Heterotrophic Communities Supplied by Ancient Organic Carbon Predominate in Deep Fennoscandian Bedrock Fluids

Abstract

The deep subsurface hosts diverse life, but the mechanisms that sustain this diversity remain elusive. Here, we studied microbial communities involved in carbon cycling in deep, dark biosphere and identified anaerobic microbial energy production mechanisms from groundwater of Fennoscandian crystalline bedrock sampled from a deep drill hole in Outokumpu, Finland, by using molecular biological analyses. Carbon cycling pathways, such as carbon assimilation, methane production and methane consumption, were studied with cbbM, rbcL, acsB, accC, mcrA and pmoA marker genes, respectively. Energy sources, i.e. the terminal electron accepting processes of sulphate-reducing and nitrate-reducing communities, were assessed with detection of marker genes dsrB and narG, respectively. While organic carbon is scarce in deep subsurface, the main carbon source for microbes has been hypothesized to be inorganic carbon dioxide. However, our results demonstrate that carbon assimilation is performed throughout the Outokumpu deep scientific drill hole water column by mainly heterotrophic microorganisms such as Clostridia. The source of carbon for the heterotrophic microbial metabolism is likely the Outokumpu bedrock, mainly composed of serpentinites and metasediments with black schist interlayers. In addition to organotrophic metabolism, nitrate and sulphate are other possible energy sources. Methanogenic and methanotrophic microorganisms are scarce, but our analyses suggest that the Outokumpu deep biosphere provides niches for these organisms; however, they are not very abundant.

Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters

“…The dominant populations in both the modern marine and old saline water biofilm formers were putative carbon- and nitrogen-fixers (MMG_Bin_93 representing 11.73% of the reads and OSG_Bin_24 representing 2.15% of the reads). The importance of previously unknown microorganisms with a simple, fermentative growth strategy has recently been recognized at the Äspö HRL [22] as well as at another site [20]. These earlier findings are consistent with the metabolic features of several biofilm populations identified here (e.g., MMR_Bin_23 and OSR_Bin_0).…”

Reactivation of Deep Subsurface Microbial Community in Response to Methane or Methanol Amendment

“…However, in the shallower fracture zone, 180 m depth, where the ratio of active cells was higher, only a small sub-population was responsive to the methane or methanol amendment. Earlier, Purkamo et al (2014) suggested that heterotrophic mechanisms such as fermenting could be community supporting strategies at certain depths of Outokumpu deep biosphere. When comparing the activated bacterial population, it was seen that at 180 m depth the Pseudomonas genus (Gammaproteobacteria) formed the majority of the activated community, whereas in the original community they were in minority.…”

“…The lithology, hydrogeochemistry and gas composition of the drillhole and fracture zones have been described previously (Ahonen et al, 2011; Kietäväinen et al, 2013; Purkamo et al, 2013; Nyyssönen et al, 2014). The fracture zones at 180 and 500 m depth are situated in a metasedimentary rock sequence, predominated by mica schist/biotite gneiss (Purkamo et al, 2014). The residence time for the fracture waters have been estimated to be between 20 and 50 Ma (Kietäväinen et al, 2014).…”

“…A diverse bacterial and archaeal community has been detected down to 2300 m depth in the drillhole (Purkamo et al, 2013, 2015, 2016; Nyyssönen et al, 2014). These communities vary at different sampling depths in response to prevailing lithology and hydrogeochemistry (Purkamo et al, 2014, 2016). Simple one-carbon compounds, such as methane and methanol are important intermediates in the deep subsurface carbon cycle, and electron acceptors such as sulfate are critical components in the oxidation processes (Kietäväinen and Purkamo, 2015).…”

Rare Biosphere Archaea Assimilate Acetate in Precambrian Terrestrial Subsurface at 2.2 km Depth

“…More specifically, the metabolic capabilities of deep terrestrial subsurface microbial communities include the pathways covering, e.g., methanogenesis [9][10][11], anaerobic methane oxidation [12], acetogenesis [4,13], sulfate reduction [14-16], oxidation of sulfur by denitrification [17], and reduction of iron [14].The Outokumpu deep scientific drill hole, located in Eastern Finland, hosts a unique environment piercing through crystalline Precambrian bedrock and its numerous saline fluid filled fracture zones. The composition of the microbial communities and the geochemical characteristics of the Outokumpu deep subsurface have been studied in detail [11,[18][19][20][21][22][23][24][25][26][27]. The metabolic strategies of the microbial communities at different depths in Outokumpu have been estimated through functional gene analysis and metagenomes [11,21].…”