TY - JOUR A1 - Yang, Sizhong A1 - Liebner, Susanne A1 - Svenning, Mette Marianne A1 - Tveit, Alexander Tøsdal T1 - Decoupling of microbial community dynamics and functions in Arctic peat soil exposed to short term warming JF - Molecular ecology N2 - Temperature is an important factor governing microbe-mediated carbon feedback from permafrost soils. The link between taxonomic and functional microbial responses to temperature change remains elusive due to the lack of studies assessing both aspects of microbial ecology. Our previous study reported microbial metabolic and trophic shifts in response to short-term temperature increases in Arctic peat soil, and linked these shifts to higher CH4 and CO2 production rates (Proceedings of the National Academy of Sciences of the United States of America, 112, E2507-E2516). Here, we studied the taxonomic composition and functional potential of samples from the same experiment. We see that along a high-resolution temperature gradient (1-30 degrees C), microbial communities change discretely, but not continuously or stochastically, in response to rising temperatures. The taxonomic variability may thus in part reflect the varied temperature responses of individual taxa and the competition between these taxa for resources. These taxonomic responses contrast the stable functional potential (metagenomic-based) across all temperatures or the previously observed metabolic or trophic shifts at key temperatures. Furthermore, with rising temperatures we observed a progressive decrease in species diversity (Shannon Index) and increased dispersion of greenhouse gas (GHG) production rates. We conclude that the taxonomic variation is decoupled from both the functional potential of the community and the previously observed temperature-dependent changes in microbial function. However, the reduced diversity at higher temperatures might help explain the higher variability in GHG production at higher temperatures. KW - microbial community KW - permafrost KW - species diversity KW - stochastic KW - temperature gradient Y1 - 2021 U6 - https://doi.org/10.1111/mec.16118 SN - 0962-1083 SN - 1365-294X VL - 30 IS - 20 SP - 5094 EP - 5104 PB - Wiley-Blackwell CY - Oxford [u.a.] ER - TY - JOUR A1 - Hashemi, Seirana A1 - Razaghi-Moghadam, Zahra A1 - Laitinen, Roosa A. E. A1 - Nikoloski, Zoran T1 - Relative flux trade-offs and optimization of metabolic network functionalities JF - Computational and structural biotechnology journal N2 - Trade-offs between traits are present across different levels of biological systems and ultimately reflect constraints imposed by physicochemical laws and the structure of underlying biochemical networks. Yet, mechanistic explanation of how trade-offs between molecular traits arise and how they relate to optimization of fitness-related traits remains elusive. Here, we introduce the concept of relative flux trade-offs and propose a constraint-based approach, termed FluTOr, to identify metabolic reactions whose fluxes are in relative trade-off with respect to an optimized fitness-related cellular task, like growth. We then employed FluTOr to identify relative flux trade-offs in the genome-scale metabolic networks of Escherichia coli, Saccharomyces cerevisiae, and Arabidopsis thaliana. For the metabolic models of E. coli and S. cerevisiae we showed that: (i) the identified relative flux trade-offs depend on the carbon source used and that (ii) reactions that participated in relative trade-offs in both species were implicated in cofactor biosynthesis. In contrast to the two microorganisms, the relative flux trade-offs for the metabolic model of A. thaliana did not depend on the available nitrogen sources, reflecting the differences in the underlying metabolic network as well as the considered environments. Lastly, the established connection between relative flux trade-offs allowed us to identify overexpression targets that can be used to optimize fitness-related traits. Altogether, our computational approach and findings demonstrate how relative flux trade-offs can shape optimization of metabolic tasks, important in biotechnological applications. KW - Trade-offs KW - Metabolic networks KW - Fluxes KW - Overexpression targets KW - Growth Y1 - 2022 U6 - https://doi.org/10.1016/j.csbj.2022.07.038 SN - 2001-0370 VL - 20 SP - 3963 EP - 3971 PB - Research Network of Computational and Structural Biotechnology (RNCSB) CY - Gotenburg ER - TY - JOUR A1 - Wassermann, Birgit A1 - Abdelfattah, Ahmed A1 - Cernava, Tomislav A1 - Wicaksono, Wisnu A1 - Berg, Gabriele T1 - Microbiome-based biotechnology for reducing food loss post harvest JF - Current opinion in biotechnology N2 - Microbiomes have an immense potential to enhance plant resilience to various biotic and abiotic stresses. However, intrinsic microbial communities respond to changes in their host's physiology and environment during plant's life cycle. The potential of the inherent plant microbiome has been neglected for a long time, especially for the postharvest period. Currently, close to 50% of all produced fruits and vegetables are lost either during production or storage. Biological