TY - JOUR
A1 - Ralevski, Alexandra
A1 - Apelt, Federico
A1 - Olas, Justyna Jadwiga
A1 - Müller-Röber, Bernd
A1 - Rugarli, Elena I.
A1 - Kragler, Friedrich
A1 - Horvath, Tamas L.
T1 - Plant mitochondrial FMT and its mammalian homolog CLUH controls development and behavior in Arabidopsis and locomotion in mice
JF - Cellular and molecular life sciences
N2 - Mitochondria in animals are associated with development, as well as physiological and pathological behaviors. Several conserved mitochondrial genes exist between plants and higher eukaryotes. Yet, the similarities in mitochondrial function between plant and animal species is poorly understood. Here, we show that FMT (FRIENDLY MITOCHONDRIA) from Arabidopsis thaliana, a highly conserved homolog of the mammalian CLUH (CLUSTERED MITOCHONDRIA) gene family encoding mitochondrial proteins associated with developmental alterations and adult physiological and pathological behaviors, affects whole plant morphology and development under both stressed and normal growth conditions. FMT was found to regulate mitochondrial morphology and dynamics, germination, and flowering time. It also affects leaf expansion growth, salt stress responses and hyponastic behavior, including changes in speed of hyponastic movements. Strikingly, Cluh(+/-) heterozygous knockout mice also displayed altered locomotive movements, traveling for shorter distances and had slower average and maximum speeds in the open field test. These observations indicate that homologous mitochondrial genes may play similar roles and affect homologous functions in both plants and animals.
KW - Arabidopsis thaliana
KW - Mitochondria
KW - FMT
KW - Hyponasty
KW - Mice
KW - CLUH;
KW - Locomotion
Y1 - 2022
U6 - https://doi.org/10.1007/s00018-022-04382-3
SN - 1420-682X
SN - 1420-9071
VL - 79
IS - 6
PB - Springer International Publishing AG
CY - Cham (ZG)
ER -
TY - JOUR
A1 - Bapolisi, Alain Murhimalika
A1 - Kielb, Patrycja
A1 - Bekir, Marek
A1 - Lehnen, Anne-Catherine
A1 - Radon, Christin
A1 - Laroque, Sophie
A1 - Wendler, Petra
A1 - Müller-Werkmeister, Henrike
A1 - Hartlieb, Matthias
T1 - Antimicrobial polymers of linear and bottlebrush architecture
BT - Probing the membrane interaction and physicochemical properties
JF - Macromolecular rapid communications : publishing the newsletters of the European Polymer Federation
N2 - Polymeric antimicrobial peptide mimics are a promising alternative for the future management of the daunting problems associated with antimicrobial resistance. However, the development of successful antimicrobial polymers (APs) requires careful control of factors such as amphiphilic balance, molecular weight, dispersity, sequence, and architecture. While most of the earlier developed APs focus on random linear copolymers, the development of APs with advanced architectures proves to be more potent. It is recently developed multivalent bottlebrush APs with improved antibacterial and hemocompatibility profiles, outperforming their linear counterparts. Understanding the rationale behind the outstanding biological activity of these newly developed antimicrobials is vital to further improving their performance. This work investigates the physicochemical properties governing the differences in activity between linear and bottlebrush architectures using various spectroscopic and microscopic techniques. Linear copolymers are more solvated, thermo-responsive, and possess facial amphiphilicity resulting in random aggregations when interacting with liposomes mimicking Escheria coli membranes. The bottlebrush copolymers adopt a more stable secondary conformation in aqueous solution in comparison to linear copolymers, conferring rapid and more specific binding mechanism to membranes. The advantageous physicochemical properties of the bottlebrush topology seem to be a determinant factor in the activity of these promising APs.
KW - antimicrobial polymers
KW - bottlebrush copolymers
KW - liposomes
KW - membrane
KW - interactions
KW - quartz crystal microbalance
Y1 - 2022
U6 - https://doi.org/10.1002/marc.202200288
SN - 1521-3927
SN - 1022-1336
VL - 43
IS - 19
PB - Wiley-VCH
CY - Weinheim
ER -
TY - JOUR
A1 - Mendes Ferreira, Clara
A1 - Dammhahn, Melanie
A1 - Eccard, Jana
T1 - Forager-mediated cascading effects on food resource species diversity
JF - Ecology and Evolution
N2 - Perceived predation risk varies in space and time. Foraging in this landscape of fear alters forager-resource interactions via cascading nonconsumptive effects. Estimating these indirect effects is difficult in natural systems. Here, we applied a novel measure to quantify the diversity at giving-up density that allows to test how spatial variation in perceived predation risk modifies the diversity of multispecies resources at local and regional spatial levels. Furthermore, we evaluated whether the nonconsumptive effects on resource species diversity can be explained by the preferences of foragers for specific functional traits and by the forager species richness. We exposed rodents of a natural community to artificial food patches, each containing an initial multispecies resource community of eight species (10 items each) mixed in sand. We sampled 35 landscapes, each containing seven patches in a spatial array, to disentangle effects at local (patch) and landscape levels. We used vegetation height as a proxy for perceived predation risk. After a period of three nights, we counted how many and which resource species were left in each patch to measure giving-up density and resource diversity at the local level (alpha diversity) and the regional level (gamma diversity and beta diversity). Furthermore, we used wildlife cameras to identify foragers and assess their species richness. With increasing vegetation height, i.e., decreasing perceived predation risk, giving-up density, and local alpha and regional gamma diversity decreased, and patches became less similar within a landscape (beta diversity increased). Foragers consumed more of the bigger and most caloric resources. The higher the forager species richness, the lower the giving-up density, and alpha and gamma diversity. Overall, spatial variation of perceived predation risk of foragers had measurable cascading effects on local and regional resource species biodiversity, independent of the forager species. Thus, nonconsumptive predation effects modify forager-resource interactions and might act as an equalizing mechanism for species coexistence.
KW - coexistence
KW - functional traits
KW - giving-up density
KW - landscape of fear
KW - perceived predation risk
Y1 - 2022
U6 - https://doi.org/10.1002/ece3.9523
SN - 2045-7758
VL - 12
IS - 11
PB - John Wiley & Sons
ER -
TY - JOUR
A1 - Berg, Gabriele
A1 - Cernava, Tomislav
T1 - The plant microbiota signature of the Anthropocene as a challenge for microbiome research
JF - Microbiome
N2 - Background:
One promise of the recently presented microbiome definition suggested that, in combination with unifying concepts and standards, microbiome research could be important for solving new challenges associated with anthropogenic-driven changes in various microbiota. With this commentary we want to further elaborate this suggestion, because we noticed specific signatures in microbiota affected by the Anthropocene.
Results:
Here, we discuss this based on a review of available literature and our own research targeting exemplarily the plant microbiome. It is not only crucial for plants themselves but also linked to planetary health. We suggest that different human activities are commonly linked to a shift of diversity and evenness of the plant microbiota, which is also characterized by a decrease of host specificity, and an increase of r-strategic microbes, pathogens, and hypermutators. The resistome, anchored in the microbiome, follows this shift by an increase of specific antimicrobial resistance (AMR) mechanisms as well as an increase of plasmid-associated resistance genes. This typical microbiome signature of the Anthropocene is often associated with dysbiosis and loss of resilience, and leads to frequent pathogen outbreaks. Although several of these observations are already confirmed by meta-studies, this issue requires more attention in upcoming microbiome studies.
Conclusions:
Our commentary aims to inspire holistic studies for the development of solutions to restore and save microbial diversity for ecosystem functioning as well as the closely connected planetary health.
Y1 - 2022
U6 - https://doi.org/10.1186/s40168-021-01224-5
SN - 2049-2618
VL - 10
IS - 1
PB - BMC
CY - London
ER -
TY - JOUR
A1 - Eccard, Jana
A1 - Mendes Ferreira, Clara
A1 - Peredo Arce, Andres
A1 - Dammhahn, Melanie
T1 - Top-down effects of foraging decisions on local, landscape and regional biodiversity of resources (DivGUD)
JF - Ecology letters
N2 - Foraging by consumers acts as a biotic filtering mechanism for biodiversity at the trophic level of resources. Variation in foraging behaviour has cascading effects on abundance, diversity, and functional trait composition of the community of resource species. Here we propose diversity at giving-up density (DivGUD), i.e. when foragers quit exploiting a patch, as a novel concept and simple measure quantifying cascading effects at multiple spatial scales. In experimental landscapes with an assemblage of plant seeds, patch residency of wild rodents decreased local alpha-DivGUD (via elevated mortality of species with large seeds) and regional gamma-DivGUD, while dissimilarity among patches in a landscape (beta-DivGUD) increased. By linking theories of adaptive foraging behaviour with community ecology, DivGUD allows to investigate cascading indirect predation effects, e.g. the ecology-of-fear framework, feedbacks between functional trait composition of resource species and consumer communities, and effects of inter-individual differences among foragers on the biodiversity of resource communities.
KW - biodiversity
KW - cascading effects
KW - foraging behaviour
KW - functional traits
KW - giving-up density
KW - landscape of fear
KW - optimal foraging
KW - patch use
Y1 - 2022
U6 - https://doi.org/10.1111/ele.13901
SN - 1461-0248
VL - 25
IS - 1
SP - 3
EP - 16
PB - Wiley-Blackwell
CY - Oxford [u.a.]
ER -
TY - JOUR
A1 - Azcorra, Hugo
A1 - Dickinson, Federico
A1 - Mendez-Dominguez, Nina
A1 - Mumm, Rebekka
A1 - Valentín, Graciela
T1 - Development of birthweight and length for gestational age and sex references in Yucatan, Mexico
JF - American journal of human biology : the official journal of the Human Biology Council
N2 - Objective To develop sex- and gestational age specific reference percentiles and curves for birth weight and length for Yucatec neonates using data from birth registers of infants born during 2015-2019. Material and methods Observational, descriptive, epidemiologic study in a 5-year period including every registered birth in the state of Yucatan, Mexico using birth registries. A total of 158 432 live, physically healthy singletons (76 442 females and 81 990 males) between 25 and 42 weeks of gestation were included in the analysis. We used the LMS method to construct smoothed reference centiles (3rd, 10th, 25th, 50th, 75th, 95th, and 97th) and curves for males and females separately. Results Mean maternal age was 26 (SD = 6.22) years. Fifty-two percent of births occurred by vaginal delivery, 37% were firstborn and similar proportions were second (33%) and third or more (30%) born. 5.5% of newborns included in the references corresponds to neonates born before 37 weeks of gestation (5.9% boys and 5.1% girls). In both sexes, the percentage of infants with a birthweight less than 2500 g was 6.7%. The birthweight at the 50th percentile for males and females at 40 weeks of gestation in this cohort was 3256 and 3167 g, respectively, and the corresponding values for birth length were 50.23 and 49.84 cm (mean differences between sexes: 89 g and 0.40 cm, respectively). Conclusion The reference percentile and curves developed in this study are useful for research purposes and can help health practitioners to assess the biological status of infants born in Yucatan.
Y1 - 2022
U6 - https://doi.org/10.1002/ajhb.23732
SN - 1042-0533
SN - 1520-6300
VL - 34
IS - 6
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Eccard, Jana
T1 - Can rolling composite wildflower blocks increase biodiversity in agricultural landscapes better than wildflowers strips?
JF - Journal of applied ecology : an official journal of the British Ecological Society
N2 - Biodiversity and abundance of wildlife has dramatically declined in agricultural landscapes. Sown, short-lived wildflower (WF) strips along the margins of crop fields are a widespread and often subsidised in agri-environmental schemes, intended to enhance biodiversity, provide refuges for wild plant and arthropod populations and to provide ecosystem services to crops. Meanwhile, WF elements are also criticised, since their functionality decreases with plant succession, the removal of aged WF strip poses an ecological trap for the attracted arthropod populations and only common and mobile species benefit. Further, insects in WF strips are impacted by pesticides from agricultural fields due to shared boundaries with crop fields and by edge effects. The performance of the measure could be improved by combining several WF strips of different successional stages, each harbouring a unique community of plants and arthropods, into persistent, composite WF block, where successional stages exist in parallel. Monitoring data on many taxa in the literature shows, that a third of species are temporarily present in an ageing WF stip, thus offering composite WF blocks should increase cumulative species richness by 28%-39% compared to annual richness in WF strips. Persistence of composite WF blocks would offer reliable refuge for animal and plant populations, also supporting their predators and herbivores. Further, WF blocks have less boundaries to crops compared to WF strips of the same area, and are less impacted by edge effects and pesticides. Policy implications. Here I suggest a change of conservation practice changing from successional WF strips to composite WF blocks. By regular removal and replacement of aged WF strips either within the block (rotational) or at its margins (rolling), the habitat heterogeneity in composite WF block could be perpetuated. Rolling composite WF blocks change locations over years, and the original location can be reconverted to arable land while a nearby WF block is still available to wildlife. A change in agricultural schemes would be necessary, since in some European countries clustered WF strips are explicitly not subsidised.
KW - AES
KW - agriculture
KW - biodiversity
KW - CAP
KW - conservation scheme
KW - field margins
KW - insects
Y1 - 2022
U6 - https://doi.org/10.1111/1365-2664.14147
SN - 0021-8901
SN - 1365-2664
VL - 59
IS - 5
SP - 1172
EP - 1177
PB - Wiley-Blackwell
CY - Oxford
ER -
TY - JOUR
A1 - Kiemel, Katrin
A1 - De Cahsan, Binia
A1 - Paraskevopoulou, Sofia
A1 - Weithoff, Guntram
A1 - Tiedemann, Ralph
T1 - Mitochondrial genomes of the freshwater monogonont rotifer Brachionus fernandoi and of two additional B. calyciflorus sensu stricto lineages from Germany and the USA (Rotifera, Brachionidae)
JF - Mitochondrial DNA. Part B-Resources
N2 - The Brachionus calyciflorus species complex was recently subdivided into four species, but genetic resources to resolve phylogenetic relationships within this complex are still lacking. We provide two complete mitochondrial (mt) genomes from B. calyciflorus sensu stricto (Germany, USA) and the mt coding sequences (cds) from a German B. fernandoi. Phylogenetic analysis placed our B. calyciflorus sensu stricto strains close to the published genomes of B. calyciflorus, forming the putative sister species to B. fernandoi. Global representatives of B. calyciflorus sensu stricto (i.e. Europe, USA, and China) are genetically closer related to each other than to B. fernandoi (average pairwise nucleotide diversity 0.079 intraspecific vs. 0.254 interspecific).
KW - Mitogenome
KW - cryptic species
KW - Brachionus calyciflorus s
KW - Brachionus
KW - fernandoi
KW - monogonont rotifer
Y1 - 2022
U6 - https://doi.org/10.1080/23802359.2022.2060765
SN - 2380-2359
VL - 7
IS - 4
SP - 646
EP - 648
PB - Routledge, Taylor & Francis Group
CY - Abingdon
ER -
TY - JOUR
A1 - Prüfer, Mareike
A1 - Wenger, Christian
A1 - Bier, Frank Fabian
A1 - Laux, Eva-Maria
A1 - Hölzel, Ralph
T1 - Activity of AC electrokinetically immobilized horseradish peroxidase
JF - Electrophoresis : microfluidics, nanoanalysis & proteomics
N2 - Dielectrophoresis (DEP) is an AC electrokinetic effect mainly used to manipulate cells. Smaller particles, like virions, antibodies, enzymes, and even dye molecules can be immobilized by DEP as well. In principle, it was shown that enzymes are active after immobilization by DEP, but no quantification of the retained activity was reported so far. In this study, the activity of the enzyme horseradish peroxidase (HRP) is quantified after immobilization by DEP. For this, HRP is immobilized on regular arrays of titanium nitride ring electrodes of 500 nm diameter and 20 nm widths. The activity of HRP on the electrode chip is measured with a limit of detection of 60 fg HRP by observing the enzymatic turnover of Amplex Red and H2O2 to fluorescent resorufin by fluorescence microscopy. The initial activity of the permanently immobilized HRP equals up to 45% of the activity that can be expected for an ideal monolayer of HRP molecules on all electrodes of the array. Localization of the immobilizate on the electrodes is accomplished by staining with the fluorescent product of the enzyme reaction. The high residual activity of enzymes after AC field induced immobilization shows the method's suitability for biosensing and research applications.
KW - AC electrokinetics
KW - dielectrophoresis
KW - enzyme activity
KW - immobilization;
KW - nanoelectrodes
Y1 - 2022
U6 - https://doi.org/10.1002/elps.202200073
SN - 0173-0835
SN - 1522-2683
SP - 1920
EP - 1933
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Delker, Carolin
A1 - Quint, Marcel
A1 - Wigge, Philip Anthony
T1 - Recent advances in understanding thermomorphogenesis signaling
JF - Current opinion in plant biology
N2 - Plants show remarkable phenotypic plasticity and are able to adjust their morphology and development to diverse environmental stimuli. Morphological acclimation responses to elevated ambient temperatures are collectively termed thermomorphogenesis. In Arabidopsis thaliana, morphological changes are coordinated to a large extent by the transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), which in turn is regulated by several thermosensing mechanisms and modulators. Here, we review recent advances in the identification of factors that regulate thermomorphogenesis of Arabidopsis seedlings by affecting PIF4 expression and PIF4 activity. We summarize newly identified thermosensing mechanisms and highlight work on the emerging topic of organ- and tissue-specificity in the regulation of thermomorphogenesis.
Y1 - 2022
U6 - https://doi.org/10.1016/j.pbi.2022.102231
SN - 1369-5266
SN - 1879-0356
VL - 68
PB - Elsevier
CY - London
ER -
TY - JOUR
A1 - Kernecker, Maria
A1 - Fienitz, Meike
A1 - Nendel, Claas
A1 - Paetzig, Marlene
A1 - Walzl, Karin Pirhofer
A1 - Raatz, Larissa
A1 - Schmidt, Martin
A1 - Wulf, Monika
A1 - Zscheischler, Jana
T1 - Transition zones across agricultural field boundaries for integrated landscape research and management of biodiversity and yields
JF - Ecological solutions and evidence
N2 - Biodiversity conservation and agricultural production have been largely framed as separate goals for landscapes in the discourse on land use. Although there is an increasing tendency to move away from this dichotomy in theory, the tendency is perpetuated by the spatially explicit approaches used in research and management practice. Transition zones (TZ) have previously been defined as areas where two adjacent fields or patches interact, and so they occur abundantly throughout agricultural landscapes. Biodiversity patterns in TZ have been extensively studied, but their relationship to yield patterns and social-ecological dimensions has been largely neglected. Focusing on European, temperate agricultural landscapes, we outline three areas of research and management that together demonstrate how TZ might be used to facilitate an integrated landscape approach: (i) plant and animal species' use and response to boundaries and the resulting effects on yield, for a deeper understanding of how landscape structure shapes quantity and quality of TZ; (ii) local knowledge on field or patch-level management and its interactions with biodiversity and yield in TZ, and (iii) conflict prevention and collaborative management across land-use boundaries.
KW - ecotones
KW - field boundaries
KW - functional traits
KW - landscape complexity;
KW - land-use conflicts
KW - local knowledge
KW - spillovers
Y1 - 2022
U6 - https://doi.org/10.1002/2688-8319.12122
SN - 2688-8319
VL - 3
IS - 1
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Voigt, Christian C.
