TY - JOUR
A1 - Stoof-Leichsenring, Kathleen R.
A1 - Huang, Sichao
A1 - Liu, Sisi
A1 - Jia, Weihan
A1 - Li, Kai
A1 - Liu, Xingqi
A1 - Pestryakova, Luidmila A.
A1 - Herzschuh, Ulrike
T1 - Sedimentary DNA identifies modern and past macrophyte diversity and its environmental drivers in high-latitude and high-elevation lakes in Siberia and China
JF - Limnology and oceanography
N2 - Arctic and alpine aquatic ecosystems are changing rapidly under recent global warming, threatening water resources by diminishing trophic status and changing biotic composition. Macrophytes play a key role in the ecology of freshwaters and we need to improve our understanding of long-term macrophytes diversity and environmental change so far limited by the sporadic presence of macrofossils in sediments.
In our study, we applied metabarcoding using the trnL P6 loop marker to retrieve macrophyte richness and composition from 179 surface-sediment samples from arctic Siberian and alpine Chinese lakes and three representative lake cores.
The surface-sediment dataset suggests that macrophyte richness and composition are mostly affected by temperature and conductivity, with highest richness when mean July temperatures are higher than 12 degrees C and conductivity ranges between 40 and 400 mu S cm(-1). Compositional turnover during the Late Pleistocene/Holocene is minor in Siberian cores and characterized by a less rich, but stable emergent macrophyte community. Richness decreases during the Last Glacial Maximum and rises during wetter and warmer climate in the Late-glacial and Mid-Holocene.
In contrast, we detect a pronounced change from emergent to submerged taxa at 14 ka in the Tibetan alpine core, which can be explained by increasing temperature and conductivity due to glacial runoff and evaporation.
Our study provides evidence for the suitability of the trnL marker to recover modern and past macrophyte diversity and its applicability for the response of macrophyte diversity to lake-hydrochemical and climate variability predicting contrasting macrophyte changes in arctic and alpine lakes under intensified warming and human impact.
Y1 - 2022
U6 - https://doi.org/10.1002/lno.12061
SN - 0024-3590
SN - 1939-5590
VL - 67
IS - 5
SP - 1126
EP - 1141
PB - Wiley-Blackwell
CY - Oxford [u.a.]
ER -
TY - JOUR
A1 - Hébert, Raphaël
A1 - Herzschuh, Ulrike
A1 - Laepple, Thomas
T1 - Millennial-scale climate variability over land overprinted by ocean temperature fluctuations
JF - Nature geoscience
N2 - Variations in regional temperature have widespread implications for society, but our understanding of the amplitude and origin of long-term natural variability is insufficient for accurate regional projections. This is especially the case for terrestrial temperature variability, which is currently thought to be weak over long timescales. By performing spectral analysis on climate reconstructions, produced using sedimentary pollen records from the Northern Hemisphere over the last 8,000 years, coupled with instrumental data, we provide a comprehensive estimate of regional temperature variability from annual to millennial timescales. We show that short-term random variations are overprinted by strong ocean-driven climate variability on multi-decadal and longer timescales. This may cause substantial and potentially unpredictable regional climatic shifts in the coming century, in contrast to the relatively muted and homogeneous warming projected by climate models. Due to the marine influence, regions characterized by stable oceanic climate at sub-decadal timescales experience stronger long-term variability, and continental regions with higher sub-decadal variability show weaker long-term variability. This fundamental relationship between the timescales provides a unique insight into the emergence of a marine-driven low-frequency regime governing terrestrial climate variability and sets the basis to project the amplitude of temperature fluctuations on multi-decadal timescales and longer.
Temperature variability over land is enhanced by ocean temperature fluctuations on millennial timescales, with implications for regional-scale climate change, according to an analysis of Northern Hemisphere proxy records and observations.
Y1 - 2022
U6 - https://doi.org/10.1038/s41561-022-01056-4
SN - 1752-0894
SN - 1752-0908
VL - 15
IS - 11
SP - 899
PB - Nature portfolio
CY - Berlin
ER -
TY - JOUR
A1 - Gutschmann, Björn
A1 - Simões, Matilde Maldonado
A1 - Schiewe, Thomas
A1 - Schröter, Edith S.
A1 - Münzberg, Marvin
A1 - Neubauer, Peter
A1 - Bockisch, Anika
A1 - Riedel, Sebastian Lothar Stefan
T1 - Continuous feeding strategy for polyhydroxyalkanoate production from solid waste animal fat at laboratory- and pilot-scale
JF - Microbial biotechnology / Society for Applied Microbiology
N2 - Bioconversion of waste animal fat (WAF) to polyhydroxyalkanoates (PHAs) is an approach to lower the production costs of these plastic alternatives. However, the solid nature of WAF requires a tailor-made process development. In this study, a double-jacket feeding system was built to thermally liquefy the WAF to employ a continuous feeding strategy. During laboratory-scale cultivations with Ralstonia eutropha Re2058/pCB113, 70% more PHA (45 g(PHA) L-1) and a 75% higher space-time yield (0.63 g(PHA) L-1 h(-1)) were achieved compared to previously reported fermentations with solid WAF. During the development process, growth and PHA formation were monitored in real-time by in-line photon density wave spectroscopy. The process robustness was further evaluated during scale-down fermentations employing an oscillating aeration, which did not alter the PHA yield although cells encountered periods of oxygen limitation. Flow cytometry with propidium iodide staining showed that more than two-thirds of the cells were viable at the end of the cultivation and viability was even little higher in the scale-down cultivations. Application of this feeding system at 150-L pilot-scale cultivation yielded in 31.5 g(PHA) L-1, which is a promising result for the further scale-up to industrial scale.
Y1 - 2022
U6 - https://doi.org/10.1111/1751-7915.14104
SN - 1751-7915
PB - Wiley
CY - Hoboken
ER -
TY - GEN
A1 - Hering, Robert
A1 - Hauptfleisch, Morgan
A1 - Kramer-Schadt, Stephanie
A1 - Stiegler, Jonas
A1 - Blaum, Niels
T1 - Effects of fences and fence gaps on the movement behavior of three southern African antelope species
T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2 - Globally, migratory ungulates are affected by fences. While field observational studies reveal the amount of animal–fence interactions across taxa, GPS tracking-based studies uncover fence effects on movement patterns and habitat selection. However, studies on the direct effects of fences and fence gaps on movement behavior, especially based on high-frequency tracking data, are scarce. We used GPS tracking on three common African antelopes (Tragelaphus strepsiceros, Antidorcas marsupialis, and T. oryx) with movement strategies ranging from range residency to nomadism in a semi-arid, Namibian savanna traversed by wildlife-proof fences that elephants have regularly breached. We classified major forms of ungulate–fence interaction types on a seasonal and a daily scale. Furthermore, we recorded the distances and times spent at fences regarding the total individual space use. Based on this, we analyzed the direct effects of fences and fence gaps on the animals’ movement behavior for the previously defined types of animal–fence interactions. Antelope-fence interactions peaked during the early hours of the day and during seasonal transitions when the limiting resource changed between water and forage. Major types of ungulate–fence interactions were quick, trace-like, or marked by halts. We found that the amount of time spent at fences was highest for nomadic eland. Migratory springbok adjusted their space use concerning fence gap positions. If the small home ranges of sedentary kudu included a fence, they frequently interacted with this fence. For springbok and eland, distance traveled along a fence declined with increasing utilization of a fence gap. All species reduced their speed in the proximity of a fence but often increased their speed when encountering the fence. Crossing a fence led to increased speeds for all species. We demonstrate that fence effects mainly occur during crucial foraging times (seasonal scale) and during times of directed movements (daily scale). Importantly, we provide evidence that fences directly alter antelope movement behaviors with negative implications for energy budgets and that persistent fence gaps can reduce the intensity of such alterations. Our findings help to guide future animal–fence studies and provide insights for wildlife fencing and fence gap planning.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1308
KW - fence ecology
KW - veterinary cordon fence
KW - ungulate
KW - movement speed
KW - fence interaction
KW - GPS
KW - Africa
KW - wildlife conservation
Y1 - 2023
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-582672
SN - 1866-8372
IS - 1308
ER -
TY - GEN
A1 - Hering, Robert
A1 - Hauptfleisch, Morgan
A1 - Jago, Mark
A1 - Smith, Taylor
A1 - Kramer-Schadt, Stephanie
A1 - Stiegler, Jonas
A1 - Blaum, Niels
T1 - Don't stop me now: Managed fence gaps could allow migratory ungulates to track dynamic resources and reduce fence related energy loss
T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2 - In semi-arid environments characterized by erratic rainfall and scattered primary production, migratory movements are a key survival strategy of large herbivores to track resources over vast areas. Veterinary Cordon Fences (VCFs), intended to reduce wildlife-livestock disease transmission, fragment large parts of southern Africa and have limited the movements of large wild mammals for over 60 years. Consequently, wildlife-fence interactions are frequent and often result in perforations of the fence, mainly caused by elephants. Yet, we lack knowledge about at which times fences act as barriers, how fences directly alter the energy expenditure of native herbivores, and what the consequences of impermeability are. We studied 2-year ungulate movements in three common antelopes (springbok, kudu, eland) across a perforated part of Namibia's VCF separating a wildlife reserve and Etosha National Park using GPS telemetry, accelerometer measurements, and satellite imagery. We identified 2905 fence interaction events which we used to evaluate critical times of encounters and direct fence effects on energy expenditure. Using vegetation type-specific greenness dynamics, we quantified what animals gained in terms of high quality food resources from crossing the VCF. Our results show that the perforation of the VCF sustains herbivore-vegetation interactions in the savanna with its scattered resources. Fence permeability led to peaks in crossing numbers during the first flush of woody plants before the rain started. Kudu and eland often showed increased energy expenditure when crossing the fence. Energy expenditure was lowered during the frequent interactions of ungulates standing at the fence. We found no alteration of energy expenditure when springbok immediately found and crossed fence breaches. Our results indicate that constantly open gaps did not affect energy expenditure, while gaps with obstacles increased motion. Closing gaps may have confused ungulates and modified their intended movements. While browsing, sedentary kudu's use of space was less affected by the VCF; migratory, mixed-feeding springbok, and eland benefited from gaps by gaining forage quality and quantity after crossing. This highlights the importance of access to vast areas to allow ungulates to track vital vegetation patches.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1278
KW - veterinary cordon fence
KW - ungulate
KW - fence ecology
KW - resource-tracking
KW - energy expenditure
KW - accelerometer
KW - GPS
KW - wildlife and habitat management
Y1 - 2022
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-570087
SN - 1866-8372
IS - 1278
ER -
TY - THES
A1 - Kürschner, Tobias
T1 - Disease transmission and persistence in dynamic landscapes
T1 - Krankheitsübertragung und Persistenz in dynamischen Landschaft
N2 - Infectious diseases are an increasing threat to biodiversity and human health. Therefore, developing a general understanding of the drivers shaping host-pathogen dynamics is of key importance in both ecological and epidemiological research. Disease dynamics are driven by a variety of interacting processes such as individual host behaviour, spatiotemporal resource availability or pathogen traits like virulence and transmission. External drivers such as global change may modify the system conditions and, thus, the disease dynamics. Despite their importance, many of these drivers are often simplified and aggregated in epidemiological models and the interactions among multiple drivers are neglected.
In my thesis, I investigate disease dynamics using a mechanistic approach that includes both bottom-up effects - from landscape dynamics to individual movement behaviour - as well as top-down effects - from pathogen virulence on host density and contact rates. To this end, I extended an established spatially explicit individual-based model that simulates epidemiological and ecological processes stochastically, to incorporate a dynamic resource landscape that can be shifted away from the timing of host population-dynamics (chapter 2). I also added the evolution of pathogen virulence along a theoretical virulence-transmission trade-off (chapter 3). In chapter 2, I focus on bottom-up effects, specifically how a temporal shift of resource availability away from the timing of biological events of host-species - as expected under global change - scales up to host-pathogen interactions and disease dynamics. My results show that the formation of temporary disease hotspots in combination with directed individual movement acted as key drivers for pathogen persistence even under highly unfavourable conditions for the host. Even with drivers like global change further increasing the likelihood of unfavourable interactions between host species and their environment, pathogens can continue to persist with heir hosts. In chapter 3, I demonstrate that the top-down effect caused by pathogen-associated mortality on its host population can be mitigated by selection for lower virulent pathogen strains when host densities are reduced through mismatches between seasonal resource availability and host life-history events. I chapter 4, I combined parts of both theoretical models into a new model that includes individual host movement decisions and the evolution of pathogenic virulence to simulate pathogen outbreaks in realistic landscapes. I was able to match simulated patterns of pathogen spread to observed patterns from long-term outbreak data of classical swine fever in wild boar in Northern Germany. The observed disease course was best explained by a simulated high virulent strain, whereas sampling schemes and vaccination campaigns could explain differences in the age-distribution of infected hosts. My model helps to understand and disentangle how the combination of individual decision making and evolution of virulence can act as important drivers of pathogen spread and persistence.
As I show across the chapters of this thesis, the interplay of both bottom-up and top-down processes is a key driver of disease dynamics in spatially structured host populations, as they ultimately shape host densities and contact rates among moving individuals. My findings are an important step towards a paradigm shift in disease ecology away from simplified assumptions towards the inclusion of mechanisms, such as complex multi-trophic interactions, and their feedbacks on pathogen spread and disease persistence. The mechanisms presented here should be at the core of realistic predictive and preventive epidemiological models.
N2 - Infektionskrankheiten stellen eine zunehmende Bedrohung für die biologische Vielfalt und die menschliche Gesundheit dar. Daher ist es sowohl für die epidemiologische als auch für die ökologische Forschung von zentraler Bedeutung, ein allgemeines Verständnis der Mechanismen, die die Wirts-Pathogen-Dynamik beeinflussen, zu entwickeln. Die Krankheitsausbrüche werden durch eine Vielzahl von interagierenden Prozessen angetrieben, wie unter anderem individuellem Wirtsverhalten, Ressourcenverfügbarkeit oder Erregermerkmale wie Virulenz. Externe Faktoren wie der globale Wandel können grundlegende Veränderungen dieser Prozesse verursachen und sich damit auch auf Krankheitsdynamiken auswirken. Trotz ihrer Bedeutung für Krankheitsausbrüche werden viele dieser Faktoren in epidemiologischen Modellen oft vereinfacht und die Wechselwirkungen zwischen den Faktoren vernachlässigt. In Anbetracht dessen, ist es sowohl für die ökologische als auch für die epidemiologische Forschung von zentraler Bedeutung, ein allgemeines Verständnis dafür zu entwickeln, wie mehrere interagierende Prozesse Wirts-Pathogen-Interaktionen beeinflussen können.
In meiner Dissertation untersuche ich die Krankheitsdynamik mittels eines mechanistischen Ansatzes, der sowohl Bottom-up-Effekte - von der Landschaftsdynamik bis zum individuellen Bewegungsverhalten - als auch Top-down-Effekte - von der Virulenz des Erregers auf die Wirtsdichte und die Kontaktraten - berücksichtigt. Zu diesem Zweck habe ich ein etabliertes, räumlich explizites, Individuen basiertes Modell, das epidemiologische und ökologische Prozesse stochastisch simuliert, um eine dynamische Ressourcenlandschaft erweitert, die zeitlich mit der Populationsdynamik der Wirte verschoben werden kann (Kapitel 2). Zusätzlich habe ich die Evolution der Virulenz von Krankheitserregern entlang eines theoretischen Verhältnisses zwischen Virulenz und Übertragung hinzugefügt (Kapitel 3). In Kapitel 2 konzentriere ich mich auf Bottom-up-Effekte, insbesondere auf die Frage, wie sich eine zeitliche Verschiebung der Ressourcenverfügbarkeit weg vom Zeitpunkt biologischer Ereignisse der Wirtsarten - wie sie im Rahmen des globalen Wandels erwartet wird - auf die Wirt-Pathogen-Interaktionen und Krankheitsdynamiken auswirkt. Meine Ergebnisse zeigen, dass die Bildung vorübergehender Krankheitsherde in Kombination mit gezielter individueller Wirtsbewegung als Schlüsselfaktoren für die Persistenz von Krankheitserregern selbst unter äußerst ungünstigen Bedingungen für den Wirt fungieren. Selbst wenn Faktoren wie der globale Wandel die Wahrscheinlichkeit ungünstiger Wechselwirkungen zwischen Wirtsarten und ihrer Umwelt weiter erhöhen, können Krankheitserreger weiterhin in ihren Wirten persistieren. In Kapitel 3 zeige ich, dass der Top-Down-Effekt, der durch die pathogen-assoziierte Mortalität verursacht wird, durch eine evolutionäre Selektion auf weniger virulente Erregerstämme abgeschwächt werden kann, wenn die Wirtsdichte durch eine zeitliche Verschiebung von saisonaler Ressourcenverfügbarkeit und dem Zeitpunkt von biologischen Ereignissen der Wirtsarten reduziert wird. In Kapitel 4 habe ich Teile der beiden theoretischen Modelle zu einem neuen Modell kombiniert, das individuelle Wirtsbewegungen und die Entwicklung der Virulenz von Krankheitserregern einbezieht, um Ausbrüche von Krankheitserregern in realistischen Landschaften zu simulieren. Es gelang mir, die simulierten Muster der Krankheitsausbreitung mit beobachteten Mustern von Langzeitausbrüchen der klassischen Schweinepest in Wildschweinen in Norddeutschland abzugleichen. Der beobachtete Krankheitsverlauf ließ sich am besten durch einen simulierten hochvirulenten Stamm erklären, während das Design der Probenentnahmen und Impfkampagnen Unterschiede in der Altersverteilung der infizierten Wirte erklären könnten. Mein Modell trägt dazu bei, zu verstehen, wie die Kombination aus individueller Bewegung und der Evolution von Virulenz als wichtige Treiber für die Ausbreitung und Persistenz des Erregers wirken können.
Wie ich in den Kapiteln dieser Arbeit zeige, ist das Zusammenspiel von Bottom-up- und Top-down-Prozessen ein entscheidender Faktor für die Krankheitsdynamik in Wirtspopulationen, da sie letztlich die Wirtsdichte und den Kontakt zwischen sich bewegenden Individuen bestimmen. Meine Ergebnisse sind ein wichtiger Schritt auf dem Weg zu einem Paradigmenwechsel in der Krankheitsökologie, weg von vereinfachten Annahmen hin zur Einbeziehung von komplexen Interaktionen und deren Rückkopplungen auf die Ausbreitung und Persistenz von Krankheitserregern. Die hier vorgestellten Mechanismen sollten den Kern realistischer Vorhersage- und Präventivmodelle für die Epidemiologie bilden.
KW - disease ecology
KW - movement ecology
KW - Krankheitsökologie
KW - Bewegungsökologie
Y1 - 2022
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-564689
ER -
TY - THES
A1 - Oberkofler, Vicky
T1 - Molecular basis of HS memory in Arabidopsis thaliana
T1 - Die molekulare Basis des Hitzestress-Gedächtnisses in Arabidopsis thaliana
N2 - Plants can be primed to survive the exposure to a severe heat stress (HS) by prior exposure to a mild HS. The information about the priming stimulus is maintained by the plant for several days. This maintenance of acquired thermotolerance, or HS memory, is genetically separable from the acquisition of thermotolerance itself and several specific regulatory factors have been identified in recent years.
On the molecular level, HS memory correlates with two types of transcriptional memory, type I and type II, that characterize a partially overlapping subset of HS-inducible genes. Type I transcriptional memory or sustained induction refers to the sustained transcriptional induction above non-stressed expression levels of a gene for a prolonged time period after the end of the stress exposure. Type II transcriptional memory refers to an altered transcriptional response of a gene after repeated exposure to a stress of similar duration and intensity. In particular, enhanced re-induction refers to a transcriptional pattern in which a gene is induced to a significantly higher degree after the second stress exposure than after the first.
This thesis describes the functional characterization of a novel positive transcriptional regulator of type I transcriptional memory, the heat shock transcription factor HSFA3, and compares it to HSFA2, a known positive regulator of type I and type II transcriptional memory. It investigates type I transcriptional memory and its dependence on HSFA2 and HSFA3 for the first time on a genome-wide level, and gives insight on the formation of heteromeric HSF complexes in response to HS. This thesis confirms the tight correlation between transcriptional memory and H3K4 hyper-methylation, reported here in a case study that aimed to reduce H3K4 hyper-methylation of the type II transcriptional memory gene APX2 by CRISPR/dCas9-mediated epigenome editing. Finally, this thesis gives insight into the requirements for a heat shock transcription factor to function as a positive regulator of transcriptional memory, both in terms of its expression profile and protein abundance after HS and the contribution of individual functional domains.
In summary, this thesis contributes to a more detailed understanding of the molecular processes underlying transcriptional memory and therefore HS memory, in Arabidopsis thaliana.
N2 - Pflanzen können darauf vorbereitet werden, einen schweren Hitzestress (HS) zu überleben, indem sie zuvor einem leichten HS ausgesetzt werden. Die Information über den Priming-Stimulus wird von der Pflanze mehrere Tage lang aufrechterhalten. Diese Aufrechterhaltung der erworbenen Thermotoleranz, das so genannte HS-Gedächtnis, ist genetisch vom Erwerb der Thermotoleranz selbst trennbar, und in den letzten Jahren wurden mehrere spezifische Regulierungsfaktoren identifiziert.
Auf molekularer Ebene korreliert das HS-Gedächtnis mit zwei Arten von Transkriptionsgedächtnis, Typ I und Typ II, die eine sich teilweise überschneidende Untergruppe von HS-induzierbaren Genen charakterisieren. Das Transkriptionsgedächtnis vom Typ I oder die anhaltende Induktion bezieht sich auf die anhaltende Transkriptionsinduktion eines Gens über das Niveau der Expression im ungestressten Zustand hinaus über einen längeren Zeitraum nach dem Ende der Stressbelastung. Das Transkriptionsgedächtnis des Typs II bezieht sich auf eine veränderte Transkriptionsreaktion eines Gens nach wiederholter Exposition gegenüber einem Hitzestress von ähnlicher Dauer und Intensität. Insbesondere bezieht sich dabei die verstärkte Re-Induktion auf ein Transkriptionsmuster, bei dem ein Gen nach der zweiten Stressexposition in deutlich höherem Maße induziert wird als nach der ersten.
Diese Arbeit beschreibt die funktionelle Charakterisierung eines neuartigen positiven Transkriptionsregulators des Typ-I-Transkriptionsgedächtnisses, des Hitzeschock-Transkriptionsfaktors HSFA3, und vergleicht ihn mit HSFA2, einem bekannten positiven Regulator des Typ-I- und Typ-II-Transkriptionsgedächtnisses. Die Arbeit untersucht das Typ-I-Transkriptionsgedächtnis und seine Abhängigkeit von HSFA2 und HSFA3 zum ersten Mal auf genomweiter Ebene und gibt Einblick in die Bildung heteromerer HSF-Komplexe als Reaktion auf HS. Diese Arbeit bestätigt den engen Zusammenhang zwischen transkriptionellem Gedächtnis und H3K4-Hypermethylierung, über den hier in einer Fallstudie berichtet wird, die darauf abzielt, die H3K4-Hypermethylierung des Typ-II-Transkriptionsgedächtnisgens APX2 durch CRISPR/dCas9-vermitteltes Epigenom-Editing zu reduzieren. Schließlich gibt diese Arbeit einen Einblick in die Anforderungen, die ein Hitzeschock-Transkriptionsfaktor erfüllen muss, damit er als positiver Regulator des Transkriptionsgedächtnisses fungieren kann, und zwar sowohl in Bezug auf sein Expressionsprofil und seine Proteinabundanz nach HS als auch in Bezug auf den Beitrag seiner einzelnen funktionellen Domänen.
Zusammenfassend trägt diese Arbeit zu einem genaueren Verständnis der molekularen Prozesse bei, die dem Transkriptionsgedächtnis und damit dem HS-Gedächtnis in Arabidopsis thaliana zugrunde liegen.
KW - Arabidopsis thaliana
KW - abiotic stress
KW - heat stress memory
KW - transcription factors
KW - HSF
KW - epigenome editing
KW - histone methylation
KW - H3K4me
KW - Arabidopsis thaliana
KW - H3K4me
KW - Hitzeschock-Transkriptionsfaktor
KW - abiotischer Stress
KW - Epigenom Editierung
KW - Hitzestress-Gedächtnis
KW - Histon Methylierung
KW - Transkriptionsfaktoren
Y1 - 2022
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-569544
ER -
TY - THES
A1 - Kahl, Sandra
T1 - Evolutionary adaptive responses to rapid climate change in plants
T1 - Evolutionäre Anpassungsstrategien von Pflanzen an den Klimawandel
BT - a case study of the widely distributed species Silene vulgaris
BT - ein Fallbeispiel der weit verbreiteten Art Silene vulgaris
N2 - The ongoing climate change is altering the living conditions for many organisms on this planet at an unprecedented pace. Hence, it is crucial for the survival of species to adapt to these changing conditions. In this dissertation Silene vulgaris is used as a model organism to understand the adaption strategies of widely distributed plant species to the current climate change. Especially plant species that possess a wide geographic range are expected to have a high phenotypic plasticity or to show genetic differentiation in response to the different climate conditions they grow in. However, they are often underrepresented in research.
In the greenhouse experiment presented in this thesis, I examined the phenotypic responses and plasticity in S. vulgaris to estimate its’ adaptation potential. Seeds from 25 wild European populations were collected along a latitudinal gradient and grown in a greenhouse under three different precipitation (65 mm, 75 mm, 90 mm) and two different temperature regimes (18°C, 21°C) that resembled a possible climate change scenario for central Europe. Afterwards different biomass and fecundity-related plant traits were measured.
The treatments significantly influenced the plants but did not reveal a latitudinal difference in response to climate treatments for most plant traits. The number of flowers per individual however, showed a stronger plasticity in northern European populations (e.g., Swedish populations) where numbers decreased more drastically with increased temperature and decreased precipitation.
To gain an even deeper understanding of the adaptation of S. vulgaris to climate change it is also important to reveal the underlying phylogeny of the sampled populations. Therefore, I analysed their population genetic structure through whole genome sequencing via ddRAD.
The sequencing revealed three major genetic clusters in the S. vulgaris populations sampled in Europe: one cluster comprised Southern European populations, one cluster Western European populations and another cluster contained central European populations. A following analysis of experimental trait responses among the clusters to the climate-change scenario showed that the genetic clusters significantly differed in biomass-related traits and in the days to flowering. However, half of the traits showed parallel response patterns to the experimental climate-change scenario.
In addition to the potential geographic and genetic adaptation differences to climate change this dissertation also deals with the response differences between the sexes in S. vulgaris. As a gynodioecious species populations of S. vulgaris consist of female and hermaphrodite
individuals and the sexes can differ in their morphological traits which is known as sexual dimorphism. As climate change is becoming an important factor influencing plant morphology it remains unclear if and how different sexes may respond in sexually dimorphic species. To examine this question the sex of each individual plant was determined during the greenhouse experiment and the measured plant traits were analysed accordingly. In general, hermaphrodites had a higher number of flowers but a lower number of leaves than females. With regards to the climate change treatment, I found that hermaphrodites showed a milder negative response to higher temperatures in the number of flowers produced and in specific leaf area (SLA) compared to females.
Synthesis – The significant treatment response in Silene vulgaris, independent of population origin in most traits suggests a high degree of universal phenotypic plasticity. Also, the three European intraspecific genetic lineages detected showed comparable parallel response patterns in half of the traits suggesting considerable phenotypic plasticity. Hence, plasticity might represent a possible adaptation strategy of this widely distributed species during ongoing and future climatic changes. The results on sexual dimorphism show that females and hermaphrodites are differing mainly in their number of flowers and females are affected more strongly by the experimental climate-change scenario. These results provide a solid knowledge basis on the sexual dimorphism in S. vulgaris under climate change, but further research is needed to determine the long-term impact on the breeding system for the species.
