TY - JOUR A1 - Riemann, Lasse A1 - Rahav, Eyal A1 - Passow, Uta A1 - Grossart, Hans-Peter A1 - de Beer, Dirk A1 - Klawonn, Isabell A1 - Eichner, Meri A1 - Benavides, Mar A1 - Bar-Zeev, Edo T1 - Planktonic aggregates as hotspots for heterotrophic diazotrophy: the plot thickens JF - Frontiers in microbiology N2 - Biological dinitrogen (N-2) fixation is performed solely by specialized bacteria and archaea termed diazotrophs, introducing new reactive nitrogen into aquatic environments. Conventionally, phototrophic cyanobacteria are considered the major diazotrophs in aquatic environments. However, accumulating evidence indicates that diverse non-cyanobacterial diazotrophs (NCDs) inhabit a wide range of aquatic ecosystems, including temperate and polar latitudes, coastal environments and the deep ocean. NCDs are thus suspected to impact global nitrogen cycling decisively, yet their ecological and quantitative importance remain unknown. Here we review recent molecular and biogeochemical evidence demonstrating that pelagic NCDs inhabit and thrive especially on aggregates in diverse aquatic ecosystems. Aggregates are characterized by reduced-oxygen microzones, high C:N ratio (above Redfield) and high availability of labile carbon as compared to the ambient water. We argue that planktonic aggregates are important loci for energetically-expensive N-2 fixation by NCDs and propose a conceptual framework for aggregate-associated N-2 fixation. Future studies on aggregate-associated diazotrophy, using novel methodological approaches, are encouraged to address the ecological relevance of NCDs for nitrogen cycling in aquatic environments. KW - aggregates KW - nitrogen fixation KW - heterotrophic bacteria KW - marine KW - aquatic KW - NCDs Y1 - 2022 U6 - https://doi.org/10.3389/fmicb.2022.875050 SN - 1664-302X VL - 13 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Zoccarato, Luca A1 - Sher, Daniel A1 - Miki, Takeshi A1 - Segre, Daniel A1 - Grossart, Hans-Peter T1 - A comparative whole-genome approach identifies bacterial traits for marine microbial interactions JF - Communications biology N2 - Luca Zoccarato, Daniel Sher et al. leverage publicly available bacterial genomes from marine and other environments to examine traits underlying microbial interactions. Their results provide a valuable resource to investigate clusters of functional and linked traits to better understand marine bacteria community assembly and dynamics. Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10% of genomes), phytohormones (3-8%) and different B vitamins (57-70%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics. Y1 - 2022 U6 - https://doi.org/10.1038/s42003-022-03184-4 SN - 2399-3642 VL - 5 IS - 1 PB - Springer Nature CY - Berlin ER - TY - JOUR A1 - Tolomeev, Aleksandr P. A1 - Dubovskaya, Olga P. A1 - Kirillin, Georgiy A1 - Buseva, Zhanna A1 - Kolmakova, Olesya A1 - Grossart, Hans-Peter A1 - Tang, Kam W. A1 - Gladyšev, Michail I. T1 - Degradation of dead cladoceran zooplankton and their contribution to organic carbon cycling in stratified lakes BT - field observation and model prediction JF - Journal of plankton research N2 - The contribution of dead zooplankton biomass to carbon cycle in aquatic ecosystems is practically unknown. Using abundance data of zooplankton in water column and dead zooplankton in sediment traps in Lake Stechlin, an ecological-mathematical model was developed to simulate the abundance and sinking of zooplankton carcasses and predict the related release of labile organic matter (LOM) into the water column. We found species-specific differences in mortality rate of the dominant zooplankton: Daphnia cucullata, Bosmina coregoni and Diaphanosoma brachyurum (0.008, 0.129 and 0.020 day(-1), respectively) and differences in their carcass sinking velocities in metalimnion (and hypolimnion): 2.1 (7.64), 14.0 (19.5) and 1.1 (5.9) m day(-1), respectively. Our model simulating formation and degradation processes of dead zooplankton predicted a bimodal distribution of the released LOM: epilimnic and metalimnic peaks of comparable intensity, ca. 1 mg DW m(-3) day(-1). Maximum degradation of carcasses up to ca. 1.7 mg DW m(-3) day(-1) occurred in the density gradient zone of metalimnion. LOM released from zooplankton carcasses into the surrounding water may stimulate microbial activity and facilitate microbial degradation of more refractory organic matter; therefore, dead zooplankton are expected to be an integral part of water column carbon source/sink dynamics in stratified lakes. KW - zooplankton carcasses KW - non-predatory mortality KW - sinking velocities KW - microbial degradation KW - Lake Stechlin KW - simulation modeling Y1 - 2022 U6 - https://doi.org/10.1093/plankt/fbac023 SN - 0142-7873 SN - 1464-3774 VL - 44 IS - 3 SP - 386 EP - 400 PB - Oxford Univ. Press CY - Oxford ER - TY - 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 - THES A1 - Hempel, Elisabeth T1 - Resolving the evolutionary history of two hippotragin antelopes using archival and ancient DNA N2 - African antelopes are iconic but surprisingly understudied in terms of their genetics, especially when it comes to their evolutionary history and genetic diversity. The age of genomics provides an opportunity to investigate evolution using whole nuclear genomes. Decreasing sequencing costs enable the recovery of multiple loci per genome, giving more power to single specimen analyses and providing higher resolution insights into species and populations that can help guide conservation efforts. This age of genomics has only recently begun for African antelopes. Many African bovids have a declining population trend and hence, are often endangered. Consequently, contemporary samples from the wild are often hard to collect. In these cases, ex situ samples from contemporary captive populations or in the form of archival or ancient DNA (aDNA) from historical museum or archaeological/paleontological specimens present a great research opportunity with the latter two even offering a window to information about the past. However, the recovery of aDNA is still considered challenging from regions with prevailing climatic conditions that are deemed adverse for DNA preservation like the African continent. This raises the question if DNA recovery from fossils as old as the early Holocene from these regions is possible. This thesis focuses on investigating the evolutionary history and genetic diversity of two species: the addax (Addax nasomaculatus) and the blue antelope (Hippotragus leucophaeus). The addax is critically endangered and might even already be extinct in the wild, while the blue antelope became extinct ~1800 AD, becoming the first extinct large African mammal species in historical times. Together, the addax and the blue antelope can inform us about current and past extinction events and the knowledge gained can help guide conservation efforts of threatened species. The three studies used ex situ samples and present the first nuclear whole genome data for both species. The addax study used historical museum specimens and a contemporary sample from a captive population. The two studies on the blue antelope used mainly historical museum specimens but also fossils, and resulted in the recovery of the oldest paleogenome from Africa at that time. The aim of the first study was to assess the genetic diversity and the evolutionary history of the addax. It found that the historical wild addax population showed only limited phylogeographic structuring, indicating that the addax was a highly mobile and panmictic population and suggesting that the current European captive population might be missing the majority of the historical mitochondrial diversity. It also found the nuclear and mitochondrial diversity in the addax to be rather low compared to other wild ungulate species. Suggestions on how to best save the remaining genetic diversity are presented. The European zoo population was shown to exhibit no or only minor levels of inbreeding, indicating good prospects for the restoration of the species in the wild. The trajectory of the addax’s effective population size indicated a major bottleneck in the late Pleistocene and a low effective population size well before recent human impact led to the species being critically endangered today. The second study set out to investigate the identities of historical blue antelope specimens using aDNA techniques. Results showed that six out of ten investigated specimens were misidentified, demonstrating the blue antelope to be one of the scarcest mammal species in historical natural history collections, with almost no bone reference material. The preliminary analysis of the mitochondrial genomes suggested a low diversity and hence low population size at the time of the European colonization of southern Africa. Study three presents the results of the analyses of two blue antelope nuclear genomes, one ~200 years old and another dating to the early Holocene, 9,800–9,300 cal years BP. A fossil-calibrated phylogeny dated the divergence time of the three historically extant Hippotragus species to ~2.86 Ma and demonstrated the blue and the sable antelope (H. niger) to be sister species. In addition, ancient gene flow from the roan (H. equinus) into the blue antelope was detected. A comparison with the roan and the sable antelope indicated that the blue antelope had a much lower nuclear diversity, suggesting a low population size since at least the early Holocene. This concurs with findings from the fossil record that show a considerable decline in abundance after the Pleistocene–Holocene