bioRxiv Channel: Centre for Microbiology and Environmental Systems Science https://biorxiv.org This feed contains articles for bioRxiv Channel "Centre for Microbiology and Environmental Systems Science " bioRxiv bioRxiv https://biorxiv.org <![CDATA[ Woeseiales transcriptional response in Arctic fjord surface sediment ]]> https://biorxiv.org/cgi/content/short/2020.06.04.134015v1?rss=1" Buongiorno, J. Sipes, K. Wasmund, K. Loy, A. Lloyd, K. G. 2020-06-05 doi:10.1101/2020.06.04.134015 Cold Spring Harbor Laboratory Press 2020-06-05 <![CDATA[ Novel taxa of Acidobacteriota involved in seafloor sulfur cycling ]]> https://biorxiv.org/cgi/content/short/2020.10.01.322446v1?rss=1" Flieder, M. Buongiorno, J. Herbold, C. Hausmann, B. Rattei, T. Lloyd, K. G. Loy, A. Wasmund, K. 2020-10-01 doi:10.1101/2020.10.01.322446 Cold Spring Harbor Laboratory Press 2020-10-01 <![CDATA[ Anaerobic microbial degradation of protein and lipid macromolecules in subarctic marine sediment ]]> https://biorxiv.org/cgi/content/short/2020.04.27.061291v1?rss=1" Pelikan, C. Wasmund, K. Glombitza, C. Hausmann, B. Herbold, C. Flieder, M. Loy, A. 2020-04-28 doi:10.1101/2020.04.27.061291 Cold Spring Harbor Laboratory Press 2020-04-28 <![CDATA[ Growth arrest in the active rare biosphere ]]> https://biorxiv.org/cgi/content/short/284430v1?rss=1" Hausmann, B. Pelikan, C. Rattei, T. Loy, A. Pester, M. 2018-03-19 doi:10.1101/284430 Cold Spring Harbor Laboratory Press 2018-03-19 <![CDATA[ Diversity decoupled from sulfur isotope fractionation in a sulfate reducing microbial community ]]> https://biorxiv.org/cgi/content/short/518837v1?rss=1" Colangelo, J. Pelikan, C. Herbold, C. Altschuler, I. Loy, A. Whyte, L. Wing, B. 2019-01-11 doi:10.1101/518837 Cold Spring Harbor Laboratory Press 2019-01-11 <![CDATA[ DNA-foraging bacteria in the seafloor ]]> https://biorxiv.org/cgi/content/short/528695v1?rss=1" Wasmund, K. Pelikan, C. Watzka, M. Richter, A. Noel, A. C. Hubert, C. R. J. Rattei, T. Hofmann, T. Herbold, C. W. Loy, A. 2019-01-23 doi:10.1101/528695 Cold Spring Harbor Laboratory Press 2019-01-23 <![CDATA[ Glacial runoff promotes deep burial of sulfur cycling-associated microorganisms in marine sediments ]]> https://biorxiv.org/cgi/content/short/661207v1?rss=1" Pelikan, C. Jaussi, M. Wasmund, K. Seidenkrantz, M.-S. Pearce, C. Kuzyk, Z. Z. A. Herbold, C. W. Roy, H. Kjeldsen, K. U. Loy, A. 2019-06-06 doi:10.1101/661207 Cold Spring Harbor Laboratory Press 2019-06-06 <![CDATA[ Bottled aqua incognita: Microbiota assembly and dissolved organic matter diversity in natural mineral waters ]]> https://biorxiv.org/cgi/content/short/154732v1?rss=1" Lesaulnier, C. C. Herbold, C. W. Pelikan, C. Berry, D. Gerard, C. Le Coz, X. Gagnot, S. Niggemann, J. Dittmar, T. Singer, G. A. Loy, A. 2017-06-23 doi:10.1101/154732 Cold Spring Harbor Laboratory Press 2017-06-23 <![CDATA[ Peatland Acidobacteria with a dissimilatory sulfur metabolism ]]> https://biorxiv.org/cgi/content/short/197269v1?rss=1" Hausmann, B. Pelikan, C. Herbold, C. W. Koestlbacher, S. Albertsen, M. Eichorst, S. A. Glavina del Rio, T. Huemer, M. Nielsen, P. H. Rattei, T. Stingl, U. Tringe, S. G. Trojan, D. Wentrup, C. Woebken, D. Pester, M. Loy, A. 2017-10-02 doi:10.1101/197269 Cold Spring Harbor Laboratory Press 2017-10-02 <![CDATA[ Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses ]]> https://biorxiv.org/cgi/content/short/053090v1?rss=1" Simon Roux Jennifer R Brum Bas E. Dutilh Shinichi Sunagawa Melissa B Duhaime Alexander Loy Bonnie T Poulos Natalie Solonenko Elena Lara Julie Poulain Stephane PESANT Stefanie Kandels-Lewis Céline Dimier Marc Picheral Sarah Searson Corinne Cruaud Adriana Alberti Carlos M. M Duarte Josep M M Gasol Dolors Vaqué Tara Oceans Coordinators Peer Bork Silvia G Acinas Patrick Wincker Matthew B Sullivan 2016-05-12 doi:10.1101/053090 Cold Spring Harbor Laboratory Press 2016-05-12 <![CDATA[ Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting ]]> https://biorxiv.org/cgi/content/short/2020.06.09.141952v1?rss=1" Mueller, A. J. Jung, M.