In summary this dissertation provides a comprehensive insight into the adaptation mechanisms and consequences of a widely distributed and gynodioecious plant species and leverages our understanding of the impact of anthropogenic climate change on plants.
N2 - Der derzeitige Klimawandel verändert die Lebensbedingungen für viele Tiere und Pflanzen auf unserem Planeten in nie da gewesenem Maße. Damit Arten überleben, ist es von besonderer Wichtigkeit, dass sich diese an die sich ändernden Klimabedingungen anpassen können. Die vorliegende Dissertation befasst sich mit der Modellpflanze Silene vulgaris und versucht zu ergründen, wie sich solch weit verbreitete Pflanzenarten an den Klimawandel anpassen. Dabei ist zu erwarten, dass sie eine hohe phänotypische Plastizität besitzen, durch die sie sich gut anpassen können oder, dass sie sich durch eine genetische Differenzierung als Antwort auf die vorherrschenden Umweltbedingungen auszeichnen. Im experimentellen Ansatz dieser Dissertation untersuchte ich daher die phänotypischen Anpassungen und die phänotypische Plastizität von S. vulgaris an ein mögliches Klimawandelszenario für Zentraleuropa. Dabei wurden die Samen von 25 europäischen Populationen gesammelt und in einem Gewächshausexperiment unter drei verschiedenen Niederschlagsbedingungen (65 mm, 75 mm, 90 mm) und zwei verschiedenen Temperaturbedingungen (18°C, 21°C) herangezogen. Im Anschluss wurden verschiedene Biomasse- und Fertilitätsmerkmale gemessen. Für ein tiefergehendes Verständnis der Anpassungsmöglichkeiten von S. vulgaris an den Klimawandel ist es zudem wichtig, auch die zugrundeliegende Phylogenie der Populationen zu verstehen. In diesem Zusammenhang nutzte ich eine genomweite Sequenziermethode mittels ddRAD.
Die Bedingungen im Gewächshausexperiment beeinflussten die Pflanzen signifikant in ihren phänotypischen Merkmalen, jedoch ließ sich kein Unterschied zwischen Population unterschiedlicher Herkunft erkennen. Lediglich die Anzahl der Blüten zeigte eine größere Plastizität in nördlichen europäischen Populationen, wo sich die Blütenzahl stärker dezimierte unter höheren Temperaturen und stärkerer Trockenheit. Die populationsgenetische Analyse ergab drei distinkte phylogenetische Gruppen für die untersuchten europäischen Populationen von S. vulgaris: eine Gruppe beinhaltete südeuropäische Populationen aus Spanien und Südfrankreich, eine weitere Gruppe bestand aus den gesammelten Individuen der westfranzösischen Populationen, während die dritte Gruppe, die Populationen aus Mittel- und Nordeuropa enthielt. Diese genetischen Gruppen wurden anschließend ebenfalls der Merkmalsanalyse unter den Gewächshausbedingungen unterzogen. Dabei stellte sich heraus, dass sich die genetischen Gruppen in ihren phänotypischen Merkmalen unterschieden, jedoch
eine ähnliche Anpassung ihrer Merkmale an die experimentellen Klimawandelbedingungen zeigten.
Der dritte Aspekt dieser Dissertation befasste sich mit möglichen Anpassungsunterschieden zwischen den Geschlechtern in S. vulgaris. Als gynodiözische Art bestehen ihre Populationen sowohl aus weiblichen, also auch aus zwittrigen Individuen. Die phänotypischen Merkmale beider Geschlechter können sich dabei unterscheiden, was man als Sexualdimorphismus bezeichnet. Es ist bereits bekannt, dass sich Pflanzenmerkmale durch den anhaltenden Klimawandel bereits verändern, jedoch ist es nicht gut erforscht, ob und wie sich die unterschiedlichen Geschlechter bei einer sexuell dimorphen Art unter diesem Selektionsdruck verhalten. Während des Gewächshausexperiments wurden daher die Geschlechter der Individuen bestimmt und die phänotypischen Unterschiede zwischen weiblichen und zwittrigen Pflanzen analysiert. Allgemein lässt sich sagen, dass zwittrige Individuen mehr Blüten aber weniger Blätter hatten als weibliche. Im Hinblick auf die experimentellen Klimawandelbedingungen konnte ich zudem feststellen, dass Hermaphroditen in ihrer spezifischen Blattfläche und der Blütenanzahl weniger stark negativ auf höhere Temperaturen reagierten.
Synthese – Die signifikanten Merkmalsanpassungen an die Gewächshausbedingungen waren unabhängig von der geographischen Herkunft oder genetischen Gruppe der Individuen. Dies lässt ein hohes Maß an universeller, phänotypischer Plastizität vermuten. Dementsprechend kann davon ausgegangen werden, dass phänotypische Plastizität ein möglicher Anpassungsmechanismus für diese weit verbreitete Art an den Klimawandel sein könnte. Im Hinblick auf den Sexualdimorphismus in S. vulgaris lässt sich sagen, dass sich beide Geschlechter vornehmlich in der Anzahl der Blüten unterscheiden und dass weibliche Pflanzen stärker von den Bedingungen des Gewächshausexperiments beeinflusst wurden. Diese Dissertation konnte damit erstmals darüber Aufschluss geben, wie sich S. vulgaris im Hinblick auf ihren Sexualdimorphismus unter Klimawandelbedingungen verhält. Weitere Forschung wird nun benötigt, um auch den Langzeiteffekt des Klimawandels auf das Fortpflanzungssystem dieser Art abschätzen zu können.
Zusammenfassend lässt sich sagen, dass die vorliegende Arbeit einen umfassenden Einblick in die Anpassungsmechanismen einer weit verbreiteten Pflanzenart an den anthropogenen Klimawandel gibt. Zudem bestärkt sie unser Verständnis der Auswirkungen, die sich daraus für eine gynodiözische Art, wie S. vulgaris ergeben.
KW - Silene vulgaris
KW - climate change
KW - plant adaptation
KW - Silene vulgaris
KW - Klimawandel
KW - Pflanzenanpassung
Y1 - 2022
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-556483
ER -
TY - JOUR
A1 - Singh, Aakanksha
A1 - Compart, Julia
A1 - AL-Rawi, Shadha Abduljaleel
A1 - Mahto, Harendra
A1 - Ahmad, Abubakar Musa
A1 - Fettke, Jörg
T1 - LIKE EARLY STARVATION 1 alters the glucan structures at the starch granule surface and thereby influences the action of both starch-synthesizing and starch-degrading enzymes
JF - The plant journal
N2 - For starch metabolism to take place correctly, various enzymes and proteins acting on the starch granule surface are crucial. Recently, two non-catalytic starch-binding proteins, pivotal for normal starch turnover in Arabidopsis leaves, namely, EARLY STARVATION 1 (ESV1) and its homolog LIKE EARLY STARVATION 1 (LESV), have been identified. Both share nearly 38% sequence homology. As ESV1 has been found to influence glucan phosphorylation via two starch-related dikinases, alpha-glucan, water dikinase (GWD) and phosphoglucan, water dikinase (PWD), through modulating the surface glucan structures of the starch granules and thus affecting starch degradation, we assess the impact of its homolog LESV on starch metabolism. Thus, the 65-kDa recombinant protein LESV and the 50-kDa ESV1 were analyzed regarding their influence on the action of GWD and PWD on the surface of the starch granules. We included starches from various sources and additionally assessed the effect of these non-enzymatic proteins on other starch-related enzymes, such as starch synthases (SSI and SSIII), starch phosphorylases (PHS1), isoamylase and beta-amylase. The data obtained indicate that starch phosphorylation, hydrolyses and synthesis were affected by LESV and ESV1. Furthermore, incubation with LESV and ESV1 together exerted an additive effect on starch phosphorylation. In addition, a stable alteration of the glucan structures at the starch granule surface following treatment with LESV and ESV1 was observed. Here, we discuss all the observed changes that point to modifications in the glucan structures at the surface of the native starch granules and present a model to explain the existing processes.
KW - starch
KW - starch metabolism
KW - starch surface structure
KW - Arabidopsis
KW - thaliana
Y1 - 2022
U6 - https://doi.org/10.1111/tpj.15855
SN - 0960-7412
SN - 1365-313X
VL - 111
IS - 3
SP - 819
EP - 835
PB - Wiley-Blackwell
CY - Oxford
ER -
TY - JOUR
A1 - Li, Xiaoping
A1 - Apriyanto, Ardha
A1 - Flores Castellanos, Junio
A1 - Compart, Julia
A1 - Muntaha, Sidratul Nur
A1 - Fettke, Jörg
T1 - Dpe2/phs1 revealed unique starch metabolism with three distinct phases characterized by different starch granule numbers per chloroplast, allowing insights into the control mechanism of granule number regulation by gene co-regulation and metabolic profiling
JF - Frontiers in Plant Science
N2 - An Arabidopsis mutant lacking both the cytosolic Disproportionating enzyme 2 (DPE2) and the plastidial glucan Phosphorylase 1 (PHS1) revealed a unique starch metabolism. Dpe2/phs1 has been reported to have only one starch granule number per chloroplast when grown under diurnal rhythm. For this study, we analyzed dpe2/phs1 in details following the mutant development, and found that it showed three distinct periods of granule numbers per chloroplast, while there was no obvious change observed in Col-0. In young plants, the starch granule number was similar to that in Col-0 at first, and then decreased significantly, down to one or no granule per chloroplast, followed by an increase in the granule number. Thus, in dpe2/phs1, control over the starch granule number is impaired, but it is not defective in starch granule initiation. The data also indicate that the granule number is not fixed, and is regulated throughout plant growth. Furthermore, the chloroplasts revealed alterations during these three periods, with a partially strong aberrant morphology in the middle phase. Interestingly, the unique metabolism was perpetuated when starch degradation was further impaired through an additional lack of Isoamylase 3 (ISA3) or Starch excess 4 (SEX4). Transcriptomic studies and metabolic profiling revealed the co-regulation of starch metabolism-related genes and a clear metabolic separation between the periods. Most senescence-induced genes were found to be up-regulated more than twice in the starch-less mature leaves. Thus, dpe2/phs1 is a unique plant material source, with which we may study starch granule number regulation to obtain a more detailed understanding.
KW - LCSM
KW - RNA-Seq
KW - metabolic-profiling
KW - starch granule number regulation
KW - starch initiation
KW - starch degradation
Y1 - 2022
U6 - https://doi.org/10.3389/fpls.2022.1039534
SN - 1664-462X
SP - 1
EP - 16
PB - Frontiers
CY - Lausanne, Schweiz
ER -
TY - JOUR
A1 - Havermann, Felix
A1 - Ghirardo, Andrea
A1 - Schnitzler, Jörg-Peter
A1 - Nendel, Claas
A1 - Hoffmann, Mathias
A1 - Kraus, David
A1 - Grote, Rüdiger
T1 - Modeling intra- and interannual variability of BVOC emissions from maize, oil-seed rape, and ryegrass
JF - Journal of advances in modeling earth systems
N2 - Air chemistry is affected by the emission of biogenic volatile organic compounds (BVOCs), which originate from almost all plants in varying qualities and quantities. They also vary widely among different crops, an aspect that has been largely neglected in emission inventories. In particular, bioenergy-related species can emit mixtures of highly reactive compounds that have received little attention so far. For such species, long-term field observations of BVOC exchange from relevant crops covering different phenological phases are scarcely available. Therefore, we measured and modeled the emission of three prominent European bioenergy crops (maize, ryegrass, and oil-seed rape) for full rotations in north-eastern Germany. Using a proton transfer reaction-mass spectrometer combined with automatically moving large canopy chambers, we were able to quantify the characteristic seasonal BVOC flux dynamics of each crop species. The measured BVOC fluxes were used to parameterize and evaluate the BVOC emission module (JJv) of the physiology-oriented LandscapeDNDC model, which was enhanced to cover de novo emissions as well as those from plant storage pools. Parameters are defined for each compound individually. The model is used for simulating total compound-specific reactivity over several years and also to evaluate the importance of these emissions for air chemistry. We can demonstrate substantial differences between the investigated crops with oil-seed rape having 37-fold higher total annual emissions than maize. However, due to a higher chemical reactivity of the emitted blend in maize, potential impacts on atmospheric OH-chemistry are only 6-fold higher.
KW - biogenic volatile organic compounds
KW - process-based modeling
KW - Zea mays
KW - Brassica napus
KW - Lolium multiflorum
KW - plant ontogenetic stage
Y1 - 2022
U6 - https://doi.org/10.1029/2021MS002683
SN - 1942-2466
VL - 14
IS - 3
PB - American Geophysical Union
CY - Washington
ER -
TY - JOUR
A1 - Schwieder, Marcel
A1 - Wesemeyer, Maximilian
A1 - Frantz, David
A1 - Pfoch, Kira
A1 - Erasmi, Stefan
A1 - Pickert, Jürgen
A1 - Nendel, Claas
A1 - Hostert, Patrick
T1 - Mapping grassland mowing events across Germany based on combined Sentinel-2 and Landsat 8 time series
JF - Remote sensing of environment
N2 - Spatially explicit knowledge on grassland extent and management is critical to understand and monitor the impact of grassland use intensity on ecosystem services and biodiversity. While regional studies allow detailed insights into land use and ecosystem service interactions, information on a national scale can aid biodiversity assessments. However, for most European countries this information is not yet widely available. We used an analysis-ready-data cube that contains dense time series of co-registered Sentinel-2 and Landsat 8 data, covering the extent of Germany. We propose an algorithm that detects mowing events in the time series based on residuals from an assumed undisturbed phenology, as an indicator of grassland use intensity. A self-adaptive ruleset enabled to account for regional variations in land surface phenology and non-stationary time series on a pixelbasis. We mapped mowing events for the years from 2017 to 2020 for permanent grassland areas in Germany. The results were validated on a pixel level in four of the main natural regions in Germany based on reported mowing events for a total of 92 (2018) and 78 (2019) grassland parcels. Results for 2020 were evaluated with combined time series of Landsat, Sentinel-2 and PlanetScope data. The mean absolute percentage error between detected and reported mowing events was on average 40% (2018), 36% (2019) and 35% (2020). Mowing events were on average detected 11 days (2018), 7 days (2019) and 6 days (2020) after the reported mowing. Performance measures varied between the different regions of Germany, and lower accuracies were found in areas that are revisited less frequently by Sentinel-2. Thus, we assessed the influence of data availability and found that the detection of mowing events was less influenced by data availability when at least 16 cloud-free observations were available in the grassland season. Still, the distribution of available observations throughout the season appeared to be critical. On a national scale our results revealed overall higher shares of less intensively mown grasslands and smaller shares of highly intensively managed grasslands. Hotspots of the latter were identified in the alpine foreland in Southern Germany as well as in the lowlands in the Northwest of Germany. While these patterns were stable throughout the years, the results revealed a tendency to lower management intensity in the extremely dry year 2018. Our results emphasize the ability of the approach to map the intensity of grassland management throughout large areas despite variations in data availability and environmental conditions.
KW - Analysis-ready data
KW - Big data
KW - Large-area mapping
KW - Germany
KW - Common agricultural policy
KW - Time series
KW - Land use intensity
KW - Optical remote sensing
KW - Multi-spectral data
KW - PlanetScope
Y1 - 2022
U6 - https://doi.org/10.1016/j.rse.2021.112795
SN - 0034-4257
SN - 1879-0704
VL - 269
PB - Elsevier
CY - New York
ER -
TY - JOUR
A1 - Tian, Fang
A1 - Qin, Wen
A1 - Zhang, Ran
A1 - Herzschuh, Ulrike
A1 - Ni, Jian
A1 - Zhang, Chengjun
A1 - Mischke, Steffen
A1 - Cao, Xianyong
T1 - Palynological evidence for the temporal stability of the plant community in the Yellow River Source Area over the last 7,400 years
JF - Vegetation history and archaeobotany
N2 - The terrestrial ecosystem in the Yellow River Source Area (YRSA) is sensitive to climate change and human impacts, although past vegetation change and the degree of human disturbance are still largely unknown. A 170-cm-long sediment core covering the last 7,400 years was collected from Lake Xingxinghai (XXH) in the YRSA. Pollen, together with a series of other environmental proxies (including grain size, total organic carbon (TOC) and carbonate content), were analysed to explore past vegetation and environmental changes for the YRSA. Dominant and common pollen components-Cyperaceae, Poaceae, Artemisia, Chenopodiaceae and Asteraceae-are stable throughout the last 7,400 years. Slight vegetation change is inferred from an increasing trend of Cyperaceae and decreasing trend of Poaceae, suggesting that alpine steppe was replaced by alpine meadow at ca. 3.5 ka cal bp. The vegetation transformation indicates a generally wetter climate during the middle and late Holocene, which is supported by increased amounts of TOC and Pediastrum (representing high water-level) and is consistent with previous past climate records from the north-eastern Tibetan Plateau. Our results find no evidence of human impact on the regional vegetation surrounding XXH, hence we conclude the vegetation change likely reflects the regional climate signal.
KW - Pollen
KW - Lake Xingxinghai
KW - Tibetan Plateau
KW - Holocene
KW - Vegetation change
KW - Regional climate
Y1 - 2022
U6 - https://doi.org/10.1007/s00334-022-00870-5
SN - 0939-6314
SN - 1617-6278
VL - 31
IS - 6
SP - 549
EP - 558
PB - Springer
CY - New York
ER -
TY - JOUR
A1 - Vatova, Mariyana
A1 - Rubin, Conrad
A1 - Grossart, Hans-Peter
A1 - Goncalves, Susana C.
A1 - Schmidt, Susanne I.
A1 - Jarić, Ivan
T1 - Aquatic fungi: largely neglected targets for conservation
JF - Frontiers in ecology and the environment
Y1 - 2022
U6 - https://doi.org/10.1002/fee.2495
SN - 1540-9295
SN - 1540-9309
VL - 20
IS - 4
SP - 207
EP - 209
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Jia, Weihan
A1 - Anslan, Sten
A1 - Chen, Fahu
A1 - Cao, Xianyong
A1 - Dong, Hailiang
A1 - Dulias, Katharina
A1 - Gu, Zhengquan
A1 - Heinecke, Liv
A1 - Jiang, Hongchen
A1 - Kruse, Stefan
A1 - Kang, Wengang
A1 - Li, Kai
A1 - Liu, Sisi
A1 - Liu, Xingqi
A1 - Liu, Ying
A1 - Ni, Jian
A1 - Schwalb, Antje
A1 - Stoof-Leichsenring, Kathleen R.
A1 - Shen, Wei
A1 - Tian, Fang
A1 - Wang, Jing
A1 - Wang, Yongbo
A1 - Wang, Yucheng
A1 - Xu, Hai
A1 - Yang, Xiaoyan
A1 - Zhang, Dongju
A1 - Herzschuh, Ulrike
T1 - Sedimentary ancient DNA reveals past ecosystem and biodiversity changes on the Tibetan Plateau: overview and prospects
JF - Quaternary science reviews : the international multidisciplinary research and review journal
N2 - Alpine ecosystems on the Tibetan Plateau are being threatened by ongoing climate warming and intensified human activities. Ecological time-series obtained from sedimentary ancient DNA (sedaDNA) are essential for understanding past ecosystem and biodiversity dynamics on the Tibetan Plateau and their responses to climate change at a high taxonomic resolution. Hitherto only few but promising studies have been published on this topic. The potential and limitations of using sedaDNA on the Tibetan Plateau are not fully understood. Here, we (i) provide updated knowledge of and a brief introduction to the suitable archives, region-specific taphonomy, state-of-the-art methodologies, and research questions of sedaDNA on the Tibetan Plateau; (ii) review published and ongoing sedaDNA studies from the Tibetan Plateau; and (iii) give some recommendations for future sedaDNA study designs. Based on the current knowledge of taphonomy, we infer that deep glacial lakes with freshwater and high clay sediment input, such as those from the southern and southeastern Tibetan Plateau, may have a high potential for sedaDNA studies. Metabarcoding (for microorganisms and plants), metagenomics (for ecosystems), and hybridization capture (for prehistoric humans) are three primary sedaDNA approaches which have been successfully applied on the Tibetan Plateau, but their power is still limited by several technical issues, such as PCR bias and incompleteness of taxonomic reference databases. Setting up high-quality and open-access regional taxonomic reference databases for the Tibetan Plateau should be given priority in the future. To conclude, the archival, taphonomic, and methodological conditions of the Tibetan Plateau are favorable for performing sedaDNA studies. More research should be encouraged to address questions about long-term ecological dynamics at ecosystem scale and to bring the paleoecology of the Tibetan Plateau into a new era.
KW - Sedimentary ancient DNA (sedaDNA)
KW - Tibetan Plateau
KW - Environmental DNA
KW - Taphonomy
KW - Ecosystem
KW - Biodiversity
KW - Paleoecology
KW - Paleogeography
Y1 - 2022
U6 - https://doi.org/10.1016/j.quascirev.2022.107703
SN - 0277-3791
SN - 1873-457X
VL - 293
PB - Elsevier
CY - Oxford
ER -
TY - JOUR
A1 - Schulte, Luise
A1 - Li, Chenzhi
A1 - Lisovski, Simeon
A1 - Herzschuh, Ulrike
T1 - Forest-permafrost feedbacks and glacial refugia help explain the unequal distribution of larch across continents
JF - Journal of biogeography
N2 - Aim: The continental-scale distribution of plant functional types, such as evergreen and summergreen needle-leaf forest, is assumed to be determined by contemporary climate. However, the distribution of summergreen needle-leaf forest of larch (Larix Mill.) differs markedly between the continents, despite relatively similar climatic conditions. The reasons for these differences are little understood. Our aim is to identify potential triggers and drivers of the current distribution patterns by comparing species' bioclimatic niches, glacial refugia and postglacial recolonization patterns.
Location: Northern hemisphere.
Taxon: Species of the genus Larix (Mill.).
Methods: We compare species distribution and dominance using species ranges and sites of dominance, as well as their occurrence on modelled permafrost extent, and active layer thickness (ALT). We compare the bioclimatic niches and calculate the niche overlap between species, using the same data in addition to modern climate data. We synthesize pollen, macrofossil and ancient DNA palaeo-evidence of past Larix occurrences of the last 60,000 years and track differences in distribution patterns through time.
Results: Bioclimatic niches show large overlaps between Asian larch species and American Larix laricina. The distribution across various degrees of permafrost extent is distinctly different for Asian L. gmelinii and L. cajanderi compared to the other species, whereas the distribution on different depths of ALT is more similar among Asian and American species. Northern glacial refugia for Larix are only present in eastern Asia and Alaska.
Main Conclusion: The dominance of summergreen larches in Asia, where evergreen conifers dominate most of the rest of the boreal forests, is dependent on the interaction of several factors which allows Asian L. gmelinii and L. cajanderi to dominate where these factors coincide. These factors include the early postglacial spread out of northern glacial refugia in the absence of competitors as well as a positive feedback mechanism between frozen ground and forest.
KW - bioclimatic niche
KW - glacial refugia
KW - larch
KW - Larix
KW - permafrost
KW - phylogeography
KW - postglacial recolonization
Y1 - 2022
U6 - https://doi.org/10.1111/jbi.14456
SN - 0305-0270
SN - 1365-2699
VL - 49
IS - 10
SP - 1825
EP - 1838
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Radosavljevic, Boris
A1 - Lantuit, Hugues
A1 - Knoblauch, Christian
A1 - Couture, Nicole
A1 - Herzschuh, Ulrike
A1 - Fritz, Michael
T1 - Arctic nearshore sediment dynamics - an example from Herschel Island - Qikiqtaruk, Canada
JF - Journal of marine science and engineering
N2 - Increasing arctic coastal erosion rates imply a greater release of sediments and organic matter into the coastal zone. With 213 sediment samples taken around Herschel Island-Qikiqtaruk, Canadian Beaufort Sea, we aimed to gain new insights on sediment dynamics and geochemical properties of a shallow arctic nearshore zone. Spatial characteristics of nearshore sediment texture (moderately to poorly sorted silt) are dictated by hydrodynamic processes, but ice-related processes also play a role. We determined organic matter (OM) distribution and inferred the origin and quality of organic carbon by C/N ratios and stable carbon isotopes delta C-13. The carbon content was higher offshore and in sheltered areas (mean: 1.0 wt.%., S.D.: 0.9) and the C/N ratios also showed a similar spatial pattern (mean: 11.1, S.D.: 3.1), while the delta C-13 (mean: -26.4 parts per thousand VPDB, S.D.: 0.4) distribution was more complex. We compared the geochemical parameters of our study with terrestrial and marine samples from other studies using a bootstrap approach. Sediments of the current study contained 6.5 times and 1.8 times less total organic carbon than undisturbed and disturbed terrestrial sediments, respectively. Therefore, degradation of OM and separation of carbon pools take place on land and continue in the nearshore zone, where OM is leached, mineralized, or transported beyond the study area.
KW - permafrost
KW - Arctic Ocean
KW - stable carbon isotopes
KW - nitrogen
KW - sediment
KW - chemistry
KW - sediment dynamics
KW - Beaufort Sea
KW - grain size
Y1 - 2022
U6 - https://doi.org/10.3390/jmse10111589
SN - 2077-1312
VL - 10
IS - 11
PB - MDPI
CY - Basel
ER -
TY - JOUR
A1 - Dallmeyer, Anne
A1 - Kleinen, Thomas
A1 - Claussen, Martin
A1 - Weitzel, Nils
A1 - Cao, Xianyong
A1 - Herzschuh, Ulrike
T1 - The deglacial forest conundrum
JF - Nature Communications
N2 - How fast the Northern Hemisphere (NH) forest biome tracks strongly warming climates is largely unknown. Regional studies reveal lags between decades and millennia. Here we report a conundrum: Deglacial forest expansion in the NH extra-tropics occurs approximately 4000 years earlier in a transient MPI-ESM1.2 simulation than shown by pollen-based biome reconstructions. Shortcomings in the model and the reconstructions could both contribute to this mismatch, leaving the underlying causes unresolved. The simulated vegetation responds within decades to simulated climate changes, which agree with pollen-independent reconstructions. Thus, we can exclude climate biases as main driver for differences. Instead, the mismatch points at a multi-millennial disequilibrium of the NH forest biome to the climate signal. Therefore, the evaluation of time-slice simulations in strongly changing climates with pollen records should be critically reassessed. Our results imply that NH forests may be responding much slower to ongoing climate changes than Earth System Models predict.
Deglacial forest expansion in the Northern Hemisphere poses a conundrum: Model results agree with the climate signal but are several millennia ahead of reconstructed forest dynamics. The underlying causes remain unsolved.
Y1 - 2022
U6 - https://doi.org/10.1038/s41467-022-33646-6
SN - 2041-1723
VL - 13
IS - 1
PB - Nature Publishing Group UK
CY - [London]
ER -
TY - JOUR
A1 - Herzschuh, Ulrike
A1 - Böhmer, Thomas
A1 - Li, Chenzhi
A1 - Cao, Xianyong
A1 - Hébert, Raphaël
A1 - Dallmeyer, Anne
A1 - Telford, Richard J.
