Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon,nitrogen, and sulfur cycling |
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Authors: | 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 Lam Austin I McDonald Jeremy A Dodsworth Tanja Woyke Brian P Hedlund |
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Institution: | 1.School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA;2.Department of Energy Joint Genome Institute, Walnut Creek, CA, USA;3.Los Alamos National Laboratory, Los Alamos, NM, USA |
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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. |
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Keywords: | Thermus Thermus oshimai Thermus thermophilus thermophiles hot springs denitrification nitrous oxide Great Basin |
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