Open Access

Complete genome sequence of Oceanithermus profundus type strain (506T)

  • Amrita Pati1,
  • Xiaojing Zhang2,
  • Alla Lapidus1,
  • Matt Nolan1,
  • Susan Lucas1,
  • Tijana Glavina Del Rio1,
  • Hope Tice1,
  • Jan-Fang Cheng1,
  • Roxane Tapia1, 2,
  • Cliff Han1, 2,
  • Lynne Goodwin1, 2,
  • Sam Pitluck1,
  • Konstantinos Liolios1,
  • Ioanna Pagani1,
  • Natalia Ivanova1,
  • Konstantinos Mavromatis1,
  • Amy Chen3,
  • Krishna Palaniappan3,
  • Loren Hauser1, 4,
  • Cynthia D. Jeffries1, 4,
  • Evelyne-Marie Brambilla5,
  • Alina Röhl6,
  • Romano Mwirichia7,
  • Manfred Rohde8,
  • Brian J. Tindall5,
  • Johannes Sikorski5,
  • Reinhard Wirth6,
  • Markus Göker5,
  • Tanja Woyke1,
  • John C. Detter1, 2,
  • James Bristow1,
  • Jonathan A. Eisen1, 9,
  • Victor Markowitz3,
  • Philip Hugenholtz1, 10,
  • Nikos C. Kyrpides1,
  • Hans-Peter Klenk5 and
  • Miriam Land1, 4
Standards in Genomic Sciences20114:4020210

https://doi.org/10.4056/sigs.1734292

Published: 29 April 2011

Abstract

Oceanithermus profundus Miroshnichenko et al. 2003 is the type species of the genus Oceanithermus, which belongs to the family Thermaceae. The genus currently comprises two species whose members are thermophilic and are able to reduce sulfur compounds and nitrite. The organism is adapted to the salinity of sea water, is able to utilize a broad range of carbohydrates, some proteinaceous substrates, organic acids and alcohols. This is the first completed genome sequence of a member of the genus Oceanithermus and the fourth sequence from the family Thermaceae. The 2,439,291 bp long genome with its 2,391 protein-coding and 54 RNA genes consists of one chromosome and a 135,351 bp long plasmid, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords

microaerophilicnon-motileGram-negativenitrate-reducingmoderate thermophilicneutrophilicchemolithoheterotrophichydrothermal vent Thermaceae GEBA

Introduction

Strain 506T (DSM 14977 = NBRC 100410 = VKM B-2274) is the type strain of Oceanithermus profundus, which is the type species of the genus Oceanithermus [1] of the family Thermaceae [2]. Together with O. desulfurans, there are currently two species placed in the genus [1,3]. The generic name derives from the Latin noun oceanus, meaning ocean and the Neo-Latin masc. substantive (from Gr. adj. thermos) thermus which means hot. Therefore, the name Oceanithermus refers to warmth-loving organisms living in the ocean. The species epithet is derived from the Latin adjective profundus meaning deep, which means pertaining to the abyss, pertaining to the depths of the ocean [1]. Strain 506T was first isolated from samples of hydrothermal fluids and chimneys collected at the 13°N hydrothermal vent field on the East Pacific Rise at a depth of 2600 m [1]. There are no further cultivated strains of this species known. The other member of the genus, O. desulfurans, is a thermophilic, sulfur-reducing bacterium isolated from a sulfide chimney in Suiyo Seamount, in the Western Pacific [3]. Here we present a summary classification and a set of features for O. profundus 506T, together with the description of the complete genomic sequencing and annotation.