A1 - Kaiser, Klara
A1 - Look, Samantha
A1 - Scharnweber, Inga Kristin
A1 - Scholz, Carolin
T1 - Wind turbines without curtailment produce large numbers of bat fatalities throughout their lifetime
BT - a call against ignorance and neglect
JF - Global ecology and conservation
N2 - Bats are protected by national and international legislation in European countries, yet many species, particularly migratory aerial insectivores, collide with wind turbines which counteracts conservation efforts. Within the European Union it is legally required to curtail the operation of wind turbines at periods of high bat activity, yet this is not practiced at old wind turbines. Based on data from the national carcass repository in Germany and from our own carcass searches at a wind park with three turbines west of Berlin, we evaluated the magnitude of bat casualties at old, potentially poor-sited wind turbines operating without curtailment. We report 88 documented bat carcasses collected by various searchers over the 20-year operation period of this wind park from 2001 to 2021. Common noctule bats (Nyctalus noctula) and common pipistrelles (Pipistrellus pipistrellus) were most often found dead at these turbines. Our search campaign in August and September 2021 yielded a total of 18 carcasses. We estimated that at least 209 bats were likely killed during our field survey, yielding more than 70 casualties/wind turbine or 39 casualties/ MW in two months. Since our campaign covered only part of the migration season, we consider this value as an underestimate. The 20-year period of the wind park emphasises the substantial impact old turbines may have on bat individuals and populations when operating without curtailments. We call for reconsidering the operation procedures of old wind turbines to stop the continuous loss of bats in Germany and other countries where turbine curtailments are even less practiced than in Germany.
KW - green-green dilemma
KW - wind energy bat conflict
KW - wildlife casualties
Y1 - 2022
U6 - https://doi.org/10.1016/j.gecco.2022.e02149
SN - 2351-9894
VL - 37
PB - Elsevier
CY - Amsterdam
ER -
TY - JOUR
A1 - Wendland, Mirko
A1 - Glowinski, Ingrid
T1 - Professionsorientierung von Praxisphasen – Ergebnisse einer Fragenbogenstudie
JF - Professionalisierung in Praxisphasen : Ergebnisse der Lehrerbildungsforschung an der Universität Potsdam (Potsdamer Beiträge zur Lehrerbildung und Bildungsforschung ; 2)
N2 - Die Professionsorientierung der Lehramtsstudiengänge ist ein zentrales Anliegen der universitären Potsdamer Lehrkräftebildung. Seit 1999 finden Evaluationen zur Professionsorientierung statt, die Diskrepanzen zwischen der gewünschten und der erfahrenen Professionsorientierung durch die Studierenden aufzeigen. Im Wintersemester 2013/14 wurden neue Studiengänge an der Universität Potsdam eingeführt. Inwieweit damit auch eine stärkere Professionsorientierung und ein stärkerer Berufsbezug erfolgt ist, ist bislang ungeklärt. In einer Onlinebefragung im Dezember 2018 wurden Studierende der Lehramtsstudiengänge der Universität Potsdam gebeten, die inhaltliche Gestaltung der Lehramtsstudiengänge sowie die Professionsorientierung der Praxisphasen, die Betreuung und Beratung im Rahmen der Praktika, den Nutzen der Praktika für Studium und Beruf und ihre Lehrer:innenkompetenz einzuschätzen. Der Beitrag stellt erste empirische Analysen dar und diskutiert Anregungen zur Weiterentwicklung der Studiengänge mit Bezug auf die Praxisstudien.
N2 - The professional orientation of the teacher training courses is a central concern of Potsdam University’s teacher training programme. Evaluations on professional orientation have been carried out since 1999. These studies repeatedly revealed discrepancies between the desired and the experienced professional orientation of the students. In winter semester 2013/14 new courses of study were introduced. It has not yet been clarified, to what extent this has led to a stronger professional orientation and a stronger occupational orientation. In an online survey in December 2018, students of the teacher education courses (at the University of Potsdam) were asked to assess the professional orientation of the courses and the practical phases, the support and advice within the framework of the internships, the benefits of the internships for study and career and their teacher competence. The article presents first empirical analyses and discusses suggestions for the further development of the degree programmes with reference to the practical studies.
Y1 - 2022
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-570876
SN - 978-3-86956-508-8
SN - 2626-3556
SN - 2626-4722
IS - 2
SP - 287
EP - 321
PB - Universitätsverlag Potsdam
CY - Potsdam
ER -
TY - JOUR
A1 - Novine, Masiar
A1 - Mattsson, Cecilie Cordua
A1 - Groth, Detlef
T1 - Network reconstruction based on synthetic data generated by a Monte Carlo approach
JF - Human biology and public health
N2 - Background: Network models are useful tools for researchers to simplify and understand investigated systems. Yet, the assessment of methods for network construction is often uncertain. Random resampling simulations can aid to assess methods, provided synthetic data exists for reliable network construction.
Objectives: We implemented a new Monte Carlo algorithm to create simulated data for network reconstruction, tested the influence of adjusted parameters and used simulations to select a method for network model estimation based on real-world data. We hypothesized, that reconstructs based on Monte Carlo data are scored at least as good compared to a benchmark.
Methods: Simulated data was generated in R using the Monte Carlo algorithm of the mcgraph package. Benchmark data was created by the huge package. Networks were reconstructed using six estimator functions and scored by four classification metrics. For compatibility tests of mean score differences, Welch’s t-test was used. Network model estimation based on real-world data was done by stepwise selection.
Samples: Simulated data was generated based on 640 input graphs of various types and sizes. The real-world dataset consisted of 67 medieval skeletons of females and males from the region of Refshale (Lolland) and Nordby (Jutland) in Denmark.
Results: Results after t-tests and determining confidence intervals (CI95%) show, that evaluation scores for network reconstructs based on the mcgraph package were at least as good compared to the benchmark huge. The results even indicate slightly better scores on average for the mcgraph package.
Conclusion: The results confirmed our objective and suggested that Monte Carlo data can keep up with the benchmark in the applied test framework. The algorithm offers the feature to use (weighted) un- and directed graphs and might be useful for assessing methods for network construction.
KW - Monte Carlo method
KW - network reconstruction
KW - mcgraph
KW - random sampling
KW - linear enamel hypoplasia
Y1 - 2022
U6 - https://doi.org/10.52905/hbph2021.3.26
SN - 2748-9957
VL - 2021
IS - 3, Summer School Supplement
PB - Universitätsverlag Potsdam
CY - Potsdam
ER -
TY - JOUR
A1 - Wilke, Liza
A1 - Boeker, Sonja
A1 - Mumm, Rebecca
A1 - Groth, Detlef
T1 - The Social status influences human growth
BT - A summary and analysis of historical data from German school girls in 1914 with comparison to modern references
JF - Human biology and public health
N2 - Background: In the animal kingdom body size is often linked to dominance and subsequently the standing in social hierarchy. Similarly, human growth has been associated and linked to socioeconomic factors, including one’s social status. This has already been proposed in the early 1900s where data on young German school girls from different social strata have been compared.
Objectives: This paper aims to summarize and analyze these results and make them accessible for non-German speakers. The full English translation of the historic work of Dikanski (Dikanski, 1914) is available as a supplement. Further, this work aims to compare the historical data with modern references, to test three hypotheses: (1) higher social class is positively associated with body height and weight, (2) affluent people from the used historical data match modern references in weight and height and (3) weight distributions are skewed in both modern and historical populations.
Methods: Comparison of historical data from 1914 with WHO and 1980s German data. The data sets, for both body weight and height for 6.0- and 7.0-year-old girls, were fitted onto centile curves and quantile correlation coefficients were calculated.
Results: In historical data social status is positively associated with body height and weight while both are also normally distributed, which marks a significant difference to modern references.
Conclusion: Social status is positively associated with height, signaling social dominance, making children of affluent classes taller. Children from the historical data do not reach the average height of modern children, even under the best environmental conditions. The children of the upper social class were not skewed in weight distribution, although they had the means to become as obese as modern children.
KW - Just so stories
KW - Summer Schools
KW - questioning solutions
KW - repetition
Y1 - 2022
U6 - https://doi.org/10.52905/hbph2021.3.22
SN - 2748-9957
VL - 2021
IS - 3, Summer School Supplement
PB - Universitätsverlag Potsdam
CY - Potsdam
ER -
TY - JOUR
A1 - Rösler, Antonia
A1 - Gasparatos, Nikolaos
A1 - Hermanussen, Michael
A1 - Scheffler, Christiane
T1 - Practicability and user-friendliness of height measurements by proof of concept APP using Augmented Reality, in 22 healthy children
JF - Human biology and public health
N2 - Background: Child growth is a dynamic process. When measured at short intervals, children’s growth shows characteristic patterns that can be of great importance for clinical purposes.
Objective: To study whether measuring height on a daily basis using an APP is practicable and user-friendly.
Methods: Recruitment took place via Snowball Sampling. Thirteen out of 14 contacted families signed up for a study period of 12 weeks with altogether 22 healthy children aged 3 to 13 years (response rate 93%). The study started with a visit to the family home for the setup of the measurement site, conventional height measuring and initial training of the new measurement process. Follow-up appointments were made at four, eight and 12 weeks. The children’s height was measured at daily intervals at their family homes over a period of three months.
Results: The parents altogether recorded 1704 height measurements and meticulously documented practicability and problems when using the device.
A 93% response rate in recruitment was achieved by maintaining a high motivation within the families. Contact with the principal investigator was permanently available, including open communication, personal training and attendance during the appointments at the family homes.
Conclusion: Measuring height by photographic display is interesting for children and parents and can be used for height measurements at home. A positive response rate of 13 out of 14 families with altogether 22 children highlights feasible recruitment and the high convenience and user-friendliness of daily APP-supported height measurements. Daily APP measurements appear to be a promising new tool for longitudinal growth studies.
KW - body height
KW - guideline
KW - augmented reality
KW - daily home-made measurements
KW - iPhone
KW - APP
Y1 - 2022
U6 - https://doi.org/10.52905/hbph2022.2.48
SN - 2748-9957
VL - 2022
IS - 2
PB - Universitätsverlag Potsdam
CY - Potsdam
ER -
TY - JOUR
A1 - Andersson, Matilda L.
A1 - Scharnweber, Inga Kristin
A1 - Eklöv, Peter
T1 - The interaction between metabolic rate, habitat choice, and resource use in a polymorphic freshwater species
JF - Ecology and evolution
N2 - Resource polymorphism is common across taxa and can result in alternate ecotypes with specific morphologies, feeding modes, and behaviors that increase performance in a specific habitat. This can result in high intraspecific variation in the expression of specific traits and the extent to which these traits are correlated within a single population. Although metabolic rate influences resource acquisition and the overall pace of life of individuals it is not clear how metabolic rate interacts with the larger suite of traits to ultimately determine individual fitness. We examined the relationship between metabolic rates and the major differences (habitat use, morphology, and resource use) between littoral and pelagic ecotypes of European perch (Perca fluviatilis) from a single lake in Central Sweden. Standard metabolic rate (SMR) was significantly higher in pelagic perch but did not correlate with resource use or morphology. Maximum metabolic rate (MMR) was not correlated with any of our explanatory variables or with SMR. Aerobic scope (AS) showed the same pattern as SMR, differing across habitats, but contrary to expectations, was lower in pelagic perch. This study helps to establish a framework for future experiments further exploring the drivers of intraspecific differences in metabolism. In addition, since metabolic rates scale with temperature and determine predator energy requirements, our observed differences in SMR across habitats will help determine ecotype-specific vulnerabilities to climate change and differences in top-down predation pressure across habitats.
KW - intraspecific variation
KW - metabolic rate
KW - morphometrics
KW - Perca
KW - fluviatilis
KW - plasticity
KW - resource use
KW - respirometry
KW - stable isotopes
Y1 - 2022
U6 - https://doi.org/10.1002/ece3.9129
SN - 2045-7758
VL - 12
IS - 8
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Ghafarian, Fatemeh
A1 - Wieland, Ralf
A1 - Lüttschwager, Dietmar
A1 - Nendel, Claas
T1 - Application of extreme gradient boosting and Shapley Additive explanations to predict temperature regimes inside forests from standard open-field meteorological data
JF - Environmental modelling & software with environment data news
N2 - Forest microclimate can buffer biotic responses to summer heat waves, which are expected to become more extreme under climate warming. Prediction of forest microclimate is limited because meteorological observation standards seldom include situations inside forests.
We use eXtreme Gradient Boosting - a Machine Learning technique - to predict the microclimate of forest sites in Brandenburg, Germany, using seasonal data comprising weather features.
The analysis was amended by applying a SHapley Additive explanation to show the interaction effect of variables and individualised feature attributions.
We evaluate model performance in comparison to artificial neural networks, random forest, support vector machine, and multi-linear regression.
After implementing a feature selection, an ensemble approach was applied to combine individual models for each forest and improve robustness over a given single prediction model.
The resulting model can be applied to translate climate change scenarios into temperatures inside forests to assess temperature-related ecosystem services provided by forests.
KW - cooling effect
KW - machine learning
KW - ensemble method
KW - ecosystem services
Y1 - 2022
U6 - https://doi.org/10.1016/j.envsoft.2022.105466
SN - 1364-8152
SN - 1873-6726
VL - 156
PB - Elsevier
CY - Oxford
ER -
TY - JOUR
A1 - Lucena-Perez, María
A1 - Bazzicalupo, Enrico
A1 - Paijmans, Johanna
A1 - Kleinman-Ruiz, Daniel
A1 - Dalén, Love
A1 - Hofreiter, Michael
A1 - Delibes, Miguel
A1 - Clavero, Miguel
A1 - Godoy, José A.
T1 - Ancient genome provides insights into the history of Eurasian lynx in Iberia and Western Europe
JF - Quaternary science reviews : the international multidisciplinary research and review journal
N2 - The Eurasian lynx (Lynx lynx) is one of the most widely distributed felids in the world. However, most of its populations started to decline a few millennia ago. Historical declines have been especially severe in Europe, and particularly in Western Europe, from where the species disappeared in the last few centuries. Here, we analyze the genome of an Eurasian lynx inhabiting the Iberian Peninsula 2500 ya, to gain insights into the phylogeographic position and genetic status of this extinct population. Also, we contextualize previous ancient data in the light of new phylogeographic studies of the species. Our results suggest that the Iberian population is part of an extinct European lineage closely related to the current Carpathian-Baltic lineages. Also, this sample holds the lowest diversity reported for the species so far, and similar to that of the highly endangered Iberian lynx. A combination of historical factors, such as a founder effect while colonizing the peninsula, together with intensified human impacts during the Holocene in the Cantabrian strip, could have led to a genetic impoverishment of the population and precipitated its extinction. Mitogenomic lineages distribution in space and time support the long-term coexistence of several lineages of Eurasian lynx in Western Europe with fluctuating ranges. While mitochondrial sequences related to the lineages currently found in Balkans and Caucasus were predominant during the Pleistocene, those more closely related to the lineage currently distributed in Central Europe prevailed during the Holocene. The use of ancient genomics has proven to be a useful tool to understand the biogeographic pattern of the Eurasian lynx in the past.
Y1 - 2022
U6 - https://doi.org/10.1016/j.quascirev.2022.107518
SN - 0277-3791
SN - 1873-457X
VL - 285
PB - Elsevier
CY - Oxford
ER -
TY - JOUR
A1 - Ostermann-Miyashita, Emu-Felicitas
A1 - König, Hannes J.
A1 - Pernat, Nadja
A1 - Bellingrath-Kimura, Sonoko Dorothea
A1 - Hibler, Sophia
A1 - Kiffner, Christian
T1 - Knowledge of returning wildlife species and willingness to participate in citizen science projects among wildlife park visitors in Germany
JF - People and nature
N2 - Successful conservation efforts have led to recent increases of large mammals such as European bison Bison bonasus, moose Alces alces and grey wolf Canis lupus and their return to former habitats in central Europe.
While embraced by some, the recovery of these species is a controversial topic and holds potential for human-wildlife conflicts.
Involving the public has been suggested to be an effective method for monitoring wildlife and mitigating associated conflicts.
To assess two interrelated prerequisites for engaging people in Citizen Science (CS)-knowledge of returning species and respondents' readiness to participate in CS activities for monitoring and managing these species-we conducted a survey (questionnaire) in two wildlife parks located in different states of Germany.
Based on 472 complete questionnaires, we developed generalized linear models to understand how sociodemographic variables and exposure to the species affected visitors' knowledge of each species, and to investigate if sociodemographic variables and knowledge influenced the likelihood of visitors to participate in CS activities.
Almost all visitors were aware of the returning wolf population, while knowledge and awareness about bison and moose were significantly lower.
Knowledge of the two herbivores differed geographically (higher knowledge of moose in the north-eastern state), possibly indicating a positive association between exposure to the species and knowledge.
However, models generally performed poorly in predicting knowledge about wildlife, suggesting that such specific knowledge is insufficiently explained by sociodemographic variables. Our model, which explained stated willingness in CS indicated that younger participants and those with higher knowledge scores in the survey were more willing to engage in CS activities.
Overall, our analyses highlight how exposure to large mammals, knowledge about wildlife and human demographics are interrelated-insights that are helpful for effectively recruiting citizen scientists for wildlife conservation.
Read the free Plain Language Summary for this article on the Journal blog.
KW - environmental awareness
KW - human-animal relationships
KW - human-wildlife conflicts
KW - social-ecological system
KW - wildlife conservation
KW - wildlife knowledge
Y1 - 2022
U6 - https://doi.org/10.1002/pan3.10379
SN - 2575-8314
VL - 4
IS - 5
SP - 1201
EP - 1215
PB - British Ecological Society; Wiley
CY - London; Hoboken, NJ
ER -
TY - JOUR
A1 - Velzen, Ellen van
A1 - Gaedke, Ursula
A1 - Klauschies, Toni
T1 - Quantifying the capacity for contemporary trait changes to drive intermittent predator-prey cycles
JF - Ecological monographs : a publication of the Ecological Society of America
N2 - A large and growing body of theory has demonstrated how the presence of trait variation in prey or predator populations may affect the amplitude and phase of predator-prey cycles. Less attention has been given to so-called intermittent cycles, in which predator-prey oscillations recurrently disappear and re-appear, despite such dynamics being observed in empirical systems and modeling studies. A comprehensive understanding of the conditions under which trait changes may drive intermittent predator-prey dynamics, as well as their potential ecological implications, is therefore missing. Here we provide a first systematic analysis of the eco-evolutionary conditions that may give rise to intermittent predator-prey cycles, investigating 16 models that incorporate different types of trait variation within prey, predators, or both. Our results show that intermittent dynamics often arise through predator-prey coevolution, but only very rarely when only one trophic level can adapt. Additionally, the frequency of intermittent cycles depends on the source of trait variation (genetic variation or phenotypic plasticity) and the genetic architecture (Mendelian or quantitative traits), with intermittency occurring most commonly through Mendelian evolution, and very rarely through phenotypic plasticity. Further analysis identified three necessary conditions for when trait variation can drive intermittent cycles. First, the intrinsic stability of the predator-prey system must depend on the traits of prey, predators, or both. Second, there must be a mechanism causing the recurrent alternation between stable and unstable states, leading to a "trait" cycle superimposed on the population dynamics. Finally, these trait dynamics must be significantly slower than the predator-prey cycles. We show how these conditions explain all the abovementioned patterns. We further show an important unexpected consequence of these necessary conditions: they are most easily met when intraspecific trait variation is at high risk of being lost. As trait diversity is positively associated with ecosystem functioning, this can have potentially severe negative consequences. This novel result highlights the importance of identifying and understanding intermittent cycles in theoretical studies and natural systems. The new approach for detecting and quantifying intermittency we develop here will be instrumental in enabling future study.
