Open Access

Complete genome sequence of the aerobic, heterotroph Marinithermus hydrothermalis type strain (T1T) from a deep-sea hydrothermal vent chimney

  • Alex Copeland1,
  • Wei Gu2,
  • Montri Yasawong3,
  • Alla Lapidus1,
  • Susan Lucas1,
  • Shweta Deshpande1,
  • Ioanna Pagani1,
  • Roxanne Tapia1, 2,
  • Jan-Fang Cheng1,
  • Lynne A. Goodwin1, 2,
  • Sam Pitluck1,
  • Konstantinos Liolios1,
  • Natalia Ivanova1,
  • Konstantinos Mavromatis1,
  • Natalia Mikhailova1,
  • Amrita Pati1,
  • Amy Chen4,
  • Krishna Palaniappan4,
  • Miriam Land1, 5,
  • Chongle Pan1, 5,
  • Evelyne-Marie Brambilla6,
  • Manfred Rohde7,
  • Brian J. Tindall6,
  • Johannes Sikorski6,
  • Markus Göker6,
  • John C. Detter1, 2,
  • James Bristow1,
  • Jonathan A. Eisen1, 8,
  • Victor Markowitz4,
  • Philip Hugenholtz1, 9,
  • Nikos C. Kyrpides1,
  • Hans-Peter Klenk6Email author and
  • Tanja Woyke1
Standards in Genomic Sciences20126:6010021

DOI: 10.4056/sigs.2435521

Published: 19 March 2012

Abstract

Marinithermus hydrothermalis Sako et al. 2003 is the type species of the monotypic genus Marinithermus. M. hydrothermalis T1T was the first isolate within the phylum “Thermus-Deinococcus” to exhibit optimal growth under a salinity equivalent to that of sea water and to have an absolute requirement for NaCl for growth. M. hydrothermalis T1T is of interest because it may provide a new insight into the ecological significance of the aerobic, thermophilic decomposers in the circulation of organic compounds in deep-sea hydrothermal vent ecosystems. This is the first completed genome sequence of a member of the genus Marinithermus and the seventh sequence from the family Thermaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,269,167 bp long genome with its 2,251 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords

strictly aerobic non-motile thermophilic neutrophilic heterotroph Gram-negative hydrothermal vent Thermaceae GEBA

Introduction

Strain T1T (= DSM 14884 = JCM 11576) is the type strain of the species M. hydrothermalis, which is the type species of the monotypic genus Marinithermus [1,2]. The genus name is derived from the Latin word ‘marinus’ meaning ‘of the sea’ and the latinized Greek word ‘thermos’ meaning ‘hot’, yielding the Neo-Latin word ‘Marinithermus’ meaning ‘an organism living in hot marine places’ [1]. The species epithet is derived from the Neo-Latin word ‘hydrothermalis’ (pertaining to a hydrothermal vent) [1]. Strain T1T was isolated in November 2000 from the surface zone of a deep-sea hydrothermal vent chimney at Suiyo Seamount in the Izu-Bonin Arc, Japan, at a depth of 1,385 m [1]. M. hydrothermalis was the first isolate within the phylum “Thermus-Deinococcus” that grew optimally under a salinity equivalent to that of sea water [1].

The absolute requirement of NaCl for growth distinguishes M. hydrothermalis from members of the genera Thermus and Meiothermus [1,3]. No further isolates have been reported for M. hydrothermalis. Here we present a summary classification and a set of features for M. hydrothermalis T1T, together with the description of the complete genomic sequencing and annotation.

