TY - JOUR A1 - Sandhage-Hofmann, Alexandra A1 - Angombe, Simon A1 - Kindermann, Liana A1 - Linstädter, Anja A1 - Mörchen, Ramona T1 - Conservation with elephants and agricultural intensification BT - effects on lignin and n-alkanes in soils of sub-Saharan Africa JF - Geoderma : an international journal of soil science N2 - Nature conservation is currently shaping many terrestrial ecosystems in Africa. This is particularly evident in Sub-Saharan Africa (SSA), where conservation is intended to recover wildlife populations, with special focus on elephants. Rising numbers of elephants induce woody biomass losses but increase soil organic carbon (SOC) stocks from decaying wood and dung. We hypothesized that these increases under wildlife conservation in SSA go along with rising contents of plant residues in SOC, traceable by the molecular markers lignin and n-alkanes. In contrast, agricultural intensification would reduce them due to lower C input and faster SOC turnover through tillage. To test this, we analyzed lignin by the CuO oxidation method and n-alkanes by fast pressurized solvent extraction in topsoils (0-10 cm) of Arenosols and corresponding plant samples (trees, grasses and crops). Sampling sites followed conservation gradients with low, medium and high elephant densities and intensification gradients with rangeland and cropland in the woodland savanna of the Namibian Zambezi Region. Patterns of lignin-derived phenols were retained in the soil, whereas n-alkanes showed shifts in chain lengths. n-Alkanes also showed no clear increase or decrease under conservation or intensification, respectively. Differently, lignin-derived phenols showed lower values under intensification than under conservation. Confirming our hypothesis, rising SOC contents with rising elephant densities (from 4.4 at low to 5.7 g kg(-1) SOC at high elephant densities) went along with an increasing accumulation of lignin-derived phenols (24.4-34.8 g kg(-1) VSCOC). This increase is associated with the input of woody debris to the soil, as indicated by V-units and carbon isotopes, modulated by clay and woody biomass. We conclude, that increasing input of woody residues into soil by browsing behaviour of elephants is an important mechanism for controlling SOC supply in the context of wildlife conservation and is traceable with lignin-derived phenols, but not with n-alkanes. KW - lignin-derived phenols KW - n-alkanes KW - soil organic carbon KW - wildlife conservation KW - agricultural intensification Y1 - 2022 U6 - https://doi.org/10.1016/j.geoderma.2022.116009 SN - 0016-7061 SN - 1872-6259 VL - 425 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Wendering, Philipp A1 - Nikoloski, Zoran T1 - Genome-scale modeling specifies the metabolic capabilities of Rhizophagus irregularis JF - mSystems N2 - Rhizophagus irregularis is one of the most extensively studied arbuscular mycorrhizal fungi (AMF) that forms symbioses with and improves the performance of many crops. Lack of transformation protocol for R. irregularis renders it challenging to investigate molecular mechanisms that shape the physiology and interactions of this AMF with plants. Here, we used all published genomics, transcriptomics, and metabolomics resources to gain insights into the metabolic functionalities of R. irregularis by reconstructing its high-quality genome-scale metabolic network that considers enzyme constraints. Extensive validation tests with the enzyme-constrained metabolic model demonstrated that it can be used to (i) accurately predict increased growth of R. irregularis on myristate with minimal medium; (ii) integrate enzyme abundances and carbon source concentrations that yield growth predictions with high and significant Spearman correlation (rS = 0.74) to measured hyphal dry weight; and (iii) simulate growth rate increases with tighter association of this AMF with the host plant across three fungal structures. Based on the validated model and system-level analyses that integrate data from transcriptomics studies, we predicted that differences in flux distributions between intraradical mycelium and arbuscles are linked to changes in amino acid and cofactor biosynthesis. Therefore, our results demonstrated that the enzyme-constrained metabolic model can be employed to pinpoint mechanisms driving developmental and physiological responses of R. irregularis to different environmental cues. In conclusion, this model can serve as a template for other AMF and paves the way to identify metabolic engineering strategies to modulate fungal metabolic traits that directly affect plant performance. IMPORTANCE Mounting evidence points to the benefits of the symbiotic interactions between the arbuscular mycorrhiza fungus Rhizophagus irregularis and crops; however, the molecular mechanisms underlying the physiological responses of this fungus to different host plants and environments remain largely unknown. We present a manually curated, enzyme-constrained, genome-scale metabolic model of R. irregularis that can accurately predict experimentally observed phenotypes. We show that this high-quality model provides an entry point into better understanding the metabolic and physiological responses of this fungus to changing environments due to the availability of different nutrients. The model can be used