KW - eco-evolutionary feedbacks
KW - ecosystem functioning
KW - intraspecific trait
KW - variation
KW - population cycles
KW - predator-prey dynamics
KW - trait dynamics
Y1 - 2022
U6 - https://doi.org/10.1002/ecm.1505
SN - 1557-7015
SN - 0012-9615
VL - 92
IS - 2
PB - Wiley
CY - New York
ER -
TY - JOUR
A1 - Stanke, Sandra
A1 - Wenger, Christian
A1 - Bier, Frank Fabian
A1 - Hölzel, Ralph
T1 - AC electrokinetic immobilization of influenza virus
JF - Electrophoresis : microfluids & proteomics
N2 - The use of alternating current (AC) electrokinetic forces, like dielectrophoresis and AC electroosmosis, as a simple and fast method to immobilize sub-micrometer objects onto nanoelectrode arrays is presented. Due to its medical relevance, the influenza virus is chosen as a model organism. One of the outstanding features is that the immobilization of viral material to the electrodes can be achieved permanently, allowing subsequent handling independently from the electrical setup. Thus, by using merely electric fields, we demonstrate that the need of prior chemical surface modification could become obsolete. The accumulation of viral material over time is observed by fluorescence microscopy. The influences of side effects like electrothermal fluid flow, causing a fluid motion above the electrodes and causing an intensity gradient within the electrode array, are discussed. Due to the improved resolution by combining fluorescence microscopy with deconvolution, it is shown that the viral material is mainly drawn to the electrode edge and to a lesser extent to the electrode surface. Finally, areas of application for this functionalization technique are presented.
KW - AC electrokinetics
KW - AC electroosmosis
KW - dielectrophoresis
KW - influenza virus
KW - nanoelectrodes
Y1 - 2022
U6 - https://doi.org/10.1002/elps.202100324
SN - 0173-0835
SN - 1522-2683
VL - 43
IS - 12
SP - 1309
EP - 1321
PB - Wiley-Blackwell
CY - Weinheim
ER -
TY - JOUR
A1 - Leins, Johannes A.
A1 - Grimm, Volker
A1 - Drechsler, Martin
T1 - Large-scale PVA modeling of insects in cultivated grasslands
BT - the role of dispersal in mitigating the effects of management schedules under climate change
JF - Ecology and evolution
N2 - In many species, dispersal is decisive for survival in a changing climate. Simulation models for population dynamics under climate change thus need to account for this factor. Moreover, large numbers of species inhabiting agricultural landscapes are subject to disturbances induced by human land use. We included dispersal in the HiLEG model that we previously developed to study the interaction between climate change and agricultural land use in single populations. Here, the model was parameterized for the large marsh grasshopper (LMG) in cultivated grasslands of North Germany to analyze (1) the species development and dispersal success depending on the severity of climate change in subregions, (2) the additional effect of grassland cover on dispersal success, and (3) the role of dispersal in compensating for detrimental grassland mowing. Our model simulated population dynamics in 60-year periods (2020-2079) on a fine temporal (daily) and high spatial (250 x 250 m(2)) scale in 107 subregions, altogether encompassing a range of different grassland cover, climate change projections, and mowing schedules. We show that climate change alone would allow the LMG to thrive and expand, while grassland cover played a minor role. Some mowing schedules that were harmful to the LMG nevertheless allowed the species to moderately expand its range. Especially under minor climate change, in many subregions dispersal allowed for mowing early in the year, which is economically beneficial for farmers. More severe climate change could facilitate LMG expansion to uninhabited regions but would require suitable mowing schedules along the path. These insights can be transferred to other species, given that the LMG is considered a representative of grassland communities. For more specific predictions on the dynamics of other species affected by climate change and land use, the publicly available HiLEG model can be easily adapted to the characteristics of their life cycle.
KW - bilinear interpolation
KW - climate change
KW - dispersal success
KW - land use
KW - large marsh grasshopper
KW - spatially explicit model
Y1 - 2022
U6 - https://doi.org/10.1002/ece3.9063
SN - 2045-7758
VL - 12
IS - 7
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Perrella, Giorgio
A1 - Bäurle, Isabel
A1 - van Zanten, Martijn
T1 - Epigenetic regulation of thermomorphogenesis and heat stress tolerance
JF - New phytologist : international journal of plant science
N2 - Many environmental conditions fluctuate and organisms need to respond effectively. This is especially true for temperature cues that can change in minutes to seasons and often follow a diurnal rhythm. Plants cannot migrate and most cannot regulate their temperature. Therefore, a broad array of responses have evolved to deal with temperature cues from freezing to heat stress. A particular response to mildly elevated temperatures is called thermomorphogenesis, a suite of morphological adaptations that includes thermonasty, formation of thin leaves and elongation growth of petioles and hypocotyl. Thermomorphogenesis allows for optimal performance in suboptimal temperature conditions by enhancing the cooling capacity. When temperatures rise further, heat stress tolerance mechanisms can be induced that enable the plant to survive the stressful temperature, which typically comprises cellular protection mechanisms and memory thereof. Induction of thermomorphogenesis, heat stress tolerance and stress memory depend on gene expression regulation, governed by diverse epigenetic processes. In this Tansley review we update on the current knowledge of epigenetic regulation of heat stress tolerance and elevated temperature signalling and response, with a focus on thermomorphogenesis regulation and heat stress memory. In particular we highlight the emerging role of H3K4 methylation marks in diverse temperature signalling pathways.
KW - chromatin remodelling
KW - elevated temperature
KW - epigenetics
KW - heat stress
KW - histone modification
KW - memory
KW - temperature response
KW - thermomorphogenesis
Y1 - 2022
U6 - https://doi.org/10.1111/nph.17970
SN - 0028-646X
SN - 1469-8137
VL - 234
IS - 4
SP - 1144
EP - 1160
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Ehrlich, Elias
A1 - Thygesen, Uffe Høgsbro
A1 - Kiørboe, Thomas
T1 - Evolution of toxins as a public good in phytoplankton
JF - Proceedings of the Royal Society of London : B, Biological sciences
N2 - Toxic phytoplankton blooms have increased in many waterbodies worldwide with well-known negative impacts on human health, fisheries and ecosystems. However, why and how phytoplankton evolved toxin production is still a puzzling question, given that the producer that pays the costs often shares the benefit with other competing algae and thus provides toxins as a 'public good' (e.g. damaging a common competitor or predator). Furthermore, blooming phytoplankton species often show a high intraspecific variation in toxicity and we lack an understanding of what drives the dynamics of coexisting toxic and non-toxic genotypes. Here, by using an individual-based two-dimensional model, we show that small-scale patchiness of phytoplankton strains caused by demography can explain toxin evolution in phytoplankton with low motility and the maintenance of genetic diversity within their blooms. This patchiness vanishes for phytoplankton with high diffusive motility, suggesting different evolutionary pathways for different phytoplankton groups. In conclusion, our study reveals that small-scale spatial heterogeneity, generated by cell division and counteracted by diffusive cell motility and turbulence, can crucially affect toxin evolution and eco-evolutionary dynamics in toxic phytoplankton species. This contributes to a better understanding of conditions favouring toxin production and the evolution of public goods in asexually reproducing organisms in general.
KW - toxic algal blooms
KW - evolution of cooperation
KW - coexistence
KW - patchiness in
KW - phytoplankton
KW - eco-evolutionary feedback
KW - spatial pattern formation
Y1 - 2022
U6 - https://doi.org/10.1098/rspb.2022.0393
SN - 0962-8452
SN - 1471-2954
VL - 289
IS - 1977
PB - Royal Society
CY - London
ER -
TY - JOUR
A1 - Cordeiro, Andre M.
A1 - Andrade, Luis
A1 - Monteiro, Catarina C.
A1 - Leitao, Guilherme
A1 - Wigge, Philip Anthony
A1 - Saibo, Nelson J. M.
T1 - Phytochrome-interacting factors
BT - a promising tool to improve crop productivity
JF - Journal of experimental botany
N2 - Review exploring the regulation of PHYTOCHROME-INTERACTING FACTORS by light, their role in abiotic stress tolerance and plant architecture, and their influence on crop productivity.
Light is a key determinant for plant growth, development, and ultimately yield. Phytochromes, red/far-red photoreceptors, play an important role in plant architecture, stress tolerance, and productivity. In the model plant Arabidopsis, it has been shown that PHYTOCHROME-INTERACTING FACTORS (PIFs; bHLH transcription factors) act as central hubs in the integration of external stimuli to regulate plant development. Recent studies have unveiled the importance of PIFs in crops. They are involved in the modulation of plant architecture and productivity through the regulation of cell division and elongation in response to different environmental cues. These studies show that different PIFs have overlapping but also distinct functions in the regulation of plant growth. Therefore, understanding the molecular mechanisms by which PIFs regulate plant development is crucial to improve crop productivity under both optimal and adverse environmental conditions. In this review, we discuss current knowledge of PIFs acting as integrators of light and other signals in different crops, with particular focus on the role of PIFs in responding to different environmental conditions and how this can be used to improve crop productivity.
KW - Cold
KW - drought
KW - grain size
KW - heat
KW - light signaling
KW - phytochrome
KW - PIF
KW - plant architecture
KW - plant breeding
KW - plant yield
KW - salinity
Y1 - 2022
U6 - https://doi.org/10.1093/jxb/erac142
SN - 0022-0957
SN - 1460-2431
VL - 73
IS - 12
SP - 3881
EP - 3897
PB - Oxford Univ. Press
CY - Oxford
ER -
TY - JOUR
A1 - Scheffler, Christiane
A1 - Hermanussen, Michael
T1 - Reply to the letter titled: "Pathologizing normal height or identifying chronic malnutrition: Public health concerns of calling stunting normal" / by Nafis Faizi, Mohd Yasir Zubair and Fazeelah Tasleem'. - New York, NY [u.a.] : Wiley Interscience. - 2022. - (American Journal of Human Biology : the Official Journal of the Human Biology Council, 16 Feb 2022. - 34(2022) 5 ). - https://doi.org/10.1002/ajhb.23735
JF - American journal of human biology : the official journal of the Human Biology Association
Y1 - 2022
U6 - https://doi.org/10.1002/ajhb.23741
SN - 1520-6300
VL - 34
IS - 5
PB - Wiley Interscience
CY - New York, NY [u.a.]
ER -
TY - JOUR
A1 - Berg-Mohnicke, Michael
A1 - Nendel, Claas
T1 - A case for object capabilities as the foundation of a distributed environmental model and simulation infrastructure
JF - Environmental modelling & software with environment data news
N2 - With the advent of increasingly powerful computational architectures, scientists use these possibilities to create simulations of ever-increasing size and complexity. Large-scale simulations of environmental systems require huge amounts of resources. Managing these in an operational way becomes increasingly complex and difficult to handle for individual scientists. State-of-the-art simulation infrastructures usually provide the necessary re-sources in a centralised setup, which often results in an all-or-nothing choice for the user. Here, we outline an alternative approach to handling this complexity, while rendering the use of high-performance hardware and large datasets still possible. It retains a number of desirable properties: (i) a decentralised structure, (ii) easy sharing of resources to promote collaboration and (iii) secure access to everything, including natural delegation of authority across levels and system boundaries. We show that the object capability paradigm will cover these issues, and present the first steps towards developing a simulation infrastructure based on these principles.
KW - Cap'n proto
KW - Scientific collaboration
KW - Co -development
KW - Communication
KW - protocol
KW - Object capability
Y1 - 2022
U6 - https://doi.org/10.1016/j.envsoft.2022.105471
SN - 1364-8152
SN - 1873-6726
VL - 156
PB - Elsevier
CY - Oxford
ER -
TY - JOUR
A1 - Sabrowski, Wiebke
A1 - Dreymann, Nico
A1 - Möller, Anja
A1 - Czepluch, Denise
A1 - Albani, Patricia P.
A1 - Theodoridis, Dimitrios
A1 - Menger, Marcus M.
T1 - The use of high-affinity polyhistidine binders as masking probes for the selection of an NDM-1 specific aptamer
JF - Scientific reports
N2 - The emergence of carbapenemase-producing multi-drug resistant Enterobacteriaceae poses a dramatic, world-wide health risk. Limited treatment options and a lack of easy-to-use methods for the detection of infections with multi-drug resistant bacteria leave the health-care system with a fast-growing challenge. Aptamers are single stranded DNA or RNA molecules that bind to their targets with high affinity and specificity and can therefore serve as outstanding detection probes. However, an effective aptamer selection process is often hampered by non-specific binding. When selections are carried out against recombinant proteins, purification tags (e.g. polyhistidine) serve as attractive side targets, which may impede protein target binding. In this study, aptamer selection was carried out against N-terminally hexa-histidine tagged New Delhi metallo-ss-lactamase 1. After 14 selection rounds binding to polyhistidine was detected rather than to New Delhi metallo-ss-lactamase 1. Hence, the selection strategy was changed. As one aptamer candidate showed remarkable binding affinity to polyhistidine, it was used as a masking probe and selection was restarted from selection round 10. Finally, after three consecutive selection rounds, an aptamer with specific binding properties to New Delhi metallo-ss-lactamase 1 was identified. This aptamer may serve as a much-needed detection probe for New Delhi metallo-ss-lactamase 1 expressing Enterobacteriaceae.
Y1 - 2022
U6 - https://doi.org/10.1038/s41598-022-12062-2
SN - 2045-2322
VL - 12
IS - 1
PB - Macmillan Publishers Limited, part of Springer Nature
CY - London
ER -
TY - JOUR
A1 - Nathan, Ran
A1 - Monk, Christopher T.
A1 - Arlinghaus, Robert
A1 - Adam, Timo
A1 - Alós, Josep
A1 - Assaf, Michael
A1 - Baktoft, Henrik
A1 - Beardsworth, Christine E.
A1 - Bertram, Michael G.
A1 - Bijleveld, Allert
A1 - Brodin, Tomas
A1 - Brooks, Jill L.
A1 - Campos-Candela, Andrea
A1 - Cooke, Steven J.
A1 - Gjelland, Karl O.
A1 - Gupte, Pratik R.
A1 - Harel, Roi
A1 - Hellstrom, Gustav
A1 - Jeltsch, Florian
A1 - Killen, Shaun S.
A1 - Klefoth, Thomas
A1 - Langrock, Roland
A1 - Lennox, Robert J.
A1 - Lourie, Emmanuel
A1 - Madden, Joah R.
A1 - Orchan, Yotam
A1 - Pauwels, Ine S.
A1 - Riha, Milan
A1 - Röleke, Manuel
A1 - Schlägel, Ulrike
A1 - Shohami, David
A1 - Signer, Johannes
A1 - Toledo, Sivan
A1 - Vilk, Ohad
A1 - Westrelin, Samuel
A1 - Whiteside, Mark A.
A1 - Jaric, Ivan
T1 - Big-data approaches lead to an increased understanding of the ecology of animal movement
JF - Science
N2 - Understanding animal movement is essential to elucidate how animals interact, survive, and thrive in a changing world. Recent technological advances in data collection and management have transformed our understanding of animal "movement ecology" (the integrated study of organismal movement), creating a big-data discipline that benefits from rapid, cost-effective generation of large amounts of data on movements of animals in the wild. These high-throughput wildlife tracking systems now allow more thorough investigation of variation among individuals and species across space and time, the nature of biological interactions, and behavioral responses to the environment. Movement ecology is rapidly expanding scientific frontiers through large interdisciplinary and collaborative frameworks, providing improved opportunities for conservation and insights into the movements of wild animals, and their causes and consequences.
Y1 - 2022
U6 - https://doi.org/10.1126/science.abg1780
SN - 0036-8075
SN - 1095-9203
VL - 375
IS - 6582
SP - 734
EP - +
PB - American Assoc. for the Advancement of Science
CY - Washington
ER -
TY - JOUR
A1 - Milles, Alexander Benedikt
A1 - Dammhahn, Melanie
A1 - Jeltsch, Florian
A1 - Schlägel, Ulrike
A1 - Grimm, Volker
T1 - Fluctuations in density-dependent selection drive the evolution of a pace-of-life syndrome within and between populations
JF - The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences
N2 - The pace-of-life syndrome (POLS) hypothesis posits that suites of traits are correlated along a slow-fast continuum owing to life history trade-offs. Despite widespread adoption, environmental conditions driving the emergence of POLS remain unclear. A recently proposed conceptual framework of POLS suggests that a slow-fast continuum should align to fluctuations in density-dependent selection. We tested three key predictions made by this framework with an ecoevolutionary agent-based population model. Selection acted on responsiveness (behavioral trait) to interpatch resource differences and the reproductive investment threshold (life history trait). Across environments with density fluctuations of different magnitudes, we observed the emergence of a common axis of trait covariation between and within populations (i.e., the evolution of a POLS). Slow-type (fast-type) populations with high (low) responsiveness and low (high) reproductive investment threshold were selected at high (low) population densities and less (more) intense and frequent density fluctuations. In support of the predictions, fast-type populations contained a higher degree of variation in traits and were associated with higher intrinsic reproductive rate (r(0)) and higher sensitivity to intraspecific competition (gamma), pointing to a universal trade-off. While our findings support that POLS aligns with density-dependent selection, we discuss possible mechanisms that may lead to alternative evolutionary pathways.
KW - pace-of-life syndrome
KW - density dependence
KW - life history
KW - trait
KW - variation
KW - model
KW - personality
Y1 - 2022
U6 - https://doi.org/10.1086/718473
SN - 0003-0147
SN - 1537-5323
VL - 199
IS - 4
SP - E124
EP - E139
PB - Univ. of Chicago Press
CY - Chicago
ER -
TY - JOUR
A1 - Ghafarian, Fatemeh
A1 - Wieland, Ralf
A1 - Nendel, Claas
T1 - Estimating the Evaporative Cooling Effect of Irrigation within and above Soybean Canopy
JF - Water
N2 - Vegetation with an adequate supply of water might contribute to cooling the land surface around it through the latent heat flux of transpiration. This study investigates the potential estimation of evaporative cooling at plot scale, using soybean as example. Some of the plants' physiological parameters were monitored and sampled at weekly intervals. A physics-based model was then applied to estimate the irrigation-induced cooling effect within and above the canopy during the middle and late season of the soybean growth period. We then examined the results of the temperature changes at a temporal resolution of ten minutes between every two irrigation rounds. During the middle and late season of growth, the cooling effects caused by evapotranspiration within and above the canopy were, on average, 4.4 K and 2.9 K, respectively. We used quality indicators such as R-squared (R-2) and mean absolute error (MAE) to evaluate the performance of the model simulation. The performance of the model in this study was better above the canopy (R-2 = 0.98, MAE = 0.3 K) than below (R-2 = 0.87, MAE = 0.9 K) due to the predefined thermodynamic condition used to estimate evaporative cooling. Moreover, the study revealed that canopy cooling contributes to mitigating heat stress conditions during the middle and late seasons of crop growth.