transition. Moreover, it suggests that the blue antelope persisted throughout the Holocene regardless of a low population size, indicating that human impact in the colonial era was a major factor in the blue antelope’s extinction. This thesis uses aDNA analyses to provide deeper insights into the evolutionary history and genetic diversity of the addax and the blue antelope. Human impact likely was the main driver of extinction in the blue antelope, and is likely the main factor threatening the addax today. This thesis demonstrates the value of ex situ samples for science and conservation, and suggests to include genetic data for conservation assessments of species. It further demonstrates the beneficial use of aDNA for the taxonomic identification of historically important specimens in natural history collections. Finally, the successful retrieval of a paleogenome from the early Holocene of Africa using shotgun sequencing shows that DNA retrieval from samples of that age is possible from regions generally deemed unfavorable for DNA preservation, opening up new research opportunities. All three studies enhance our knowledge of African antelopes, contributing to the general understanding of African large mammal evolution and to the conservation of these and similarly threatened species. N2 - Afrikanische Antilopen sind sehr bekannte Tiere. Allerdings sind sie genetisch wenig untersucht, vor allem hinsichtlich ihrer Evolutionsgeschichte und genetischen Diversität. Das Zeitalter der Genomik ermöglicht es, Evolution mit Hilfe von kompletten nukleären Genomen zu untersuchen. Durch sinkende Sequenzierkosten können zahlreiche Genloci pro Genom gewonnen werden, wodurch Analysen mit nur einem Exemplar mehr Aussagekraft zukommt und tiefere Erkenntnisse über Arten und Populationen zulassen, die Artenschutzbemühungen unterstützen können. Für afrikanische Antilopen hat dieses Zeitalter gerade erst begonnen. Viele afrikanische Boviden haben einen sinkenden Populationstrend und sind daher häufig gefährdet. Dies erschwert es oft, Proben freilebender Tiere zu bekommen. In diesen Fällen bieten ex situ Proben von in Gefangenschaft lebenden Tieren oder in Form von alter DNA (aDNA) aus naturhistorischen Sammlungen eine gute Forschungsmöglichkeit. Letztere ermöglicht zudem den Zugang zu Informationen aus der Vergangenheit. Es gilt noch immer als Herausforderung, aDNA aus Regionen zu erlangen, deren Bedingungen schlecht für den Erhalt von DNA sind. Dies wirft die Frage auf, ob es möglich ist, aDNA aus Fossilien vom Beginn des Holozäns aus Afrika zu erhalten. Das Ziel dieser Doktorarbeit war die Erforschung der Evolutionsgeschichte und der genetischen Diversität der Mendesantilope (Addax nasomaculatus) und des Blaubocks (Hippotragus leucophaeus). Die Mendesantilope ist vom Aussterben bedroht und könnte in freier Wildbahn bereits ausgestorben sein. Der Blaubock starb ca. 1800 aus und war das erste afrikanische Großsäugetier, das in historischer Zeit ausstarb. Beide Arten können unsere Kenntnisse über derzeitige und vergangene Aussterbeereignisse erweitern, um den Schutz bedrohter Arten zu unterstützen. Die drei Studien dieser Doktorarbeit nutzten ex situ Proben und präsentieren die ersten kompletten nukleären Genome dieser beiden Arten. Die Studie über die Mendesantilope nutzte historische Präparate aus naturhistorischen Sammlungen sowie eine rezente Probe eines Tieres aus Gefangenschaft. Beide Blaubock-Studien nutzten vor allem Präparate aus naturhistorischen Sammlungen, aber auch Fossilien, woraus das zu diesem Zeitpunkt älteste Paläogenom aus Afrika resultierte. Die erste Studie untersuchte die genetische Diversität und Evolutionsgeschichte der Mendesantilope. Es zeigte sich, dass ihre historische Wildpopulation nur eine geringe phylogeographische Strukturierung aufwies, was auf eine sehr mobile und panmiktische Population hindeutet. Dies legt nahe, dass die rezente europäische Zoopopulation vermutlich Großteile der historischen mitochondrialen Diversität verloren hat. Zusätzlich zeigte sich, dass die nukleäre und mitochondriale Diversität relativ gering waren im Vergleich zu anderen wilden Huftierarten. Es werden Möglichkeiten zum Erhalt der verbliebenen Diversität aufgezeigt. Die europäische Zoopopulation zeigte keine beziehungsweise nur geringe Anzeichen von Inzucht, was für gute Wiederauswilderungsaussichten spricht. Die effektive Populationsgröße der Mendesantilope weist einen starken genetischen Flaschenhals im späten Pleistozän auf. Zudem war sie bereits deutlich niedrig, bevor der derzeitige menschliche Einfluss zu ihrer heutigen Bedrohung führte. Die zweite Stude untersuchte mit Hilfe von aDNA die Identitäten historischer Blaubock-Präparate. Nur vier der zehn untersuchten Präparate stellten sich als Blauböcke heraus. Somit ist der Blaubock eine der seltensten Säugetierarten in naturhistorischen Sammlungen, für die es zudem kaum Knochenreferenzmaterial gibt. Die vorläufige Analyse des mitochondrialen Genoms deutet auf eine geringe Diversität und daher eine geringe Populationsgröße zur Zeit der europäischen Kolonialisierung Südafrikas hin. Die dritte Studie analysierte zwei nukleäre Blaubockgenome, ein ~200 Jahre altes Präparat und eines aus dem frühen Holozän, 9.800–9.300 Jahre. Ein mit Hilfe von Fossilien kalibrierter Stammbaum datiert die Aufspaltung der drei historisch rezenten Hippotragus-Arten auf ~2,86 Mio. Jahre und zeigt die Rappenantilope (H. niger) und den Blaubock als Schwesterarten. Darüber hinaus wurde früherer Genfluss der Pferdeantilope (H. equinus) zum Blaubock festgestellt. Der Vergleich der drei Hippotragus-Arten legt nahe, dass der Blaubock eine deutlich geringere nukleäre Diversität besaß und somit seit mindestens dem frühen Holozän nur über eine geringe Populationsgröße verfügte. Dies stimmt mit Ergebnissen aus dem Fossilbericht überein, die eine deutliche Häufigkeitsabnahme nach dem Übergang des Pleistozäns zum Holozän aufzeigen. Außerdem suggeriert es, dass der Blaubock unabhängig von einer geringen Populationsgröße das Holozän überdauerte und sein Aussterben stark durch den Menschen während der Kolonialzeit beeinflusst wurde. Diese Doktorarbeit bietet mit Hilfe von aDNA gewonnene Erkenntnisse über die Evolutionsgeschichte und die genetische Diversität der Mendesantilope und des Blaubocks. Der menschliche Einfluss war vermutlich der Hauptaussterbegrund des Blaubocks. Dies gilt wahrscheinlich ebenso für die heutige Bedrohung der Mendesantilope. Diese Doktorarbeit zeigt den Wert von ex situ Proben für die Wissenschaft und den Artenschutz und legt die Einbindung von genetischen Daten für die Bewertung des Gefährdungsstatus einer Art nahe. Des Weiteren demonstriert sie die Nutzung von aDNA für taxonomische Bestimmungen von historisch wichtigen Präparaten in naturhistorischen Sammlungen. Die erfolgreiche Gewinnung eines Paläogenoms aus dem frühen Holozän Afrikas mittels shotgun-Sequenzierung zeigt, dass die DNA-Gewinnung aus Proben diesen Alters aus Regionen möglich ist, deren Bedingungen allgemein als ungünstig für den Erhalt von DNA gelten. Dies eröffnet neue Forschungsmöglichkeiten. Alle drei Studien erweitern unser Wissen über afrikanische Antilopen und tragen damit zum allgemeinen Verständnis der Evolution von afrikanischen Großsäugetieren sowie zu deren Erhalt und dem ähnlich gefährdeter Arten bei. KW - Addax nasomaculatus KW - antelope KW - aDNA KW - conservation KW - museomics KW - extinction KW - South Africa KW - Blue antelope KW - Hippotragus leucophaeus KW - bluebuck KW - Addax nasomaculatus KW - Blaubock KW - Hippotragus leucophaeus KW - Südafrika KW - aDNA KW - Antilope KW - Artenschutz KW - Aussterben KW - museomics Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-647718 ER - TY - THES A1 - Küken, Anika T1 - Predictions from constraint-based approaches including enzyme kinetics N2 - The metabolic state of an organism reflects the entire phenotype that is jointly affected by genetic and environmental changes. Due to the complexity of metabolism, system-level modelling approaches have become indispensable tools to obtain new insights into biological functions. In particular, simulation and analysis of metabolic networks using constraint-based modelling approaches have helped the analysis of metabolic fluxes. However, despite ongoing improvements in prediction of reaction flux through a system, approaches to directly predict metabolite concentrations from large-scale metabolic networks remain elusive. In this thesis, we present a computational approach for inferring concentration ranges from genome-scale metabolic models endowed with mass action kinetics. The findings specify a molecular mechanism underling facile control of concentration ranges for components in large-scale metabolic networks. Most importantly, an extended version of the approach can be used to predict concentration ranges without knowledge of kinetic parameters, provided measurements of concentrations in a reference state. We show that the approach is applicable with large-scale kinetic and stoichiometric metabolic models of organisms from different kingdoms of life. By challenging the predictions of concentration ranges in the genome-scale metabolic network of Escherichia coli with real-world data sets, we further demonstrate the prediction power and limitations of the approach. To predict concentration ranges in other species, e.g. model plant species Arabidopsis thaliana, we would rely on estimates of kinetic parameters (i.e. enzyme catalytic rates) since plant-specific enzyme catalytic rates are poorly documented. Using the constraint-based approach of Davidi et al. for estimation