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High-Quality Draft Genome Sequence of the Thermus Amyloliquefaciens Type Strain YIM 77409(T) with an Incomplete Denitrification Pathway

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High-Quality Draft Genome Sequence of the Thermus Amyloliquefaciens Type Strain YIM 77409(T) with an Incomplete Denitrification Pathway Lawrence Berkeley National Laboratory Recent Work Title High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409(T) with an incomplete denitrification pathway. Permalink https://escholarship.org/uc/item/49c6b0bb Journal Standards in genomic sciences, 11(1) ISSN 1944-3277 Authors Zhou, En-Min Murugapiran, Senthil K Mefferd, Chrisabelle C et al. Publication Date 2016 DOI 10.1186/s40793-016-0140-3 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Zhou et al. Standards in Genomic Sciences (2016) 11:20 DOI 10.1186/s40793-016-0140-3 SHORTGENOMEREPORT Open Access High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409T with an incomplete denitrification pathway En-Min Zhou1,2, Senthil K. Murugapiran2, Chrisabelle C. Mefferd2, Lan Liu3, Wen-Dong Xian1, Yi-Rui Yin1, Hong Ming1, Tian-Tian Yu1, Marcel Huntemann4, Alicia Clum4, Manoj Pillay4, Krishnaveni Palaniappan4, Neha Varghese4, Natalia Mikhailova4, Dimitrios Stamatis4, T. B. K. Reddy4, Chew Yee Ngan4, Chris Daum4, Nicole Shapiro4, Victor Markowitz4, Natalia Ivanova4, Alexander Spunde4, Nikos Kyrpides4, Tanja Woyke4, Wen-Jun Li1,3 and Brian P. Hedlund2,5* Abstract Thermus amyloliquefaciens type strain YIM 77409T is a thermophilic, Gram-negative, non-motile and rod-shaped bacterium isolated from Niujie Hot Spring in Eryuan County, Yunnan Province, southwest China. In the present study we describe the features of strain YIM 77409T together with its genome sequence and annotation. The genome is 2,160,855 bp long and consists of 6 scaffolds with 67.4 % average GC content. A total of 2,313 genes were predicted, comprising 2,257 protein-coding and 56 RNA genes. The genome is predicted to encode a complete glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle. Additionally, a large number of transporters and enzymes for heterotrophy highlight the broad heterotrophic lifestyle of this organism. A denitrification gene cluster included genes predicted to encode enzymes for the sequential reduction of nitrate to nitrous oxide, consistent with the incomplete denitrification phenotype of this strain. Keywords: Thermus, Thermus amyloliquefaciens, Thermophiles, Hot springs, Denitrification Introduction strains also can grow as facultative anaerobes using Thermus species have been isolated from both natural nitrogen oxides, sulfur, or metals as terminal electron and man-made thermal environments such as hot acceptors under oxygen-deprived conditions [8–10]. springs, hot domestic water, deep mines, composting Cava et al. [11] demonstrated that different T. ther- systems, and sewage sludge [1–5]. The genus has mophilus strains can grow anaerobically by reducing attracted considerable attention as a source of thermo- nitrate to nitrite or by reducing nitrite to a gaseous stable enzymes, which have important biotechnological nitrogen product. applications [6], and as a model organism to study the The nitrogen biogeochemical cycle has been investi- mechanisms involved in bacterial adaptation to extreme gated in a few geothermal systems [12], including Great environments [7]. Members of the genus Thermus were Boiling Spring, a ~80 °C hot spring in the U.S. Great formerly considered to be strictly aerobic, based on the Basin [13–15]. Studies in GBS revealed a high flux of characteristics of the type species Thermus aquaticus nitrous oxide, particularly in the ~80 °C source pool, [2]. However, many studies have shown that Thermus suggesting the importance of incomplete denitrifiers in high-temperature environments. A subsequent cultiva- * Correspondence: [email protected] tion and physiological study of heterotrophic denitrifiers 2School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA 5Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, suggested a significant role of T. oshimai and T. thermo- Las Vegas, NV, USA philus in denitrification in this hot spring [16]. A Full list of author information is available at the end of the article © 2016 Zhou et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Zhou et al. Standards in Genomic Sciences (2016) 11:20 Page 2 of 9 Fig. 1 Maximum-likelihood phylogenetic tree of the genus Thermus to highlight the position of Thermus amyloliquefaciens strain YIM 77409T. The tree was reconstructed based on 1374 aligned positions that