A1 - Kruse, Stefan
T1 - Reversals in temperature-precipitation correlations in the Northern Hemisphere extratropics during the Holocene
JF - Geophysical research letters
N2 - Future precipitation levels remain uncertain because climate models have struggled to reproduce observed variations in temperature-precipitation correlations. Our analyses of Holocene proxy-based temperature-precipitation correlations and hydrological sensitivities from 2,237 Northern Hemisphere extratropical pollen records reveal a significant latitudinal dependence and temporal variations among the early, middle, and late Holocene. These proxy-based variations are largely consistent with patterns obtained from transient climate simulations (TraCE21k). While high latitudes and subtropical monsoon areas show mainly stable positive correlations throughout the Holocene, the mid-latitude pattern is temporally and spatially more variable. In particular, we identified a reversal from positive to negative temperature-precipitation correlations in the eastern North American and European mid-latitudes from the early to mid-Holocene that mainly related to slowed down westerlies and a switch to moisture-limited convection under a warm climate. Our palaeoevidence of past temperature-precipitation correlation shifts identifies those regions where simulating past and future precipitation levels might be particularly challenging.
Y1 - 2022
U6 - https://doi.org/10.1029/2022GL099730
SN - 0094-8276
SN - 1944-8007
VL - 49
IS - 22
PB - American Geophysical Union
CY - Washington
ER -
TY - JOUR
A1 - Kruse, Stefan
A1 - Herzschuh, Ulrike
T1 - Regional opportunities for tundra conservation in the next 1000 years
JF - eLife
N2 - The biodiversity of tundra areas in northern high latitudes is threatened by invasion of forests under global warming. However, poorly understood nonlinear responses of the treeline ecotone mean the timing and extent of tundra losses are unclear, but policymakers need such information to optimize conservation efforts. Our individual-based model LAVESI, developed for the Siberian tundra-taiga ecotone, can help improve our understanding. Consequently, we simulated treeline migration trajectories until the end of the millennium, causing a loss of tundra area when advancing north. Our simulations reveal that the treeline follows climate warming with a severe, century-long time lag, which is overcompensated by infilling of stands in the long run even when temperatures cool again. Our simulations reveal that only under ambitious mitigation strategies (relative concentration pathway 2.6) will ~30% of original tundra areas remain in the north but separated into two disjunct refugia.
KW - Larix gmelinii
KW - Larix cajanderi
KW - nonlinear response
KW - treeline ecotone
KW - tundra
KW - Ecology
KW - Short Report
Y1 - 2022
U6 - https://doi.org/10.7554/eLife.75163
SN - 2050-084X
VL - 11
PB - eLife Sciences Publications
CY - Cambridge
ER -
TY - JOUR
A1 - Zhang, Naimeng
A1 - Cao, Xianyong
A1 - Xu, Qinghai
A1 - Huang, Xiaozhong
A1 - Herzschuh, Ulrike
A1 - Shen, Zhongwei
A1 - Peng, Wei
A1 - Liu, Sisi
A1 - Wu, Duo
A1 - Wang, Jian
A1 - Xia, Huan
A1 - Zhang, Dongju
A1 - Chen, Fahu
T1 - Vegetation change and human-environment interactions in the Qinghai Lake Basin, northeastern Tibetan Plateau, since the last deglaciation
JF - Catena
N2 - The nature of the interaction between prehistoric humans and their environment, especially the vegetation, has long been of interest. The Qinghai Lake Basin in North China is well-suited to exploring the interactions between prehistoric humans and vegetation in the Tibetan Plateau, because of the comparatively dense distribution of archaeological sites and the ecologically fragile environment. Previous pollen studies of Qinghai Lake have enabled a detailed reconstruction of the regional vegetation, but they have provided relatively little information on vegetation change within the Qinghai Lake watershed. To address the issue we conducted a pollen-based vegetation reconstruction for an archaeological site (YWY), located on the southern shore of Qinghai Lake. We used high temporal-resolution pollen records from the YWY site and from Qinghai Lake, spanning the interval since the last deglaciation (15.3 kyr BP to the present) to quantitatively reconstruct changes in the local and regional vegetation using Landscape Reconstruction Algorithm models. The results show that, since the late glacial, spruce forest grew at high altitudes in the surrounding mountains, while the lakeshore environment was occupied mainly by shrub-steppe. From the lateglacial to the middle Holocene, coniferous woodland began to expand downslope and reached the YWY site at 7.1 kyr BP. The living environment of the local small groups of Paleolithic-Epipaleolithic humans (during 15.3-13.1 kyr BP and 9-6.4 kyr BP) changed from shrub-steppe to coniferous forest-steppe. The pollen record shows no evidence of pronounced changes in the vegetation community corresponding to human activity. However, based on a comparison of the local and regional vegetation reconstructions, low values of biodiversity and a significant increase in two indicators of vegetation degradation, Chenopodiaceae and Rosaceae, suggest that prehistoric hunters-gatherers likely disturbed the local vegetation during 9.0-6.4 kyr BP. Our findings are a preliminary attempt to study human-environment interactions at Paleolithic-Epipaleolithic sites in the region, and they contribute to ongoing environmental archaeology research in the Tibetan Plateau.
KW - Quantitative vegetation reconstruction
KW - Local and regional vegetation
KW - dynamics
KW - Paleolithic-Epipaleolithic human-environment
KW - interactions
KW - Northeastern Tibetan Plateau
Y1 - 2022
U6 - https://doi.org/10.1016/j.catena.2021.105892
SN - 0341-8162
SN - 1872-6887
VL - 210
PB - Elsevier
CY - Amsterdam
ER -
TY - JOUR
A1 - Li, Chenzhi
A1 - Postl, Alexander K.
A1 - Böhmer, Thomas
A1 - Cao, Xianyong
A1 - Dolman, Andrew M.
A1 - Herzschuh, Ulrike
T1 - Harmonized chronologies of a global late Quaternary pollen dataset (LegacyAge 1.0)
JF - Earth system science data : ESSD
N2 - We present a chronology framework named LegacyAge 1.0 containing harmonized chronologies for 2831 pollen records (downloaded from the Neotoma Paleoecology Database and the supplementary Asian datasets) together with their age control points and metadata in machine-readable data formats.
All chronologies use the Bayesian framework implemented in Bacon version 2.5.3. Optimal parameter settings of priors (accumulation.shape, memory.strength, memory.mean, accumulation.rate, and thickness) were identified based on information in the original publication or iteratively after preliminary model inspection.
The most common control points for the chronologies are radiocarbon dates (86.1 %), calibrated by the latest calibration curves (IntCal20 and SHCal20 for the terrestrial radiocarbon dates in the Northern Hemisphere and Southern Hemisphere and Marine20 for marine materials).
The original publications were consulted when dealing with outliers and inconsistencies. Several major challenges when setting up the chronologies included the waterline issue (18.8% of records), reservoir effect (4.9 %), and sediment deposition discontinuity (4.4 %).
Finally, we numerically compare the LegacyAge 1.0 chronologies to those published in the original publications and show that the reliability of the chronologies of 95.4% of records could be improved according to our assessment.
Our chronology framework and revised chronologies provide the opportunity to make use of the ages and age uncertainties in synthesis studies of, for example, pollen-based vegetation and climate change.
The LegacyAge 1.0 dataset, including metadata, datings, harmonized chronologies, and R code used, is openaccess and available at PANGAEA (https://doi.org/10.1594/PANGAEA.933132; Li et al., 2021) and Zenodo (https://doi.org/10.5281/zenodo.5815192; Li et al., 2022), respectively.
Y1 - 2022
U6 - https://doi.org/10.5194/essd-14-1331-2022
SN - 1866-3508
SN - 1866-3516
VL - 14
IS - 3
SP - 1331
EP - 1343
PB - Copernics Publications
CY - Katlenburg-Lindau
ER -
TY - JOUR
A1 - Heim, Birgit
A1 - Lisovski, Simeon
A1 - Wieczorek, Mareike
A1 - Morgenstern, Anne
A1 - Juhls, Bennet
A1 - Shevtsova, Iuliia
A1 - Kruse, Stefan
A1 - Boike, Julia
A1 - Fedorova, Irina
A1 - Herzschuh, Ulrike
T1 - Spring snow cover duration and tundra greenness in the Lena Delta, Siberia
BT - two decades of MODIS satellite time series (2001-2021)
JF - Environmental research letters
N2 - The Lena Delta in Siberia is the largest delta in the Arctic and as a snow-dominated ecosystem particularly vulnerable to climate change.
Using the two decades of MODerate resolution Imaging Spectroradiometer satellite acquisitions, this study investigates interannual and spatial variability of snow-cover duration and summer vegetation vitality in the Lena Delta.
We approximated snow by the application of the normalized difference snow index and vegetation greenness by the normalized difference vegetation index (NDVI). We consolidated the analyses by integrating reanalysis products on air temperature from 2001 to 2021, and air temperature, ground temperature, and the date of snow-melt from time-lapse camera (TLC) observations from the Samoylov observatory located in the central delta.
We extracted spring snow-cover duration determined by a latitudinal gradient. The 'regular year' snow-melt is transgressing from mid-May to late May within a time window of 10 days across the delta.
We calculated yearly deviations per grid cell for two defined regions, one for the delta, and one focusing on the central delta. We identified an ensemble of early snow-melt years from 2012 to 2014, with snow-melt already starting in early May, and two late snow-melt years in 2004 and 2017, with snow-melt starting in June. In the times of TLC recording, the years of early and late snow-melt were confirmed.
In the three summers after early snow-melt, summer vegetation greenness showed neither positive nor negative deviations. Whereas, vegetation greenness was reduced in 2004 after late snow-melt together with the lowest June monthly air temperature of the time series record. Since 2005, vegetation greenness is rising, with maxima in 2018 and 2021.
The NDVI rise since 2018 is preceded by up to 4 degrees C warmer than average June air temperature. The ongoing operation of satellite missions allows to monitor a wide range of land surface properties and processes that will provide urgently needed data in times when logistical challenges lead to data gaps in land-based observations in the rapidly changing Arctic.
KW - Arctic vegetation
KW - tundra
KW - snow cover duration
KW - NDVI
KW - NDSI
KW - MODIS
KW - Lena Delta
Y1 - 2022
U6 - https://doi.org/10.1088/1748-9326/ac8066
SN - 1748-9326
VL - 17
IS - 8
PB - IOP Publ. Ltd.
CY - Bristol
ER -
TY - JOUR
A1 - Stuenzi, Simone Maria
A1 - Kruse, Stefan
A1 - Boike, Julia
A1 - Herzschuh, Ulrike
A1 - Oehme, Alexander
A1 - Pestryakova, Luidmila A.
A1 - Westermann, Sebastian
A1 - Langer, Moritz
T1 - Thermohydrological impact of forest disturbances on ecosystem-protected permafrost
JF - Journal of geophysical research : Biogeosciences
N2 - Boreal forests cover over half of the global permafrost area and protect underlying permafrost. Boreal forest development, therefore, has an impact on permafrost evolution, especially under a warming climate.
Forest disturbances and changing climate conditions cause vegetation shifts and potentially destabilize the carbon stored within the vegetation and permafrost. Disturbed permafrost-forest ecosystems can develop into a dry or swampy bush- or grasslands, shift toward broadleaf- or evergreen needleleaf-dominated forests, or recover to the pre-disturbance state.
An increase in the number and intensity of fires, as well as intensified logging activities, could lead to a partial or complete ecosystem and permafrost degradation. We study the impact of forest disturbances (logging, surface, and canopy fires) on the thermal and hydrological permafrost conditions and ecosystem resilience.
We use a dynamic multilayer canopy-permafrost model to simulate different scenarios at a study site in eastern Siberia. We implement expected mortality, defoliation, and ground surface changes and analyze the interplay between forest recovery and permafrost. We find that forest loss induces soil drying of up to 44%, leading to lower active layer thicknesses and abrupt or steady decline of a larch forest, depending on disturbance intensity.
Only after surface fires, the most common disturbances, inducing low mortality rates, forests can recover and overpass pre-disturbance leaf area index values. We find that the trajectory of larch forests after surface fires is dependent on the precipitation conditions in the years after the disturbance. Dryer years can drastically change the direction of the larch forest development within the studied period.
KW - permafrost
KW - boreal forest
KW - periglacial process
KW - Siberia
KW - larch forest
KW - disturbance
Y1 - 2022
U6 - https://doi.org/10.1029/2021JG006630
SN - 2169-8953
SN - 2169-8961
VL - 127
IS - 5
PB - American Geophysical Union
CY - Washington
ER -
TY - JOUR
A1 - Andreev, Andrei
A1 - Nazarova, Larisa B.
A1 - Lenz, Marlene M.
A1 - Böhmer, Thomas
A1 - Syrykh, Ludmila
A1 - Wagner, Bernd
A1 - Melles, Martin
A1 - Pestryakova, Luidmila A.
A1 - Herzschuh, Ulrike
T1 - Late Quaternary paleoenvironmental reconstructions from sediments of Lake Emanda (Verkhoyansk Mountains, East Siberia)
JF - Journal of quaternary science : JQS
N2 - Continuous pollen and chironomid records from Lake Emanda (65 degrees 17'N, 135 degrees 45'E) provide new insights into the Late Quaternary environmental history of the Yana Highlands (Yakutia). Larch forest with shrubs (alders, pines, birches) dominated during the deposition of the lowermost sediments suggesting its Early Weichselian [Marine Isotope Stage (MIS) 5] age. Pollen- and chironomid-based climate reconstructions suggest July temperatures (T-July) slightly lower than modern. Gradually increasing amounts of herb pollen and cold stenotherm chironomid head capsules reflect cooler and drier environments, probably during the termination of MIS 5. T-July dropped to 8 degrees C. Mostly treeless vegetation is reconstructed during MIS 3. Tundra and steppe communities dominated during MIS 2. Shrubs became common after similar to 14.5 ka BP but herb-dominated habitats remained until the onset of the Holocene. Larch forests with shrub alder and dwarf birch dominated after the Holocene onset, ca. 11.7 ka BP. Decreasing amounts of shrub pollen during the Lateglacial are assigned to the Older Dryas and Younger Dryas with T-July similar to 7.5 degrees C. T-July increased up to 13 degrees C. Shrub stone pine was present after similar to 7.5 ka BP. The vegetation has been similar to modern since ca. 5.8 ka BP. Chironomid diversity and concentration in the sediments increased towards the present day, indicating the development of richer hydrobiological communities in response to the Holocene thermal maximum.
KW - chironomids
KW - environmental reconstructions
KW - Late Quaternary
KW - pollen
Y1 - 2022
U6 - https://doi.org/10.1002/jqs.3419
SN - 0267-8179
SN - 1099-1417
VL - 37
IS - 5
SP - 884
EP - 899
PB - Wiley
CY - New York, NY [u.a.]
ER -
TY - JOUR
A1 - Herzschuh, Ulrike
A1 - Li, Chenzhi
A1 - Boehmer, Thomas
A1 - Postl, Alexander K.
A1 - Heim, Birgit
A1 - Andreev, Andrei A.
A1 - Cao, Xianyong
A1 - Wieczorek, Mareike
A1 - Ni, Jian
T1 - LegacyPollen 1.0
BT - a taxonomically harmonized global late Quaternary pollen dataset of 2831 records with standardized chronologies
JF - Earth system science data : ESSD
N2 - Here we describe the LegacyPollen 1.0, a dataset of 2831 fossil pollen records with metadata, a harmonized taxonomy, and standardized chronologies.
A total of 1032 records originate from North America, 1075 from Europe, 488 from Asia, 150 from Latin America, 54 from Africa, and 32 from the Indo-Pacific.
The pollen data cover the late Quaternary (mostly the Holocene). The original 10 110 pollen taxa names (including variations in the notations) were harmonized to 1002 terrestrial taxa (including Cyperaceae), with woody taxa and major herbaceous taxa harmonized to genus level and other herbaceous taxa to family level.
The dataset is valuable for synthesis studies of, for example, taxa areal changes, vegetation dynamics, human impacts (e.g., deforestation), and climate change at global or continental scales.
The harmonized pollen and metadata as well as the harmonization table are available from PANGAEA (https://doi.org/10.1594/PANGAEA.929773; Herzschuh et al., 2021). R code for the harmonization is provided at Zenodo (https://doi.org/10.5281/zenodo.5910972; Herzschuh et al., 2022) so that datasets at a customized harmonization level can be easily established.
Y1 - 2022
U6 - https://doi.org/10.5194/essd-14-3213-2022
SN - 1866-3508
SN - 1866-3516
VL - 14
IS - 7
SP - 3213
EP - 3227
PB - Copernicus
CY - Göttingen
ER -
TY - JOUR
A1 - Glückler, Ramesh
A1 - Geng, Rongwei
A1 - Grimm, Lennart
A1 - Baisheva, Izabella
A1 - Herzschuh, Ulrike
A1 - Stoof-Leichsenring, Kathleen R.
A1 - Kruse, Stefan
A1 - Andreev, Andrej Aleksandrovic
A1 - Pestryakova, Luidmila
A1 - Dietze, Elisabeth
T1 - Holocene wildfire and vegetation dynamics in Central Yakutia, Siberia, reconstructed from lake-sediment proxies
JF - Frontiers in Ecology and Evolution
N2 - Wildfires play an essential role in the ecology of boreal forests.
In eastern Siberia, fire activity has been increasing in recent years, challenging the livelihoods of local communities. Intensifying fire regimes also increase disturbance pressure on the boreal forests, which currently protect the permafrost beneath from accelerated degradation.
However, long-term relationships between changes in fire regime and forest structure remain largely unknown.
We assess past fire-vegetation feedbacks using sedimentary proxy records from Lake Satagay, Central Yakutia, Siberia, covering the past c. 10,800 years.
Results from macroscopic and microscopic charcoal analyses indicate high amounts of burnt biomass during the Early Holocene, and that the present-day, low-severity surface fire regime has been in place since c. 4,500 years before present.
A pollen-based quantitative reconstruction of vegetation cover and a terrestrial plant record based on sedimentary ancient DNA metabarcoding suggest a pronounced shift in forest structure toward the Late Holocene.
Whereas the Early Holocene was characterized by postglacial open larch-birch woodlands, forest structure changed toward the modern, mixed larch-dominated closed-canopy forest during the Mid-Holocene.
We propose a potential relationship between open woodlands and high amounts of burnt biomass, as well as a mediating effect of dense larch forest on the climate-driven intensification of fire regimes.
Considering the anticipated increase in forest disturbances (droughts, insect invasions, and wildfires), higher tree mortality may force the modern state of the forest to shift toward an open woodland state comparable to the Early Holocene.
Such a shift in forest structure may result in a positive feedback on currently intensifying wildfires.
These new long-term data improve our understanding of millennial-scale fire regime changes and their relationships to changes of vegetation in Central Yakutia, where the local population is already being confronted with intensifying wildfire seasons.
KW - fire
KW - larch
KW - boreal
KW - forest
KW - Russia
KW - charcoal
KW - pollen
KW - ancient DNA
Y1 - 2022
U6 - https://doi.org/10.3389/fevo.2022.962906
SN - 2296-701X
VL - 10
PB - Frontiers Media
CY - Lausanne
ER -
TY - JOUR
A1 - Bizic, Mina
A1 - Ionescu, Danny
A1 - Karnatak, Rajat
A1 - Musseau, Camille L.
A1 - Onandia, Gabriela
A1 - Berger, Stella A.
A1 - Nejstgaard, Jens C.
A1 - Lischeid, Gunnar
A1 - Gessner, Mark O.
A1 - Wollrab, Sabine
A1 - Grossart, Hans-Peter
T1 - Land-use type temporarily affects active pond community structure but not gene expression patterns
JF - Molecular ecology
N2 - Changes in land use and agricultural intensification threaten biodiversity and ecosystem functioning of small water bodies. We studied 67 kettle holes (KH) in an agricultural landscape in northeastern Germany using landscape-scale metatranscriptomics to understand the responses of active bacterial, archaeal and eukaryotic communities to land-use type. These KH are proxies of the millions of small standing water bodies of glacial origin spread across the northern hemisphere. Like other landscapes in Europe, the study area has been used for intensive agriculture since the 1950s. In contrast to a parallel environmental DNA study that suggests the homogenization of biodiversity across KH, conceivably resulting from long-lasting intensive agriculture, land-use type affected the structure of the active KH communities during spring crop fertilization, but not a month later. This effect was more pronounced for eukaryotes than for bacteria. In contrast, gene expression patterns did not differ between months or across land-use types, suggesting a high degree of functional redundancy across the KH communities. Variability in gene expression was best explained by active bacterial and eukaryotic community structures, suggesting that these changes in functioning are primarily driven by interactions between organisms. Our results indicate that influences of the surrounding landscape result in temporary changes in the activity of different community members. Thus, even in KH where biodiversity has been homogenized, communities continue to respond to land management. This potential needs to be considered when developing sustainable management options for restoration purposes and for successful mitigation of further biodiversity loss in agricultural landscapes.
KW - agriculture
KW - eRNA
KW - land use
KW - metacommunity
KW - transcriptomics
Y1 - 2022
U6 - https://doi.org/10.1111/mec.16348
SN - 0962-1083
SN - 1365-294X
VL - 31
IS - 6
SP - 1716
EP - 1734
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Tolomeev, Aleksandr P.
A1 - Dubovskaya, Olga P.
A1 - Kirillin, Georgiy
A1 - Buseva, Zhanna
A1 - Kolmakova, Olesya
A1 - Grossart, Hans-Peter
A1 - Tang, Kam W.
A1 - Gladyšev, Michail I.
T1 - Degradation of dead cladoceran zooplankton and their contribution to organic carbon cycling in stratified lakes
BT - field observation and model prediction
JF - Journal of plankton research
N2 - The contribution of dead zooplankton biomass to carbon cycle in aquatic ecosystems is practically unknown. Using abundance data of zooplankton in water column and dead zooplankton in sediment traps in Lake Stechlin, an ecological-mathematical model was developed to simulate the abundance and sinking of zooplankton carcasses and predict the related release of labile organic matter (LOM) into the water column. We found species-specific differences in mortality rate of the dominant zooplankton: Daphnia cucullata, Bosmina coregoni and Diaphanosoma brachyurum (0.008, 0.129 and 0.020 day(-1), respectively) and differences in their carcass sinking velocities in metalimnion (and hypolimnion): 2.1 (7.64), 14.0 (19.5) and 1.1 (5.9) m day(-1), respectively. Our model simulating formation and degradation processes of dead zooplankton predicted a bimodal distribution of the released LOM: epilimnic and metalimnic peaks of comparable intensity, ca. 1 mg DW m(-3) day(-1). Maximum degradation of carcasses up to ca. 1.7 mg DW m(-3) day(-1) occurred in the density gradient zone of metalimnion. LOM released from zooplankton carcasses into the surrounding water may stimulate microbial activity and facilitate microbial degradation of more refractory organic matter; therefore, dead zooplankton are expected to be an integral part of water column carbon source/sink dynamics in stratified lakes.
KW - zooplankton carcasses
KW - non-predatory mortality
KW - sinking velocities
KW - microbial degradation
KW - Lake Stechlin
KW - simulation modeling
Y1 - 2022
U6 - https://doi.org/10.1093/plankt/fbac023
SN - 0142-7873
SN - 1464-3774
VL - 44
IS - 3
SP - 386
EP - 400
PB - Oxford Univ. Press
CY - Oxford
ER -
TY - THES
A1 - Nwosu, Ebuka Canisius
T1 - Sedimentary DNA-based reconstruction of cyanobacterial communities from Lake Tiefer See, NE Germany, for the last 11,000 years
N2 - Climate change and human-driven eutrophication promote the spread of harmful cyanobacteria blooms in lakes worldwide, which affects water quality and impairs the aquatic food chain. In recent times, sedimentary ancient DNA-based (sedaDNA) studies were used to probe how centuries of climate and environmental changes have affected cyanobacterial assemblages in temperate lakes. However, there is a lack of information on the consistency between sediment-deposited cyanobacteria communities versus those of the water column, and on the individual role of natural climatic changes versus human pressure on cyanobacteria community dynamics over multi-millennia time scales.
Therefore, this thesis uses sedimentary ancient DNA of Lake Tiefer See in northeastern Germany to trace the deposition of cyanobacteria along the water column into the sediment, and to reconstruct cyanobacteria communities spanning the last 11,000 years using a set of molecular techniques including quantitative PCR, biomarkers, metabarcoding, and metagenome sequence analyses.
The results of this thesis proved that cyanobacterial composition and species richness did not significantly differ among different water depths, sediment traps, and surface sediments. This means that the cyanobacterial community composition from the sediments reflects the water column communities. However, there is a skewed sediment deposition of different cyanobacteria groups because of DNA alteration and/or deterioration during transport along the water column to the sediment. Specifically, single filament taxa, such as Planktothrix, are poorly represented in sediments despite being abundant in the water column as shown by an additional study of the thesis on cyanobacteria seasonality. In contrast, aggregate-forming taxa, like Aphanizomenon, are relatively overrepresented in sediment although they are not abundant in the water column. These different deposition patterns of cyanobacteria taxa should be considered in future DNA-based paleolimnological investigations. The thesis also reveals a substantial increase in total cyanobacteria abundance during the Bronze Age which is not apparent in prior phases of the early to middle Holocene and is suggested to be caused by human farming, deforestation, and excessive nutrient addition to the lake. Not only cyanobacterial abundance was influenced by human activity but also cyanobacteria community composition differed significantly between phases of no, moderate, and intense human impact.
The data presented in this thesis are the first on sedimentary cyanobacteria DNA since the early Holocene in a temperate lake. The results bring together archaeological, historical climatic, and limnological data with deep DNA-sequencing and paleoecology to reveal a legacy impact of human pressure on lake cyanobacteria populations dating back to approximately 4000 years.
N2 - Der Klimawandel und die vom Menschen verursachte Eutrophierung fördern die Ausbreitung schädlicher Cyanobakterienblüten in Seen weltweit, was die Wasserqualität und die aquatische Nahrungskette beeinträchtigt. In jüngster Zeit wurden sedimentäre DNA (sedaDNA)-Studien verwendet, um zu untersuchen, wie sich klimatische- und menschliche Umweltveränderungen von Jahrhunderten auf Cyanobakteriengemeinschaften in Seen ausgewirkt haben. Jedoch fehlen bislang Informationen, wie repräsentativ die im Sediment abgelagerten Cyanobakterien und deren DNA für die Gemeinschaften der Wassersäule sind, sowie zur individuellen Rolle natürlicher klimatischer Veränderungen gegenüber dem menschlichen Einflusses auf die Dynamik von Cyanobakterien über Zeitskalen von Jahrtausenden.
Daher wurde in dieser Arbeit sedimentäre alte DNA (sedaDNA) des Tiefen Sees in Nordostdeutschland verwendet, um die Ablagerung von Cyanobakterien entlang der Wassersäule in das Sediment zu verfolgen. Ein Hauptteil dieser Arbeit bildete jedoch die Rekonstruktion von Cyanobakteriengemeinschaften der letzten 11.000 Jahre, unter Verwendung einer Reihe von molekularen Techniken, darunter quantitative PCR, Biomarker, Metabarcoding und Metagenom-Sequenzanalysen.
