Open Access

Complete genome sequence of Thermaerobacter marianensis type strain (7p75aT)

  • Cliff Han1, 2,
  • Wei Gu1, 2,
  • Xiaojing Zhang1, 2,
  • Alla Lapidus1,
  • Matt Nolan1,
  • Alex Copeland1,
  • Susan Lucas1,
  • Tijana Glavina Del Rio1,
  • Hope Tice1,
  • Jan-Fang Cheng1,
  • Roxane Tapia1, 2,
  • Lynne Goodwin1, 2,
  • Sam Pitluck1,
  • Ioanna Pagani1,
  • Natalia Ivanova1,
  • Konstantinos Mavromatis1,
  • Natalia Mikhailova1,
  • Amrita Pati1,
  • Amy Chen3,
  • Krishna Palaniappan3,
  • Miriam Land1, 4,
  • Loren Hauser1, 4,
  • Yun-Juan Chang1, 4,
  • Cynthia D. Jeffries1, 4,
  • Susanne Schneider5,
  • Manfred Rohde6,
  • Markus Göker5,
  • Rüdiger Pukall5,
  • Tanja Woyke1,
  • James Bristow1,
  • Jonathan A. Eisen1, 7,
  • Victor Markowitz3,
  • Philip Hugenholtz1,
  • Nikos C. Kyrpides1,
  • Hans-Peter Klenk5 and
  • John C. Detter1, 2
Standards in Genomic Sciences20103:3030337

https://doi.org/10.4056/sigs.1373474

Published: 31 December 2010

Abstract

Thermaerobacter marianensis Takai et al. 1999 is the type species of the genus Thermaerobacter, which belongs to the Clostridiales family Incertae Sedis XVII. The species is of special interest because T. marianensis is an aerobic, thermophilic marine bacterium, originally isolated from the deepest part in the western Pacific Ocean (Mariana Trench) at the depth of 10.897m. Interestingly, the taxonomic status of the genus has not been clarified until now. The genus Thermaerobacter may represent a very deep group within the Firmicutes or potentially a novel phylum. The 2,844,696 bp long genome with its 2,375 protein-coding and 60 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords

strictly aerobic none-motile Gram-variable thermophilic chemoheterotrophic deep-sea family Incertae Sedis XVII Clostridiales GEBA

Introduction

Strain 7p75aT (= DSM 12885 = ATCC 700841 = JCM 10246) is the type strain of T. marianensis which is the type species of the genus Thermaerobacter [1,2]. Currently, there are five species placed in the genus Thermaerobacter [1,3]. The generic name derives from the Greek words ‘thermos’ meaning ‘hot’, ‘aeros’(air) and the Neo-Latin word ‘bacter’ meaning ‘a rod’, which altogether means able to grow at high temperatures in the presence of air [2]. The species epithet is derived from the Neo-Latin word ‘marianensis’ pertaining to the Mariana Trench, the location from which the strain was isolated from [2]. T. marianensis strain 7p75aT was isolated from a mud sample of the Challenger Deep in the Mariana Trench at the depth of 10,897 m [2]. No further isolates have been obtained for T. marianensis. Other members of the genus Thermaerobacter were isolated from mud of the bottom of the Challenger Deep [2], shallow marine hydrothermal vent, Japan [4], water sediment slurries of the run-off channel of New Lorne Bore, Australia [5], a coastal hydrothermal beach, Japan [6] and from food sludge compost, Japan [7]. Here we present a summary classification and a set of features for T. marianensis 7p75aT, together with the description of the complete genomic sequencing and annotation.

Classification and features

The 16S rRNA gene sequences of T. marianensis 7p75aT share 98.3 to 98.6% sequence identity with the other type strains of the genus Thermaerobacter [2,8] and T. nagasakiensis being the closest relative. Outside the genus members of the recently proposed genus “Calditerricola” (88.6%) [9] and the genus Moorella (88.1%) [10] share the highest degree of sequence similarity. The genomic survey sequence database (gss) contains as best hits several 16S rRNA gene sequence from The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific [11] at a similarity level of only 84%. No phylotypes from environmental samples database (env_nt) could be linked to the species T. marianensis or even the genus Thermaerobacter, indicating a rather rare occurrence of members of this genus in the habitats screened thus far (as of November 2010).

A representative genomic 16S rRNA sequence of T. marianensis 7p75aT was compared using NCBI BLAST under default values (e.g., considering only the best 250 hits) with the most recent release of the Greengenes database [12] and the relative frequencies of taxa and keywords, weighted by BLAST scores, were determined. The five most frequent genera were Thermaerobacter (39.7%), Moorella (35.3%), Geobacillus (6.4%), Thermoactinomyces (3.6%) and Bacillus (3.4%). Regarding hits to sequences from other members of the genus, the average identity within HSPs (high-scoring segment pairs) was 98.1%, whereas the average coverage by HSPs was 96.3%. The species yielding the highest score was Thermaerobacter subterraneus. The five most frequent keywords within the labels of environmental samples which yielded hits were ‘compost(ing)’ (6.1%), ‘municipal’ (2.9%), ‘scale’ (2.7%) and ‘process/stages’ (2.6%). Environmental samples which yielded hits of a higher score than the highest scoring species were not found.