-Y. Strachan, C. R. Herbold, C. W. Kirkegaard, R. H. Wagner, M. Daims, H. 2020-06-10 doi:10.1101/2020.06.09.141952 Cold Spring Harbor Laboratory Press 2020-06-10 <![CDATA[ A refined set of rRNA-targeted oligonucleotide probes for in situ detection and quantification of ammonia-oxidizing bacteria ]]> https://biorxiv.org/cgi/content/short/2020.05.27.119446v1?rss=1" Lukumbuzya, M. Kristensen, J. M. Kitzinger, K. Pommerening-Roeser, A. Nielsen, P. H. Wagner, M. Daims, H. Pjevac, P. 2020-05-27 doi:10.1101/2020.05.27.119446 Cold Spring Harbor Laboratory Press 2020-05-27 <![CDATA[ Ammonia-oxidizing archaea possess a wide range of cellular ammonia affinities ]]> https://biorxiv.org/cgi/content/short/2021.03.02.433310v1?rss=1" Jung, M.-Y. Sedlacek, C. J. Kits, K. D. Mueller, A. J. Rhee, S.-K. Hink, L. Nicol, G. W. Bayer, B. Lehtovirta-Morley, L. Wright, C. L. de la Torre, J. R. Herbold, C. W. Pjevac, P. Daims, H. Wagner, M. 2021-03-02 doi:10.1101/2021.03.02.433310 Cold Spring Harbor Laboratory Press 2021-03-02 <![CDATA[ Sustained nitrogen loss in a symbiotic association of Comammox Nitrospira and Anammox bacteria ]]> https://biorxiv.org/cgi/content/short/2020.10.12.336248v1?rss=1" Gottshall, E. Y. Bryson, S. J. Cogert, K. I. Landreau, M. Sedlacek, C. J. Stahl, D. A. Daims, H. Winkler, M. 2020-10-12 doi:10.1101/2020.10.12.336248 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ A novel oxidase from Alcaligenes sp. HO-1 oxidizes hydroxylamine to N2 ]]> https://biorxiv.org/cgi/content/short/2020.08.20.256677v1?rss=1" Wu, M.-R. Miao, L.-L. Liu, Y. Hou, T.-T. Ai, G.-M. Ma, L. Zhu, H.-Z. Zhu, Y.-X. Gao, X.-Y. Qin, Y.-L. Wu, T. Shen, X.-H. Jiang, C.-Y. Herbold, C. W. Wagner, M. Li, D.-F. Liu, Z.-P. Liu, S.-J. 2020-08-20 doi:10.1101/2020.08.20.256677 Cold Spring Harbor Laboratory Press 2020-08-20 <![CDATA[ Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira ]]> https://biorxiv.org/cgi/content/short/2020.03.05.977850v1?rss=1" Daebeler, A. Kitzinger, K. Koch, H. Herbold, C. W. Steinfeder, M. Schwarz, J. Zechmeister, T. Karst, S. M. Albertsen, M. Nielsen, P. H. Wagner, M. Daims, H. 2020-03-06 doi:10.1101/2020.03.05.977850 Cold Spring Harbor Laboratory Press 2020-03-06 <![CDATA[ Transcriptomic response of Nitrosomonas europaea transitioned from ammonia- to oxygen-limited steady-state growth ]]> https://biorxiv.org/cgi/content/short/765727v1?rss=1" Sedlacek, C. J. Giguere, A. T. Dobie, M. D. Mellbye, B. L. Ferrell, R. V. Woebken, D. Sayavedra-Soto, L. Bottomley, P. Daims, H. Wagner, M. Pjevac, P. 2019-09-11 doi:10.1101/765727 Cold Spring Harbor Laboratory Press 2019-09-11 <![CDATA[ AmoA-targeted polymerase chain reaction primers for the specific detection and quantification of comammox Nitrospira in the environment ]]> https://biorxiv.org/cgi/content/short/096891v1?rss=1" Pjevac, P. Schauberger, C. Poghosyan, L. Herbold, C. W. van Kessel, M. A. Daebeler, A. Steinberger, M. Jetten, M. S. Lucker, S. Wagner, M. Daims, H. 2016-12-27 doi:10.1101/096891 Cold Spring Harbor Laboratory Press 2016-12-27 <![CDATA[ Cultivation and genomic analysis of Candidatus Nitrosocaldus islandicus, a