Abstract
To get insights into microbial diversity and biogeochemical processes in the terrestrial deep subsurface aquifer, we sequenced the metagenome of artesian water collected at a 2.8 km deep oil exploration borehole 5P in Western Siberia, Russia. We obtained 71 metagenome-assembled genomes (MAGs), altogether comprising 93% of the metagenome. Methanogenic archaea accounted for about 20% of the community and mostly belonged to hydrogenotrophic Methanobacteriaceae; acetoclastic and methylotrophic lineages were less abundant. ANME archaea were not found. The most numerous bacteria were the Firmicutes, Ignavibacteriae, Deltaproteobacteria, Chloroflexi, and Armatimonadetes. Most of the community was composed of anaerobic heterotrophs. Only six MAGs belonged to sulfate reducers. These MAGs accounted for 5% of the metagenome and were assigned to the Firmicutes, Deltaproteobacteria, Candidatus Kapabacteria, and Nitrospirae. Organotrophic bacteria carrying cytochrome c oxidase genes and presumably capable of aerobic respiration mostly belonged to the Chloroflexi, Ignavibacteriae, and Armatimonadetes. They accounted for 13% of the community. The first complete closed genomes were obtained for members of the Ignavibacteriae SJA-28 lineage and the candidate phylum Kapabacteria. Metabolic reconstruction of the SJA-28 bacterium, designated Candidatus Tepidiaquacella proteinivora, predicted that it is an anaerobe growing on proteinaceous substrates by fermentation or anaerobic respiration. The Ca. Kapabacteria genome contained both the sulfate reduction pathway and cytochrome c oxidase. Presumably, the availability of buried organic matter of Mesozoic marine sediments, long-term recharge of the aquifer with meteoric waters and its spatial heterogeneity provided the conditions for the development of microbial communities, taxonomically and functionally more diverse than those found in oligotrophic underground ecosystems.
Highlights
Deep subsurface environments provide the largest habitats for prokaryotes in terms of size (Whitman et al, 1998)
Organic matter buried since their formation provides energy sources and organic carbon, which enable the development of various organotrophic microorganisms
The microbial community of an aquifer broached by the 3P borehole in the Parabel district (Tomsk region, Russia) was characterized by 16S rRNA profiling and cultivation; it was found to consist mostly of chemolithoautotrophs, – sulfate-reducing Firmicutes and hydrogenotrophic methanogenic archaea (Frank et al, 2016)
Summary
Deep subsurface environments provide the largest habitats for prokaryotes in terms of size (Whitman et al, 1998). In the lithoautotrophic communities characteristic of igneous rocks, the main source of energy is molecular hydrogen of abiotic origin, and the content of organic carbon is extremely low Such microbial communities are usually characterized by low diversity and contain sulfate-reducing or methanogenic microorganisms (Moser et al, 2005; Chivian et al, 2008). The microbial community of the second aquifer, accessed via the 1-R borehole in the Byelii Yar district, has been analyzed by metagenomics This community was more complex: it lacked methanogens and comprised sulfatereducing Firmicutes and Deltaproteobacteria, as well as various presumably organotrophic members of the phyla Chlorofexi, Ignavibacteriae, Ca. Aminicenantes, Ca. Riflebacteria and BRC1 (Kadnikov et al, 2018). We successfully recovered high-quality metagenome-assembled genomes of the vast majority of community members that enabled us to perform an accurate metabolic reconstruction and propose an ecological model of the deep subsurface aquifer
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