Classification and features

A representative genomic 16S rRNA sequence of strain 506T was compared using NCBI BLAST under default settings (e.g., considering only the high-scoring segment pairs (HSPs) from the best 250 hits) with the most recent release of the Greengenes database [4] and the relative frequencies, weighted by BLAST scores, of taxa and keywords (reduced to their stem) [5] were determined. The five most frequent genera were Thermus (52.0%), Meiothermus (37.0%), Oceanithermus (7.6%), Marinithermus (2.0%) and Vulcanithermus (1.4%) (156 hits in total). Regarding the four hits to sequences from members of the species, the average identity within HSPs was 99.6%, whereas the average coverage by HSPs was 94.8%. Regarding the two hits to sequences from other members of the genus, the average identity within HSPs was 99.3%, whereas the average coverage by HSPs was 91.0%. Among all other species, the one yielding the highest score was O. desulfurans, which corresponded to an identity of 99.3% and an HSP coverage of 91.0%. The highest-scoring environmental sequence was EU555123 (‘Microbial Sulfide Hydrothermal Vent Field Juan de Fuca Ridge Dudley hydrothermal vent clone 4132B16’), which showed an identity of 99.1% and an HSP coverage of 98.0%. The five most frequent keywords within the labels of environmental samples which yielded hits were ‘spring’ (8.2%), ‘hot’ (6.2%), ‘microbi’ (4.5%), ‘geochem, nation, park, yellowston’ (2.8%) and ‘hydrotherm/vent’ (2.5%) (94 hits in total). The five most frequent keywords within the labels of environmental samples which yielded hits of a higher score than the highest scoring species were ‘hydrotherm/vent’ (12.2%), ‘field, microbi, ridg’ (6.1%), ‘fluid’ (5.9%), ‘dudlei, fuca, juan, sulfid’ (3.1%) and ‘degre, east, north, ocean, pacif, rise’ (3.0%) (3 hits in total). These 16S BLAST results are a confirmation of the kind of environment from which the living strain was isolated and therefore fits the description of the isolate.

Figure 1 shows the phylogenetic neighborhood of O. profundus in a 16S rRNA based tree. The sequences of the two identical 16S rRNA gene copies in the genome differ by one nucleotide from the previously published 16S rRNA sequence (AJ430586).
Figure 1.

Phylogenetic tree highlighting the position of O. profundus relative to the other type strains within the family Thermaceae. The tree was inferred from 1,420 aligned characters [6,7] of the 16S rRNA gene sequence under the maximum likelihood criterion [8]. Rooting was initially done using the midpoint method [9] and then checked for its accordance with the current taxonomy (see Table 1) and rooted accordingly. The branches are scaled in terms of the expected number of substitutions per site. Numbers to the right of bifurcations are support values from 1,000 bootstrap replicates [10] if larger than 60%. Lineages with type strain genome sequencing projects that are registered in GOLD [11] but remain unpublished are labeled with one asterisk, published genomes with two asterisks [1214].

The cells of O. profundus are described as non-motile, rod-shaped, 0.5–0.7 µm in diameter and of various lengths (Figure 2). When grown on proteinaceous substrates, old cultures of O. profundus form filaments and large spheres resembling the ‘rotund bodies’ typical of aged cells of Thermus species [1,15]. The organism is Gram-negative and non spore-forming (Table 1).
Figure 2.

Scanning electron micrograph of O. profundus 506T

Table 1.

Classification and general features of O. profundus 506T according to the MIGS recommendations [16].

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [17]

 

Phylum “Deinococcus-Thermus

TAS [18,19]

 

Class Deinococci

TAS [20,21]

 

Order Thermales

TAS [21,22]

 

Family Thermaceae

TAS [21,23]

 

Genus Oceanithermus

TAS [1]

 

Species Oceanithermus profundus

TAS [1]

 

Type strain 506

TAS [1]

 

Gram stain

negative

TAS [1]

 

Cell shape

rod-shaped

TAS [1]

 

Motility

non-motile

TAS [1]

 

Sporulation

none

TAS [1]

 

Temperature range

40–68°C

TAS [1]

 

Optimum temperature

60°C

TAS [1]

 

Salinity

1%–5%, optimum 3% NaCl

TAS [1]

MIGS-22

Oxygen requirement

microaerophile

TAS [1]

 

