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Research article - Peer-reviewed, 2021

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;

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. 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.

Published in

Nature Communications

2021, volume: 12, number: 1, article number: 4253

Authors' information

Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment
Mehrshad, Maliheh
Uppsala University
Lopez-Fernandez, Margarita
Linnaeus University
Sundh, John
Stockholm University
Bell, Emma
Swiss Federal Institute of Technology in Lausanne (EFPL)
Linnaeus University
Swedish University of Agricultural Sciences, Department of Plant Biology
Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment
Bernier-Latmani, Rizlan
Swiss Federal Institute of Technology in Lausanne (EFPL)
Uppsala University
Swedish University of Agricultural Sciences, Department of Aquatic Sciences and Assessment
Dopson, Mark
Linnaeus University

UKÄ Subject classification

Microbiology

Publication Identifiers

DOI: https://doi.org/10.1038/s41467-021-24549-z

URI (permanent link to this page)

https://res.slu.se/id/publ/112838