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...
Published in: | Nature Communications |
---|---|
Main Authors: | , , , , , , , , |
Format: | Text |
Language: | unknown |
Published: |
Berlin, NATURE RESEARCH
2021
|
Subjects: | |
Online Access: | https://doi.org/10.1038/s41467-021-24549-z https://infoscience.epfl.ch/record/287594/files/s41467-021-24549-z.pdf http://infoscience.epfl.ch/record/287594 |
id |
ftinfoscience:oai:infoscience.epfl.ch:287594 |
---|---|
record_format |
openpolar |
spelling |
ftinfoscience:oai:infoscience.epfl.ch:287594 2023-05-15T16:12:53+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 2021-07-31T00:25:41Z https://doi.org/10.1038/s41467-021-24549-z https://infoscience.epfl.ch/record/287594/files/s41467-021-24549-z.pdf http://infoscience.epfl.ch/record/287594 unknown Berlin, NATURE RESEARCH isi:000675329200009 doi:10.1038/s41467-021-24549-z https://infoscience.epfl.ch/record/287594/files/s41467-021-24549-z.pdf http://infoscience.epfl.ch/record/287594 http://infoscience.epfl.ch/record/287594 Text 2021 ftinfoscience https://doi.org/10.1038/s41467-021-24549-z 2023-02-13T23:06:09Z 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. Ecological constraints on microbial niches in oligotrophic deep groundwaters remain elusive. This study provides support for the existence of a common core microbiome in two deep groundwater biomes of the Fennoscandian Shield using a genome-resolved, integrated omics analysis. Text Fennoscandian EPFL Infoscience (Ecole Polytechnique Fédérale Lausanne) Nature Communications 12 1 |
institution |
Open Polar |
collection |
EPFL Infoscience (Ecole Polytechnique Fédérale Lausanne) |
op_collection_id |
ftinfoscience |
language |
unknown |
description |
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. Ecological constraints on microbial niches in oligotrophic deep groundwaters remain elusive. This study provides support for the existence of a common core microbiome in two deep groundwater biomes of the Fennoscandian Shield using a genome-resolved, integrated omics analysis. |
format |
Text |
author |
Mehrshad, Maliheh Lopez-Fernandez, Margarita Sundh, John Bell, Emma Simone, Domenico Buck, Moritz Bernier-Latmani, Rizlan Bertilsson, Stefan Dopson, Mark |
spellingShingle |
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 |
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 |
Berlin, NATURE RESEARCH |
publishDate |
2021 |
url |
https://doi.org/10.1038/s41467-021-24549-z https://infoscience.epfl.ch/record/287594/files/s41467-021-24549-z.pdf http://infoscience.epfl.ch/record/287594 |
genre |
Fennoscandian |
genre_facet |
Fennoscandian |
op_source |
http://infoscience.epfl.ch/record/287594 |
op_relation |
isi:000675329200009 doi:10.1038/s41467-021-24549-z https://infoscience.epfl.ch/record/287594/files/s41467-021-24549-z.pdf http://infoscience.epfl.ch/record/287594 |
op_doi |
https://doi.org/10.1038/s41467-021-24549-z |
container_title |
Nature Communications |
container_volume |
12 |
container_issue |
1 |
_version_ |
1765998492008841216 |