Sondersammlungen
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Publication Antiviral defense systems in the rumen microbiome(2025) Sáenz, Johan S.; Rios-Galicia, Bibiana; Seifert, JanaThe continuous interaction between phages and their respective hosts has resulted in the evolution of multiple bacterial immune mechanisms. However, the diversity and prevalence of antiviral defense systems in complex communities are still unknown. We therefore investigated the diversity and abundance of viral defense systems in 3,038 high-quality bacterial and archaeal genomes from the rumen. In total, 14,241 defense systems and 31,948 antiviral-related genes were identified. Those genes represented 114 unique system types grouped into 49 families. We observed a high prevalence of defense systems in the genomes. However, the number of defense systems, defense system families, and system density varied widely from genome to genome. Additionally, the number of defense system per genome correlated positively with the number of defense system families and the genome size. Restriction modification, Abi, and cas system families were the most common, but many rare systems were present in only 1% of the genomes. Antiviral defense systems are prevalent and diverse in the rumen, but only a few are dominant, indicating that most systems are rarely present. However, the collection of systems throughout the rumen may represent a pool of mechanisms that can be shared by different members of the community and modulate the phage–host interaction.Publication Data on transgenerational memory effects of photosynthetic efficiency of twelve wheat varieties under elevated carbon dioxide concentration and reduced soil water availability(2025) Berauer, Bernd J.; Chaudhary, Suraj; Kottmann, Lorenz; Schweiger, Andreas H.This data represents ACi curves of twelve winter wheat varieties, which were grown under elevated and ambient CO2 concentrations within a FACE experiment and the subsequent F1 generation was exposed to ambient and elevated CO2 concentrations in a highly controlled environment using climate chambers. The 12 winter wheat genotypes (Triticum aestivum L.) were selected based on their susceptibilty to leaf rust (Puccinia triticina Eriks.) and Fusarium head blight (Fusarium graminearum Schwabe) according to the descriptive variety list of the German Federal Office of Plant Varietes (Beschreibende Sortenliste, Bundessortenamt 2024). The aim was to obtain a diverse set of varieties with the widest possible range of susceptibilities to leaf rust and fusarium head blight. Photosynthesis was measured using the novel Dynamic Assimilation Technique, thus not with the common steady-state approach. The individual wheat plants were measured twice, once under saturating soil water availability (θFC) and once under reduced soil water availability (θcsoil). θcsoil represents the gravimetric water content when the soil matric potential drops below the root matric potential, thus the onset of plant drought stress (sensu Cai et al. [2]). The photosynthesis data was used to fit ACi curves and extract the maximum Rubisco carboxylation rate [Vcmax], maximum rate of electron transport [Jmax] and dark respiration [Rd]. At both measurements we determined BBCH and plant height to quantify plant morphological development, as well as leaf water potential to quantify plant ecohydrologic status. At the end of the experiment, biomass was harvested and reported. Further, we provide environmental data of the climate chambers in use. Within the data repository, we provide comprehensive experimental data on the investigation of transgenerational memory effects on photosynthetic efficiency. We provide photosynthetic raw data as well as processed (merged) and derived (extracted ACi fit) data. Additionally, we provide the R-code to reproduce the calculation of the derived parameters. Data on transgenerational memory effects (that is, the influence of the parental environment on offspring phenotype and performance) are scarce, i.e. on the adaptive capacity of the photosynthetic apparatus. Thus, the data provided here can contribute to closing this gap. The highly controlled environment allows to closely investigate cause-effect relationships, thereby contributing to a mechanistic understanding of the transgenerational memory effects on photosynthetic efficiency and how this is altered by reduced soil water availability. By using a recently developed methodological approach, the data contributes to further investigate the quality of the method and establish it within the field of plant ecophysiology.Publication Enhanced crop diversity but not smaller field size benefit bats in agricultural landscapes(2025) Hiller, Thomas; Gall, Friederike; Grass, Ingo; Hiller, Thomas; Ecology of Tropical Agricultural Systems, University of Hohenheim, Stuttgart, Germany; Gall, Friederike; Ecology of Tropical Agricultural Systems, University of Hohenheim, Stuttgart, Germany; Grass, Ingo; Ecology of Tropical Agricultural