Skip to main content
Download PDF
  • Short genome report
  • Open access
  • Published:

High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409T with an incomplete denitrification pathway

Standards in Genomic Sciences volume 11, Article number: 20 (2016) Cite this article

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.

Introduction

Thermus species have been isolated from both natural and man-made thermal environments such as hot springs, hot domestic water, deep mines, composting systems, and sewage sludge [1–5]. The genus has attracted considerable attention as a source of thermostable enzymes, which have important biotechnological applications [6], and as a model organism to study the mechanisms involved in bacterial adaptation to extreme environments [7]. Members of the genus Thermus were formerly considered to be strictly aerobic, based on the characteristics of the type species Thermus aquaticus [2]. However, many studies have shown that Thermus strains also can grow as facultative anaerobes using nitrogen oxides, sulfur, or metals as terminal electron acceptors under oxygen-deprived conditions [8–10]. Cava et al. [11] demonstrated that different T. thermophilus strains can grow anaerobically by reducing nitrate to nitrite or by reducing nitrite to a gaseous nitrogen product.

The nitrogen biogeochemical cycle has been investigated in a few geothermal systems [12], including Great Boiling Spring, a ~80 °C hot spring in the U.S. Great Basin [13–15]. Studies in GBS revealed a high flux of nitrous oxide, particularly in the ~80 °C source pool, suggesting the importance of incomplete denitrifiers in high-temperature environments. A subsequent cultivation and physiological study of heterotrophic denitrifiers suggested a significant role of T. oshimai and T. thermophilus in denitrification in this hot spring [16]. A following study of the whole genomes of one strain from each species, T. oshimai JL-2 and T. thermophilus JL-18, revealed that they have genes encoding the sequential reduction of nitrate to nitrous oxide but lack genes encoding the nitrous oxide reductase, and explains their incomplete denitrification phenotype [17].

Thermus amyloliquefaciens strain YIM 77409T was isolated in the course of an investigation of the culturable thermophiles that inhabit geothermal springs in Yunnan Province, southwest China [18]. Strain YIM 77409T was cultured from a sediment sample collected from Niujie Hot Spring using the serial dilution technique on T5 agar. This organism was able to grow anaerobically 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, Thermus amyloliquefaciens , according to its ability to digest starch [18]. The highest 16S rRNA gene sequence pairwise similarities for strain YIM 77409T were found with the type strain of T. scotoductus SE-1T (97.6 %), T. antranikianii HN3-7T (96.6 %), T. caliditerrae YIM 77925T (96.5 %), and T. tengchongensis YIM 77924T (96.1 %) using EzTaxon-e [19]. The sequence similarities were less than 96.0 % with all other species. Phylogenetic analyses based on the 16S rRNA gene sequences show that YIM 77409T together with T. caliditerrae , T. scotoductus , T. antranikianii , and T. tengchongensis constitute a distinct monophyletic group within the genus Thermus (Fig. 1). The DNA-DNA hybridization value between strains YIM 77409T and T. scotoductus SE-1T was 30.6 ± 1.6 % [18], which was lower than the threshold value (70 %) for the recognition of microbial species [20]. Similarly, the average nucleotide identity (ANI) score between the two strains based on genome-wide comparisons was 86.6  %, according to the algorithm proposed by Goris et al. [21], which is lower than the ANI threshold range (95–96 %) for species demarcation [22]. Those results indicate that strain YIM 77409T represents a distinct genospecies in the genus Thermus [18].

Fig. 1
figure 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

Full size image

Strain YIM 77409T is Gram-negative, facultatively anaerobic, non-motile, and rod shaped (Fig. 2). Cells are 0.4–0.6 μm wide and 1.5–4.5 μm long. Colonies grown on an R2A, T5, and Thermus agar plates for 2 days are yellow and circular. The strain degrades starch and is positive for nitrate reduction. The predominant menaquinone is MK-8. Major fatty acids (>10 %) are iso-C15:0 and iso-C17:0. The polar lipids consist of aminophospholipid, one unidentified phospholipid, and two unidentified glycolipids. Minimum Information about the Genome Sequence [23] of type strain YIM 77409T is provided in Table 1.