to design metabolic engineering strategies to tailor R. irregularis metabolism toward improving the performance of host plants. KW - Rhizophagus irregularis KW - metabolic modeling Y1 - 2022 U6 - https://doi.org/10.1128/msystems.01216-21 SN - 2379-5077 VL - 7 IS - 1 PB - American Society for Microbiology CY - Washington, DC ER - TY - CHAP A1 - Fayyaz, Susann A1 - Hartmann, Bolette A1 - Hanack, Katja A1 - Michelchen, Sophia A1 - Kreiling, Reinhard T1 - Development of a hematopoietic stem cell (murine system) based system as an alternative for the in vivo T-cell-dependent antibody response (TDAR) assay within the EOGRTS: case-study with Parabens T2 - Toxicology letters Y1 - 2022 U6 - https://doi.org/10.1016/j.toxlet.2022.07.483 SN - 0378-4274 SN - 1879-3169 VL - 368 SP - S175 EP - S176 PB - Elsevier Science CY - Amsterdam [u.a.] ER - TY - THES A1 - Karakas, Esra T1 - High-resolution studies of epistasis in tomato metabolism T1 - Hochauflösende Studien zur Epistasierung des Tomatenstoffwechsels N2 - The inclusion of exotic germplasm serves as a crucial means to enhance allelic and consequently phenotypic diversity in inbred crop species. Such species have experienced a reduction in diversity due to artificial selection focused on a limited set of traits. The natural biodiversity within ecosystems presents an opportunity to explore various traits influencing plant survival, reproductive fitness and yield potential. In agricultural research, the study of wild species closely related to cultivated plants serves as a means to comprehend the genetic foundations of past domestication events and the polymorphisms essential for future breeding efforts to develop superior varieties. In order to examine the metabolic composition, pinpoint quantitative trait loci (QTL) and facilitate their resolution an extensive large-scale analysis of metabolic QTL (mQTL) was conducted on tomato backcross inbred lines (BILs) derived from a cross between the wild species S. pennellii (5240) incorporated into the background of S. lycopersicum cv. LEA determinate inbred which can be grown in open fields and cv. TOP indeterminate which can be grown in greenhouse conditions. A large number of mQTL associated with primary secondary and lipid metabolism in fruit were identified across the two BIL populations. Epistasis, the interactions between genes at different loci, has been an interest in molecular and quantitative genetics for many decades. The study of epistasis requires the analysis of very large populations with multiple independent genotypes that carry specific genomic regions. In order to understand the genetic basis of tomato fruit metabolism, I extended the work to investigate epistatic interactions of the genomic regions. In addition, two candidate genes were identified through quantitative trait loci underlying fruit-specific sucrose and jasmonic acid derivatives. Finally, in this study, I assessed the genetic framework of fruit metabolic traits with a high level of detail, utilizing the newly created Solanum pennellii (5240) backcrossed introgression lines (n=3000). This investigation resulted in the discovery of promising candidate loci associated with significant fruit quality traits, including those to the abundance of glutamic acid and aspartic acid crucial elements contributing to the development of acidity and flavors. N2 - Die Einbeziehung von exotischem Keimplasma ist ein wichtiges Mittel zur Verbesserung der allelischen und folglich auch der phänotypischen Vielfalt bei Inzuchtpflanzenarten. Bei diesen Arten hat die künstliche Selektion, die sich auf eine begrenzte Anzahl von Merkmalen konzentriert, zu einem Rückgang der Vielfalt geführt. Die natürliche Artenvielfalt in Ökosystemen bietet die Möglichkeit, verschiedene Merkmale zu erforschen, die das Überleben, die Reproduktionsfähigkeit und das Ertragspotenzial von Pflanzen beeinflussen. In der Agrarforschung dient die Untersuchung von Wildarten, die eng mit Kulturpflanzen verwandt sind, als Mittel zum Verständnis der genetischen Grundlagen vergangener Domestizierungsereignisse und der Polymorphismen, die für künftige Züchtungsbemühungen zur Entwicklung besserer Sorten wichtig sind. Um die metabolische Zusammensetzung zu untersuchen, quantitative Merkmalsloci (QTL) zu identifizieren und ihre Auflösung zu erleichtern, wurde eine umfangreiche Analyse metabolischer QTL (mQTL) an Tomaten-Rückkreuzungs-Inzuchtlinien (BILs) durchgeführt, die aus einer Kreuzung zwischen der Wildart S. pennellii (5240), die in den Hintergrund von S. lycopersicum cv. LEA determinate inbred, die im Freiland angebaut werden kann, und cv. TOP indeterminate, die unter Gewächshausbedingungen angebaut werden kann. In den beiden BIL-Populationen wurde eine große Anzahl von mQTL identifiziert, die mit dem primären Sekundär- und Lipidstoffwechsel in der Frucht in Verbindung stehen. Epistase, die Wechselwirkungen zwischen Genen an verschiedenen Loci, ist seit vielen Jahrzehnten ein Thema in der molekularen und quantitativen Genetik. Die Untersuchung der Epistase erfordert die Analyse sehr großer Populationen mit mehreren unabhängigen Genotypen, die bestimmte genomische Regionen tragen. Um die genetischen Grundlagen des Tomatenfruchtstoffwechsels zu verstehen, habe ich die Arbeit erweitert, um epistatische Interaktionen der genomischen