KW - canopy cooling effects
KW - shading cooling
KW - canopy-air temperature
KW - energy
KW - balance
KW - the Penman-Monteith equation
Y1 - 2022
U6 - https://doi.org/10.3390/w14030319
SN - 2073-4441
VL - 14
IS - 3
PB - MDPI
CY - Basel
ER -
TY - JOUR
A1 - Boeker, Sonja
A1 - Hermanussen, Michael
A1 - Scheffler, Christiane
T1 - Dental age is an independent marker of biological age
JF - Human biology and public health
N2 - Background: Biological age markers are a crucial indicator whether children are decelerated in growth tempo. Skeletal maturation is the standard measure. Yet, it relies on exposing children to x-radiation. Dental eruption is a potential, but highly debated, radiation free alternative.
Objectives: We assess the interrelationship between dental eruption and other maturational markers. We hypothesize that dental age correlates with body height and skeletal age. We further evaluate how the three different variables behave in cohorts from differing social backgrounds.
Sample and Method: Dental, skeletal and height data from the 1970s to 1990s from Guatemalan boys were converted into standard deviation scores, using external references for each measurement. The boys, aged between 7 and 12, derived from different social backgrounds (middle SES (N = 6529), low-middle SES (N = 736), low SES Ladino (N = 3653) and low SES Maya (N = 4587).
Results: Dental age shows only a weak correlation with skeletal age (0.18) and height (0.2). The distinction between cohorts differs according to each of the three measurements. All cohorts differ significantly in height. In skeletal maturation, the middle SES cohort is significantly advanced compared to all other cohorts. The periodically malnourished cohorts of low SES Mayas and Ladinos are significantly delayed in dental maturation compared to the well-nourished low-middle and middle class Ladino children.
Conclusion: Dental development is an independent system, that is regulated by different mechanisms than skeletal development and growth. Tooth eruption is sensitive to nutritional status, whereas skeletal age is more sensitive to socioeconomic background.
KW - dental eruption
KW - biological age
KW - skeletal age
KW - growth tempo
KW - maturation
KW - malnutrition
Y1 - 2022
U6 - https://doi.org/10.52905/hbph2021.3.24
SN - 2748-9957
VL - 2021
IS - 3, Summer School Supplement
PB - Universitätsverlag Potsdam
CY - Potsdam
ER -
TY - JOUR
A1 - Hermanussen, Michael
A1 - Groth, Detlef
A1 - Scheffler, Christiane
T1 - Human growth data analyses and statistics
BT - The 4th Gülpe International Student Summer School
JF - Human biology and public health
N2 - Students learn by repetition. Repetition is essential, but repetition needs questioning, and questioning the repertoire belongs to the essential tasks of student education. Guiding students to questioning was and is our prime motive to offer our International Student Summer Schools. The data were critically discussed among the students, in the twilight of Just So Stories, common knowledge, and prompted questioning of contemporary solutions. For these schools, the students bring their own data, carry their preliminary concepts, and in group discussions, they may have to challenge these concepts. Catch-up growth is known to affect long bone growth, but different opinions exist to what extent it also affects body proportions. Skeletal age and dental development are considered appropriate measures of maturation, but it appears that both system develop independently and are regulated by different mechanisms. Body weight distributions are assumed to be skewed, yet, historic data disproved this assumption. Many discussions focused on current ideas of global growth standards as a common yardstick for all populations world-wide, with new statistical tools being developed including network reconstruction and evaluation of the reconstructs to determine the confidence of graph prediction methods.
KW - Just so stories
KW - Summer Schools
KW - questioning solutions
KW - repetition
Y1 - 2022
U6 - https://doi.org/10.52905/hbph2021.3.29
SN - 2748-9957
VL - 2021
IS - 3, Summer School Supplement
PB - Universitätsverlag Potsdam
CY - Potsdam
ER -
TY - JOUR
A1 - Mumm, Rebekka
A1 - Hermanussen, Michael
T1 - The dilemma of misclassifying weight in short and in historic population
JF - Human biology and public health
N2 - Background: Clinicians often refer anthropometric measures of a child to so-called “growth standards” and “growth references. Over 140 countries have meanwhile adopted WHO growth standards.
Objectives: The present study was conducted to thoroughly examine the idea of growth standards as a common yardstick for all populations. Weight depends on height. We became interested in whether also weight-for-height depends on height. First, we studied the age-group effect on weight-for-height. Thereafter, we tested the applicability of weight-for-height references in short and in historic populations.
Sample and Methods: We analyzed body height and body weight and weight-for-height of 3795 healthy boys and 3726 healthy girls aged 2 to 5 years measured in East-Germany between 1986 and 1990.
We chose contemporary height and weight charts from Germany, the UK, and the WHO growth chart and compared these with three geographically commensurable growth charts from the end of the 19th century.
Results: We analyzed body height and body weight and weight-for-height of 3795 healthy boys and 3726 healthy girls aged 2 to 5 years measured in East-Germany between 1986 and 1990.
We chose contemporary height and weight charts from Germany, the UK, and the WHO growth chart and compared these with three geographically commensurable growth charts of the end of the 19th century.
Conclusion: Weight-for-height depends on age and sex and apart from the nutritional state, reflects body proportion and body built particularly during infancy and early childhood. Populations with a relatively short average height are prone to high values of weight-for-height for arithmetic reasons independent of the nutritional state.
KW - growth standards
KW - growth references
KW - body mass index
KW - nutritional status
Y1 - 2022
U6 - https://doi.org/10.52905/hbph2021.3.28
SN - 2748-9957
VL - 2021
IS - 3, Summer School Supplement
PB - Universitätsverlag Potsdam
CY - Potsdam
ER -
TY - JOUR
A1 - Hermanussen, Michael
A1 - Scheffler, Christiane
T1 - Evidence of chronic undernutrition in late 19th century German infants of all social classes
JF - Human biology and public health
N2 - 125 years ago, European infants grew differently from modern infants. We show weight gains of 20 healthy children weighed longitudinally from birth to age 1 year, published by Camerer in 1882. The data illustrate the historically prevalent concepts of infant nutrition practiced by German civil servants, lawyers, merchants, university professors, physicians, foresters and farmers. Breastfeeding by the mother was not truly appreciated in those days; children were often breastfed by wet nurses or received bottled milk. Bottle feeding mainly used diluted cow’s milk with some added carbohydrates, without evidence that appropriate amounts of oil, butter or other fatty components were added. French children from 1914 showed similar weight gain patterns suggesting similar feeding practices. The historical data suggest that energy deficient infant formula was fed regularly in the late 19th and early 20th century Europe, regardless of wealth and social class. The data question current concerns that temporarily feeding energy deficient infant formula may warrant serious anxieties regarding long-term cognitive, social and emotional behavioral development.
KW - chronic undernutrition
KW - breastfeeding
KW - historical growth
KW - social class
KW - translation
Y1 - 2022
U6 - https://doi.org/10.52905/hbph2022.2.42
SN - 2748-9957
VL - 2022
IS - 2
PB - Universitätsverlag Potsdam
CY - Potsdam
ER -
TY - JOUR
A1 - Haueis, Lisa
A1 - Stech, Marlitt
A1 - Kubick, Stefan
T1 - A Cell-free Expression Pipeline for the Generation and Functional Characterization of Nanobodies
JF - Frontiers in Bioengineering and Biotechnology
N2 - Cell-free systems are well-established platforms for the rapid synthesis, screening, engineering and modification of all kinds of recombinant proteins ranging from membrane proteins to soluble proteins, enzymes and even toxins. Also within the antibody field the cell-free technology has gained considerable attention with respect to the clinical research pipeline including antibody discovery and production. Besides the classical full-length monoclonal antibodies (mAbs), so-called "nanobodies" (Nbs) have come into focus. A Nb is the smallest naturally-derived functional antibody fragment known and represents the variable domain (VHH, similar to 15 kDa) of a camelid heavy-chain-only antibody (HCAb). Based on their nanoscale and their special structure, Nbs display striking advantages concerning their production, but also their characteristics as binders, such as high stability, diversity, improved tissue penetration and reaching of cavity-like epitopes. The classical way to produce Nbs depends on the use of living cells as production host. Though cell-based production is well-established, it is still time-consuming, laborious and hardly amenable for high-throughput applications. Here, we present for the first time to our knowledge the synthesis of functional Nbs in a standardized mammalian cell-free system based on Chinese hamster ovary (CHO) cell lysates. Cell-free reactions were shown to be time-efficient and easy-to-handle allowing for the "on demand" synthesis of Nbs. Taken together, we complement available methods and demonstrate a promising new system for Nb selection and validation.
KW - cell-free protein synthesis
KW - In vitro transcription
KW - translation
KW - nanobody
KW - VHH
KW - camelid
KW - CHO cell lysate
Y1 - 2022
U6 - https://doi.org/10.3389/fbioe.2022.896763
SN - 2296-4185
VL - 10
PB - Frontiers Media
CY - Lausanne
ER -
TY - JOUR
A1 - Dammhahn, Melanie
A1 - Lange, Pauline
A1 - Eccard, Jana
T1 - The landscape of fear has individual layers
BT - an experimental test of among-individual differences in perceived predation risk during foraging
JF - Oikos
N2 - Perceived predation risk varies in space and time creating a landscape of fear. This key feature of an animal's environment is classically studied as a species-specific property. However, individuals differ in how they solve the tradeoff between safety and reward and may, hence, differ consistently and predictively in perceived predation risk across landscapes. To test this hypothesis, we quantified among-individual differences in boldness and activity and exposed behaviourally phenotyped male bank voles Myodes glareolus individually to two different experimental landscapes of risks in large outdoor enclosures and provided resources as discrete food patches. We manipulated perceived predation risk via vegetation height between 2 and > 30 cm and quantified patch use indirectly via RFID-logging and giving-up densities. We statistically disentangled among-individual differences in microhabitat use from spatially varying perceived risk, i.e. landscape of fear. We found that individuals varied in mean vegetation height of their foraging microhabitats and that this microhabitat selection matched the intrinsic individual differences in perceived risk. As predicted by the patch use model, all individual's perceived higher risks when foraging in lower vegetation. However, individuals differed in their reaction norm slopes of perceived risk to vegetation height, and these differences in slopes were consistent across two different landscapes of risks and resources. We interpret these results as evidence for individual landscapes of fear, which could be predicted by among-individual differences in activity and boldness. Since perceived predation risk affects when and where to forage, among-individual differences in fear responses could act as a mode of intraspecific niche complementarity (i.e. individual niche specialization), help explain behavioural type by environment correlations, and will likely have cascading indirect effects on lower trophic levels.
KW - activity
KW - behavioural reaction norm
KW - giving-up density
KW - patch use;
KW - optimal foraging
KW - personality
KW - risk allocation
KW - rodents
Y1 - 2022
U6 - https://doi.org/10.1111/oik.09124
SN - 0030-1299
SN - 1600-0706
VL - 2022
IS - 6
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Krumbholz, Julia
A1 - Ishida, Keishi
A1 - Baunach, Martin
A1 - Teikari, Jonna
A1 - Rose, Magdalena M.
A1 - Sasso, Severin
A1 - Hertweck, Christian
A1 - Dittmann, Elke
T1 - Deciphering chemical mediators regulating specialized metabolism in a symbiotic cyanobacterium
JF - Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker. International edition
N2 - Genomes of cyanobacteria feature a variety of cryptic biosynthetic pathways for complex natural products, but the peculiarities limiting the discovery and exploitation of the metabolic dark matter are not well understood. Here we describe the discovery of two cell density-dependent chemical mediators, nostoclide and nostovalerolactone, in the symbiotic model strain Nostoc punctiforme, and demonstrate their pronounced impact on the regulation of specialized metabolism. Through transcriptional, bioinformatic and labeling studies we assigned two adjacent biosynthetic gene clusters to the biosynthesis of the two polyketide mediators. Our findings provide insight into the orchestration of specialized metabolite production and give lessons for the genomic mining and high-titer production of cyanobacterial bioactive compounds.
KW - Biosynthesis
KW - Cyanobacteria
KW - Genomic Mining
KW - Quorum Sensing
KW - Specialized
KW - Metabolism
Y1 - 2022
U6 - https://doi.org/10.1002/anie.202204545
SN - 1433-7851
SN - 1521-3773
PB - Wiley-VCH
CY - Weinheim
ER -
TY - JOUR
A1 - Dreymann, Nico
A1 - Wuensche, Julia
A1 - Sabrowski, Wiebke
A1 - Moeller, Anja
A1 - Czepluch, Denise
A1 - Vu Van, Dana
A1 - Füssel, Susanne
A1 - Menger, Marcus M.
T1 - Inhibition of Human Urokinase-Type Plasminogen Activator (uPA) Enzyme Activity and Receptor Binding by DNA Aptamers as Potential Therapeutics through Binding to the Different Forms of uPA
JF - International journal of molecular sciences
N2 - Urokinase-type plasminogen activator is widely discussed as a marker for cancer prognosis and diagnosis and as a target for cancer therapies. Together with its receptor, uPA plays an important role in tumorigenesis, tumor progression and metastasis. In the present study, systematic evolution of ligands by exponential enrichment (SELEX) was used to select single-stranded DNA aptamers targeting different forms of human uPA. Selected aptamers allowed the distinction between HMW-uPA and LMW-uPA, and therefore, presumably, have different binding regions. Here, uPAapt-02-FR showed highly affine binding with a K-D of 0.7 nM for HMW-uPA and 21 nM for LMW-uPA and was also able to bind to pro-uPA with a K-D of 14 nM. Furthermore, no cross-reactivity to mouse uPA or tissue-type plasminogen activator (tPA) was measured, demonstrating high specificity. Suppression of the catalytic activity of uPA and inhibition of uPAR-binding could be demonstrated through binding with different aptamers and several of their truncated variants. Since RNA aptamers are already known to inhibit uPA-uPAR binding and other pathological functions of the uPA system, these aptamers represent a novel, promising tool not only for detection of uPA but also for interfering with the pathological functions of the uPA system by additionally inhibiting uPA activity.
KW - biomarker
KW - cancer
KW - cancer therapy
KW - DNA aptamer
KW - microscale thermophoresis (MST)
KW - SELEX
KW - surface plasmon resonance spectroscopy (SPR)
KW - uPA
KW - uPAR
KW - urokinase
Y1 - 2022
U6 - https://doi.org/10.3390/ijms23094890
SN - 1661-6596
SN - 1422-0067
VL - 23
IS - 9
PB - MDPI
CY - Basel
ER -
TY - JOUR
A1 - Palma-Vera, Sergio E.
A1 - Reyer, Henry
A1 - Langhammer, Martina
A1 - Reinsch, Norbert
A1 - Derezanin, Lorena
A1 - Fickel, Jörns
A1 - Qanbari, Saber
A1 - Weitzel, Joachim M.
A1 - Franzenburg, Soeren
A1 - Hemmrich-Stanisak, Georg
A1 - Schön, Jennifer
T1 - Genomic characterization of the world's longest selection experiment in mouse reveals the complexity of polygenic traits
JF - BMC Biology
N2 - Background
Long-term selection experiments are a powerful tool to understand the genetic background of complex traits. The longest of such experiments has been conducted in the Research Institute for Farm Animal Biology (FBN), generating extreme mouse lines with increased fertility, body mass, protein mass and endurance. For >140 generations, these lines have been maintained alongside an unselected control line, representing a valuable resource for understanding the genetic basis of polygenic traits. However, their history and genomes have not been reported in a comprehensive manner yet. Therefore, the aim of this study is to provide a summary of the breeding history and phenotypic traits of these lines along with their genomic characteristics. We further attempt to decipher the effects of the observed line-specific patterns of genetic variation on each of the selected traits.
Results
Over the course of >140 generations, selection on the control line has given rise to two extremely fertile lines (>20 pups per litter each), two giant growth lines (one lean, one obese) and one long-distance running line. Whole genome sequencing analysis on 25 animals per line revealed line-specific patterns of genetic variation among lines, as well as high levels of homozygosity within lines. This high degree of distinctiveness results from the combined effects of long-term continuous selection, genetic drift, population bottleneck and isolation. Detection of line-specific patterns of genetic differentiation and structural variation revealed multiple candidate genes behind the improvement of the selected traits.
Conclusions
The genomes of the Dummerstorf trait-selected mouse lines display distinct patterns of genomic variation harbouring multiple trait-relevant genes. Low levels of within-line genetic diversity indicate that many of the beneficial alleles have arrived to fixation alongside with neutral alleles. This study represents the first step in deciphering the influence of selection and neutral evolutionary forces on the genomes of these extreme mouse lines and depicts the genetic complexity underlying polygenic traits.
KW - Mouse
KW - Fertility
KW - Body mass
KW - Endurance
KW - Selective breeding
KW - Genetic
KW - drift
KW - Bottleneck
KW - Whole genome sequencing
KW - Single-nucleotide
KW - polymorphism
KW - Structural variation
Y1 - 2022
U6 - https://doi.org/10.1186/s12915-022-01248-9
SN - 1741-7007
VL - 20
IS - 1
PB - BMC
CY - London
ER -
TY - JOUR
A1 - Blickensdörfer, Lukas
A1 - Schwieder, Marcel
A1 - Pflugmacher, Dirk
A1 - Nendel, Claas
A1 - Erasmi, Stefan
A1 - Hostert, Patrick
T1 - Mapping of crop types and crop sequences with combined time series of Sentinel-1, Sentinel-2 and Landsat 8 data for Germany
JF - Remote sensing of environment : an interdisciplinary journal
N2 - Monitoring agricultural systems becomes increasingly important in the context of global challenges like climate change, biodiversity loss, population growth, and the rising demand for agricultural products. High-resolution, national-scale maps of agricultural land are needed to develop strategies for future sustainable agriculture.
However, the characterization of agricultural land cover over large areas and for multiple years remains challenging due to the locally diverse and temporally variable characteristics of cultivated land.
We here propose a workflow for generating national agricultural land cover maps on a yearly basis that accounts for varying environmental conditions. We tested the approach by mapping 24 agricultural land cover classes in Germany for the three years 2017, 2018, and 2019, in which the meteorological conditions strongly differed.
We used a random forest classifier and dense time series data from Sentinel-2 and Landsat 8 in combination with monthly Sentinel-1 composites and environmental data and evaluated the relative importance of optical, radar, and environmental data.
Our results show high overall accuracy and plausible class accuracies for the most dominant crop types across different years despite the strong inter-annual meteorological variability and the presence of drought and nondrought years. The maps show high spatial consistency and good delineation of field parcels.
Combining optical, SAR, and environmental data increased overall accuracies by 6% to 10% compared to single sensor approaches, in which optical data outperformed SAR. Overall accuracy ranged between 78% and 80%, and the mapped areas aligned well with agricultural statistics at the regional and national level.
Based on the multi-year dataset we mapped major crop sequences of cereals and leaf crops. Most crop sequences were dominated by winter cereals followed by summer cereals.
Monocultures of summer cereals were mainly revealed in the Northwest of Germany. We showcased that high spatial and thematic detail in combination with annual mapping will stimulate research on crop cycles and studies to assess the impact of environmental policies on management decisions.
Our results demonstrate the capabilities of integrated optical time series and SAR data in combination with variables describing local and seasonal environmental conditions for annual large-area crop type mapping.