Carbon source

carbohydrates

TAS [1]

 

Energy metabolism

chemoorganoheterotroph, lithoheterotroph, organotroph

TAS [1]

MIGS-6

Habitat

deep sea, hydrothermal vent, marine

TAS [1]

MIGS-15

Biotic relationship

free-living

TAS [1]

MIGS-14

Pathogenicity

none

NAS

 

Biosafety level

1

NAS [24]

 

Isolation

deep-sea hot vent

TAS [1]

MIGS-4

Geographic location

East Pacific Rise

TAS [1]

MIGS-5

Sample collection time

1999

TAS [1]

MIGS-4.1

Latitude

12.8

TAS [1]

MIGS-4.2

Longitude

103.93

TAS [1]

MIGS-4.3

Depth

2,600 m

TAS [1]

MIGS-4.4

Altitude

−2,600 m

NAS

Evidence codes - IDA: Inferred from Direct Assay (first time in publication); 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 of the Gene Ontology project [25] If the evidence code is IDA, then the property was directly observed by one of the authors or an expert mentioned in the acknowledgements.

O. profundus is microaerophilic, only being able to grow at oxygen concentrations below 6% [1]. No growth has been observed in an atmosphere of air, either in liquid medium or on plates. In an agar tube containing 5 ml of basal medium supplemented with 2 g sucrose and 1 g tryptone per liter with air in the headspace (10 ml), growth occurs in a zone located 20 mm below the agar/air interface [1]. Alternatively, the organism grows anaerobically using nitrate as the electron acceptor. O. profundus grows within a temperature range of 40–68ºC, optimal growth being observed at 60ºC. At 60ºC, it grows between pH 5.5 and 8.4, with an optimum around 7.5 [1]. Strain 506T grows at NaCl concentrations ranging from 10 to 50 g/l, with an optimum at 30 g/1 [1]. The organism is oxidase- and catalase positive and is able to utilize a wide spectrum of carbohydrates in the presence of either nitrate or oxygen [1]. The highest cell yield is observed in the presence of nitrate with fructose, maltose, sucrose, trehalose, galactose, rhamnose or xylose. Glucose, lactose and starch are utilized, but no growth has been reported with ribose, galactose, arabinose, dextrin or cellobiose [1]. Acetate and propionate are produced during growth with sucrose as a growth substrate and nitrate as the electron acceptor. Nitrite is the only product of denitrification [1]. O. profundus grows well with complex proteinaceous substrates such as beef extract, tryptone or papaic digest of soybean (1-1.5 g/l). However, growth is strongly inhibited by higher concentrations of these substrates [1]. The isolate does not grow with Casamino acids or yeast extract as sole sources of carbon and energy, though 100 mg/l yeast extract is required for growth [1]. O. profundus is able to utilize acetate, pyruvate and propionate as growth substrates. It also grows with methanol, ethanol and mannitol, though the cell yield is lower [1]. O. profundus is able to grow lithoheterotrophically using molecular hydrogen as the energy source, yeast extract as the carbon source and nitrate as the electron acceptor. Other electron acceptors (sulfate, elemental sulfur, thiosulfate and nitrite) do not support growth, regardless of growth substrate [1]. Detailed studies on the metabolism of maltose, acetate, pyruvate, and hydrogen have been undertaken by Fedosov et al. [26].

Chemotaxonomy

The polar lipid pattern of strain 506T comprises three phospholipids, whereas glycolipids have not been detected [1]. This differentiates the organism from members of the genera Vulcanithermus, Rhabdothermus, Thermus and Meiothermus, where phospholipids and glycolipids have both been detected [27,28]. It should be noted that the major phospholipid detected in O. profundus has the same Rf and staining behavior as the 2′-O-(1, 2-diacyl-sn-glycero-3-phospho)–3′-O-(α-N-acetyl-glucosaminyl)-N-glyceroyl alkylamine reported to occur in members of the genera Meiothermus and Thermus [29]. On the basis of Rf value and staining behavior this lipid also appears to be present in members of the genera Vulcanithermus and Rhabdothermus, which also synthesize glycolipids [30,31]. Although members of the genus Deinococcus may also produce glycolipids in addition to a novel series of phosphoglycolipids [32,33] the latter are absent in members of the genera Thermus and Meiothermus. The absence of glycolipids was one of the arguments for Miroshnichenko et al. for placing strain 506T in a new genus [1].

