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, 5Email author
Standards in Genomic Sciences201611:20

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

Received: 4 September 2015

Accepted: 10 December 2015

Published: 27 February 2016

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 ThermophilesHot springsDenitrification

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 [15]. 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 [810]. 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 [1315]. 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

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

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

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

Table 1

Classification and general features of Thermus amyloliquefaciens strain YIM 77409T [23]

MIGS ID

Property

Term

Evidence codea

 

Classification

Domain Bacteria

TAS [45]

  

Phylum Deinococcus-Thermus

TAS [46]

  

Class Deinococci

TAS [47, 48]

  

Order Thermales

TAS [48, 49]

  

Family Thermaceae

TAS [48, 50]

  

Genus Thermus

TAS [2, 51, 52]

  

Species Thermus amyloliquefaciens

TAS [18]

  

Type strain: YIM 77409T

TAS [18]

 

Gram stain

Negative

TAS [18]

 

Cell shape

Rod

TAS [18]

 

Motility

Non-motile

TAS [18]

 

Sporulation

Nonsporulating

TAS [18]

 

Temperature range

50–70 °C

TAS [18]

 

Optimum temperature

60–65 °C

TAS [18]

 

pH range; Optimum

6.0–8.0; 7.0

TAS [18]

 

Carbon source

Glucose, sucrose, glycerol, maltose, raffinose, trehalose, rhamnose, inositol, xylitol, mannitol, sodium malate, mannose and L-arabinose

TAS [18]

MIGS-6

Habitat

Terrestrial hot springs

TAS [18]

MIGS-6.3

Salinity

Not reported

 

MIGS-22

Oxygen requirement

Facultatively anaerobic

TAS [18]

MIGS-15

Biotic relationship

Free-living

TAS [18]

MIGS-14

Pathogenicity

Non-pathogen

NAS

MIGS-4

Geographic location

Niujie hot spring in Eryuan County, Yunnan Province, southwest China

TAS [18]

MIGS-5

Sample collection

2010

NAS

MIGS-4.1

Latitude

N 26°15'01. 4"

NAS

MIGS-4.2

Longitude

E 99°59'22. 3"

NAS

MIGS-4.4

Altitude

2060 m

NAS

IDA Inferred from Direct Assay, TAS Traceable Author Statement (i.e., a direct report exists in the literature), NAS Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [53]

a Evidence codes

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

MIGS ID

Property

Term

MIGS 31

Finishing quality

Permanent Draft

MIGS-28

Libraries used

PacBio 10 kb

MIGS 29

Sequencing platforms

PacBio RS

MIGS 31.2

Fold coverage

384.9X PacBio

MIGS 30

Assemblers

HGAP version 2.1.1

MIGS 32

Gene calling method

Prodigal 2.5; GenePRIMP

 

Locus Tag

BS74

 

Genbank ID

JQMV00000000

 

GenBank Date of Release

August 28, 2014

 

Database: IMG

2579778517

 

GOLD ID

Gp0050852

 

BIOPROJECT

PRJNA234787

MIGS 13

Source Material Identifier

YIM 77409T

 

Project relevance

Biotechnological

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

Attribute

Value

% of Totala

Genome size (bp)

2,160,855

100.0

DNA coding (bp)

2,031,100

94.0

DNA G + C (bp)

1,457,281

67.4

DNA scaffolds

6

100.0

Total genes

2,313

100.0

Protein coding genes

2,257

97.6

RNA genes

56

2.4

Pseudo genesb

74

3.2

Genes in internal clusters

1,932

83.5

Genes with function prediction

1,839

79.5

Genes assigned to COGs

1,558

67.4

Genes with Pfam domains

1,842

79.6

Genes with signal peptides

110

4.8

Genes with transmembrane helices

439

19.0

CRISPR repeats

5

 

aThe total is based on either the size of the genome in base pairs or the total number of protein coding genes in the annotated genome

bPseudogenes may also be counted as protein coding or RNA genes, so is not additive under total gene count