KW - agricultural land cover
KW - analysis-ready data
KW - time series
KW - large-area mapping
KW - optical remote sensing
KW - SAR
KW - big data
KW - multi-sensor
Y1 - 2022
U6 - https://doi.org/10.1016/j.rse.2021.112831
SN - 0034-4257
SN - 1879-0704
VL - 269
PB - Elsevier
CY - New York
ER -
TY - JOUR
A1 - Kühn, Elisabeth
A1 - Becker, Marc
A1 - Harpke, Alexander
A1 - Kühn, Ingolf
A1 - Kuhlicke, Christian
A1 - Schmitt, Thomas
A1 - Settele, Josef
A1 - Musche, Martin
T1 - The benefits of counting butterflies: recommendations for a successful citizen science project
JF - Ecology and Society
N2 - Citizen science (CS) projects, being popular across many fields of science, have recently also become a popular tool to collect biodiversity data. Although the benefits of such projects for science and policy making are well understood, relatively little is known about the benefits participants get from these projects as well as their personal backgrounds and motivations. Furthermore, very little is known about their expectations. We here examine these aspects, with the citizen science project "German Butterfly Monitoring" as an example. A questionnaire was sent to all participants of the project and the responses to the questionnaire indicated the following: center dot Most transect walkers do not have a professional background in this field, though they do have a high educational level, and are close to retirement, with a high number of females; center dot An important motivation to join the project is to preserve the natural environment and to contribute to scientific knowledge; center dot Participants benefit by enhancing their knowledge about butterflies and especially their ability to identify different species (taxonomic knowledge); center dot Participants do not have specific expectations regarding the project beyond proper management and coordination, but have an intrinsic sense of working for a greater good. The willingness to join a project is higher if the project contributes to the solution of a problem discussed in the media (here, insect decline). Based on our findings from the analysis of the questionnaire we can derive a set of recommendations for establishing a successful CS project. These include the importance of good communication, e.g., by explaining what the (scientific) purpose of the project is and what problems are to be solved with the help of the data collected in the project. The motivation to join a CS project is mostly intrinsic and CS is a good tool to engage people during difficult times such as the COVID-19 pandemic, giving participants the feeling of doing something useful.
KW - COVID-19 pandemic
KW - gender gap
KW - insect decline
KW - intrinsic motivation
KW - monitoring
Y1 - 2022
U6 - https://doi.org/10.5751/ES-12861-270238
SN - 1708-3087
VL - 27
IS - 2
PB - Resilience Alliance
CY - Wolfville
ER -
TY - JOUR
A1 - Jesus, Sonia A.
A1 - Schmidt, Anke
A1 - Fickel, Jörns
A1 - Doherr, Marcus G.
A1 - Boonprasert, Khajohnpat
A1 - Thitaram, Chatchote
A1 - Sariya, Ladawan
A1 - Ratanakron, Parntep
A1 - Hildebrandt, Thomas Bernd
T1 - Assessing coagulation parameters in healthy Asian Elephants (Elephas maximus) from European and thai populations
JF - Animals
N2 - Simple Summary Asian elephants (Elephas maximus) are considered endangered and their population is in continuous decline. Understanding their social interactions, health, and welfare status has been a topic of intense research in recent decades. Coagulation assessments have been underutilized in wildlife but can give valuable information on individual health. This study aims to increase the knowledge of the coagulation status in healthy Asian elephants from different backgrounds and age groups, using a fast point-of-care analyzer. This tool can be further used in either routine health check-ups performed by caretakers or in a clinical emergency, such as in cases of elephant endotheliotropic herpesvirus hemorrhagic disease outbreaks. We have also investigated the presence of genomic mutations in one coagulation factor-factor VII-where a disorder was previously reported in an Asian elephant. Hereby, we report new reference values for coagulation parameters, such as coagulation times and fibrinogen concentration of Asian elephants assessed in Thailand and in Europe, as well as several single point mutations found in the exons of Elephas maximus coagulation F7 gene. We found the point-of-care analyzer used in this study to be very practical and user friendly for a zoo and field environment and hope that this project will incentivize further coagulation studies in Asian elephants and in other wildlife species. The Asian elephant population is continuously declining due to several extrinsic reasons in their range countries, but also due to diseases in captive populations worldwide. One of these diseases, the elephant endotheliotropic herpesvirus (EEHV) hemorrhagic disease, is very impactful because it particularly affects Asian elephant calves. It is commonly fatal and presents as an acute and generalized hemorrhagic syndrome. Therefore, having reference values of coagulation parameters, and obtaining such values for diseased animals in a very short time, is of great importance. We analyzed prothrombin time (PT), activated partial thromboplastin time (aPTT), and fibrinogen concentrations using a portable and fast point-of-care analyzer (VetScan Pro) in 127 Asian elephants from Thai camps and European captive herds. We found significantly different PT and aPTT coagulation times between elephants from the two regions, as well as clear differences in fibrinogen concentration. Nevertheless, these alterations were not expected to have biological or clinical implications. We have also sequenced the coagulation factor VII gene of 141 animals to assess the presence of a previously reported hereditary coagulation disorder in Asian elephants and to investigate the presence of other mutations. We did not find the previously reported mutation in our study population. Instead, we discovered the presence of several new single nucleotide polymorphisms, two of them being considered as deleterious by effect prediction software.
KW - coagulation
KW - Asian elephant
KW - EEHV
KW - factor VII
KW - F7 gene
KW - prothrombin
KW - activated PTT
KW - fibrinogen
Y1 - 2022
U6 - https://doi.org/10.3390/ani12030361
SN - 2076-2615
VL - 12
IS - 3
PB - MDPI
CY - Basel
ER -
TY - JOUR
A1 - Stelbrink, Björn
A1 - von Rintelen, Thomas
A1 - Richter, Kirsten
A1 - Finstermeier, Knut
A1 - Frahnert, Sylke
A1 - Cracraft, Joel
A1 - Hofreiter, Michael
T1 - Insights into the geographical origin and phylogeographical patterns of Paradisaea birds-of-paradise
JF - Zoological journal of the Linnean Society
N2 - Birds-of-paradise represent a textbook example for geographical speciation and sexual selection. Perhaps the most iconic genus is Paradisaea, which is restricted to New Guinea and a few surrounding islands. Although several species concepts have been applied in the past to disentangle the different entities within this genus, no attempt has been made so far to uncover phylogeographical patterns based on a genetic dataset that includes multiple individuals per species. Here, we applied amplicon sequencing for the mitochondrial fragment Cytb for a total of 69 museum specimens representing all seven Paradisaea species described and inferred both phylogenetic relationships and colonization pathways across the island. Our analyses show that the most recent common ancestor of the diverging lineages within Paradisaea probably originated in the Late Miocene in the eastern part of the Central Range and suggest that tectonic processes played a key role in shaping the diversification and distribution of species. All species were recovered as monophyletic, except for those within the apoda-minor-raggiana clade, which comprises the allopatric and parapatric species P. apoda, P. minor and P. raggiana. The comparatively young divergence times, together with possible instances of mitochondrial introgression and incomplete lineage sorting, suggest recent speciation in this clade.
KW - amplicon sequencing
KW - Cytb
KW - historical DNA
KW - molecular clock
KW - molecular phylogeny
KW - museomics
KW - New Guinea
KW - Paradisaeidae
Y1 - 2022
U6 - https://doi.org/10.1093/zoolinnean/zlac010
SN - 0024-4082
SN - 1096-3642
VL - 196
IS - 4
SP - 1394
EP - 1407
PB - Oxford Univ. Press
CY - Oxford
ER -
TY - JOUR
A1 - Eckert, Silvia
A1 - Herden, Jasmin
A1 - Stift, Marc
A1 - Durka, Walter
A1 - Kleunen, Mark van
A1 - Joshi, Jasmin Radha
T1 - Traces of genetic but not epigenetic adaptation in the invasive goldenrod Solidago canadensis despite the absence of population structure
JF - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2 - Biological invasions may result from multiple introductions, which might compensate for reduced gene pools caused by bottleneck events, but could also dilute adaptive processes. A previous common-garden experiment showed heritable latitudinal clines in fitness-related traits in the invasive goldenrod Solidago canadensis in Central Europe. These latitudinal clines remained stable even in plants chemically treated with zebularine to reduce epigenetic variation. However, despite the heritability of traits investigated, genetic isolation-by-distance was non-significant. Utilizing the same specimens, we applied a molecular analysis of (epi)genetic differentiation with standard and methylation-sensitive (MSAP) AFLPs. We tested whether this variation was spatially structured among populations and whether zebularine had altered epigenetic variation. Additionally, we used genome scans to mine for putative outlier loci susceptible to selection processes in the invaded range. Despite the absence of isolation-by-distance, we found spatial genetic neighborhoods among populations and two AFLP clusters differentiating northern and southern Solidago populations. Genetic and epigenetic diversity were significantly correlated, but not linked to phenotypic variation. Hence, no spatial epigenetic patterns were detected along the latitudinal gradient sampled. Applying genome-scan approaches (BAYESCAN, BAYESCENV, RDA, and LFMM), we found 51 genetic and epigenetic loci putatively responding to selection. One of these genetic loci was significantly more frequent in populations at the northern range. Also, one epigenetic locus was more frequent in populations in the southern range, but this pattern was lost under zebularine treatment. Our results point to some genetic, but not epigenetic adaptation processes along a large-scale latitudinal gradient of S. canadensis in its invasive range.
T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1271
KW - AFLP
KW - MSAP
KW - cytosine methylation
KW - spatial autocorrelation
KW - genome scan
Y1 - 2022
U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-566758
SN - 1866-8372
SP - 1
EP - 17
PB - Universitätsverlag Potsdam
CY - Potsdam
ER -
TY - JOUR
A1 - Eckert, Silvia
A1 - Herden, Jasmin
A1 - Stift, Marc
A1 - Durka, Walter
A1 - Kleunen, Mark van
A1 - Joshi, Jasmin
T1 - Traces of genetic but not epigenetic adaptation in the invasive goldenrod Solidago canadensis despite the absence of population structure
JF - Frontiers in Ecology and Evolution
N2 - Biological invasions may result from multiple introductions, which might compensate for reduced gene pools caused by bottleneck events, but could also dilute adaptive processes. A previous common-garden experiment showed heritable latitudinal clines in fitness-related traits in the invasive goldenrod Solidago canadensis in Central Europe. These latitudinal clines remained stable even in plants chemically treated with zebularine to reduce epigenetic variation. However, despite the heritability of traits investigated, genetic isolation-by-distance was non-significant. Utilizing the same specimens, we applied a molecular analysis of (epi)genetic differentiation with standard and methylation-sensitive (MSAP) AFLPs. We tested whether this variation was spatially structured among populations and whether zebularine had altered epigenetic variation. Additionally, we used genome scans to mine for putative outlier loci susceptible to selection processes in the invaded range. Despite the absence of isolation-by-distance, we found spatial genetic neighborhoods among populations and two AFLP clusters differentiating northern and southern Solidago populations. Genetic and epigenetic diversity were significantly correlated, but not linked to phenotypic variation. Hence, no spatial epigenetic patterns were detected along the latitudinal gradient sampled. Applying genome-scan approaches (BAYESCAN, BAYESCENV, RDA, and LFMM), we found 51 genetic and epigenetic loci putatively responding to selection. One of these genetic loci was significantly more frequent in populations at the northern range. Also, one epigenetic locus was more frequent in populations in the southern range, but this pattern was lost under zebularine treatment. Our results point to some genetic, but not epigenetic adaptation processes along a large-scale latitudinal gradient of S. canadensis in its invasive range.
KW - AFLP
KW - MSAP
KW - cytosine methylation
KW - spatial autocorrelation
KW - genome scan
Y1 - 2022
U6 - https://doi.org/10.3389/fevo.2022.856453
SN - 2296-701X
VL - 10
SP - 1
EP - 17
PB - Frontiers
CY - Lausanne, Schweiz
ER -
TY - JOUR
A1 - Ghoddousi, Arash
A1 - Van Cayzeele, Corinna
A1 - Negahdar, Pegah
A1 - Soofi, Mahmood
A1 - Kh. Hamidi, Amirhossein
A1 - Bleyhl, Benjamin
A1 - Fandos, Guillermo
A1 - Khorozyan, Igor
A1 - Waltert, Matthias
A1 - Kuemmerle, Tobias
T1 - Understanding spatial patterns of poaching pressure using ranger logbook data to optimize future patrolling strategies
JF - Ecological applications : a publication of the Ecological Society of America
N2 - Poaching is driving many species toward extinction, and as a result, lowering poaching pressure is a conservation priority. This requires understanding where poaching pressure is high and which factors determine these spatial patterns. However, the cryptic and illegal nature of poaching makes this difficult.
Ranger patrol data, typically recorded in protected area logbooks, contain information on patrolling efforts and poaching detection and should thus provide opportunities for a better understanding of poaching pressure. However, these data are seldom analyzed and rarely used to inform adaptive management strategies.
We developed a novel approach to making use of analog logbook records to map poaching pressure and to test environmental criminology and predator-prey relationship hypotheses explaining poaching patterns. We showcase this approach for Golestan National Park in Iran, where poaching has substantially depleted ungulate populations. We digitized data from >4800 ranger patrols from 2014 to 2016 and used an occupancy modeling framework to relate poaching to (1) accessibility, (2) law enforcement, and (3) prey availability factors. Based on predicted poaching pressure and patrolling intensity, we provide suggestions for future patrol allocation strategies. Our results revealed a low probability (12%) of poacher detection during patrols. Poaching distribution was best explained by prey availability, indicating that poachers target areas with high concentrations of ungulates. Poaching pressure was estimated to be high (>0.49) in 39% of our study area. To alleviate poaching pressure, we recommend ramping up patrolling intensity in 12% of the national park, which could be achievable by reducing excess patrols in about 20% of the park.
However, our results suggest that for 27% of the park, it is necessary to improve patrolling quality to increase detection probability of poaching, for example, by closing temporal patrolling gaps or expanding informant networks. Our approach illustrates that analog ranger logbooks are an untapped resource for evidence-based and adaptive planning of protected area management. Using this wealth of data can open up new avenues to better understand poaching and its determinants, to expand effectiveness assessments to the past, and, more generally, to allow for strategic conservation planning in protected areas.
KW - illegal hunting
KW - large herbivores
KW - megafauna
KW - occupancy modeling
KW - patrolling optimization
KW - protected area
KW - rangers
KW - ungulates
Y1 - 2022
U6 - https://doi.org/10.1002/eap.2601
SN - 1051-0761
SN - 1939-5582
VL - 32
IS - 5
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Wendering, Philipp
A1 - Nikoloski, Zoran
T1 - COMMIT
BT - Consideration of metabolite leakage and community composition improves microbial community reconstructions
JF - PLoS Computational Biology : a new community journal / publ. by the Public Library of Science (PLoS) in association with the International Society for Computational Biology (ISCB)
N2 - Composition and functions of microbial communities affect important traits in diverse hosts, from crops to humans. Yet, mechanistic understanding of how metabolism of individual microbes is affected by the community composition and metabolite leakage is lacking. Here, we first show that the consensus of automatically generated metabolic reconstructions improves the quality of the draft reconstructions, measured by comparison to reference models. We then devise an approach for gap filling, termed COMMIT, that considers metabolites for secretion based on their permeability and the composition of the community. By applying COMMIT with two soil communities from the Arabidopsis thaliana culture collection, we could significantly reduce the gap-filling solution in comparison to filling gaps in individual reconstructions without affecting the genomic support. Inspection of the metabolic interactions in the soil communities allows us to identify microbes with community roles of helpers and beneficiaries. Therefore, COMMIT offers a versatile fully automated solution for large-scale modelling of microbial communities for diverse biotechnological applications.
Author summaryMicrobial communities are important in ecology, human health, and crop productivity. However, detailed information on the interactions within natural microbial communities is hampered by the community size, lack of detailed information on the biochemistry of single organisms, and the complexity of interactions between community members. Metabolic models are comprised of biochemical reaction networks based on the genome annotation, and can provide mechanistic insights into community functions. Previous analyses of microbial community models have been performed with high-quality reference models or models generated using a single reconstruction pipeline. However, these models do not contain information on the composition of the community that determines the metabolites exchanged between the community members. In addition, the quality of metabolic models is affected by the reconstruction approach used, with direct consequences on the inferred interactions between community members. Here, we use fully automated consensus reconstructions from four approaches to arrive at functional models with improved genomic support while considering the community composition. We applied our pipeline to two soil communities from the Arabidopsis thaliana culture collection, providing only genome sequences. Finally, we show that the obtained models have 90% genomic support and demonstrate that the derived interactions are corroborated by independent computational predictions.
Y1 - 2022
U6 - https://doi.org/10.1371/journal.pcbi.1009906
SN - 1553-734X
SN - 1553-7358
VL - 18
IS - 3
PB - Public Library of Science
CY - San Fransisco
ER -
TY - JOUR
A1 - Küken, Anika
A1 - Langary, Damoun
A1 - Nikoloski, Zoran
T1 - The hidden simplicity of metabolic networks is revealed by multireaction dependencies
JF - Science Advances
N2 - Understanding the complexity of metabolic networks has implications for manipulation of their functions. The complexity of metabolic networks can be characterized by identifying multireaction dependencies that are challenging to determine due to the sheer number of combinations to consider. Here, we propose the concept of concordant complexes that captures multireaction dependencies and can be efficiently determined from the algebraic structure and operational constraints of metabolic networks. The concordant complexes imply the existence of concordance modules based on which the apparent complexity of 12 metabolic networks of organisms from all kingdoms of life can be reduced by at least 78%. A comparative analysis against an ensemble of randomized metabolic networks shows that the metabolic network of Escherichia coli contains fewer concordance modules and is, therefore, more tightly coordinated than expected by chance. Together, our findings demonstrate that metabolic networks are considerably simpler than what can be perceived from their structure alone.
Y1 - 2022
U6 - https://doi.org/10.1126/sciadv.abl6962
SN - 2375-2548
VL - 8
IS - 13
PB - American Assoc. for the Advancement of Science
CY - Washington
ER -
TY - JOUR
A1 - Omranian, Sara
A1 - Nikoloski, Zoran
T1 - CUBCO+: prediction of protein complexes based on min-cut network partitioning into biclique spanned subgraphs
JF - Applied Network Science
N2 - High-throughput proteomics approaches have resulted in large-scale protein–protein interaction (PPI) networks that have been employed for the prediction of protein complexes. However, PPI networks contain false-positive as well as false-negative PPIs that affect the protein complex prediction algorithms. To address this issue, here we propose an algorithm called CUBCO+ that: (1) employs GO semantic similarity to retain only biologically relevant interactions with a high similarity score, (2) based on link prediction approaches, scores the false-negative edges, and (3) incorporates the resulting scores to predict protein complexes. Through comprehensive analyses with PPIs from Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens, we show that CUBCO+ performs as well as the approaches that predict protein complexes based on recently introduced graph partitions into biclique spanned subgraphs and outperforms the other state-of-the-art approaches. Moreover, we illustrate that in combination with GO semantic similarity, CUBCO+ enables us to predict more accurate protein complexes in 36% of the cases in comparison to CUBCO as its predecessor.
KW - Protein complexes
KW - Protein–protein interaction
KW - Network clustering
KW - Species comparison
Y1 - 2022
U6 - https://doi.org/10.1007/s41109-022-00508-5
SN - 2364-8228
VL - 7
PB - Springer International Publishing
CY - Cham
ER -
TY - JOUR
A1 - Tong, Hao
A1 - Nankar, Amol N.