Die Ergebnisse dieser Arbeit beweisen, dass die Cyanobakterien-Zusammensetzung und der Artenreichtum zwischen verschiedenen Wassertiefen, Sedimentfallen und Oberflächensedimenten nicht signifikant unterschiedlich ist. Das bedeutet, dass die Zusammensetzung der Cyanobakteriengemeinschaften aus den Sedimenten die Gemeinschaften der Wassersäule widerspiegelt. Aufgrund von DNA-Veränderungen und/oder -Abbau während des Transports entlang der Wassersäule zum Sediment kommt es jedoch zu einer verzerrten Sedimentablagerung verschiedener Cyanobakterien Arten. Insbesondere sind filamentose Arten wie Planktothrix in Sedimenten schlecht vertreten, obwohl sie, laut Ergebnissen einer zusätzlichen Studie dieser Arbeit zur Saisonalität von Cyanobakterien, in der Wassersäule reichlich vorhanden sind. Im Gegensatz dazu sind aggregatbildende Arten wie Aphanizomenon in Sedimenten relativ gesehen überrepräsentiert, obwohl sie in der Wassersäule relativ selten vorkommen. Diese unterschiedlichen Muster zur Sedimentablagerung verschiedener Cyanobakterien Arten sollten in zukünftigen DNA-basierten paläolimnologischen Untersuchungen berücksichtigt werden. Die Dissertation zeigt auch eine deutliche Zunahme der Cyanobakterien Abundanz während der Bronzezeit, die in vorhergehenden Phasen des frühen und mittleren Holozäns nicht erkennbar war. Dies ist wahrscheinlich durch menschliche Landwirtschaft, Entwaldung und übermäßige Nährstoffzufuhr in den See verursacht worden. Nicht nur die Abundanz von Cyanobakterien wurde durch menschliche Aktivitäten beeinflusst, sondern auch die Zusammensetzung von deren Gemeinschaften, die sich signifikant zwischen Phasen unterscheidet, die durch keinen, moderaten, und intensiven menschlichen Einfluss gekennzeichnet sind.
Die in dieser Dissertation präsentierten Daten sind die ersten zu sedimentärer Cyanobakterien-DNA seit dem frühen Holozän eines Sees der gemäßigte Klimazone. Die Ergebnisse vereinen archäologische, historische, klimatische und limnologische Daten mit hochaufgelöster und Hochdurchsatz-DNA-Sequenzierung und belegen, dass der menschliche Einfluss auf Cyanobakteriengemeinschaften in Seen etwa 4000 Jahre zurückreicht.
KW - anthropogenic impact
KW - paleoecology
KW - high throughput sequencing
KW - cyanobacteria biomarker
KW - microbial diversity
KW - microbial ecology
KW - 7-methylheptadecane
KW - 7-Methylheptadecan
KW - anthropogene Einwirkung
KW - Cyanobakterien-Biomarker
KW - hoher Durchsatz Sequenzierung
KW - mikrobielle Vielfalt
KW - mikrobielle Ökologie
KW - Paläoökologie
Y1 - 2022
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-563590
ER -
TY - THES
A1 - Schulte, Luise
T1 - Dynamics of Larix (Mill.) species in Siberia during the last 50,000 years inferred from sedimentary ancient DNA
T1 - Die Dynamik sibirischer Lärchenarten (Larix Mill.) während der
der letzten 50.000 Jahre, untersucht mittels sedimentärer alter DNA
N2 - The deciduous needle tree larch (Larix Mill.) covers more than 80% of the Asian boreal forests. Only a few Larix species constitute the vast forests and these species differ markedly in their ecological traits, most importantly in their ability to grow on and stabilize underlying permafrost. The pronounced dominance of the summergreen larches makes the Asian boreal forests unique, as the rest of the northern hemisphere boreal forests is almost exclusively dominated by evergreen needle-leaf forests. Global warming is impacting the whole world but is especially pronounced in the arctic and boreal regions. Although adapted to extreme climatic conditions, larch forests are sensitive to varying climatic conditions. By their sheer size, changes in Asian larch forests as range shifts or changes in species composition and the resulting vegetation-climate feedbacks are of global relevance. It is however still uncertain if larch forests will persist under the ongoing warming climate or if they will be replaced by evergreen forests. It is therefore of great importance to understand how these ecosystems will react to future climate warmings and if they will maintain their dominance. One step in the better understanding of larch dynamics is to study how the vast dominant forests developed and why they only established in northern Asia. A second step is to study how the species reacted to past changes in the climate.
The first objective of this thesis was to review and identify factors promoting Asian larch dominance. I achieved this by synthesizing and comparing reported larch occurrences and influencing components on the northern hemisphere continents in the present and in the past. The second objective was to find a possibility to directly study past Larix populations in Siberia and specifically their genetic variation, enabling the study of geographic movements. For this, I established chloroplast enrichment by hybridization capture from sedimentary ancient DNA (sedaDNA) isolated from lake sediment records. The third objective was to use the established method to track past larch populations, their glacial refugia during the Last Glacial Maximum (LGM) around 21,000 years before present (ka BP), and their post-glacial migration patterns.
To study larch promoting factors, I compared the present state of larch species ranges, areas of dominance, their bioclimatic niches, and the distribution on different extents and thaw depths of permafrost. The species comparison showed that the bioclimatic niches greatly overlap between the American and Asian species and that it is only in the extremely continental climates in which only the Asian larch species can persist. I revealed that the area of dominance is strongly connected to permafrost extent but less linked to permafrost seasonal thaw depths. Comparisons of the paleorecord of larch between the continents suggest differences in the recolonization history. Outside of northern Asia and Alaska, glacial refugial populations of larch were confined to the southern regions and thus recolonization could only occur as migration from south to north. Alaskan larch populations could not establish wide-range dominant forest which could be related to their own genetically depletion as separated refugial population. In Asia, it is still unclear whether or not the northern refugial populations contributed and enhanced the postglacial colonization or whether they were replaced by populations invading from the south in the course of climate warming. Asian larch dominance is thus promoted partly by adaptions to extremely continental climates and by adaptations to grow on continuous permafrost but could be also connected to differences in glacial survival and recolonization history of Larix species.
Except for extremely rare macrofossil findings of fossilized cones, traditional methods to study past vegetation are not able to distinguish between larch species or populations. Within the scope of this thesis, I therefore established a method to retrieve genetic information of past larch populations to distinguish between species. Using the Larix chloroplast genome as target, I successfully applied the method of DNA target enrichment by hybridization capture on sedaDNA samples from lake records and showed that it is able to distinguish between larch species. I then used the method on samples from lake records from across Siberia dating back up to 50 ka BP. The results allowed me to address the question of glacial survival and post-glacial recolonization mode in Siberian larch species. The analyzed pattern showed that LGM refugia were almost exclusively constituted by L. gmelinii, even in sites of current L. sibirica distribution. For included study sites, L. sibirica migrated into its extant northern distribution area only in the Holocene. Consequently, the post-glacial recolonization of L. sibirica was not enhanced by northern glacial refugia. In case of sites in extant distribution area of L. gmelinii, the absence of a genetic turn-over point to a continuous population rather than an invasion of southern refugia. The results suggest that climate has a strong influence on the distribution of Larix species and that species may also respond differently to future climate warming. Because species differ in their ecological characteristics, species distribution is also relevant with respect to further feedbacks between vegetation and climate.
With this thesis, I give an overview of present and past larch occurrences and evaluate which factors promote their dominance. Furthermore, I provide the tools to study past Larix species and give first important insights into the glacial history of Larix populations.
N2 - Der sommergrüne Nadelbaum Lärche (Larix Mill.) bedeckt mehr als 80 % der Fläche der borealen Wälder Asiens. Nur wenige Lärchenarten bilden ausgedehnte Wälder und diese Arten unterscheiden sich deutlich in ihren ökologischen Eigenschaften, vor allem in ihrer Fähigkeit, auf Permafrost zu wachsen und diesen zu stabilisieren. Die ausgeprägte Dominanz der sommergrünen Lärchen macht die asiatischen borealen Wälder einzigartig, da der Rest der borealen Wälder der Nordhalbkugel fast ausschließlich von immergrünen Nadelwäldern dominiert wird. Die Klimaerwärmung wirkt sich auf die ganze Welt aus, ist aber in den arktischen und borealen Regionen besonders ausgeprägt. Obwohl die Lärchenwälder an extreme klimatische Bedingungen angepasst sind, reagieren sie empfindlich auf klimatische Schwankungen. Aufgrund ihrer schieren Größe sind Veränderungen in asiatischen Lärchenwäldern, wie z. B. Verschiebungen des Verbreitungsgebiets oder Veränderungen in der Artenzusammensetzung und die daraus resultierenden Rückkopplungen zwischen Vegetation und Klima, von globaler Bedeutung. Es ist jedoch noch ungewiss, ob die Lärchenwälder unter der fortschreitenden Klimaerwärmung bestehen bleiben oder durch immergrüne Wälder ersetzt werden. Es ist daher von großer Bedeutung zu verstehen, wie diese Ökosysteme auf die künftige Klimaerwärmung reagieren werden und ob sie ihre Dominanz behalten werden. Ein Schritt zum besseren Verständnis der Lärchendynamik besteht darin, zu untersuchen, wie die riesigen dominanten Wälder von heute entstanden sind und warum sie sich nur in Nordasien etabliert haben. In einem zweiten Schritt soll untersucht werden, wie die Art auf vergangene Klimaveränderungen reagiert hat.
Das erste Ziel dieser Arbeit bestand darin, die Faktoren zu ermitteln, die die Dominanz der asiatischen Lärche begünstigen. Dies erreichte ich, indem ich die dokumentierten Lärchenvorkommen und die sie beeinflussenden Komponenten auf den Kontinenten der nördlichen Hemisphäre in der Gegenwart und in der Vergangenheit gesammelt und verglichen habe. Das zweite Ziel bestand darin, eine Möglichkeit zu finden, frühere Lärchenpopulationen in Sibirien und insbesondere ihre genetische Variation direkt zu studieren, um geografische Bewegungen untersuchen zu können. Dafür etablierte ich die Methode der Anreicherung von Chloroplasten durch Hybridisierung von alter sedimentärer DNA (sedaDNA) isoliert aus Seesedimenten. Das dritte Ziel bestand darin, die etablierte Methode zu nutzen, um vergangene Lärchenpopulationen, ihre eiszeitlichen Refugien während des letzten glazialen Maximums (LGM) um ca. 21.000 Jahre vor der Gegenwart (ka BP) und ihre nacheiszeitlichen Migrationsmuster zu verfolgen.
Um die Faktoren zu untersuchen, die die Ausbreitung der Lärche begünstigen, verglich ich den gegenwärtigen Stand der Verbreitungsgebiete der Lärchenarten, die Gebiete, in denen sie vorherrschen, ihre bioklimatischen Nischen und die Verteilung auf verschiedene Ausdehnungen und Auftautiefen des Permafrosts. Der Artenvergleich zeigte, dass sich die bioklimatischen Nischen der amerikanischen und asiatischen Arten stark überschneiden und dass nur in den extrem kontinentalen Klimazonen ausschließlich die asiatischen Lärchenarten überleben können. Es zeigte sich, dass das Verbreitungsgebiet stark mit der Permafrostausdehnung zusammenhängt, aber weniger mit der saisonalen Auftautiefe des Permafrosts. Der Vergleich vergangener Lärchenvorkommen zwischen den Kontinenten deutet auf Unterschiede in der Rekolonisationsgeschichte hin. Außerhalb Nordasiens und Alaskas waren die eiszeitlichen Lärchenpopulationen auf die südlichen Regionen beschränkt, so dass die Wiederbesiedlung nur als Wanderung von Süden nach Norden erfolgen konnte. Die Lärchenpopulationen in Alaska konnten keinen weiträumig dominanten Wald etablieren, was mit ihrer eigenen genetischen Verarmung als abgeschiedene Refugialpopulation zusammenhängen könnte. In Asien ist noch unklar, ob die nördlichen Refugialpopulationen zur nacheiszeitlichen Besiedlung beigetragen und diese verstärkt haben oder ob sie im Zuge der Klimaerwärmung durch von Süden eindringende Populationen ersetzt wurden. Die Dominanz der asiatischen Lärche wird also zum Teil durch Anpassungen an das extrem kontinentale Klima und durch Anpassungen an das Wachstum auf kontinuierlichem Permafrost begünstigt, könnte aber auch mit Unterschieden in der glazialen Überlebens- und Rekolonisationsgeschichte der Larix-Arten zusammenhängen.
Abgesehen von den äußerst seltenen Makrofossilienfunden versteinerter Zapfen sind die herkömmlichen Methoden zur Untersuchung der vergangenen Vegetation nicht in der Lage, zwischen Lärchenarten oder -populationen zu unterscheiden. Im Rahmen dieser Arbeit habe ich daher eine Methode zur Gewinnung genetischer Informationen früherer Lärchenpopulationen entwickelt, um zwischen den Arten zu unterscheiden. Unter Verwendung des Larix-Chloroplastengenoms habe ich die Methode der DNA-Anreicherung durch Hybridisierung erfolgreich auf sedaDNA-Proben aus See-sedimentbohrkernen angewandt und gezeigt, dass die Methode erlaubt zwischen Lärchenarten zu unterscheiden. Anschließend wendete ich die Methode auf Proben aus Seen in ganz Sibirien an, die bis zu 50 ka BP zurückreichen. Anhand der Ergebnisse konnte ich zur Beantwortung der Frage beitragen, welche sibirische Lärchenarten während des LGM überlebten und wie die postglaziale Wiederbesiedlung stattfand.
Das analysierte Muster zeigte, dass die LGM-Refugien fast ausschließlich von L. gmelinii gebildet wurden, selbst an Orten, an denen heute L. sibirica verbreitet ist. In den untersuchten Gebieten ist L. sibirica erst im Holozän in ihr heutiges nördliches Verbreitungsgebiet eingewandert. Folglich wurde die nacheiszeitliche Wiederbesiedlung von L. sibirica nicht durch nördliche eiszeitliche Refugien gefördert. Im Falle der Standorte im heutigen Verbreitungsgebiet von L. gmelinii deutet das Fehlen eines Wechsels genetischer Variation eher auf eine kontinuierliche Population als auf eine Invasion aus südlichen Refugien hin. Die Ergebnisse deuten darauf hin, dass das Klima einen starken Einfluss auf die Verbreitung von Larix-Arten hat und die Arten auch auf zukünftige Klimaerwärmung unterschiedlich reagieren könnten. Da die Arten sich in ihren ökologischen Eigenschaften unterscheiden, ist eine Änderung in der Verbreitung der Arten auch im Hinblick auf weitere Rückkopplungen zwischen Vegetation und Klima relevant.
In dieser Arbeit gebe ich einen Überblick über die heutigen und früheren Lärchenvorkommen und bewerte, welche Faktoren ihre Dominanz begünstigen. Darüber hinaus stelle ich eine Methode zur Untersuchung vergangener Lärchenarten bereit und gebe erste wichtige Einblicke in ihre glaziale Geschichte.
KW - ancient DNA
KW - ancient sedimentary DNA
KW - Larix
KW - larch
KW - glacial refugia
KW - postglacial recolonization
KW - phylogeography
KW - hybridization capture
KW - target enrichment
KW - shotgun sequencing
KW - chloroplast
KW - Siberia
KW - Larix
KW - Sibirien
KW - alte DNA
KW - alte sedimentäre DNA
KW - Chloroplast
KW - glaziale Refugien
KW - Lärche
KW - Phylogeographie
KW - nacheiszeitliche Wiederbesiedlung
KW - Shotgun Sequenzierung
Y1 - 2022
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-558782
ER -
TY - GEN
A1 - Li, Xiaoping
A1 - Apriyanto, Ardha
A1 - Flores Castellanos, Junio
A1 - Compart, Julia
A1 - Muntaha, Sidratul Nur
A1 - Fettke, Jörg
T1 - Dpe2/phs1 revealed unique starch metabolism with three distinct phases characterized by different starch granule numbers per chloroplast, allowing insights into the control mechanism of granule number regulation by gene co-regulation and metabolic profiling
T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2 - An Arabidopsis mutant lacking both the cytosolic Disproportionating enzyme 2 (DPE2) and the plastidial glucan Phosphorylase 1 (PHS1) revealed a unique starch metabolism. Dpe2/phs1 has been reported to have only one starch granule number per chloroplast when grown under diurnal rhythm. For this study, we analyzed dpe2/phs1 in details following the mutant development, and found that it showed three distinct periods of granule numbers per chloroplast, while there was no obvious change observed in Col-0. In young plants, the starch granule number was similar to that in Col-0 at first, and then decreased significantly, down to one or no granule per chloroplast, followed by an increase in the granule number. Thus, in dpe2/phs1, control over the starch granule number is impaired, but it is not defective in starch granule initiation. The data also indicate that the granule number is not fixed, and is regulated throughout plant growth. Furthermore, the chloroplasts revealed alterations during these three periods, with a partially strong aberrant morphology in the middle phase. Interestingly, the unique metabolism was perpetuated when starch degradation was further impaired through an additional lack of Isoamylase 3 (ISA3) or Starch excess 4 (SEX4). Transcriptomic studies and metabolic profiling revealed the co-regulation of starch metabolism-related genes and a clear metabolic separation between the periods. Most senescence-induced genes were found to be up-regulated more than twice in the starch-less mature leaves. Thus, dpe2/phs1 is a unique plant material source, with which we may study starch granule number regulation to obtain a more detailed understanding.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1286
KW - LCSM
KW - RNA-Seq
KW - metabolic-profiling
KW - starch granule number regulation
KW - starch initiation
KW - starch degradation
Y1 - 2022
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-571250
SN - 1866-8372
IS - 1286
ER -
TY - JOUR
A1 - Muntaha, Sidratul Nur
A1 - Li, Xiaoping
A1 - Compart, Julia
A1 - Apriyanto, Ardha
A1 - Fettke, Jörg
T1 - Carbon pathways during transitory starch degradation in Arabidopsis differentially affect the starch granule number and morphology in the dpe2/phs1 mutant background
JF - Plant physiology and biochemistry : an official journal of the Federation of European Societies of Plant Physiology
N2 - The Arabidopsis knockout mutant lacking both the cytosolic disproportionating enzyme 2 (DPE2) and the plastidial phosphorylase (PHS1) had a dwarf-growth phenotype, a reduced and uneven distribution of starch within the plant rosettes, and a lower starch granule number per chloroplast under standard growth conditions. In contrast, a triple mutant impaired in starch degradation by its additional lack of the glucan, water dikinase (GWD) showed improved plant growth, a starch-excess phenotype, and a homogeneous starch distribution. Furthermore, the number of starch granules per chloroplast was increased and was similar to the wild type. We concluded that ongoing starch degradation is mainly responsible for the observed phenotype of dpe2/phs1. Next, we generated two further triple mutants lacking either the phosphoglucan, water dikinase (PWD), or the disproportionating enzyme 1 (DPE1) in the background of the double mutant. Analysis of the starch metabolism revealed that even minor ongoing starch degradation observed in dpe2/phs1/pwd maintained the double mutant phenotype. In contrast, an additional blockage in the glucose pathway of starch breakdown, as in dpe2/phs1/ dpe1, resulted in a nearly starch-free phenotype and massive chloroplast degradation. The characterized mutants were discussed in the context of starch granule formation.
KW - Starch granules
KW - Starch metabolism
KW - Starch granule number per
KW - chloroplast
KW - Starch morphology
KW - LCSM
KW - Arabidopsis thaliana
Y1 - 2022
U6 - https://doi.org/10.1016/j.plaphy.2022.03.033
SN - 0981-9428
SN - 1873-2690
VL - 180
SP - 35
EP - 41
PB - Elsevier
CY - Paris
ER -
TY - JOUR
A1 - Kamali, Bahareh
A1 - Stella, Tommaso
A1 - Berg-Mohnicke, Michael
A1 - Pickert, Jürgen
A1 - Groh, Jannis
A1 - Nendel, Claas
T1 - Improving the simulation of permanent grasslands across Germany by using multi-objective uncertainty-based calibration of plant-water dynamics
JF - European journal of agronomy
N2 - The dynamics of grassland ecosystems are highly complex due to multifaceted interactions among their soil, water, and vegetation components.
Precise simulations of grassland productivity therefore rely on accurately estimating a variety of parameters that characterize different processes of these systems.
This study applied three calibration schemes - a Single-Objective (SO-SUFI2), a Multi-Objective Pareto (MO-Pareto), and, a novel Uncertainty-Based Multi-Objective (MO-SUFI2) - to estimate the parameters of MONICA (Model for Nitrogen and Carbon Simulation) agro-ecosystem model in grassland ecosystems across Germany.
The MO-Pareto model is based on a traditional Pareto optimality concept, while the MO-SUFI2 optimizes multiple target variables considering their level of prediction uncertainty.
We used measurements of leaf area index, aboveground biomass, and soil moisture from experimental data at five sites with different intensities of cutting regimes (from two to five cutting events per season) to evaluate model performance.
Both MO-Pareto and MO-SUFI2 outperformed SO-SUFI2 during calibration and validation.
The comparison of the two MO approaches shows that they do not necessarily conflict with each other, but MO-SUFI2 provides complementary information for better estimations of model parameter uncertainty.
We used the obtained parameter ranges to simulate grassland productivity across Germany under different cutting regimes and quantified the uncertainty associated with estimated productivity across regions.
The results showed higher uncertainty in intensively managed grasslands compared to extensively managed grasslands, partially due to a lack of high-resolution input information concerning cutting dates. Furthermore, the additional information on the quantified uncertainty provided by our proposed MO-SUFI2 method adds deeper insights on confidence levels of estimated productivity.
Benefiting from additional management data collected at high resolution and ground measurements on the composition of grassland species mixtures appear to be promising solutions to reduce uncertainty and increase model reliability.
KW - intensively managed grasslands
KW - extensively managed grasslands
KW - grassland productivity
KW - pareto optimality
Y1 - 2022
U6 - https://doi.org/10.1016/j.eja.2022.126464
SN - 1161-0301
SN - 1873-7331
VL - 134
PB - Elsevier
CY - Amsterdam
ER -
TY - JOUR
A1 - Reinhard, Johanna E.
A1 - Geißler, Katja
A1 - Blaum, Niels
T1 - Grass and ground dwelling beetle community responses to holistic and wildlife grazing management using a cross-fence comparison in Western Kalahari rangeland, Namibia
JF - Journal of insect conservation : an international journal devoted to the conservation of insects and related invertebrates
N2 - Savannahs are often branded by livestock grazing with resulting land degradation. Holistic management of livestock was proposed to contribute to biodiversity conservation by simulating native wildlife grazing behaviour. This study attempts the comparison of the impact of a holistic management regime to a wildlife grazing management regime on grass and ground-dwelling beetle species diversity on neighboring farms in Namibian rangeland. Results show that the response of biodiversity in species richness and composition to holistic management of livestock differs substantially from wildlife grazing with a positive impact. From a total of 39 identified species of ground-dwelling beetles (Coleoptera: Tenebrionidae, Carabidae) from 29 genera, eight species were found to be indicators for holistic management of livestock and three were found to be indicators for wildlife grazed rangeland. Observations suggest that holistic management of livestock may contribute to biodiversity conservation, but the differential effect of grazing management on species assemblages suggests that livestock grazing cannot replace native wildlife herbivory. Implications for insect conservation An adaptive management strategy such as holistic management used in this study shows the potential to support high beetle biodiversity. Holistic management of livestock thus aspects in favour for a sustainable form of grazing management for insect conservation even though it does not functionally replace grazing by native wildlife.
KW - Beetle conservation
KW - Land use management
KW - Biodiversity
KW - Insect conservation
KW - Wildlife management
Y1 - 2022
U6 - https://doi.org/10.1007/s10841-022-00410-6
SN - 1366-638X
SN - 1572-9753
VL - 26
SP - 711
EP - 720
PB - Springer
CY - Dordrecht
ER -
TY - JOUR
A1 - Rosso, Pablo
A1 - Nendel, Claas
A1 - Gilardi, Nicolas
A1 - Udroiu, Cosmin
A1 - Chlebowski, Florent
T1 - Processing of remote sensing information to retrieve leaf area index in barley
BT - a comparison of methods
JF - Precision agriculture
N2 - Leaf area index (LAI) is a key variable in understanding and modeling crop-environment interactions.
With the advent of increasingly higher spatial resolution satellites and sensors mounted on remotely piloted aircrafts (RPAs), the use of remote sensing in precision agriculture is becoming more common.
Since also the availability of methods to retrieve LAI from image data have also drastically expanded, it is necessary to test simultaneously as many methods as possible to understand the advantages and disadvantages of each approach.
Ground-based LAI data from three years of barley experiments were related to remote sensing information using vegetation indices (VI), machine learning (ML) and radiative transfer models (RTM), to assess the relative accuracy and efficacy of these methods.
The optimized soil adjusted vegetation index and a modified version of the Weighted Difference Vegetation Index performed slightly better than any other retrieval method. However, all methods yielded coefficients of determination of around 0.7 to 0.9.
The best performing machine learning algorithms achieved higher accuracies when four Sentinel-2 bands instead of 12 were used.
Also, the good performance of VIs and the satisfactory performance of the 4-band RTM, strongly support the synergistic use of satellites and RPAs in precision agriculture. One of the methods used, Sen2-Agri, an open source ML-RTM-based operational system, was also able to accurately retrieve LAI, although it is restricted to Sentinel-2 and Landsat data.
This study shows the benefits of testing simultaneously a broad range of retrieval methods to monitor crops for precision agriculture.
KW - leaf area index
KW - vegetation indices
KW - machine learning
KW - radiative transfer models
Y1 - 2022
U6 - https://doi.org/10.1007/s11119-022-09893-4
SN - 1385-2256
SN - 1573-1618
VL - 23
IS - 4
SP - 1449
EP - 1472
PB - Springer
CY - Dordrecht
ER -
TY - JOUR
A1 - Kamali, Bahareh
A1 - Lorite, Ignacio J.
A1 - Webber, Heidi A.
A1 - Rezaei, Ehsan Eyshi
A1 - Gabaldon-Leal, Clara
A1 - Nendel, Claas
A1 - Siebert, Stefan
A1 - Ramirez-Cuesta, Juan Miguel
A1 - Ewert, Frank
A1 - Ojeda, Jonathan J.
T1 - Uncertainty in climate change impact studies for irrigated maize cropping systems in southern Spain
JF - Scientific reports
N2 - This study investigates the main drivers of uncertainties in simulated irrigated maize yield under historical conditions as well as scenarios of increased temperatures and altered irrigation water availability.
Using APSIM, MONICA, and SIMPLACE crop models, we quantified the relative contributions of three irrigation water allocation strategies, three sowing dates, and three maize cultivars to the uncertainty in simulated yields.
The water allocation strategies were derived from historical records of farmer's allocation patterns in drip-irrigation scheme of the Genil-Cabra region, Spain (2014-2017).
By considering combinations of allocation strategies, the adjusted R-2 values (showing the degree of agreement between simulated and observed yields) increased by 29% compared to unrealistic assumptions of considering only near optimal or deficit irrigation scheduling. The factor decomposition analysis based on historic climate showed that irrigation strategies was the main driver of uncertainty in simulated yields (66%).
However, under temperature increase scenarios, the contribution of crop model and cultivar choice to uncertainty in simulated yields were as important as irrigation strategy. This was partially due to different model structure in processes related to the temperature responses.
Our study calls for including information on irrigation strategies conducted by farmers to reduce the uncertainty in simulated yields at field scale.
