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. 2008 Mar;18(3):442-8.
doi: 10.1101/gr.7136508. Epub 2008 Jan 24.

The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota

Tomoyuki Kosaka  1 , Souichiro Kato, Takefumi Shimoyama, Shunichi Ishii, Takashi Abe, Kazuya Watanabe
Affiliations

The genome of Pelotomaculum thermopropionicum reveals niche-associated evolution in anaerobic microbiota

Tomoyuki Kosaka et al. Genome Res. 2008 Mar.

Abstract

The anaerobic biodegradation of organic matter is accomplished by sequential syntrophic catabolism by microbes in different niches. Pelotomaculum thermopropionicum is a representative syntrophic bacterium that catalyzes the intermediate bottleneck step in the anaerobic-biodegradation process, whereby volatile fatty acids (VFAs) and alcohols produced by upstream fermenting bacteria are converted to acetate, hydrogen, and carbon dioxide (substrates for downstream methanogenic archaea). To reveal genomic features that contribute to our understanding of the ecological niche and evolution of P. thermopropionicum, we sequenced its 3,025,375-bp genome and performed comparative analyses with genomes of other community members available in the databases. In the genome, 2920 coding sequences (CDSs) were identified. These CDSs showed a distinct distribution pattern in the functional categories of the Clusters of Orthologous Groups database, which is considered to reflect the niche of this organism. P. thermopropionicum has simple catabolic pathways, in which the propionate-oxidizing methylmalonyl-CoA pathway constitutes the backbone and is linked to several peripheral pathways. Genes for most of the important catabolic enzymes are physically linked to those for PAS-domain-containing regulators, suggesting that the catabolic pathways are regulated in response to environmental conditions and/or global cellular situations rather than specific substrates. Comparative analyses of codon usages revealed close evolutionary relationships between P. thermopropionicum and other niche members, while it was distant from phylogenetically related sugar-fermenting bacteria. These analyses suggest that P. thermopropionicum has evolved as a syntrophy specialist by interacting with niche-associated microbes.

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Figures

Figure 1.
Figure 1.
Metabolic interactions in the anaerobic biodegradation process. Italic letters indicate representative organisms in the anaerobic microbiota, whose genomes have been determined; (Pth) Pelotomaculum thermopropionicum; (Moth) Moorella thermoacetica; (Tte) Thermoanaerobacter tengcongensis; (Swol) Syntrophomonas wolfei; (Cth) Clostridium thermocellum; (Cac) Clostridium acetobutylicum; (Sac) Syntrophus aciditrophicus; (Sfu) Syntrophobacter fumaroxidans; (Pac) Propionibacterium acnes; (Bfr) Bacteroides fragilis; (Tde) Treponema denticola; (Msth) Methanosaeta thermophila; (Mtth) Methanothermobacter thermautotrophicus; (Mhu) Methanospirillum hungatei; (Mma) Methanococcus maripaludis; (Mac) Methanosarcina acetivorans. For more information about these organisms, refer to Supplemental Table S1.
Figure 2.
Figure 2.
Overview of the metabolism of P. thermopropionicum. Substrates of alcohol dehydrogenases (ADH) and aldehyde dehydrogenases (AdDH) are not identified, and they are listed below the cell. (MQ) Menaquinone.
Figure 3.
Figure 3.
Evolutionary relationships among the organisms analyzed in this study. (A) A neighbor-joining tree based on 16S rRNA gene sequences. (Black circles) Branch nodes supported by the Bootstrap analysis (>70%). (B) A UPGMA tree based on gene contents. (C) A self-organization map (SOM) based on codon usages. Each point represents one CDS, and CDSs of one organism are presented with the same color. Italic letters indicate organism names; (Chy) Carboxydothermus hydrogenoformans; (Lla) Lactococcus lactis; (Lpl) Lactobacillus plantarum; (Efa) Enterococcus faecalis; (Bsu) Bacillus subtilis; (Wsu) Wolinella succinogenes; (Dde) Desulfovibrio desulfuricans; (Gsu) Geobacter sulfurreducens; (Zmo) Zymomonas mobilis; (Pae) Pseudomonas aeruginosa; (Tma) Thermotoga maritima. Refer to the legend of Figure 1 for other organisms and to Supplemental Table S1 for more information about these organisms.
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