Fig. 2
figure 2

Scanning electron microscopy image of Thermus amyloliquefaciens strain YIM 77409T grown in Thermus medium broth at 65 °C for 24 h

Full size image
Table 1 Classification and general features of Thermus amyloliquefaciens strain YIM 77409T [23]
Full size table

Genome sequencing information

Genome project history

T. amyloliquefaciens strain YIM 77409T was selected for whole genome sequencing based on its phylogenetic position, denitrifying phenotype, and also for its biotechnological potential. Comparison of the genome of this organism to that of other sequenced Thermus species may provide insights into the molecular basis of the denitrification process in this genus. The genome project for strain YIM 77409T was deposited in the Genomes OnLine Database [24] and the complete sequences were deposited in GenBank. Sequencing, finishing, and annotation were performed by the Department of Energy Joint Genome Institute (Walnut Creek, CA, USA) using state of the art sequencing technology [25]. A summary of the project information associated with MIGS version 2.0 compliance [23] is shown in Table 2.

Table 2 Project information
Full size table

Growth conditions and genomic DNA preparation

T. amyloliquefaciens type strain YIM 77409T was grown aerobically in Thermus medium at 65 °C for 2 days [18] and DNA was isolated from 0.5–1.0 g of cell pellet using the Joint Genome Institute CTAB bacterial genomic DNA isolation protocol [26].

Genome sequencing and assembly

The draft genome of T. amyloliquefaciens type strain YIM 77409T was generated at the DOE JGI using Pacific Biosciences sequencing technology [27]. A PacBio SMRTbell™ library was constructed and sequenced on the PacBio RS platform using three SMRT cells, which generated 264,235 filtered subreads totaling 751.5 Mbp with an N50 contig length of 2,065,958 bp. All general aspects of library construction and sequencing can be found at the JGI website. All raw reads were assembled using HGAP version 2.1.1 [28]. The final draft assembly produced 6 contigs in 6 scaffolds, totaling 2.16 Mbp in size. The input read coverage was 384.9 × .

Genome annotation

Genes were identified using Prodigal [29] as part of the JGI microbial annotation pipeline [30], followed by a round of manual curation using the JGI GenePRIMP pipeline [31]. The predicted coding sequences were translated and used to search against the Integrated Microbial Genomes non-redundant database, UniProt, TIGRfam, Pfam, PRIAM, KEGG, COG, and InterPro databases. These data sources were combined to assert a product description for each predicted protein. The rRNA genes are predicted using hmmsearch tool from the package HMMER 3.0 [32] and a set of in-house curated HMMs derived from an alignment of full-length rRNA genes selected from IMG isolate genomes; tRNA genes were found using tRNAscan-SE 1.3.1 [33]; other non-coding RNAs and regulatory RNA features were found by searching the genome for the corresponding Rfam profiles using INFERNAL 1.0.2 package [34]. Additional gene prediction analysis and manual functional annotation was performed using the Integrated Microbial Genomes Expert Review platform developed by the JGI [35]. The analysis of the genome presented here and the annotations are for the version available through IMG (2579778517).

Genome properties

The T. amyloliquefaciens YIM 77409T high quality draft genome is 2,160,855 bp long with a 67.4 % G + C content. The genomes comprise 2,257 protein-coding genes and 56 RNA genes. The coding regions accounted for 94 % of the whole genome and 1,839 genes were assigned to a putative function with the remaining annotated as hypothetical proteins. A total of 1,558 genes (67.4 %) were assigned to COGs. The properties and the statistics of the genome are presented in Table 3. The distribution of genes into COG functional categories is presented in Table 4.

