Archaeal methanogenesis in a deep terrestrial aquifer driven by Methanothermobacter tomskensis sp. nov.
5 affiliations
- 1Skryabin Institute of Biochemistry and Physiology of Microorganisms, Federal Research Center Pushchino Center for Biological Research of the Russian Academy of Sciences
- 2Laboratory of Biochemistry and Molecular Biology, Tomsk State University
- 3Winogradsky Institute of Microbiology, Research Centre of Biotechnology of the Russian Academy of Sciences
- 4Institute of Bioengineering, Research Centre of Biotechnology of the Russian Academy of Sciences
- 5Shirshov Institute of Oceanology, Russian Academy of Sciences
Abstract
Methanogenic archaea, capable of producing organic matter from hydrogen and CO ₂ emanating from the mantle, constitute one of the key functional groups of microorganisms in the deep subsurface. Although the diversity of methanogenic inhabitants of the deep biosphere has been studied in detail, the activity of methanogens in these biotopes remains virtually uncharacterized. We have measured the rate of hyrogenotrophic methanogenesis in water from the model borehole 3P (2.7 km deep), located near the small town of Parabel in the Tomsk Region. The potential rate of hydrogenotrophic methanogenesis, measured using ¹⁴ C-labeled sodium bicarbonate, was 5.45 ± 0.528 nmol CH ₄ /dm ³ /day (0.00545 ± 0.0005 nmol CH ₄ /cm ³ /day) - a value compatible to the methanogenic archaeal activity known for anaerobic sediments of surface water bodies. The 16S rRNA gene profiles of water from well 3P were dominated by s single phylotype assigned to the genus Methanothermobacter ; it accounted for 25.54% of the total microbial community. A MAG (metagenome assembled genome) designated 3P-20-051 and belonging to the genus Methanothermobacter was assembled from the water metagenome of well 3P. According to GTDB taxonomy, this MAG represents a novel species within the genus. The closest validly described relative of MAG 3P-20-001 was Methanothermobacter marburgensis with an ANI of 92.66%. Following the characterization of this MAG, a strain of methanogenic archaea designated as K4 T was isolated in pure culture. Morphological, physiological, genotypic, and phylogenetic data indicate that this strain represents a new species of the genus Methanothermobacter, for which we propose the name Methanothermobacter tomskensis sp. nov. Comparison of the strain K4 T genome with MAG 3P-20-051 showed that they were nearly identical: the ANI value was 99.96%. Thus, M. tomskensis sp. nov. indeed, represents a dominant methanogenic lineage revealed by metagenomics. Strain K4 T is characterized by an obligately hydrogenotrophic metabolism and possibly represents the main producer of organic matter in the deep horizons of the thermal aquifer.
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BibTeX
@article{trubitsyn2026archaeal,
title = {{Archaeal methanogenesis in a deep terrestrial aquifer driven by Methanothermobacter tomskensis sp. nov.}},
author = {Vladimir E. Trubitsyn and Igor I. Rusanov and Viktoria I. Rechkina and Vitaly V. Kadnikov and Daria N. Zasko and Alexey V. Beletsky and Nikolai V. Pimenov and Nikolai V. Ravin and Viktoria A. Shcherbakova and Olga V. Karnachuk},
journal = {Frontiers in Microbiology},
year = {2026},
month = oct,
doi = {10.3389/fmicb.2026.1973590},
url = {https://www.frontiersin.org/articles/10.3389/fmicb.2026.1973590/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Archaeal methanogenesis in a deep terrestrial aquifer driven by Methanothermobacter tomskensis sp. nov.
AU - Vladimir E. Trubitsyn
AU - Igor I. Rusanov
AU - Viktoria I. Rechkina
AU - Vitaly V. Kadnikov
AU - Daria N. Zasko
AU - Alexey V. Beletsky
AU - Nikolai V. Pimenov
AU - Nikolai V. Ravin
AU - Viktoria A. Shcherbakova
AU - Olga V. Karnachuk
PY - 2026
DA - 2026/10/15
JO - Frontiers in Microbiology
DO - 10.3389/fmicb.2026.1973590
UR - https://www.frontiersin.org/articles/10.3389/fmicb.2026.1973590/full
AB - Methanogenic archaea, capable of producing organic matter from hydrogen and CO ₂ emanating from the mantle, constitute one of the key functional groups of microorganisms in the deep subsurface. Although the diversity of methanogenic inhabitants of the deep biosphere has been studied in detail, the activity of methanogens in these biotopes remains virtually uncharacterized. We have measured the rate of hyrogenotrophic methanogenesis in water from the model borehole 3P (2.7 km deep), located near the small town of Parabel in the Tomsk Region. The potential rate of hydrogenotrophic methanogenesis, measured using ¹⁴ C-labeled sodium bicarbonate, was 5.45 ± 0.528 nmol CH ₄ /dm ³ /day (0.00545 ± 0.0005 nmol CH ₄ /cm ³ /day) - a value compatible to the methanogenic archaeal activity known for anaerobic sediments of surface water bodies. The 16S rRNA gene profiles of water from well 3P were dominated by s single phylotype assigned to the genus Methanothermobacter ; it accounted for 25.54% of the total microbial community. A MAG (metagenome assembled genome) designated 3P-20-051 and belonging to the genus Methanothermobacter was assembled from the water metagenome of well 3P. According to GTDB taxonomy, this MAG represents a novel species within the genus. The closest validly described relative of MAG 3P-20-001 was Methanothermobacter marburgensis with an ANI of 92.66%. Following the characterization of this MAG, a strain of methanogenic archaea designated as K4 T was isolated in pure culture. Morphological, physiological, genotypic, and phylogenetic data indicate that this strain represents a new species of the genus Methanothermobacter, for which we propose the name Methanothermobacter tomskensis sp. nov. Comparison of the strain K4 T genome with MAG 3P-20-051 showed that they were nearly identical: the ANI value was 99.96%. Thus, M. tomskensis sp. nov. indeed, represents a dominant methanogenic lineage revealed by metagenomics. Strain K4 T is characterized by an obligately hydrogenotrophic metabolism and possibly represents the main producer of organic matter in the deep horizons of the thermal aquifer.
SN - 1664-302X
ER -