A1 - Liu, Jintao
A1 - Todorova, Velichka
A1 - Ganeva, Daniela
A1 - Grozeva, Stanislava
A1 - Tringovska, Ivanka
A1 - Pasev, Gancho
A1 - Radeva-Ivanova, Vesela
A1 - Gechev, Tsanko
A1 - Kostova, Dimitrina
A1 - Nikoloski, Zoran
T1 - Genomic prediction of morphometric and colorimetric traits in Solanaceous fruits
JF - Horticulture research
N2 - Selection of high-performance lines with respect to traits of interest is a key step in plant breeding. Genomic prediction allows to determine the genomic estimated breeding values of unseen lines for trait of interest using genetic markers, e.g. single-nucleotide polymorphisms (SNPs), and machine learning approaches, which can therefore shorten breeding cycles, referring to genomic selection (GS). Here, we applied GS approaches in two populations of Solanaceous crops, i.e. tomato and pepper, to predict morphometric and colorimetric traits. The traits were measured by using scoring-based conventional descriptors (CDs) as well as by Tomato Analyzer (TA) tool using the longitudinally and latitudinally cut fruit images. The GS performance was assessed in cross-validations of classification-based and regression-based machine learning models for CD and TA traits, respectively. The results showed the usage of TA traits and tag SNPs provide a powerful combination to predict morphology and color-related traits of Solanaceous fruits. The highest predictability of 0.89 was achieved for fruit width in pepper, with an average predictability of 0.69 over all traits. The multi-trait GS models are of slightly better predictability than single-trait models for some colorimetric traits in pepper. While model validation performs poorly on wild tomato accessions, the usage as many as one accession per wild species in the training set can increase the transferability of models to unseen populations for some traits (e.g. fruit shape for which predictability in unseen scenario increased from zero to 0.6). Overall, GS approaches can assist the selection of high-performance Solanaceous fruits in crop breeding.
Y1 - 2022
U6 - https://doi.org/10.1093/hr/uhac072
SN - 2052-7276
VL - 9
PB - Oxford Univ. Press
CY - Cary
ER -
TY - JOUR
A1 - Huß, Sebastian
A1 - Judd, Rika Siedah
A1 - Koper, Kaan
A1 - Maeda, Hiroshi A.
A1 - Nikoloski, Zoran
T1 - An automated workflow that generates atom mappings for large-scale metabolic models and its application to Arabidopsis thaliana
JF - The plant journal
N2 - Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determines cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux analysis (MFA), which relies on the patterns of isotope labeling of metabolites in the network. The application of MFA also requires a stoichiometric model with atom mappings that are currently not available for the majority of large-scale metabolic network models, particularly of plants. While automated approaches such as the Reaction Decoder Toolkit (RDT) can produce atom mappings for individual reactions, tracing the flow of individual atoms of the entire reactions across a metabolic model remains challenging. Here we establish an automated workflow to obtain reliable atom mappings for large-scale metabolic models by refining the outcome of RDT, and apply the workflow to metabolic models of Arabidopsis thaliana. We demonstrate the accuracy of RDT through a comparative analysis with atom mappings from a large database of biochemical reactions, MetaCyc. We further show the utility of our automated workflow by simulating N-15 isotope enrichment and identifying nitrogen (N)-containing metabolites which show enrichment patterns that are informative for flux estimation in future N-15-MFA studies of A. thaliana. The automated workflow established in this study can be readily expanded to other species for which metabolic models have been established and the resulting atom mappings will facilitate MFA and graph-theoretic structural analyses with large-scale metabolic networks.
KW - atom mapping
KW - genome-scale metabolic model
KW - isotopic labeling
KW - metabolic
KW - flux analysis
KW - technical advance
Y1 - 2022
U6 - https://doi.org/10.1111/tpj.15903
SN - 0960-7412
SN - 1365-313X
VL - 111
IS - 5
SP - 1486
EP - 1500
PB - Wiley-Blackwell
CY - Oxford [u.a.]
ER -
TY - JOUR
A1 - Wendt, Martin
A1 - Kulanek, Dustin
A1 - Varga, Zoltan
A1 - Rakosy, Laszlo
A1 - Schmitt, Thomas
T1 - Pronounced mito-nuclear discordance and various Wolbachia infections in the water ringlet Erebia pronoe have resulted in a complex phylogeographic structure
JF - Scientific reports
N2 - Several morphological and mitochondrial lineages of the alpine ringlet butterfly species Erebia pronoe have been described, indicating a complex phylogenetic structure. However, the existing data were insufficient and allow neither a reconstruction of the biogeographic history, nor an assessment of the genetic lineages. Therefore, we analysed mitochondrial (COI, NDI) and nuclear (EF1 alpha, RPS5) gene sequences and compared them with sequences from the sister species Erebia melas. Additionally, we combined this information with morphometric data of the male genitalia and the infection patterns with Wolbachia strains, based on a WSP analysis. We obtained a distinct phylogeographic structure within the E. pronoe-melas complex with eight well-distinguishable geographic groups, but also a remarkable mito-nuclear discordance. The mito-nuclear discordance in E. melas and E. pronoe glottis can be explained by different ages of Wolbachia infections with different Wolbachia strains, associated selective sweeps, and hybridisation inhibition. Additionally, we found indications for incipient speciation of E. pronoe glottis in the Pyrenees and a pronounced range dynamic within and among the other high mountain systems of Europe. Our results emphasize the importance of combined approaches in reconstructing biogeographic patterns and evaluating phylogeographic splits.
Y1 - 2022
U6 - https://doi.org/10.1038/s41598-022-08885-8
SN - 2045-2322
VL - 12
IS - 1
PB - Nature Portfolio
CY - Berlin
ER -
TY - JOUR
A1 - Habel, Jan Christian
A1 - Ulrich, Werner
A1 - Eberle, Jonas
A1 - Schmitt, Thomas
T1 - Species community structures of Afrotropical butterflies differ depending on the monitoring method
JF - Biodiversity and conservation
N2 - Standardised biodiversity assessment is crucial to understand community structures and population dynamics of animals.
There exist various methods to monitor biodiversity. Approaches differ depending on the target species group and the aim of study, and show advantages and disadvantages.
The obtained data and results are influenced by local environmental conditions and seasonal variability.
In a comparative approach, we studied butterfly diversity and community structure in the dryland savannah biome of south-eastern Kenya with two different methods, transect counts and bait trapping.
We repeatedly collected data throughout the dry and rainy seasons, in both near natural and anthropogenically influenced landscapes. Significantly more species and individuals were recorded by transect counts than by bait trapping, though the larger and more mobile Nymphalid species (and in particular representatives of the genus Charaxes) were comparatively overrepresented in traps.
The transect data revealed much more pronounced effects of land-use and seasonality than the trap data. These results show that the choice of data collection methods must depend on the general research question, habitat conditions and season. To study the relative variation of species diversity and abundance, the collection of a fraction of the total species diversity might be sufficient.
However, if the focus is on a largely complete recording of species diversity, the use of various collection methods is essential. More specifically, our data clearly demonstrate that transect counts represent a reasonable method for assessing butterfly diversity for the African dryland savannah region, but fails to fully capture occurrences of all species. Bait trapping can be used only as a supplementary method for assessing some few highly mobile low-density species.
KW - monitoring
KW - transect count
KW - bait trap
KW - population dynamic
KW - disturbance
KW - seasonality
Y1 - 2022
U6 - https://doi.org/10.1007/s10531-021-02332-2
SN - 0960-3115
SN - 1572-9710
VL - 31
IS - 1
SP - 245
EP - 259
PB - Springer
CY - Dordrecht
ER -
TY - JOUR
A1 - Reeve, Holly A.
A1 - Nicholson, Jake
A1 - Altaf, Farieha
A1 - Lonsdale, Thomas H.
A1 - Preissler, Janina
A1 - Lauterbach, Lars
A1 - Lenz, Oliver
A1 - Leimkühler, Silke
A1 - Hollmann, Frank
A1 - Paul, Caroline E.
A1 - Vincent, Kylie A.
T1 - A hydrogen-driven biocatalytic approach to recycling synthetic analogues of NAD(P)H
JF - Chemical communications : ChemComm
N2 - We demonstrate a recycling system for synthetic nicotinamide cofactor analogues using a soluble hydrogenase with turnover number of >1000 for reduction of the cofactor analogues by H-2.
Coupling this system to an ene reductase, we show quantitative conversion of N-ethylmaleimide to N-ethylsuccinimide.
The biocatalyst system retained >50% activity after 7 h.
Y1 - 2022
U6 - https://doi.org/10.1039/d2cc02411j
SN - 1359-7345
SN - 1364-548X
VL - 58
IS - 75
SP - 10540
EP - 10543
PB - Royal Society of Chemistry
CY - Cambridge
ER -
TY - JOUR
A1 - Krebs, Simon K.
A1 - Rakotoarinoro, Nathanael
A1 - Stech, Marlitt
A1 - Zemella, Anne
A1 - Kubick, Stefan
T1 - A CHO-based cell-free dual fluorescence reporter system for the straightforward assessment of amber suppression and scFv functionality
JF - Frontiers in Bioengineering and Biotechnology
N2 - Incorporation of noncanonical amino acids (ncAAs) with bioorthogonal reactive groups by amber suppression allows the generation of synthetic proteins with desired novel properties. Such modified molecules are in high demand for basic research and therapeutic applications such as cancer treatment and in vivo imaging. The positioning of the ncAA-responsive codon within the protein's coding sequence is critical in order to maintain protein function, achieve high yields of ncAA-containing protein, and allow effective conjugation. Cell-free ncAA incorporation is of particular interest due to the open nature of cell-free systems and their concurrent ease of manipulation. In this study, we report a straightforward workflow to inquire ncAA positions in regard to incorporation efficiency and protein functionality in a Chinese hamster ovary (CHO) cell-free system. As a model, the well-established orthogonal translation components Escherichia coli tyrosyl-tRNA synthetase (TyrRS) and tRNATyr(CUA) were used to site-specifically incorporate the ncAA p-azido-l-phenylalanine (AzF) in response to UAG codons. A total of seven ncAA sites within an anti-epidermal growth factor receptor (EGFR) single-chain variable fragment (scFv) N-terminally fused to the red fluorescent protein mRFP1 and C-terminally fused to the green fluorescent protein sfGFP were investigated for ncAA incorporation efficiency and impact on antigen binding. The characterized cell-free dual fluorescence reporter system allows screening for ncAA incorporation sites with high incorporation efficiency that maintain protein activity. It is parallelizable, scalable, and easy to operate. We propose that the established CHO-based cell-free dual fluorescence reporter system can be of particular interest for the development of antibody-drug conjugates (ADCs).
KW - expanded genetic code
KW - orthogonal system
KW - noncanonical amino acid
KW - unnatural amino acid
KW - antibody
KW - cell-free protein synthesis
KW - mRFP1
KW - sfGFP
Y1 - 2022
U6 - https://doi.org/10.3389/fbioe.2022.873906
SN - 2296-4185
VL - 10
PB - Frontiers Media
CY - Lausanne
ER -
TY - JOUR
A1 - Montes-Osuna, Nuria
A1 - Cernava, Tomislav
A1 - Gomez-Lama Cabanas, Carmen
A1 - Berg, Gabriele
A1 - Mercado-Blanco, Jesus
T1 - Identification of volatile organic compounds emitted by two beneficial endophytic pseudomonas strains from olive roots
JF - Plants
N2 - The production of volatile organic compounds (VOCs) represents a promising strategy of plant-beneficial bacteria to control soil-borne phytopathogens.
Pseudomonas sp. PICF6 and Pseudomonas simiae PICF7 are two indigenous inhabitants of olive roots displaying effective biological control against Verticillium dahliae. Additionally, strain PICF7 is able to promote the growth of barley and Arabidopsis thaliana, VOCs being involved in the growth of the latter species.
In this study, the antagonistic capacity of these endophytic bacteria against relevant phytopathogens (Verticillium spp., Rhizoctonia solani, Sclerotinia sclerotiorum and Fusarium oxysporum f.sp. lycopersici) was assessed. Under in vitro conditions, PICF6 and PICF7 were only able to antagonize representative isolates of V. dahliae and V. longisporum. Remarkably, both strains produced an impressive portfolio of up to twenty VOCs, that included compounds with reported antifungal (e.g., 1-undecene, (methyldisulfanyl) methane and 1-decene) or plant growth promoting (e.g., tridecane, 1-decene) activities. Moreover, their volatilomes differed strongly in the absence and presence of V. dahliae.
For example, when co incubated with the defoliating pathotype of V. dahliae, the antifungal compound 4-methyl-2,6-bis(2-methyl-2-propanyl)phenol was produced. Results suggest that volatiles emitted by these endophytes may differ in their modes of action, and that potential benefits for the host needs further investigation in planta.
KW - biological control agents
KW - olive rhizobacteria
KW - Pseudomonas sp
KW - PICF6
KW - Pseudomonas simiae PICF7
KW - root endophytes
KW - Verticillium dahliae
KW - volatilome
Y1 - 2022
U6 - https://doi.org/10.3390/plants11030318
SN - 2223-7747
VL - 11
IS - 3
PB - MDPI
CY - Basel
ER -
TY - JOUR
A1 - Aichner, Bernhard
A1 - Dubbert, David
A1 - Kiel, Christine
A1 - Kohnert, Katrin
A1 - Ogashawara, Igor
A1 - Jechow, Andreas
A1 - Harpenslager, Sarah-Faye
A1 - Hölker, Franz
A1 - Nejstgaard, Jens Christian
A1 - Grossart, Hans-Peter
A1 - Singer, Gabriel
A1 - Wollrab, Sabine
A1 - Berger, Stella Angela
T1 - Spatial and seasonal patterns of water isotopes in northeastern German lakes
JF - Earth system science data : ESSD
N2 - Water stable isotopes (delta O-18 and delta H-2) were analyzed in samples collected in lakes, associated with riverine systems in northeastern Germany, throughout 2020. The dataset (Aichner et al., 2021; https://doi.org/10.1594/PANGAEA.935633) is derived from water samples collected at (a) lake shores (sampled in March and July 2020), (b) buoys which were temporarily installed in deep parts of the lake (sampled monthly from March to October 2020), (c) multiple spatially distributed spots in four selected lakes (in September 2020), and (d) the outflow of Muggelsee (sampled biweekly from March 2020 to January 2021). At shores, water was sampled with a pipette from 40-60 cm below the water surface and directly transferred into a measurement vial, while at buoys a Limnos water sampler was used to obtain samples from 1 m below the surface. Isotope analysis was conducted at IGB Berlin, using a Picarro L2130-i cavity ring-down spectrometer, with a measurement uncertainty of < 0.15 parts per thousand (delta O-18) and < 0.0 parts per thousand (delta H-2). The data give information about the vegetation period and the full seasonal isotope amplitude in the sampled lakes and about spatial isotope variability in different branches of the associated riverine systems.
Y1 - 2022
U6 - https://doi.org/10.5194/essd-14-1857-2022
SN - 1866-3508
SN - 1866-3516
VL - 14
IS - 4
SP - 1857
EP - 1867
PB - Copernicus
CY - Göttingen
ER -
TY - JOUR
A1 - Villalba, Luis Alberto
A1 - Karnatak, Rajat
A1 - Grossart, Hans-Peter
A1 - Wollrab, Sabine
T1 - Flexible habitat choice of pelagic bacteria increases system stability and energy flow through the microbial loop
JF - Limnology and oceanography : L & O
N2 - Pelagic bacteria can be classified into free-living and particle-attached life modes, which either dwell in the water column or attach to suspended particles. Bacteria with a generalist life style, however, can actively shift between these two habitats. Globally increasing densities of natural and artificial particles enhance habitat heterogeneity, with potential consequences for system stability and trophic transfer through aquatic food webs. To better decipher the dynamics of microbial communities, we investigated the influence of adaptive vs. fixed habitat choice on species coexistence for a simplified bacterial community by analyzing a corresponding food web model, consisting of two specialist bacterial prey species (free and attached), a generalist bacterial prey species with the ability to shift between both habitats, and two protist predators, specialized on either water or particle compartment. For simplicity we assume a shared resource pool, considering particles only for colonization but not as a source for nutrients or carbon, that is, inert particles like microplastics or inorganic sediments. The model predicts coexistence on a cyclic attractor between fixed and flexible bacteria, if the costs for adaptive habitat choice can be balanced by adaptation speed. The presence of adaptive prey dampens predator-prey cycle amplitudes, contributing to system stabilization resulting in higher mean predator biomass compared to specialist prey only. Thus, in pelagic microbial systems, flexible habitat choice at the prey level has important implications for system stability and magnitude of energy flow through the microbial loop.
Y1 - 2022
U6 - https://doi.org/10.1002/lno.12091
SN - 0024-3590
SN - 1939-5590
VL - 67
IS - 6
SP - 1402
EP - 1415
PB - Wiley-Blackwell
CY - Oxford [u.a.]
ER -
TY - JOUR
A1 - Ilicic, Doris
A1 - Grossart, Hans-Peter
T1 - Basal parasitic fungi in marine food webs-a mystery yet to unravel
JF - Journal of Fungi
N2 - Although aquatic and parasitic fungi have been well known for more than 100 years, they have only recently received increased awareness due to their key roles in microbial food webs and biogeochemical cycles. There is growing evidence indicating that fungi inhabit a wide range of marine habitats, from the deep sea all the way to surface waters, and recent advances in molecular tools, in particular metagenome approaches, reveal that their diversity is much greater and their ecological roles more important than previously considered. Parasitism constitutes one of the most widespread ecological interactions in nature, occurring in almost all environments. Despite that, the diversity of fungal parasites, their ecological functions, and, in particular their interactions with other microorganisms remain largely speculative, unexplored and are often missing from current theoretical concepts in marine ecology and biogeochemistry. In this review, we summarize and discuss recent research avenues on parasitic fungi and their ecological potential in marine ecosystems, e.g., the fungal shunt, and emphasize the need for further research.
KW - basal fungi
KW - parasites
KW - Chytridiomycota
KW - Rozellomycota
KW - food web
KW - biological carbon pump
Y1 - 2022
U6 - https://doi.org/10.3390/jof8020114
SN - 2309-608X
VL - 8
IS - 2
PB - MDPI
CY - Basel
ER -
TY - JOUR
A1 - Mbebi, Alain J.
A1 - Breitler, Jean-Christophe
A1 - Bordeaux, M'elanie
A1 - Sulpice, Ronan
A1 - McHale, Marcus
A1 - Tong, Hao
A1 - Toniutti, Lucile
A1 - Castillo, Jonny Alonso
A1 - Bertrand, Benoit
A1 - Nikoloski, Zoran
T1 - A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids
JF - G3: Genes, genomes, genetics
N2 - Genomic prediction has revolutionized crop breeding despite remaining issues of transferability of models to unseen environmental conditions and environments. Usage of endophenotypes rather than genomic markers leads to the possibility of building phenomic prediction models that can account, in part, for this challenge. Here, we compare and contrast genomic prediction and phenomic prediction models for 3 growth-related traits, namely, leaf count, tree height, and trunk diameter, from 2 coffee 3-way hybrid populations exposed to a series of treatment-inducing environmental conditions. The models are based on 7 different statistical methods built with genomic markers and ChlF data used as predictors. This comparative analysis demonstrates that the best-performing phenomic prediction models show higher predictability than the best genomic prediction models for the considered traits and environments in the vast majority of comparisons within 3-way hybrid populations. In addition, we show that phenomic prediction models are transferrable between conditions but to a lower extent between populations and we conclude that chlorophyll a fluorescence data can serve as alternative predictors in statistical models of coffee hybrid performance. Future directions will explore their combination with other endophenotypes to further improve the prediction of growth-related traits for crops.