of enzyme catalytic rates, we obtain values for 168 plant enzymes. The approach depends on quantitative proteomics data and flux estimates obtained from constraint-based model of plant leaf metabolism integrating maximal rates of selected enzymes, plant-specific constraints on fluxes through canonical pathways, and growth measurements from Arabidopsis thaliana rosette under ten conditions. We demonstrate a low degree of plant enzyme saturation, supported by the agreement between concentrations of nicotinamide adenine dinucleotide, adenosine triphosphate, and glyceraldehyde 3-phosphate, based on our maximal in vivo catalytic rates, and available quantitative metabolomics data. Hence, our results show genome-wide estimation for plant-specific enzyme catalytic rates is feasible. These can now be readily employed to study resource allocation, to predict enzyme and metabolite concentrations using recent constrained-based modelling approaches. Constraint-based methods do not directly account for kinetic mechanisms and corresponding parameters. Therefore, a number of workflows have already been proposed to approximate reaction kinetics and to parameterize genome-scale kinetic models. We present a systems biology strategy to build a fully parameterized large-scale model of Chlamydomonas reinhardtii accounting for microcompartmentalization in the chloroplast stroma. Eukaryotic algae comprise a microcompartment, the pyrenoid, essential for the carbon concentrating mechanism (CCM) that improves their photosynthetic performance. Since the experimental study of the effects of microcompartmentation on metabolic pathways is challenging, we employ our model to investigate compartmentation of fluxes through the Calvin-Benson cycle between pyrenoid and stroma. Our model predicts that ribulose-1,5-bisphosphate, the substrate of Rubisco, and 3-phosphoglycerate, its product, diffuse in and out of the pyrenoid. We also find that there is no major diffusional barrier to metabolic flux between the pyrenoid and stroma. Therefore, our computational approach represents a stepping stone towards understanding of microcompartmentalized CCM in other organisms. This thesis provides novel strategies to use genome-scale metabolic networks to predict and integrate metabolite concentrations. Therefore, the presented approaches represent an important step in broadening the applicability of large-scale metabolic models to a range of biotechnological and medical applications. N2 - Der Stoffwechsel eines Organismus spiegelt den gesamten Phänotyp wieder, welcher durch genetische und umweltbedingte Veränderungen beeinflusst wird. Aufgrund der Komplexität des Stoffwechsels sind Modellierungsansätze, welche das ganzheitliches System betrachten, zu unverzichtbaren Instrumenten geworden, um neue Einblicke in biologische Funktionen zu erhalten. Insbesondere die Simulation und Analyse von Stoffwechselnetzwerken mithilfe von Constraint-basierten Modellierungsansätzen hat die Analyse von Stoffwechselflüssen erleichtert. Trotz kontinuierlicher Verbesserungen bei der Vorhersage des Reaktionsflusses durch ein System, sind Ansätze zur direkten Vorhersage von Metabolitkonzentrationen aus metabolischen Netzwerken kaum vorhanden. In dieser Arbeit stellen wir einen Ansatz vor, mit welchem Konzentrationsbereiche aus genomweiten metabolischen Netzwerken, die mit einer Massenwirkungskinetik ausgestattet sind, abgeleitet werden können. Die Ergebnisse zeigen einen molekularen Mechanismus auf, welcher der Steuerung von Konzentrationsbereichen für Komponenten in metabolischen Netzwerken zugrunde liegt. Eine erweiterte Version des Ansatzes kann verwendet werden, um Konzentrationsbereiche ohne Kenntnis der kinetischen Parameter vorherzusagen, vorausgesetzt, dass Messungen von Konzentrationen in einem Referenzzustand vorhanden sind. Wir zeigen, dass der Ansatz mit kinetischen und stöchiometrischen Stoffwechselmodellen von Organismen aus verschiedenen taxonomischen Reichen anwendbar ist. Indem wir die Vorhersagen von Konzentrationsbereichen im genomweiten Stoffwechselnetzwerk von Escherichia coli mit realen Datensätzen validieren, demonstrieren wir die Vorhersagekraft und die Grenzen des Ansatzes. Um Konzentrationsbereiche in anderen Spezies vorherzusagen, z.B. der Modellpflanzenspezies Arabidopsis thaliana, stützen wir uns auf Schätzungen der kinetischen Parameter (d.h. der katalytischen Enzymraten), da tatsächlich gemessene, pflanzenspezifische katalytische Enzymraten nur unzureichend dokumentiert sind. Unter Verwendung des Constraint-basierten Ansatzes von Davidi et al. zur Abschätzung der katalytischen Enzymraten erhalten wir Werte für 168 pflanzliche Enzyme. Der Ansatz hängt von quantitativen Proteomikdaten und Schätzungen des Reaktionsflusses ab, die aus einem Constraint-basierten Modell des Pflanzenblattmetabolismus unter Einbeziehung der maximalen Raten ausgewählter Enzyme, pflanzenspezifischen Einschränkungen des Flusses durch kanonische Pfade und Wachstumsmessungen aus Rosetten von Arabidopsis thaliana unter zehn Bedingungen erhalten wurden. Wir fanden einen niedrigen Grad an Sättigung der Pflanzenenzyme, der durch die Übereinstimmung zwischen den Konzentrationen von Nicotinamidadenindinukleotid, Adenosintriphosphat und Glycerinaldehyd-3-phosphat auf der Grundlage unserer maximalen in vivo katalytischen Raten und den verfügbaren quantitativen Metabolomikdaten gestützt wird. Daher zeigen unsere Ergebnisse, dass genomweite Schätzungen für pflanzenspezifische Enzymkatalyseraten möglich sind. Diese können nun leicht verwendet werden, um die Ressourcenzuweisung zu untersuchen und die Enzym- und Metabolitenkonzentrationen unter Verwendung neuerer Constraint-basierter Modellierungsansätze vorherzusagen. Constraint-basierte Methoden berücksichtigen kinetische Mechanismen und entsprechende Parameter nicht direkt. Daher wurden einige Methoden entwickelt, welche die Reaktionskinetik approximieren und systemumfassende kinetische Modelle zu parametrisieren. Wir präsentieren eine systembiologische Strategie zur Erstellung eines vollständig parametrisierten Modells von Chlamydomonas reinhardtii, welches die Mikrokompartimentierung im Chloroplaststroma berücksichtigt. Eukaryotische Algen besitzen ein Mikrokompartiment, den Pyrenoiden, der für den Kohlenstoffkonzentrationsmechanismus (KKM) unerlässlich ist und die Photosyntheseleistung verbessert. Die experimentelle Untersuchung der Auswirkungen der Mikrokompartimentierung auf Stoffwechselwege stellt eine Herausforderung dar. Daher verwenden wir unser Modell um die Kompartimentierung von Reaktionsflüssen durch den Calvin-Benson-Zyklus zwischen Pyrenoid und Stroma zu untersuchen. Unser Modell sagt voraus, dass Ribulose-1,5-Bisphosphat, das Substrat von Rubisco, und 3-Phosphoglycerat , das Produkt, in den Pyrenoid hinein und aus ihm heraus diffundieren. Weiter stellen wir fest, dass es keine wesentliche Diffusionsbarriere zwischen dem Pyrenoid und dem Stroma gibt. Somit bietet unser Ansatz eine Möglichkeit um ein Verständnis des mikrokompartimentierten KKM auch in anderen Organismen zu erlangen. Diese Dissertation zeigt neue Strategien um metabolische Netzwerke zur Vorhersage von Metabolitkonzentrationen zu nutzen und selbige zu integrieren. Daher stellen die Ansätze einen wichtigen Schritt zur Anwendbarkeit von genomweiten Stoffwechselmodellen auf eine Reihe von biotechnologischen und medizinischen Anwendungen dar. KW - constraint-based modeling KW - metabolism KW - metabolic networks Y1 - 2020 ER - TY - JOUR A1 - Küken, Anika A1 - Nikoloski, Zoran T1 - Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways JF - Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants N2 - Successfully designed and implemented plant-specific synthetic metabolic pathways hold promise to increase crop yield and nutritional value. Advances in synthetic biology have already demonstrated the capacity to design artificial biological pathways whose behavior can be predicted and controlled in microbial systems. However, the transfer of these advances to model plants and crops faces the lack of characterization of plant cellular pathways and increased complexity due to compartmentalization and multicellularity. Modern computational developments provide the means to test the feasibility of plant synthetic metabolic pathways despite gaps in the accumulated knowledge of plant metabolism. Here, we provide a succinct systematic review of optimization-based and retrobiosynthesis approaches that can be used to design and in silico test synthetic metabolic pathways in large-scale plant context-specific metabolic models. In addition, by surveying the existing case studies, we highlight the challenges that these approaches face when applied to plants. Emphasis is placed on understanding the effect that metabolic designs can have on native metabolism, particularly with respect to metabolite concentrations and thermodynamics of biochemical reactions. In addition, we discuss the computational developments that may help to transform the identified challenges into opportunities for plant synthetic biology. Y1 - 2019 U6 - https://doi.org/10.1104/pp.18.01273 SN - 0032-0889 SN - 1532-2548 VL - 179 IS - 3 SP - 894 EP - 906 PB - American Society of Plant Physiologists CY - Rockville ER - TY - GEN A1 - König, Christian A1 - Weigelt, Patrick A1 - Taylor, Amanda A1 - Stein, Anke A1 - Dawson, Wayne A1 - Essl, Franz A1 - Pergl, Jan A1 - Pyšek, Petr A1 - Kleunen, Mark van A1 - Winter, Marten A1 - Chatelain, Cyrille A1 - Wieringa, Jan J. A1 - Krestov, Pavel A1 - Kreft, Holger T1 - Source pools and disharmony of the world’s island floras