Regionen zu untersuchen. Darüber hinaus wurden zwei Kandidatengene identifiziert, die über quantitative Merkmalsloci den fruchttypischen Saccharose- und Jasmonsäurederivaten zugrunde liegen. Schließlich habe ich in dieser Studie das genetische Gerüst der Fruchtstoffwechselmerkmale mit einem hohen Detaillierungsgrad bewertet, wobei ich die neu geschaffenen Solanum pennellii (5240) Rückkreuzungslinien (n=3000) verwendet habe. Diese Untersuchung führte zur Entdeckung vielversprechender Kandidatenloci, die mit bedeutenden Fruchtqualitätsmerkmalen assoziiert sind, einschließlich derjenigen, die mit der Fülle von Glutaminsäure und Asparaginsäure in Verbindung stehen - entscheidende Elemente, die zur Entwicklung von Säure und Aromen beitragen. KW - Epistasis KW - QTL mapping KW - metabolomics KW - backcross inbred line (BIL) KW - Epistase KW - QTL KW - Metabolomik KW - Rückkreuzungsinzuchtlinie (BIL) Y1 - 2024 ER - TY - JOUR A1 - Matz, Timon W. A1 - Wang, Yang A1 - Kulshreshtha, Ritika A1 - Sampathkumar, Arun A1 - Nikoloski, Zoran T1 - Topological properties accurately predict cell division events and organization of shoot apical meristem in Arabidopsis thaliana JF - Development : Company of Biologists N2 - Cell division and the resulting changes to the cell organization affect the shape and functionality of all tissues. Thus, understanding the determinants of the tissue-wide changes imposed by cell division is a key question in developmental biology. Here, we use a network representation of live cell imaging data from shoot apical meristems (SAMs) in Arabidopsis thaliana to predict cell division events and their consequences at the tissue level. We show that a support vector machine classifier based on the SAM network properties is predictive of cell division events, with test accuracy of 76%, which matches that based on cell size alone. Furthermore, we demonstrate that the combination of topological and biological properties, including cell size, perimeter, distance and shared cell wall between cells, can further boost the prediction accuracy of resulting changes in topology triggered by cell division. Using our classifiers, we demonstrate the importance of microtubule-mediated cell-to-cell growth coordination in influencing tissue-level topology. Together, the results from our network-based analysis demonstrate a feedback mechanism between tissue topology and cell division in A. thaliana SAMs. KW - Arabidopsis thaliana KW - cell division KW - classification models KW - networks KW - shoot apical meristem KW - topology Y1 - 2022 U6 - https://doi.org/10.1242/dev.201024 SN - 0950-1991 SN - 1477-9129 VL - 149 IS - 16 PB - Company of Biologists CY - Cambridge ER - TY - JOUR A1 - Mollavali, Mohanna A1 - Börnke, Frederik T1 - Characterization of trehalose-6-phosphate synthase and trehalose-6-phosphate phosphatase genes of tomato (Solanum lycopersicum L.) and analysis of their differential expression in response to temperature JF - International journal of molecular sciences N2 - In plants, the trehalose biosynthetic pathway plays key roles in the regulation of carbon allocation and stress adaptation. Engineering of the pathway holds great promise to increase the stress resilience of crop plants. The synthesis of trehalose proceeds by a two-step pathway in which a trehalose-phosphate synthase (TPS) uses UDP-glucose and glucose-6-phosphate to produce trehalose-6 phosphate (T6P) that is subsequently dephosphorylated by trehalose-6 phosphate phosphatase (TPP). While plants usually do not accumulate high amounts of trehalose, their genome encodes large families of putative trehalose biosynthesis genes, with many members lacking obvious enzymatic activity. Thus, the function of putative trehalose biosynthetic proteins in plants is only vaguely understood. To gain a deeper insight into the role of trehalose biosynthetic proteins in crops, we assessed the enzymatic activity of the TPS/TPP family from tomato (Solanum lycopersicum L.) and investigated their expression pattern in different tissues as well as in response to temperature shifts. From the 10 TPS isoforms tested, only the 2 proteins belonging to class I showed enzymatic activity, while all 5 TPP isoforms investigated were catalytically active. Most of the TPS/TPP family members showed the highest expression in mature leaves, and promoter-reporter gene studies suggest that the two class I TPS genes have largely overlapping expression patterns within the vasculature, with only subtle differences in expression in fruits and flowers. The majority of tomato TPS/TPP genes were induced by heat stress, and individual family members also responded to cold. This suggests that trehalose biosynthetic pathway genes could play an important role during temperature stress adaptation. In summary, our study represents a further step toward the exploitation of the TPS and TPP gene families for the improvement of tomato stress resistance. KW - trehalose metabolism KW - heat stress KW - Solanum lycopersicum KW - yeast complementation Y1 - 2022 U6 - https://doi.org/10.3390/ijms231911436 SN - 1661-6596 SN - 1422-0067 VL - 23 IS - 19 PB - MDPI CY - Basel ER - TY - JOUR A1 - Gätjen, Dominic A1 - Wieczorek, Marek A1 - Listek, Martin A1 - Tomszak, Florian A1 - Nölle, Volker A1 - Hanack, Katja A1 - Droste, Miriam Susanna