Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling

Senthil K. Murugapiran, Marcel Huntemann, Chia Lin Wei, James Han, J. C. Detter, Cliff Han, Tracy H. Erkkila, Hazuki Teshima, Amy Chen, Nikos Kyrpides, Konstantinos Mavrommatis, Victor Markowitz, Ernest Szeto, Natalia Ivanova, Ioanna Pagani, Amrita Pati, Lynne Goodwin, Lin Peters, Sam Pitluck, Jenny LamAustin I. McDonald, Jeremy A. Dodsworth, Tanja Woyke, Brian P. Hedlund

Research output: Contribution to journalArticlepeer-review

16 Scopus citations

Abstract

The complete genomes of Thermus oshimai JL-2 and T. thermophilus JL-18 each consist of a circular chromosome, 2.07 Mb and 1.9 Mb, respectively, and two plasmids ranging from 0.27 Mb to 57.2 kb. Comparison of the T. thermophilus JL-18 chromosome with those from other strains of T. thermophilus revealed a high degree of synteny, whereas the megaplasmids from the same strains were highly plastic. The T. oshimai JL-2 chromosome and megaplasmids shared little or no synteny with other sequenced Thermus strains. Phylogenomic analyses using a concatenated set of conserved proteins confirmed the phylogenetic and taxonomic assignments based on 16S rRNA phylogenetics. Both chromosomes encode a complete glycolysis, tricarboxylic acid (TCA) cycle, and pentose phosphate pathway plus glucosidases, glycosidases, proteases, and peptidases, highlighting highly versatile heterotrophic capabilities. Megaplasmids of both strains contained a gene cluster encoding enzymes predicted to catalyze the sequential reduction of nitrate to nitrous oxide; however, the nitrous oxide reductase required for the terminal step in denitrification was absent, consistent with their incomplete denitrification phenotypes. A sox gene cluster was identified in both chromosomes, suggesting a mode of chemolithotrophy. In addition, nrf and psr gene clusters in T. oshmai JL-2 suggest respiratory nitrite ammonification and polysulfide reduction as possible modes of anaerobic respiration.

Original languageEnglish (US)
Pages (from-to)449-468
Number of pages20
JournalStandards in Genomic Sciences
Volume7
Issue number3
DOIs
StatePublished - 2013

Keywords

  • Denitrification
  • Great basin
  • Hot springs
  • Nitrous oxide
  • Thermophiles
  • Thermus
  • Thermus oshimai
  • Thermus thermophilus

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