Classification and features

A representative genomic 16S rRNA sequence of M. hydrothermalis T1T was compared using NCBI BLAST [4,5] 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 [6] and the relative frequencies of taxa and keywords (reduced to their stem [7]) were determined, weighted by BLAST scores. The most frequently occurring genera were Thermus (91.0%), Oceanithermus (4.9%), Marinithermus (3.3%) and Thermothrix (0.8%) (118 hits in total). Regarding the two hits to sequences from members of the species, the average identity within HSPs was 100.0%, whereas the average coverage by HSPs was 98.0%. Among all other species, the one yielding the highest score was O. profundus (NR_027212), which corresponded to an identity of 91.9% and HSP coverage of 93.3%. (Note that the Greengenes database uses the INSDC (= EMBL/NCBI/DDBJ) annotation, which is not an authoritative source for nomenclature or classification.) The highest-scoring environmental sequence was EU555123 [8] (‘Microbial Sulfide Hydrothermal Vent Field Juan de Fuca Ridge Dudley hydrothermal vent clone 4132B16’), which showed an identity of 91.6% and HSP coverage of 92.1%. The most frequently occurring keywords within the labels of all environmental samples which yielded hits were ‘spring’ (6.9%), ‘hot’ (5.3%), ‘microbi’ (3.7%), ‘nation, park, yellowston’ (3.2%) and ‘skin’ (3.0%) (132 hits in total). Environmental samples which yielded hits of a higher score than the highest scoring species were not found. These key words are in accordance with the biotope of the strain T1T in the original description [1], although ‘skin’ indicates the possible presence of relatives in a moderate environment.

Figure 1 shows the phylogenetic neighborhood of M. hydrothermalis T1T in a 16S rRNA based tree. The sequences of the three identical 16S rRNA gene copies in the genome differ by two nucleotides from the previously published 16S rRNA sequence (AB079382).
Figure 1.

Phylogenetic tree highlighting the position of M. hydrothermalis relative to the type strains of the other species within the family Thermaceae. The tree was inferred from 1,426 aligned characters [9,10] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [11]. Rooting was done initially using the midpoint method [12] and then checked for its agreement with the current classification (Table 1). The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 850 ML bootstrap replicates [13] (left) and from 1,000 maximum-parsimony bootstrap replicates [14] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [15] are labeled with an asterisk, those also listed as ‘Complete and Published’ with two asterisks [1619].

The cells of strain T1T are Gram-negative, non-motile, straight rods measuring 7.5–9.4 µm by 0.9–1.0 µm during the exponential growth phase [1] (Figure 2 and Table 1). In the stationary growth phase the cells tend to form filaments [1]. Rotund bodies were not observed from the cells [1]. Cells of strain T1T have an envelope which consists of a cytoplasmic membrane with a simple outline and a cell wall with an inner, electron-dense thin layer, which presumably represents the peptidoglycan [1]. Colonies are whitish and have 2.5–3.0 mm of diameter [1]. The organism is an obligate heterotroph and grows only under strictly aerobic culture conditions [1]. Growth was not observed in anaerobic or autotrophic culture conditions [1]. However, it should be noted that according to Mori and colleagues [32] this was tested only in the presence of sulfide. Steinsbu and colleagues [3] argue that it is therefore possible that M. hydrothermalis has the capability of anaerobic growth under unreduced conditions, as has been observed for Rhabdothermus arcticus, Vulcanithermus mediatlanticus, O. profundus and O. desulfurans [3,3234]. Unlike members of the genus Thermus, reactions were negative for catalase- and cytochrome oxidase and hydrolysis of gelatin, starch or casein was negative [1]. Growth occurs over the temperature range of 50.0–72.5°C (optimum 67.5°C), pH range 6.25–7.75 (optimum pH 7.0), and at NaCl concentrations in the range 0.5–4.5% (optimum 3%) [1]. The generation time under the above listed optimal condition and in medium MJYPV is about 30 minutes [1]. M. hydrothermalis T1T differs from the members of the genera Oceanithermus by having a higher optimal temperature for growth and a higher oxygen tolerance [3]. Strain T1T is able to utilize complex organic substrates such as Casamino acids, tryptone and yeast extract as sole energy and carbon sources [1].
Figure 2.

Scanning electron micrograph of M. hydrothermalis T1T

Table 1.

Classification and general features of M. hydrothermalis T1T according to the MIGS recommendations [20] and the NamesforLife database [21].