T1 - A switchable secrete-and-capture system enables efficient selection of Pichia pastoris clones producing high yields of Fab fragments JF - Journal of immunological methods N2 - Pichia pastoris (syn. Komagataella phaffii) represents a commonly used expression system in the biotech industry. High clonal variation of transformants, however, typically results in a broad range of specific productivities for secreted proteins. To isolate rare clones with exceedingly high product titers, an extensive number of clones need to be screened. In contrast to high-throughput screenings of P. pastoris clones in microtiter plates, secrete-and -capture methodologies have the potential to efficiently isolate high-producer clones among millions of cells through fluorescence-activated cell sorting (FACS).Here, we describe a novel approach for the non-covalent binding of fragment antigen-binding (Fab) proteins to the cell surface for the isolation of high-producing clones. Eight different single-chain variable fragment (scFv)-based capture matrices specific for the constant part of the Fabs were fused to the Saccharomyces cerevisiae alpha -agglutinin (SAG1) anchor protein for surface display in P. pastoris. By encoding the capture matrix on an episomal plasmid harboring inherently unstable autonomously replicating sequences (ARS), this secrete-and -capture system offers a switchable scFv display. Efficient plasmid clearance upon removal of selective pres-sure enabled the direct use of isolated clones for subsequent Fab production. Flow-sorted clones (n = 276) displaying high amounts of Fabs showed a significant increase in median Fab titers detected in the cell-free supernatant (CFS) compared to unsorted clones (n = 276) when cells were cultivated in microtiter plates (fac-tor in the range of-21-49). Fab titers of clones exhibiting the highest product titer observed for each of the two approaches were increased by up to 8-fold for the sorted clone. Improved Fab yields of sorted cells vs. unsorted cells were confirmed in an upscaled shake flask cultivation of selected candidates (factor in the range of-2-3). Hence, the developed display-based selection method proved to be a valuable tool for efficient clone screening in the early stages of our bioprocess development. KW - Fab fragment production KW - Pichia pastoris KW - FACS KW - yeast surface display high throughput screening Y1 - 2022 U6 - https://doi.org/10.1016/j.jim.2022.113383 SN - 0022-1759 SN - 1872-7905 VL - 511 PB - Elsevier Science CY - Amsterdam [u.a.] 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 - 1460-2423 VL - 32 IS - 11 SP - 933 EP - 948 PB - Oxford Univ. Press CY - Cary 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 - Langary, Damoun A1 - Küken, Anika A1 - Nikoloski, Zoran T1 - The effective deficiency of biochemical networks JF - Scientific reports N2 - The deficiency of a (bio)chemical reaction network can be conceptually interpreted as a measure of its ability to support exotic dynamical behavior and/or multistationarity. The classical definition of deficiency relates to the capacity of a network to permit variations of the complex formation rate vector at steady state, irrespective of the network kinetics. However, the deficiency is by definition completely insensitive to the fine details of the directionality of reactions as well as bounds on reaction fluxes. While the classical definition of deficiency can be readily applied in the analysis of unconstrained, weakly reversible networks, it only provides an upper bound in the cases where relevant constraints on reaction fluxes are imposed. Here we propose the concept of effective deficiency, which provides a more accurate assessment of the network’s capacity to permit steady state variations at the complex level for constrained networks of any reversibility patterns. The effective deficiency relies on the concept of nonstoichiometric balanced complexes, which we have already shown to be present in real-world biochemical networks operating under flux constraints. Our results demonstrate that the effective deficiency of real-world biochemical networks is smaller than the classical deficiency, indicating the effects of reaction directionality and flux bounds on the variation of the complex formation rate vector at steady state. Y1 - 2023 U6 - https://doi.org/10.1038/s41598-023-41767-1 SN - 2045-2322 VL - 13 PB - Springer Nature CY - London 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 - Nendel, Claas A1 - Reckling, Moritz A1 - Debaeke, Philippe A1 - Schulz, Susanne A1 - Berg-Mohnicke, Michael A1 - Constantin, Julie A1 - Fronzek, Stefan A1 - Hoffmann, Munir A1 - Jakšić, Snežana A1 - Kersebaum, Kurt-Christian A1 - Klimek-Kopyra, Agnieszka A1 - Raynal, Hélène A1 - Schoving, Céline A1 - Stella, Tommaso A1 - Battisti, Rafael T1 - Future area expansion outweighs increasing drought risk for soybean in Europe JF - Global change biology N2 - The European Union is highly dependent on soybean imports from overseas to meet its protein demands. Individual Member States have been quick to declare self-sufficiency targets for plant-based proteins, but detailed strategies are still lacking. Rising global temperatures have painted an image of a bright future for soybean production in Europe, but emerging climatic risks such