The Potential for CH&lt;sub&gt;4&lt;/sub&gt; Production by Syntrophic Microbial Communities in Diverse Deep Aquifers Associated with an Accretionary Prism and its Overlying Sedimentary Layers

Matsushita, Makoto; Ishikawa, Shugo; Magara, Kenta; Sato, Yu; Kimura, Hiroyuki

doi:10.1264/jsme2.me19103

Cited by 6 publications

(5 citation statements)

References 60 publications

(85 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Fermentative Firmicutes and Deltaproteobacteria capable of oxidizing low-molecular-weight organics could be involved in syntrophic associations with methanogens or anaerobic respiring organisms. An important role for syntropy in deep subsurface environments has been reported (Gray et al, 2010;Kimura et al, 2010;Matsushita et al, 2020).…”

Section: Diversity Of Environmental Conditions and Microbial Processementioning

confidence: 99%

Microbial Life in the Deep Subsurface Aquifer Illuminated by Metagenomics

et al. 2020

View full text Add to dashboard Buy / Rent full text

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.

show abstract

Section: Diversity Of Environmental Conditions and Microbial Processementioning

confidence: 99%

Microbial Life in the Deep Subsurface Aquifer Illuminated by Metagenomics

et al. 2020

View full text Add to dashboard Buy / Rent full text

show abstract

“…This difference in abundances could be attributed to the existing environmental conditions of that sample which may have favoured the growth of specific groups. Syntropy has been reported to play an important role in deep subsurface environments ( Matsushita et al, 2020 ). Autotrophic taxa proficient of C fixation (e.g., Cyanobacteria), also capable H 2 -based metabolism ( Puente-Sánchez et al, 2018 ), Chloroflexi, and NH 4 oxidizing/ methanogenic archaeal groups are observed to associate with organotrophic acetate assimilating Bacteroidetes ( Kadnikov et al, 2020 ), fermentative Firmicutes and Fusobacteria members ( Rogers et al, 1998 ; Gupta et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

Depth wide distribution and metabolic potential of chemolithoautotrophic microorganisms reactivated from deep continental granitic crust underneath the Deccan Traps at Koyna, India

Mandal

Bose²,

Ramesh³

et al. 2022

Front. Microbiol.

View full text Add to dashboard Buy / Rent full text

Characterization of inorganic carbon (C) utilizing microorganisms from deep crystalline rocks is of major scientific interest owing to their crucial role in global carbon and other elemental cycles. In this study we investigate the microbial populations from the deep [up to 2,908 meters below surface (mbs)] granitic rocks within the Koyna seismogenic zone, reactivated (enriched) under anaerobic, high temperature (50°C), chemolithoautotrophic conditions. Subsurface rock samples from six different depths (1,679–2,908 mbs) are incubated (180 days) with CO2 (+H2) or HCO3− as the sole C source. Estimation of total protein, ATP, utilization of NO3- and SO42− and 16S rRNA gene qPCR suggests considerable microbial growth within the chemolithotrophic conditions. We note a better response of rock hosted community towards CO2 (+H2) over HCO3−. 16S rRNA gene amplicon sequencing shows a depth-wide distribution of diverse chemolithotrophic (and a few fermentative) Bacteria and Archaea. Comamonas, Burkholderia-Caballeronia-Paraburkholderia, Ralstonia, Klebsiella, unclassified Burkholderiaceae and Enterobacteriaceae are reactivated as dominant organisms from the enrichments of the deeper rocks (2335–2,908 mbs) with both CO2 and HCO3−. For the rock samples from shallower depths, organisms of varied taxa are enriched under CO2 (+H2) and HCO3−. Pseudomonas, Rhodanobacter, Methyloversatilis, and Thaumarchaeota are major CO2 (+H2) utilizers, while Nocardioides, Sphingomonas, Aeromonas, respond towards HCO3−. H2 oxidizing Cupriavidus, Hydrogenophilus, Hydrogenophaga, CO2 fixing Cyanobacteria Rhodobacter, Clostridium, Desulfovibrio and methanogenic archaea are also enriched. Enriched chemolithoautotrophic members show good correlation with CO2, CH4 and H2 concentrations of the native rock environments, while the organisms from upper horizons correlate more to NO3−, SO42−, Fe and TIC levels of the rocks. Co-occurrence networks suggest close interaction between chemolithoautotrophic and chemoorganotrophic/fermentative organisms. Carbon fixing 3-HP and DC/HB cycles, hydrogen, sulfur oxidation, CH4 and acetate metabolisms are predicted in the enriched communities. Our study elucidates the presence of live, C and H2 utilizing Bacteria and Archaea in deep subsurface granitic rocks, which are enriched successfully. Significant impact of depth and geochemical controls on relative distribution of various chemolithotrophic species enriched and their C and H2 metabolism are highlighted. These endolithic microorganisms show great potential for answering the fundamental questions of deep life and their exploitation in CO2 capture and conversion to useful products.

