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Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater

Mehrshad, Maliheh and Lopez-Fernandez, Margarita and Sundh, John and Bell, Emma and Simone, Domenico and Buck, Moritz and Bernier-Latmani, Rizlan and Bertilsson, Stefan and Dopson, Mark (2021). Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater. Nature Communications. 12 , 4253
[Research article]

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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.

Authors/Creators:Mehrshad, Maliheh and Lopez-Fernandez, Margarita and Sundh, John and Bell, Emma and Simone, Domenico and Buck, Moritz and Bernier-Latmani, Rizlan and Bertilsson, Stefan and Dopson, Mark
Title:Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater
Series Name/Journal:Nature Communications
Year of publishing :2021
Volume:12
Article number:4253
Number of Pages:12
ISSN:2041-1723
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 1 Natural sciences > 106 Biological Sciences (Medical to be 3 and Agricultural to be 4) > Microbiology (Microbiology in the medical area to be 30109)
URN:NBN:urn:nbn:se:slu:epsilon-p-112838
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-112838
Additional ID:
Type of IDID
DOI10.1038/s41467-021-24549-z
ID Code:24893
Faculty:NJ - Fakulteten för naturresurser och jordbruksvetenskap
Department:(NL, NJ) > Dept. of Aquatic Sciences and Assessment
(NL, NJ) > Dept. of Plant Biology and Forest Genetics (until 131231)
Deposited By: SLUpub Connector
Deposited On:13 Aug 2021 13:25
Metadata Last Modified:13 Aug 2021 13:31

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