as drought have so far not been included in any of those outlooks. Here, we present simulations of future soybean production and the most prominent risk factors across Europe using an ensemble of climate and soybean growth models. Projections suggest a substantial increase in potential soybean production area and productivity in Central Europe, while southern European production would become increasingly dependent on supplementary irrigation. Average productivity would rise by 8.3% (RCP 4.5) to 8.7% (RCP 8.5) as a result of improved growing conditions (plant physiology benefiting from rising temperature and CO2 levels) and farmers adapting to them by using cultivars with longer phenological cycles. Suitable production area would rise by 31.4% (RCP 4.5) to 37.7% (RCP 8.5) by the mid-century, contributing considerably more than productivity increase to the production potential for closing the protein gap in Europe. While wet conditions at harvest and incidental cold spells are the current key challenges for extending soybean production, the models and climate data analysis anticipate that drought and heat will become the dominant limitations in the future. Breeding for heat-tolerant and water-efficient genotypes is needed to further improve soybean adaptation to changing climatic conditions. KW - genotypes KW - legumes KW - maturity groups KW - protein crops KW - protein transition KW - resilience Y1 - 2022 U6 - https://doi.org/10.1111/gcb.16562 SN - 1354-1013 SN - 1365-2486 VL - 29 IS - 5 SP - 1340 EP - 1358 PB - Wiley-Blackwell CY - Ocford [u.a] ER - TY - JOUR A1 - Shikangalah, Rosemary A1 - Mapani, Benjamin A1 - Mapaure, Isaac A1 - Herzschuh, Ulrike T1 - Responsiveness of Dichrostachys cinerea to seasonal variations in temperature and rainfall in central Namibia JF - Flora N2 - Woody plants provide natural archives of climatic variation which can be investigated by applying dendroclimatological methods. Such studies are limited in Southern Africa but have great potential of improving our understanding of past climates and plant functional adaptations in the region. This study therefore investigated the responsiveness of Dichrostachys cinerea to seasonal variations in temperature and rainfall at two sites in central Namibia, Waterberg and Kuzikus. Dichrostachys cinerea is one of the encroacher species thriving well in Namibia. A moving correlation and response function analysis were used to test its responsiveness to seasonal climatic variations over time. Dichrostachys cinerea growth rings showed relationships to late summer warming, lasting up to half of the rainy season. The results also revealed that past temperatures had been fluctuating and their influence on growth rings had been intensifying over the years, but to varying extents between the two sites. Temperature was a more important determinant of ring growth at the drier site (Kuzikus), while rainfall was more important at the wetter site (Waterberg). Growth ring responsiveness to rainfall was not immediate but showed a rather lagged pattern. We conclude that D. cinerea differentially responds to variations in rainfall and temperature across short climatic gradients. This study showed that the species, due to its somewhat wide ecological amplitude, has great potential for dendroclimatological studies in tropical regions. KW - Dendroclimatology KW - Dichrostachys cinerea KW - Growth rings KW - Namibia KW - Seasonal variation Y1 - 2021 U6 - https://doi.org/10.1016/j.flora.2021.151974 SN - 0367-2530 SN - 1618-0585 VL - 286 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Pohanková, Eva A1 - Hlavinka, Petr A1 - Kersebaum, Kurt-Christian A1 - Rodríguez, Alfredo A1 - Balek, Jan A1 - Bednařík, Martin A1 - Dubrovský, Martin A1 - Gobin, Anne A1 - Hoogenboom, Gerrit A1 - Moriondo, Marco A1 - Nendel, Claas A1 - Olesen, Jørgen E. E. A1 - Rötter, Reimund Paul A1 - Ruiz-Ramos, Margarita A1 - Shelia, Vakhtang A1 - Stella, Tommaso A1 - Hoffmann, Munir Paul A1 - Takáč, Jozef A1 - Eitzinger, Josef A1 - Dibari, Camilla A1 - Ferrise, Roberto A1 - Bláhová, Monika A1 - Trnka, Miroslav T1 - Expected effects of climate change on the production and water use of crop rotation management reproduced by crop model ensemble for Czech Republic sites JF - European journal of agronomy N2 - Crop rotation, fertilization and residue management affect the water balance and crop production and can lead to different sensitivities to climate change. To assess the impacts of climate change on crop rotations (CRs), the crop model ensemble (APSIM,AQUACROP, CROPSYST, DAISY, DSSAT, HERMES, MONICA) was used. The yields and water balance of two CRs with the same set of crops (winter wheat, silage maize, spring barley and winter rape) in a continuous transient run from 1961 to 2080 were simulated. CR1 was without cover crops and without manure application. Straw after the harvest was exported from the fields. CR2 included cover crops, manure application and crop residue retention left on field. Simulations were performed using two soil types (Chernozem, Cambisol) within three sites in the Czech Republic, which represent temperature and precipitation gradients for crops in Central Europe. For the description of future climatic conditions, seven climate scenarios were used. Six of them had increasing CO & nbsp;concentrations