Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater
Abstract 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 om...
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crspringernat:10.1038/s41467-021-24549-z 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 http://dx.doi.org/10.1038/s41467-021-24549-z http://www.nature.com/articles/s41467-021-24549-z.pdf http://www.nature.com/articles/s41467-021-24549-z en eng Springer Science and Business Media LLC https://creativecommons.org/licenses/by/4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Nature Communications volume 12, issue 1 ISSN 2041-1723 General Physics and Astronomy General Biochemistry, Genetics and Molecular Biology General Chemistry journal-article 2021 crspringernat https://doi.org/10.1038/s41467-021-24549-z 2022-01-04T15:17:54Z Abstract 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. Article in Journal/Newspaper Fennoscandian Springer Nature (via Crossref) Nature Communications 12 1 |
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Springer Nature (via Crossref) |
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English |
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General Physics and Astronomy General Biochemistry, Genetics and Molecular Biology General Chemistry |
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General Physics and Astronomy General Biochemistry, Genetics and Molecular Biology General Chemistry 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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General Physics and Astronomy General Biochemistry, Genetics and Molecular Biology General Chemistry |
description |
Abstract 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 |
Article in Journal/Newspaper |
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 |
Springer Science and Business Media LLC |
publishDate |
2021 |
url |
http://dx.doi.org/10.1038/s41467-021-24549-z http://www.nature.com/articles/s41467-021-24549-z.pdf http://www.nature.com/articles/s41467-021-24549-z |
genre |
Fennoscandian |
genre_facet |
Fennoscandian |
op_source |
Nature Communications volume 12, issue 1 ISSN 2041-1723 |
op_rights |
https://creativecommons.org/licenses/by/4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1038/s41467-021-24549-z |
container_title |
Nature Communications |
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12 |
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1 |
_version_ |
1765998596132438016 |