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ISME J. 2014 Jul;8(7):1522-33. doi: 10.1038/ismej.2013.251. Epub 2014 Jan 30.

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

Author information

  • 11] GNS Science, Extremophiles Research Group, Wairakei Research Centre, Taupo, New Zealand [2] Department of Biological Sciences, University of Waikato, Hamilton, New Zealand.
  • 21] GNS Science, Extremophiles Research Group, Wairakei Research Centre, Taupo, New Zealand [2] Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
  • 31] GNS Science, Extremophiles Research Group, Wairakei Research Centre, Taupo, New Zealand [2] Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.
  • 4Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.
  • 5Department of Biological Sciences, University of Waikato, Hamilton, New Zealand.
  • 6GNS Science, Extremophiles Research Group, Wairakei Research Centre, Taupo, New Zealand.

Abstract

Most of the lineages of bacteria have remained unknown beyond environmental surveys using molecular markers. Until the recent characterisation of several strains, the phylum Armatimonadetes (formerly known as 'candidate division OP10') was a dominant and globally-distributed lineage within this 'uncultured majority'. Here we report the first Armatimonadetes genome from the thermophile Chthonomonas calidirosea T49(T) and its role as a saccharide scavenger in a geothermal steam-affected soil environment. Phylogenomic analysis indicates T49(T) to be related closely to the phylum Chloroflexi. The predicted genes encoding for carbohydrate transporters (27 carbohydrate ATP-binding cassette transporter-related genes) and carbohydrate-metabolising enzymes (including at least 55 putative enzymes with glycosyl hydrolase domains) within the 3.43 Mb genome help explain its ability to utilise a wide range of carbohydrates as well as its inability to break down extracellular cellulose. The presence of only a single class of branched amino acid transporter appears to be the causative step for the requirement of isoleucine for growth. The genome lacks many commonly conserved operons (for example, lac and trp). Potential causes for this, such as dispersion of functionally related genes via horizontal gene transfer from distant taxa or recent genome recombination, were rejected. Evidence suggests T49(T) relies on the relatively abundant σ-factors, instead of operonic organisation, as the primary means of transcriptional regulation. Examination of the genome with physiological data and environmental dynamics (including interspecific interactions) reveals ecological factors behind the apparent elusiveness of T49(T) to cultivation and, by extension, the remaining 'uncultured majority' that have so far evaded conventional microbiological techniques.

PMID:
24477196
PMCID:
PMC4069393
DOI:
10.1038/ismej.2013.251
[PubMed - indexed for MEDLINE]
Free PMC Article
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