Rapid Reactivation of Deep Subsurface Microbes in the Presence of C-1 Compounds

Abstract

Microorganisms in the deep biosphere are believed to conduct little metabolic activity due to low nutrient availability in these environments. However, destructive penetration to long-isolated bedrock environments during construction of underground waste repositories can lead to increased nutrient availability and potentially affect the long-term stability of the repository systems, Here, we studied how microorganisms present in fracture fluid from a depth of 500 m in Outokumpu, Finland, respond to simple carbon compounds (C-1 compounds) in the presence or absence of sulphate as an electron acceptor. C-1 compounds such as methane and methanol are important intermediates in the deep subsurface carbon cycle, and electron acceptors such as sulphate are critical components of oxidation processes. Fracture fluid samples were incubated in vitro with either methane or methanol in the presence or absence of sulphate as an electron acceptor. Metabolic response was measured by staining the microbial cells with fluorescent dyes that indicate metabolic activity and transcriptional response with RT-qPCR. Our results show that deep subsurface microbes exist in dormant states but rapidly reactivate their transcription and respiration systems in the presence of C-1 substrates, particularly methane. Microbial activity was further enhanced by the addition of sulphate as an electron acceptor. Sulphate- and nitrate-reducing microbes were particularly responsive to the addition of C-1 compounds and sulphate. These taxa are common in deep biosphere environments and may be affected by conditions disturbed by bedrock intrusion, as from drilling and excavation for long-term storage of hazardous waste.

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

“…In our study, we investigated the acetate cycling with DNA SIP, and RNA-targeted cell activation. The previous study from Outokumpu showed the fast activation of dormant cells in the presence of C-1 compounds [91]. A further study by Rajala and Bomberg [66] demonstrated the similar response to C-1 compounds on RNA level, indicating that our incubation time of three hours was sufficient with regards to the RNA synthesis.…”

Acetate Activates Deep Subsurface Fracture Fluid Microbial Communities in Olkiluoto, Finland

“…The size of the archaeal population in the fracture groundwaters was determined using primers ARC344f [27] and Ar744r (reverse complement from [28]) flanking the V4-V6 region of the archaeal 16S rRNA gene, as described in [3]. Sulphate reducers (dsrB) were quantified, as described in [24], and bacterial nitrate reducers (narG) and archaeal methanogens (mcrA) were determined according to [29] and [20] respectively.…”

Fluctuations in populations of subsurface methane oxidizers in coordination with changes in electron acceptor availability

“…the activity of subsurface communities can be enhanced (Rajala et al 2015). Large 46 disturbances such as CO2 (Morozova et al 2010(Morozova et al , 2011 and H2 injection (Bagnoud et al 47 2016), hydraulic fracking (Daly et al 2016), and drilling (Purkamo et al 2013) have also 48 been reported to alter natural subsurface communities.…”