control of spoilage and storage diseases is still lacking sufficiency. Today, novel multiomics technologies allow us to study the microbiome and its responses on a community level, which will help to advance current classic approaches and develop more effective and robust microbiome-based solutions for fruit and vegetable storability, quality, and safety. Y1 - 2022 U6 - https://doi.org/10.1016/j.copbio.2022.102808 SN - 0958-1669 SN - 1879-0429 VL - 78 PB - Elsevier Science CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Arnold, Patrick A1 - Hagemann, Justus A1 - Gilissen, Emmanuel A1 - Hofreiter, Michael T1 - Otter shrew mitogenomes (Afrotheria, Potamogalidae) reconstructed from historical museum skins JF - Mitochondrial DNA. Part B N2 - African otter shrews (Potamogalidae) are Afrotherian mammals adapted to a semi-aquatic lifestyle. Given their rareness, genetic data on otter shrews are limited. By applying laboratory methods tuned for the recovery of archival DNA and an iterative mapping approach, we reconstructed whole mitochondrial genomes of the Giant (Potamogale velox) and Ruwenzori pygmy otter shrew (Micropotamogale ruwenzorii) from historical museum skins. Phylogenetic analyses are consistent with previous reports in recovering a sister relationship between African otter shrews and Malagasy tenrecs. The long branches separating both lineages, however, support their recognition as separate families. KW - tenrecs KW - Afrotheria KW - Africa KW - historical DNA Y1 - 2022 U6 - https://doi.org/10.1080/23802359.2022.2122747 SN - 2380-2359 VL - 7 IS - 9 SP - 1699 EP - 1701 PB - Taylor & Francis Group CY - London ER - TY - JOUR A1 - Thongthaisong, Patch A1 - Kasada, Minoru A1 - Grossart, Hans-Peter A1 - Wollrab, Sabine T1 - Critical role of parasite-mediated energy pathway on community response to nutrient enrichment JF - Ecology and evolution N2 - Parasites form an integral part of food webs, however, they are often ignored in classic food web theory or limited to the investigation of trophic transmission pathways. Specifically, direct consumption of parasites by nonhost predators is rarely considered, while it can contribute substantially to energy flow in food webs. In aquatic systems, chytrids constitute a major group of fungal parasites whose free-living infective stages (zoospores) form a highly nutritional food source to zooplankton. Thereby, the consumption of zoospores can create an energy pathway from otherwise inedible phytoplankton to zooplankton ( "mycoloop "). This parasite-mediated energy pathway might be of special importance during phytoplankton blooms dominated by inedible or toxic primary producers like cyanobacteria, which are on the rise with eutrophication and global warming. We theoretically investigated community dynamics and energy transfer in a food web consisting of an edible nonhost and an inedible host phytoplankton species, a parasitic fungus, and a zooplankton species grazing on edible phytoplankton and fungi. Food web dynamics were investigated along a nutrient gradient contrasting nonadaptive zooplankton species representative for filter feeders like cladocerans and zooplankton with the ability to actively adapt their feeding preferences like many copepod species. Overall, the importance of the mycoloop for zooplankton increases with nutrient availability. This increase is smooth for nonadaptive consumers. For adaptive consumers, we observe an abrupt shift from an almost exclusive preference for edible phytoplankton at low nutrient levels to a strong preference for parasitic fungi at high nutrient levels. The model predicts that parasitic fungi could contribute up to 50% of the zooplankton diet in nutrient-rich environments, which agrees with empirical observations on zooplankton gut content from eutrophic systems during blooms of inedible diatoms or cyanobacteria. Our findings highlight the role of parasite-mediated energy pathways for predictions of energy flow and community composition under current and future environmental change. KW - adaptive preference KW - energy flow KW - food web KW - mycoloop KW - parasite-mediated KW - energy pathway KW - parasites KW - parasitic fungi Y1 - 2022 U6 - https://doi.org/10.1002/ece3.9622 SN - 2045-7758 VL - 12 IS - 12 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Wicaksono, Wisnu Adi A1 - Erschen, Sabine A1 - Krause, Robert A1 - Müller, Henry A1 - Cernava, Tomislav A1 - Berg, Gabriele T1 - Enhanced survival of multi-species biofilms under stress is promoted by low-abundant but antimicrobial-resistant keystone species JF - Journal of hazardous materials : environmental control, risk assessment, impact and management N2 - Multi-species biofilms are more resistant against stress compared to single-species biofilms. However, the mechanisms underlying this common observation remain elusive. Therefore, we studied biofilm formation of well-known opportunistic pathogens (Acinetobacter baumanii, Enterococcus faecium, Escherichia coli, Staphylococcus haemolyticus and Stenotrophomonas maltophilia) in various approaches. Synergistic effects in their multi species biofilms were observed. Using