Systems, University of Hohenheim, Stuttgart, GermanyContext: Farmland biodiversity continues to decline due to the expansion and intensification of agriculture. Historically, efforts to conserve farmland biodiversity have focused on conserving habitats outside agricultural production areas. More recently, attention has turned to the conservation potential of the cropland matrix, where reducing field size and increasing crop diversity to promote crop heterogeneity can significantly benefit farmland biodiversity. Bats are one group of farmland species that have experienced dramatic declines over recent decades. Objectives: Here we investigated the effects of crop heterogeneity (crop diversity, field size) and landscape structural elements (e.g. length of linear structures, distance to forest, proportion of semi-natural habitat) on the activity of bat functional groups. Results: Increasing crop diversity led to greater bat activity, especially for open space foraging bats. However, contrary expectations, bat activity was not affected by heterogeneity in crop configuration, i.e. field edge density. Furthermore, structural landscape elements, including hedgerows and distance to forest, were important predictors of bat activity, especially for species that hunt in highly cluttered spaces. While crop diversity clearly benefited bat activity, the lack of effect of crop configurational heterogeneity on bat foraging activity may suggest heterogeneityarea trade-offs and intensive pesticide use in small-scale vegetable production. Conclusions: Therefore, in addition to maintaining high levels of crop diversity, promoting hedgerows and tree lines between farmland and woodland may facilitate bat activity across the agricultural landscape matrix. The combination of high crop heterogeneity and structural elements provides favorable hunting grounds for bats and may promote their conservation in agricultural landscapes.Publication Insect conservation in agricultural landscapes needs both high crop heterogeneity and semi-natural habitats(2024) Tassoni, Sara; Becker, David; Kasten, Marit Kinga; Moriníere, Jérôme; Grass, IngoIdentifying landscapes that are suitable for both biodiversity conservation and agricultural production is a major challenge. Traditionally, much research has focused on biodiversity conservation outside of agricultural production areas, e.g., in semi-natural habitats. In contrast, recent research has mainly focused on the potential of crop heterogeneity. This includes both compositional (crop diversity) and configurational heterogeneity (field border density). However, if and how crop heterogeneity, and semi-natural habitats interact to shape insect diversity in agricultural landscapes remains poorly understood. Here we investigated the combined effects of crop diversity, field border density, and semi-natural habitats (i.e., grassland proportion, hedge density) on insect diversity. We sampled insect communities from 14 – 17 June 2021 with pan traps in 27 study landscapes (500 m x 500 m) covering independent gradients of these landscape variables and identified a total of 587 insect species with DNA metabarcoding. We found that field border density mediated the effects of crop diversity, grassland proportion, and hedge density on insect richness. At low levels of field border density (i.e., landscapes with mostly large fields), effects were either neutral (crop diversity), negative (grassland proportion) or weakly positive (hedge density). By contrast, at high levels of field border density, crop diversity, grassland proportion, and hedge density all exerted positive effects on insect richness. Responses to crop heterogeneity and semi-natural habitat differed among trophic groups of insects (decomposers, herbivores, parasitoids, predators). While variation in richness of herbivorous insects followed the patterns of the overall richness, decomposer richness was not related to any of the investigated variables. Predator richness increased with hedge density in landscapes, whereas parasitoid richness increased when high levels of field border density and grassland proportion coincided. Our study shows that increasing crop heterogeneity is a viable strategy for promoting insect diversity in agricultural landscapes. However, the effects of the amount of remaining semi-natural habitats, such as grassland or hedges, are mediated by configurational heterogeneity, and vary between trophic groups. Efforts to conserve insects in agricultural landscapes must therefore focus on both increasing the heterogeneity of the crop matrix by promoting crop diversity and increasing the density of field borders, while also maintaining or restoring semi-natural habitats as important source habitats for insect species.Publication Mating-type analysis in Diaporthe isolates from soybean in central Europe(2025) Hosseini, Behnoush; Käfer, Lena Sophia; Link, Tobias Immanuel; Cai, LeiSpecies of the genus Diaporthe have a mating-type system with the two mating