Diversity and distribution of thermophilic hydrogenogenic carboxydotrophs revealed by microbial community analysis in sediments from multiple hydrothermal environments in Japan

Abstract

In hydrothermal environments, carbon monoxide (CO) utilisation by thermophilic hydrogenogenic carboxydotrophs may play an important role in microbial ecology by reducing toxic levels of CO and providing H 2 for fuelling microbial communities. We evaluated thermophilic hydrogenogenic carboxydotrophs by microbial community analysis. First, we analysed the correlation between carbon monoxide dehydrogenase (CODH)–energy-converting hydrogenase (ECH) gene cluster and taxonomic affiliation by surveying an increasing genomic database. We identified 71 genome-encoded CODH–ECH gene clusters, including 46 whose owners were not reported as hydrogenogenic carboxydotrophs. We identified 13 phylotypes showing > 98.7% identity with these taxa as potential hydrogenogenic carboxydotrophs in hot springs. Of these, Firmicutes phylotypes such as Parageobacillus , Carboxydocella , Caldanaerobacter, and Carboxydothermus were found in different environmental conditions and distinct microbial communities. The relative abundance of the potential thermophilic hydrogenogenic carboxydotrophs was low. Most of them did not show any symbiotic networks with other microbes, implying that their metabolic activities might be low. Electronic supplementary material The online version of this article (10.1007/s00203-019-01661-9) contains supplementary material, which is available to authorized users.

Draft Genome Sequence of Thermanaeromonas sp. Strain C210, Isolated in the Presence of Carbon Monoxide

“…The amino acid sequence identities of these three CODHs of strain C210 to their orthologs in T. toyohensis ToBE T were Ͼ85%. These results were consistent with the fact that strain C210 was enriched in the presence of CO and with recent bioinformatics-based analyses showing that the genus Thermanaeromonas includes possible hydrogen-evolving, CO-oxidizing bacteria (16)(17)(18).…”

Diversity analysis of thermophilic hydrogenogenic carboxydotrophs by carbon monoxide dehydrogenase amplicon sequencing using new primers

“…Amplicon sequencing which reveals the community structure in high-resolution with deeply sequenced target genes is another option for diversity estimation of thermophilic hydrogenogenic carboxydotrophs. A recent bioinformatics-based analysis identified 71 genomes harboring the CODH–ECH gene clusters from ~ 140,000 prokaryotic genomes analyzed, which expanded the diversity estimation of potential hydrogenogenic carboxydotrophs to four phyla, 26 genera, and 43 species and provided the reference for amplicon sequencing (Omae et al 2019 ). By using the 16S rRNA gene sequences retrieved from these 71 genomes as a reference in microbial community analysis, we revealed that multiple species of potential thermophilic hydrogenogenic carboxydotrophs in the phylum Firmicutes were distributed in a wide variety of terrestrial hydrothermal environments in culture-independent way (Omae et al 2019 ).…”

“…A recent bioinformatics-based analysis identified 71 genomes harboring the CODH–ECH gene clusters from ~ 140,000 prokaryotic genomes analyzed, which expanded the diversity estimation of potential hydrogenogenic carboxydotrophs to four phyla, 26 genera, and 43 species and provided the reference for amplicon sequencing (Omae et al 2019 ). By using the 16S rRNA gene sequences retrieved from these 71 genomes as a reference in microbial community analysis, we revealed that multiple species of potential thermophilic hydrogenogenic carboxydotrophs in the phylum Firmicutes were distributed in a wide variety of terrestrial hydrothermal environments in culture-independent way (Omae et al 2019 ). However, we were unable to define hydrogenogenic carboxydotrophs by the 16S rRNA gene sequence alone, because strains with and without hydrogenogenic carboxydotrophy exist within a single species (Omae et al 2019 ).…”

“…By using the 16S rRNA gene sequences retrieved from these 71 genomes as a reference in microbial community analysis, we revealed that multiple species of potential thermophilic hydrogenogenic carboxydotrophs in the phylum Firmicutes were distributed in a wide variety of terrestrial hydrothermal environments in culture-independent way (Omae et al 2019 ). However, we were unable to define hydrogenogenic carboxydotrophs by the 16S rRNA gene sequence alone, because strains with and without hydrogenogenic carboxydotrophy exist within a single species (Omae et al 2019 ). Additionally, phylogenetically novel hydrogenogenic carboxydotrophs may remain unidentified by the 16S-targeted amplicon sequencing based on the 71 reference genomes.…”

“…In the present study, to address the diversity of hydrogenogenic carboxydotrophs, we designed multiple degenerate primers which effectively amplified CODHech genes, enabling amplicon sequencing that target those species. To cover the major taxa of thermophilic hydrogenogenic carboxydotrophs which are predicted to be widely distributed across environments (Fukuyama et al 2020 ; Omae et al 2019 ), the new primers were designed to amplify the CODHech genes identified in Firmicutes (hereafter called “FirmiCODHech genes”). The FirmiCODHech genes were derived from 20 species within 12 genera, including one uncultivated strain, and formed three subclades within Clades E and F. Amplicon sequencing by these primers in hot spring sediment samples with or without incubation under CO gas successfully identified phylogenetically novel CODHech genes which may be derived from uncultured hydrogenogenic carboxydotrophs, as well as those of known species.…”