KW - genomic prediction
KW - phenomic prediction
KW - 3-way coffee hybrids
KW - chlorophyll a fluorescence
KW - GenPred
KW - Shared Data Resource
Y1 - 2022
U6 - https://doi.org/10.1093/g3journal/jkac170
SN - 2160-1836
VL - 12
IS - 9
PB - Genetics Soc. of America
CY - Pittsburgh, PA
ER -
TY - JOUR
A1 - Malacrinò, Antonino
A1 - Abdelfattah, Ahmed
A1 - Berg, Gabriele
A1 - Benitez, Maria-Soledad
A1 - Bennett, Alison E.
A1 - Böttner, Laura
A1 - Xu, Shuqing
A1 - Schena, Leonardo
T1 - Exploring microbiomes for plant disease management
JF - Biological control : theory and application in pest management
N2 - Microbiome science is revolutionizing many concepts of plant biology, ecology, and evolution.
Understanding plant microbiomes is key to developing solutions that protect crop health without impacting the environment.
In this perspective article, we highlight the importance of both the structure and functions of plant-associated microbial communities in protecting their host from pathogens.
These new findings have a high potential to aid biocontrol programs and to replace traditional chemical products, guiding the transition towards a sustainable production.
KW - microbiota
KW - metagenomics
KW - plant pathogen
KW - plant protection
Y1 - 2022
U6 - https://doi.org/10.1016/j.biocontrol.2022.104890
SN - 1049-9644
SN - 1090-2112
VL - 169
PB - Academic Press
CY - San Diego, Calif.
ER -
TY - JOUR
A1 - Moradian, Hanieh
A1 - Roch, Toralf
A1 - Anthofer, Larissa
A1 - Lendlein, Andreas
A1 - Gossen, Manfred
T1 - Chemical modification of uridine modulates mRNA-mediated proinflammatory and antiviral response in primary human macrophages
JF - Molecular therapy
N2 - In vitro transcribed (IVT)-mRNA has been accepted as a promising therapeutic modality. Advances in facile and rapid production technologies make IVT-mRNA an appealing alternative to protein- or virus-based medicines.
Robust expression levels, lack of genotoxicity, and their manageable immunogenicity benefit its clinical applicability.
We postulated that innate immune responses of therapeutically relevant human cells can be tailored or abrogated by combinations of 5'-end and internal IVT-mRNA modifications.
Using primary human macrophages as targets, our data show the particular importance of uridine modifications for IVT-mRNA performance.
Among five nucleotide modification schemes tested, 5-methoxy-uridine outperformed other modifications up to 4-fold increased transgene expression, triggering moderate proinflammatory and non-detectable antiviral responses.
Macrophage responses against IVT-mRNAs exhibiting high immunogenicity (e.g., pseudouridine) could be minimized upon HPLC purification. Conversely, 5'-end modifications had only modest effects on mRNA expression and immune responses.
Our results revealed how the uptake of chemically modified IVT-mRNA impacts human macrophages, responding with distinct patterns of innate immune responses concomitant with increased transient transgene expression.
We anticipate our findings are instrumental to predictively address specific cell responses required for a wide range of therapeutic applications from eliciting controlled immunogenicity in mRNA vaccines to, e.g., completely abrogating cell activation in protein replacement therapies.
Y1 - 2022
U6 - https://doi.org/10.1016/j.omtn.2022.01.004
SN - 2162-2531
VL - 27
SP - 854
EP - 869
PB - Cell Press
CY - Cambridge
ER -
TY - JOUR
A1 - Weyrich, Alexandra
A1 - Guerrero-Altamirano, Tania P.
A1 - Yasar, Selma
A1 - Czirjak, Gábor-Árpád
A1 - Wachter, Bettina
A1 - Fickel, Jörns
T1 - First Steps towards the development of epigenetic biomarkers in female cheetahs (Acinonyx jubatus)
JF - Life : open access journal
N2 - Free-ranging cheetahs (Acinonyx jubatus) are generally healthy, whereas cheetahs under human care, such as those in zoological gardens, suffer from ill-defined infectious and degenerative pathologies. These differences are only partially explained by husbandry management programs because both groups share low genetic diversity. However, mounting evidence suggests that physiological differences between populations in different environments can be tracked down to differences in epigenetic signatures. Here, we identified differentially methylated regions (DMRs) between free-ranging cheetahs and conspecifics in zoological gardens and prospect putative links to pathways relevant to immunity, energy balance and homeostasis. Comparing epigenomic DNA methylation profiles obtained from peripheral blood mononuclear cells (PBMCs) from eight free-ranging female cheetahs from Namibia and seven female cheetahs living in zoological gardens within Europe, we identified DMRs of which 22 were hypermethylated and 23 hypomethylated. Hypermethylated regions in cheetahs under human care were located in the promoter region of a gene involved in host-pathogen interactions (KLC1) and in an intron of a transcription factor relevant for the development of pancreatic beta-cells, liver, and kidney (GLIS3). The most canonical mechanism of DNA methylation in promoter regions is assumed to repress gene transcription. Taken together, this could indicate that hypermethylation at the promoter region of KLC1 is involved in the reduced immunity in cheetahs under human care. This approach can be generalized to characterize DNA methylation profiles in larger cheetah populations under human care with a more granular longitudinal data collection, which, in the future, could be used to monitor the early onset of pathologies, and ultimately translate into the development of biomarkers with prophylactic and/or therapeutic potential.
KW - animals under human care
KW - captivity
KW - carnivore
KW - DNA methylation;
KW - felidae
KW - free-ranging
KW - wildlife
Y1 - 2022
U6 - https://doi.org/10.3390/life12060920
SN - 2075-1729
VL - 12
IS - 6
PB - MDPI
CY - Basel
ER -
TY - JOUR
A1 - Zappa, Luca
A1 - Schlaffer, Stefan
A1 - Brocca, Luca
A1 - Vreugdenhil, Mariette
A1 - Nendel, Claas
A1 - Dorigo, Wouter
T1 - How accurately can we retrieve irrigation timing and water amounts from (satellite) soil moisture?
JF - International journal of applied earth observation and geoinformation
N2 - While ensuring food security worldwide, irrigation is altering the water cycle and generating numerous environmental side effects. As detailed knowledge about the timing and the amounts of water used for irrigation over large areas is still lacking, remotely sensed soil moisture has proved potential to fill this gap.
However, the spatial resolution and revisit time of current satellite products represent a major limitation to accurately estimating irrigation. This work aims to systematically quantify their impact on the retrieved irrigation information, hence assessing the value of satellite soil moisture for estimating irrigation timing and water amounts.
In a real-world experiment, we modeled soil moisture using actual irrigation and meteorological data, obtained from farmers and weather stations, respectively. Modeled soil moisture was compared against various remotely sensed products differing in terms of spatio-temporal resolution to test the hypothesis that high-resolution observations can disclose the irrigation signal from individual fields while coarse-scale satellite products cannot.
Then, in a synthetic experiment, we systematically investigated the effect of soil moisture spatial and temporal resolution on the accuracy of irrigation estimates. The analysis was further elaborated by considering different irrigation scenarios and by adding realistic amounts of random errors in the soil moisture time series.
We show that coarse-scale remotely sensed soil moisture products achieve higher correlations with rainfed simulations, while high-resolution satellite observations agree significantly better with irrigated simulations, suggesting that high-resolution satellite soil moisture can inform on field-scale (similar to 40 ha) irrigation. A thorough analysis of the synthetic dataset showed that satisfactory results, both in terms of detection (F-score > 0.8) and quantification (Pearson's correlation > 0.8), are found for noise-free soil moisture observations either with a temporal sampling up to 3 days or if at least one-third of the pixel covers the irrigated field(s).
However, irrigation water amounts are systematically underestimated for temporal samplings of more than one day, and decrease proportionally to the spatial resolution, i.e., coarsening the pixel size leads to larger irrigation underestimations.
Although lower spatial and temporal resolutions decrease the detection and quantification accuracies (e.g., R between 0.6 and 1 depending on the irrigation rate and spatio-temporal resolution), random errors in the soil moisture time series have a stronger negative impact (Pearson R always smaller than 0.85).
As expected, better performances are found for higher irrigation rates, i.e. when more water is supplied during an irrigation event. Despite the potentially large underestimations, our results suggest that high-resolution satellite soil moisture has the potential to track and quantify irrigation, especially over regions where large volumes of irrigation water are applied to the fields, and given that low errors affect the soil moisture observations.
KW - remote sensing
KW - soil moisture
KW - irrigation
KW - detection
KW - quantification
KW - sentinel-1
Y1 - 2022
U6 - https://doi.org/10.1016/j.jag.2022.102979
SN - 1569-8432
SN - 1872-826X
VL - 113
PB - Elsevier
CY - Amsterdam
ER -
TY - JOUR
A1 - Ionescu, Danny
A1 - Bizic, Mina
A1 - Karnatak, Rajat
A1 - Musseau, Camille L.
A1 - Onandia, Gabriela
A1 - Kasada, Minoru
A1 - Berger, Stella A.
A1 - Nejstgaard, Jens Christian
A1 - Ryo, Masahiro
A1 - Lischeid, Gunnar
A1 - Gessner, Mark O.
A1 - Wollrab, Sabine
A1 - Grossart, Hans-Peter
T1 - From microbes to mammals: Pond biodiversity homogenization across different land-use types in an agricultural landscape
JF - Ecological monographs
N2 - Local biodiversity patterns are expected to strongly reflect variation in topography, land use, dispersal boundaries, nutrient supplies, contaminant spread, management practices, and other anthropogenic influences. Contrary to this expectation, studies focusing on specific taxa revealed a biodiversity homogenization effect in areas subjected to long-term intensive industrial agriculture. We investigated whether land use affects biodiversity levels and community composition (alpha- and beta-diversity) in 67 kettle holes (KH) representing small aquatic islands embedded in the patchwork matrix of a largely agricultural landscape comprising grassland, forest, and arable fields. These KH, similar to millions of standing water bodies of glacial origin, spread across northern Europe, Asia, and North America, are physico-chemically diverse and differ in the degree of coupling with their surroundings. We assessed aquatic and sediment biodiversity patterns of eukaryotes, Bacteria, and Archaea in relation to environmental features of the KH, using deep-amplicon-sequencing of environmental DNA (eDNA). First, we asked whether deep sequencing of eDNA provides a representative picture of KH aquatic biodiversity across the Bacteria, Archaea, and eukaryotes. Second, we investigated if and to what extent KH biodiversity is influenced by the surrounding land use. We hypothesized that richness and community composition will greatly differ in KH from agricultural land use compared with KH in grasslands and forests. Our data show that deep eDNA amplicon sequencing is useful for in-depth assessments of cross-domain biodiversity comprising both micro- and macro-organisms, but has limitations with respect to single-taxa conservation studies. Using this broad method, we show that sediment eDNA, integrating several years to decades, depicts the history of agricultural land-use intensification. Aquatic biodiversity was best explained by seasonality, whereas land-use type explained little of the variation. We concluded that, counter to our hypothesis, land use intensification coupled with landscape wide nutrient enrichment (including atmospheric deposition), groundwater connectivity between KH and organismal (active and passive) dispersal in the tight network of ponds, resulted in a biodiversity homogenization in the KH water, leveling off today's detectable differences in KH biodiversity between land-use types. These findings have profound implications for measures and management strategies to combat current biodiversity loss in agricultural landscapes worldwide.
KW - biodiversity homogenization
KW - eDNA
KW - intensive agriculture
KW - kettle hole;
KW - land use
Y1 - 2022
U6 - https://doi.org/10.1002/ecm.1523
SN - 0012-9615
SN - 1557-7015
VL - 92
IS - 3
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Souto-Veiga, Rodrigo
A1 - Groeneveld, Juergen
A1 - Enright, Neal J.
A1 - Fontaine, Joseph B.
A1 - Jeltsch, Florian
T1 - Declining pollination success reinforces negative climate and fire change impacts in a serotinous, fire-killed plant
JF - Plant ecology : an international journal
N2 - Climate change projections predict that Mediterranean-type ecosystems (MTEs) are becoming hotter and drier and that fires will become more frequent and severe.
While most plant species in these important biodiversity hotspots are adapted to hot, dry summers and recurrent fire, the Interval Squeeze framework suggests that reduced seed production (demographic shift), reduced seedling establishment after fire (post fire recruitment shift), and reduction in the time between successive fires (fire interval shift) will threaten fire killed species under climate change.
One additional potential driver of accelerated species decline, however, has not been considered so far: the decrease in pollination success observed in many ecosystems worldwide has the potential to further reduce seed accumulation and thus population persistence also in these already threatened systems.
Using the well-studied fire-killed and serotinous shrub species Banksia hookeriana as an example, we apply a new spatially implicit population simulation model to explore population dynamics under past (1988-2002) and current (2003-2017) climate conditions, deterministic and stochastic fire regimes, and alternative scenarios of pollination decline.
Overall, model results suggest that while B. hookeriana populations were stable under past climate conditions, they will not continue to persist under current (and prospective future) climate.
Negative effects of climatic changes and more frequent fires are reinforced by the measured decline in seed set leading to further reduction in the mean persistence time by 12-17%.
These findings clearly indicate that declining pollination rates can be a critical factor that increases further the pressure on the persistence of fire-killed plants.
Future research needs to investigate whether other fire-killed species are similarly threatened, and if local population extinction may be compensated by recolonization events, facilitating persistence in spatially structured meta-communities.
KW - climate change
KW - fire frequency
KW - interval squeeze
KW - pollination
KW - process-based simulation model
KW - mediterranean-type ecosystem
Y1 - 2022
U6 - https://doi.org/10.1007/s11258-022-01244-7
SN - 1385-0237
SN - 1573-5052
VL - 223
IS - 7
SP - 863
EP - 881
PB - Springer
CY - Dordrecht
ER -
TY - JOUR
A1 - Hagberg, Linda
A1 - Celemin, Enrique
A1 - Irisarri, Iker
A1 - Hawlitschek, Oliver
A1 - Bella, Jose L.
A1 - Mott, Tami
A1 - Pereira, Ricardo J.
T1 - Extensive introgression at late stages of species formation
BT - insights from grasshopper hybrid zones
JF - Molecular ecology
N2 - The process of species formation is characterized by the accumulation of multiple reproductive barriers. The evolution of hybrid male sterility, or Haldane's rule, typically characterizes later stages of species formation, when reproductive isolation is strongest.
Yet, understanding how quickly reproductive barriers evolve and their consequences for maintaining genetic boundaries between emerging species remains a challenging task because it requires studying taxa that hybridize in nature.
Here, we address these questions using the meadow grasshopper Pseudochorthippus parallelus, where populations that show multiple reproductive barriers, including hybrid male sterility, hybridize in two natural hybrid zones. Using mitochondrial data, we infer that such populations diverged some 100,000 years ago, at the beginning of the last glacial cycle in Europe.
Nuclear data show that contractions at multiple glacial refugia, and post-glacial expansions have facilitated genetic differentiation between lineages that today interact in hybrid zones.
We find extensive introgression throughout the sampled species range, irrespective of the current strength of reproductive isolation. Populations exhibiting hybrid male sterility in two hybrid zones show repeatable patterns of genomic differentiation, consistent with shared genomic constraints affecting ancestral divergence or with the role of those regions in reproductive isolation.
Together, our results suggest that reproductive barriers that characterize late stages of species formation can evolve relatively quickly, particularly when associated with strong demographic changes. Moreover, we show that such barriers persist in the face of extensive gene flow, allowing future studies to identify associated genomic regions.
KW - Haldane's rule
KW - hybridization
KW - Pseudochorthippus parallelus
KW - speciation
KW - sterility
Y1 - 2022
U6 - https://doi.org/10.1111/mec.16406
SN - 0962-1083
SN - 1365-294X
VL - 31
IS - 8
SP - 2384
EP - 2399
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Schittko, Conrad
A1 - Onandia, Gabriela
A1 - Bernard-Verdier, Maud
A1 - Heger, Tina
A1 - Jeschke, Jonathan M.
A1 - Kowarik, Ingo
A1 - Maaß, Stefanie
A1 - Joshi, Jasmin
T1 - Biodiversity maintains soil multifunctionality and soil organic carbon in novel urban ecosystems
JF - Journal of ecology
N2 - Biodiversity in urban ecosystems has the potential to increase ecosystem functions and support a suite of services valued by society, including services provided by soils. Specifically, the sequestration of carbon in soils has often been advocated as a solution to mitigate the steady increase in CO2 concentration in the atmosphere as a key driver of climate change. However, urban ecosystems are also characterized by an often high level of ecological novelty due to profound human-mediated changes, such as the presence of high numbers of non-native species, impervious surfaces or other disturbances. Yet it is poorly understood whether and how biodiversity affects ecosystem functioning and services of urban soils under these novel conditions. In this study, we assessed the influence of above- and below-ground diversity, as well as urbanization and plant invasions, on multifunctionality and organic carbon stocks of soils in non-manipulated grasslands along an urbanization gradient in Berlin, Germany. We focused on plant diversity (measured as species richness and functional trait diversity) and, in addition, on soil organism diversity as a potential mediator for the relationship of plant species diversity and ecosystem functioning. Our results showed positive effects of plant diversity on soil multifunctionality and soil organic carbon stocks along the entire gradient. Structural equation models revealed that plant diversity enhanced soil multifunctionality and soil organic carbon by increasing the diversity of below-ground organisms. These positive effects of plant diversity on soil multifunctionality and soil fauna were not restricted to native plant species only, but were also exerted by non-native species, although to a lesser degree. Synthesis. We conclude that enhancing diversity in plants and soil fauna of urban grasslands can increase the multifunctionality of urban soils and also add to their often underestimated but very valuable role in mitigating effects of climate change.
KW - Anthropocene
KW - biological invasions
KW - ecosystem function and services;
KW - functional diversity
KW - global change
KW - non-native species
KW - novel
KW - ecosystems
KW - urbanization
Y1 - 2022
U6 - https://doi.org/10.1111/1365-2745.13852
SN - 0022-0477
SN - 1365-2745
VL - 110
IS - 4
SP - 916
EP - 934
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Hilgers, Leon
A1 - Hartmann, Stefanie
A1 - Pfaender, Jobst
A1 - Lentge-Maass, Nora
A1 - Marwoto, Ristiyanti M.
A1 - von Rintelen, Thomas
A1 - Hofreiter, Michael
T1 - Evolutionary divergence and radula diversification in two ecomorphs from an adaptive radiation of freshwater snails
JF - Genes
N2 - (1) Background:
Adaptive diversification of complex traits plays a pivotal role in the evolution of organismal diversity. In the freshwater snail genus Tylomelania, adaptive radiations were likely promoted by trophic specialization via diversification of their key foraging organ, the radula.
(2) Methods:
To investigate the molecular basis of radula diversification and its contribution to lineage divergence, we used tissue-specific transcriptomes of two sympatric Tylomelania sarasinorum ecomorphs.
(3) Results:
We show that ecomorphs are genetically divergent lineages with habitat-correlated abundances. Sequence divergence and the proportion of highly differentially expressed genes are significantly higher between radula transcriptomes compared to the mantle and foot. However, the same is not true when all differentially expressed genes or only non-synonymous SNPs are considered. Finally, putative homologs of some candidate genes for radula diversification (hh, arx, gbb) were also found to contribute to trophic specialization in cichlids and Darwin's finches.