Menaquinones are the sole respiratory lipoquinones detected, with MK-8 predominating (95%) and MK-9 being present in smaller proportions (5%) [1]. The predominance of MK-8 is consistent with reports of MK-8 in members of the genera Thermus, Meiothermus [34,35], Marinithermus [36] Vulcanithermus, Rhabdothermus, Truepera, Deinobacterium and Deinococcus [3033,37]. However, the presence of MK-9, albeit at only 5%, appears to be a unique feature of O. profundus.

The fatty acids comprise mainly iso- and anteiso-branched fatty acids though iso-unsaturated fatty acids are also present [1]. The major fatty acids are iso-C15:1ω7 (7.7%), iso-C15:0 (33.2%), iso-C16:1ω8 (2.6 iso-C16:0 (3.3%), iso-C17:1ω7c (18.8%), iso-C17:0 (12.3%), anteiso-C15:0 (5.1%) and anteiso-C17:0 (5.4%) [1]. The presence of iso- and anteiso-branched fatty acids is a feature of members of the genera Deinococcus, Thermus, Meiothermus, Vulcanithermus, Rhabdothermus and Marinithermus [27,28,3034,37]. The presence of unsaturated branched-chain fatty acids is a distinctive feature of members of the genera Oceanithermus, Vulcanithermus and Rhabdothermus within the family Thermaceae. The unsaturated fatty acid content of the isolate is also higher (33-37%) as compared to the closest relative O. desulfurans (18%) [3].

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [38] and is part of the Genomic Encyclopedia of Bacteria and Archaea project [39]. The genome project is deposited in the Genome On Line Database [11] and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2.
Table 2.

Genome sequencing project information

MIGS ID

Property

Term

MIGS-31

Finishing quality

Finished

MIGS-28

Libraries used

Three genomic libraries: one 454 pyrosequence standard library, one 454 PE library (17 kb insert size), one Illumina library

MIGS-29

Sequencing platforms

Illumina GAii, 454 GS FLX Titanium

MIGS-31.2

Sequencing coverage

85.5 × Illumina; 197.3 × pyrosequence

MIGS-30

Assemblers

Newbler version 2.3-PreRelease-8-23-2009, Velvet, phrap

MIGS-32

Gene calling method

Prodigal 1.4, GenePRIMP

 

INSDC ID

CP002361 chromosome

 

CP002362 plasmid OCEPR01

 

Genbank Date of Release

December 7, 2010

 

GOLD ID

Gc01553

 

NCBI project ID

40223

 

Database: IMG-GEBA

2503508010

MIGS-13

Source material identifier

DSM 14977

 

Project relevance

Tree of Life, GEBA

Growth conditions and DNA isolation

O. profundus strain 506T, DSM 14977, was grown anaerobically in DSMZ medium 975 (Oceanithermus profundus medium) [40] at 60°C. DNA was isolated from 0.5–1 g of cell paste using Jetflex Genomic DNA Purification Kit following the standard protocol as recommended by the manufacturer, but with an additional proteinase K (20 µl) digestion for 45 min at 58°C. DNA is available through the DNA Bank Network [41].