novel obligately thermophilic ammonia-oxidizing Thaumarchaeon ]]> https://biorxiv.org/cgi/content/short/235028v1?rss=1" Daebeler, A. Herbold, C. Vierheilig, J. Sedlacek, C. J. Pjevac, P. Albersten, M. Kirkegaard, R. H. de la Torre, J. R. Daims, H. Wagner, M. 2017-12-15 doi:10.1101/235028 Cold Spring Harbor Laboratory Press 2017-12-15 <![CDATA[ Evolutionary recent dual obligatory symbiosis among adelgids indicates a transition between fungus and insect associated lifestyles ]]> https://biorxiv.org/cgi/content/short/2020.10.16.342642v1?rss=1" Szabo, G. Schulz, F. Manzano-Marin, A. Toenshoff, E. R. Horn, M. 2020-10-16 doi:10.1101/2020.10.16.342642 Cold Spring Harbor Laboratory Press 2020-10-16 <![CDATA[ Acquisition of a type 3 secretion signal in an housekeeping enzyme shaped glycogen metabolism in Chlamydia ]]> https://biorxiv.org/cgi/content/short/2020.10.11.335026v1?rss=1" Triboulet, S. N'Gadjaga, M. D. Niragire, B. Köstlbacher, S. Horn, M. Subtil, A. 2020-10-12 doi:10.1101/2020.10.11.335026 Cold Spring Harbor Laboratory Press 2020-10-12 <![CDATA[ Happens in the best of subfamilies: Replacement and internalisation of co-obligate Serratia endosymbionts in Lachninae aphids ]]> https://biorxiv.org/cgi/content/short/059816v1?rss=1" Alejandro Manzano-Marín Gitta Szabó Jean-Christophe Simon Matthias Horn Amparo Latorre 2016-06-19 doi:10.1101/059816 Cold Spring Harbor Laboratory Press 2016-06-19 <![CDATA[ The hidden pangenome: comparative genomics reveals pervasive diversity in symbiotic and free-living sulfur-oxidizing bacteria ]]> https://biorxiv.org/cgi/content/short/2020.12.11.421487v1?rss=1" Ansorge, R. Romano, S. Sayavedra, L. Rubin-Blum, M. Gruber-Vodicka, H. R. Scilipoti, S. Molari, M. Dubilier, N. Petersen, J. 2020-12-11 doi:10.1101/2020.12.11.421487 Cold Spring Harbor Laboratory Press 2020-12-11 <![CDATA[ Anaerobic sulfur oxidation underlies adaptation of a chemosynthetic symbiont to oxic-anoxic interfaces ]]> https://biorxiv.org/cgi/content/short/2020.03.17.994798v1?rss=1" Bulgheresi, S. Paredes, G. F. Viehboek, T. Lee, R. Palatinszky, M. Mausz, M. Reipert, S. Schintlmeister, A. Volland, J.-M. Hirschfeld, C. Wagner, M. Berry, D. Markert, S. Koenig, L. 2020-03-18 doi:10.1101/2020.03.17.994798 Cold Spring Harbor Laboratory Press 2020-03-18 <![CDATA[ Diversity matters: Deep-sea mussels harbor multiple symbiont strains ]]> https://biorxiv.org/cgi/content/short/531459v1?rss=1" Ansorge, R. Romano, S. Sayavedra, L. Kupczok, A. Tegetmeyer, H. E. Dubilier, N. Petersen, J. 2019-01-26 doi:10.1101/531459 Cold Spring Harbor Laboratory Press 2019-01-26 <![CDATA[ Vitamin and amino acid auxotrophy in anaerobic consortia operating under methanogenic condition ]]> https://biorxiv.org/cgi/content/short/128660v1?rss=1" Hubalek, V. Buck, M. Tan, B. Foght, J. Wendeberg, A. Berry, D. Bertilsson, S. Eiler, A. 2017-04-19 doi:10.1101/128660 Cold Spring Harbor Laboratory Press 2017-04-19 <![CDATA[ Ecology and evolution of chlamydial symbionts of arthropods ]]> https://biorxiv.org/cgi/content/short/2022.03.11.483957v1?rss=1" Halter, T. Koestlbacher, S. Collingro, A. Sixt, B. S. Toenshoff, E. R. Hendrickx, F. Kostanjsek, R. Horn, M. 2022-03-13 doi:10.1101/2022.03.11.483957 Cold Spring Harbor Laboratory Press 2022-03-13 <![CDATA[ One to host them all: genomics of the diverse bacterial endosymbionts of the spider Oedothorax gibbosus ]]> https://biorxiv.org/cgi/content/short/2022.05.31.494226v1?rss=1" Halter, T. Köstlbacher, S. Rattei, T. Hendrickx, F. Manzano-Marin, A. Horn, M. 2022-05-31 doi:10.1101/2022.05.31.494226 Cold Spring