according RCP 8.5, one had no CO2 increase in the future. The output of an ensemble expected higher productivity by 0.82 t/ha/year and 2.04 t/ha/year for yields and aboveground biomass in the future (2051-2080). However, if the direct effect of a CO2 increase is not considered, the average yields for lowlands will be lower. Compared to CR1, CR2 showed higher average yields of 1.26 t/ha/year for current climatic conditions and 1.41 t/ha/year for future climatic conditions. For the majority of climate change scenarios, the crop model ensemble agrees on the projected yield increase in C3 crops in the future for CR2 but not for CR1. Higher agreement for future yield increases was found for Chernozem, while for Cambisol, lower yields under dry climate scenarios are expected. For silage maize, changes in simulated yields depend on locality. If the same hybrid will be used in the future, then yield reductions should be expected within lower altitudes. The results indicate the potential for higher biomass production from cover crops, but CR2 is associated with almost 120 mm higher evapotranspiration compared to that of CR1 over a 5-year cycle for lowland stations in the future, which in the case of the rainfed agriculture could affect the long-term soil water balance. This could affect groundwater replenishment, especially for locations with fine textured soils, although the findings of this study highlight the potential for the soil water-holding capacity to buffer against the adverse weather conditions. KW - Yields KW - Evapotranspiration KW - Winter wheat KW - Silage maize KW - Spring barley KW - Winter oilseed rape Y1 - 2022 U6 - https://doi.org/10.1016/j.eja.2021.126446 SN - 1161-0301 SN - 1873-7331 VL - 134 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Wang, Enli A1 - He, Di A1 - Wang, Jing A1 - Lilley, Julianne M. A1 - Christy, Brendan A1 - Hoffmann, Munir P. A1 - O'Leary, Garry A1 - Hatfield, Jerry L. A1 - Ledda, Luigi A1 - Deligios, Paola A. A1 - Grant, Brian A1 - Jing, Qi A1 - Nendel, Claas A1 - Kage, Henning A1 - Qian, Budong A1 - Rezaei, Ehsan Eyshi A1 - Smith, Ward A1 - Weymann, Wiebke A1 - Ewert, Frank T1 - How reliable are current crop models for simulating growth and seed yield of canola across global sites and under future climate change? JF - Climatic change N2 - To better understand how climate change might influence global canola production, scientists from six countries have completed the first inter-comparison of eight crop models for simulating growth and seed yield of canola, based on experimental data from six sites across five countries. A sensitivity analysis was conducted with a combination of five levels of atmospheric CO2 concentrations, seven temperature changes, five precipitation changes, together with five nitrogen application rates. Our results were in several aspects different from those of previous model inter-comparison studies for wheat, maize, rice, and potato crops. A partial model calibration only on phenology led to very poor simulation of aboveground biomass and seed yield of canola, even from the ensemble median or mean. A full calibration with additional data of leaf area index, biomass, and yield from one treatment at each site reduced simulation error of seed yield from 43.8 to 18.0%, but the uncertainty in simulation results remained large. Such calibration (with data from one treatment) was not able to constrain model parameters to reduce simulation uncertainty across the wide range of environments. Using a multi-model ensemble mean or median reduced the uncertainty of yield simulations, but the simulation error remained much larger than observation errors, indicating no guarantee that the ensemble mean/median would predict the correct responses. Using multi-model ensemble median, canola yield was projected to decline with rising temperature (2.5-5.7% per degrees C), but to increase with increasing CO2 concentration (4.6-8.3% per 100-ppm), rainfall (2.1-6.1% per 10% increase), and nitrogen rates (1.3-6.0% per 10% increase) depending on locations. Due to the large uncertainty, these results need to be treated with caution. We further discuss the need to collect new data to improve modelling of several key physiological processes of canola for increased confidence in future climate impact assessments. KW - AgMIP KW - Brassica napus L. KW - Model calibration KW - Model improvement; KW - Multimodel ensemble KW - Sensitivity analysis Y1 - 2022 U6 - https://doi.org/10.1007/s10584-022-03375-2 SN - 0165-0009 SN - 1573-1480 VL - 172 IS - 1-2 PB - Springer Nature CY - Dordrecht ER - TY - JOUR A1 - McHuron, Elizabeth A. A1 - Adamczak, Stephanie A1 - Arnould, John P. Y. A1 - Ashe, Erin A1 - Booth, Cormac A1 - Bowen, W. Don A1 - Christiansen, Fredrik A1 - Chudzinska, Magda A1 - Costa, Daniel P. A1 - Fahlman, Andreas A1 - Farmer, Nicholas A. A1 - Fortune, Sarah M. E. A1 - Gallagher, Cara A. A1 - Keen, Kelly A. A1 - Madsen, Peter T. A1 - McMahon, Clive R. A1 - Nabe-Nielsen, Jacob A1 - Noren, Dawn P. A1 - Noren, Shawn R. A1 - Pirotta, Enrico A1 - Rosen, David A. S. A1 - Speakman, Cassie N. A1 - Villegas-Amtmann, Stella A1 - Williams, Rob T1 - Key questions in marine mammal bioenergetics JF - Conservation physiology N2 - Bioenergetic approaches are increasingly used to understand how marine mammal