types MAT1-1 and MAT1-2, like other ascomycetes. They can either be heterothallic, which means that any isolate only possesses one of the two mating types and needs a mating partner for sexual reproduction, or homothallic, which means that they possess both mating types and are self-fertile. For several Diaporthe species, no sexual reproduction has been observed so far. Using PCR with primers specific to the defining genes MAT1-1-1 and MAT1-2-1 , we determined the mating types of 33 isolates of Diaporthe caulivora , D. eres , D. longicolla , and D. novem from central Europe. In addition, we partially sequenced the mating-type genes of 25 isolates. We found that different D. longicolla isolates either possess MAT1-1-1 or MAT1-2-1, making the species heterothallic, which is in contrast to previous studies and the general assumption that D. longicolla only reproduces asexually. D. eres and D. novem were also found to be heterothallic. Using genomic sequence information and re-sequencing of DNA and RNA, we identified the MAT1-1-1 gene in D. caulivora and present here the full sequence of the mating-type locus of this homothallic species. Finally, we used sequence information from MAT1-1-1 and MAT1-2-1 , respectively, for improved phylogenetic resolution of our isolates.Publication Metabolome fingerprinting reveals the presence of multiple nitrification inhibitors in biomass and root exudates of Thinopyrum intermedium(2024) Issifu, Sulemana; Acharya, Prashamsha; Schöne, Jochen; Kaur-Bhambra, Jasmeet; Gubry-Rangin, Cecile; Rasche, FrankBiological Nitrification Inhibition (BNI) encompasses primarily NH4 +-induced release of secondary metabolites to impede the rhizospheric nitrifying microbes from per- forming nitrification. The intermediate wheatgrass Thinopyrum intermedium (Kernza®) is known for exuding several nitrification inhibition traits, but its BNI potential has not yet been identified. We hypothesized Kernza® to evince BNI potential through the presence and release of multiple BNI metabolites. The presence of BNI metabolites in the biomass of Kernza® and annual winter wheat (Triticum aestivum) and in the root exudates of hydroponically grown Kernza®, were fingerprinted using HPLC-DAD and GC–MS/MS analyses. Growth bioassays involving ammonia-oxidizing bacteria (AOB) and archaea (AOA) strains were conducted to assess the influence of the crude root metabolome of Kernza® and selected metabolites on nitrification. In most instances, significant concentrations of various metabolites with BNI potential were observed in the leaf and root biomass of Kernza® compared to annual winter wheat. Furthermore, NH4 + nutrition triggered the exudation of various phenolic BNI metabolites. Crude root exudates of Kernza® inhibited multiple AOB strains and completely inhibited N. viennensis. Vanillic acid, caffeic acid, vanillin, and phenylalanine suppressed the growth of all AOB and AOA strains tested, and reduced soil nitrification, while syringic acid and 2,6-dihydroxybenzoic acid were ineffective. We demonstrated the considerable role of the Kernza® metabolome in suppressing nitrification through active exudation of multiple nitrification inhibitors.Publication The non-nutritive sweetener rebaudioside a enhances phage infectivity(2025) Marongiu, Luigi; Brzozowska, Ewa; Brykała, Jan; Burkard, Markus; Schmidt, Herbert; Szermer-Olearnik, Bożena; Venturelli, Sascha; Marongiu, Luigi; Department of Nutritional Biochemistry, University of Hohenheim, Garbenstraße 30, 70599, Stuttgart, Germany; Brzozowska, Ewa; Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 12 R. Weigl St, 53114, Wroclaw, Poland; Brykała, Jan; Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 12 R. Weigl St, 53114, Wroclaw, Poland; Burkard, Markus; Department of Nutritional Biochemistry, University of Hohenheim, Garbenstraße 30, 70599, Stuttgart, Germany; Schmidt, Herbert; Department of Food Microbiology, Institute of Food Science and Biotechnology, University of Hohenheim, Garbenstraße 28, 70599, Stuttgart, Germany; Szermer-Olearnik, Bożena; Department of Experimental Oncology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 12 R. Weigl St, 53114, Wroclaw, Poland; Venturelli, Sascha; Department of Nutritional Biochemistry, University of Hohenheim, Garbenstraße 30, 70599, Stuttgart, GermanyNon-nutritive sweeteners (NNS) are widely employed in foodstuffs. However, it has become increasingly evident that their consumption is associated with bacterial dysbiosis, which, in turn, is linked to several health conditions, including a higher risk of type 2 diabetes and cancer. Among the NNS, stevia, whose main component is rebaudioside A (rebA), is gaining popularity in the organic food market segment. While the effect of NNS on bacteria has been established, the impact of these sweeteners on bacterial viruses (phages) has been neglected, even though phages are crucial elements in maintaining microbial eubiosis. The present study sought to provide a proof-of-concept of the impact of