Table 3 Genome statistics
Full size table
Table 4 Number of genes associated with general COG functional categories
Full size table

Insights from the genome sequence

Comparisons with other Thermus spp. genomes

Twenty-two Thermus genomes from 12 different species have been sequenced, including T. amyloliquefaciens type strain YIM 77409T , and 7 of them have finished genome sequences. The phylogenetic coverage of these genomes is shown in Fig. 1 and their basic properties are summarized in Table 5. The Thermus genomes range in size from 2.04 Mb ( Thermus sp. RLM) to 2.56 Mb ( T. tengchongensis YIM 77401); GC contents vary from 64.8 % ( T. scotoductus DSM 8553T ) to 69.5 % ( T. thermophilus HB8T), predicted gene number range from 2,043 (T. sp. RLM) to 2,789 ( T. brockianus ). The genome size (2.16 Mb) and GC contents (67.4 %) of strain YIM 77409T are around the average value, but the gene number of this strain is lower than the average, possibly indicating gene loss through genomic streamlining in this species. In addition, the percentage of protein-coding genes with functional prediction (79.5 %) is higher than the average, whereas the percentage of protein-coding genes with COGs (67.4 %) is similar to the average of the genus Thermus .

Table 5 Comparison of basic genome features of Thermus strains
Full size table

Profiles of metabolic network and pathway

The T. amyloliquefaciens YIM 77409T genome encodes genes for complete glycolysis, gluconeogenesis, tricarboxylic acid cycle, pyruvate dehydrogenase, and pentose phosphate pathway. Twenty ABC transporters were identified in the YIM 77409T genome, including amino acid, oligopeptide/dipeptide, N-acetyl-D-glucosamine, maltose, nucleoside, sugar, phosphonate, phosphate, thiamin, cation, and ammonium transporters as well as other permeases. The genome also encodes glucosidases, glycosidases, proteases, and peptidases. The finding of three genes probably coding for esterase (BS74_RS04020, BS74_RS04625, BS74_RS10315) and one gene probably coding for amylopullulanase (BS74_RS00620) are consistent with the observed lipase and amylase activities observed in strain YIM 77409T . A number of genes assigned to a classical electron transport chain have been identified in the strain YIM 77409T genome. Respiratory complex I NADH quinone oxidoreductases consists of NADH quinone oxidoreductase chains A-N (BS74_RS03070-BS74_RS03135), NADH quinone oxidoreductase subunit 15 (BS74_RS02790), and two quinone oxidoreductases (BS74_RS00610, BS74_RS06600). Complex II consists of succinate dehydrogenase (cytochrome b 556 subunit SdhC (BS74_RS07950), SdhA (BS74_RS07940), SdhB (BS74_RS07935), and SdhD (BS74_RS07945). A four-subunit cytochrome bc 1 complex found in T. thermophilus was also identified in strain YIM 77409T (BS74_RS10415-BS74_RS10430) [36, 37]. The terminal cytochrome oxidase is encoded by four cytochrome c oxidase genes ctaC1 (BS74_RS00820), caaA (BS74_RS00825), ctaD2 (BS74_RS04775), and ctaC2 (BS74_RS04780). Other cytochrome c oxidase genes observed in T. scotoductus SA-01, ctaH, ctaE1, ctaE2, ctaD1, and coxM (TSC_C00960-TSC_C01000), were not found in the YIM 77409T genome.