Harbor Laboratory Press 2022-05-31 <![CDATA[ Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction ]]> https://biorxiv.org/cgi/content/short/2023.06.27.546762v1?rss=1" 60% taxonomically resolved, uncultured family-level lineages and recommendations on existing dsrAB primers for environmental surveys. Our work summarizes insights into the inferred ecophysiology of newly discovered SRM, puts SRM diversity into context of the major recent changes in bacterial and archaeal taxonomy, and provides an up-to-date framework to study SRM in a global context. One sentence summarySulfate/sulfite reducing microorganisms are shaping Earths interconnected sulfur and carbon cycles since the Archaean: this legacy unfolds in 27 archaeal and bacterial phyla encountered in diverse marine, terrestrial, and deep-subsurface environments. ]]> Diao, M. Dyksma, S. Koeksoy, E. Ngugi, D. K. Anantharaman, K. Loy, A. Pester, M. 2023-06-27 doi:10.1101/2023.06.27.546762 Cold Spring Harbor Laboratory Press 2023-06-27 <![CDATA[ A novel taurine-respiring murine gut bacterium contributes to colonization resistance against enteropathogens ]]> https://biorxiv.org/cgi/content/short/2022.10.05.510937v1?rss=1" Ye, H. Borusak, S. Eberl, C. Hanson, B. T. Zwirzitz, B. Herbold, C. Pjevac, P. Hausmann, B. Stecher, B. Schleheck, D. Loy, A. 2022-10-05 doi:10.1101/2022.10.05.510937 Cold Spring Harbor Laboratory Press 2022-10-05 <![CDATA[ Sulfoquinovose is differently degraded by the mouse and human gut microbiota and not metabolized by the host ]]> https://biorxiv.org/cgi/content/short/2025.01.22.634256v1?rss=1" Krasenbrink, J. Hanson, B. T. Weiss, A. S. Borusak, S. Tanabe, T. S. Lang, M. Aichinger, G. Hausmann, B. Berry, D. Richter, A. Marko, D. Mussmann, M. Schleheck, D. Stecher, B. Loy, A. 2025-01-22 doi:10.1101/2025.01.22.634256 Cold Spring Harbor Laboratory Press 2025-01-22 <![CDATA[ Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts ]]> https://biorxiv.org/cgi/content/short/2025.01.10.632322v1?rss=1" Kujawska, M. Seki, D. Chalklen, L. Malsom, J. Goatcher, S. Christoforou, I. Mitra, S. Crouch, L. Hall, L. J. 2025-01-11 doi:10.1101/2025.01.10.632322 Cold Spring Harbor Laboratory Press 2025-01-11 <![CDATA[ Pervasive phosphorylation by phage T7 kinase disarms bacterial defenses ]]> https://biorxiv.org/cgi/content/short/2024.12.20.629319v1?rss=1" Bartolec, T. Mitosch, K. Potel, C. Corona, F. Yang, A. L. J. Burtscher, M. L. Koumoutsi, A. Becher, I. Bobonis, J. Karcher, N. Galardini, M. Typas, A. Savitski, M. M. 2024-12-20 doi:10.1101/2024.12.20.629319 Cold Spring Harbor Laboratory Press 2024-12-20 <![CDATA[ The methane-cycling microbiome in intact and degraded permafrost soils of the pan-Arctic ]]> https://biorxiv.org/cgi/content/short/2024.12.16.628686v1?rss=1" Wang, H. Lindemann, E. Liebmann, P. Varsadiya, M. Svenning, M. M. Waqas, M. Petters, S. Richter, A. Guggenberger, G. Barta, J. Urich, T. 2024-12-16 doi:10.1101/2024.12.16.628686 Cold Spring Harbor Laboratory Press 2024-12-16 <![CDATA[ Soil microbes prefer organic acids over sugars in simulated root exudation ]]> https://biorxiv.org/cgi/content/short/2024.12.03.626624v1?rss=1" Wiesenbauer, J. Gorka, S. Jenab, K. Schuster, R. Kumar, N. Rottensteiner, C. Koenig, A. Kraemer, S. Inselsbacher, E. Kaiser, C. 2024-12-03 doi:10.1101/2024.12.03.626624 Cold Spring Harbor Laboratory Press 2024-12-03 <![CDATA[ Soil bacterial neutral lipid fatty acids: Markers for carbon storage or necromass? ]]> https://biorxiv.org/cgi/content/short/2024.12.02.626346v1?rss=1" Gorka, S. Canarini, A. Schmidt, H. Kaiser, C. 