Figure 1 shows the phylogenetic neighborhood of T. marianensis 7p75aT in a 16S rRNA based tree. The sequences of the two 16S rRNA gene copies differ from each other by two nucleotides, and differ by up to two nucleotides from the previously published 16S rRNA sequence (AB011495), which contains one ambiguous base call.
Figure 1.

Phylogenetic tree highlighting the position of T. marianensis 7p75aT relative to the other type strains within the family. The tree was inferred from 1,489 aligned characters [13,14] of the 16S rRNA gene sequence under the maximum likelihood criterion [15] and rooted in accordance with the current taxonomy. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates [16] if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [17] are shown in blue, published genomes in bold.

The cells of T. marianensis are generally rod-shaped (0.3–0.6 × 2–7 µm), straight to slightly curved with rounded ends (Figure 2). The cells can be arranged in pairs [2]. T. marianensis is a Gram-positive, spore-forming bacterium (Table 1). At stationary phase cells, may stain Gram-negative. Motility and flagella have not been observed [2], but genes for biosynthesis and assembly of flagella have been identified in the here reported genome sequence. The organism is a strictly aerobic chemoheterotroph. T. marianensis is a typical marine bacterium and requires sea salts (0.5–5%, optimum 2%) in media for good growth [2]. The temperature range for growth is between 50°C and 80°C, with an optimum at 75°C [2]. The pH range for growth is 5.4–9.5, with an optimum at pH 7.0–7.5 [2]. T. marianensis is able to grow on yeast extract, peptone and casein. It utilizes carbohydrates like starch, xylan, chitin, maltose, maltotriose, cellobiose, lactose, trehalose, sucrose, glucose, galactose, xylose, mannitol, inositol. The strain is also able to grow on amino acids like casamino acids, valine, isoleucine, cysteine, proline, serine, threonine, asparagine, glutamine, aspartate, glutamate, lysine, arginine and histidine. T. marianensis is able to grow well on various carboxylic acids like propionate, 2-aminobutyric acid, malate, pyruvate, tartarate, succinate, lactate, acetate and glycerol [2]
Figure 2.

Scanning electron micrograph of T. marianensis 7p75aT

Table 1.

Classification and general features of T. marianens 7p75aT according to the MIGS recommendations [18].

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [19]

 

Phylum Firmicutes

TAS [2022]

 

Class Clostridia

TAS [20,23,24]

 

Order Clostridiales

TAS [20,25,26]

 

Family Incertae sedis XVII

TAS [20]

 

Genus Thermaerobacter

TAS [2,5,27]

 

Species Thermaerobacter marianensis

TAS [2,27]

 

Type strain 7p75a

TAS [2]

 

Gram stain

variable, slightly Gram-positive

TAS [2]

 

Cell shape

straight to slightly rods with rounded ends, singly or in pairs

TAS [2]

 

Motility

non-motile

TAS [2]

 

Sporulation

terminal, round spores (rarely detectable)

IDA

 

Temperature range

50°C–80°C

TAS [2]

 

Optimum temperature

75

TAS [2]

 

Salinity

requirement for sea salts (0.5–5%)

TAS [2]

MIGS-22

Oxygen requirement

strictly aerobic

TAS [2]

 

Carbon source

carbohydrates

TAS [2]

 

Energy source

chemoheterotrophic

TAS [2]

MIGS-6

Habitat

mud

TAS [2]

MIGS-15

Biotic relationship

free-living

NAS

MIGS-14

Pathogenicity

none

NAS

 

Biosafety level

1

TAS [28]

 

Isolation

marine mud sample

TAS [2]

MIGS-4

Geographic location

Challenger Deep; Mariana Trench

TAS [2]

MIGS-5

Sample collection time

1996

TAS [2]

MIGS-4.1

Latitude

11.35

TAS [2]

MIGS-4.2

Longitude

142.41

TAS [2]

MIGS-4.3

Depth

10,897 m

TAS [2]

MIGS-4.4

Altitude

−10,897 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 [29]. If the evidence code is IDA, then the property was directly observed by one of the authors or an expert mentioned in the acknowledgements.

Chemotaxonomy

The cellular polyamines of the strain 7p75aT were identified as N4-bis(aminopropyl)spermidine, agmatine, spermidine, and spermine [30,31]. The major cellular fatty acids were composed of 15-methyl-hexadecanic acid (52.3%), myristoleic acid (27.6%) and 14-methyl hexadecanoic acid (9.3%) [2]. No data are available for polar lipids and peptidoglycan type of the cell wall.