metatranscriptomics, changes in the gene expression of the involved members became evident, and provided explanations for the improved survivability under nutrient limitation and exposure to disinfectants. Genes encoding proteins for vitamin B6 synthesis and iron uptake were linked to synergism in the multi-species biofilm under nutrient-limited conditions. Our study indicates that sub-lethal concentrations of an alcohol-based disinfectant enhance biofilm yields in multi-species assemblages. A reduction of the dominant taxa in the multi-species biofilm under disinfectant pressure allowed minor taxa to bloom. The findings underline the importance of minor but antimicrobial-resistant species that serve as "protectors" for the whole assemblage due to upregulation of genes involved in defence mechanisms and biofilm formation. This ultimately results in an increase in the total yield of the multi-species biofilm. We conclude that inter-species interactions may be crucial for the survival of opportunistic pathogens; especially under conditions that are typically found under hospital settings. KW - Biofilm KW - Opportunistic pathogen KW - Synergism KW - Multi-species KW - Metatranscriptomic Y1 - 2022 U6 - https://doi.org/10.1016/j.jhazmat.2021.126836 SN - 0304-3894 SN - 1873-3336 VL - 422 PB - Science Direct CY - New York, NY [u.a.] ER - TY - JOUR A1 - Olimi, Expedito A1 - Bickel, Samuel A1 - Wicaksono, Wisnu Adi A1 - Kusstatscher, Peter A1 - Matzer, Robert A1 - Cernava, Tomislav A1 - Berg, Gabriele T1 - Deciphering the microbial composition of biodynamic preparations and their effects on the apple rhizosphere microbiome JF - Frontiers in soil science N2 - Soil microbial communities are crucial for plant growth and are already depleted by anthropogenic activities. The application of microbial transplants provides a strategy to restore beneficial soil traits, but less is known about the microbiota of traditional inoculants used in biodynamic agriculture. In this study, we used amplicon sequencing and quantitative PCR to decipher microbial communities of composts, biodynamic manures, and plant preparations from Austria and France. In addition, we investigated the effect of extracts derived from biodynamic manure and compost on the rhizosphere microbiome of apple trees. Microbiota abundance, composition, and diversity of biodynamic manures, plant preparations, and composts were distinct. Microbial abundances ranged between 1010-1011 (bacterial 16S rRNA genes) and 109-1011 (fungal ITS genes). The bacterial diversity was significantly higher in biodynamic manures compared to compost without discernible differences in abundance. Fungal diversity was not significantly different while abundance was increased in biodynamic manures. The microbial communities of biodynamic manures and plant preparations were specific for each production site, but all contain potentially plant-beneficial bacterial genera. When applied in apple orchards, biodynamic preparations (extracts) had the non-significant effect of reducing bacterial and fungal abundance in apple rhizosphere (4 months post-application), while increasing fungal and lowering bacterial Shannon diversity. One to four months after inoculation, individual taxa indicated differential abundance. We observed the reduction of the pathogenic fungus Alternaria, and the enrichment of potentially beneficial bacterial genera such as Pseudomonas. Our study paves way for the science-based adaptation of empirically developed biodynamic formulations under different farming practices to restore the vitality of agricultural soils. KW - biodynamic farming KW - compost microbiome KW - biodynamic manures KW - biodynamic preparations KW - rhizosphere microbiome KW - 16S rRNA/ITS amplicon sequencing KW - organic soil amendments Y1 - 2022 U6 - https://doi.org/10.3389/fsoil.2022.1020869 SN - 2673-8619 VL - 2 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Ullrich, Jessica A1 - Göhmann, Philip Jonas A1 - Zemella, Anne A1 - Kubick, Stefan T1 - Oligomerization of the heteromeric γ-aminobutyric acid receptor GABAB in a eukaryotic cell-free system JF - Scientific reports N2 - Understanding the assembly mechanism and function of membrane proteins is a fundamental problem in biochemical research. Among the membrane proteins, G protein-coupled receptors (GPCRs) represent the largest class in the human body and have long been considered to function as monomers. Nowadays, the oligomeric assembly of GPCRs is widely accepted, although the functional importance and therapeutic intervention remain largely unexplored. This is partly due to difficulties in the heterologous production of membrane proteins. Cell-free protein synthesis (CFPS) with its endogenous endoplasmic reticulum-derived structures has proven as a technique to address this issue. In this study, we investigate for the first time the conceptual CFPS of a heteromeric GPCR, the gamma-aminobutyric acid receptor type B (GABA(B)), from its protomers BR1 and BR2 using a eukaryotic cell-free lysate. Using a fluorescence-based proximity ligation assay, we provide evidence for colocalization and thus suggesting