Genome sequencing and assembly

The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website [42]. Pyrosequencing reads were assembled using the Newbler assembler version 2.3-PreRelease-8-23-2009 (Roche). The initial Newbler assembly, consisting of nine contigs in four scaffolds, was converted into a phrap assembly by [43] making fake reads from the consensus, to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (208 Mb) was assembled with Velvet [44] and the consensus sequences were shredded into 1.5 kb overlapped fake reads and assembled together with the 454 data. The 454 draft assembly was based on 306.1 Mb 454 draft data and all of the 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20. The Phred/Phrap/Consed software package [43] was used for sequence assembly and quality assessment in the subsequent finishing process. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with gapResolution [42], Dupfinisher, or sequencing cloned bridging PCR fragments with subcloning or transposon bombing (Epicentre Biotechnologies, Madison, WI) [45]. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F.Chang, unpublished). A total of 177 additional reactions were necessary to close gaps and to raise the quality of the finished sequence. Illumina reads were also used to correct potential base errors and increase consensus quality using a software Polisher developed at JGI [46]. The error rate of the completed genome sequence is less than 1 in 100,000. Together, the combination of the Illumina and 454 sequencing platforms provided 282.8 × coverage of the genome. The final assembly contained 1,258,374 pyrosequence and 5,792,221 Illumina reads.

Genome annotation

Genes were identified using Prodigal [47] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [48]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes - Expert Review (IMG-ER) [49].

Genome properties

The genome consists of a 2,303,940 bp long chromosome with a G+C content of 70% and a 135,351 bp plasmid with a G+C content of 66% (Table 3 and Figure 3). Of the 2,445 genes predicted, 2,391 were protein-coding genes, and 54 RNAs; 18 pseudogenes were also identified. The majority of the protein-coding genes (69.9%) were assigned with a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.
Figure 3.

Graphical circular map of chromosome (map of plasmid not shown). From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Table 3.

Genome Statistics

Attribute

Value

% of Total

Genome size (bp)

2,439,291

100.00%

DNA coding region (bp)

2,265,747

92.89%

DNA G+C content (bp)

1,702,985

69.81%

Number of replicons

2

 

Extrachromosomal elements

1

 

Total genes

2,445

100.00%

RNA genes

54

2.21%

rRNA operons

2

 

Protein-coding genes

2,391

97.79%

Pseudo genes

18

0.74%

Genes with function prediction

1,709

69.90%

Genes in paralog clusters

25

1.02%

Genes assigned to COGs

1,772

72.47%

Genes assigned Pfam domains

1,842

75.34%

Genes with signal peptides

615

25.15%

Genes with transmembrane helices

654

26.75%

CRISPR repeats

0

 
Table 4.

Number of genes associated with the general COG functional categories

Code

value

%age

Description

J

150

7.7

Translation, ribosomal structure and biogenesis

A

1

0.0

RNA processing and modification

K

90

4.6

Transcription

L

91

4.7

Replication, recombination and repair

B

1

0.0

Chromatin structure and dynamics

D

27

1.4

Cell cycle control, cell division, chromosome partitioning

Y

0

0.0

Nuclear structure

V

31

1.6

Defense mechanisms

T

80

4.1

Signal transduction mechanisms

M

79

4.1

Cell wall/membrane/envelope biogenesis

N

23

1.2

Cell motility

Z

0

0.0

Cytoskeleton

W

0

0.0

Extracellular structures

U

47

2.4

Intracellular trafficking, secretion, and vesicular transport

O

82

4.2

Posttranslational modification, protein turnover, chaperones

C

154

7.9

Energy production and conversion

G

125

6.4

Carbohydrate transport and metabolism

E

203

10.4

Amino acid transport and metabolism

F

72

3.7

Nucleotide transport and metabolism

H

93

4.8

Coenzyme transport and metabolism

I

66

3.4

Lipid transport and metabolism

P

100

5.1

Inorganic ion transport and metabolism

Q

31

1.6

Secondary metabolites biosynthesis, transport and catabolism

R

244

12.5

General function prediction only

S

155

8.0

Function unknown

-

673

27.6

Not in COGs

Declarations

Acknowledgements

This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2.