Y1 - 2022
U6 - https://doi.org/10.1038/s41598-022-08056-9
SN - 2045-2322
VL - 12
IS - 1
PB - Macmillan Publishers Limited,
CY - London
ER -
TY - THES
A1 - Mahto, Harendra
T1 - In vitro analysis of Early Starvation 1 (ESV1) and Like Early Starvation 1 (LESV) on starch degradation with focus on glucan, water dikinase (GWD) and phosphoglucan, water dikinase (PWD)
N2 - Starch is an insoluble polyglucan, comprises of two polymers, namely, the branched α-1,4: α-1,6-D-glucan amylopectin and the almost unbranched α-1,4-D-glucan amylose. The growth of all plants is directly dependent on the accumulation of transitory starch during the daytime when photosynthesis takes place and subsequently starch degradation during the night. Starch phosphorylation takes place by starch-related dikinases called α-glucan, water dikinase (GWD), and phosphoglucan, water dikinase (PWD), and is a very important step in starch degradation. The biochemical mechanisms of phosphorylation of starch are not properly understood. Recent studies have found that there are two starch binding proteins namely, Early Starvation1 (ESV1) and Like Early Starvation1 (LESV), which play an important role in starch metabolism. It has been shown that ESV1 and LESV proteins affect the starch phosphorylation activity of GWD and PWD enzymes, which control the rate of degradation of starch granules. In this thesis, various in vitro assays were performed to identify and understand the mechanism of recombinant proteins; ESV1 and LESV on the starch degradation. The starch degradation was performed by phosphorylation enzymes, GWD and PWD separately. In various enzymatic assays, the influence of the ESV1 and LESV on the actions of GWD and PWD on the surfaces of different native starch granules were analysed. Furthermore, ESV1 and LESV have specifically shown influences on the phosphorylation activities of GWD and PWD on the starch granule surfaces in an antagonistic pattern in such a way that, the GWD mediated phosphorylation were significantly reduced while PWD mediated phosphorylation were significantly increased respectively. In another set of experiments, ISA and BAM hydrolyzing enzymes were used to alter the structure of starch, and then determine the effect of both dikinases mediated phosphorylation in the presence of ESV1 and LESV on the altered starch granules surfaces. In these results, significant decreases in both GWD and PWD mediated phosphorylation were observed in all the treatments containing either ESV1 or LESV proteins only or both ESV1 and LESV. It was also found that LESV preferentially binds to both amylose and amylopectin, while ESV1 binds to highly ordered glucans such as maltodextrins and amylopectin, which are crystalline in structure. Both ESV1 or LESV proteins either individually or in combination have shown influence on the activity of GWD and PWD phosphate incorporation into the starch granules via reduction even though at different percentages depending on the sources of starch, therefore it is difficult to distinguish the specific function between them. The biochemical studies have shown that protein-glucan interaction specifically between ESV1 or LESV or in combination with different species of starch granules has very strong surface binding, or it might be possible that both the proteins not only bind to the surface of the starch granules but also have entered deep inside the glucan structure of the starch granules. However, the results also revealed that ESV1 and LESV did not alter the autophosphorylation of the dikinases. Also, the chain length distribution pattern of the released glucan chains after treatment of starch with ISA enzyme was evaluated with respect to the degree of polymerization (DP) of the different starch granules. Capillary electrophoresis was employed to study the effect of LESV and ESV1 on the chain length distribution. In summary, this study confirms that ESV1 and LESV play an important role in organizing and regulating the starch metabolism process. In the later half, studies were performed to monitor whether the metabolism of carbohydrates and partitioning, contribute to the higher salt tolerance of the facultative halophyte Hordeum marinum when compared to glycophyte Hordeum vulgare. Seedlings with the same size from both species were hydroponically grown at 0, 150, and 300 mM of NaCl for 3 weeks. H. marinum maintained a high relative growth rate, which was found concomitant in higher aptitude plants to maintain efficient shoot tissue hydration and integrity of membrane under salt conditions when compared to H. vulgare. Hence, our data suggested that the change in the starch storage, distribution of soluble sugar concentrations between source and sink organs, and also changes in the level of enzymes involved in the starch metabolism was significant to give insights into the importance of carbohydrate metabolism in barley species with regards to the salt tolerance. Although these results are still in their nascent state, it could be vital for other researchers to formulate future studies. The preliminary results which were studies about the carbohydrate metabolism and partitioning in salt responses in the halophyte H. marinum and the glycophyte H. vulgare revealed that salt tolerance in barley species is not due to osmotic adjustments, but due to other reasons that were not explored in the past studies. However, the activity of DPE2 in H. vulgare was not hampered by the presence of NaCl as observed. While Pho1 and Pho2, activities were highly increased in cultivated barley. These findings could be suggestive of a possible role of these enzymes in the responses of carbohydrate metabolism to salinity. When sea and cultivated barley species were compared, it was discovered that the former had more versatility in carbohydrate metabolism and distribution.
N2 - Stärke ist ein unlösliches Polyglucan, das aus zwei Polymeren besteht, nämlich dem verzweigten α-1,4: α-1,6-D-Glucan Amylopektin und dem fast unverzweigten α-1,4-D-Glucan Amylose. Das Wachstum aller Pflanzen hängt direkt von der Akkumulation transitorischer Stärke während des Tages, wenn die Photosynthese stattfindet, und dem anschließenden Stärkeabbau während der Nacht ab. Die Phosphorylierung von Stärke erfolgt durch stärkeverwandte Dikinasen, die α-Glucan-Wasser-Dikinase (GWD) und Phosphoglucan-Wasser-Dikinase (PWD), und ist ein entscheidender Schritt beim Stärkeabbau. Die biochemischen Mechanismen der Phosphorylierung von Stärke sind nicht genau bekannt. Jüngste Studien haben ergeben, dass es zwei stärkebindende Proteine gibt, nämlich Early Starvation1 (ESV1) und Like Early Starvation1 (LESV), die eine wichtige Rolle im Stärkestoffwechsel spielen. Es hat sich gezeigt, dass ESV1- und LESV-Proteine die Stärkephosphorylierungsaktivität der GWD- und PWD-Enzyme beeinflussen, die die Geschwindigkeit des Abbaus von Stärkekörnern steuern. In dieser Arbeit wurden verschiedene In-vitro-Tests durchgeführt, um den Mechanismus der rekombinanten Proteine ESV1 und LESV auf den Stärkeabbau zu identifizieren und zu verstehen.Der Stärkeabbau wurde von den Phosphorylierungsenzymen GWD und PWD getrennt durchgeführt. In verschiedenen enzymatischen Assays wurde der Einfluss von ESV1 und LESV auf die Wirkung von GWD und PWD auf die Oberflächen verschiedener nativer Stärkekörner analysiert. Darüber hinaus haben ESV1 und LESV spezifisch Einflüsse auf die Phosphorylierungsaktivitäten von GWD und PWD auf den Oberflächen der Stärkekörner in einem antagonistischen Muster gezeigt, so dass die GWD-vermittelte Phosphorylierung signifikant reduziert wurde, während die PWD-vermittelte Phosphorylierung signifikant erhöht wurde. In einer anderen Versuchsreihe wurden ISA- und BAM verwendet, um die Struktur der Stärke zu verändern und dann die Auswirkungen der durch beide Dikinasen vermittelten Phosphorylierung in Gegenwart von ESV1 und LESV auf die veränderten Oberflächen der Stärkekörner zu bestimmen. In diesen Ergebnissen wurde ein signifikanter Rückgang der GWD- und PWD-vermittelten Phosphorylierung in allen Behandlungen beobachtet, die entweder nur ESV1- oder LESV-Proteine oder sowohl ESV1 als auch LESV enthielten. Es wurde auch festgestellt, dass LESV vorzugsweise an Amylose und Amylopektin bindet, während ESV1 an hochgeordnete Glucane wie Maltodextrine und Amylopektin bindet, die eine kristalline Struktur aufweisen. Sowohl ESV1- als auch LESV-Proteine haben entweder einzeln oder in Kombination einen Einfluss auf die Aktivität des GWD- und PWD-Phosphateinbaus in die Stärkekörner durch Reduktion gezeigt, jedoch zu unterschiedlichen Prozentsätzen, je nach Stärkequelle, so dass es schwierig ist, ihre spezifische Funktion zu unterscheiden. Die biochemischen Untersuchungen zeigen, dass die Protein-Glucan-Interaktion speziell zwischen ESV1 oder LESV oder in Kombination mit verschiedenen Arten von Stärkekörnern eine sehr starke Oberflächenbindung aufweist, oder es ist möglich, dass beide Proteine nicht nur an die Oberfläche der Stärkekörner binden, sondern auch tief in die Glucanstruktur der Stärkekörner eingedrungen sind. Die Ergebnisse zeigten jedoch auch, dass ESV1 und LESV die Autophosphorylierung der Dikinasen nicht veränderten. Außerdem wurde die Kettenlängenverteilung der freigesetzten Glucanketten nach Behandlung der Stärke mit dem ISA-Enzym im Hinblick auf den Polymerisationsgrad (DP) der verschiedenen Stärkekörner bewertet. Mit Hilfe der Kapillarelektrophorese wurde die Wirkung von LESV und ESV1 auf die Kettenlängenverteilung untersucht. Zusammenfassend bestätigt diese Studie, dass ESV1 und LESV eine wichtige Rolle bei der Organisation und Regulierung des Stärkestoffwechsels spielen. In der zweiten Hälfte wurden Untersuchungen durchgeführt, um zu prüfen, ob der Stoffwechsel von Kohlenhydraten und deren Verteilung zu der höheren Salztoleranz des fakultativen Halophyten Hordeum marinum im Vergleich zum Glykophyten Hordeum vulgare beitragen. Die gleich großen Sämlinge beider Arten wurden 3 Wochen lang bei 0, 150 und 300 mM NaCl hydroponisch gezogen. H. marinum wies eine hohe relative Wachstumsrate auf, die mit einer höheren Fähigkeit der Pflanzen einherging, unter Salzbedingungen eine effiziente Hydratation des Sprossgewebes und die Integrität der Membran aufrechtzuerhalten, als dies bei H. vulgare der Fall war. Unsere Daten deuten also darauf hin, dass die Veränderungen in der Stärkespeicherung, die Verteilung der Konzentrationen löslicher Zucker zwischen Source- und Sinkorganen und auch die Veränderungen in der Menge der am Stärkestoffwechsel beteiligten Enzyme von Bedeutung sind und Einblicke in die Bedeutung des Kohlenhydratstoffwechsels bei Gerstenarten im Hinblick auf die Salztoleranz geben. Obwohl sich diese Ergebnisse noch im Anfangsstadium befinden, könnten sie für andere Forscher bei der Formulierung künftiger Studien von entscheidender Bedeutung sein. Die vorläufigen Ergebnisse der Studien über den Kohlenhydratstoffwechsel und die Verteilung der Kohlenhydrate bei Salzreaktionen im Halophyten H. marinum und im Glykophyten H. vulgare haben gezeigt, dass die Salztoleranz bei Gerstenarten nicht auf osmotische Anpassungen zurückzuführen ist, sondern auf andere Gründe, die in den bisherigen Studien nicht untersucht wurden. Die Aktivität von DPE2 in H. vulgare wurde jedoch nicht wie beobachtet durch die Anwesenheit von NaCl beeinträchtigt. Dagegen waren die Aktivitäten von Pho1 und Pho2 in kultivierter Gerste stark erhöht. Diese Ergebnisse könnten auf eine mögliche Rolle dieser Enzyme bei der Reaktion des Kohlenhydratstoffwechsels auf den Salzgehalt hinweisen. Beim Vergleich von Meeres- und Kulturgerstenarten wurde festgestellt, dass erstere eine größere Vielseitigkeit im Kohlenhydratstoffwechsel und in der Kohlenhydratverteilung aufweisen.
KW - Arabidopsis thaliana
KW - starch phosphorylation
KW - phosphoglucan
KW - starch granule surface
KW - Early Starvation 1
Y1 - 2022
ER -
TY - JOUR
A1 - Peter, Lena
A1 - Wendering, Désirée Jacqueline
A1 - Schlickeiser, Stephan
A1 - Hoffmann, Henrike
A1 - Noster, Rebecca
A1 - Wagner, Dimitrios Laurin
A1 - Zarrinrad, Ghazaleh
A1 - Münch, Sandra
A1 - Picht, Samira
A1 - Schulenberg, Sarah
A1 - Moradian, Hanieh
A1 - Mashreghi, Mir-Farzin
A1 - Klein, Oliver
A1 - Gossen, Manfred
A1 - Roch, Toralf
A1 - Babel, Nina
A1 - Reinke, Petra
A1 - Volk, Hans-Dieter
A1 - Amini, Leila
A1 - Schmueck-Henneresse, Michael
T1 - Tacrolimus-resistant SARS-CoV-2-specific T cell products to prevent and treat severe COVID-19 in immunosuppressed patients
JF - Molecular therapy methods and clinical development
N2 - Solid organ transplant (SOT) recipients receive therapeutic immunosuppression that compromises their immune response to infections and vaccines. For this reason, SOT patients have a high risk of developing severe coronavirus disease 2019 (COVID-19) and an increased risk of death from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. Moreover, the efficiency of immunotherapies and vaccines is reduced due to the constant immunosuppression in this patient group. Here, we propose adoptive transfer of SARS-CoV-2-specific T cells made resistant to a common immunosuppressant, tacrolimus, for optimized performance in the immunosuppressed patient. Using a ribonucleoprotein approach of CRISPR-Cas9 technology, we have generated tacrolimus-resistant SARS-CoV-2-specific T cell products from convalescent donors and demonstrate their specificity and function through characterizations at the single-cell level, including flow cytometry, single-cell RNA (scRNA) Cellular Indexing of Transcriptomes and Epitopes (CITE), and T cell receptor (TCR) sequencing analyses. Based on the promising results, we aim for clinical validation of this approach in transplant recipients. Additionally, we propose a combinatory approach with tacrolimus, to prevent an overshooting immune response manifested as bystander T cell activation in the setting of severe COVID-19 immunopathology, and tacrolimus-resistant SARS-CoV-2-specific T cell products, allowing for efficient clearance of viral infection. Our strategy has the potential to prevent severe COVID-19 courses in SOT or autoimmunity settings and to prevent immunopathology while providing viral clearance in severe non-transplant COVID-19 cases.
Y1 - 2022
U6 - https://doi.org/10.1016/j.omtm.2022.02.012
SN - 2329-0501
VL - 25
SP - 52
EP - 73
PB - Cell Press
CY - Cambridge
ER -
TY - JOUR
A1 - Abdelilah-Seyfried, Salim
A1 - Iruela-Arispe, M. Luisa
A1 - Penninger, Josef M.
A1 - Tournier-Lasserve, Elisabeth
A1 - Vikkula, Miikka
A1 - Cleaver, Ondine
T1 - Recalibrating vascular malformations and mechanotransduction by pharmacological intervention
JF - Journal of clinical investigation
Y1 - 2022
U6 - https://doi.org/10.1172/JCI160227
SN - 0021-9738
SN - 1558-8238
VL - 132
IS - 8
PB - American Society for Clinical Investigation
CY - Ann Arbor
ER -
TY - JOUR
A1 - Xu, Huizhen
A1 - Giannetti, Alessandro
A1 - Sugiyama, Yuki
A1 - Zheng, Wenna
A1 - Schneider, René
A1 - Watanabe, Yoichiro
A1 - Oda, Yoshihisa
A1 - Persson, Staffan
T1 - Secondary cell wall patterning-connecting the dots, pits and helices
JF - Open biology
N2 - All plant cells are encased in primary cell walls that determine plant morphology, but also protect the cells against the environment. Certain cells also produce a secondary wall that supports mechanically demanding processes, such as maintaining plant body stature and water transport inside plants. Both these walls are primarily composed of polysaccharides that are arranged in certain patterns to support cell functions. A key requisite for patterned cell walls is the arrangement of cortical microtubules that may direct the delivery of wall polymers and/or cell wall producing enzymes to certain plasma membrane locations. Microtubules also steer the synthesis of cellulose-the load-bearing structure in cell walls-at the plasma membrane. The organization and behaviour of the microtubule array are thus of fundamental importance to cell wall patterns. These aspects are controlled by the coordinated effort of small GTPases that probably coordinate a Turing's reaction-diffusion mechanism to drive microtubule patterns. Here, we give an overview on how wall patterns form in the water-transporting xylem vessels of plants. We discuss systems that have been used to dissect mechanisms that underpin the xylem wall patterns, emphasizing the VND6 and VND7 inducible systems, and outline challenges that lay ahead in this field.
KW - plant cell wall
KW - microtubules
KW - xylem
KW - cell wall patterning
KW - cellulose
Y1 - 2022
U6 - https://doi.org/10.1098/rsob.210208
SN - 2046-2441
VL - 12
IS - 5
PB - Royal Society
CY - London
ER -
TY - JOUR
A1 - Agne, Stefanie
A1 - Naylor, Gavin J. P.
A1 - Preick, Michaela
A1 - Yang, Lei
A1 - Thiel, Ralf
A1 - Weigmann, Simon
A1 - Paijmans, Johanna L. A.
A1 - Barlow, Axel
A1 - Hofreiter, Michael
A1 - Straube, Nicolas
T1 - Taxonomic identification of two poorly known lantern shark species based on mitochondrial DNA from wet-collection paratypes
JF - Frontiers in Ecology and Evolution
N2 - Etmopteridae (lantern sharks) is the most species-rich family of sharks, comprising more than 50 species.
Many species are described from few individuals, and re-collection of specimens is often hindered by the remoteness of their sampling sites.
For taxonomic studies, comparative morphological analysis of type specimens housed in natural history collections has been the main source of evidence.
In contrast, DNA sequence information has rarely been used.
Most lantern shark collection specimens, including the types, were formalin fixed before long-term storage in ethanol solutions.
The DNA damage caused by both fixation and preservation of specimens has excluded these specimens from DNA sequence-based phylogenetic analyses so far.
However, recent advances in the field of ancient DNA have allowed recovery of wet-collection specimen DNA sequence data.
Here we analyse archival mitochondrial DNA sequences, obtained using ancient DNA approaches, of two wet-collection lantern shark paratype specimens, namely Etmopterus litvinovi and E. pycnolepis, for which the type series represent the only known individuals.
Target capture of mitochondrial markers from single-stranded DNA libraries allows for phylogenetic placement of both species.
Our results suggest synonymy of E. benchleyi with E. litvinovi but support the species status of E. pycnolepis. This revised taxonomy is helpful for future conservation and management efforts, as our results indicate a larger distribution range of E. litvinovi. This study further demonstrates the importance of wet-collection type specimens as genetic resource for taxonomic research.
KW - type specimens
KW - Etmopterus litvinovi
KW - Etmopterus pycnolepis
KW - deep-sea
KW - sharks
KW - archival DNA
Y1 - 2022
U6 - https://doi.org/10.3389/fevo.2022.910009
SN - 2296-701X
VL - 10
PB - Frontiers Media
CY - Lausanne
ER -
TY - JOUR
A1 - Stiegler, Jonas
A1 - Lins, Alisa
A1 - Dammhahn, Melanie
A1 - Kramer-Schadt, Stephanie
A1 - Ortmann, Sylvia
A1 - Blaum, Niels
T1 - Personality drives activity and space use in a mammalian herbivore
JF - Movement Ecology
N2 - Background
Animal personality has emerged as a key concept in behavioral ecology. While many studies have demonstrated the influence of personality traits on behavioral patterns, its quantification, especially in wild animal populations, remains a challenge. Only a few studies have established a link between personality and recurring movements within home ranges, although these small-scale movements are of key importance for identifying ecological interactions and forming individual niches. In this regard, differences in space use among individuals might reflect different exploration styles between behavioral types along the shy-bold continuum.
Methods
We assessed among-individual differences in behavior in the European hare (Lepus europaeus), a characteristic mammalian herbivore in agricultural landscapes using a standardized box emergence test for captive and wild hares. We determined an individuals’ degree of boldness by measuring the latencies of behavioral responses in repeated emergence tests in captivity. During capture events of wild hares, we conducted a single emergence test and recorded behavioral responses proven to be stable over time in captive hares. Applying repeated novel environment tests in a near-natural enclosure, we further quantified aspects of exploration and activity in captive hares. Finally, we investigated whether and how this among-individual behavioral variation is related to general activity and space use in a wild hare population. Wild and captive hares were treated similarly and GPS-collared with internal accelerometers prior to release to the wild or the outdoor enclosure, respectively. General activity was quantified as overall dynamic body acceleration (ODBA) obtained from accelerometers. Finally, we tested whether boldness explained variation in (i) ODBA in both settings and (ii) variation in home ranges and core areas across different time scales of GPS-collared hares in a wild population.
Results
We found three behavioral responses to be consistent over time in captive hares. ODBA was positively related to boldness (i.e., short latencies to make first contact with the new environment) in both captive and wild hares. Space use in wild hares also varied with boldness, with shy individuals having smaller core areas and larger home ranges than bold conspecifics (yet in some of the parameter space, this association was just marginally significant).
Conclusions
Against our prediction, shy individuals occupied relatively large home ranges but with small core areas. We suggest that this space use pattern is due to them avoiding risky, and energy-demanding competition for valuable resources. Carefully validated, activity measurements (ODBA) from accelerometers provide a valuable tool to quantify aspects of animal personality along the shy-bold continuum remotely. Without directly observing—and possibly disturbing—focal individuals, this approach allows measuring variability in animal personality, especially in species that are difficult to assess with experiments. Considering that accelerometers are often already built into GPS units, we recommend activating them at least during the initial days of tracking to estimate individual variation in general activity and, if possible, match them with a simple novelty experiment. Furthermore, information on individual behavioral types will help to facilitate mechanistic understanding of processes that drive spatial and ecological dynamics in heterogeneous landscapes.
KW - Animal personality
KW - Movement ecology
KW - Inter-individual differences
KW - ODBA
KW - Energy expenditure
KW - European hare
Y1 - 2022
U6 - https://doi.org/10.1186/s40462-022-00333-6
SN - 2051-3933
VL - 10
PB - BioMed Central (BMC), Springer Nature
CY - London
ER -
TY - JOUR
A1 - Hering, Robert
A1 - Hauptfleisch, Morgan
A1 - Jago, Mark
A1 - Smith, Taylor
A1 - Kramer-Schadt, Stephanie
A1 - Stiegler, Jonas
A1 - Blaum, Niels
T1 - Don't stop me now: Managed fence gaps could allow migratory ungulates to track dynamic resources and reduce fence related energy loss
JF - Frontiers in Ecology and Evolution
N2 - In semi-arid environments characterized by erratic rainfall and scattered primary production, migratory movements are a key survival strategy of large herbivores to track resources over vast areas. Veterinary Cordon Fences (VCFs), intended to reduce wildlife-livestock disease transmission, fragment large parts of southern Africa and have limited the movements of large wild mammals for over 60 years. Consequently, wildlife-fence interactions are frequent and often result in perforations of the fence, mainly caused by elephants. Yet, we lack knowledge about at which times fences act as barriers, how fences directly alter the energy expenditure of native herbivores, and what the consequences of impermeability are. We studied 2-year ungulate movements in three common antelopes (springbok, kudu, eland) across a perforated part of Namibia's VCF separating a wildlife reserve and Etosha National Park using GPS telemetry, accelerometer measurements, and satellite imagery. We identified 2905 fence interaction events which we used to evaluate critical times of encounters and direct fence effects on energy expenditure. Using vegetation type-specific greenness dynamics, we quantified what animals gained in terms of high quality food resources from crossing the VCF. Our results show that the perforation of the VCF sustains herbivore-vegetation interactions in the savanna with its scattered resources. Fence permeability led to peaks in crossing numbers during the first flush of woody plants before the rain started. Kudu and eland often showed increased energy expenditure when crossing the fence. Energy expenditure was lowered during the frequent interactions of ungulates standing at the fence. We found no alteration of energy expenditure when springbok immediately found and crossed fence breaches. Our results indicate that constantly open gaps did not affect energy expenditure, while gaps with obstacles increased motion. Closing gaps may have confused ungulates and modified their intended movements. While browsing, sedentary kudu's use of space was less affected by the VCF; migratory, mixed-feeding springbok, and eland benefited from gaps by gaining forage quality and quantity after crossing. This highlights the importance of access to vast areas to allow ungulates to track vital vegetation patches.
KW - veterinary cordon fence
KW - ungulate
KW - fence ecology
KW - resource-tracking
KW - energy expenditure
KW - accelerometer
KW - GPS
KW - wildlife and habitat management
Y1 - 2022
U6 - https://doi.org/10.3389/fevo.2022.907079
SN - 2296-701X
SP - 1
EP - 18
PB - Frontiers
CY - Lausanne, Schweiz
ER -
TY - JOUR
A1 - Hering, Robert
A1 - Hauptfleisch, Morgan
A1 - Kramer-Schadt, Stephanie
A1 - Stiegler, Jonas
A1 - Blaum, Niels
T1 - Effects of fences and fence gaps on the movement behavior of three southern African antelope species
JF - Frontiers in Conservation Science
N2 - Globally, migratory ungulates are affected by fences. While field observational studies reveal the amount of animal–fence interactions across taxa, GPS tracking-based studies uncover fence effects on movement patterns and habitat selection. However, studies on the direct effects of fences and fence gaps on movement behavior, especially based on high-frequency tracking data, are scarce. We used GPS tracking on three common African antelopes (Tragelaphus strepsiceros, Antidorcas marsupialis, and T. oryx) with movement strategies ranging from range residency to nomadism in a semi-arid, Namibian savanna traversed by wildlife-proof fences that elephants have regularly breached. We classified major forms of ungulate–fence interaction types on a seasonal and a daily scale. Furthermore, we recorded the distances and times spent at fences regarding the total individual space use. Based on this, we analyzed the direct effects of fences and fence gaps on the animals’ movement behavior for the previously defined types of animal–fence interactions. Antelope-fence interactions peaked during the early hours of the day and during seasonal transitions when the limiting resource changed between water and forage. Major types of ungulate–fence interactions were quick, trace-like, or marked by halts. We found that the amount of time spent at fences was highest for nomadic eland. Migratory springbok adjusted their space use concerning fence gap positions. If the small home ranges of sedentary kudu included a fence, they frequently interacted with this fence. For springbok and eland, distance traveled along a fence declined with increasing utilization of a fence gap. All species reduced their speed in the proximity of a fence but often increased their speed when encountering the fence. Crossing a fence led to increased speeds for all species. We demonstrate that fence effects mainly occur during crucial foraging times (seasonal scale) and during times of directed movements (daily scale). Importantly, we provide evidence that fences directly alter antelope movement behaviors with negative implications for energy budgets and that persistent fence gaps can reduce the intensity of such alterations. Our findings help to guide future animal–fence studies and provide insights for wildlife fencing and fence gap planning.
KW - fence ecology
KW - veterinary cordon fence
KW - ungulate
KW - movement speed
KW - fence interaction
KW - GPS
KW - Africa
KW - wildlife conservation
Y1 - 2022
U6 - https://doi.org/10.3389/fcosc.2022.959423
SN - 2673-611X
VL - 3
SP - 1
EP - 19
PB - Frontiers
CY - Lausanne, Schweiz
ER -
TY - JOUR
A1 - Irob, Katja
A1 - Blaum, Niels
A1 - Baldauf, Selina
A1 - Kerger, Leon
A1 - Strohbach, Ben
A1 - Kanduvarisa, Angelina
A1 - Lohmann, Dirk
A1 - Tietjen, Britta
T1 - Browsing herbivores improve the state and functioning of savannas
BT - A model assessment of alternative land-use strategies
JF - Ecology and evolution
N2 - Changing climatic conditions and unsustainable land use are major threats to savannas worldwide. Historically, many African savannas were used intensively for livestock grazing, which contributed to widespread patterns of bush encroachment across savanna systems. To reverse bush encroachment, it has been proposed to change the cattle-dominated land use to one dominated by comparatively specialized browsers and usually native herbivores. However, the consequences for ecosystem properties and processes remain largely unclear. We used the ecohydrological, spatially explicit model EcoHyD to assess the impacts of two contrasting, herbivore land-use strategies on a Namibian savanna: grazer- versus browser-dominated herbivore communities. We varied the densities of grazers and browsers and determined the resulting composition and diversity of the plant community, total vegetation cover, soil moisture, and water use by plants. Our results showed that plant types that are less palatable to herbivores were best adapted to grazing or browsing animals in all simulated densities. Also, plant types that had a competitive advantage under limited water availability were among the dominant ones irrespective of land-use scenario. Overall, the results were in line with our expectations: under high grazer densities, we found heavy bush encroachment and the loss of the perennial grass matrix. Importantly, regardless of the density of browsers, grass cover and plant functional diversity were significantly higher in browsing scenarios. Browsing herbivores increased grass cover, and the higher total cover in turn improved water uptake by plants overall. We concluded that, in contrast to grazing-dominated land-use strategies, land-use strategies dominated by browsing herbivores, even at high herbivore densities, sustain diverse vegetation communities with high cover of perennial grasses, resulting in lower erosion risk and bolstering ecosystem services.