Genes involved in denitrification

Denitrification is a respiratory process to reduce nitrate or nitrite stepwise to nitrogen gas (NO3 − → NO2 − → NO → N2O → N2), and plays a major role in converting bioavailable nitrogen to recalcitrant dinitrogen gas [38]. Denitrification normally occurs under oxygen-limiting conditions, and is catalyzed by four types of nitrogen oxide reductases in sequence: nitrate reductase (Nar or Nap), nitrite reductase (Nir), nitric oxide reductase (Nor), and nitrous oxide reductase (Nos) [39, 40]. Previous studies have demonstrated that some Thermus species have incomplete denitrification phenotypes terminating with the production of nitrite or nitrous oxide [16, 41]. This incomplete denitrification is partly encoded by a conjugative element (nitrate conjugative element, NCE) that can be transferred among strains [42]. The NCE is composed of two main operons, nar and nrc, and the transcription factors DnrS and DnrT, which are required for their expression under anaerobic conditions when nitrate is present [43, 44]. The periplasmic nitrate reductase subunits NapB and NapC were not found in the genome of T. amyloliquefaciens YIM 77409T , consistent with the use of the Nar system in the Thermales . Figure 3 shows the organization of the nar operon and neighboring genes involved in denitrification in T. amyloliquefaciens YIM 77409T , T. tengchongensis YIM 77401, and T. scotoductus SA-01. They are located on the chromosome in strains YIM 77409T and YIM 77401, as in T. scotoductus SA-01. However, these gene clusters are located on megaplasmids in T. thermophilus and T. oshimai strains [17]. The nar operons show a high degree of synteny and consist of narCGHJIKT encoding the associated periplasmic cytochrome NarC, the membrane-bound nitrate reductase (NarGHI), the dedicated chaperone NarJ, the nitrate/proton symporter (NarK1), which might also function in nitrite extrusion in T. thermophilus HB8T, and the nitrate/nitrite antiporter (NarK2). Regulatory protein A and a denitrification regulator gene operon dnrST are adjacent to the nar operons. Strain YIM 77409T contains a putative nirS, which encodes the isofunctional tetraheme cytochrome cd1-containing nitrite reductase. The nirK, encoding a Cu-containing nitrite reductase in T. scotoductus SA-01, is absent in strain YIM 77409T and YIM 77401. Genes encoding conserved hypothetical proteins, coenzyme PQQ synthesis protein (PqqE), and nitric oxide reductase subunit b (NorB) and c (NorC) were also presented in the YIM 77409T genome. Genes encoding the periplasmic multicopper enzyme nitrous oxide reductase (Nos), which catalyzes the last step of the denitrification (N2O → N2), were not observed in the YIM 77409T genome or in any Thermus spp. genomes. Physiological experiments with nitrate as the sole terminal electron acceptor also confirm that strain YIM 77409T can convert nitrate to nitrous oxide under anaerobic conditions, but not to nitrogen gas.

Fig. 3
figure 3

Molecular organization of identified nar operon and neighboring genes involved in denitrification located on the chromosome of T. amyloliquefaciens YIM 77409T, T. tengchongensis YIM 77401, and T. scotoductus SA-01. Fe: heme protein-containing nitrite reductase, Cu: copper-containing nitrite reductase. Numbers below the genes indicate the provisional ORF numbers in T. amyloliquefaciens YIM 77409T and T. tengchongensis YIM 77401, the locations in the chromosome are indicated below. nar: nitrate reductase gene; nir: nitrite reductase gene; nor: nitric oxide reductase gene; dnr: denitrification regulator gene [43, 55, 56]. This figure is modified from Murugapiran et al. [17]

Full size image

Conclusions

The genus Thermus is the archetypal thermophilic bacterium and has been isolated from both natural and man-made thermal environments. Members of this genus are of significance as a source of thermophilic enzymes of great biotechnological interest and as an excellent laboratory models to study the molecular basis of thermal stability. Here, we report the annotation of a high quality draft genome sequence of Thermus amyloliquefaciens YIM 77409T . Analysis of the genome revealed that strain YIM 77409T encodes enzymes involved in complete glycolysis, pentose phosphate pathway, tricarboxylic acid cycle, pyruvate dehydrogenase, and pentose phosphate pathway. The genome sequence of strain YIM 77409T provides insights to better understand the molecular mechanisms of the incomplete denitrification phenotype and the ecological roles that Thermus species play in nitrogen cycling. Combined analysis of this genome and other Thermus genomes also provides important insights into the evolution and ecology of this group and the role it may play in the high-temperature nitrogen biogeochemical cycle.

Abbreviations

GBS:

Great Boiling Spring

CTAB:

cetyl trimethyl ammonium bromide

PacBio:

Pacific Biosciences

ANI:

average nucleotide identity

NCE:

nitrate conjugative element

References

  1. Yabe S, Kato A, Hazaka M, Yokota A. Thermaerobacter composti sp. nov., a novel extremely thermophilic bacterium isolated from compost. J Gen Appl Microbiol. 2009;55(5):323–8.

