Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater
While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analy...
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ftpubmed:oai:pubmedcentral.nih.gov:8275790 2023-05-15T16:12:59+02:00 Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater Mehrshad, Maliheh Lopez-Fernandez, Margarita Sundh, John Bell, Emma Simone, Domenico Buck, Moritz Bernier-Latmani, Rizlan Bertilsson, Stefan Dopson, Mark 2021-07-12 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8275790/ http://www.ncbi.nlm.nih.gov/pubmed/34253732 https://doi.org/10.1038/s41467-021-24549-z en eng Nature Publishing Group UK http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8275790/ http://www.ncbi.nlm.nih.gov/pubmed/34253732 http://dx.doi.org/10.1038/s41467-021-24549-z © The Author(s) 2021 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/) . CC-BY Nat Commun Article Text 2021 ftpubmed https://doi.org/10.1038/s41467-021-24549-z 2021-07-25T00:30:54Z While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome. Text Fennoscandian PubMed Central (PMC) Nature Communications 12 1 |
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Article Mehrshad, Maliheh Lopez-Fernandez, Margarita Sundh, John Bell, Emma Simone, Domenico Buck, Moritz Bernier-Latmani, Rizlan Bertilsson, Stefan Dopson, Mark Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater |
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Article |
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While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome. |
format |
Text |
author |
Mehrshad, Maliheh Lopez-Fernandez, Margarita Sundh, John Bell, Emma Simone, Domenico Buck, Moritz Bernier-Latmani, Rizlan Bertilsson, Stefan Dopson, Mark |
author_facet |
Mehrshad, Maliheh Lopez-Fernandez, Margarita Sundh, John Bell, Emma Simone, Domenico Buck, Moritz Bernier-Latmani, Rizlan Bertilsson, Stefan Dopson, Mark |
author_sort |
Mehrshad, Maliheh |
title |
Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater |
title_short |
Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater |
title_full |
Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater |
title_fullStr |
Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater |
title_full_unstemmed |
Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater |
title_sort |
energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater |
publisher |
Nature Publishing Group UK |
publishDate |
2021 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8275790/ http://www.ncbi.nlm.nih.gov/pubmed/34253732 https://doi.org/10.1038/s41467-021-24549-z |
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Fennoscandian |
genre_facet |
Fennoscandian |
op_source |
Nat Commun |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8275790/ http://www.ncbi.nlm.nih.gov/pubmed/34253732 http://dx.doi.org/10.1038/s41467-021-24549-z |
op_rights |
© The Author(s) 2021 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/) . |
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CC-BY |
op_doi |
https://doi.org/10.1038/s41467-021-24549-z |
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Nature Communications |
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12 |
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1 |
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1765998584752242688 |