populations could be affected by a changing and disturbed aquatic environment. There remain considerable gaps in our knowledge of marine mammal bioenergetics, which hinder the application of bioenergetic studies to inform policy decisions. We conducted a priority-setting exercise to identify high-priority unanswered questions in marine mammal bioenergetics, with an emphasis on questions relevant to conservation and management. Electronic communication and a virtual workshop were used to solicit and collate potential research questions from the marine mammal bioenergetic community. From a final list of 39 questions, 11 were identified as 'key'questions because they received votes from at least 50% of survey participants. Key questions included those related to energy intake (prey landscapes, exposure to human activities) and expenditure (field metabolic rate, exposure to human activities, lactation, time-activity budgets), energy allocation priorities, metrics of body condition and relationships with survival and reproductive success and extrapolation of data from one species to another. Existing tools to address key questions include labelled water, animal-borne sensors, mark-resight data from long-term research programs, environmental DNA and unmanned vehicles. Further validation of existing approaches and development of new methodologies are needed to comprehensively address some key questions, particularly for cetaceans. The identification of these key questions can provide a guiding framework to set research priorities, which ultimately may yield more accurate information to inform policies and better conserve marine mammal populations. Y1 - 2022 U6 - https://doi.org/10.1093/conphys/coac055 SN - 2051-1434 VL - 10 IS - 1 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Sporbert, Maria A1 - Jakubka, Desiree A1 - Bucher, Solveig Franziska A1 - Hensen, Isabell A1 - Freiberg, Martin A1 - Heubach, Katja A1 - König, Andreas A1 - Nordt, Birgit A1 - Plos, Carolin A1 - Blinova, Ilona A1 - Bonn, Aletta A1 - Knickmann, Barbara A1 - Koubek, Tomáš A1 - Linstädter, Anja A1 - Mašková, Tereza A1 - Primack, Richard B. A1 - Rosche, Christoph A1 - Shah, Manzoor A. A1 - Stevens, Albert-Dieter A1 - Tielbörger, Katja A1 - Träger, Sabrina A1 - Wirth, Christian A1 - Römermann, Christine T1 - Functional traits influence patterns in vegetative and reproductive plant phenology - a multi-botanical garden study JF - New phytologist N2 - Phenology has emerged as key indicator of the biological impacts of climate change, yet the role of functional traits constraining variation in herbaceous species' phenology has received little attention. Botanical gardens are ideal places in which to investigate large numbers of species growing under common climate conditions. We ask whether interspecific variation in plant phenology is influenced by differences in functional traits. We recorded onset, end, duration and intensity of initial growth, leafing out, leaf senescence, flowering and fruiting for 212 species across five botanical gardens in Germany. We measured functional traits, including plant height, absolute and specific leaf area, leaf dry matter content, leaf carbon and nitrogen content and seed mass and accounted for species' relatedness. Closely related species showed greater similarities in timing of phenological events than expected by chance, but species' traits had a high degree of explanatory power, pointing to paramount importance of species' life-history strategies. Taller plants showed later timing of initial growth, and flowered, fruited and underwent leaf senescence later. Large-leaved species had shorter flowering and fruiting durations. Taller, large-leaved species differ in their phenology and are more competitive than smaller, small-leaved species. We assume climate warming will change plant communities' competitive hierarchies with consequences for biodiversity. KW - botanical gardens KW - first flowering day KW - growing season length KW - leaf KW - traits KW - PhenObs phenological network KW - phylogeny Y1 - 2022 U6 - https://doi.org/10.1111/nph.18345 SN - 0028-646X SN - 1469-8137 VL - 235 IS - 6 SP - 2199 EP - 2210 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Vences, Miguel A1 - Köhler, Jörn A1 - Crottini, Angelica A1 - Hofreiter, Michael A1 - Hutter, Carl R. A1 - du Preez, Louis A1 - Preick, Michaela A1 - Rakotoarison, Andolalao A1 - Rancilhac, Loïs A1 - Raselimanana, Achille P. A1 - Rosa, Gonçalo M. A1 - Scherz, Mark D. A1 - Glaw, Frank T1 - An integrative taxonomic revision and redefinition of Gephyromantis (Laurentomantis) malagasius based on archival DNA analysis reveals four new mantellid frog species from Madagascar JF - Vertebrate zoology N2 - The subgenus Laurentomantis in the genus Gephyromantis contains some of the least known amphibian species of Madagascar. The six currently valid nominal species are rainforest frogs known from few individuals, hampering a full understanding of the species diversity of the clade. We assembled data on specimens collected during field surveys over the past 30 years and integrated analysis of mitochondrial and nuclear-encoded genes of 88 individuals, a comprehensive bioacoustic analysis, and morphological comparisons to delimit a minimum of nine species-level lineages in the subgenus. To