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [22]

 

Phylum “Deinococcus-Thermus

TAS [2325]

 

Class Deinococci

TAS [26,27]

 

Order Thermales

TAS [26,28]

 

Family Thermaceae

TAS [26,29]

 

Genus Marinithermus

TAS [1]

 

Species Marinithermus hydrothermalis

TAS [1]

 

Type strain T1

TAS [1]

 

Gram stain

negative

TAS [1]

 

Cell shape

straight rods

TAS [1]

 

Motility

non-motile

TAS [1]

 

Sporulation

none

NAS

 

Temperature range

50.0°C–72.5°C

TAS [1]

 

Optimum temperature

67.5°C

TAS [1]

 

Salinity

0.5–4.5%, optimum 3% NaCl

TAS [1]

MIGS-22

Oxygen requirement

strictly aerobic

TAS [1]

 

Carbon source

casamino acids, yeast extract, tryptone

TAS [1]

 

Energy metabolism

neutrophilic heterotroph

TAS [1]

MIGS-6

Habitat

deep-sea, hydrothermal vent, marine

TAS [1]

MIGS-15

Biotic relationship

free-living

NAS

MIGS-14

Pathogenicity

not reported

 
 

Biosafety level

1

TAS [30]

 

Isolation

deep-sea hydrothermal vent chimny

TAS [1]

MIGS-4

Geographic location

Suiyo Seamount, Izu-Bonin Arc, Japan

TAS [1]

MIGS-5

Sample collection time

November 2000

TAS [1]

MIGS-4.1

Latitude

28.65

TAS [1]

MIGS-4.2

Longitude

140.82

TAS [1]

MIGS-4.3

Depth

1,385 m

TAS [1]

MIGS-4.4

Altitude

− 1,385 m

TAS [1]

Evidence codes - 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 [31].

Strain T1T shares with its closest related genome-sequenced neighbors, O. profundus [17], Meiothermus silvanus [18] and Thermus thermophilus [16] (Figure 1), the presence of two linked 5S-23S rRNA gene clusters, with two 16S rRNA genes located separately in the genomes, but has one surplus, third 16S rRNA gene copy.

Chemotaxonomy

The major cellular fatty acids of strain T1T, when grown at 67.5°C, were iso-C15:0 (40.4%), iso-C17:0 (28.5%), C16:0 (12.9%), anteiso-C15:0 (6.0%), anteiso-C17:0 (5.4%), iso-C16:0 (2.8%) and iso 3-OH C11:0 (1.0%). Menaquinone-8 was the major respiratory quinone. The fatty acid and respiratory quinone composition were similar to those of members of the genus Thermus, as described previously [35,36]. However, the presence of iso 3-OH C11:0 in strain T1T distinguishes it from Thermus species [1].

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [37], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [38]. The genome project is deposited in the Genomes OnLine Database [15] 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

Four genomic libraries: one 454 pyrosequence standard library, two 454 PE libraries (7.0 kb insert size), one Illumina library

MIGS-29

Sequencing platforms

Illumina GAii, 454 GS FLX Titanium

MIGS-31.2

Sequencing coverage

1,608.4 × Illumina; 58.1 × pyrosequence

MIGS-30

Assemblers

Newbler version 2.3, Velvet version 0.7.63, phrap version SPS - 4.24

MIGS-32

Gene calling method

Prodigal 1.4, GenePRIMP

 

INSDC ID

CP002630

 

Genbank Date of Release

April 15, 2011

 

GOLD ID

Gc001721

 

NCBI project ID

50827

 

Database: IMG-GEBA

2504643006

MIGS-13

Source material identifier

DSM 14884

 

Project relevance

Tree of Life, GEBA

Growth conditions and DNA isolation

M. hydrothermalis T1T, DSM 14884, was grown in DSMZ medium 973 (Marinithermus hydrothermalis medium) [39] at 70°C. DNA was isolated from 0.5–1 g of cell paste using MasterPure Gram-positive DNA purification kit (Epicentre MGP04100) following the standard protocol as recommended by the manufacturer, with modification st/DL for cell lysis as described in Wu et al. [38]. DNA is available through the DNA Bank Network [40].