Authors’ Affiliations

(1)
DOE Joint Genome Institute
(2)
Bioscience Division, Los Alamos National Laboratory
(3)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(4)
Oak Ridge National Laboratory
(5)
DSMZ - German Collection of Microorganisms and Cell Cultures GmbH
(6)
Microbiology - Archaeenzentrum, University of Regensburg
(7)
Jomo Kenyatta University of Agriculture and Technology
(8)
HZI - Helmholtz Centre for Infection Research
(9)
University of California Davis Genome Center
(10)
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland

References

  1. Miroshnichenko ML, L’haridon S, Jeanthon C, Antipov AN, Kostrikina NA, Tindall BJ, Schumann P, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA. Oceanithermus profundus gen. nov., sp. nov., a thermophilic, microaerophilic, facultatively chemolithoheterotrophic bacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2003; 53:747–752. PubMed doi:10.1099/ijs.0.02367-0View ArticlePubMedGoogle Scholar
  2. Da Costa MS, Rainey FA. Family I. Thermaceae fam. nov. In: Bergey’s Manual of Systematic Bacteriology 2001. Boone DR, Castenholz RW, Garrity GM (eds), 2nd edn, vol. 1, pp. 403–404. New York: Springer.Google Scholar
  3. Mori K, Kakegawa T, Higashi Y, Nakamura K, Maruyama A, Hanada S. Oceanithermus desulfurans sp. nov., a novel thermophilic, sulfur-reducing bacterium isolated from a sulfide chimney in Suiyo Seamount. Int J Syst Evol Microbiol 2004; 54:1561–1566. PubMed doi:10.1099/ijs.0.02962-0View ArticlePubMedGoogle Scholar
  4. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL. Greengenes, a Chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006; 72:5069–5072. PubMed doi:10.1128/AEM.03006-05PubMed CentralView ArticlePubMedGoogle Scholar
  5. Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems 1980; 14:130–137.View ArticleGoogle Scholar
  6. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452–464. PubMed doi:10.1093/bioinformatics/18.3.452View ArticlePubMedGoogle Scholar
  7. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552. PubMedView ArticlePubMedGoogle Scholar
  8. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web-servers. Syst Biol 2008; 57:758–771. PubMed doi:10.1080/10635150802429642View ArticlePubMedGoogle Scholar
  9. Hess PN, De Moraes Russo CA. An empirical test of the midpoint rooting method. Biol J Linn Soc Lond 2007; 92:669–674. doi:10.1111/j.1095-8312.2007.00864.xView ArticleGoogle Scholar
  10. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary? Lect Notes Comput Sci 2009; 5541:184–200. doi:10.1007/978-3-642-02008-7_13View ArticleGoogle Scholar
  11. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38:D346–D354. PubMed doi:10.1093/nar/gkp848PubMed CentralView ArticlePubMedGoogle Scholar
  12. Sikorski J, Tindall BJ, Lowry S, Lucas S, Nolan M, Copeland A, Rio TGD, Tice H, Cheng JF, Han C, et al. Complete genome sequence of Meiothermus silvanus type strain (VI-R2T). Stand Genomic Sci 2010; 3:37–46. PubMed doi:10.4056/sigs.1042812PubMed CentralView ArticlePubMedGoogle Scholar
  13. Tindall BJ, Sikorski J, Lucas S, Goltsman E, Copeland A, Rio TGD, Nolan M, Tice H, Cheng JF, Han C, et al. Complete genome sequence of Meiothermus ruber type strain (21T). Stand Genomic Sci 2010; 3:26–36. PubMed doi:10.4056/sigs.1032748PubMed CentralView ArticlePubMedGoogle Scholar
  14. Ivanova N, Rohde C, Munk C, Nolan M, Lucas S, Glavina Del Rio T, Tice H, Deshpande S, Cheng JF, Tapia R, et al. Complete genome sequence of Truepera radiovictrix type strain (RQ-24T). Stand Genomic Sci 2011; 4:91–99. PubMed doi:10.4056/sigs.1563919PubMed CentralView ArticlePubMedGoogle Scholar