clarify the identity of the species Gephyromantis malagasius, we applied a target-enrichment approach to a sample of the 110 year old holotype of Microphryne malagasia Methuen and Hewitt, 1913 to assign this specimen to a lineage based on a mitochondrial DNA barcode. The holotype clustered unambiguously with specimens previously named G. ventrimaculatus. Consequently we propose to consider Trachymantis malagasia ventrimaculatus Angel, 1935 as a junior synonym of Gephyromantis malagasius. Due to this redefinition of G. malagasius, no scientific name is available for any of the four deep lineages of frogs previously subsumed under this name, all characterized by red color ventrally on the hindlimbs. These are here formally named as Gephyromantis fiharimpe sp. nov., G. matsilo sp. nov., G. oelkrugi sp. nov., and G. portonae sp. nov. The new species are distinguishable from each other by genetic divergences of >4% uncorrected pairwise distance in a fragment of the 16S rRNA marker and a combination of morphological and bioacoustic characters. Gephyromantis fiharimpe and G. matsilo occur, respectively, at mid-elevations and lower elevations along a wide stretch of Madagascar's eastern rainforest band, while G. oelkrugi and G. portonae appear to be more range-restricted in parts of Madagascar's North East and Northern Central East regions. Open taxonomic questions surround G. horridus, to which we here assign specimens from Montagne d'Ambre and the type locality Nosy Be; and G. ranjomavo, which contains genetically divergent populations from Marojejy, Tsaratanana, and Ampotsidy. KW - Amphibia KW - Anura KW - archival DNA KW - Mantellidae KW - new species KW - phylogeography Y1 - 2022 U6 - https://doi.org/10.3897/vz.72.e78830 SN - 1864-5755 SN - 2625-8498 VL - 72 SP - 271 EP - 309 PB - Senckenberg Gesellschaft für Naturforschung CY - Frankfurt am Main ER - TY - JOUR A1 - Esmaeilishirazifard, Elham A1 - Usher, Louise A1 - Trim, Carol A1 - Denise, Hubert A1 - Sangal, Vartul A1 - Tyson, Gregory H. A1 - Barlow, Axel A1 - Redway, Keith F. A1 - Taylor, John D. A1 - Kremyda-Vlachou, Myrto A1 - Davies, Sam A1 - Loftus, Teresa D. A1 - Lock, Mikaella M. G. A1 - Wright, Kstir A1 - Dalby, Andrew A1 - Snyder, Lori A. S. A1 - Wuster, Wolfgang A1 - Trim, Steve A1 - Moschos, Sterghios A. T1 - Bacterial adaptation to venom in snakes and arachnida JF - Microbiology spectrum N2 - Notwithstanding their 3 to 5% mortality, the 2.7 million envenomation-related injuries occurring annually-predominantly across Africa, Asia, and Latin America-are also major causes of morbidity. Venom toxin-damaged tissue will develop infections in some 75% of envenomation victims, with E. faecalis being a common culprit of disease; however, such infections are generally considered to be independent of envenomation. Animal venoms are considered sterile sources of antimicrobial compounds with strong membrane-disrupting activity against multidrug-resistant bacteria. However, venomous bite wound infections are common in developing nations. Investigating the envenomation organ and venom microbiota of five snake and two spider species, we observed venom community structures that depend on the host venomous animal species and evidenced recovery of viable microorganisms from black-necked spitting cobra (Naja nigricollis) and Indian ornamental tarantula (Poecilotheria regalis) venoms. Among the bacterial isolates recovered from N. nigricollis, we identified two venom-resistant, novel sequence types of Enterococcus faecalis whose genomes feature 16 virulence genes, indicating infectious potential, and 45 additional genes, nearly half of which improve bacterial membrane integrity. Our findings challenge the dogma of venom sterility and indicate an increased primary infection risk in the clinical management of venomous animal bite wounds. IMPORTANCE Notwithstanding their 3 to 5% mortality, the 2.7 million envenomation-related injuries occurring annually-predominantly across Africa, Asia, and Latin America-are also major causes of morbidity. Venom toxin-damaged tissue will develop infections in some 75% of envenomation victims, with E. faecalis being a common culprit of disease; however, such infections are generally considered to be independent of envenomation. Here, we provide evidence on venom microbiota across snakes and arachnida and report on the convergent evolution mechanisms that can facilitate adaptation to black-necked cobra venom in two independent E. faecalis strains, easily misidentified by biochemical diagnostics. Therefore, since inoculation with viable and virulence gene-harboring bacteria can occur during envenomation, acute infection risk management following envenomation is warranted, particularly for immunocompromised and malnourished victims in resource-limited settings. These results shed light on how bacteria evolve for survival in one of the most extreme environments on Earth and how venomous bites must be also treated for infections. KW - drug resistance evolution KW - extremophiles KW - genome analysis KW - microbiome KW - multidrug resistance KW - venom Y1 - 2022 U6 - https://doi.org/10.1128/spectrum.02408-21 SN - 2165-0497 VL - 10 IS - 3 PB - American Society for Microbiology CY - Birmingham, Ala. ER - TY - JOUR A1 - 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 -