    Article  CAS  PubMed  Google Scholar 

  2. Brock TD, Freeze H. Thermus aquaticus gen. n. and sp. n., a nonsporulating extreme thermophile. J Bacteriol. 1969;98(1):289–97.

    PubMed Central  CAS  PubMed  Google Scholar 

  3. Kristjánsson JK, Hjörleifsdóttir S, Marteinsson VT, Alfredsson GA. Thermus scotoductus, sp. nov., a pigment-producing thermophilic bacterium from hot tap water in Iceland and including Thermus sp. X-1. Syst Appl Microbiol. 1994;17(1):44–50.

    Article  Google Scholar 

  4. Yu T-T, Yao J-C, Ming H, Yin Y-R, Zhou E-M, Liu M-J, et al. Thermus tengchongensis sp. nov., isolated from a geothermally heated soil sample in Tengchong, Yunnan, south-west China. Antonie Van Leeuwenhoek. 2013;103(3):513–8.

    Article  PubMed  Google Scholar 

  5. Kieft T, Fredrickson J, Onstott T, Gorby Y, Kostandarithes H, Bailey T, et al. Dissimilatory reduction of Fe (III) and other electron acceptors by a Thermus isolate. Appl Environ Microbiol. 1999;65(3):1214–21.

    PubMed Central  CAS  PubMed  Google Scholar 

  6. Bruins ME, Janssen AE, Boom RM. Thermozymes and their applications. Appl Biochem Biotechnol. 2001;90(2):155–86.

    Article  CAS  PubMed  Google Scholar 

  7. Rothschild LJ, Mancinelli RL. Life in extreme environments. Nature. 2001;409(6823):1092–101.

    Article  CAS  PubMed  Google Scholar 

  8. Gihring TM, Banfield JF. Arsenite oxidation and arsenate respiration by a new Thermus isolate. FEMS Microbiol Lett. 2001;204(2):335–40.

    Article  CAS  PubMed  Google Scholar 

  9. Balkwill DL, Kieft T, Tsukuda T, Kostandarithes HM, Onstott T, Macnaughton S, et al. Identification of iron-reducing Thermus strains as Thermus scotoductus. Extremophiles. 2004;8(1):37–44.

    Article  CAS  PubMed  Google Scholar 

  10. Skirnisdottir S, Hreggvidsson GO, Holst O, Kristjansson JK. Isolation and characterization of a mixotrophic sulfur-oxidizing Thermus scotoductus. Extremophiles. 2001;5(1):45–51. doi:10.1007/s007920000172.

    Article  CAS  PubMed  Google Scholar 

  11. Cava F, Zafra O, Da Costa MS, Berenguer J. The role of the nitrate respiration element of Thermus thermophilus in the control and activity of the denitrification apparatus. Environ Microbiol. 2008;10(2):522–33.

    Article  CAS  PubMed  Google Scholar 

  12. Hamilton TL, Koonce E, Howells A, Havig JR, Jewell T, José R, et al. Competition for ammonia influences the structure of chemotrophic communities in geothermal springs. Appl Environ Microbiol. 2014;80(2):653–61.

    Article  PubMed Central  PubMed  Google Scholar 

  13. Dodsworth JA, Hungate BA, Hedlund BP. Ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium in two US Great Basin hot springs with abundant ammonia-oxidizing archaea. Environ Microbiol. 2011;13(8):2371–86. doi:10.1111/j.1462-2920.2011.02508.x.

    Article  CAS  PubMed  Google Scholar 

  14. Dodsworth JA, Hungate B, de la Torre JR, Jiang H, Hedlund BP. Measuring nitrification, denitrification, and related biomarkers in terrestrial geothermal ecosystems. Methods Enzymol. 2011;486:171–203.