T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Island disharmony refers to the biased representation of higher taxa on islands compared to their mainland source regions and represents a central concept in island biology. Here, we develop a generalizable framework for approximating these source regions and conduct the first global assessment of island disharmony and its underlying drivers. We compiled vascular plant species lists for 178 oceanic islands and 735 mainland regions. Using mainland data only, we modelled species turnover as a function of environmental and geographic distance and predicted the proportion of shared species between each island and mainland region. We then quantified the over- or under-representation of families on individual islands (representational disharmony) by contrasting the observed number of species against a null model of random colonization from the mainland source pool, and analysed the effects of six family-level functional traits on the resulting measure. Furthermore, we aggregated the values of representational disharmony per island to characterize overall taxonomic bias of a given flora (compositional disharmony), and analysed this second measure as a function of four island biogeographical variables. Our results indicate considerable variation in representational disharmony both within and among plant families. Examples of generally over-represented families include Urticaceae, Convolvulaceae and almost all pteridophyte families. Other families such as Asteraceae and Orchidaceae were generally under-represented, with local peaks of over-representation in known radiation hotspots. Abiotic pollination and a lack of dispersal specialization were most strongly associated with an insular over-representation of families, whereas other family-level traits showed minor effects. With respect to compositional disharmony, large, high-elevation islands tended to have the most disharmonic floras. Our results provide important insights into the taxon- and island-specific drivers of disharmony. The proposed framework allows overcoming the limitations of previous approaches and provides a quantitative basis for incorporating functional and phylogenetic approaches into future studies of island disharmony. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1211 KW - assembly processes KW - biotic filtering KW - dispersal filtering KW - environmental filtering KW - generalized dissimilarity modelling KW - island disharmony KW - island syndromes KW - source regions KW - vascular plants Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-525101 SN - 1866-8372 IS - 1 ER - TY - THES A1 - Kindermann, Liana T1 - Trees, shrubs, and land-use change T1 - Bäume, Büsche und Landnutzungswandel BT - The future of carbon storage in an African Savanna BT - Die Zukunft der Kohlenstoffspeicherung in einer Afrikanischen Savanne N2 - The global drylands cover nearly half of the terrestrial surface and are home to more than two billion people. In many drylands, ongoing land-use change transforms near-natural savanna vegetation to agricultural land to increase food production. In Southern Africa, these heterogenous savanna ecosystems are also recognized as habitats of many protected animal species, such as elephant, lion and large herds of diverse herbivores, which are of great value for the tourism industry. Here, subsistence farmers and livestock herder communities often live in close proximity to nature conservation areas. Although these land-use transformations are different regarding the future they aspire to, both processes, nature conservation with large herbivores and agricultural intensification, have in common, that they change the vegetation structure of savanna ecosystems, usually leading to destruction of trees, shrubs and the woody biomass they consist of. Such changes in woody vegetation cover and biomass are often regarded as forms of land degradation and forest loss. Global forest conservation approaches and international programs aim to stop degradation processes, also to conserve the carbon bound within wood from volatilization into earth’s atmosphere. In search for mitigation options against global climate change savannas are increasingly discussed as potential carbon sinks. Savannas, however, are not forests, in that they are naturally shaped by and adapted to disturbances, such as wildfires and herbivory. Unlike in forests, disturbances are necessary for stable, functioning savanna ecosystems and prevent these ecosystems from forming closed forest stands. Their consequently lower levels of carbon storage in woody vegetation have long been the reason for savannas to be overlooked as a potential carbon sink but recently the question was raised if carbon sequestration programs (such as REDD+) could also be applied to savanna ecosystems. However, heterogenous vegetation structure and chronic disturbances hamper the quantification of carbon stocks in savannas, and current procedures of carbon storage estimation entail high uncertainties due to methodological obstacles. It is therefore challenging to assess how future land-use changes such as agricultural intensification or increasing wildlife densities will impact the carbon storage balance of African drylands. In this thesis, I address the research gap of accurately quantifying carbon storage in vegetation and soils of disturbance-prone savanna ecosystems. I further analyse relevant drivers for both ecosystem compartments and their implications for future carbon storage under land-use change. Moreover, I show that in savannas different carbon storage pools vary in their persistence to disturbance, causing carbon bound in shrub vegetation to be most likely to experience severe losses under land-use change while soil organic carbon stored in subsoils is least likely to be impacted by land-use change in the future. I start with summarizing conventional approaches to carbon storage assessment and where and for which reasons they fail to accurately estimated savanna ecosystem carbon storage. Furthermore, I outline which future-making processes drive land-use change in Southern Africa along two pathways of land-use transformation and how these are likely to influence carbon storage. In the following chapters, I propose a new method of carbon storage estimation which is adapted to the specific conditions of disturbance-prone ecosystems and demonstrate the advantages of this approach in relation to existing forestry methods. Specifically, I highlight sources for previous over- and underestimation of savanna carbon stocks which the proposed methodology resolves. In the following chapters, I apply the new method to analyse impacts of land-use change on carbon storage in woody vegetation in conjunction with the soil compartment. With this interdisciplinary approach, I can demonstrate that indeed both, agricultural intensification and nature conservation with large herbivores, reduce woody carbon storage above- and belowground, but partly sequesters this carbon into the soil organic carbon stock. I then quantify whole-ecosystem carbon storage in different ecosystem compartments (above- and belowground woody carbon in shrubs and trees, respectively, as well as topsoil and subsoil organic carbon) of two savanna vegetation types (scrub savanna and savanna woodland). Moreover, in a space-for-time substitution I analyse how land-use changes impact carbon storage in each compartment and in the whole ecosystem. Carbon storage compartments are found to differ in their persistence to land-use change with carbon bound in shrub biomass being least persistent to future changes and subsoil organic carbon being most stable under changing land-use. I then explore which individual land-use change effects act as drivers of carbon storage through Generalized Additive Models (GAMs) and uncover non-linear effects, especially of elephant browsing, with implications for future carbon storage. In the last chapter, I discuss my findings in the larger context of this thesis and discuss relevant implications for land-use change and future-making decisions in rural Africa. N2 - Weltweit bedecken Trockengebiete fast die Hälfte der Erdoberfläche und sind die Heimat von mehr als zwei Milliarden Menschen. In vielen Regionen wird durch den fortschreitenden Landnutzungswandel die naturnahe Savannenvegetation in landwirtschaftliche Flächen umgewandelt, um die Nahrungsmittelproduktion zu steigern. Im südlichen Afrika sind diese diversen Savannenökosysteme auch als Lebensraum für viele geschützte Tierarten wie Elefanten, Löwen und große Herden vielfältiger Pflanzenfresser bekannt, die großen Wert für die Tourismusbranche haben. Im Umfeld vieler großer Schutzgebiete leben Kleinbauern und Viehhirten oft in unmittelbarer Nachbarschaft zu diesen – oft gefährlichen – Tieren. Obwohl sich beide Landnutzungen im Hinblick darauf unterscheiden welche Zukunftsvision verfolgt wird, haben sie doch beide gemeinsam, dass sowohl Schutzgebiete mit großen Pflanzenfressern wie Elefanten als auch die Landwirtschaft, die Vegetationsstruktur von Savannenökosystemen verändern. In der Regel reduzieren beide Prozesse die holzige Biomasse im Ökosystem, indem Bäume und Sträucher entfernt, zerstört oder durch Fraßverhalten und Holzeinschlag geschädigt werden. Solche Veränderungen der holzigen Vegetationsschicht samt Einflüssen auf die Biomasse werden oft als Formen von Umweltzerstörung oder Waldverlust betrachtet. Globale Waldschutzkonzepte und internationale Programme zielen darauf ab, solche Degradationsprozesse zu stoppen und den im Holz gebundenen Kohlenstoff