@article{StachDeepPimenteletal.2025, author = {Stach, Tom Lennard and Deep, Aman and Pimentel, Iris Madge and Buchner, Dominik and Borton, Mikayla A. and Soares, Andr{\´e} and Starke, J{\"o}rn and Bornemann, Till L.V. and Rehsen, Philipp M. and Dreger, Ken L. and Boenigk, Jens and Vos, Matthijs and Leese, Florian and Beißer, Daniela and Probst, Alexander J.}, title = {Complex compositional and metabolic response of river sediment microbiomes to multiple anthropogenic stressors}, series = {ISME Communications}, volume = {2025}, journal = {ISME Communications}, publisher = {Oxford Academic}, doi = {10.1093/ismeco/ycaf079}, pages = {32}, year = {2025}, abstract = {Rivers face constant anthropogenic stress, resulting in significant changes in microbial community composition. What remains unclear is whether stream microbiomes exhibit distinct resilience patterns in composition and/or activity upon exposure to different stressors. By subjecting 64 river-connected mesocosms to multiple stressors, we show that sediment microbiomes of small lowland rivers are highly sensitive to low flow velocity. This stress results in altered community compositions incapable of mitigating the applied stressor within a two-week timeframe despite functional stability (inferred via metagenomics). Transcriptomics revealed a systematic heat shock response in the community and a highly active, metabolically versatile, uncharacterized anaerobic keystone species. Increases in temperature (+ 3.5°C) or salinity (+ 0.5 mS/cm) elicited minor responses at community and transcriptomic levels (e.g., upregulation of photosystems). Following a two-week recovery, transcriptomic-inferred stress responses vanished completely, underscoring the river microbiome resilience. Given the complex community responses observed at the activity and compositional levels, we conclude that maintaining natural river flow is vital to preventing energy loss and reduced microbiome activity in river sediments.}, language = {en} } @article{DeepSieberBodenetal., author = {Deep, Aman and Sieber, Guido and Boden, Lisa and David, Gwendoline M. and Baikova, Daria and Buchner, Dominik and Starke, J{\"o}rn and Stach, Tom Lennard and Reinders, Torben and Hadžiomerović, Una and Beszteri, S{\´a}ra and Probst, Alexander J. and Boenigk, Jens and Beißer, Daniela}, title = {A metatranscriptomic exploration of fungal and bacterial contributions to allochthonous leaf litter decomposition in the streambed}, series = {PeerJ}, volume = {2025}, journal = {PeerJ}, publisher = {PeerJ Publishing}, doi = {10.7717/peerj.19120}, pages = {20 Seiten}, abstract = {The decomposition of organic matter is essential for sustaining the health of freshwater ecosystems by enabling nutrient recycling, sustaining food webs, and shaping habitat conditions, which collectively enhance ecosystem resilience and productivity. Bacteria and fungi play a crucial role in this process by breaking down coarse particulate organic matter (CPOM), such as leaf litter, into nutrients available for other organisms. However, the specific contribution of bacteria and their functional interactions with fungi in freshwater sediments have yet to be thoroughly explored. In the following study, we enriched organic matter through the addition of alder (Alnus glutinosa) leaves into artificial stream channels (AquaFlow mesocosms). We then investigated enzyme expression, metabolic pathways, and community composition of fungi and bacteria involved in the degradation of CPOM through metatranscriptomics and amplicon sequencing. Enzymes involved in the degradation of lignin, cellulose, and hemicellulose were selectively upregulated with increased organic matter. Analysis of ITS and 16S rRNA gene sequences revealed that during decomposition, fungal communities were predominantly composed of Basidiomycota and Ascomycota, while bacterial communities were largely dominated by Pseudomonadota and Bacteroidota. The similar gene expression patterns of CPOM degradation related enzymes observed between bacteria and fungi indicate potential functional interaction between these microbial groups. This correlation in enzyme expression may indicate that bacteria and fungi are jointly involved in the breakdown of coarse particulate organic matter, potentially through mutualistic interaction. This study uncovers the specific enzymatic activities of bacteria and fungi and the importance of microbial interactions in organic matter decomposition, revealing their central role in facilitating nutrient cycling and maintaining the ecological health and stability of freshwater ecosystems.}, language = {en} }