    Article  CAS  PubMed  Google Scholar 

  15. Edwards TA, Calica NA, Huang DA, Manoharan N, Hou W, Huang L, et al. Cultivation and characterization of thermophilic Nitrospira species from geothermal springs in the US Great Basin, China, and Armenia. FEMS Microbiol Ecol. 2013;85(2):283–92.

    Article  CAS  PubMed  Google Scholar 

  16. Hedlund BP, McDonald A, Lam J, Dodsworth JA, Brown J, Hungate B. Potential role of Thermus thermophilus and T. oshimai in high rates of nitrous oxide (N2O) production in ~80 °C hot springs in the US Great Basin. Geobiology. 2011;9(6):471–80.

    Article  CAS  PubMed  Google Scholar 

  17. Murugapiran SK, Huntemann M, Wei C-L, Han J, Detter JC, Han C, et al. Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling. Stand Genomic Sci. 2013;7(3):449–68.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  18. Yu T-T, Ming H, Yao J-C, Zhou E-M, Park D-J, Hozzein WN, et al. Thermus amyloliquefaciens sp. nov., isolated from a hot spring sediment sample. Int J Syst Evol Microbiol. 2015;65(8):2491–5.

    Article  CAS  PubMed  Google Scholar 

  19. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol. 2012;62(Pt 3):716–21.

    Article  CAS  PubMed  Google Scholar 

  20. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, et al. Report of the ad hoc Committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol. 1987;37(4):463–4.

    Article  Google Scholar 

  21. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol. 2007;57(1):81–91.

    Article  CAS  PubMed  Google Scholar 

  22. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol. 2014;64(Pt 2):346–51.

    Article  CAS  PubMed  Google Scholar 

  23. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26(5):541–7.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  24. Reddy T, Thomas AD, Stamatis D, Bertsch J, Isbandi M, Jansson J, et al. The Genomes OnLine Database (GOLD) v. 5: a metadata management system based on a four level (meta) genome project classification. Nucleic Acids Res. 2014:gku950.

  25. Mavromatis K, Land ML, Brettin TS, Quest DJ, Copeland A, Clum A, et al. The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation. 2012.

    Google Scholar 

  26. DOE Joint Genome Institute http://my.jgi.doe.gov/general.

  27. Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, et al. Real-time DNA sequencing from single polymerase molecules. Science. 2009;323(5910):133–8.

    Article  CAS  PubMed  Google Scholar 

  28. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods. 2013;10(6):563–9.

    Article  CAS  PubMed  Google Scholar 

  29. Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11(1):119.

    Article  PubMed Central  PubMed  Google Scholar 

  30. Mavromatis K, Ivanova NN, Chen I-MA, Szeto E, Markowitz VM, Kyrpides NC. The DOE-JGI Standard operating procedure for the annotations of microbial genomes. Stand Genomic Sci. 2009;1(1):63.

    Article  PubMed Central  PubMed  Google Scholar 

  31. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, et al. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Meth. 2010;7(6):455–7.

    Article  CAS  Google Scholar 

  32. Eddy SR. Accelerated profile HMM searches. PLoS Comput Biol. 2011;7(10):e1002195.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  33. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25(5):0955–964.

    Article  CAS  Google Scholar 

  34. Nawrocki EP, Kolbe DL, Eddy SR. Infernal 1.0: inference of RNA alignments. Bioinformatics. 2009;25(10):1335–7.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  35. Markowitz VM, Mavromatis K, Ivanova NN, Chen I-MA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009;25(17):2271–8.

    Article  CAS  PubMed  Google Scholar 

  36. Mooser D, Maneg O, Corvey C, Steiner T, Malatesta F, Karas M, et al. A four-subunit cytochrome bc 1 complex complements the respiratory chain of Thermus thermophilus. Biochimica et Biophysica Acta (BBA)-Bioenergetics. 2005;1708(2):262–74.