remained after the application of the Lane mask to the 16S rRNA gene sequences using MEGA 5.0 [54]. Complete deletion of gaps and missing data and Kimura’s two-parameter model was applied. Bootstrap analysis was based on 1000 resamplings. Nodes supported in >75 % (black circles) or >50 % (grey circles) of bootstrap pseudoreplicates (1000 resamplings) for both maximum-likelihood and neighbor-joining methods are indicated. Bar, 0.02 changes per nucleotide. The number of genomes available for each species is included in parentheses (see Table 5) and the asterisk indicates that the genome of the type strain is available. The 16S rRNA gene sequences from Marinithermus hydrothermalis T1T/AB079382 and Rhabdothermus arcticus 2 M70-1T/HM856631 were used as outgroups following study of the whole genomes of one strain from antranikianii HN3-7T (96.6 %), T. caliditerrae YIM each species, T. oshimai JL-2 and T. thermophilus JL-18, 77925T (96.5 %), and T. tengchongensis YIM 77924T revealed that they have genes encoding the sequential (96.1 %) using EzTaxon-e [19]. The sequence similarities reduction of nitrate to nitrous oxide but lack genes en- were less than 96.0 % with all other species. Phylogenetic coding the nitrous oxide reductase, and explains their analyses based on the 16S rRNA gene sequences show incomplete denitrification phenotype [17]. that YIM 77409T together with T. caliditerrae, T. scoto- Thermus amyloliquefaciens strain YIM 77409T was ductus, T. antranikianii,andT. tengchongensis constitute isolated in the course of an investigation of the cultur- a distinct monophyletic group within the genus Thermus able thermophiles that inhabit geothermal springs in (Fig. 1). The DNA-DNA hybridization value between Yunnan Province, southwest China [18]. Strain YIM strains YIM 77409T and T. scotoductus SE-1T was 30.6 ± 77409T was cultured from a sediment sample collected 1.6 % [18], which was lower than the threshold value from Niujie Hot Spring using the serial dilution tech- (70 %) for the recognition of microbial species [20]. nique on T5 agar. This organism was able to grow an- Similarly, the average nucleotide identity (ANI) score aerobically using nitrate as a terminal electron acceptor, and may potentially impact the nitrogen biogeochemical cycle. Here we describe a summary classification and a set of the features of Thermus amyloliquefaciens type strain YIM 77409T, together with the genome sequence description and annotation. This work may help to better understand the physiological characters as well as the ecological role of this organism in hot spring ecosystems. Organism information Classification and features A taxonomic study using a polyphasic approach placed strain YIM 77409T in the genus Thermus within the family Thermaceae of the phylum Deinococcus-Thermus and resulted in the description of a novel species, Ther- mus amyloliquefaciens, according to its ability to digest starch [18]. The highest 16S rRNA gene sequence pair- Fig. 2 Scanning electron microscopy image of Thermus T wise similarities for strain YIM 77409T were found with amyloliquefaciens strain YIM 77409 grown in Thermus medium broth at 65 °C for 24 h the type strain of T. scotoductus SE-1T (97.6 %), T. Zhou et al. Standards in Genomic Sciences (2016) 11:20 Page 3 of 9 between the two strains based on genome-wide compar- consist of aminophospholipid, one unidentified isons was 86.6 %, according to the algorithm proposed phospholipid, and two unidentified glycolipids. Mini- by Goris et al. [21], which is lower than the ANI thresh- mum Information about the Genome Sequence [23] old range (95–96 %) for species demarcation [22]. Those of type strain YIM 77409T is provided in Table 1. results indicate that strain YIM 77409T represents a dis- tinct genospecies in the genus Thermus [18]. Genome sequencing information Strain YIM 77409T is Gram-negative, facultatively Genome project history anaerobic, non-motile, and rod shaped (Fig. 2). Cells T. amyloliquefaciens strain YIM 77409T was selected for are 0.4–0.6 μm wide and 1.5–4.5 μm long. Colonies whole genome sequencing based on its phylogenetic grownonanR2A,T5,andThermus agar plates for position, denitrifying phenotype, and also for its biotech- 2 days are yellow and circular. The strain degrades nological potential. Comparison of the genome of this starch and is positive for nitrate reduction. The pre- organism to that of other sequenced Thermus species dominant menaquinone is MK-8. Major fatty acids may provide insights into the molecular basis of the de- (>10 %) are iso-C15:0 and iso-C17:0. The polar lipids nitrification
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