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 [41]. Pyrosequencing reads were assembled using the Newbler assembler (Roche). The initial Newbler assembly consisting of 70 contigs in one scaffold was converted into a phrap [42] assembly by making fake reads from the consensus, to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (3,943.0 Mb) was assembled with Velvet [43] and the consensus sequences were shredded into 2.0 kb overlapped fake reads and assembled together with the 454 data. The 454 draft assembly was based on 167.5 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 [42] 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 [41], Dupfinisher [44], or sequencing cloned bridging PCR fragments with subcloning. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F. Chang, unpublished). A total of 97 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 [45]. 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 1,666.5 × coverage of the genome. The final assembly contained 458,684 pyrosequence and 48,027,166 Illumina reads.

Genome annotation

Genes were identified using Prodigal [46] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [47]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) non-redundant 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) platform [48].

Genome properties

The genome consists of a 2,269,167 bp long chromosome with a 68.1% GC content (Figure 3 and Table 3). Of the 2,310 genes predicted, 2,251 were protein-coding genes, and 59 RNAs; 46 pseudogenes were also identified. The majority of the protein-coding genes (75.5%) 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 the chromosome. 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)

2,269,167

100.00%

DNA coding region (bp)

2,092,686

92.22%

DNA G+C content (bp)

1,544,754

68.08%

Number of replicons

1

 

Extrachromosomal elements

0

 

Total genes

2,310

100.00%

RNA genes

59

2.55%

RNA operons

2*

 

Protein-coding genes

2,251

97.45%

Pseudo genes

46

1.99%

Genes with function prediction

1,743

75.45%

Genes in paralog clusters

963

41.69%

Genes assigned to COGs

1,858

80.43%

Genes assigned Pfam domains

1,840

79.65%

Genes with signal peptides

479

20.74%

Genes with transmembrane helices

512

22.16%

CRISPR repeats

4

 

* but three 16S rRNA genes

Table 4.

Number of genes associated with the general COG functional categories

Code

Value

%age

Description

J

151

7.5

Translation, ribosomal structure and biogenesis

A

0

0.0

RNA processing and modification

K

96

4.7

Transcription

L

99

4.9

Replication, recombination and repair

B

2

0.1

Chromatin structure and dynamics

D

27

1.3

Cell cycle control, cell division, chromosome partitioning

Y

0

0.0

Nuclear structure

V

30

1.5

Defense mechanisms

T

73

3.6

Signal transduction mechanisms

M

108

5.3

Cell wall/membrane/envelope biogenesis

N

21

1.0

Cell motility

Z

0

0.0

Cytoskeleton

W

0

0.0

Extracellular structures

U

49

2.4

Intracellular trafficking, secretion, and vesicular transport

O

86

4.2

Posttranslational modification, protein turnover, chaperones

C

149

7.4

Energy production and conversion

G

125

6.2

Carbohydrate transport and metabolism

E

215

10.6

Amino acid transport and metabolism

F

67

3.3

Nucleotide transport and metabolism

H

117

5.8

Coenzyme transport and metabolism

I

77

3.8

Lipid transport and metabolism

P

94

4.6

Inorganic ion transport and metabolism

Q

33

1.6

Secondary metabolites biosynthesis, transport and catabolism

R

255

12.6

General function prediction only

S

154

7.6

Function unknown

-

452

19.6

Not in COGs

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Helga Pomrenke (DSMZ) for growing M. hydrothermalis cultures. 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)
Department of Biochemistry, Srinakharinwirot University
(4)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(5)
Oak Ridge National Laboratory
(6)
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures
(7)
HZI - Helmholtz Centre for Infection Research
(8)
University of California Davis Genome Center
(9)
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland

References

  1. 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
  2. Euzeby JP. List of bacterial names with standing in nomenclature: a folder available on the Internet. Int J Syst Bacteriol 1997; 47:590–592. PubMed doi:10.1099/00207713-47-2-590View ArticlePubMedGoogle Scholar
  3. Steinsbu BO, Tindall BJ, Torsvik VL, 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 2010. [Epub ahead of print, doi: 10.1099/ijs.0.027839-0].
  4. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410. PubMedView ArticlePubMedGoogle Scholar
  5. Korf I, Yandell M, Bedell J. BLAST. Sebastopol, CA, O’Reilly, 2003.Google Scholar
  6. 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
  7. Porter MF. An algorithm for suffix stripping. Program: electronic library and information systems 1980; 14:130–137.View ArticleGoogle Scholar
  8. Zhou H, Li J, Peng X, Meng J, Wang F, Ai Y. Microbial diversity of a sulfide black smoker in main endeavour hydrothermal vent field, Juan de Fuca Ridge. J Microbiol 2009; 47:235–247. PubMed doi:10.1007/s12275-008-0311-zView ArticlePubMedGoogle Scholar
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods). 4.0 b10. Sunderland, Sinauer Associates, 2002.Google Scholar
  15. 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
  16. Henne A, Bruggemann H, Raasch C, Wiezer A, Hartsch T, Liesegang H, Johann A, Lienard T, Gohl O, Martinez-Arias R, et al. The genome sequence of the extreme thermophile Thermus thermophilus. Nat Biotechnol 2004; 22:547–553. PubMed doi:10.1038/nbt956View ArticlePubMedGoogle Scholar
  17. Pati A, Zhang X, Lapidus A, Nolan M, Lucas S, Del Rio TG, Tice H, Cheng JF, Tapia R, Han C, et al. Complete genome sequence of Oceanithermus profundus type strain (506T). Stand Genomic Sci 2011; 4:210–220. PubMed doi:10.4056/sigs.1734292PubMed CentralView ArticlePubMedGoogle Scholar
  18. Sikorski J, Tindall BJ, Lowry S, Lucas S, Nolan M, Copeland A, Glavina Del Rio T, Tice H, Cheng JF, Han C, et al. Complete genome sequence of Meiothermus silvanus type strain (VI-R2 T). Stand Genomic Sci 2010; 3:37–46. PubMed doi:10.4056/sigs.1042812PubMed CentralView ArticlePubMedGoogle Scholar
  19. Tindall BJ, Sikorski J, Lucas S, Goltsman E, Copeland A, Glavina Del Rio T, 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
  20. 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
  21. Garrity G. NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser. Microbiol Today 2010; 37:9.Google Scholar
  22. 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
  23. 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.
  24. 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
  25. 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
  26. 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.0.02358-0
  27. 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
  28. 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
  29. 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
  30. BAuA. Classification of bacteria and archaea in risk groups. TRBA 466. Germany, Bundesanstalt für Arbeitsschutz und Arbeitsmedizin, 2010. p 125.Google Scholar
  31. 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. The Gene Ontology Consortium. Nat Genet 2000; 25:25–29. PubMed doi:10.1038/75556PubMed CentralView ArticlePubMedGoogle Scholar
  32. 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
  33. 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
  34. Miroshnichenko ML, L’Haridon S, Nercessian O, Antipov AN, Kostrikina NA, Tindall BJ, Schumann P, Spring S, Stackebrandt E, Bonch-Osmolovskaya EA, et al. 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
  35. 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
  36. Prado A, da Costa MS, Madeira VMC. Effect of growth temperature on the lipid composition of two strains of Thermus sp. J Gen Microbiol 1988; 134:1653–1660.Google Scholar
  37. 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
  38. 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
  39. List of growth media used at DSMZ: http://www.dsmz.de/catalogues/catalogue-microorganisms/culture-technology/list-of-media-for-microorganisms.html.
  40. 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
  41. DOE Joint Genome Institute. http://www.jgi.doe.gov.
  42. Phrap and Phred for Windows. MacOS, Linux and Unix. http://www.phrap.com.
  43. 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
  44. Han C, Chain P. Finishing repeat regions automatically with Dupfinisher. In: Proceeding of the 2006 international conference on bioinformatics & computational biology. Arabnia HR, Valafar H (eds), CSREA Press. June 26–29, 2006: 141–146.
  45. 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. 2008; Marco Island, FL.
  46. 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
  47. 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
  48. Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, 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

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