Detecting Seismically-Sustained Deep Subsurface CH4-cycling Chemolithoautotrophic Microbial Communities Using Multi-Omic Analyses and NanoSIMS
EMSL Project ID
49952
Abstract
The specific objective of the proposed JGI/EMSL project is to document the microbial ecosystem of an active fault zone at 3.5 to 3.6 kilometers depth in South Africa. More specifically, the goal is to delineate how the syntrophic chemolithoautotrophic microbial communities that exist in the deep subsurface respond to pulses of H2 released during seismic activity. We hypothesize that the H2 pulses are rapidly consumed by hydrogenotrophic methanogens and sulfate reducing bacteria (SRB), and that as the pH2 declines between seismic events the anaerobic methane oxidizers and anaerobic sulfide oxidizing bacteria (ASOB) consume the metabolic products of the methanogens (CH4) and SRB (HS- of FeS). We also hypothesize that the ASOB may utilize H2 as an alternative electron donor during the H2 pulses and then switch to microbially produced sulfide as pH2 declines. A corollary to these hypotheses is that during the seismically induced-H2 pulses, dissolved inorganic carbon will be fixed primarily by methanogens and SRB by acetyl-CoA fixation pathways. In between pulses when pH2 is low, CH4 will be oxidized to form dissolved inorganic carbon that then is taken up primarily by ASOB using the Calvin-Benson-Bassham (CBB) cycle. Based upon previous CH4 isotopic analyses from subsurface fracture water in South Africa we also predict that the clumped isotopic signature of the CH4 (e.g. Delat13CH3D and Delta12CH2D2) will reflect mixing between a more deeply-sourced, abiogenic CH4 isotopic signature and a biogenic signature which reflects the ambient temperature of the fault zone. We will test these hypotheses using a combination of isotopic labeling experiments followed by SIP-protein and lipid and nano-SIMS analyses and metagenomic analyses of biofilms incubated under similar conditions. More broadly, we hypothesize that the syntrophic interactions between the microbial clades remove thermodynamic bottlenecks and enable diverse metabolic reactions to occur under the oligotrophic conditions that dominate the subsurface. The site that we are proposing to study offers an ideal opportunity to test this hypothesis, both in situ, and by performing laboratory incubations of subsurface biofilms and fault zone water collected from the site. Temporal samples for geochemical analyses will enable thermodynamic calculations for each of the principal active autotrophic metabolisms, e.g. methanogenesis, methanotrophy, sulfate-reduction, H2 oxidation coupled to denitrification and anaerobic sulfide oxidation. If the hypothesis is true, then it implies that the transport of microbial species and colonization of deep subsurface sites occurs in a structured manner with primary producers representing keystone species. The samples being collected will be unique in that they will represent both biofilms attached to mineral substrates and planktonic communities. Very few studies, if any, have reported on the differences in both the metabolic potential (i.e. through metagenomic sequencing) and active metabolism (i.e. through metatranscriptomics and metaproteomics) of the sessile versus suspended microbial constituents of a deep subsurface ecosystem.The specific aim of this proposed JGI/EMSL project is to document the shifts in microbial communities trapped in an active fault zone at 3.5 to 3.6 kilometers depth in South Africa in response to seismic events. More specifically, the goal is to delineate how the syntrophic chemolithoautotrophic microbial communities that exist in the deep subsurface respond to pulses of H2 released during seismic activity. We hypothesize that the dissolved H2 pulses triggered by cataclastic quartz/water reactions that occur during seismic events are rapidly consumed by hydrogenotrophic methanogens and sulfate reducing bacteria (SRB) while producing CH4 and HS-, respectively. NH4+, NO3- and NO2- are also released by fluid inclusion rupture during seismic events. As the pH2 declines during H2-consumption by methanogens and SRB, anaerobic methane oxidizers and anaerobic sulfide oxidizing bacteria (ASOB) consume the metabolic products of the methanogens (CH4) and SRB (HS- or FeS). We also hypothesize that ASOB may utilize H2 as an alternative electron donor during the H2 pulses and then switch to microbially produced sulfide as pH2 declines. A corollary to these hypotheses is that during the seismically induced-H2 pulses, dissolved inorganic carbon will be fixed primarily by methanogens and SRB by acetyl-CoA fixation pathways. In between pulses when pH2 is low, CH4 will be oxidized to form dissolved inorganic carbon that then is taken up primarily by ASOB using the Calvin-Benson-Bassham (CBB) cycle. N2-fixation may occur just after the seismic event when H2 concentrations are high, but before the less conservative dissolved nitrogen species migrate into the fault zone.
We have observed previously that these syntrophic interactions between these subsurface microbial clades mitigate thermodynamic bottlenecks and enable diverse metabolic reactions to occur under the oligotrophic conditions that normally dominate the subsurface. The borehole into the fault zone that we propose to study offers an unprecedented opportunity to test this hypothesis because the environment should alternate between H2-rich, high-energy flux during seismic activity and low-energy flux during the quiescent periods between seismic events. We will collect microbial, geochemical and isotopic samples that we can utilize to monitor H2 pulses and the concomitant changes in the in situ syntrophic microbial cycling of carbon through gene expression and NanoSIMS analyses. We will also perform 13C- and 15N-enriched laboratory incubations on subsurface biofilms collected during borehole incubations and planktonic communities concentrated from fault zone water. We propose using the facilities provided by EMSL and JGI to analyze these samples to address the following questions:
1. Do seismogenically-generated pulses of H2 cause a downstream cycling of CH4 and sulfide in syntrophic chemolithotrophic microbial communities?
2. Do any of the anaerobic CH4-oxidizing microorganisms have novel genomes representing as yet undiscovered archaea or bacteria that combine CH4 oxidation and electron acceptor pathways in new ways?
3. Do the syntrophic anaerobic CH4 and HS- oxidizing consortia exhibit spatial arrangements that resemble those found in seafloor sediments and what does this tell us about the means of electron transfer?
4. Does N2 fixation occur in the microbial consortia and, if so, which members perform it?
Project Details
Project type
FICUS Research
Start Date
2017-10-01
End Date
2019-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Co-Investigator(s)
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