show abstract

“…With the exception of several reads present in seafloor sediments near a methane seep off the coast of Oregon [ 66 ] and one read in Guaymas Basin sediment [ 67 ], all reads were found in samples from continental or island subsurface sites 400–1200 m deep (Table S 8 ). Most of the reads originated from a Pleistocene basaltic aquifer in Iceland [ 68 , 69 ]; an additional location in the same Paleozoic dolomite aquifer accessed by BLM1 and in the overlying Miocene volcanic units in Nevada [ 20 ]; in Neogene-Paleogene and Cretaceous gas reservoirs in Japan [ 70 , 71 ]; and in Upper Cretaceous coal bed gas reservoirs in Alberta, Canada [ 72 , 73 ]. A single CDA sequence read originated from a biofilm in an anaerobic geothermal reactor in Denmark; which could have originated from subsurface geothermal water that supplied the facility [ 74 ].…”

Section: Discussionmentioning

confidence: 99%

Evolutionary stasis of a deep subsurface microbial lineage

Becraft

Lau

Bezuidt

et al. 2021

ISME J

View full text Add to dashboard Buy / Rent full text

Sulfate-reducing bacteria Candidatus Desulforudis audaxviator (CDA) were originally discovered in deep fracture fluids accessed via South African gold mines and have since been found in geographically widespread deep subsurface locations. In order to constrain models for subsurface microbial evolution, we compared CDA genomes from Africa, North America and Eurasia using single cell genomics. Unexpectedly, 126 partial single amplified genomes from the three continents, a complete genome from of an isolate from Eurasia, and metagenome-assembled genomes from Africa and Eurasia shared >99.2% average nucleotide identity, low frequency of SNP’s, and near-perfectly conserved prophages and CRISPRs. Our analyses reject sample cross-contamination, recent natural dispersal, and unusually strong purifying selection as likely explanations for these unexpected results. We therefore conclude that the analyzed CDA populations underwent only minimal evolution since their physical separation, potentially as far back as the breakup of Pangea between 165 and 55 Ma ago. High-fidelity DNA replication and repair mechanisms are the most plausible explanation for the highly conserved genome of CDA. CDA presents a stark contrast to the current model organisms in microbial evolutionary studies, which often develop adaptive traits over far shorter periods of time.

show abstract

The Potential for CH<sub>4</sub> Production by Syntrophic Microbial Communities in Diverse Deep Aquifers Associated with an Accretionary Prism and its Overlying Sedimentary Layers

Cited by 6 publications

References 60 publications

Microbial Life in the Deep Subsurface Aquifer Illuminated by Metagenomics

Microbial Life in the Deep Subsurface Aquifer Illuminated by Metagenomics

Depth wide distribution and metabolic potential of chemolithoautotrophic microorganisms reactivated from deep continental granitic crust underneath the Deccan Traps at Koyna, India

Evolutionary stasis of a deep subsurface microbial lineage

Contact Info

Product

Resources

About