title: Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling.
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.
authors.affiliation: School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA.
authors.forename: Senthil K
authors.initials: SK
authors.lastname: Murugapiran
authors.forename: Marcel
authors.initials: M
authors.lastname: Huntemann
authors.forename: Chia-Lin
authors.initials: CL
authors.lastname: Wei
authors.forename: James
authors.initials: J
authors.lastname: Han
authors.forename: J C
authors.initials: JC
authors.lastname: Detter
authors.forename: Cliff
authors.initials: C
authors.lastname: Han
authors.forename: Tracy H
authors.initials: TH
authors.lastname: Erkkila
authors.forename: Hazuki
authors.initials: H
authors.lastname: Teshima
authors.forename: Amy
authors.initials: A
authors.lastname: Chen
authors.forename: Nikos
authors.initials: N
authors.lastname: Kyrpides
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Mavrommatis
authors.forename: Victor
authors.initials: V
authors.lastname: Markowitz
authors.forename: Ernest
authors.initials: E
authors.lastname: Szeto
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.forename: Ioanna
authors.initials: I
authors.lastname: Pagani
authors.forename: Amrita
authors.initials: A
authors.lastname: Pati
authors.forename: Lynne
authors.initials: L
authors.lastname: Goodwin
authors.forename: Lin
authors.initials: L
authors.lastname: Peters
authors.forename: Sam
authors.initials: S
authors.lastname: Pitluck
authors.forename: Jenny
authors.initials: J
authors.lastname: Lam
authors.forename: Austin I
authors.initials: AI
authors.lastname: McDonald
authors.forename: Jeremy A
authors.initials: JA
authors.lastname: Dodsworth
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.forename: Brian P
authors.initials: BP
authors.lastname: Hedlund
keywords: Great Basin; Thermus; Thermus oshimai; Thermus thermophilus; denitrification; hot springs; nitrous oxide; thermophiles
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