  15. Brock TD, Edwards MR. Fine structure of Thermus aquaticus, an extreme thermophile. J Bacteriol 1970; 104:509–517. PubMedPubMed CentralPubMedGoogle Scholar
  16. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541–547. PubMed doi:10.1038/nbt1360PubMed CentralView ArticlePubMedGoogle Scholar
  17. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576–4579. PubMed doi:10.1073/pnas.87.12.4576PubMed CentralView ArticlePubMedGoogle Scholar
  18. Garrity GM, Lilburn TG, Cole JR, Harrison SH, Euzéby J, Tindall BJ. Taxonomic outline of the Bacteria and Archaea, Release 7.7 March 6, 2007. Part 2 — The Bacteria: Phyla “Aquificae”, “Thermotogae”, “Thermodesulfobacteria”, “Deinococcus-Thermus”, “Chrysiogenetes”, “Chloroflexi”, “Thermomicrobia”, “Nitrospira”, “Deferribacteres”, “Cyanobacteria”, and “Chlorobi”. http://www.taxonomicoutline.org/index.php/toba/article/view/187/211 2007.
  19. Weisburg WG, Giovannoni SJ, Woese CR. The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction. Syst Appl Microbiol 1989; 11:128–134. PubMedView ArticlePubMedGoogle Scholar
  20. Garrity GM, Holt JG. Class I. Deinococci class. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 395.View ArticleGoogle Scholar
  21. List Editor. 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; 52:685–690. PubMed doi:10.1099/ijs.0.02358-0Google Scholar
  22. Rainey FA, da Costa MS. Order II. Thermales ord. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 403.Google Scholar
  23. da Costa MS, Rainey FA. Family I. Thermaceae fam. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 403–404.Google Scholar
  24. Classification of bacteria and archaea in risk groups. http://www.baua.de TRBA 466.
  25. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25–29. PubMed doi:10.1038/75556PubMed CentralView ArticlePubMedGoogle Scholar
  26. Fedosov DV, Podkopaeva DA, Miroshnichenko ML, Bonch-Osmolovskaya EA, Lebedinsky AV, Grabovich MY. Metabolism of the thermophilic bacterium Oceanithermus profundus. Microbiology 2008; 77:159–165. PubMed doi:10.1134/S0026261708020069View ArticleGoogle Scholar
  27. Donato MM, Seleiro EA, Da Costa MS. Polar lipid and fatty acid composition of strains of the genus Thermus. Syst Appl Microbiol 1990; 13:234–239.View ArticleGoogle Scholar
  28. Donato MM, Seleiro EA, Da Costa MS. Polar lipid and fatty acid composition of strains of Thermus ruber. Syst Appl Microbiol 1991; 14:235–239.View ArticleGoogle Scholar
  29. Yang YL, Yang FL, Jao SC, Chen MY, Tsay SS, Zou W, Wu SH. Structural elucidation of phosphoglycolipids from strains of the bacterial thermophiles Thermus and Meiothermus. J Lipid Res 2006; 47:1823–1832. PubMed doi:10.1194/jlr.M600034-ILR200View ArticlePubMedGoogle Scholar
  30. Steinsbu BO, Tindall BJ, Torsvik VL, Ingunn H, Thorseth IH, Daae FL, Pedersen RB. Rhabdothermus arcticus gen. nov., sp. nov., a novel member of the family Thermaceae isolated from a hydrothermal vent chimney from Soria Moria vent field at the Arctic Mid-Ocean Ridge. Int J Syst Evol Microbiol 2010Google Scholar
  31. Miroshnichenko ML, L’Haridon S, Nercessian O, Antipov AN, Kostrikina NA, Tindall BJ, Schumann P, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA, Jeanthon C. Vulcanithermus mediatlanticus gen. nov., sp. nov., a novel member of the family Thermaceae from a deep-sea hot vent. Int J Syst Evol Microbiol 2003; 53:1143–1148. PubMed doi:10.1099/ijs.0.02579-0View ArticlePubMedGoogle Scholar