2024-12-02 doi:10.1101/2024.12.02.626346 Cold Spring Harbor Laboratory Press 2024-12-02 <![CDATA[ The adaptation of chlamydiae to facultative host multicellularity ]]> https://biorxiv.org/cgi/content/short/2024.11.28.625222v1?rss=1" Helmlinger, L. Arthofer, P. Cyran, N. Collingro, A. Horn, M. 2024-11-28 doi:10.1101/2024.11.28.625222 Cold Spring Harbor Laboratory Press 2024-11-28 <![CDATA[ Contribution of ammonia oxidizers to inorganic carbon fixation in the dark ocean ]]> https://biorxiv.org/cgi/content/short/2024.11.16.623942v1?rss=1" Bayer, B. Kitzinger, K. Paul, N. L. Albers, J. B. Saito, M. A. Wagner, M. Carlson, C. A. Santoro, A. E. 2024-11-16 doi:10.1101/2024.11.16.623942 Cold Spring Harbor Laboratory Press 2024-11-16 <![CDATA[ Strong family- and guild-specific responses of arbuscular mycorrhizal fungi to long-term deficiencies and imbalances of N, P and K ]]> https://biorxiv.org/cgi/content/short/2024.11.06.622229v1?rss=1" Jenab, K. Alteio, L. Guseva, K. Gorka, S. Darcy, S. Fuchslueger, L. Canarini, A. Martin, V. S. Wiesenbauer, J. Spiegel, F. Imai, B. Schmidt, H. Hage-Ahmed, K. Poetsch, E. Richter, A. Jansa, J. Kaiser, C. 2024-11-08 doi:10.1101/2024.11.06.622229 Cold Spring Harbor Laboratory Press 2024-11-08 <![CDATA[ Shewanella is a putative producer of polyunsaturated fatty acids in the gut soil of the composting earthworm Eisenia fetida ]]> https://biorxiv.org/cgi/content/short/2024.03.31.587473v1?rss=1" Wittlinger, J.-P. Castejon, N. Hausmann, B. Berry, D. Schnorr, S. L. 2024-04-01 doi:10.1101/2024.03.31.587473 Cold Spring Harbor Laboratory Press 2024-04-01 <![CDATA[ Entorhinal grid-like codes for visual space during memory formation ]]> https://biorxiv.org/cgi/content/short/2024.09.27.615339v1?rss=1" Graichen, L. P. Linder, M. S. Keuter, L. Jensen, O. Doeller, C. F. Lamm, C. Staudigl, T. Wagner, I. C. 2024-09-27 doi:10.1101/2024.09.27.615339 Cold Spring Harbor Laboratory Press 2024-09-27 <![CDATA[ Novel high-quality amoeba genomes reveal widespread codon usage mismatch between giant viruses and their hosts ]]> https://biorxiv.org/cgi/content/short/2024.09.23.614596v1?rss=1" Willemsen, A. Manzano-Marin, A. Horn, M. 2024-09-25 doi:10.1101/2024.09.23.614596 Cold Spring Harbor Laboratory Press 2024-09-25 <![CDATA[ Human-derived microRNA 21 regulates indole and L-tryptophan biosynthesis transcripts in a prominent gut symbiont ]]> https://biorxiv.org/cgi/content/short/2024.08.15.608161v1?rss=1" Flanagan, K. Gassner, K. Lang, M. Ozelyte, J. Hausmann, B. Crepaz, D. Pjevac, P. Gasche, C. Berry, D. Vesely, C. Pereira, F. C. 2024-08-15 doi:10.1101/2024.08.15.608161 Cold Spring Harbor Laboratory Press 2024-08-15 <![CDATA[ Niche and spatial partitioning restrain ecological equivalence among microbes along aquatic redox gradient ]]> https://biorxiv.org/cgi/content/short/2024.08.09.607300v1?rss=1" Kajan, K. Kirkegaard, R. Pjevac, P. Orlic, S. Mehrshad, M. 2024-08-09 doi:10.1101/2024.08.09.607300 Cold Spring Harbor Laboratory Press 2024-08-09 <![CDATA[ Distinct microbial communities are linked to organic matter properties in millimetre-sized soil aggregates ]]> https://biorxiv.org/cgi/content/short/2024.08.01.606122v1?rss=1" Simon, E. Guseva, K. Darcy, S. Alteio, L. Pjevac, P. Schmidt, H. Jenab, K. Ranits, C. Kaiser, C. 2024-08-03 doi:10.1101/2024.08.01.606122 Cold Spring Harbor Laboratory Press 2024-08-03 <![CDATA[ Bacteria face trade-offs in the decomposition of complex biopolymers ]]> https://biorxiv.org/cgi/content/short/2023.10.03.560709v1?rss=1" Guseva, K. Mohrlok, M. Alteio, L. Schmidt, H. Pollak, S. Kaiser, C. 