    Article  CAS  Google Scholar 

  37. Janzon J, Ludwig B, Malatesta F. Electron transfer kinetics of soluble fragments indicate a direct interaction between complex III and the caa 3 oxidase in Thermus thermophilus. Iubmb Life. 2007;59(8–9):563–9.

    Article  CAS  PubMed  Google Scholar 

  38. Knowles R. Denitrification. Microbiol Rev. 1982;46(1):43.

    PubMed Central  CAS  PubMed  Google Scholar 

  39. Kraft B, Strous M, Tegetmeyer HE. Microbial nitrate respiration-genes, enzymes and environmental distribution. J Biotechnol. 2011;155(1):104–17.

    Article  CAS  PubMed  Google Scholar 

  40. Zumft WG. Cell biology and molecular basis of denitrification. Microbiol Mol Biol Rev. 1997;61(4):533–616.

    PubMed Central  CAS  PubMed  Google Scholar 

  41. Ramı́rez-Arcos S, Fernández-Herrero LA, Berenguer J. A thermophilic nitrate reductase is responsible for the strain specific anaerobic growth of Thermus thermophilus HB8. Biochimica et Biophysica Acta (BBA)-Gene Structure and Expression. 1998;1396(2):215–27.

    Article  Google Scholar 

  42. Ramírez-Arcos S, Fernández-Herrero LA, Marín I, Berenguer J. Anaerobic growth, a property horizontally transferred by an Hfr-like mechanism among extreme thermophiles. J Bacteriol. 1998;180(12):3137–43.

    PubMed Central  PubMed  Google Scholar 

  43. Cava F, Zafra O, Magalon A, Blasco F, Berenguer J. A new type of NADH dehydrogenase specific for nitrate respiration in the extreme thermophile Thermus thermophilus. J Biol Chem. 2004;279(44):45369–78.

    Article  CAS  PubMed  Google Scholar 

  44. Cava F, Berenguer J. Biochemical and regulatory properties of a respiratory island encoded by a conjugative plasmid in the extreme thermophile Thermus thermophilus. Biochem Soc Trans. 2006;34(1):97–100.

    Article  CAS  PubMed  Google Scholar 

  45. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria and Eucarya. Proc Natl Acad Sci U S A. 1990;87:4576–9.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  46. Weisburg W, Giovannoni S, Woese C. The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction. Syst Appl Microbiol. 1989;11(2):128–34.

    Article  CAS  PubMed  Google Scholar 

  47. Garrity GM, Holt JG, Class I. Deinococci class. nov. In: Garrity GM, Boone DR, Castenholz RW, editors. Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1. New York: Springer; 2001. p. 395.

    Chapter  Google Scholar 

  48. Validation List No. 85: validation of publication of new names and new combinations previously effectively published outside the IJSEM. Int J Syst Evol Microbiol. 2002;52(3):685–90.

  49. Rainey FA, da Costa MS. Order II. Thermales ord. nov. In: Garrity GM, Boone DR, Castenholz RW, editors. Bergey’s manual of systematic bacteriology, second edition, volume 1. New York: Springer; 2001. p. 403.

    Google Scholar 

  50. da Costa MS, Rainey FA. Family I. Thermaceae fam. nov. In: Garrity GM, Boone DR, Castenholz RW, editors. Bergey’s manual of systematic bacteriology, second edition, volume 1. New York: Springer; 2001. p. 403–4.

    Google Scholar 

  51. Nobre MF, Trüper HG, da Costa MS. Transfer of Thermus ruber (Loginova et al. 1984), Thermus silvanus (Tenreiro et al. 1995), and Thermus chliarophilus (Tenreiro et al. 1995) to Meiothermus gen. nov. as Meiothermus ruber comb, nov., Meiothermus silvanus comb. nov., and Meiothermus chliarophilus comb. nov., respectively, and emendation of the genus Thermus. Int J Syst Evol Microbiol. 1999;49(4):1951.