vor der Verflüchtigung in die Erdatmosphäre zu bewahren. Auf der Suche nach Möglichkeiten zur Eindämmung des globalen Klimawandels werden Savannen zunehmend als potenzielle Kohlenstoffsenken diskutiert. Savannen sind von Wäldern jedoch fundamental verschieden, da sie von Natur aus durch starke Störungen, wie z. B. Elefantenfraß und Buschfeuer, geprägt und an diese evolutionär angepasst sind. Anders als in Wäldern sind hier Störungen für Funktion und Stabilität von offenen Savannenökosysteme notwendig und verhindern, dass sie sich zu geschlossenen Waldbeständen oder undurchdringlichen Gestrüppen entwickeln. Folglich ist die Kohlenstoffspeicherung in der holzigen Vegetation in Savannen geringer als in Wäldern und dies war lange Zeit der Grund dafür, dass Savannen keine Beachtung als potenzielle Kohlenstoffsenke fanden. In letzter Zeit wurde jedoch zunehmend die Frage aufgeworfen, ob Programme zur Kohlenstoffbindung (wie REDD+) auch auf Savannenökosysteme angewendet werden könnten. Die heterogene Vegetationsstruktur und chronischen Störungen erschweren jedoch erheblich die Quantifizierung der Kohlenstoffvorräte in Savannen, so dass die derzeitigen Verfahren zur Schätzung der Kohlenstoffspeicherung aufgrund methodischer Hindernisse mit großen Unsicherheiten verbunden sind. Daher ist es auch schwierig abzuschätzen, wie sich künftige Landnutzungsänderungen wie die Intensivierung der Landwirtschaft oder die Erhöhung von Wildtierdichten auf die Kohlenstoffspeicher der afrikanischen Trockengebiete auswirken werden. In dieser Arbeit fasse ich zunächst die konventionellen Ansätze zur Quantifizierung von Kohlenstoffspeichern zusammen und zeige auf, wo und aus welchen Gründen sie in Savannenökosystemen versagen. Darüber hinaus skizziere ich entlang zweier Pfade der Landnutzungsänderung, welche Zukunftsvorstellungen den Landnutzungswandel im südlichen Afrika vorantreiben und wie diese voraussichtlich die Kohlenstoffspeicherung beeinflussen werden. In den folgenden Kapiteln entwickele ich eine neue Methode zur Schätzung der Kohlenstoffspeicherung, die an die spezifischen Bedingungen störungsanfälliger Ökosysteme angepasst ist, und zeige die Vorteile dieses Ansatzes gegenüber den bisherigen forstwirtschaftlichen Methoden auf. In den beiden daran anschließenden Kapiteln wende ich die neue Methode an, um die Auswirkungen von Landnutzungsänderungen auf die Kohlenstoffspeicherung zu analysieren und berücksichtige dabei auch das Verhältnis von holziger Biomasse zu im Boden gespeichertem Kohlenstoff. Mit diesem interdisziplinären Ansatz kann ich zeigen, dass sowohl die Intensivierung der Landwirtschaft als auch der Naturschutz mit großen Pflanzenfressern die ober- und unterirdische Kohlenstoffspeicherung in Büschen und Bäumen verringern, dieser Kohlenstoff jedoch nicht verloren geht, sondern teilweise in den organischen Kohlenstoffbestand des Bodens eingelagert wird. Anschließend quantifiziere ich die Kohlenstoffspeicherung im gesamten Ökosystem sowie in verschiedenen Ökosystemkompartimenten (ober- und unterirdischer Holzkohlenstoff in Sträuchern bzw. Bäumen sowie organischer Kohlenstoff im Ober- und Unterboden) von zwei verschiedenen Vegetationstypen der Studienregion. Darüber hinaus analysiere ich in einer Raum-Zeit-Substitution, wie sich zukünftige Landnutzungsänderungen auf die Kohlenstoffspeicherung in jedem Kompartiment und im gesamten Ökosystem auswirken. Die hier untersuchten Kohlenstoffspeicher unterscheiden sich in ihrer Beständigkeit gegenüber Landnutzungsänderungen, wobei jener Kohlenstoff, der in der Strauchbiomasse gebunden ist sich als am wenigsten beständig gegenüber künftigen Änderungen herausgestellt hat; demgegenüber ist der organische Kohlenstoff im Unterboden bei veränderter Landnutzung am stabilsten. Anschließend untersuche ich mit Hilfe von statistischen Modellen (Generalized Additive Models, GAMs), welche individuellen Landnutzungsfaktoren die Kohlenstoffspeicherung beeinflussen, und decke nichtlineare Effekte auf. Insbesondere Elefantenfraß kann zunächst positive Auswirkungen auf die Kohlenstoffspeicherung haben, die sich bei weiterer Intensivierung jedoch ins Gegenteil verkehrt. Dies muss bei zukünftigen Planungen berücksichtigt werden. Im letzten Kapitel diskutiere ich meine Ergebnisse im größeren Kontext dieser Arbeit und erörtere relevante Implikationen für Landnutzungsänderungen und zukünftige Entscheidungen. KW - biology KW - plant ecology KW - carbon storage KW - savanna KW - woodland KW - vegetation ecology KW - disturbance ecology KW - soil organic carbon KW - Biologie KW - Kohlenstoffspeicherung KW - Störungsökologie KW - Pflanzenökologie KW - Savanne KW - Organischer Bodenkohlenstoff KW - Vegetationsökologie KW - Baumsavanne Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-648943 ER - TY - JOUR A1 - Zwickel, Theresa A1 - Kahl, Sandra A1 - Rychlik, Michael A1 - Müller, Marina E. H. T1 - Chemotaxonomy of Mycotoxigenic Small-Spored Alternaria Fungi BT - Do Multitoxin Mixtures Act as an Indicator for Species Differentiation? JF - Frontiers in microbiology N2 - Necrotrophic as well as saprophytic small-spored Altemaria (A.) species are annually responsible for major losses of agricultural products, such as cereal crops, associated with the contamination of food and feedstuff with potential health-endangering Altemaria toxins. Knowledge of the metabolic capabilities of different species-groups to form mycotoxins is of importance for a reliable risk assessment. 93 Altemaria strains belonging to the four species groups Alternaria tenuissima, A. arborescens, A. altemata, and A. infectoria were isolated from winter wheat kernels harvested from fields in Germany and Russia and incubated under equal conditions. Chemical analysis by means of an HPLC-MS/MS multi-Alternaria-toxin-method showed that 95% of all strains were able to form at least one of the targeted 17 non-host specific Altemaria toxins. Simultaneous production of up to 15 (modified) Altemaria toxins by members of the A. tenuissima, A. arborescens, A. altemata species-groups and up to seven toxins by A. infectoria strains was demonstrated. Overall tenuazonic acid was the most extensively formed mycotoxin followed by alternariol and alternariol mono methylether, whereas altertoxin I was the most frequently detected toxin. Sulfoconjugated modifications of alternariol, alternariol mono methylether, altenuisol and altenuene were frequently determined. Unknown perylene quinone derivatives were additionally detected. Strains of the species-group A. infectoria could be segregated from strains of the other three species-groups due to significantly lower toxin levels and the specific production of infectopyrone. Apart from infectopyrone, alterperylenol was also frequently produced by 95% of the A. infectoria strains. Neither by the concentration nor by the composition of the targeted Altemaria toxins a differentiation between the species-groups A. altemata, A. tenuissima and A. arborescens was possible. KW - small-spored Alternaria fungi KW - Alternaria species-groups KW - Alternaria mycotoxins KW - chemotaxonomy KW - secondary metabolite profiling KW - LC-MS/MS KW - wheat KW - perylene quinone derivatives Y1 - 2018 U6 - https://doi.org/10.3389/fmicb.2018.01368 SN - 1664-302X VL - 9 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Neiber, Marco Thomas A1 - Kahl, Sandra A1 - Wiggering, Benedikt A1 - Glaubrecht, Matthias T1 - Adding the West-African riverine component BT - Revision of the Recent freshwater snails belonging to Pseudocleopatra Thiele, 1928 (Caenogastropoda, Cerithioidea, Paludomidae) JF - Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists N2 - While Africa’s lacustrine gastropod fauna, in particular of Lake Tanganyika, has received much attention, the continent’s riverine malacofauna has long been neglected. Pseudocleopatra is a relatively poorly known paludomid gastropod genus with species found throughout the lower reaches of the West African Volta and Congo rivers. In the course of ongoing systematic revisions of African paludomids, we present here a morphometric analysis and revision of the recent species assigned to the genus, i.e., P. togoensis, P. voltana, P. dartevellei and P. bennikei, to improve taxonomic acuity for this group. We use available museum material for geometric morphometrics, multivariate ratio analysis and comparisons of radular and opercular characters. Our results demonstrate that the four recent species of Pseudocleopatra are clearly distinguishable on the basis of ratios of shell measurements as well as radular and opercular characters. Pseudocleopatra has generic-level synapomorphies including: concentric opercula with relatively large paucispiral nuclei, and rachidian radular teeth with usually 13–20 cusps. On the basis of this characterisation, the nominal species Cleopatra broecki is transferred to Pseudocleopatra. Additionally, the nominal taxon P. bennikei is synonymized with P. broecki n. comb. The phylogenetic relationships of Pseudocleopatra are currently unknown, but the observed tendency of some fossil taxa assigned to Pseudocleopatra towards thalassoidism, i.e., the resemblance to marine gastropods, has led to the hypothesis that some of the thalassoid endemics in Lake Tanganyika may have originated from or be related to Pseudocleopatra. Should this hypothesis be correct, which is in need of testing by molecular genetic methods when suitable samples become available, Pseudocleopatra may play a crucial role in understanding of the evolution of thalassoidism in African Paludomidae. KW - Africa KW - Congo River KW - Volta River KW - thalassoidism KW - geometric morphometrics KW - multivariate ratio analysis Y1 - 2019 U6 - https://doi.org/10.11646/zootaxa.4674.3.1 SN - 1175-5326 SN - 1175-5334 VL - 4674 IS - 3 SP - 301 EP - 328 PB - Magnolia Press CY - Auckland ER - TY - JOUR A1 - Kahl, Sandra A1 - Lenhard, Michael A1 - Joshi, Jasmin Radha T1 - Compensatory mechanisms to climate change in the widely distributed species Silene vulgaris JF - The journal of ecology N2 - The adaptation of plants to future climatic conditions is crucial for their survival. Not surprisingly, phenotypic responses to climate change have already been observed in many plant populations. These responses may be due to evolutionary adaptive changes or phenotypic plasticity. Especially plant species with a wide geographic range are either expected to show genetic differentiation in response to differing climate conditions or to have a high phenotypic plasticity. We investigated phenotypic responses and plasticity as an estimate of the adaptive potential in the widespread species Silene vulgaris. In a greenhouse experiment, 25 European populations covering a geographic range from the Canary Islands to Sweden were exposed to three experimental precipitation and two temperature regimes mimicking a possible climate-change scenario for central Europe. We hypothesized that southern populations have a better performance under high temperature and drought conditions, as they are already adapted to a comparable environment. We found that our treatments significantly influenced the plants, but did not reveal a latitudinal difference in response to climate treatments for most plant traits. Only flower number showed a stronger plasticity in northern European populations (e.g. Swedish populations) where numbers decreased more drastically with increased temperature and decreased precipitation treatment. Synthesis. The significant treatment response in Silene vulgaris, independent of population origin - except for the number of flowers produced - suggests a high degree of universal phenotypic plasticity in this widely distributed species. This reflects the likely adaptation strategy of the species and forms the basis for a successful survival strategy during upcoming climatic changes. However, as flower number, a strongly fitness-related trait, decreased more strongly in northern populations under a climate-change scenario, there might be limits to adaptation even in this widespread, plastic species. KW - climate change KW - global change ecology KW - latitudinal gradient KW - local adaptation KW - phenotypic plasticity KW - plant performance KW - temperature increase Y1 - 2019 U6 - https://doi.org/10.1111/1365-2745.13133 SN - 0022-0477 SN - 1365-2745 VL - 107 IS - 4 SP - 1918 EP - 1930 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Bornhorst, Dorothee A1 - Seyfried, Salim T1 - Strong as a hippo’s heart BT - Biomechanical hippo signaling during zebrafish cardiac development JF - Frontiers in cell and developmental biology N2 - The heart is comprised of multiple tissues that contribute to its physiological functions. During development, the growth of myocardium and endocardium is coupled and morphogenetic processes within these separate tissue layers are integrated. Here, we discuss the roles of mechanosensitive Hippo signaling in growth and morphogenesis of the zebrafish heart. Hippo signaling is involved in defining numbers of cardiac progenitor cells derived from the secondary heart field, in restricting the growth of the epicardium, and in guiding trabeculation and outflow tract formation. Recent work also shows that myocardial chamber dimensions serve as a blueprint for Hippo signaling-dependent growth of the endocardium. Evidently, Hippo pathway components act at the crossroads of various signaling pathways involved in embryonic zebrafish heart development. Elucidating how biomechanical Hippo signaling guides heart morphogenesis has direct implications for our understanding of cardiac physiology and pathophysiology. KW - Hippo signaling KW - Yap1/Wwtr1 (Taz) KW - cardiac development KW - mechanobiology KW - endocardium KW - myocardium KW - zebrafish KW - intra-organ-communication Y1 - 2021 U6 - https://doi.org/10.3389/fcell.2021.731101 SN - 2296-634X VL - 9 SP - 1 EP - 10 PB - Frontiers Media CY - Lausanne, Schweiz ER - TY - JOUR A1 - Szangolies, Leonna A1 - Rohwäder, Marie-Sophie A1 - Jeltsch, Florian T1 - Single large AND several small habitat patches BT - a community perspective on their importance for biodiversity JF - Basic and applied ecology : Journal of the Gesellschaft für Ökologie N2 - The debate whether single large or several small (SLOSS) patches benefit biodiversity has existed for decades, but recent literature provides increasing evidence for the importance of small habitats. Possible beneficial mechanisms include reduced presence of preda-tors and competitors in small habitat areas or specific functions such as stepping stones for dispersal. Given the increasing amount of studies highlighting individual behavioral differences that may influence these functions, we hypothesize that the advantage of small versus large habitat patches not only depends on patch functionality but also on the presence of animal personalities (i.e., risk-tolerant vs. risk-averse). Using an individual-based, spatially-explicit community model, we analyzed the diversity of mammal communities in landscapes consisting of a few large habitat islands interspersed with different amounts and sizes of small habitat patches. Within these heterogeneous environments, individuals compete for resources and form home-ranges, with only risk-tolerant individuals using habitat edges. Results show that when risk-tolerant individuals exist, small patches increase species diversity. A strong peak occurs at approximately 20% habitat cover in small patches when those small habitats are only used for foraging but not for breeding and home-range core position. Additional usage as stepping stones for juvenile dispersal further increases species persistence. Over-all, our results reveal that a combination of a few large and several small habitat patches promotes biodiversity by enhancing land-scape heterogeneity. Here, heterogeneity is created by pronounced differences in habitat functionality, increasing edge density, and variability in habitat use by different behavioral types. The finding that a combination of single large AND several small (SLASS) patches is needed for effective biodiversity preservation has implications for advancing landscape conservation. Particularly in struc-turally poor agricultural areas, modern technology enables precise management with the opportunity to create small foraging habitats by excluding less profitable agricultural land from cultivation. KW - SLOSS KW - fragmentation KW - heterogeneity KW - community KW - coexistence KW - coviability KW - competition KW - home-ranges KW - inter-individual difference KW - personality Y1 - 2022 U6 - https://doi.org/10.1016/j.baae.2022.09.004 SN - 1439-1791 SN - 1618-0089 VL - 65 SP - 16 EP - 27 PB - Elsevier CY - München ER - TY - JOUR A1 - Banerjee, Pallavi A1 - Silva, Daniel Varon A1 - Lipowsky, Reinhard A1 - Santer, Mark T1 - The importance of side branches of glycosylphosphatidylinositol anchors BT - a molecular dynamics perspective JF - Glycobiology N2 - Many proteins are anchored to the cell surface of eukaryotes using a unique family of glycolipids called glycosylphosphatidylinositol (GPI) anchors. These glycolipids also exist without a covalently bound protein, in particular on the cell surfaces of protozoan parasites where they are densely populated. GPIs and GPI-anchored proteins participate in multiple cellular processes such as signal transduction, cell adhesion, protein trafficking and pathogenesis of Malaria, Toxoplasmosis, Trypanosomiasis and prion diseases, among others. All GPIs share a common conserved glycan core modified in a cell-dependent manner with additional side glycans or phosphoethanolamine residues. Here, we use atomistic molecular dynamic simulations and perform a systematic study to evaluate the structural properties of GPIs with different side chains inserted in lipid bilayers. Our results show a flop-down orientation of GPIs with respect to the membrane surface and the presentation of the side chain residues to the solvent. This finding agrees well with experiments showing the role of the side residues as active epitopes for recognition of GPIs by macrophages and induction of GPI-glycan-specific immune responses. Protein-GPI interactions were investigated by attaching parasitic GPIs to Green Fluorescent Protein. GPIs are observed to recline on the membrane surface and pull down the attached protein close to the membrane facilitating mutual contacts between protein, GPI and the lipid bilayer. This model is efficient in evaluating the interaction of GPIs and GPI-anchored proteins with membranes and can be extended to study other parasitic GPIs and proteins and develop GPI-based immunoprophylaxis to treat infectious diseases. KW - conformation KW - GFP KW - glycan recognition KW - GPI KW - molecular dynamics Y1 - 2022 U6 - https://doi.org/10.1093/glycob/cwac037 SN - 0959-6658 SN - 1460-2423 VL - 32 IS - 11 SP - 933 EP - 948 PB - Oxford Univ. Press CY - Cary ER - TY - JOUR A1 - Küken, Anika A1 - Treves, Haim A1 - Nikoloski, Zoran T1 - A simulation-free constrained regression approach for flux estimation in isotopically nonstationary metabolic flux analysis with applications in microalgae JF - Frontiers in plant science : FPLS N2 - Introduction Flux phenotypes from different