2023-10-03 doi:10.1101/2023.10.03.560709 Cold Spring Harbor Laboratory Press 2023-10-03 <![CDATA[ Acidotolerant soil nitrite oxidiser 'Candidatus Nitrobacter laanbroekii' NHB1 alleviates constraints on growth of acidophilic soil ammonia oxidisers ]]> https://biorxiv.org/cgi/content/short/2024.07.06.601931v1?rss=1" Hink, L. Bachtsevani, E. Meng, Y. Sedlacek, C. J. Lee, S. Daims, H. Wagner, M. Gubry-Rangin, C. de Boer, W. Hazard, C. Prosser, J. I. Nicol, G. W. 2024-07-07 doi:10.1101/2024.07.06.601931 Cold Spring Harbor Laboratory Press 2024-07-07 <![CDATA[ Microflora Danica: the atlas of Danish environmental microbiomes ]]> https://biorxiv.org/cgi/content/short/2024.06.27.600767v1?rss=1" Singleton, C. M. Jensen, T. B. Delogu, F. Sorensen, E. A. Jorgensen, V. R. Karst, S. M. Yang, Y. Knudsen, K. S. Sereika, M. Petriglieri, F. Knuttson, S. Dall, S. M. Kirkegaard, R. H. Kristensen, J. M. Woodcroft, B. J. Speth, D. R. Aroney, S. The Microflora Danica Consortium, Wagner, M. Dueholm, M. M. Nielsen, P. H. Albertsen, M. 2024-06-27 doi:10.1101/2024.06.27.600767 Cold Spring Harbor Laboratory Press 2024-06-27 <![CDATA[ Genome-wide sweeps create fundamental ecological units in the human gut microbiome ]]> https://biorxiv.org/cgi/content/short/2024.05.25.595854v1?rss=1" Yu, X. A. Strachan, C. R. Herbold, C. W. Lang, M. Gasche, C. Makristathis, A. Segata, N. Pollak, S. Tett, A. Polz, M. F. 2024-05-25 doi:10.1101/2024.05.25.595854 Cold Spring Harbor Laboratory Press 2024-05-25 <![CDATA[ Insights into the early-life chemical exposome of Nigerian infants and potential correlations with the developing gut microbiome ]]> https://biorxiv.org/cgi/content/short/2023.11.08.566030v1?rss=1" View larger version (30K): org.highwire.dtl.DTLVardef@61ad1aorg.highwire.dtl.DTLVardef@ab99a5org.highwire.dtl.DTLVardef@1f44c17org.highwire.dtl.DTLVardef@1af8857_HPS_FORMAT_FIGEXP M_FIG C_FIG ]]> Oesterle, I. Ayeni, K. I. Ezekiel, C. N. Berry, D. Rompel, A. Warth, B. 2023-11-11 doi:10.1101/2023.11.08.566030 Cold Spring Harbor Laboratory Press 2023-11-11 <![CDATA[ The interplay between light, arsenic and H2O2 controls oxygenic photosynthesis in a Precambrian analog cyanobacterial mat. ]]> https://biorxiv.org/cgi/content/short/2024.04.27.591451v1?rss=1" Castillejos Sepulveda, A. Speth, D. R. Kerl, C. Doherty-Weason, D. Vignale, F. A. Santha, K. Chennu, A. Mohr, W. Merz, E. de Beer, D. Farias, M. E. Klatt, J. 2024-04-27 doi:10.1101/2024.04.27.591451 Cold Spring Harbor Laboratory Press 2024-04-27 <![CDATA[ Discordance between phylogenomic datasets in aphids: who is telling the truth? ]]> https://biorxiv.org/cgi/content/short/2024.04.12.589189v1?rss=1" Jousselin, E. Coeur d'acier, A. Clamens, A.-l. Galan, M. Cruaud, C. Barbe, V. Manzano-Marin, A. 2024-04-15 doi:10.1101/2024.04.12.589189 Cold Spring Harbor Laboratory Press 2024-04-15 <![CDATA[ Unexpectedly dense colonization of soil pore space by microbes ]]> https://biorxiv.org/cgi/content/short/2024.04.10.588810v1?rss=1" Schmidt, H. Schlueter, S. Raynaud, X. Felde, V. J. Zeller-Plumhoff, B. Richter, A. Nunan, N. 2024-04-13 doi:10.1101/2024.04.10.588810 Cold Spring Harbor Laboratory Press 2024-04-13 <![CDATA[ Expanding the cultivated human archaeome by targeted isolation of novel Methanobrevibacter strains from fecal samples ]]> https://biorxiv.org/cgi/content/short/2024.04.10.588852v1?rss=1" Duller, S. Vrbancic, S. Szydlowski, L. Mahnert, A. Blohs, M. Predl, M. Kumpitsch, C. Zrim, V. Hoegenauer, C. Kosciolek, T. Schmitz, R. A. Eberhard, A. Dragovan, M. Schmidberger, L. Zurabischvili, T. Weinberger, V. Moser, A. M. Kolb, D. Pernitsch, D. Mohammadzadeh, R. Kuehnast, T. Rattei, T. Moissl-Eichinger, C. 