    Google Scholar 

  52. Skerman V, McGowan V, Sneath P, Moore W, Moore LV. Approved lists. Int J Syst Bacteriol. 1980;30:225–420.

    Article  Google Scholar 

  53. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25(1):25–9.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  54. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011;28(10):2731–9.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  55. Cava F, Laptenko O, Borukhov S, Chahlafi Z, Blas-Galindo E, Gómez-Puertas P, et al. Control of the respiratory metabolism of Thermus thermophilus by the nitrate respiration conjugative element NCE. Mol Microbiol. 2007;64(3):630–46.

    Article  CAS  PubMed  Google Scholar 

  56. Gounder K, Brzuszkiewicz E, Liesegang H, Wollherr A, Daniel R, Gottschalk G, et al. Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01. BMC Genomics. 2011;12(1):577.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. Additional support was supported by the Key Project of International Cooperation of Ministry of Science & Technology (MOST) (No. 2013DFA31980), Natural Science Foundation of China (No. 31470139), National Science Foundation grant (OISE-0968421). E-M Zhou received the Scholarship Award for Excellent Doctoral Student granted by Yunnan Province, and China Scholarship Council (CSC, File No. 201307030004). W-J Li was also supported by the Guangdong Province Higher Vocational Colleges & Schools Pearl River Scholar Funded Scheme (2014). B.P. Hedlund was also funded by a gift from Greg Fullmer through the UNLV Foundation.

Author information

Authors and Affiliations

  1. Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People’s Republic of China

    En-Min Zhou, Wen-Dong Xian, Yi-Rui Yin, Hong Ming, Tian-Tian Yu & Wen-Jun Li

  2. School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA

    En-Min Zhou, Senthil K. Murugapiran, Chrisabelle C. Mefferd & Brian P. Hedlund

  3. State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People’s Republic of China

    Lan Liu & Wen-Jun Li

  4. Department of Energy Joint Genome Institute, Walnut Creek, CA, USA

    Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, T. B. K. Reddy, Chew Yee Ngan, Chris Daum, Nicole Shapiro, Victor Markowitz, Natalia Ivanova, Alexander Spunde, Nikos Kyrpides & Tanja Woyke

  5. Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV, USA

    Brian P. Hedlund

Authors
  1. En-Min Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Senthil K. Murugapiran
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Chrisabelle C. Mefferd
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lan Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Wen-Dong Xian
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yi-Rui Yin
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Hong Ming
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Tian-Tian Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Marcel Huntemann
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Alicia Clum
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Manoj Pillay
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Krishnaveni Palaniappan
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Neha Varghese
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Natalia Mikhailova
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Dimitrios Stamatis
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. T. B. K. Reddy
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Chew Yee Ngan
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Chris Daum
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Nicole Shapiro
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. Victor Markowitz
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. Natalia Ivanova
    View author publications

    You can also search for this author in PubMed Google Scholar

  22. Alexander Spunde
    View author publications

    You can also search for this author in PubMed Google Scholar

  23. Nikos Kyrpides
    View author publications

    You can also search for this author in PubMed Google Scholar

  24. Tanja Woyke
    View author publications

    You can also search for this author in PubMed Google Scholar

  25. Wen-Jun Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  26. Brian P. Hedlund
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Brian P. Hedlund.

Additional information

Competing interests

None of the authors have any competing interests in the manuscript.

Authors’ contributions

WJL and HM supplied the strain. EMZ, CRC, LL, YRY, HM, TTY, and WDX performed the laboratory experiments. MH, AC, MP, KP, NV, NM, DS, TBKR, CYN, CD, NS, VM, NI, AS, NK, and TW were involved in aspects of genome production including sequencing, assembling, annotation and GenBank submission. EMZ, SKM, WJL, and BPH analyzed the genomic data and drafted the manuscript. All authors read and approved the final manuscript.

Rights and permissions

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.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zhou, EM., Murugapiran, S.K., Mefferd, C.C. et al. High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409T with an incomplete denitrification pathway. Stand in Genomic Sci 11, 20 (2016). https://doi.org/10.1186/s40793-016-0140-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1186/s40793-016-0140-3

Keywords

Environmental Microbiome

ISSN: 2524-6372