organisms and growth conditions allow better understanding of differential metabolic networks functions. Fluxes of metabolic reactions represent the integrated outcome of transcription, translation, and post-translational modifications, and directly affect growth and fitness. However, fluxes of intracellular metabolic reactions cannot be directly measured, but are estimated via metabolic flux analysis (MFA) that integrates data on isotope labeling patterns of metabolites with metabolic models. While the application of metabolomics technologies in photosynthetic organisms have resulted in unprecedented data from 13CO2-labeling experiments, the bottleneck in flux estimation remains the application of isotopically nonstationary MFA (INST-MFA). INST-MFA entails fitting a (large) system of coupled ordinary differential equations, with metabolite pools and reaction fluxes as parameters. Here, we focus on the Calvin-Benson cycle (CBC) as a key pathway for carbon fixation in photosynthesizing organisms and ask if approaches other than classical INST-MFA can provide reliable estimation of fluxes for reactions comprising this pathway. Methods First, we show that flux estimation with the labeling patterns of all CBC intermediates can be formulated as a single constrained regression problem, avoiding the need for repeated simulation of time-resolved labeling patterns. Results We then compare the flux estimates of the simulation-free constrained regression approach with those obtained from the classical INST-MFA based on labeling patterns of metabolites from the microalgae Chlamydomonas reinhardtii, Chlorella sorokiniana and Chlorella ohadii under different growth conditions. Discussion Our findings indicate that, in data-rich scenarios, simulation-free regression-based approaches provide a suitable alternative for flux estimation from classical INST-MFA since we observe a high qualitative agreement (rs=0.89) to predictions obtained from INCA, a state-of-the-art tool for INST-MFA. KW - metabolic flux analysis KW - INST-MFA KW - regression KW - 13C labeling KW - algae Y1 - 2023 U6 - https://doi.org/10.3389/fpls.2023.1140829 SN - 1664-462X VL - 14 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Wojcik, Laurie Anne Myriam A1 - Ceulemans, Ruben A1 - Gaedke, Ursula T1 - Functional diversity buffers the effects of a pulse perturbation on the dynamics of tritrophic food webs JF - Ecology and Evolution N2 - Biodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: This loss may hamper ecosystems’ ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of human-induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. We investigated the effects of functional diversity on the robustness, that is, resistance, resilience, and elasticity, using a tritrophic—and thus more realistic—plankton food web model. We compared a non-adaptive food chain with no diversity within the individual trophic levels to a more diverse food web with three adaptive trophic levels. The species fitness differences were balanced through trade-offs between defense/growth rate for prey and selectivity/half-saturation constant for predators. We showed that the resistance, resilience, and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occurred. Importantly, we found that a more diverse food web was generally more resistant and resilient but its elasticity was context-dependent. Particularly, functional diversity reduced the probability of a regime shift toward a non-desirable alternative state. The basal-intermediate interaction consistently determined the robustness against a nutrient pulse despite the complex influence of the shape and type of the dynamical attractors. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience, and potentially elasticity as functional diversity declines. KW - functional diversity KW - nutrient spike KW - pulse perturbation KW - regime shift KW - robustness KW - tritrophic food web Y1 - 2021 U6 - https://doi.org/10.1002/ece3.8214 SN - 2045-7758 N1 - Wojcik and Ceulemans shared first authorship. VL - 11 IS - 22 SP - 15639 EP - 15663 PB - John Wiley & Sons, Inc. CY - Hoboken (New Jersey) ER - TY - GEN A1 - Zwickel, Theresa A1 - Kahl, Sandra A1 - Klaffke, Horst A1 - Rychlik, Michael A1 - Müller, Marina E. H. T1 - Spotlight on the underdogs BT - an analysis of underrepresented alternaria mycotoxins formed depending on varying substrate, time and temperature conditions N2 - Alternaria (A.) is a genus of widespread fungi capable of producing numerous, possibly health-endangering Alternaria toxins (ATs), which are usually not the focus of attention. The formation of ATs depends on the species and complex interactions of various environmental factors and is not fully understood. In this study the influence of temperature (7 °C, 25 °C), substrate (rice, wheat kernels) and incubation time (4, 7, and 14 days) on the production of thirteen ATs and three sulfoconjugated ATs by three different Alternaria isolates from the species groups A. tenuissima and A. infectoria was determined. High-performance liquid chromatography coupled with tandem mass spectrometry was used for quantification. Under nearly all conditions, tenuazonic acid was the most extensively produced toxin. At 25 °C and with increasing incubation time all toxins were formed in high amounts by the two A. tenuissima strains on both substrates with comparable mycotoxin profiles. However, for some of the toxins, stagnation or a decrease in production was observed from day 7 to 14. As opposed to the A. tenuissima strains, the A. infectoria strain only produced low amounts of ATs, but high concentrations of stemphyltoxin III. The results provide an essential insight into the quantitative in vitro AT formation under different environmental conditions, potentially transferable to different field and storage conditions T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 353 KW - Alternaria infectoria KW - A. tenuissima KW - mycotoxin profile KW - wheat KW - rice KW - Alternaria toxin sulfates KW - modified Alternaria toxins KW - altertoxins KW - altenuic acid KW - HPLC-MS/MS Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-400438 ER - TY - JOUR A1 - Romero Mujalli, Daniel A1 - Rochow, Markus A1 - Kahl, Sandra A1 - Paraskevopoulou, Sofia A1 - Folkertsma, Remco A1 - Jeltsch, Florian A1 - Tiedemann, Ralph T1 - Adaptive and nonadaptive plasticity in changing environments BT - Implications for sexual species with different life history strategies JF - Ecology and evolution N2 - Populations adapt to novel environmental conditions by genetic changes or phenotypic plasticity. Plastic responses are generally faster and can buffer fitness losses under variable conditions. Plasticity is typically modeled as random noise and linear reaction norms that assume simple one-to- one genotype–phenotype maps and no limits to the phenotypic response. Most studies on plasticity have focused on its effect on population viability. However, it is not clear, whether the advantage of plasticity depends solely on environmental fluctuations or also on the genetic and demographic properties (life histories) of populations. Here we present an individual-based model and study the relative importance of adaptive and nonadaptive plasticity for populations of sexual species with different life histories experiencing directional stochastic climate change. Environmental fluctuations were simulated using differentially autocorrelated climatic stochasticity or noise color, and scenarios of directiona climate change. Nonadaptive plasticity was simulated as a random environmental effect on trait development, while adaptive plasticity as a linear, saturating, or sinusoidal reaction norm. The last two imposed limits to the plastic response and emphasized flexible interactions of the genotype with the environment. Interestingly, this assumption led to (a) smaller phenotypic than genotypic variance in the population (many-to- one genotype–phenotype map) and the coexistence of polymorphisms, and (b) the maintenance of higher genetic variation—compared to linear reaction norms and genetic determinism—even when the population was exposed to a constant environment for several generations. Limits to plasticity led to genetic accommodation, when costs were negligible, and to the appearance of cryptic variation when limits were exceeded. We found that adaptive plasticity promoted population persistence under red environmental noise and was particularly important for life histories with low fecundity. Populations produing more offspring could cope with environmental fluctuations solely by genetic changes or random plasticity, unless environmental change was too fast. KW - developmental canalization KW - environmental change KW - genetic accommodation KW - Individual-based models KW - limits KW - many-to-one genotype–phenotype map KW - noise color KW - phenotypic plasticity KW - reaction norms KW - stochastic fluctuations Y1 - 2020 U6 - https://doi.org/10.1002/ece3.7485 SN - 2045-7758 VL - 11 IS - 11 SP - 6341 EP - 6357 PB - John Wiley & Sons, Inc. CY - New Jersey ER - TY - THES A1 - Kahl, Sandra T1 - Evolutionary adaptive responses to rapid climate change in plants T1 - Evolutionäre Anpassungsstrategien von Pflanzen an den Klimawandel BT - a case study of the widely distributed species Silene vulgaris BT - ein Fallbeispiel der weit verbreiteten Art Silene vulgaris N2 - The ongoing climate change is altering the living conditions for many organisms on this planet at an unprecedented pace. Hence, it is crucial for the survival of species to adapt to these changing conditions. In this