2024-04-11 doi:10.1101/2024.04.10.588852 Cold Spring Harbor Laboratory Press 2024-04-11 <![CDATA[ The predicted secreted proteome of activated sludge microorganisms indicate distinct nutrient niches ]]> https://biorxiv.org/cgi/content/short/2024.02.27.582363v1?rss=1" 100 heme-binding motifs. Myxococcota have exceptionally large secreted protein complements, probably related to predatory lifestyles and/or complex cell cycles. Many Gammaproteobacteria MAGs (mostly former Betaproteobacteria) encode few or no secreted hydrolases, but many periplasmic substrate-binding proteins and ABC- and TRAP-transporters, suggesting they are mostly sustained by small molecules. Together, this study provides a comprehensive overview of how WWTPs microorganisms interact with the environment, providing new insights into their functioning and niche partitioning. ImportanceWastewater treatment plants are critical biotechnological systems that clean wastewater, allowing the water to reenter the environment and limit eutrophication and pollution. They are also increasingly important for recovery of resources. They function primarily by the activity of microorganisms, which act as a living sponge, taking-up and transforming nutrients, organic material and pollutants. Despite much research, many microorganisms in WWTPs are uncultivated and poorly characterized, limiting our understanding of their functioning. Here, we analyzed a large collection of high-quality metagenome-assembled genomes from WWTPs for encoded secreted enzymes and proteins, with special emphasis on those used to degrade organic material. This analysis showed highly distinct secreted proteome profiles among different major phylogenetic groups of microorganisms, thereby providing new insights into how different groups function and co-exist in activated sludge. This knowledge will contribute to a better understanding of how to efficiently manage and exploit WWTP microbiomes. ]]> Wasmund, K. Singleton, C. Dueholm, M. S. Wagner, M. Nielsen, P. H. 2024-02-29 doi:10.1101/2024.02.27.582363 Cold Spring Harbor Laboratory Press 2024-02-29 <![CDATA[ Mechanism of bacterial predation via ixotrophy ]]> https://biorxiv.org/cgi/content/short/2024.01.29.577165v1?rss=1" Lien, Y.-W. Amendola, D. Lee, K. S. Bartlau, N. Xu, J. Furusawa, G. Polz, M. F. Stocker, R. Weiss, G. L. PIlhofer, M. 2024-01-29 doi:10.1101/2024.01.29.577165 Cold Spring Harbor Laboratory Press 2024-01-29 <![CDATA[ Nitrous oxide respiration in acidophilic methanotrophs ]]> https://biorxiv.org/cgi/content/short/2024.01.15.574570v1?rss=1" Awala, S. I. Gwak, J.-H. Kim, Y. Jung, M.-Y. Dunfield, P. F. Wagner, M. Rhee, S.-K. 2024-01-16 doi:10.1101/2024.01.15.574570 Cold Spring Harbor Laboratory Press 2024-01-16 <![CDATA[ Candidatus Nitrosocosmicus members are the dominant archaea associated with pepper (Capsicum annuum L.) and ginseng (Panax ginseng C.A. Mey.) plants rhizospheres ]]> https://biorxiv.org/cgi/content/short/2024.01.08.574571v1?rss=1" Lee, U.-J. Gwak, J.-H. Choi, S. Jung, M.-Y. Lee, T. K. Ryu, H. Awala, S. I. Wanek, W. Wagner, M. Quan, Z.-X. Rhee, S.