(4) Conclusions:
Our results are in line with diversifying selection on the radula driving Tylomelania ecomorph divergence and indicate that some molecular pathways may be especially prone to adaptive diversification, even across phylogenetically distant animal groups.
KW - speciation
KW - adaptive radiation
KW - molluscs
KW - RNAseq
KW - regulatory evolution
KW - trophic specialization
Y1 - 2022
U6 - https://doi.org/10.3390/genes13061029
SN - 2073-4425
VL - 13
IS - 6
PB - MDPI
CY - Basel
ER -
TY - JOUR
A1 - Escalante, Ignacio
A1 - Dominguez, Marisol
A1 - Gomez-Ruiz, Daisy Alejandra
A1 - Machado, Glauco
T1 - Benefits and costs of mixed-species aggregations in Harvestmen (Arachnida: Opiliones)
JF - Frontiers in ecology and evolution
N2 - Many animals form aggregations with individuals of the same species (single-species aggregations, SSA). Less frequently, individuals may also aggregate with individuals of other species (mixed-species aggregations, MSA). Although the benefits and costs of SSA have been intensively studied, the same is not true for MSA. Here, we first review the cases of MSA in harvestmen, an arachnid order in which the records of MSA are more frequent than other arthropod orders. We then propose several benefits and costs of MSA in harvestmen, and contrast them with those of SSA. Second, using field-gathered data we describe gregariousness in seven species of Prionostemma harvestmen from Costa Rica. These species form MSA, but individuals are also found solitarily or in SSA. We tested one possible benefit and one possible cost of gregariousness in Prionostemma harvestmen. Regarding the benefit, we hypothesized that individuals missing legs would be more exposed to predation than eight-legged individuals and thus they should be found preferentially in aggregations, where they would be more protected from predators. Our data, however, do not support this hypothesis. Regarding the cost, we hypothesized that gregariousness increases the chances of parasitism. We found no support for this hypothesis either because both mite prevalence and infestation intensity did not differ between solitary or aggregated individuals. Additionally, the type of aggregation (SSA or MSA) was not associated with the benefit or the cost we explored. This lack of effect may be explained by the fluid membership of the aggregations, as we found high turnover over time in the number of individuals and species composition of the aggregations. In conclusion, we hope our review and empirical data stimulate further studies on MSA, which remains one of the most elusive forms of group living in animals.
KW - alarm signals
KW - aggregation size
KW - autotomy
KW - chemical defenses
KW - dilution
KW - effect
KW - ectoparasitism
KW - group living
KW - roosting site
Y1 - 2022
U6 - https://doi.org/10.3389/fevo.2021.766323
SN - 2296-701X
VL - 9
PB - Frontiers Media
CY - Lausanne
ER -
TY - JOUR
A1 - Raffeiner, Margot
A1 - Üstün, Suayib
A1 - Guerra, Tiziana
A1 - Spinti, Daniela
A1 - Fitzner, Maria
A1 - Sonnewald, Sophia
A1 - Baldermann, Susanne
A1 - Börnke, Frederik
T1 - The Xanthomonas type-III effector XopS stabilizes CaWRKY40a to regulate defense responses and stomatal immunity in pepper (Capsicum annuum)
JF - The plant cell
N2 - As a critical part of plant immunity, cells that are attacked by pathogens undergo rapid transcriptional reprogramming to minimize virulence. Many bacterial phytopathogens use type III effector (T3E) proteins to interfere with plant defense responses, including this transcriptional reprogramming. Here, we show that Xanthomonas outer protein S (XopS), a T3E of Xanthomonas campestris pv. vesicatoria (Xcv), interacts with and inhibits proteasomal degradation of WRKY40, a transcriptional regulator of defense gene expression. Virus-induced gene silencing of WRKY40 in pepper (Capsicum annuum) enhanced plant tolerance to Xcv infection, indicating that WRKY40 represses immunity. Stabilization of WRKY40 by XopS reduces the expression of its targets, which include salicylic acid-responsive genes and the jasmonic acid signaling repressor JAZ8. Xcv bacteria lacking XopS display significantly reduced virulence when surface inoculated onto susceptible pepper leaves. XopS delivery by Xcv, as well as ectopic expression of XopS in Arabidopsis thaliana or Nicotiana benthamiana, prevented stomatal closure in response to bacteria and biotic elicitors. Silencing WRKY40 in pepper or N. benthamiana abolished XopS's ability to prevent stomatal closure. This suggests that XopS interferes with both preinvasion and apoplastic defense by manipulating WRKY40 stability and downstream gene expression, eventually altering phytohormone crosstalk to promote pathogen proliferation.
Y1 - 2022
U6 - https://doi.org/10.1093/plcell/koac032
SN - 1040-4651
SN - 1532-298X
VL - 34
IS - 5
SP - 1684
EP - 1708
PB - Oxford Univ. Press
CY - Cary
ER -
TY - JOUR
A1 - Minutillo, Serena A.
A1 - Ruano-Rosa, David
A1 - Abdelfattah, Ahmed
A1 - Schena, Leonardo
A1 - Malacrino, Antonino
T1 - The fungal microbiome of wheat flour includes potential mycotoxin producers
JF - Foods
N2 - Consumers are increasingly demanding higher quality and safety standards for the products they consume, and one of this is wheat flour, the basis of a wide variety of processed products. This major component in the diet of many communities can be contaminated by microorganisms before the grain harvest, or during the grain storage right before processing. These microorganisms include several fungal species, many of which produce mycotoxins, secondary metabolites that can cause severe acute and chronic disorders. Yet, we still know little about the overall composition of fungal communities associated with wheat flour. In this study, we contribute to fill this gap by characterizing the fungal microbiome of different types of wheat flour using culture-dependent and -independent techniques. Qualitatively, these approaches suggested similar results, highlighting the presence of several fungal taxa able to produce mycotoxins. In-vitro isolation of fungal species suggest a higher frequency of Penicillium, while metabarcoding suggest a higher abundance of Alternaria. This discrepancy might reside on the targeted portion of the community (alive vs. overall) or in the specific features of each technique. Thus, this study shows that commercial wheat flour hosts a wide fungal diversity with several taxa potentially representing concerns for consumers, aspects that need more attention throughout the food production chain.
KW - Penicillium
KW - Alternaria
KW - post-harvest
KW - metabarcoding
Y1 - 2022
U6 - https://doi.org/10.3390/foods11050676
SN - 2304-8158
VL - 11
IS - 5
PB - MDPI
CY - Basel
ER -
TY - JOUR
A1 - Wassermann, Birgit
A1 - Abdelfattah, Ahmed
A1 - Wicaksono, Wisnu Adi
A1 - Kusstatscher, Peter
A1 - Müller, Henry
A1 - Cernava, Tomislav
A1 - Goertz, Simon
A1 - Rietz, Steffen
A1 - Abbadi, Amine
A1 - Berg, Gabriele
T1 - The Brassica napus seed microbiota is cultivar-specific and transmitted via paternal breeding lines
JF - Microbial biotechnology
N2 - Seed microbiota influence germination and plant health and have the potential to improve crop performance, but the factors that determine their structure and functions are still not fully understood.
Here, we analysed the impact of plant-related and external factors on seed endophyte communities of 10 different oilseed rape (Brassica napus L.) cultivars from 26 field sites across Europe.
All seed lots harboured a high abundance and diversity of endophytes, which were dominated by six genera: Ralstonia, Serratia, Enterobacter, Pseudomonas, Pantoea, and Sphingomonas.
The cultivar was the main factor explaining the variations in bacterial diversity, abundance and composition. In addition, the latter was significantly influenced by diverse biotic and abiotic factors, for example host germination rates and disease resistance against Plasmodiophora brassicae.
A set of bacterial biomarkers was identified to discriminate between characteristics of the seeds, for example Sphingomonas for improved germination and Brevundimonas for disease resistance.
Application of a Bayesian community approach suggested vertical transmission of seed endophytes, where the paternal parent plays a major role and might even determine the germination performance of the offspring.
This study contributes to the understanding of seed microbiome assembly and underlines the potential of the microbiome to be implemented in crop breeding and biocontrol programmes.
Y1 - 2022
U6 - https://doi.org/10.1111/1751-7915.14077
SN - 1751-7915
VL - 15
IS - 9
SP - 2379
EP - 2390
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Manna, Vincenzo
A1 - Zoccarato, Luca
A1 - Banchi, Elisa
A1 - Arnosti, Carol
A1 - Grossart, Hans-Peter
A1 - Celussi, Mauro
T1 - Linking lifestyle and foraging strategies of marine bacteria
BT - selfish behaviour of particle-attached bacteria in the northern Adriatic Sea
JF - Environmental microbiology reports
N2 - Microbe-mediated enzymatic hydrolysis of organic matter entails the production of hydrolysate, the recovery of which may be more or less efficient. The selfish uptake mechanism, recently discovered, allows microbes to hydrolyze polysaccharides and take up large oligomers, which are then degraded in the periplasmic space. By minimizing the hydrolysate loss, selfish behaviour may be profitable for free-living cells dwelling in a patchy substrate landscape. However, selfish uptake seems to be tailored to algal-derived polysaccharides, abundant in organic particles, suggesting that particle-attached microbes may use this strategy. We tracked selfish polysaccharides uptake in surface microbial communities of the northeastern Mediterranean Sea, linking the occurrence of this processing mode with microbial lifestyle. Additionally, we set up fluorescently labelled polysaccharides incubations supplying phytodetritus to investigate a 'pioneer' scenario for particle-attached microbes. Under both conditions, selfish behaviour was almost exclusively carried out by particle-attached microbes, suggesting that this mechanism may represent an advantage in the race for particle exploitation. Our findings shed light on the selfish potential of particle-attached microbes, suggesting multifaceted foraging strategies exerted by particle colonizers.
Y1 - 2022
U6 - https://doi.org/10.1111/1758-2229.13059
SN - 1758-2229
VL - 14
IS - 4
SP - 549
EP - 558
PB - Wiley
CY - Hoboken
ER -
TY - JOUR
A1 - Zhang, Kai
A1 - Hu, Jiege
A1 - Yang, Shuai
A1 - Xu, Wei
A1 - Wang, Zhichao
A1 - Zhuang, Peiwen
A1 - Grossart, Hans-Peter
A1 - Luo, Zhuhua
T1 - Biodegradation of polyester polyurethane by the marine fungus Cladosporium halotolerans 6UPA1
JF - Journal of hazardous materials
N2 - Lack of degradability and the accumulation of polymeric wastes increase the risk for the health of the environment. Recently, recycling of polymeric waste materials becomes increasingly important as raw materials for polymer synthesis are in short supply due to the rise in price and supply chain disruptions. As an important polymer, polyurethane (PU) is widely used in modern life, therefore, PU biodegradation is desirable to avoid its accumulation in the environment. In this study, we isolated a fungal strain Cladosporium halotolerans from the deep sea which can grow in mineral medium with a polyester PU (Impranil DLN) as a sole carbon source. Further, we demonstrate that it can degrade up to 80% of Impranil PU after 3 days of incubation at 28 celcius by breaking the carbonyl groups (1732 cm(-1)) and C-N-H bonds (1532 cm(-1) and 1247 cm(-1)) as confirmed by Fourier-transform infrared (FTIR) spectroscopy analysis. Gas chromatography-mass spectrometry (GC-MS) analysis revealed polyols and alkanes as PU degradation intermediates, indicating the hydrolysis of ester and urethane bonds. Esterase and urease activities were detected in 7 days-old cultures with PU as a carbon source. Transcriptome analysis showed a number of extracellular protein genes coding for enzymes such as cutinase, lipase, peroxidase and hydrophobic surface binding proteins A (HsbA) were expressed when cultivated on Impranil PU. The yeast two-hybrid assay revealed that the hydrophobic surface binding protein ChHsbA1 directly interacts with inducible esterases, ChLip1 (lipase) and ChCut1 (cutinase). Further, the KEGG pathway for "fatty acid degradation " was significantly enriched in Impranil PU inducible genes, indicating that the fungus may use the degradation intermediates to generate energy via this pathway. Taken together, our data indicates secretion of both esterase and hydrophobic surface binding proteins by C. halotolerans plays an important role in Impranil PU absorption and subsequent degradation. Our study provides a mechanistic insight into Impranil PU biodegradation by deep sea fungi and provides the basis for future development of biotechnological PU recycling.
KW - Impranil PU degradation
KW - Lipase
KW - Cutinase
KW - HsbA
KW - Fatty acid degradation
Y1 - 2022
U6 - https://doi.org/10.1016/j.jhazmat.2022.129406
SN - 0304-3894
SN - 1873-3336
VL - 437
PB - Elsevier
CY - Amsterdam
ER -
TY - JOUR
A1 - Perkins, Anita K.
A1 - Santos, Isaac R.
A1 - Rose, Andrew L.
A1 - Schulz, Kai G.
A1 - Grossart, Hans-Peter
A1 - Eyre, Bradley D.
A1 - Kelaher, Brendan P.
A1 - Oakes, Joanne M.
T1 - Production of dissolved carbon and alkalinity during macroalgal wrack degradation on beaches
BT - a mesocosm experiment with implications for blue carbon
JF - Biogeochemistry
N2 - Marine macroalgae are a key primary producer in coastal ecosystems, but are often overlooked in blue carbon inventories. Large quantities of macroalgal detritus deposit on beaches, but the fate of wrack carbon (C) is little understood. If most of the wrack carbon is respired back to CO2, there would be no net carbon sequestration. However, if most of the wrack carbon is converted to bicarbonate (alkalinity) or refractory DOC, wrack deposition would represent net carbon sequestration if at least part of the metabolic products (e.g., reduced Fe and S) are permanently removed (i.e., long-term burial) and the DOC is not remineralised. To investigate the release of macroalgal C via porewater and its potential to contribute to C sequestration (blue carbon), we monitored the degradation of Ecklonia radiata in flow-through mesocosms simulating tidal flushing on sandy beaches. Over 60 days, 81% of added E. radiata organic matter (OM) decomposed. Per 1 mol of detritus C, the degradation produced 0.48 +/- 0.34 mol C of dissolved organic carbon (DOC) (59%) and 0.25 +/- 0.07 mol C of dissolved inorganic carbon (DIC) (31%) in porewater, and a small amount of CO2 (0.3 +/- 0.0 mol C; ca. 3%) which was emitted to the atmosphere. A significant amount of carbonate alkalinity was found in porewater, equating to 33% (0.27 +/- 0.05 mol C) of the total degraded C. The degradation occurred in two phases. In the first phase (days 0-3), 27% of the OM degraded, releasing highly reactive DOC. In the second phase (days 4-60), the labile DOC was converted to DIC. The mechanisms underlying E. radiata degradation were sulphate reduction and ammonification. It is likely that the carbonate alkalinity was primarily produced through sulphate reduction. The formation of carbonate alkalinity and semi-labile or refractory DOC from beach wrack has the potential to play an overlooked role in coastal carbon cycling and contribute to marine carbon sequestration.
KW - Tidal pumping
KW - Organic matter degradation
KW - Carbon cycle
KW - Mineralisation
KW - Porewater exchange
KW - Submarine groundwater discharge
Y1 - 2022
U6 - https://doi.org/10.1007/s10533-022-00946-4
SN - 0168-2563
SN - 1573-515X
VL - 160
IS - 2
SP - 159
EP - 175
PB - Springer
CY - Dordrecht
ER -
TY - JOUR
A1 - Li, Zhen
A1 - Wang, Yongbo
A1 - Herzschuh, Ulrike
A1 - Cao, Xianyong
A1 - Ni, Jian
A1 - Zhao, Yan
T1 - Pollen-based biome reconstruction on the Qinghai-Tibetan Plateau during the past 15,000 years
JF - Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences
N2 - Reconstruction of past vegetation change is critical for better understanding the potential impact of future global change on the fragile alpine ecosystems of the Qinghai-Tibetan Plateau (QTP). In this paper, pollen assemblages comprising 58 records from the QTP, spanning the past 15 kyrs, were collected to reconstruct biome compositions using a standard approach. Six forest biomes were identified mainly on the southeastern plateau, exhibiting a pattern of gradual expansion along the eastern margin during early to mid-Holocene times. The alpine meadow biome was separately identified based on an updated scheme, and showed notable westward expansions towards lower latitudes and higher altitudes during early Holocene times. Consistent patterns of migration could also be identified for the alpine steppe biome, which moved eastward during the late Holocene after 4 ka. As the dominant biome type, temperate steppe was distributed widely over the QTP with minor migration patterns, except for a progressive expansion to lower altitudes in the late Holocene times. The desert biome was inferred mainly as covering the northwestern plateau and the Qaidam Basin, in relatively restricted areas. The spatial distribution of the reconstructed biomes represent the large-scale vegetation gradient on the QTP. Monsoonal precipitation expressed predominant controls on the development of alpine ecosystems, while the variations in desert vegetation responded to regional moisture brought by the mid-latitude Westerlies. Temperature changes played relatively minor roles in the variations of alpine vegetation, but exerted more significant impacts on the forest biomes.
KW - biomization
KW - pollen
KW - vegetation migration
KW - Qinghai-Tibetan Plateau
KW - holocene
Y1 - 2022
U6 - https://doi.org/10.1016/j.palaeo.2022.111190
SN - 0031-0182
SN - 1872-616X
VL - 604
PB - Elsevier
CY - Amsterdam
ER -
TY - JOUR
A1 - Alshareef, Nouf Owdah
A1 - Otterbach, Sophie L.
A1 - Allu, Annapurna Devi
A1 - Woo, Yong H.
A1 - de Werk, Tobias
A1 - Kamranfar, Iman
A1 - Müller-Röber, Bernd
A1 - Tester, Mark
A1 - Balazadeh, Salma
A1 - Schmöckel, Sandra M.
T1 - NAC transcription factors ATAF1 and ANAC055 affect the heat stress response in Arabidopsis
JF - Scientific reports
N2 - Pre-exposing (priming) plants to mild, non-lethal elevated temperature improves their tolerance to a later higher-temperature stress (triggering stimulus), which is of great ecological importance. 'Thermomemory' is maintaining this tolerance for an extended period of time. NAM/ATAF1/2/ CUC2 (NAC) proteins are plant-specific transcription factors (TFs) that modulate responses to abiotic stresses, including heat stress (HS). Here, we investigated the potential role of NACs for thermomemory. We determined the expression of 104 Ara bidopsis NAC genes after priming and triggering heat stimuli, and found ATAF1 expression is strongly induced right after priming and declines below control levels thereafter during thermorecovery. Knockout mutants of ATAF1 show better thermomemory than wild type, revealing a negative regulatory role. Differential expression analyses of RNA-seq data from ATAF1 overexpressor, ataf1 mutant and wild-type plants after heat priming revealed five genes that might be priming-associated direct targets of ATAF1: AT2G31260 (ATG9), AT2G41640 (GT61), AT3G44990 (XTH31), AT4G27720 and AT3G23540. Based on co-expression analyses applied to the aforementioned RNA-seq profiles, we identified ANAC055 to be transcriptionally co-regulated with ATAF1. Like atafl, anac055 mutants show improved thermomemory, revealing a potential co-control of both NACTFs over thermomemory. Our data reveals a core importance of two NAC transcription factors, ATAF1 and ANAC055, for thermomemory.
Y1 - 2022
U6 - https://doi.org/10.1038/s41598-022-14429-x
SN - 2045-2322
VL - 12
IS - 1
PB - Nature Research
CY - Berlin
ER -
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 - 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 -