Table 4

Number of genes associated with general COG functional categories

Code

Value

%age

Description

J

179

10.4

Translation, ribosomal structure and biogenesis

A

4

0.2

RNA processing and modification

K

76

4.4

Transcription

L

63

3.7

Replication, recombination and repair

B

2

0.1

Chromatin structure and dynamics

D

22

1.3

Cell cycle control, Cell division, chromosome partitioning

V

35

2.0

Defense mechanisms

T

66

3.8

Signal transduction mechanisms

M

77

4.5

Cell wall/membrane biogenesis

N

16

0.9

Cell motility

U

14

0.8

Intracellular trafficking and secretion

O

90

5.2

Posttranslational modification, protein turnover, chaperones

C

131

7.6

Energy production and conversion

G

105

6.1

Carbohydrate transport and metabolism

E

183

10.6

Amino acid transport and metabolism

F

75

4.4

Nucleotide transport and metabolism

H

121

7.0

Coenzyme transport and metabolism

I

91

5.3

Lipid transport and metabolism

P

82

4.8

Inorganic ion transport and metabolism

Q

40

2.3

Secondary metabolites biosynthesis, transport and catabolism

R

170

9.9

General function prediction only

S

68

4.0

Function unknown

-

755

32.6

Not in COGs

The total is based on the total number of protein coding genes in the genome

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

Genome Name

Status

Genome Size (Mb)

GC Content (%)

Gene Count

No. of protein coding genes with function prediction

Percentage (%)

No. of protein coding genes with COGs

Percentage (%)

IMG Genome ID

T. amyloliquefaciens YIM 77409T

Draft

2.16

67.4

2313

1839

79.5

1558

67.4

2579778517

T. scotoductus SA-01

Finished

2.36

64.9

2514

1878

74.7

1704

67.8

649633105

T. scotoductus KI2

Draft

2.48

65.5

2643

2159

81.7

1808

68.4

2574179778

T. scotoductus DSM 8553T

Draft

2.07

64.8

2305

1816

78.8

1484

64.4

2518645614

T. antranikianii DSM 12462T

Draft

2.17

64.8

2321

1939

83.5

1654

71.3

2522572193

T. caliditerrae YIM 77777T

Draft

2.22

67.2

2327

1901

81.7

1646

70.7

2582581225

T. tengchongensis YIM 77401

Draft

2.56

66.4

2750

2158

78.5

1818

66.1

2574179781

T. arciformis CGMCC 1.6992T

Draft

2.44

68.7

2672

2052

76.8

1704

63.8

2617270932

T. thermophilus HB8T

Finished

2.12

69.5

2302

1498

65.1

1550

67.3

637000323

T. thermophilus JL-18

Finished

2.31

69.0

2508

1984

79.1

1717

68.5

2508501108

T. thermophilus SG0.5JP17-16

Finished

2.30

68.7

2488

2024

81.4

1700

68.3

2505679077

T. thermophilus HB27

Finished

2.13

69.4

2273

1517

66.7

1562

68.7

637000322

T. thermophilus ATCC 33923

Draft

2.15

69.4

2366

1928

81.5

1603

67.8

2554235155

T. islandicus DSM 21543T

Draft

2.26

68.4

2470

1965

79.6

1654

67.0

2524614852

T. oshimai JL-2

Finished

2.40

68.6

2548

2018

79.2

1735

68.1

2508501045

T. oshimai DSM 12092T

Draft

2.26

68.7

2409

1960

81.4

1700

70.6

2515154080

T. igniterrae ATCC 700962T

Draft

2.23

68.8

2379

1962

82.5

1661

69.8

2515154172

T. aquaticus Y51MC23

Draft

2.34

68.1

2595

1740

67.1

1530

59.0

645058872

T. brockianus

Draft

2.48

66.8

2789

2004

71.9

1709

61.3

2502171156

T. sp. CCB_US3_UF1

Finished

2.26

68.6

2333

1935

82.9

1655

70.9

2511231187

T. sp. RLM

Draft

2.04

68.3

2043

1636

80.1

1326

64.9

2513237279

T. sp. NMX2.A1

Draft

2.29

65.3

2522

1954

77.5

1666

66.1

2514885041

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

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]

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

Declarations

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.

Open AccessThis 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.

Authors’ Affiliations

(1)
Yunnan Institute of Microbiology, Yunnan University
(2)
School of Life Sciences, University of Nevada Las Vegas
(3)
State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University
(4)
Department of Energy Joint Genome Institute
(5)
Nevada Institute of Personalized Medicine, University of Nevada Las Vegas

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© Zhou et al. 2016