A metagenomic window into the 2-km-deep terrestrial subsurface aquifer revealed multiple pathways of organic matter decomposition

Abstract

We have sequenced metagenome of the microbial community of a deep subsurface thermal aquifer in the Tomsk Region of the Western Siberia, Russia. Our goal was the recovery of near-complete genomes of the community members to enable accurate reconstruction of metabolism and ecological roles of the microbial majority, including previously unstudied lineages. The water, obtained via a 2.6 km deep borehole 1-R, was anoxic, with a slightly alkaline pH, and a temperature around 45°C. Microbial community, as revealed by 16S rRNA gene profiling over 2 years, mostly consisted of sulfate-reducing Firmicutes and Deltaproteobacteria, and uncultured lineages of the phyla Chlorofexi, Ignavibacteriae and Aminicenantes (OP8). 25 composite genomes with more than 90% completeness were recovered from metagenome and used for metabolic reconstruction. Members of uncultured lineages of Chlorofexi and Ignavibacteriae are likely involved in degradation of carbohydrates by fermentation, and are also capable of aerobic and anaerobic respiration. The Chlorofexi bacterium has the Wood-Ljungdahl pathway of CO2 fixation. The recently identified candidate phylum Riflebacteria accounted for 5%-10% of microbial community. Metabolic reconstruction of a member of Riflebacteria predicted that it is an anaerobe capable to grow on carbohydrates by fermentation or dissimilatory Fe(III) reduction.

Microbial Life in the Deep Subsurface Aquifer Illuminated by Metagenomics

“…higher than in waters collected at the 3P Parabel (Frank et al, 2016) and 1-R Byelii Yar boreholes (Kadnikov et al, 2018) and varied from year to year (90.4 mg L −1 in 2016 and 23.3 mg L −1 in 2015). The water contained dissolved hydrogen sulfide at concentrations of 15.7 mg L −1 in 2016 and 7.6 mg L −1 in 2015.…”

“…All 12 Chloroflexi MAGs were assigned to the class Anaerolinea, members of which have been identified from diverse environments, including marine and freshwater sediments and deep subsurface aquifers (Yamada and Sekiguchi, 2009). They were also found in the Western Siberian deep subsurface (Kadnikov et al, 2018). Only one MAG, Ch72, was classified at the genus level, being assigned to the Thermanaerothrix, sharing 83.69% AAI with the only cultured species of this genus, thermophilic anaerobic bacterium Thermanaerothrix daxensis, isolated from a deep hot aquifer in France (Grégoire et al, 2011).…”

“…The second important functional group is sulfate reducers. Like methanogens, they are typical members of both lithoautotrophic and organotrophic microbial communities of the deep subsurface ecosystems, including Western Siberia (Moser et al, 2005;Chivian et al, 2008;Frank et al, 2016;Kadnikov et al, 2018). The sulfate reduction pathway was revealed in two genomes of Firmicutes (Ch2 and Ch87) and in the members of Deltaproteobacteria (Ch28 and Ch74), Ca.…”

Contrasting Variable and Stable Subsurface Microbial Populations: an ecological time series analysis from the Deep Mine Microbial Observatory, South Dakota, USA

“…Subsurface Anaerolineales have been found in hydrothermal sediments off of Japan where they are suggested to be mediating anaerobic heterotrophy or mixotrophy (Fullerton and Moyer, 2016) as well as in a Siberian deep aquifer where they are implicated in aerobic and anaerobic respiration and fermentation (Kadnikov et al, 2018). The Anaerolineales contain complete Acetyl-CoA carbon fixation pathways, suggesting the potential for in situ carbon fixation.…”

“…Benk et al (2019) targeted the very shallow subsurface over a three-year time series in concert with DOM analysis and found considerable temporal variability in the alpha diversity of groundwater communities that was correlated with the alpha diversity of DOM itself (Benk et al, 2019). Kadnikov et al (2018) accessed a Siberian borehole over a five-year time period, but do not report a time series analysis of microbial diversity (Kadnikov et al, 2018).…”