KW - browsing
KW - ecohydrology
KW - land use
KW - plant community
KW - savanna
KW - wildlife
KW - management
Y1 - 2022
U6 - https://doi.org/10.1002/ece3.8715
SN - 2045-7758
VL - 12
IS - 3
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Van den Wyngaert, Silke
A1 - Ganzert, Lars
A1 - Seto, Kensuke
A1 - Rojas-Jimenez, Keilor
A1 - Agha, Ramsy
A1 - Berger, Stella A.
A1 - Woodhouse, Jason
A1 - Padisak, Judit
A1 - Wurzbacher, Christian
A1 - Kagami, Maiko
A1 - Grossart, Hans-Peter
T1 - Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits
JF - ISME journal
N2 - Zoosporic fungi of the phylum Chytridiomycota (chytrids) regularly dominate pelagic fungal communities in freshwater and marine environments. Their lifestyles range from obligate parasites to saprophytes. Yet, linking the scarce available sequence data to specific ecological traits or their host ranges constitutes currently a major challenge. We combined 28 S rRNA gene amplicon sequencing with targeted isolation and sequencing approaches, along with cross-infection assays and analysis of chytrid infection prevalence to obtain new insights into chytrid diversity, ecology, and seasonal dynamics in a temperate lake. Parasitic phytoplankton-chytrid and saprotrophic pollen-chytrid interactions made up the majority of zoosporic fungal reads. We explicitly demonstrate the recurrent dominance of parasitic chytrids during frequent diatom blooms and saprotrophic chytrids during pollen rains. Distinct temporal dynamics of diatom-specific parasitic clades suggest mechanisms of coexistence based on niche differentiation and competitive strategies. The molecular and ecological information on chytrids generated in this study will aid further exploration of their spatial and temporal distribution patterns worldwide. To fully exploit the power of environmental sequencing for studies on chytrid ecology and evolution, we emphasize the need to intensify current isolation efforts of chytrids and integrate taxonomic and autecological data into long-term studies and experiments.
Y1 - 2022
U6 - https://doi.org/10.1038/s41396-022-01267-y
SN - 1751-7362
SN - 1751-7370
VL - 16
IS - 9
SP - 2242
EP - 2254
PB - Springer Nature
CY - London
ER -
TY - JOUR
A1 - Groh, Jannis
A1 - Diamantopoulos, Efstathios
A1 - Duan, Xiaohong
A1 - Ewert, Frank
A1 - Heinlein, Florian
A1 - Herbst, Michael
A1 - Holbak, Maja
A1 - Kamali, Bahareh
A1 - Kersebaum, Kurt-Christian
A1 - Kuhnert, Matthias
A1 - Nendel, Claas
A1 - Priesack, Eckart
A1 - Steidl, Jörg
A1 - Sommer, Michael
A1 - Pütz, Thomas
A1 - Vanderborght, Jan
A1 - Vereecken, Harry
A1 - Wallor, Evelyn
A1 - Weber, Tobias K. D.
A1 - Wegehenkel, Martin
A1 - Weihermüller, Lutz
A1 - Gerke, Horst H.
T1 - Same soil, different climate: Crop model intercomparison on translocated lysimeters
JF - Vadose zone journal
N2 - Crop model intercomparison studies have mostly focused on the assessment of predictive capabilities for crop development using weather and basic soil data from the same location. Still challenging is the model performance when considering complex interrelations between soil and crop dynamics under a changing climate. The objective of this study was to test the agronomic crop and environmental flux-related performance of a set of crop models. The aim was to predict weighing lysimeter-based crop (i.e., agronomic) and water-related flux or state data (i.e., environmental) obtained for the same soil monoliths that were taken from their original environment and translocated to regions with different climatic conditions, after model calibration at the original site. Eleven models were deployed in the study. The lysimeter data (2014-2018) were from the Dedelow (Dd), Bad Lauchstadt (BL), and Selhausen (Se) sites of the TERENO (TERrestrial ENvironmental Observatories) SOILCan network. Soil monoliths from Dd were transferred to the drier and warmer BL site and the wetter and warmer Se site, which allowed a comparison of similar soil and crop under varying climatic conditions. The model parameters were calibrated using an identical set of crop- and soil-related data from Dd. Environmental fluxes and crop growth of Dd soil were predicted for conditions at BL and Se sites using the calibrated models. The comparison of predicted and measured data of Dd lysimeters at BL and Se revealed differences among models. At site BL, the crop models predicted agronomic and environmental components similarly well. Model performance values indicate that the environmental components at site Se were better predicted than agronomic ones. The multi-model mean was for most observations the better predictor compared with those of individual models. For Se site conditions, crop models failed to predict site-specific crop development indicating that climatic conditions (i.e., heat stress) were outside the range of variation in the data sets considered for model calibration. For improving predictive ability of crop models (i.e., productivity and fluxes), more attention should be paid to soil-related data (i.e., water fluxes and system states) when simulating soil-crop-climate interrelations in changing climatic conditions.
Y1 - 2022
U6 - https://doi.org/10.1002/vzj2.20202
SN - 1539-1663
VL - 21
IS - 4
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Dunker, Susanne
A1 - Boyd, Matthew
A1 - Durka, Walter
A1 - Erler, Silvio
A1 - Harpole, W. Stanley
A1 - Henning, Silvia
A1 - Herzschuh, Ulrike
A1 - Hornick, Thomas
A1 - Knight, Tiffany
A1 - Lips, Stefan
A1 - Mäder, Patrick
A1 - Švara, Elena Motivans
A1 - Mozarowski, Steven
A1 - Rakosy, Demetra
A1 - Römermann, Christine
A1 - Schmitt-Jansen, Mechthild
A1 - Stoof-Leichsenring, Kathleen
A1 - Stratmann, Frank
A1 - Treudler, Regina
A1 - Virtanen, Risto
A1 - Wendt-Potthoff, Katrin
A1 - Wilhelm, Christian
T1 - The potential of multispectral imaging flow cytometry for environmental monitoring
JF - Cytometry part A
N2 - Environmental monitoring involves the quantification of microscopic cells and particles such as algae, plant cells, pollen, or fungal spores. Traditional methods using conventional microscopy require expert knowledge, are time-intensive and not well-suited for automated high throughput. Multispectral imaging flow cytometry (MIFC) allows measurement of up to 5000 particles per second from a fluid suspension and can simultaneously capture up to 12 images of every single particle for brightfield and different spectral ranges, with up to 60x magnification. The high throughput of MIFC has high potential for increasing the amount and accuracy of environmental monitoring, such as for plant-pollinator interactions, fossil samples, air, water or food quality that currently rely on manual microscopic methods. Automated recognition of particles and cells is also possible, when MIFC is combined with deep-learning computational techniques. Furthermore, various fluorescence dyes can be used to stain specific parts of the cell to highlight physiological and chemical features including: vitality of pollen or algae, allergen content of individual pollen, surface chemical composition (carbohydrate coating) of cells, DNA- or enzyme-activity staining. Here, we outline the great potential for MIFC in environmental research for a variety of research fields and focal organisms. In addition, we provide best practice recommendations.
KW - environmental monitoring
KW - imaging flow cytometry
KW - plant traits
Y1 - 2022
U6 - https://doi.org/10.1002/cyto.a.24658
SN - 1552-4922
SN - 1552-4930
VL - 101
IS - 9
SP - 782
EP - 799
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Cao, Xianyong
A1 - Chen, Jianhui
A1 - Tian, Fang
A1 - Xu, Qinghai
A1 - Herzschuh, Ulrike
A1 - Telford, Richard
A1 - Huang, Xiaozhong
A1 - Zheng, Zhuo
A1 - Shen, Caiming
A1 - Li, Wenjia
T1 - Long-distance modern analogues bias results of pollen-based precipitation reconstructions
JF - Science bulletin
Y1 - 2022
U6 - https://doi.org/10.1016/j.scib.2022.01.003
SN - 2095-9273
SN - 2095-9281
VL - 67
IS - 11
SP - 1115
EP - 1117
PB - Elsevier
CY - Amsterdam
ER -
TY - JOUR
A1 - Schulte, Luise
A1 - Meucci, Stefano
A1 - Stoof-Leichsenring, Kathleen R.
A1 - Heitkam, Tony
A1 - Schmidt, Nicola
A1 - von Hippel, Barbara
A1 - Andreev, Andrei A.
A1 - Diekmann, Bernhard
A1 - Biskaborn, Boris
A1 - Wagner, Bernd
A1 - Melles, Martin
A1 - Pestryakova, Lyudmila A.
A1 - Alsos, Inger G.
A1 - Clarke, Charlotte
A1 - Krutovsky, Konstantin
A1 - Herzschuh, Ulrike
T1 - Larix species range dynamics in Siberia since the Last Glacial captured from sedimentary ancient DNA
JF - Communications biology
N2 - Climate change is expected to cause major shifts in boreal forests which are in vast areas of Siberia dominated by two species of the deciduous needle tree larch (Larix). The species differ markedly in their ecosystem functions, thus shifts in their respective ranges are of global relevance.
However, drivers of species distribution are not well understood, in part because paleoecological data at species level are lacking. This study tracks Larix species distribution in time and space using target enrichment on sedimentary ancient DNA extracts from eight lakes across Siberia. We discovered that Larix sibirica, presently dominating in western Siberia, likely migrated to its northern distribution area only in the Holocene at around 10,000 years before present (ka BP), and had a much wider eastern distribution around 33 ka BP. Samples dated to the Last Glacial Maximum (around 21 ka BP), consistently show genotypes of L. gmelinii.
Our results suggest climate as a strong determinant of species distribution in Larix and provide temporal and spatial data for species projection in a changing climate.
Using ancient sedimentary DNA from up to 50 kya, dramatic distributional shifts are documented in two dominant boreal larch species, likely guided by environmental changes suggesting climate as a strong determinant of species distribution.
Y1 - 2022
U6 - https://doi.org/10.1038/s42003-022-03455-0
SN - 2399-3642
VL - 5
IS - 1
PB - Springer Nature
CY - London
ER -
TY - JOUR
A1 - Riemann, Lasse
A1 - Rahav, Eyal
A1 - Passow, Uta
A1 - Grossart, Hans-Peter
A1 - de Beer, Dirk
A1 - Klawonn, Isabell
A1 - Eichner, Meri
A1 - Benavides, Mar
A1 - Bar-Zeev, Edo
T1 - Planktonic aggregates as hotspots for heterotrophic diazotrophy: the plot thickens
JF - Frontiers in microbiology
N2 - Biological dinitrogen (N-2) fixation is performed solely by specialized bacteria and archaea termed diazotrophs, introducing new reactive nitrogen into aquatic environments.
Conventionally, phototrophic cyanobacteria are considered the major diazotrophs in aquatic environments. However, accumulating evidence indicates that diverse non-cyanobacterial diazotrophs (NCDs) inhabit a wide range of aquatic ecosystems, including temperate and polar latitudes, coastal environments and the deep ocean. NCDs are thus suspected to impact global nitrogen cycling decisively, yet their ecological and quantitative importance remain unknown. Here we review recent molecular and biogeochemical evidence demonstrating that pelagic NCDs inhabit and thrive especially on aggregates in diverse aquatic ecosystems. Aggregates are characterized by reduced-oxygen microzones, high C:N ratio (above Redfield) and high availability of labile carbon as compared to the ambient water.
We argue that planktonic aggregates are important loci for energetically-expensive N-2 fixation by NCDs and propose a conceptual framework for aggregate-associated N-2 fixation. Future studies on aggregate-associated diazotrophy, using novel methodological approaches, are encouraged to address the ecological relevance of NCDs for nitrogen cycling in aquatic environments.
KW - aggregates
KW - nitrogen fixation
KW - heterotrophic bacteria
KW - marine
KW - aquatic
KW - NCDs
Y1 - 2022
U6 - https://doi.org/10.3389/fmicb.2022.875050
SN - 1664-302X
VL - 13
PB - Frontiers Media
CY - Lausanne
ER -
TY - JOUR
A1 - Cao, Xianyong
A1 - Tian, Fang
A1 - Herzschuh, Ulrike
A1 - Ni, Jian
A1 - Xu, Qinghai
A1 - Li, Wenjia
A1 - Zhang, Yanrong
A1 - Luo, Mingyu
A1 - Chen, Fahu
T1 - Human activities have reduced plant diversity in eastern China over the last two millennia
JF - Global change biology
N2 - Understanding the history and regional singularities of human impact on vegetation is key to developing strategies for sustainable ecosystem management. In this study, fossil and modern pollen datasets from China are employed to investigate temporal changes in pollen composition, analogue quality, and pollen diversity during the Holocene. Anthropogenic disturbance and vegetation's responses are also assessed. Results reveal that pollen assemblages from non-forest communities fail to provide evidence of human impact for the western part of China (annual precipitation less than 400 mm and/or elevation more than 3000 m.a.s.l.), as inferred from the stable quality of modern analogues, principal components, and diversity of species and communities throughout the Holocene. For the eastern part of China, the proportion of fossil pollen spectra with good modern analogues increases from ca. 50% to ca. 80% during the last 2 millennia, indicating an enhanced intensity of anthropogenic disturbance on vegetation. This disturbance has caused the pollen spectra to become taxonomically less diverse over space (reduced abundances of arboreal taxa and increased abundances of herbaceous taxa), highlighting a reduced south-north differentiation and divergence from past vegetation between regions in the eastern part of China. We recommend that care is taken in eastern China when basing the development of ecosystem management strategies on vegetation changes in the region during the last 2000 years, since humans have significantly disturbed the vegetation during this period.
KW - analogue quality
KW - human-vegetation interaction
KW - land use
KW - latitudinal
KW - zonation
KW - plant diversity
KW - pollen
Y1 - 2022
U6 - https://doi.org/10.1111/gcb.16274
SN - 1354-1013
SN - 1365-2486
VL - 28
IS - 16
SP - 4962
EP - 4976
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Apriyanto, Ardha
A1 - Compart, Julia
A1 - Zimmermann, Vincent
A1 - Alseekh, Saleh
A1 - Fernie, Alisdair R.
A1 - Fettke, Jörg
T1 - Indication that starch and sucrose are biomarkers for oil yield in oil palm (Elaeis guineensis Jacq.)
JF - Food chemistry
N2 - Oil palm (Elaeis guineensis Jacq.) is the most productive oil-producing crop per hectare of land. The oil that accumulates in the mesocarp tissue of the fruit is the highest observed among fruit-producing plants. A comparative analysis between high-, medium-, and low-yielding oil palms, particularly during fruit development, revealed unique characteristics. Metabolomics analysis was able to distinguish accumulation patterns defining of the various developmental stages and oil yield. Interestingly, high- and medium-yielding oil palms exhibited substantially increased sucrose levels compared to low-yielding palms. In addition, parameters such as starch granule morphology, granule size, total starch content, and starch chain length distribution (CLD) differed significantly among the oil yield categories with a clear correlation between oil yield and various starch parameters. These results provide new insights into carbohydrate and starch metabolism for biosynthesis of oil palm fruits, indicating that starch and sucrose can be used as novel, easy-to-analyze, and reliable biomarker for oil yield.
KW - carbohydrate
KW - mesocarp
KW - metabolites
KW - oil palm
KW - oil yield
KW - sucrose;
KW - starch
Y1 - 2022
U6 - https://doi.org/10.1016/j.foodchem.2022.133361
SN - 0308-8146
SN - 1873-7072
VL - 393
PB - Elsevier
CY - New York, NY [u.a.]
ER -
TY - JOUR
A1 - Zielhofer, Christoph
A1 - Schmidt, Johannes
A1 - Reiche, Niklas
A1 - Tautenhahn, Marie
A1 - Ballasus, Helen
A1 - Burkart, Michael
A1 - Linstädter, Anja
A1 - Dietze, Elisabeth
A1 - Kaiser, Knut
A1 - Mehler, Natascha
T1 - The lower Havel River Region (Brandenburg, Germany)
BT - a 230-Year-Long historical map record indicates a decrease in surface water areas and groundwater levels
JF - Water
N2 - Instrumental data show that the groundwater and lake levels in Northeast Germany have decreased over the past decades, and this process has accelerated over the past few years. In addition to global warming, the direct influence of humans on the local water balance is suspected to be the cause. Since the instrumental data usually go back only a few decades, little is known about the multidecadal to centennial-scale trend, which also takes long-term climate variation and the long-term influence by humans on the water balance into account. This study aims to quantitatively reconstruct the surface water areas in the Lower Havel Inner Delta and of adjacent Lake Gulpe in Brandenburg. The analysis includes the calculation of surface water areas from historical and modern maps from 1797 to 2020. The major finding is that surface water areas have decreased by approximately 30% since the pre-industrial period, with the decline being continuous. Our data show that the comprehensive measures in Lower Havel hydro-engineering correspond with groundwater lowering that started before recent global warming. Further, large-scale melioration measures with increasing water demands in the upstream wetlands beginning from the 1960s to the 1980s may have amplified the decline in downstream surface water areas.
KW - long-term hydrological changes
KW - historical maps
KW - review of written
KW - sources
KW - preindustrial to industrial period
KW - hydro-engineering history;
KW - effects of global warming
KW - drying trend
KW - wetlands
KW - drainage works to
KW - create cropland
KW - Lower Havel River Region
KW - Brandenburg
KW - Germany
Y1 - 2022
U6 - https://doi.org/10.3390/w14030480
SN - 2073-4441
VL - 14
IS - 3
PB - MDPI
CY - Basel
ER -
TY - JOUR
A1 - Kamali, Bahareh
A1 - Jahanbakhshi, Farshid
A1 - Dogaru, Diana
A1 - Dietrich, Jörg
A1 - Nendel, Claas
A1 - AghaKouchak, Amir
T1 - Probabilistic modeling of crop-yield loss risk under drought: a spatial showcase for sub-Saharan Africa
JF - Environmental research letters
N2 - Assessing the risk of yield loss in African drought-affected regions is key to identify feasible solutions for stable crop production. Recent studies have demonstrated that Copula-based probabilistic methods are well suited for such assessment owing to reasonably inferring important properties in terms of exceedance probability and joint dependence of different characterization. However, insufficient attention has been given to quantifying the probability of yield loss and determining the contribution of climatic factors. This study applies the Copula theory to describe the dependence between drought and crop yield anomalies for rainfed maize, millet, and sorghum crops in sub-Saharan Africa (SSA). The environmental policy integrated climate model, calibrated with Food and Agriculture Organization country-level yield data, was used to simulate yields across SSA (1980-2012). The results showed that the severity of yield loss due to drought had a higher magnitude than the severity of drought itself. Sensitivity analysis to identify factors contributing to drought and high-temperature stresses for all crops showed that the amount of precipitation during vegetation and grain filling was the main driver of crop yield loss, and the effect of temperature was stronger for sorghum than for maize and millet. The results demonstrate the added value of probabilistic methods for drought-impact assessment. For future studies, we recommend looking into factors influencing drought and high-temperature stresses as individual/concurrent climatic extremes.
KW - Copula theory
KW - crop model
KW - drought stress
KW - joint probability
KW - risk
Y1 - 2022
U6 - https://doi.org/10.1088/1748-9326/ac4ec1
SN - 1748-9326
VL - 17
IS - 2
PB - IOP Publishing
CY - Bristol
ER -
TY - JOUR
A1 - Hoang, Yen
A1 - Gryzik, Stefanie
A1 - Hoppe, Ines
A1 - Rybak, Alexander
A1 - Schädlich, Martin
A1 - Kadner, Isabelle
A1 - Walther, Dirk
A1 - Vera, Julio
A1 - Radbruch, Andreas
A1 - Groth, Detlef
A1 - Baumgart, Sabine
A1 - Baumgrass, Ria
T1 - PRI: Re-analysis of a public mass cytometry dataset reveals patterns of effective tumor treatments
JF - Frontiers in immunology
N2 - Recently, mass cytometry has enabled quantification of up to 50 parameters for millions of cells per sample. It remains a challenge to analyze such high-dimensional data to exploit the richness of the inherent information, even though many valuable new analysis tools have already been developed. We propose a novel algorithm "pattern recognition of immune cells (PRI)" to tackle these high-dimensional protein combinations in the data. PRI is a tool for the analysis and visualization of cytometry data based on a three or more-parametric binning approach, feature engineering of bin properties of multivariate cell data, and a pseudo-multiparametric visualization. Using a publicly available mass cytometry dataset, we proved that reproducible feature engineering and intuitive understanding of the generated bin plots are helpful hallmarks for re-analysis with PRI. In the CD4(+)T cell population analyzed, PRI revealed two bin-plot patterns (CD90/CD44/CD86 and CD90/CD44/CD27) and 20 bin plot features for threshold-independent classification of mice concerning ineffective and effective tumor treatment. In addition, PRI mapped cell subsets regarding co-expression of the proliferation marker Ki67 with two major transcription factors and further delineated a specific Th1 cell subset. All these results demonstrate the added insights that can be obtained using the non-cluster-based tool PRI for re-analyses of high-dimensional cytometric data.
KW - multi-parametric analysis
KW - re-analysis
KW - combinatorial protein
KW - expression
KW - high-dimensional cytometry data
KW - mass cytometry data
KW - pattern perception
Y1 - 2022
U6 - https://doi.org/10.3389/fimmu.2022.849329
SN - 1664-3224
VL - 13
PB - Frontiers Media
CY - Lausanne
ER -
TY - JOUR
A1 - Esmaeilishirazifard, Elham
A1 - Usher, Louise
A1 - Trim, Carol
A1 - Denise, Hubert
A1 - Sangal, Vartul
A1 - Tyson, Gregory H.
A1 - Barlow, Axel
A1 - Redway, Keith F.
A1 - Taylor, John D.
A1 - Kremyda-Vlachou, Myrto
A1 - Davies, Sam
A1 - Loftus, Teresa D.
A1 - Lock, Mikaella M. G.
A1 - Wright, Kstir
A1 - Dalby, Andrew
A1 - Snyder, Lori A. S.
A1 - Wuster, Wolfgang
A1 - Trim, Steve
A1 - Moschos, Sterghios A.
T1 - Bacterial adaptation to venom in snakes and arachnida
JF - Microbiology spectrum
N2 - Notwithstanding their 3 to 5% mortality, the 2.7 million envenomation-related injuries occurring annually-predominantly across Africa, Asia, and Latin America-are also major causes of morbidity. Venom toxin-damaged tissue will develop infections in some 75% of envenomation victims, with E. faecalis being a common culprit of disease; however, such infections are generally considered to be independent of envenomation.
Animal venoms are considered sterile sources of antimicrobial compounds with strong membrane-disrupting activity against multidrug-resistant bacteria.
However, venomous bite wound infections are common in developing nations. Investigating the envenomation organ and venom microbiota of five snake and two spider species, we observed venom community structures that depend on the host venomous animal species and evidenced recovery of viable microorganisms from black-necked spitting cobra (Naja nigricollis) and Indian ornamental tarantula (Poecilotheria regalis) venoms. Among the bacterial isolates recovered from N. nigricollis, we identified two venom-resistant, novel sequence types of Enterococcus faecalis whose genomes feature 16 virulence genes, indicating infectious potential, and 45 additional genes, nearly half of which improve bacterial membrane integrity.
Our findings challenge the dogma of venom sterility and indicate an increased primary infection risk in the clinical management of venomous animal bite wounds. IMPORTANCE Notwithstanding their 3 to 5% mortality, the 2.7 million envenomation-related injuries occurring annually-predominantly across Africa, Asia, and Latin America-are also major causes of morbidity. Venom toxin-damaged tissue will develop infections in some 75% of envenomation victims, with E. faecalis being a common culprit of disease; however, such infections are generally considered to be independent of envenomation. Here, we provide evidence on venom microbiota across snakes and arachnida and report on the convergent evolution mechanisms that can facilitate adaptation to black-necked cobra venom in two independent E. faecalis strains, easily misidentified by biochemical diagnostics.
Therefore, since inoculation with viable and virulence gene-harboring bacteria can occur during envenomation, acute infection risk management following envenomation is warranted, particularly for immunocompromised and malnourished victims in resource-limited settings.
These results shed light on how bacteria evolve for survival in one of the most extreme environments on Earth and how venomous bites must be also treated for infections.
KW - drug resistance evolution
KW - extremophiles
KW - genome analysis
KW - microbiome
KW - multidrug resistance
KW - venom
Y1 - 2022
U6 - https://doi.org/10.1128/spectrum.02408-21
SN - 2165-0497
VL - 10
IS - 3
PB - American Society for Microbiology
CY - Birmingham, Ala.
ER -
TY - JOUR
A1 - Vences, Miguel
A1 - Köhler, Jörn
A1 - Crottini, Angelica
A1 - Hofreiter, Michael
A1 - Hutter, Carl R.
A1 - du Preez, Louis
A1 - Preick, Michaela
A1 - Rakotoarison, Andolalao
A1 - Rancilhac, Loïs
A1 - Raselimanana, Achille P.
A1 - Rosa, Gonçalo M.
A1 - Scherz, Mark D.
A1 - Glaw, Frank
T1 - An integrative taxonomic revision and redefinition of Gephyromantis (Laurentomantis) malagasius based on archival DNA analysis reveals four new mantellid frog species from Madagascar
JF - Vertebrate zoology
N2 - The subgenus Laurentomantis in the genus Gephyromantis contains some of the least known amphibian species of Madagascar. The six currently valid nominal species are rainforest frogs known from few individuals, hampering a full understanding of the species diversity of the clade. We assembled data on specimens collected during field surveys over the past 30 years and integrated analysis of mitochondrial and nuclear-encoded genes of 88 individuals, a comprehensive bioacoustic analysis, and morphological comparisons to delimit a minimum of nine species-level lineages in the subgenus. To clarify the identity of the species Gephyromantis malagasius, we applied a target-enrichment approach to a sample of the 110 year old holotype of Microphryne malagasia Methuen and Hewitt, 1913 to assign this specimen to a lineage based on a mitochondrial DNA barcode. The holotype clustered unambiguously with specimens previously named G. ventrimaculatus. Consequently we propose to consider Trachymantis malagasia ventrimaculatus Angel, 1935 as a junior synonym of Gephyromantis malagasius. Due to this redefinition of G. malagasius, no scientific name is available for any of the four deep lineages of frogs previously subsumed under this name, all characterized by red color ventrally on the hindlimbs. These are here formally named as Gephyromantis fiharimpe sp. nov., G. matsilo sp. nov., G. oelkrugi sp. nov., and G. portonae sp. nov. The new species are distinguishable from each other by genetic divergences of >4% uncorrected pairwise distance in a fragment of the 16S rRNA marker and a combination of morphological and bioacoustic characters. Gephyromantis fiharimpe and G. matsilo occur, respectively, at mid-elevations and lower elevations along a wide stretch of Madagascar's eastern rainforest band, while G. oelkrugi and G. portonae appear to be more range-restricted in parts of Madagascar's North East and Northern Central East regions. Open taxonomic questions surround G. horridus, to which we here assign specimens from Montagne d'Ambre and the type locality Nosy Be; and G. ranjomavo, which contains genetically divergent populations from Marojejy, Tsaratanana, and Ampotsidy.