dissertation Silene vulgaris is used as a model organism to understand the adaption strategies of widely distributed plant species to the current climate change. Especially plant species that possess a wide geographic range are expected to have a high phenotypic plasticity or to show genetic differentiation in response to the different climate conditions they grow in. However, they are often underrepresented in research. In the greenhouse experiment presented in this thesis, I examined the phenotypic responses and plasticity in S. vulgaris to estimate its’ adaptation potential. Seeds from 25 wild European populations were collected along a latitudinal gradient and grown in a greenhouse under three different precipitation (65 mm, 75 mm, 90 mm) and two different temperature regimes (18°C, 21°C) that resembled a possible climate change scenario for central Europe. Afterwards different biomass and fecundity-related plant traits were measured. The treatments significantly influenced the plants but did not reveal a latitudinal difference in response to climate treatments for most plant traits. The number of flowers per individual however, showed a stronger plasticity in northern European populations (e.g., Swedish populations) where numbers decreased more drastically with increased temperature and decreased precipitation. To gain an even deeper understanding of the adaptation of S. vulgaris to climate change it is also important to reveal the underlying phylogeny of the sampled populations. Therefore, I analysed their population genetic structure through whole genome sequencing via ddRAD. The sequencing revealed three major genetic clusters in the S. vulgaris populations sampled in Europe: one cluster comprised Southern European populations, one cluster Western European populations and another cluster contained central European populations. A following analysis of experimental trait responses among the clusters to the climate-change scenario showed that the genetic clusters significantly differed in biomass-related traits and in the days to flowering. However, half of the traits showed parallel response patterns to the experimental climate-change scenario. In addition to the potential geographic and genetic adaptation differences to climate change this dissertation also deals with the response differences between the sexes in S. vulgaris. As a gynodioecious species populations of S. vulgaris consist of female and hermaphrodite individuals and the sexes can differ in their morphological traits which is known as sexual dimorphism. As climate change is becoming an important factor influencing plant morphology it remains unclear if and how different sexes may respond in sexually dimorphic species. To examine this question the sex of each individual plant was determined during the greenhouse experiment and the measured plant traits were analysed accordingly. In general, hermaphrodites had a higher number of flowers but a lower number of leaves than females. With regards to the climate change treatment, I found that hermaphrodites showed a milder negative response to higher temperatures in the number of flowers produced and in specific leaf area (SLA) compared to females. Synthesis – The significant treatment response in Silene vulgaris, independent of population origin in most traits suggests a high degree of universal phenotypic plasticity. Also, the three European intraspecific genetic lineages detected showed comparable parallel response patterns in half of the traits suggesting considerable phenotypic plasticity. Hence, plasticity might represent a possible adaptation strategy of this widely distributed species during ongoing and future climatic changes. The results on sexual dimorphism show that females and hermaphrodites are differing mainly in their number of flowers and females are affected more strongly by the experimental climate-change scenario. These results provide a solid knowledge basis on the sexual dimorphism in S. vulgaris under climate change, but further research is needed to determine the long-term impact on the breeding system for the species. In summary this dissertation provides a comprehensive insight into the adaptation mechanisms and consequences of a widely distributed and gynodioecious plant species and leverages our understanding of the impact of anthropogenic climate change on plants. N2 - Der derzeitige Klimawandel verändert die Lebensbedingungen für viele Tiere und Pflanzen auf unserem Planeten in nie da gewesenem Maße. Damit Arten überleben, ist es von besonderer Wichtigkeit, dass sich diese an die sich ändernden Klimabedingungen anpassen können. Die vorliegende Dissertation befasst sich mit der Modellpflanze Silene vulgaris und versucht zu ergründen, wie sich solch weit verbreitete Pflanzenarten an den Klimawandel anpassen. Dabei ist zu erwarten, dass sie eine hohe phänotypische Plastizität besitzen, durch die sie sich gut anpassen können oder, dass sie sich durch eine genetische Differenzierung als Antwort auf die vorherrschenden Umweltbedingungen auszeichnen. Im experimentellen Ansatz dieser Dissertation untersuchte ich daher die phänotypischen Anpassungen und die phänotypische Plastizität von S. vulgaris an ein mögliches Klimawandelszenario für Zentraleuropa. Dabei wurden die Samen von 25 europäischen Populationen gesammelt und in einem Gewächshausexperiment unter drei verschiedenen Niederschlagsbedingungen (65 mm, 75 mm, 90 mm) und zwei verschiedenen Temperaturbedingungen (18°C, 21°C) herangezogen. Im Anschluss wurden verschiedene Biomasse- und Fertilitätsmerkmale gemessen. Für ein tiefergehendes Verständnis der Anpassungsmöglichkeiten von S. vulgaris an den Klimawandel ist es zudem wichtig, auch die zugrundeliegende Phylogenie der Populationen zu verstehen. In diesem Zusammenhang nutzte ich eine genomweite Sequenziermethode mittels ddRAD. Die Bedingungen im Gewächshausexperiment beeinflussten die Pflanzen signifikant in ihren phänotypischen Merkmalen, jedoch ließ sich kein Unterschied zwischen Population unterschiedlicher Herkunft erkennen. Lediglich die Anzahl der Blüten zeigte eine größere Plastizität in nördlichen europäischen Populationen, wo sich die Blütenzahl stärker dezimierte unter höheren Temperaturen und stärkerer Trockenheit. Die populationsgenetische Analyse ergab drei distinkte phylogenetische Gruppen für die untersuchten europäischen Populationen von S. vulgaris: eine Gruppe beinhaltete südeuropäische Populationen aus Spanien und Südfrankreich, eine weitere Gruppe bestand aus den gesammelten Individuen der westfranzösischen Populationen, während die dritte Gruppe, die Populationen aus Mittel- und Nordeuropa enthielt. Diese genetischen Gruppen wurden anschließend ebenfalls der Merkmalsanalyse unter den Gewächshausbedingungen unterzogen. Dabei stellte sich heraus, dass sich die genetischen Gruppen in ihren phänotypischen Merkmalen unterschieden, jedoch eine ähnliche Anpassung ihrer Merkmale an die experimentellen Klimawandelbedingungen zeigten. Der dritte Aspekt dieser Dissertation befasste sich mit möglichen Anpassungsunterschieden zwischen den Geschlechtern in S. vulgaris. Als gynodiözische Art bestehen ihre Populationen sowohl aus weiblichen, also auch aus zwittrigen Individuen. Die phänotypischen Merkmale beider Geschlechter können sich dabei unterscheiden, was man als Sexualdimorphismus bezeichnet. Es ist bereits bekannt, dass sich Pflanzenmerkmale durch den anhaltenden Klimawandel bereits verändern, jedoch ist es nicht gut erforscht, ob und wie sich die unterschiedlichen Geschlechter bei einer sexuell dimorphen Art unter diesem Selektionsdruck verhalten. Während des Gewächshausexperiments wurden daher die Geschlechter der Individuen bestimmt und die phänotypischen Unterschiede zwischen weiblichen und zwittrigen Pflanzen analysiert. Allgemein lässt sich sagen, dass zwittrige Individuen mehr Blüten aber weniger Blätter hatten als weibliche. Im Hinblick auf die experimentellen Klimawandelbedingungen konnte ich zudem feststellen, dass Hermaphroditen in ihrer spezifischen Blattfläche und der Blütenanzahl weniger stark negativ auf höhere Temperaturen reagierten. Synthese – Die signifikanten Merkmalsanpassungen an die Gewächshausbedingungen waren unabhängig von der geographischen Herkunft oder genetischen Gruppe der Individuen. Dies lässt ein hohes Maß an universeller, phänotypischer Plastizität vermuten. Dementsprechend kann davon ausgegangen werden, dass phänotypische Plastizität ein möglicher Anpassungsmechanismus für diese weit verbreitete Art an den Klimawandel sein könnte. Im Hinblick auf den Sexualdimorphismus in S. vulgaris lässt sich sagen, dass sich beide Geschlechter vornehmlich in der Anzahl der Blüten unterscheiden und dass weibliche Pflanzen stärker von den Bedingungen des Gewächshausexperiments beeinflusst wurden. Diese Dissertation konnte damit erstmals darüber Aufschluss geben, wie sich S. vulgaris im Hinblick auf ihren Sexualdimorphismus unter Klimawandelbedingungen verhält. Weitere Forschung wird nun benötigt, um auch den Langzeiteffekt des Klimawandels auf das Fortpflanzungssystem dieser Art abschätzen zu können. Zusammenfassend lässt sich sagen, dass die vorliegende Arbeit einen umfassenden Einblick in die Anpassungsmechanismen einer weit verbreiteten Pflanzenart an den anthropogenen Klimawandel gibt. Zudem bestärkt sie unser Verständnis der Auswirkungen, die sich daraus für eine gynodiözische Art, wie S. vulgaris ergeben. KW - Silene vulgaris KW - climate change KW - plant adaptation KW - Silene vulgaris KW - Klimawandel KW - Pflanzenanpassung Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-556483 ER -