Electing a candidate: a speculative history of the bacterial phylum OP10

Abstract

Summary In 1998, a cultivation‐independent survey of the microbial community in Obsidian Pool, Yellowstone National Park, detected 12 new phyla within the Domain Bacteria. These were dubbed ‘candidate divisions’ OP1 to OP12. Since that time the OP10 candidate division has been commonly detected in various environments, usually as part of the rare biosphere, but occasionally as a predominant community component. Based on 16S rRNA gene phylogeny, OP10 comprises at least 12 class‐level subdivisions. However, despite this broad ecological and evolutionary diversity, all OP10 bacteria have eluded cultivation until recently. In 2011, two reference species of OP10 were taxonomically validated, removing the phylum from its ‘candidate’ status. Construction of a highly resolved phylogeny based on 29 universally conserved genes verifies its standing as a unique bacterial phylum. In the following paper we summarize what is known and what is suspected about the newest described bacterial phylum, the Armatimonadetes.

Humboldt’s spa: microbial diversity is controlled by temperature in geothermal environments

“…Candidate division OP11 was found in highest abundance at temperatures below 60 1C. Armatimonadetes (OP10) reached its highest relative abundance between 50-80 1C, which is consistent with previous environmental and culture-based studies of this group (Stott et al, 2008;Dunfield et al, 2012) (Supplementary Figure S8a). pH was also observed to have some influence on the relative abundances of different phyla, although both Bacteria and Archaea were observed in all pH ranges (Supplementary Figure S8b).…”

Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes

“…The PhyloPhlAn pipeline presents an expansion in the scope of analysis, with the inclusion of both a large number (B400) of highly conserved proteins and (currently 3737) microbial genomes. The analysis (Figure 2 and Supplementary Figure 1) confirmed previous findings (Dunfield et al, 2012) of the deeply branching nature of T49 T /Armatimonadetes lineage and the strong association, and probably the common ancestry with the phylum Chloroflexi. In addition, the analysis confirmed our previously inferred cladal relationships with the other phyla, including Actinobacteria, Deinococcus-Thermus and Cyanobacteria.…”

“…In combination with the results of previous community and physiological studies (Stott et al, 2008;Lee et al, 2011;Dunfield et al, 2012), the genomic analysis presented here has allowed us to more accurately define the ecological role of T49 T and provided some insight into the ecology of the phylum Armatimonadetes. Physiological data, characteristics of carbohydrate-active enzymes and a large array of carbohydrate transporters, all indicate that T49 T has a chemoheterotrophic carbohydratebased primary metabolism that targets soluble/ amorphous carbohydrates.…”

“…Until recently, this division had no cultivated strains, yet contained just over 600 full-length phylotypes in the SILVA database version 114 (Pruesse et al, 2007). Phylotypes grouping within candidate division OP10 were detected in a wide range of environments, including soil, geothermal springs, freshwater sediments and bioreactors (Bond et al, 1995;Hugenholtz et al, 1998;Lehours et al, 2007;Stott et al, 2008;Dunfield et al, 2012), suggesting a broad range of metabolic capabilities and ecological roles. The first reported cultivated strains of candidate division OP10, strains T49 T and P488, were isolated from geothermally heated soils in New Zealand (Stott et al, 2008).…”

“…To date, three species from the Armatimonadetes have been formally described: C. calidirosea T49 T (Lee et al, 2011), Fimbriimonas ginsengisoli GSoil348 T and the phylum type species, Armatimonas rosea YO-36 T (Tamaki et al, 2011). These strains are only distantly related, with 16S rRNA gene sequence similarities of o80% (Dunfield et al, 2012).…”