KW - Amphibia
KW - Anura
KW - archival DNA
KW - Mantellidae
KW - new species
KW - phylogeography
Y1 - 2022
U6 - https://doi.org/10.3897/vz.72.e78830
SN - 1864-5755
SN - 2625-8498
VL - 72
SP - 271
EP - 309
PB - Senckenberg Gesellschaft für Naturforschung
CY - Frankfurt am Main
ER -
TY - JOUR
A1 - Sporbert, Maria
A1 - Jakubka, Desiree
A1 - Bucher, Solveig Franziska
A1 - Hensen, Isabell
A1 - Freiberg, Martin
A1 - Heubach, Katja
A1 - König, Andreas
A1 - Nordt, Birgit
A1 - Plos, Carolin
A1 - Blinova, Ilona
A1 - Bonn, Aletta
A1 - Knickmann, Barbara
A1 - Koubek, Tomáš
A1 - Linstädter, Anja
A1 - Mašková, Tereza
A1 - Primack, Richard B.
A1 - Rosche, Christoph
A1 - Shah, Manzoor A.
A1 - Stevens, Albert-Dieter
A1 - Tielbörger, Katja
A1 - Träger, Sabrina
A1 - Wirth, Christian
A1 - Römermann, Christine
T1 - Functional traits influence patterns in vegetative and reproductive plant phenology - a multi-botanical garden study
JF - New phytologist
N2 - Phenology has emerged as key indicator of the biological impacts of climate change, yet the role of functional traits constraining variation in herbaceous species' phenology has received little attention. Botanical gardens are ideal places in which to investigate large numbers of species growing under common climate conditions. We ask whether interspecific variation in plant phenology is influenced by differences in functional traits. We recorded onset, end, duration and intensity of initial growth, leafing out, leaf senescence, flowering and fruiting for 212 species across five botanical gardens in Germany. We measured functional traits, including plant height, absolute and specific leaf area, leaf dry matter content, leaf carbon and nitrogen content and seed mass and accounted for species' relatedness. Closely related species showed greater similarities in timing of phenological events than expected by chance, but species' traits had a high degree of explanatory power, pointing to paramount importance of species' life-history strategies. Taller plants showed later timing of initial growth, and flowered, fruited and underwent leaf senescence later. Large-leaved species had shorter flowering and fruiting durations. Taller, large-leaved species differ in their phenology and are more competitive than smaller, small-leaved species. We assume climate warming will change plant communities' competitive hierarchies with consequences for biodiversity.
KW - botanical gardens
KW - first flowering day
KW - growing season length
KW - leaf
KW - traits
KW - PhenObs phenological network
KW - phylogeny
Y1 - 2022
U6 - https://doi.org/10.1111/nph.18345
SN - 0028-646X
SN - 1469-8137
VL - 235
IS - 6
SP - 2199
EP - 2210
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Derežanin, Lorena
A1 - Blažytė, Asta
A1 - Dobrynin, Pavel
A1 - Duchêne, David A.
A1 - Grau, José Horacio
A1 - Jeon, Sungwon
A1 - Kliver, Sergei
A1 - Koepfli, Klaus-Peter
A1 - Meneghini, Dorina
A1 - Preick, Michaela
A1 - Tomarovsky, Andrey
A1 - Totikov, Azamat
A1 - Fickel, Jörns
A1 - Förster, Daniel W.
T1 - Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae
JF - Molecular ecology
N2 - Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes and searching for species-specific structural variants. Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observed species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This argues strongly for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance.
KW - adaptation
KW - gene family evolution
KW - genomics
KW - mustelids
KW - positive
KW - selection
KW - structural variation
Y1 - 2022
U6 - https://doi.org/10.1111/mec.16443
SN - 0962-1083
SN - 1365-294X
VL - 31
IS - 10
SP - 2898
EP - 2919
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Garbulowski, Mateusz
A1 - Smolinska, Karolina
A1 - Çabuk, Uğur
A1 - Yones, Sara A.
A1 - Celli, Ludovica
A1 - Yaz, Esma Nur
A1 - Barrenas, Fredrik
A1 - Diamanti, Klev
A1 - Wadelius, Claes
A1 - Komorowski, Jan
T1 - Machine learning-based analysis of glioma grades reveals co-enrichment
JF - Cancers
N2 - Simple Summary Gliomas are heterogenous types of cancer, therefore the therapy should be personalized and targeted toward specific pathways. We developed a methodology that corrected strong batch effects from The Cancer Genome Atlas datasets and estimated glioma grade-specific co-enrichment mechanisms using machine learning. Our findings created hypotheses for annotations, e.g., pathways, that should be considered as therapeutic targets. Gliomas develop and grow in the brain and central nervous system. Examining glioma grading processes is valuable for improving therapeutic challenges. One of the most extensive repositories storing transcriptomics data for gliomas is The Cancer Genome Atlas (TCGA). However, such big cohorts should be processed with caution and evaluated thoroughly as they can contain batch and other effects. Furthermore, biological mechanisms of cancer contain interactions among biomarkers. Thus, we applied an interpretable machine learning approach to discover such relationships. This type of transparent learning provides not only good predictability, but also reveals co-predictive mechanisms among features. In this study, we corrected the strong and confounded batch effect in the TCGA glioma data. We further used the corrected datasets to perform comprehensive machine learning analysis applied on single-sample gene set enrichment scores using collections from the Molecular Signature Database. Furthermore, using rule-based classifiers, we displayed networks of co-enrichment related to glioma grades. Moreover, we validated our results using the external glioma cohorts. We believe that utilizing corrected glioma cohorts from TCGA may improve the application and validation of any future studies. Finally, the co-enrichment and survival analysis provided detailed explanations for glioma progression and consequently, it should support the targeted treatment.
KW - glioma
KW - machine learning
KW - batch effect
KW - TCGA
KW - co-enrichment
KW - rough sets
Y1 - 2022
U6 - https://doi.org/10.3390/cancers14041014
SN - 2072-6694
VL - 14
IS - 4
PB - MDPI
CY - Basel
ER -
TY - JOUR
A1 - Ilicic, Doris
A1 - Woodhouse, Jason Nicholas
A1 - Karsten, Ulf
A1 - Zimmermann, Jonas
A1 - Wichard, Thomas
A1 - Quartino, Maria Liliana
A1 - Campana, Gabriela Laura
A1 - Livenets, Alexandra
A1 - Van den Wyngaert, Silke
A1 - Grossart, Hans-Peter
T1 - Antarctic Glacial Meltwater Impacts the Diversity of Fungal Parasites Associated With Benthic Diatoms in Shallow Coastal Zones
JF - Frontiers in microbiology
N2 - Aquatic ecosystems are frequently overlooked as fungal habitats, although there is increasing evidence that their diversity and ecological importance are greater than previously considered. Aquatic fungi are critical and abundant components of nutrient cycling and food web dynamics, e.g., exerting top-down control on phytoplankton communities and forming symbioses with many marine microorganisms. However, their relevance for microphytobenthic communities is almost unexplored. In the light of global warming, polar regions face extreme changes in abiotic factors with a severe impact on biodiversity and ecosystem functioning. Therefore, this study aimed to describe, for the first time, fungal diversity in Antarctic benthic habitats along the salinity gradient and to determine the co-occurrence of fungal parasites with their algal hosts, which were dominated by benthic diatoms. Our results reveal that Ascomycota and Chytridiomycota are the most abundant fungal taxa in these habitats. We show that also in Antarctic waters, salinity has a major impact on shaping not just fungal but rather the whole eukaryotic community composition, with a diversity of aquatic fungi increasing as salinity decreases. Moreover, we determined correlations between putative fungal parasites and potential benthic diatom hosts, highlighting the need for further systematic analysis of fungal diversity along with studies on taxonomy and ecological roles of Chytridiomycota.
KW - Antarctica
KW - aquatic fungi
KW - Chytridiomycota
KW - phytoplankton host
KW - salinity gradient
KW - Illumina amplicon sequencing
KW - Carlini Station
Y1 - 2022
U6 - https://doi.org/10.3389/fmicb.2022.805694
SN - 1664-302X
IS - 13
PB - Frontiers Media
CY - Lausanne
ER -
TY - JOUR
A1 - Zoccarato, Luca
A1 - Sher, Daniel
A1 - Miki, Takeshi
A1 - Segre, Daniel
A1 - Grossart, Hans-Peter
T1 - A comparative whole-genome approach identifies bacterial traits for marine microbial interactions
JF - Communications biology
N2 - Luca Zoccarato, Daniel Sher et al. leverage publicly available bacterial genomes from marine and other environments to examine traits underlying microbial interactions.
Their results provide a valuable resource to investigate clusters of functional and linked traits to better understand marine bacteria community assembly and dynamics.
Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities.
We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10% of genomes), phytohormones (3-8%) and different B vitamins (57-70%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions.
Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.
Y1 - 2022
U6 - https://doi.org/10.1038/s42003-022-03184-4
SN - 2399-3642
VL - 5
IS - 1
PB - Springer Nature
CY - Berlin
ER -
TY - JOUR
A1 - Potente, Giacomo
A1 - Léveillé-Bourret, Étienne
A1 - Yousefi, Narjes
A1 - Choudhury, Rimjhim Roy
A1 - Keller, Barbara
A1 - Diop, Seydina Issa
A1 - Duijsings, Daniël
A1 - Pirovano, Walter
A1 - Lenhard, Michael
A1 - Szövényi, Péter
A1 - Conti, Elena
T1 - Comparative genomics elucidates the origin of a supergene controlling floral heteromorphism
JF - Molecular biology and evolution : MBE
N2 - Supergenes are nonrecombining genomic regions ensuring the coinheritance of multiple, coadapted genes. Despite the importance of supergenes in adaptation, little is known on how they originate. A classic example of supergene is the S locus controlling heterostyly, a floral heteromorphism occurring in 28 angiosperm families. In Primula, heterostyly is characterized by the cooccurrence of two complementary, self-incompatible floral morphs and is controlled by five genes clustered in the hemizygous, ca. 300-kb S locus. Here, we present the first chromosome-scale genome assembly of any heterostylous species, that of Primula veris (cowslip). By leveraging the high contiguity of the P. veris assembly and comparative genomic analyses, we demonstrated that the S-locus evolved via multiple, asynchronous gene duplications and independent gene translocations. Furthermore, we discovered a new whole-genome duplication in Ericales that is specific to the Primula lineage. We also propose a mechanism for the origin of S-locus hemizygosity via nonhomologous recombination involving the newly discovered two pairs of CFB genes flanking the S locus. Finally, we detected only weak signatures of degeneration in the S locus, as predicted for hemizygous supergenes. The present study provides a useful resource for future research addressing key questions on the evolution of supergenes in general and the S locus in particular: How do supergenes arise? What is the role of genome architecture in the evolution of complex adaptations? Is the molecular architecture of heterostyly supergenes across angiosperms similar to that of Primula?
KW - genome architecture
KW - supergene
KW - heterostyly
KW - evolutionary genomics
KW - chromosome-scale genome assembly
KW - primula
Y1 - 2022
U6 - https://doi.org/10.1093/molbev/msac035
SN - 0737-4038
SN - 1537-1719
VL - 39
IS - 2
PB - Oxford Univ. Press
CY - Oxford
ER -
TY - GEN
A1 - Huu, Cuong Nguyen
A1 - Plaschil, Sylvia
A1 - Himmelbach, Axel
A1 - Kappel, Christian
A1 - Lenhard, Michael
T1 - Female self-incompatibility type in heterostylous Primula is determined by the brassinosteroid-inactivating cytochrome P450 CYP734A50
T2 - Current biology
N2 - Most flowering plants are hermaphrodites, with flowers having both male and female reproductive organs. One widespread adaptation to limit self-fertilization is self-incompatibility (SI), where self-pollen fails to fertilize ovules.(1,2) In homomorphic SI, many morphologically indistinguishable mating types are found, although in heteromorphic SI, the two or three mating types are associated with different floral morphologies.(3-6) In heterostylous Primula, a hemizygous supergene determines a short-styled S-morph and a long-styled L-morph, corresponding to two different mating types, and full seed set only results from inter morph crosses.(7-9) Style length is controlled by the brassinosteroid (BR)-inactivating cytochrome P450 CYP734A50,(10) yet it remains unclear what defines the male and female incompatibility types. Here, we show that CYP734A50 also determines the female incompatibility type. Inactivating CYP734A50 converts short S-morph styles into long styles with the same incompatibility behavior as L-morph styles, and this effect can be mimicked by exogenous BR treatment. In vitro responses of S-and L-morph pollen grains and pollen tubes to increasing BR levels could only partly explain their different in vivo behavior, suggesting both direct and indirect effects of the different BR levels in S-versus L-morph stigmas and styles in controlling pollen performance. This BR-mediated SI provides a novel mechanism for preventing self-fertilization. The joint control of morphology and SI by CYP734A50 has important implications for the evolutionary buildup of the heterostylous syndrome and provides a straightforward explanation for why essentially all of the derived self-compatible homostylous Primula species are long homostyles.(11)
KW - heteromorphic self-incompatibility
KW - heterostyly
KW - Primula forbesii
KW - brassinosteroid
KW - CYP734A50
KW - supergene
KW - pleiotropy
Y1 - 2022
U6 - https://doi.org/10.1016/j.cub.2021.11.046
SN - 0960-9822
SN - 1879-0445
VL - 32
IS - 3
SP - 671
EP - 676, E1-E5
PB - Cell Press
CY - Cambridge, Mass.
ER -
TY - JOUR
A1 - Oberkofler, Vicky
A1 - Bäurle, Isabel
T1 - Inducible epigenome editing probes for the role of histone H3K4 methylation in Arabidopsis heat stress memory
JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants
N2 - A temperature-inducible epigenome editing system to knock down histone methylation can be used to study the role of histone H3K4 methylation during heat stress memory in Arabidopsis.
Histone modifications play a crucial role in the integration of environmental signals to mediate gene expression outcomes. However, genetic and pharmacological interference often causes pleiotropic effects, creating the urgent need for methods that allow locus-specific manipulation of histone modifications, preferably in an inducible manner. Here, we report an inducible system for epigenome editing in Arabidopsis (Arabidopsis thaliana) using a heat-inducible dCas9 to target a JUMONJI (JMJ) histone H3 lysine 4 (H3K4) demethylase domain to a locus of interest. As a model locus, we target the ASCORBATE PEROXIDASE2 (APX2) gene that shows transcriptional memory after heat stress (HS), correlating with H3K4 hyper-methylation. We show that dCas9-JMJ is targeted in a HS-dependent manner to APX2 and that the HS-induced overaccumulation of H3K4 trimethylation (H3K4me3) decreases when dCas9-JMJ binds to the locus. This results in reduced HS-mediated transcriptional memory at the APX2 locus. Targeting an enzymatically inactive JMJ protein in an analogous manner affected transcriptional memory less than the active JMJ protein; however, we still observed a decrease in H3K4 methylation levels. Thus, the inducible targeting of dCas9-JMJ to APX2 was effective in reducing H3K4 methylation levels. As the effect was not fully dependent on enzyme activity of the eraser domain, the dCas9-JMJ fusion protein may act in part independently of its demethylase activity. This underlines the need for caution in the design and interpretation of epigenome editing studies. We expect our versatile inducible epigenome editing system to be especially useful for studying temporal dynamics of chromatin modifications.
Y1 - 2022
U6 - https://doi.org/10.1093/plphys/kiac113
SN - 0032-0889
SN - 1532-2548
VL - 189
IS - 2
SP - 703
EP - 714
PB - Oxford University Press
CY - Oxford
ER -
TY - JOUR
A1 - Welke, Robert-William
A1 - Sperber, Hannah Sabeth
A1 - Bergmann, Ronny
A1 - Koikkarah, Amit
A1 - Menke, Laura
A1 - Sieben, Christian
A1 - Krüger, Detlev H.
A1 - Chiantia, Salvatore
A1 - Herrmann, Andreas
A1 - Schwarzer, Roland
T1 - Characterization of hantavirus N protein intracellular dynamics and localization
JF - Viruses
N2 - Hantaviruses are enveloped viruses that possess a tri-segmented, negative-sense RNA genome.
The viral S-segment encodes the multifunctional nucleocapsid protein (N), which is involved in genome packaging, intracellular protein transport, immunoregulation, and several other crucial processes during hantavirus infection.
In this study, we generated fluorescently tagged N protein constructs derived from Puumalavirus (PUUV), the dominant hantavirus species in Central, Northern, and Eastern Europe.
We comprehensively characterized this protein in the rodent cell line CHO-K1, monitoring the dynamics of N protein complex formation and investigating co-localization with host proteins as well as the viral glycoproteins Gc and Gn.
We observed formation of large, fibrillar PUUV N protein aggregates, rapidly coalescing from early punctate and spike-like assemblies.
Moreover, we found significant spatial correlation of N with vimentin, actin, and P-bodies but not with microtubules. N constructs also co-localized with Gn and Gc albeit not as strongly as the glycoproteins associated with each other.
Finally, we assessed oligomerization of N constructs, observing efficient and concentration-dependent multimerization, with complexes comprising more than 10 individual proteins.
KW - hantavirus
KW - N protein
KW - oligomerization
KW - actin
KW - P-bodies
KW - vimentin
KW - Number and Brightness
KW - Puumalavirus
KW - macromolecular assemblies
Y1 - 2022
U6 - https://doi.org/10.3390/v14030457
SN - 1999-4915
VL - 14
IS - 3
PB - MDPI
CY - Basel
ER -
TY - JOUR
A1 - Belluardo, Francesco
A1 - Scherz, Mark D.
A1 - Santos, Barbara
A1 - Andreone, Franco
A1 - Antonelli, Alexandre
A1 - Glaw, Frank
A1 - Munoz-Pajares, A. Jesus
A1 - Randrianirina, Jasmin E.
A1 - Raselimanana, Achille P.
A1 - Vences, Miguel
A1 - Crottini, Angelica
T1 - Molecular taxonomic identification and species-level phylogeny of the narrow-mouthed frogs of the genus Rhombophryne (Anura: Microhylidae: Cophylinae) from Madagascar
JF - Systematics and biodiversity
N2 - The study of diamond frogs (genus Rhombophryne, endemic to Madagascar) has been historically hampered by the paucity of available specimens, because of their low detectability in the field. Over the last 10 years, 13 new taxa have been described, and 20 named species are currently recognized. Nevertheless, undescribed diversity within the genus is probably large, calling for a revision of the taxonomic identification of published records and an update of the known distribution of each lineage. Here we generate DNA sequences of the mitochondrial 16S rRNA gene of all specimens available to us, revise the genetic data from public databases, and report all deeply divergent mitochondrial lineages of Rhombophryne identifiable from these data. We also generate a multi-locus dataset (including five mitochondrial and eight nuclear markers; 9844 bp) to infer a species-level phylogenetic hypothesis for the diversification of this genus and revise the distribution of each lineage. We recognize a total of 10 candidate species, two of which are identified here for the first time. The genus Rhombophryne is here proposed to be divided into six main species groups, and phylogenetic relationships among some of them are not fully resolved. These frogs are primarily distributed in northern Madagascar, and most species are known from only few localities. A previous record of this genus from the Tsingy de Bemaraha (western Madagascar) is interpreted as probably due to a mislabelling and should not be considered further unless confirmed by new data. By generating this phylogenetic hypothesis and providing an updated distribution of each lineage, our findings will facilitate future species descriptions, pave the way for evolutionary studies, and provide valuable information for the urgent conservation of diamond frogs.
KW - amphibians
KW - candidate species
KW - diamond frogs
KW - mitochondrial lineages
KW - northern Madagascar
KW - species-identification
KW - systematics
Y1 - 2022
U6 - https://doi.org/10.1080/14772000.2022.2039320
SN - 1477-2000
SN - 1478-0933
VL - 20
IS - 1
SP - 1
EP - 13
PB - Routledge, Taylor & Francis Group
CY - Abingdon
ER -
TY - JOUR
A1 - Numberger, Daniela
A1 - Zoccarato, Luca
A1 - Woodhouse, Jason Nicholas
A1 - Ganzert, Lars
A1 - Sauer, Sascha
A1 - García Márquez, Jaime Ricardo
A1 - Domisch, Sami
A1 - Grossart, Hans-Peter
A1 - Greenwood, Alex
T1 - Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens
JF - The science of the total environment : an international journal for scientific research into the environment and its relationship with man
N2 - Freshwater ecosystems are characterized by complex and highly dynamic microbial communities that are strongly structured by their local environment and biota. Accelerating urbanization and growing city populations detrimentally alter freshwater environments. To determine differences in freshwater microbial communities associated with urban-ization, full-length 16S rRNA gene PacBio sequencing was performed in a case study from surface waters and sedi-ments from a wastewater treatment plant, urban and rural lakes in the Berlin-Brandenburg region, Northeast Germany. Water samples exhibited highly habitat specific bacterial communities with multiple genera showing clear urban signatures. We identified potentially harmful bacterial groups associated with environmental parameters specific to urban habitats such as Alistipes, Escherichia/Shigella, Rickettsia and Streptococcus. We demonstrate that urban-ization alters natural microbial communities in lakes and, via simultaneous warming and eutrophication and creates favourable conditions that promote specific bacterial genera including potential pathogens. Our findings are evidence to suggest an increased potential for long-term health risk in urbanized waterbodies, at a time of rapidly expanding global urbanization. The results highlight the urgency for undertaking mitigation measures such as targeted lake restoration projects and sustainable water management efforts.
KW - Urbanization
KW - Urban waters
KW - Wastewater
KW - Lakes
KW - Microbial community
KW - composition
KW - Humanization
KW - Full-length 16S rRNA PacBio sequencing
Y1 - 2022
U6 - https://doi.org/10.1016/j.scitotenv.2022.157321
SN - 0048-9697
SN - 1879-1026
VL - 845
PB - Elsevier
CY - Amsterdam
ER -
TY - JOUR
A1 - Mehner, Thomas
A1 - Attermeyer, Katrin
A1 - Brauns, Mario
A1 - Brothers, Soren
A1 - Hilt, Sabine
A1 - Scharnweber, Inga Kristin
A1 - Dorst, Renee Minavan
A1 - Vanni, Michael J.
A1 - Gaedke, Ursula
T1 - Trophic transfer efficiency in lakes
JF - Ecosystems
N2 - Trophic transfer efficiency (TTE) is usually calculated as the ratio of production rates between two consecutive trophic levels. Although seemingly simple, TTE estimates from lakes are rare. In our review, we explore the processes and structures that must be understood for a proper lake TTE estimate.
We briefly discuss measurements of production rates and trophic positions and mention how ecological efficiencies, nutrients (N, P) and other compounds (fatty acids) affect energy transfer between trophic levels and hence TTE.
Furthermore, we elucidate how TTE estimates are linked with size-based approaches according to the Metabolic Theory of Ecology, and how food-web models can be applied to study TTE in lakes.
Subsequently, we explore temporal and spatial heterogeneity of production and TTE in lakes, with a particular focus on the links between benthic and pelagic habitats and between the lake and the terrestrial environment.
We provide an overview of TTE estimates from lakes found in the published literature. Finally, we present two alternative approaches to estimating TTE. First, TTE can be seen as a mechanistic quantity informing about the energy and matter flow between producer and consumer groups.
This approach is informative with respect to food-web structure, but requires enormous amounts of data. The greatest uncertainty comes from the proper consideration of basal production to estimate TTE of omnivorous organisms.
An alternative approach is estimating food-chain and food-web efficiencies, by comparing the heterotrophic production of single consumer levels or the total sum of all heterotrophic production including that of heterotrophic bacteria to the total sum of primary production.
We close the review by pointing to a few research questions that would benefit from more frequent and standardized estimates of TTE in lakes.
KW - stoichiometry
KW - production rates
KW - trophic position
KW - fatty acids
KW - land-water coupling
KW - food-web models
Y1 - 2022
U6 - https://doi.org/10.1007/s10021-022-00776-3
SN - 1432-9840
SN - 1435-0629
VL - 25
IS - 8
SP - 1628
EP - 1652
PB - Springer
CY - New York
ER -
TY - THES
A1 - Wijesingha Ahchige, Micha
T1 - Canalization of plant metabolism and yield
T1 - Kanalisierung des Pflanzenmetabolismus und -ertrags
N2 - Plant metabolism is the main process of converting assimilated carbon to different crucial compounds for plant growth and therefore crop yield, which makes it an important research topic. Although major advances in understanding genetic principles contributing to metabolism and yield have been made, little is known about the genetics responsible for trait variation or canalization although the concepts have been known for a long time. In light of a growing global population and progressing climate change, understanding canalization of metabolism and yield seems ever-more important to ensure food security. Our group has recently found canalization metabolite quantitative trait loci (cmQTL) for tomato fruit metabolism, showing that the concept of canalization applies on metabolism. In this work two approaches to investigate plant metabolic canalization and one approach to investigate yield canalization are presented.
In the first project, primary and secondary metabolic data from Arabidopsis thaliana and Phaseolus vulgaris leaf material, obtained from plants grown under different conditions was used to calculate cross-environment coefficient of variations or fold-changes of metabolite levels per genotype and used as input for genome wide association studies. While primary metabolites have lower CV across conditions and show few and mostly weak associations to genomic regions, secondary metabolites have higher CV and show more, strong metabolite to genome associations. As candidate genes, both potential regulatory genes as well as metabolic genes, can be found, albeit most metabolic genes are rarely directly related to the target metabolites, suggesting a role for both potential regulatory mechanisms as well as metabolic network structure for canalization of metabolism.
In the second project, candidate genes of the Solanum lycopersicum cmQTL mapping are selected and CRISPR/Cas9-mediated gene-edited tomato lines are created, to validate the genes role in canalization of metabolism. Obtained mutants appeared to either have strong aberrant developmental phenotypes or appear wild type-like. One phenotypically inconspicuous mutant of a pantothenate kinase, selected as candidate for malic acid canalization shows a significant increase of CV across different watering conditions. Another such mutant of a protein putatively involved in amino acid transport, selected as candidate for phenylalanine canalization shows a similar tendency to increased CV without statistical significance. This potential role of two genes involved in metabolism supports the hypothesis of structural relevance of metabolism for its own stability.
In the third project, a mutant for a putative disulfide isomerase, important for thylakoid biogenesis, is characterized by a multi-omics approach. The mutant was characterized previously in a yield stability screening and showed a variegated leaf phenotype, ranging from green leaves with wild type levels of chlorophyll over differently patterned variegated to completely white leaves almost completely devoid of photosynthetic pigments. White mutant leaves show wild type transcript levels of photosystem assembly factors, with the exception of ELIP and DEG orthologs indicating a stagnation at an etioplast to chloroplast transition state. Green mutant leaves show an upregulation of these assembly factors, possibly acting as overcompensation for partially defective disulfide isomerase, which seems sufficient for proper chloroplast development as confirmed by a wild type-like proteome. Likely as a result of this phenotype, a general stress response, a shift to a sink-like tissue and abnormal thylakoid membranes, strongly alter the metabolic profile of white mutant leaves. As the severity and pattern of variegation varies from plant to plant and may be effected by external factors, the effect on yield instability, may be a cause of a decanalized ability to fully exploit the whole leaf surface area for photosynthetic activity.
