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Cited by 115Microbial Community Ecology and PhysiologyGenomics and Phylogenetic StudiesMicrobial metabolism and enzyme function

A Deeply Branching Thermophilic Bacterium with an Ancient Acetyl-CoA Pathway Dominates a Subsurface Ecosystem

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Takami, Hideto, Noguchi, Hideki, Takaki, Yoshihiro, Uchiyama, Ikuo, Toyoda, Atsushi, Nishi, Shinro, Chee, Gab-Joo, Arai, Wataru +4 more·2012·PLoS ONE
DOI 10.1371/journal.pone.0030559PMC PMC3267732
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Abstract

A nearly complete genome sequence of Candidatus 'Acetothermum autotrophicum', a presently uncultivated bacterium in candidate division OP1, was revealed by metagenomic analysis of a subsurface thermophilic microbial mat community. Phylogenetic analysis based on the concatenated sequences of proteins common among 367 prokaryotes suggests that Ca. 'A. autotrophicum' is one of the earliest diverging bacterial lineages. It possesses a folate-dependent Wood-Ljungdahl (acetyl-CoA) pathway of CO(2) fixation, is predicted to have an acetogenic lifestyle, and possesses the newly discovered archaeal-autotrophic type of bifunctional fructose 1,6-bisphosphate aldolase/phosphatase. A phylogenetic analysis of the core gene cluster of the acethyl-CoA pathway, shared by acetogens, methanogens, some sulfur- and iron-reducers and dechlorinators, supports the hypothesis that the core gene cluster of Ca. 'A. autotrophicum' is a particularly ancient bacterial pathway. The habitat, physiology and phylogenetic position of Ca. 'A. autotrophicum' support the view that the first bacterial and archaeal lineages were H(2)-dependent acetogens and methanogenes living in hydrothermal environments.

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  • Sulfate reducers, acetogens and methanogens appear to be the most common inhabitants of ecosystems situated deep within the crust.

    “Sulfate reducers, acetogens and methanogens appear to be the most common inhabitants of ecosystems situated deep within the crust [184–188].”

    From Early bioenergetic evolution (2013) · cites this paper as [185]

    The Discussion (page unavailable) describes a numerically abundant bacterium in a subsurface microbial mat whose metabolism is predicted to include acetogenesis. It does not establish that sulfate reducers, acetogens, and methanogens are collectively the most common inhabitants of ecosystems deep within the crust; its account of this mat also discusses methanotrophs, which are not methanogens. (LLM, conf=0.86)

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Authors
Takami, H., Noguchi, H., Takaki, Y., Uchiyama, I., Toyoda, A., Nishi, S., Chee, G.-J., Arai, W., Nunoura, T., Itoh, T., Hattori, M., & Takai, K.
Affiliations
  • Japan Agency for Marine-Earth Science and Technology (JP)
  • Tokyo Institute of Technology (JP)
  • National Institute for Basic Biology (JP)
  • National Institute of Genetics (JP)
  • The University of Tokyo (JP)
Corresponding author
Takami, Hideto
ORCID
Venue
PLoS ONE
Publisher
Public Library of Science (PLoS)
Published
2012-01-27
Volume
7
Issue
1
Pages
e30559
ISSN
1932-6203 (ISSN-L)
DOI
10.1371/journal.pone.0030559
PMC
PMC3267732
OpenAlex
W2070267953
Cited by
115
References
4
Citations by year
2026: 1 · 2025: 2 · 2024: 8 · 2023: 1 · 2022: 5 · 2021: 7 · 2020: 9 · 2019: 15 · 2018: 12 · 2017: 9 · 2016: 10 · 2015: 12 · 2014: 6 · 2013: 12 · 2012: 5
FWCI
9.92
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS ONE (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • Figshare (submittedVersion, cc-by)
Funders
  • Ministry of Education, Culture, Sports, Science and Technology
  • University of Tokyo
  • Kitasato University
  • University of California, San Diego
  • Japan Society for the Promotion of Science (21244077)
  • Japan Science and Technology Agency
  • Japan Agency for Marine-Earth Science and Technology
  • National Institute for Basic Biology
Topics
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial metabolism and enzyme function
Keywords
thermophilic bacteria, Wood-Ljungdahl pathway, acetyl-CoA pathway, CO2 fixation, acetogenesis, methanogenic archaea, hydrothermal environments, metagenomics, genome sequence
MeSH terms
Acetyl Coenzyme A, Bacteria, Codon, DNA, Ribosomal, Energy Metabolism, Genes, Bacterial, Gluconeogenesis, Molecular Sequence Data, Phylogeny, Temperature, Cluster Analysis, Ecosystem, Metabolic Networks and Pathways

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