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Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression

Identifying mechanisms by which bacterial species evolve and maintain genomic diversity is particularly challenging for the uncultured lineages that dominate the surface ocean. A longitudinal analysis of bacterial genes, genomes, and transcripts during a coastal phytoplankton bloom revealed two co-o...

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Autores principales: Nowinski, Brent, Feng, Xiaoyuan, Preston, Christina M., Birch, James M., Luo, Haiwei, Whitman, William B., Moran, Mary Ann
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10203303/
https://www.ncbi.nlm.nih.gov/pubmed/36871069
http://dx.doi.org/10.1038/s41396-023-01390-4
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author Nowinski, Brent
Feng, Xiaoyuan
Preston, Christina M.
Birch, James M.
Luo, Haiwei
Whitman, William B.
Moran, Mary Ann
author_facet Nowinski, Brent
Feng, Xiaoyuan
Preston, Christina M.
Birch, James M.
Luo, Haiwei
Whitman, William B.
Moran, Mary Ann
author_sort Nowinski, Brent
collection PubMed
description Identifying mechanisms by which bacterial species evolve and maintain genomic diversity is particularly challenging for the uncultured lineages that dominate the surface ocean. A longitudinal analysis of bacterial genes, genomes, and transcripts during a coastal phytoplankton bloom revealed two co-occurring, highly related Rhodobacteraceae species from the deeply branching and uncultured NAC11-7 lineage. These have identical 16S rRNA gene amplicon sequences, yet their genome contents assembled from metagenomes and single cells indicate species-level divergence. Moreover, shifts in relative dominance of the species during dynamic bloom conditions over 7 weeks confirmed the syntopic species’ divergent responses to the same microenvironment at the same time. Genes unique to each species and genes shared but divergent in per-cell inventories of mRNAs accounted for 5% of the species’ pangenome content. These analyses uncover physiological and ecological features that differentiate the species, including capacities for organic carbon utilization, attributes of the cell surface, metal requirements, and vitamin biosynthesis. Such insights into the coexistence of highly related and ecologically similar bacterial species in their shared natural habitat are rare.
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spelling pubmed-102033032023-05-24 Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression Nowinski, Brent Feng, Xiaoyuan Preston, Christina M. Birch, James M. Luo, Haiwei Whitman, William B. Moran, Mary Ann ISME J Article Identifying mechanisms by which bacterial species evolve and maintain genomic diversity is particularly challenging for the uncultured lineages that dominate the surface ocean. A longitudinal analysis of bacterial genes, genomes, and transcripts during a coastal phytoplankton bloom revealed two co-occurring, highly related Rhodobacteraceae species from the deeply branching and uncultured NAC11-7 lineage. These have identical 16S rRNA gene amplicon sequences, yet their genome contents assembled from metagenomes and single cells indicate species-level divergence. Moreover, shifts in relative dominance of the species during dynamic bloom conditions over 7 weeks confirmed the syntopic species’ divergent responses to the same microenvironment at the same time. Genes unique to each species and genes shared but divergent in per-cell inventories of mRNAs accounted for 5% of the species’ pangenome content. These analyses uncover physiological and ecological features that differentiate the species, including capacities for organic carbon utilization, attributes of the cell surface, metal requirements, and vitamin biosynthesis. Such insights into the coexistence of highly related and ecologically similar bacterial species in their shared natural habitat are rare. Nature Publishing Group UK 2023-03-04 2023-06 /pmc/articles/PMC10203303/ /pubmed/36871069 http://dx.doi.org/10.1038/s41396-023-01390-4 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Nowinski, Brent
Feng, Xiaoyuan
Preston, Christina M.
Birch, James M.
Luo, Haiwei
Whitman, William B.
Moran, Mary Ann
Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression
title Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression
title_full Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression
title_fullStr Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression
title_full_unstemmed Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression
title_short Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression
title_sort ecological divergence of syntopic marine bacterial species is shaped by gene content and expression
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10203303/
https://www.ncbi.nlm.nih.gov/pubmed/36871069
http://dx.doi.org/10.1038/s41396-023-01390-4
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