  32. Embley TM, O’Donnell AG, Wait R, Rostron J. Lipid and cell wall amino acid composition in the classification of members of the genus Deinococcus. Syst Appl Microbiol 1987; 10:20–27.View ArticleGoogle Scholar
  33. Ferreira AC, Nobre MF, Rainey FA, Silva MT, Wait R, Burghardt J, Chung AP, Da Costa MS. Deinococcus geothermalis sp. nov. and Deinococcus murrayi sp. nov., two extremely radiation-resistant and slightly thermophilic species from hot springs. Int J Syst Bacteriol 1997; 47:939–947. PubMed doi:10.1099/00207713-47-4-939View ArticlePubMedGoogle Scholar
  34. Hensel R, Demharter W, Kandler O, Kroppenstedt RM, Stackebrandt E. Chemotaxonomic and molecular-genetic studies of the genus Thermus: evidence for a phylogenetic relationship of Thermus aquaticus and Thermus ruber to the genus Deinococcus. Int J Syst Bacteriol 1986; 36:444–453. doi:10.1099/00207713-36-3-444View ArticleGoogle Scholar
  35. Chung AP, Rainey F, Nobre MF, Burghardt J, Da Costa MS. Meiothermus cerbereus sp. nov., a new slightly thermophilic species with high levels of 3-hydroxy fatty acids. Int J Syst Bacteriol 1997; 47:1225–1230. PubMed doi:10.1099/00207713-47-4-1225View ArticlePubMedGoogle Scholar
  36. Sako Y, Nakagawa S, Takai K, Horikoshi K. Marinithermus hydrothermalis gen. nov., sp. nov., a strictly aerobic, thermophilic bacterium from a deep-sea hydrothermal vent chimney. Int J Syst Evol Microbiol 2003; 53:59–65. PubMed doi:10.1099/ijs.0.02364-0View ArticlePubMedGoogle Scholar
  37. Ekman JV, Raulio M, Busse HJ, Fewer DP, Salkinoja-Salonen M. Deinobacterium chartae gen. nov., sp. nov., an extremely radiation-resistant, biofilm-forming bacterium isolated from a Finnish paper mill. Int J Syst Evol Microbiol 2011; 61:540–548. PubMed doi:10.1099/ijs.0.017970-0View ArticlePubMedGoogle Scholar
  38. Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175–182. PubMed doi:10.1016/j.syapm.2010.03.003View ArticlePubMedGoogle Scholar
  39. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009; 462:1056–1060. PubMed doi:10.1038/nature08656PubMed CentralView ArticlePubMedGoogle Scholar
  40. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php
  41. Gemeinholzer B, Dröge G, Zetzsche H, Haszprunar G, Klenk HP, Güntsch A, Berendsohn WG, Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreservation and Biobanking 2011; 9:51–55. doi:10.1089/bio.2010.0029View ArticlePubMedGoogle Scholar
  42. DOE Joint Genome Institute. http://www.jgi.doe.gov
  43. Phrap and Phred for Windows. MacOS, Linux, and Unix. http://www.phrap.com
  44. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829. PubMed doi:10.1101/gr.074492.107PubMed CentralView ArticlePubMedGoogle Scholar
  45. Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, et al. Complete genome sequence of Kytococcus sedentarius type strain (541T). Stand Genomic Sci 2009; 1:12–20. PubMed doi:10.4056/sigs.761PubMed CentralView ArticlePubMedGoogle Scholar
  46. Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for using ultra short reads in microbial genome assembly and finishing. AGBT, Marco Island, FL, 2008.Google Scholar
  47. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-119PubMed CentralView ArticlePubMedGoogle Scholar
  48. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455–457. PubMed doi:10.1038/nmeth.1457View ArticlePubMedGoogle Scholar
  49. Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271–2278. PubMed doi:10.1093/bioinformatics/btp393View ArticlePubMedGoogle Scholar

Copyright

© The Author(s) 2011