NNS on phage infectivity by assessing the binding of rebA to phage proteins involved in the infection process of enteropathogenic bacteria, namely the fiber protein gp17 of Yersinia enterocolitica phage φYeO3-12 and the tubular baseplate protein gp31 of Klebsiella pneumoniae phage 32. We employed docking analysis and a panel of in vitro confirmatory tests (microscale thermophoresis, RedStarch ™ depolymerization, adsorption, and lysis rates). Docking analysis indicated that NNS can bind to both fiber and baseplate proteins. Confirmatory assays demonstrated that rebA can bind gp31 and that such binding increased the protein’s enzymatic activity. Moreover, the binding of rebA to gp17 resulted in a decrease in the adsorption rate of the recombinant protein to its host but increased the Yersinia bacteriolysis caused by the whole phage compared to unexposed controls. These results support the hypothesis that NNS can impair phage infectivity, albeit the resulting effect on the microbiome remains to be elucidated.Publication Prostaglandin E2 signaling through prostaglandin E receptor subtype 2 and Nurr1 induces fibroblast growth factor 23 production(2024) Feger, Martina; Hammerschmidt, Katharina; Liesche, lona; Rausch, Steffen; Alber, Jana; Föller, MichaelBone cells produce fibroblast growth factor 23 (FGF23), a hormone regulating renal phosphate and vitamin D homeostasis, and a paracrine factor produced in further tissues. Chronic kidney disease and cardiovascular disorders are associated with early elevations of plasma FGF23 levels associated with clinical outcomes. FGF23 production is dependent on many conditions including inflammation. Prostaglandin E2 (PGE2) is a major eicosanoid with a broad role in pain, inflammation, and fever. Moreover, it regulates renal blood flow, renin secretion, natriuresis as well as bone formation through prostaglandin E receptor 2 (EP2). Here, we studied the role of PGE2 and its signaling for the production of FGF23. Osteoblast-like UMR-106 cells were exposed to EP receptor agonists, antagonists or RNAi. Wild type and EP2 knockout mice were treated with stable EP2 agonist misoprostol. Fgf23 or Nurr1 gene expression was determined by quantitative real-time PCR, hormone and further blood parameters by enzyme-linked immunosorbent assay and colorimetric methods. PGE2 and EP2 agonists misoprostol and butaprost enhanced FGF23 production in UMR-106 cells, effects mediated by EP2 and transcription factor Nurr1. A single dose of misoprostol up-regulated bone Fgf23 expression and FGF23 serum levels in wild type mice with subtle effects on parameters of mineral metabolism only. Compared to wild type mice, the FGF23 effect of misoprostol was significantly lower in EP2-deficient mice. To conclude, PGE2 signaling through EP2 and Nurr1 induces FGF23 production. Given the broad physiological and pathophysiological implications of PGE2 signaling, this effect is likely of clinical relevance.Publication tsCRISPR based identification of Rab proteins required for the recycling of Drosophila TRPL ion channel(2024) Zeger, Matthias; Stanisławczyk, Lena Sarah; Bulić,Marija; Binder, Andrea Maria; Huber, ArminIn polarized cells, the precise regulation of protein transport to and from the plasma membrane is crucial to maintain cellular function. Dysregulation of intracellular protein transport in neurons can lead to neurodegenerative diseases such as Retinitis Pigmentosa, Alzheimer’s and Parkinson’s disease. Here we used the light-dependent transport of the TRPL (transient receptor potential-like) ion channel in Drosophila photoreceptor cells to study the role of Rab proteins in TRPL recycling. TRPL is located in the rhabdomeric membrane of dark-adapted flies, but it is transported out of the rhabdomere upon light exposure and localizes at the Endoplasmatic Reticulum within 12 h. Upon subsequent dark adaptation, TRPL is recycled back to the rhabdomeric membrane within 90 min. To screen for Rab proteins involved in TRPL recycling, we established a tissue specific (ts) CRISPR/Cas9-mediated knock- out of individual Rab genes in Drosophila photoreceptors and assessed TRPL localization using an eGFP tagged TRPL protein in the intact eyes of these mutants. We observed severe TRPL recycling defects in the knockouts of Rab3, Rab4, Rab7, Rab32, and RabX2. Using immunohistochemistry, we further showed that Rab3 and RabX2 each play a significant role in TRPL recycling and also influence TRPL transport. We localized Rab3 to the late endosome in Drosophila photoreceptors and observed disruption of TRPL transport to the ER in Rab3 knock-out mutants. TRPL transport from the ER to the rhabdomere ensues from the trans-Golgi where RabX2 is located. We observed accumulated TRPL at the trans-Golgi in RabX2 knock-out mutants. In summary, our study reveals the requirement of specific Rab proteins for different steps of TRPL transport in photoreceptor cells and provides evidence for a unique retrograde recycling pathway of TRPL from the ER via the trans-Golgi