Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater
MetadataShow full item record
Mehrshad, M... [et al.]. Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater. Nat Commun 12, 4253 (2021). [https://doi.org/10.1038/s41467-021-24549-z]
SponsorshipUnited States Department of Energy (DOE) DE-AC02-05CH11231; Swedish Research Council; European Commission 2018-04311 2017-04422 2014-4398; Swedish Nuclear Fuel and Waste Management Company (SKB); Crafoord Foundation 20180599 20130557; Nova Center for University Studies, Research and Development; Familjen Hellmans Stiftelse; Carl Tryggers Foundation KF16: 18; Swedish Research Council European Commission; Science for Life Laboratory; Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX) at Uppsala University b2013127 SNIC 2019/3-22 SNIC 2020/5-19; SciLifeLab-WABI bioinformatics grant; Knut and Alice Wallenberg Foundation as part of the National Bioinformatics Infrastructure Sweden at SciLifeLab
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.