N2 - Der pflanzliche Stoffwechsel ist der Hauptprozess, der assimilierten Kohlenstoff in unterschiedliche Stoffe umwandelt, die wichtig für das Pflanzenwachstum und somit den Ertrag sind, weswegen es ein wichtiges Forschungsthema ist. Obwohl große Fortschritte beim Verständnis der genetischen Prinzipien, die zum Stoffwechsel und Ertrag beitragen, gemacht wurden, ist noch relativ wenig über die genetischen Prinzipien bekannt, die für die Variation oder Kanalisierung von Eigenschaften verantwortlich sind, obwohl diese Konzepte schon lange bekannt sind. In Anbetracht einer wachsenden Weltbevölkerung und des fortschreitenden Klimawandels, scheint es immer wichtiger zu sein, Kanalisierung von Metabolismus und Ertrag zu verstehen, um Ernährungssicherheit zu garantieren. Unsere Gruppe hat kürzlich metabolisch kanalisierte quantitative Merkmalsregionen für den Stoffwechsel von Tomatenfrüchten gefunden und damit gezeigt, dass sich das Konzept der Kanalisierung sich auf den Stoffwechsel anwenden lässt. In dieser Arbeit werden zwei Ansätze zu Untersuchung von Kanalisierung des pflanzlichen Stoffwechsels und ein Ansatz zur Untersuchung von Ertragskanalisierung präsentiert.
Im ersten Projekt, wurden Daten von Primär- und Sekundärmetaboliten von Arabidopsis thaliana und Phaseolus vulgaris, gewonnen von Pflanzen, die unter unterschiedlichen Bedingungen wuchsen, verwendet, um den Variationskoeffizient (VarK) oder die relative Änderung von Stoffgehalten umweltübergreifend für jeden Genotyp zu berechnen und als Eingabe für genomweite Assoziationsstudien verwendet. Während Primärmetabolite über unterschiedliche Umweltbedingungen einen geringeren VarK haben und nur wenige eher schwache Assoziationen zu genomischen Regionen zeigen, haben Sekundärstoffe einen höheren VarK und zeigen mehr und stärkere Assoziationen zwischen Metabolit und Genom. Als Kandidatengene können sowohl potenziell regulatorische, als auch metabolische Gene gefunden werden, jedoch sind metabolische Gene selten direkt zu den Zielmetaboliten verbunden, was für eine Rolle von sowohl regulatorischen Mechanismen als auch metabolischer Netzwerkstruktur für die Kanalisierung des Stoffwechsels spricht.
Im zweiten Projekt wurden Kandidatengene aus der Solanum lycopersicum cmQTL-Kartierung, ausgewählt und CRISPR/Cas9-vermittelte, genomeditierte Tomatenlinien erschaffen, um die Rolle dieser Gene in der Kanalisierung des Metabolismus zu validieren. Erhaltene Mutanten zeigten entweder starke Fehlentwicklungsphänotypen oder erschienen wildtypähnlich. Eine phänotypisch unauffällige Mutante einer Pantothensäurekinase, die als Kandidat für die Kanalisierung von Apfelsäure gewählt wurde, zeigte einen signifikanten Anstieg des VarK über unterschiedliche Bewässerungsbedingungen. Eine andere solche Mutante eines Proteins, welches mutmaßlich im Aminosäuretransport involviert ist, welches als Kandidat für die Kanalisierung von Phenylalanin gewählt wurde, zeigt eine ähnliche Tendenz zu einem erhöhten VarK ohne statistische Signifikanz. Diese potenzielle Rolle von zwei Genen, die im Stoffwechsel involviert sind, unterstützt die Hypothese einer strukturellen Relevanz des Metabolismus für seine eigene Stabilität.
Im dritten Projekt wurde eine Mutante einer mutmaßlichen Disulfid-Isomerase, welche wichtig für die Thylakoidbiogenese ist, durch einen Multiomik Ansatz charakterisiert. Die Mutante wurde vorher in einer Ertragsstabilitäts-Selektierung charakterisiert und zeigte einen panaschierten Blattphänotyp, welcher von grünen Blättern mit Wildtyp Chlorophyllgehalt über unterschiedlich gemustert panaschierte Blätter bis zu komplett weißen Blätter reichte, die fast gar keine photosynthetischen Pigmente enthielten. Weiße Blätter der Mutante zeigen Wildtyp Transkriptlevel von Photosystem-Aufbaufaktoren, mit der Ausnahme von ELIP und DEG Orthologen, was indikativ für eine Stagnation in einer Etioplast-zu-Chloroplast-Übergangsphase ist. Grüne Blätter der Mutante zeigen eine Hochregulierung dieser Aufbaufaktoren, was möglicherweise als Überkompensation für eine partiell defekte Disulfid-Isomerase wirkt und letztlich ausreichend für Chloroplastenentwicklung zu sein scheint, was wiederum durch ein wildtyp-ähnliches Proteom bestätigt wird. Wahrscheinlich als Effekt dieses Phänotyps ändern, eine generelle Stressantwort, eine Umschaltung zu einem Senke-ähnlichen Gewebe und abnormale Thylakoidmembranen, stark das metabolische Profil von weißen Blättern der Mutante. Da der Schweregrad und das Muster der Panaschierung von Pflanze zu Pflanze unterschiedlich ist und durch äußere Faktoren beeinflusst sein könnte, könnte der Effekt auf die Ertragsstabilität eine Folge einer dekanalisierten Fähigkeit sein die ganze Blattoberfläche für photosynthetische Aktivität zu nutzen.
KW - canalization
KW - phenotypic variation
KW - metabolism
KW - CRISPR/Cas9
KW - GWAS
KW - CRISPR/Cas9
KW - GWAS
KW - Kanalisierung
KW - Metabolismus
KW - phänotypische Variation
Y1 - 2022
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-548844
ER -
TY - JOUR
A1 - Tabatabaei, Iman
A1 - Alseekh, Saleh
A1 - Shahid, Mohammad
A1 - Leniak, Ewa
A1 - Wagner, Mateusz
A1 - Mahmoudi, Henda
A1 - Thushar, Sumitha
A1 - Fernie, Alisdair R.
A1 - Murphy, Kevin M.
A1 - Schmöckel, Sandra M.
A1 - Tester, Mark
A1 - Müller-Röber, Bernd
A1 - Skirycz, Aleksandra
A1 - Balazadeh, Salma
T1 - The diversity of quinoa morphological traits and seed metabolic composition
JF - Scientific data
N2 - Quinoa (Chenopodium quinoa Willd.) is an herbaceous annual crop of the amaranth family (Amaranthaceae). It is increasingly cultivated for its nutritious grains, which are rich in protein and essential amino acids, lipids, and minerals. Quinoa exhibits a high tolerance towards various abiotic stresses including drought and salinity, which supports its agricultural cultivation under climate change conditions. The use of quinoa grains is compromised by anti-nutritional saponins, a terpenoid class of secondary metabolites deposited in the seed coat; their removal before consumption requires extensive washing, an economically and environmentally unfavorable process; or their accumulation can be reduced through breeding. In this study, we analyzed the seed metabolomes, including amino acids, fatty acids, and saponins, from 471 quinoa cultivars, including two related species, by liquid chromatography - mass spectrometry. Additionally, we determined a large number of agronomic traits including biomass, flowering time, and seed yield. The results revealed considerable diversity between genotypes and provide a knowledge base for future breeding or genome editing of quinoa.
Y1 - 2022
U6 - https://doi.org/10.1038/s41597-022-01399-y
SN - 2052-4463
VL - 9
IS - 1
PB - Nature Research
CY - Berlin
ER -
TY - JOUR
A1 - Leong, Jia Xuan
A1 - Raffeiner, Margot
A1 - Spinti, Daniela
A1 - Langin, Gautier
A1 - Franz-Wachtel, Mirita
A1 - Guzman, Andrew R.
A1 - Kim, Jung-Gun
A1 - Pandey, Pooja
A1 - Minina, Alyona E.
A1 - Macek, Boris
A1 - Hafren, Anders
A1 - Bozkurt, Tolga O.
A1 - Mudgett, Mary Beth
A1 - Börnke, Frederik
A1 - Hofius, Daniel
A1 - Uestuen, Suayib
T1 - A bacterial effector counteracts host autophagy by promoting degradation of an autophagy component
JF - The EMBO journal
N2 - Beyond its role in cellular homeostasis, autophagy plays anti- and promicrobial roles in host-microbe interactions, both in animals and plants.
One prominent role of antimicrobial autophagy is to degrade intracellular pathogens or microbial molecules, in a process termed xenophagy.
Consequently, microbes evolved mechanisms to hijack or modulate autophagy to escape elimination.
Although well-described in animals, the extent to which xenophagy contributes to plant-bacteria interactions remains unknown.
Here, we provide evidence that Xanthomonas campestris pv. vesicatoria (Xcv) suppresses host autophagy by utilizing type-III effector XopL. XopL interacts with and degrades the autophagy component SH3P2 via its E3 ligase activity to promote infection.
Intriguingly, XopL is targeted for degradation by defense-related selective autophagy mediated by NBR1/Joka2, revealing a complex antagonistic interplay between XopL and the host autophagy machinery.
Our results implicate plant antimicrobial autophagy in the depletion of a bacterial virulence factor and unravel an unprecedented pathogen strategy to counteract defense-related autophagy in plant-bacteria interactions.
KW - autophagy
KW - effectors
KW - immunity
KW - ubiquitination
KW - xenophagy
Y1 - 2022
U6 - https://doi.org/10.15252/embj.2021110352
SN - 1460-2075
VL - 41
IS - 13
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Mitzscherling, Julia
A1 - MacLean, Joana
A1 - Lipus, Daniel
A1 - Bartholomäus, Alexander
A1 - Mangelsdorf, Kai
A1 - Lipski, André
A1 - Roddatis, Vladimir
A1 - Liebner, Susanne
A1 - Wagner, Dirk
T1 - Nocardioides alcanivorans sp. nov., a novel hexadecane-degrading species isolated from plastic waste
JF - International journal of systematic and evolutionary microbiology
N2 - Strain NGK65(T), a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill.
Strain NGK65(T) hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 degrees C. in 0-1% NaCl and at pH 7.5-8.0. Glycerol, D-glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate. sucrose, acetate, pyruvate and hexadecane were used as sole carbon sources.
The predominant membrane fatty acids were iso-C-16:0 followed by iso-C(17:)0 and C-18:1 omega 9c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and hydroxyphosphatidylinositol.
The cell-wall peptidoglycan type was A3 gamma, with LL-diaminopimelic acid and glycine as the diagnostic amino acids. MK 8 (H-4) was the predominant menaquinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK65(T) belongs to the genus Nocardioides (phylum Actinobacteria). appearing most closely related to Nocardioides daejeonensis MJ31(T) (98.6%) and Nocardioides dubius KSL-104(T) (98.3%).
The genomic DNA G+C content of strain NGK65(T) was 68.2%.
Strain NGK65(T) and the type strains of species involved in the analysis had average nucleotide identity values of 78.3-71.9% as well as digital DNA-DNA hybridization values between 22.5 and 19.7%, which clearly indicated that the isolate represents a novel species within the genus Nocardioides.
Based on phenotypic and molecular characterization, strain NGK65(T) can clearly be differentiated from its phylogenetic neighbours to establish a novel species, for which the name Nocardioides alcanivorans sp. nov. is proposed.
The type strain is NGK65(T) (=DSM 113112(T)=NCCB 100846(T)).
KW - Nocardioides alcanivorans
KW - hexadecane
KW - plastic degradation
KW - terrestrial
KW - plastisphere
KW - bacteria
Y1 - 2022
U6 - https://doi.org/10.1099/ijsem.0.005319
SN - 1466-5026
SN - 1466-5034
VL - 72
IS - 4
PB - Microbiology Society
CY - London
ER -
TY - JOUR
A1 - Hagemann, Justus
A1 - Conejero, Carles
A1 - Stillfried, Milena
A1 - Mentaberre, Gregorio
A1 - Castillo-Contreras, Raquel
A1 - Fickel, Jörns
A1 - Lopez-Olvera, Jorge Ramón
T1 - Genetic population structure defines wild boar as an urban exploiter species in Barcelona, Spain
JF - The science of the total environment : an international journal for scientific research into the environment and its relationship with man
N2 - Urban wildlife ecology is gaining relevance as metropolitan areas grow throughout the world, reducing natural habitats and creating new ecological niches.
However, knowledge is still scarce about the colonisation processes of such urban niches, the establishment of new communities, populations and/or species, and the related changes in behaviour and life histories of urban wildlife.
Wild boar (Sus scrofa) has successfully colonised urban niches throughout Europe.
The aim of this study is to unveil the processes driving the establishment and maintenance of an urban wild boar population by analysing its genetic structure.
A set of 19 microsatellite loci was used to test whether urban wild boars in Barcelona, Spain, are an isolated population or if gene flow prevents genetic differentiation between rural and urban wild boars.
This knowledge will contribute to the understanding of the effects of synurbisation and the associated management measures on the genetic change of large mammals in urban ecosystems. Despite the unidirectional gene flow from rural to urban areas, the urban wild boars in Barcelona form an island population genotypically differentiated from the surrounding rural ones.
The comparison with previous genetic studies of urban wild boar populations suggests that forest patches act as suitable islands for wild boar genetic differentiation.
Previous results and the genetic structure of the urban wild boar population in Barcelona classify wild boar as an urban exploiter species.
These wild boar peri-urban island populations are responsible for conflict with humans and thus should be managed by reducing the attractiveness of urban areas.
The management of peri-urban wild boar populations should aim at reducing migration into urban areas and preventing phenotypic changes (either genetic or plastic) causing habituation of wild boars to humans and urban environments.
KW - gene flow
KW - island population
KW - population genetics
KW - sus scrofa
KW - synurbisation
KW - urban ecology
Y1 - 2022
U6 - https://doi.org/10.1016/j.scitotenv.2022.155126
SN - 0048-9697
SN - 1879-1026
VL - 833
PB - Elsevier Science
CY - Amsterdam [u.a.]
ER -
TY - JOUR
A1 - Hilt, Sabine
A1 - Grossart, Hans-Peter
A1 - McGinnis, Daniel F.
A1 - Keppler, Frank
T1 - Potential role of submerged macrophytes for oxic methane production in aquatic ecosystems
JF - Limnology and oceanography
N2 - Methane (CH4) from aquatic ecosystems contributes to about half of total global CH4 emissions to the atmosphere. Until recently, aquatic biogenic CH4 production was exclusively attributed to methanogenic archaea living under anoxic or suboxic conditions in sediments, bottom waters, and wetlands. However, evidence for oxic CH4 production (OMP) in freshwater, brackish, and marine habitats is increasing. Possible sources were found to be driven by various planktonic organisms supporting different OMP mechanisms. Surprisingly, submerged macrophytes have been fully ignored in studies on OMP, yet they are key components of littoral zones of ponds, lakes, and coastal systems. High CH4 concentrations in these zones have been attributed to organic substrate production promoting classic methanogenesis in the absence of oxygen. Here, we review existing studies and argue that, similar to terrestrial plants and phytoplankton, macroalgae and submerged macrophytes may directly or indirectly contribute to CH4 formation in oxic waters. We propose several potential direct and indirect mechanisms: (1) direct production of CH4; (2) production of CH4 precursors and facilitation of their bacterial breakdown or chemical conversion; (3) facilitation of classic methanogenesis; and (4) facilitation of CH4 ebullition. As submerged macrophytes occur in many freshwater and marine habitats, they are important in global carbon budgets and can strongly vary in their abundance due to seasonal and boom-bust dynamics. Knowledge on their contribution to OMP is therefore essential to gain a better understanding of spatial and temporal dynamics of CH4 emissions and thus to substantially reduce current uncertainties when estimating global CH4 emissions from aquatic ecosystems.
Y1 - 2022
U6 - https://doi.org/10.1002/lno.12095
SN - 0024-3590
SN - 1939-5590
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Hannigan, Sara
A1 - Nendel, Claas
A1 - Krull, Marcos
T1 - Effects of temperature on the movement and feeding behaviour of the large lupine beetle, Sitona gressorius
JF - Journal of pest science
N2 - Even though the effects of insect pests on global agricultural productivity are well recognised, little is known about movement and dispersal of many species, especially in the context of global warming. This work evaluates how temperature and light conditions affect different movement metrics and the feeding rate of the large lupine beetle, an agricultural pest responsible for widespread damage in leguminous crops. By using video recordings, the movement of 384 beetles was digitally analysed under six different temperatures and light conditions in the laboratory. Bayesian linear mixed-effect models were used to analyse the data. Furthermore, the effects of temperature on the daily diffusion coefficient of beetles were estimated by using hidden Markov models and random walk simulations. Results of this work show that temperature, light conditions, and beetles' weight were the main factors affecting the flight probability, displacement, time being active and the speed of beetles. Significant variations were also observed in all evaluated metrics. On average, beetles exposed to light conditions and higher temperatures had higher mean speed and flight probability. However, beetles tended to stay more active at higher temperatures and less active at intermediate temperatures, around 20 degrees C. Therefore, both the diffusion coefficient and displacement of beetles were lower at intermediate temperatures. These results show that the movement behaviour and feeding rates of beetles can present different relationships in the function of temperature. It also shows that using a single diffusion coefficient for insects in spatially explicit models may lead to over- or underestimation of pest spread.
KW - Agricultural pests
KW - Diffusion
KW - Hidden Markov models
KW - Movement ecology
Y1 - 2022
U6 - https://doi.org/10.1007/s10340-022-01510-7
SN - 1612-4758
SN - 1612-4766
SP - 389
EP - 402
PB - Springer
CY - Heidelberg
ER -
TY - JOUR
A1 - Li, Shuang
A1 - Abdulkadir, Nafi'u
A1 - Schattenberg, Florian
A1 - da Rocha, Ulisses Nunes
A1 - Grimm, Volker
A1 - Müller, Susann
A1 - Liu, Zishu
T1 - Stabilizing microbial communities by looped mass transfer
JF - Proceedings of the National Academy of Sciences of the United States of America : PNAS
N2 - Building and changing a microbiome at will and maintaining it over hundreds of generations has so far proven challenging. Despite best efforts, complex microbiomes appear to be susceptible to large stochastic fluctuations. Current capabilities to assemble and control stable complex microbiomes are limited. Here, we propose a looped mass transfer design that stabilizes microbiomes over long periods of time. Five local microbiomes were continuously grown in parallel for over 114 generations and connected by a loop to a regional pool. Mass transfer rates were altered and microbiome dynamics were monitored using quantitative high-throughput flow cytometry and taxonomic sequencing of whole communities and sorted subcommunities. Increased mass transfer rates reduced local and temporal variation in microbiome assembly, did not affect functions, and overcame stochasticity, with all microbiomes exhibiting high constancy and increasing resistance. Mass transfer synchronized the structures of the five local microbiomes and nestedness of certain cell types was eminent. Mass transfer increased cell number and thus decreased net growth rates mu'. Subsets of cells that did not show net growth mu'SCx were rescued by the regional pool R and thus remained part of the microbiome. The loop in mass transfer ensured the survival of cells that would otherwise go extinct, even if they did not grow in all local microbiomes or grew more slowly than the actual dilution rate D would allow. The rescue effect, known from metacommunity theory, was the main stabilizing mechanism leading to synchrony and survival of subcommunities, despite differences in cell physiological properties, including growth rates.
KW - microbial ecology
KW - metacommunity assembly
KW - stability
KW - microbial
KW - community cytometry
KW - single-cell analytics
Y1 - 2022
U6 - https://doi.org/10.1073/pnas.2117814119
SN - 1091-6490
VL - 119
IS - 17
PB - National Acad. of Sciences
CY - Washington
ER -
TY - JOUR
A1 - Pohanková, Eva
A1 - Hlavinka, Petr
A1 - Kersebaum, Kurt-Christian
A1 - Rodríguez, Alfredo
A1 - Balek, Jan
A1 - Bednařík, Martin
A1 - Dubrovský, Martin
A1 - Gobin, Anne
A1 - Hoogenboom, Gerrit
A1 - Moriondo, Marco
A1 - Nendel, Claas
A1 - Olesen, Jørgen E. E.
A1 - Rötter, Reimund Paul
A1 - Ruiz-Ramos, Margarita
A1 - Shelia, Vakhtang
A1 - Stella, Tommaso
A1 - Hoffmann, Munir Paul
A1 - Takáč, Jozef
A1 - Eitzinger, Josef
A1 - Dibari, Camilla
A1 - Ferrise, Roberto
A1 - Bláhová, Monika
A1 - Trnka, Miroslav
T1 - Expected effects of climate change on the production and water use of crop rotation management reproduced by crop model ensemble for Czech Republic sites
JF - European journal of agronomy
N2 - Crop rotation, fertilization and residue management affect the water balance and crop production and can lead to different sensitivities to climate change. To assess the impacts of climate change on crop rotations (CRs), the crop model ensemble (APSIM,AQUACROP, CROPSYST, DAISY, DSSAT, HERMES, MONICA) was used. The yields and water balance of two CRs with the same set of crops (winter wheat, silage maize, spring barley and winter rape) in a continuous transient run from 1961 to 2080 were simulated. CR1 was without cover crops and without manure application. Straw after the harvest was exported from the fields. CR2 included cover crops, manure application and crop residue retention left on field. Simulations were performed using two soil types (Chernozem, Cambisol) within three sites in the Czech Republic, which represent temperature and precipitation gradients for crops in Central Europe. For the description of future climatic conditions, seven climate scenarios were used. Six of them had increasing CO & nbsp;concentrations according RCP 8.5, one had no CO2 increase in the future. The output of an ensemble expected higher productivity by 0.82 t/ha/year and 2.04 t/ha/year for yields and aboveground biomass in the future (2051-2080). However, if the direct effect of a CO2 increase is not considered, the average yields for lowlands will be lower. Compared to CR1, CR2 showed higher average yields of 1.26 t/ha/year for current climatic conditions and 1.41 t/ha/year for future climatic conditions. For the majority of climate change scenarios, the crop model ensemble agrees on the projected yield increase in C3 crops in the future for CR2 but not for CR1. Higher agreement for future yield increases was found for Chernozem, while for Cambisol, lower yields under dry climate scenarios are expected. For silage maize, changes in simulated yields depend on locality. If the same hybrid will be used in the future, then yield reductions should be expected within lower altitudes. The results indicate the potential for higher biomass production from cover crops, but CR2 is associated with almost 120 mm higher evapotranspiration compared to that of CR1 over a 5-year cycle for lowland stations in the future, which in the case of the rainfed agriculture could affect the long-term soil water balance. This could affect groundwater replenishment, especially for locations with fine textured soils, although the findings of this study highlight the potential for the soil water-holding capacity to buffer against the adverse weather conditions.
KW - Yields
KW - Evapotranspiration
KW - Winter wheat
KW - Silage maize
KW - Spring barley
KW - Winter oilseed rape
Y1 - 2022
U6 - https://doi.org/10.1016/j.eja.2021.126446
SN - 1161-0301
SN - 1873-7331
VL - 134
PB - Elsevier
CY - Amsterdam
ER -
TY - JOUR
A1 - Wang, Enli
A1 - He, Di
A1 - Wang, Jing
A1 - Lilley, Julianne M.
A1 - Christy, Brendan
A1 - Hoffmann, Munir P.
A1 - O'Leary, Garry
A1 - Hatfield, Jerry L.
A1 - Ledda, Luigi
A1 - Deligios, Paola A.
A1 - Grant, Brian
A1 - Jing, Qi
A1 - Nendel, Claas
A1 - Kage, Henning
A1 - Qian, Budong
A1 - Rezaei, Ehsan Eyshi
A1 - Smith, Ward
A1 - Weymann, Wiebke
A1 - Ewert, Frank
T1 - How reliable are current crop models for simulating growth and seed yield of canola across global sites and under future climate change?
JF - Climatic change
N2 - To better understand how climate change might influence global canola production, scientists from six countries have completed the first inter-comparison of eight crop models for simulating growth and seed yield of canola, based on experimental data from six sites across five countries. A sensitivity analysis was conducted with a combination of five levels of atmospheric CO2 concentrations, seven temperature changes, five precipitation changes, together with five nitrogen application rates. Our results were in several aspects different from those of previous model inter-comparison studies for wheat, maize, rice, and potato crops. A partial model calibration only on phenology led to very poor simulation of aboveground biomass and seed yield of canola, even from the ensemble median or mean. A full calibration with additional data of leaf area index, biomass, and yield from one treatment at each site reduced simulation error of seed yield from 43.8 to 18.0%, but the uncertainty in simulation results remained large. Such calibration (with data from one treatment) was not able to constrain model parameters to reduce simulation uncertainty across the wide range of environments. Using a multi-model ensemble mean or median reduced the uncertainty of yield simulations, but the simulation error remained much larger than observation errors, indicating no guarantee that the ensemble mean/median would predict the correct responses. Using multi-model ensemble median, canola yield was projected to decline with rising temperature (2.5-5.7% per degrees C), but to increase with increasing CO2 concentration (4.6-8.3% per 100-ppm), rainfall (2.1-6.1% per 10% increase), and nitrogen rates (1.3-6.0% per 10% increase) depending on locations. Due to the large uncertainty, these results need to be treated with caution. We further discuss the need to collect new data to improve modelling of several key physiological processes of canola for increased confidence in future climate impact assessments.
KW - AgMIP
KW - Brassica napus L.
KW - Model calibration
KW - Model improvement;
KW - Multimodel ensemble
KW - Sensitivity analysis
Y1 - 2022
U6 - https://doi.org/10.1007/s10584-022-03375-2
SN - 0165-0009
SN - 1573-1480
VL - 172
IS - 1-2
PB - Springer Nature
CY - Dordrecht
ER -
TY - JOUR
A1 - McHuron, Elizabeth A.
A1 - Adamczak, Stephanie
A1 - Arnould, John P. Y.
A1 - Ashe, Erin
A1 - Booth, Cormac
A1 - Bowen, W. Don
A1 - Christiansen, Fredrik
A1 - Chudzinska, Magda
A1 - Costa, Daniel P.
A1 - Fahlman, Andreas
A1 - Farmer, Nicholas A.
A1 - Fortune, Sarah M. E.
A1 - Gallagher, Cara A.
A1 - Keen, Kelly A.
A1 - Madsen, Peter T.
A1 - McMahon, Clive R.
A1 - Nabe-Nielsen, Jacob
A1 - Noren, Dawn P.
A1 - Noren, Shawn R.
A1 - Pirotta, Enrico
A1 - Rosen, David A. S.
A1 - Speakman, Cassie N.
A1 - Villegas-Amtmann, Stella
A1 - Williams, Rob
T1 - Key questions in marine mammal bioenergetics
JF - Conservation physiology
N2 - Bioenergetic approaches are increasingly used to understand how marine mammal populations could be affected by a changing and disturbed aquatic environment. There remain considerable gaps in our knowledge of marine mammal bioenergetics, which hinder the application of bioenergetic studies to inform policy decisions. We conducted a priority-setting exercise to identify high-priority unanswered questions in marine mammal bioenergetics, with an emphasis on questions relevant to conservation and management. Electronic communication and a virtual workshop were used to solicit and collate potential research questions from the marine mammal bioenergetic community. From a final list of 39 questions, 11 were identified as 'key'questions because they received votes from at least 50% of survey participants. Key questions included those related to energy intake (prey landscapes, exposure to human activities) and expenditure (field metabolic rate, exposure to human activities, lactation, time-activity budgets), energy allocation priorities, metrics of body condition and relationships with survival and reproductive success and extrapolation of data from one species to another. Existing tools to address key questions include labelled water, animal-borne sensors, mark-resight data from long-term research programs, environmental DNA and unmanned vehicles. Further validation of existing approaches and development of new methodologies are needed to comprehensively address some key questions, particularly for cetaceans. The identification of these key questions can provide a guiding framework to set research priorities, which ultimately may yield more accurate information to inform policies and better conserve marine mammal populations.
Y1 - 2022
U6 - https://doi.org/10.1093/conphys/coac055
SN - 2051-1434
VL - 10
IS - 1
PB - Oxford Univ. Press
CY - Oxford
ER -