Environmentally dependent interactions shape patterns in gene content across natural microbiomes.

Autor: Crocker K; Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.; Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL, USA.; Center for Living Systems, The University of Chicago, Chicago, IL, USA., Lee KK; Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.; Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL, USA.; Center for Living Systems, The University of Chicago, Chicago, IL, USA., Chakraverti-Wuerthwein M; Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL, USA.; Center for Living Systems, The University of Chicago, Chicago, IL, USA.; Biophysical Sciences Graduate Program, The University of Chicago, Chicago, IL, USA., Li Z; Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.; Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL, USA.; Department of Physics, The University of Illinois at Urbana-Champaign, Urbana, IL, USA., Tikhonov M; Department of Physics, Washington University in St. Louis, St. Louis, MO, USA., Mani M; Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA.; Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.; NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, USA.; National Institute for Theory and Mathematics in Biology, Northwestern University and The University of Chicago, Chicago, IL, USA., Gowda K; Department of Microbiology, The Ohio State University, Columbus, OH, USA. karna.gowda@gmail.com.; Biophysics Graduate Program, The Ohio State University, Columbus, OH, USA. karna.gowda@gmail.com., Kuehn S; Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA. seppe.kuehn@gmail.com.; Center for the Physics of Evolving Systems, The University of Chicago, Chicago, IL, USA. seppe.kuehn@gmail.com.; Center for Living Systems, The University of Chicago, Chicago, IL, USA. seppe.kuehn@gmail.com.; National Institute for Theory and Mathematics in Biology, Northwestern University and The University of Chicago, Chicago, IL, USA. seppe.kuehn@gmail.com.
Jazyk: angličtina
Zdroj: Nature microbiology [Nat Microbiol] 2024 Aug; Vol. 9 (8), pp. 2022-2037. Date of Electronic Publication: 2024 Jul 08.
DOI: 10.1038/s41564-024-01752-4
Abstrakt: Sequencing surveys of microbial communities in hosts, oceans and soils have revealed ubiquitous patterns linking community composition to environmental conditions. While metabolic capabilities restrict the environments suitable for growth, the influence of ecological interactions on patterns observed in natural microbiomes remains uncertain. Here we use denitrification as a model system to demonstrate how metagenomic patterns in soil microbiomes can emerge from pH-dependent interactions. In an analysis of a global soil sequencing survey, we find that the abundances of two genotypes trade off with pH; nar gene abundances increase while nap abundances decrease with declining pH. We then show that in acidic conditions strains possessing nar fail to grow in isolation but are enriched in the community due to an ecological interaction with nap genotypes. Our study provides a road map for dissecting how associations between environmental variables and gene abundances arise from environmentally modulated community interactions.
(© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)
Databáze: MEDLINE
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