-K. 2024-01-08 doi:10.1101/2024.01.08.574571 Cold Spring Harbor Laboratory Press 2024-01-08 <![CDATA[ Novel nitrifying symbiont lineages are vertically inherited and widespread in marine sponges ]]> https://biorxiv.org/cgi/content/short/2023.12.23.573102v1?rss=1" Glasl, B. Luter, H. M. Damjanovic, K. Kitzinger, K. Mueller, A. J. Mahler, L. Engelberts, J. P. Rix, L. Osvatic, J. T. Hausmann, B. Seneca, J. Daims, H. Pjevac, P. Wagner, M. 2023-12-23 doi:10.1101/2023.12.23.573102 Cold Spring Harbor Laboratory Press 2023-12-23 <![CDATA[ Characteristics of putative keystones in the healthy adult human gut microbiome as determined by correlation network analysis ]]> https://biorxiv.org/cgi/content/short/2023.11.20.567895v1?rss=1" Bauchinger, F. Seki, D. Berry, D. 2023-11-21 doi:10.1101/2023.11.20.567895 Cold Spring Harbor Laboratory Press 2023-11-21 <![CDATA[ Chlamydiae in cnidarians: Shared functional potential despite broad taxonomic diversity ]]> https://biorxiv.org/cgi/content/short/2023.11.19.567766v1?rss=1" Maire, J. Collingro, A. Horn, M. van Oppen, M. J. H. 2023-11-20 doi:10.1101/2023.11.19.567766 Cold Spring Harbor Laboratory Press 2023-11-20 <![CDATA[ The Parkinson's drug entacapone disrupts gut microbiome homeostasis via iron sequestration ]]> https://biorxiv.org/cgi/content/short/2023.11.12.566429v1?rss=1" Pereira, F. C. Ge, X. Kristensen, J. M. Kirkegaard, R. H. Maritsch, K. Zu, Y. Decorte, M. Hausmann, B. Berry, D. Wasmund, K. Schintlmeister, A. Boettcher, T. Cheng, J.-X. Wagner, M. 2023-11-12 doi:10.1101/2023.11.12.566429 Cold Spring Harbor Laboratory Press 2023-11-12 <![CDATA[ Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants ]]> https://biorxiv.org/cgi/content/short/2023.10.25.562895v1?rss=1" Wagner, M. Hu, H. Kristensen, J. M. Pjevac, P. Kitzinger, K. Herbold, C. W. Hausmann, B. Dueholm, M. K. D. Nielsen, P. H. 2023-10-29 doi:10.1101/2023.10.25.562895 Cold Spring Harbor Laboratory Press 2023-10-29 <![CDATA[ Soil fungi remain active and invest in storage compounds during drought independent of future climate conditions ]]> https://biorxiv.org/cgi/content/short/2023.10.23.563577v1?rss=1" Canarini, A. Fuchslueger, L. Schnecker, J. Metze, D. Nelson, D. Kahmen, A. Watzka, M. Poetsch, E. M. Schaumberger, A. Bahn, M. Richter, A. 2023-10-23 doi:10.1101/2023.10.23.563577 Cold Spring Harbor Laboratory Press 2023-10-23 <![CDATA[ Maximizing Efficiency in SedaDNA Analysis: A Novel Extract Pooling Approach ]]> https://biorxiv.org/cgi/content/short/2023.10.17.562718v1?rss=1" Oberreiter, V. Gelabert, P. Brueck, F. Franz, S. Zelger, E. Szedlacsek, S. Cheronet, O. Tenorio Cano, F. Exler, F. Zagorc, B. Karavanic, I. Banda, M. Gasparyan, B. Straus, L. G. Gonzalez Morales, M. R. Kappelman, J. Stahlschmidt, M. Rattei, T. Kraemer, S. M. Sawyer, S. Pinhasi, R. 2023-10-20 doi:10.1101/2023.10.17.562718 Cold Spring Harbor Laboratory Press 2023-10-20 <![CDATA[ Microclimate Shapes the Phylosymbiosis of Rodent Gut Microbiota in Jordan's Great Rift Valley ]]> https://biorxiv.org/cgi/content/short/2023.08.01.551195v1?rss=1" Al-khlifeh, e. M. Khadem, S. Hausmann, B. M. Berry, D. 2023-08-01 doi:10.1101/2023.08.01.551195 Cold Spring Harbor Laboratory Press 2023-08-01 <![CDATA[ Evolution of an alternative genetic code in the Providencia symbiont of the haematophagous leech Haementeria acuecueyetzin ]]> https://biorxiv.org/cgi/content/short/2023.03.27.534433v1?rss=1" Manzano-Marin, A. Kvist, S. Oceguera-Figueroa, A. 2023-03-27 doi:10.1101/2023.03.27.534433 Cold Spring Harbor Laboratory Press 2023-03-27 <![CDATA[ Co-obligate symbioses have repeatedly evolved across aphids, but partner identity and nutritional contributions vary across lineages ]]> https://biorxiv.org/cgi/content/short/2022.08.28.505559v1?rss=1" Manzano-Marin, A. Coeur d'acier, A. Clamens, A.-L. Cruaud, C. Barbe, V. Jousselin, E. 2022-08-29 doi:10.1101/2022.08.28.505559 Cold Spring Harbor Laboratory Press 2022-08-29