heterodimerization. We prove the heterodimeric assembly by a bioluminescence resonance energy transfer saturation assay providing the manufacturability of a heterodimeric GPCR by CFPS. Additionally, we show the binding of a fluorescent orthosteric antagonist, demonstrating the feasibility of combining the CFPS of GPCRs with pharmacological applications. These results provide a simple and powerful experimental platform for the synthesis of heteromeric GPCRs and open new perspectives for the modelling of protein-protein interactions. Accordingly, the presented technology enables the targeting of protein assemblies as a new interface for pharmacological intervention in disease-relevant dimers. Y1 - 2022 U6 - https://doi.org/10.1038/s41598-022-24885-0 SN - 2045-2322 VL - 12 IS - 1 PB - Springer Nature CY - [London] ER - TY - JOUR A1 - Egli, Lukas A1 - Mehrabi, Zia A1 - Seppelt, Ralf T1 - More farms, less specialized landscapes, and higher crop diversity stabilize food supplies JF - Environmental research letters N2 - Theoretical and empirical studies show increased diversity in crops, supply chains, and markets helps stabilize food systems. At the same time global commodity markets and industrial agriculture have driven homogenization of local and regional production systems, and consolidated power in fewer larger specialized farms and distributers. This is a global challenge, with no obvious global solutions. An important question therefore, is how individual countries can build their own resilience through maintaining or increasing diversity within their borders. Here we show, using farm level data from Germany, that spreading production risk by growing the same crops across different farms carries stabilizing benefits by allowing for increased spatiotemporal asynchrony within crops. We also find that increasing asynchrony between the year-to-year production of different crops has stabilizing effects on food supply. Importantly, the benefits of increasing crop diversity are lower in specialized landscapes growing the same crop on large patches. Our results illustrate clear benefits of diversified crops, producers, and agricultural landscapes to buffer supply side shocks, and for incorporation in subsidies and other regulatory measures aimed at stabilizing food systems. KW - agroecology KW - climate variability KW - resilience KW - spatial heterogeneity KW - supply shocks Y1 - 2021 U6 - https://doi.org/10.1088/1748-9326/abf529 SN - 1748-9326 VL - 16 IS - 5 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Meier, Laura A1 - Brauns, Mario A1 - Grimm, Volker A1 - Weitere, Markus A1 - Frank, Karin T1 - MASTIFF: a mechanistic model for cross-scale analyses of the functioning of multiple stressed riverine ecosystems JF - Ecological modelling : international journal on ecological modelling and engineering and systems ecolog N2 - Riverine ecosystems provide various ecosystem services. One of these services is the biological control of eutrophication by grazing macroinvertebrates. However, riverine ecosystems are subject to numerous stressors that affect community structure, functions, and stability properties. To manage rivers in response to these stressors, a better understanding of the ecological functions underlying services is needed. This requires consideration of local and regional processes, which requires a metacommunity approach that links local food webs through drift and dispersal. This takes into account long-distance interactions that can compensate for local effects of stressors. Our modular model MASTIFF (Multiple Aquatic STressors In Flowing Food webs) is stage-structured, spatially explicit, and includes coupled food webs consisting of benthic resource-consumer interactions between biofilm and three competing macroinvertebrate functional types. River segments are unidirectionally connected through organismal drift and bidirectionally connected through dispersal. Climate and land use stressors along the river can be accounted for. Biocontrol of biofilm eutrophication is used as an exemplary functional indicator. We present the model and the underlying considerations, and show in an exemplary application that explicit consideration of drift and dispersal is essential for understanding the spatiotemporal biocontrol of eutrophication. The combination of drift and dispersal reduced eutrophication events. While dispersal events were linked to specific periods in the species life cycles and therefore had limited potential to control, drift was ubiquitous and thus responded more readily to changing habitat conditions. This indicates that drift is an important factor for coping with stress situations. Finally, we outline and discuss the potential and possibilities of MASTIFF as a tool for mechanistic, cross-scale analyses of multiple stressors to advance knowledge of riverine ecosystem functioning. KW - modeling KW - riverine ecosystems KW - drift and dispersal KW - multiple stressors KW - functioning KW - biocontrol of eutrophication Y1 - 2022 U6 - https://doi.org/10.1016/j.ecolmodel.2022.110007 SN - 0304-3800 SN - 1872-7026 VL - 470 PB - Elsevier CY - Amsterdam ER -