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [32], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [33]. The genome project is deposited in the Genome OnLine Database [17,34] 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 (9 kb insert size), one Illumina library

MIGS-29

Sequencing platforms

Illumina GAii, 454 GS FLX, Titanium

MIGS-31.2

Sequencing coverage

340.8 × Illumina; 91.0 × pyrosequence

MIGS-30

Assemblers

Newbler version 2.1-PreRelease-4-28-2009-gcc-3.4.6, phrap, Velvet

MIGS-32

Gene calling method

Prodigal 1.4, GenePRIMP

 

INSDC ID

CP002244

 

Genbank Date of Release

December 29, 2010

 

GOLD ID

Gi03961

 

NCBI project ID

38025

 

Database: IMG-GEBA

2503538005

MIGS-13

Source material identifier

DSM 12885

 

Project relevance

Tree of Life, GEBA

Growth conditions and DNA isolation1

T. marianensis 7p75aT, DSM 12885, was grown in half strength DSMZ medium 514 (Bacto Marine Broth) [35] at 65°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/LALM for cell lysis as described in Wu et al. [33].

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 2.1-PreRelease-4-28-2009-gcc-3.4.6-threads (Roche). The initial Newbler assembly consisting of 30 contigs was converted into a phrap assembly by making fake reads from the consensus, collecting the read pairs in the 454 paired end library. Illumina GAii sequencing data (969.0 Mb) was assembled with Velvet [36] 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 216.6 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 following 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) [37]. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F.Chang, unpublished). A total of 132 additional reactions and 4 shatter libraries 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 [38]. 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 431.8 × coverage of the genome. Final assembly contained 689,185 pyrosequence and 26,930,845 Illumina reads.

Genome annotation

Genes were identified using Prodigal [39] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [40]. 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) platform [41].

Genome properties

The genome consists of a 2,844,696 bp long chromosome with a GC content of 72.5% (Table 3 and Figure 3). Of the 2,435 genes predicted, 2,375 were protein-coding genes, and 60 RNAs; 48 pseudogenes were also identified. The majority of the protein-coding genes (74.1%) 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)

2,844,696

100.00%

DNA Coding region (bp)

2,412,792

84.82%

DNA G+C content (bp)

2,061,895

72.48%

Number of replicons

1

 

Extrachromosomal elements

0

 

Total genes

2,435

100.00%

RNA genes

60

2.46%

rRNA operons

2

 

Protein-coding genes

2,375

97.54%

Pseudo genes

48

1.97%

Genes with function prediction

1,804

74.09%

Genes in paralog clusters

288

11.83%

Genes assigned to COGs

1,870

76.80%

Genes assigned Pfam domains

1,996

81.56%

Genes with signal peptides

737

30.27%

Genes with transmembrane helices

647

26.57%

CRISPR repeats

2

 
Table 4.

Number of genes associated with the general COG functional categories

Code

value

% age

Description

J

140

6.8

Translation, ribosomal structure and biogenesis

A

0

0.0

RNA processing and modification

K

126

6.1

Transcription

L

99

4.8

Replication, recombination and repair

B

0

0.0

Chromatin structure and dynamics

D

29

1.4

Cell cycle control, cell division, chromosome partitioning

Y

0

0.0

Nuclear structure

V

34

1.7

Defense mechanisms

T

79

3.8

Signal transduction mechanisms

M

101

4.9

Cell wall/membrane/envelope biogenesis

N

49

2.4

Cell motility

Z

0

0.0

Cytoskeleton

W

0

0.0

Extracellular structures

U

49

2.4

Intracellular trafficking, secretion, and vesicular transport

O

73

3.5

Posttranslational modification, protein turnover, chaperones

C

133

6.4

Energy production and conversion

G

108

5.2

Carbohydrate transport and metabolism

E

264

12.8

Amino acid transport and metabolism

F

63

3.1

Nucleotide transport and metabolism

H

96

4.7

Coenzyme transport and metabolism

I

71

3.4

Lipid transport and metabolism

P

108

5.2

Inorganic ion transport and metabolism

Q

44

2.1

Secondary metabolites biosynthesis, transport and catabolism

R

233

11.3

General function prediction only

S

166

8.0

Function unknown

-

565

23.2

Not in COGs

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Gabriele Gehrich-Schröter (DSMZ) for growing T. marianensis 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)
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)
HZI - Helmholtz Centre for Infection Research
(7)
University of California Davis Genome Center

References

  1. Garrity G. NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser. Microbiol Today 2010; 7:1.Google Scholar
  2. Takai K, Inoue A, Horikoshi K. Thermaerobacter marianensis gen. nov., sp. nov., an aerobic extremely thermophilic marine bacterium from the 11,000 m deep Mariana Trench. Int J Syst Bacteriol 1999; 49:619–628. PubMed doi:https://doi.org/10.1099/00207713-49-2-619View ArticlePubMedGoogle Scholar
  3. Euzéby 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:https://doi.org/10.1099/00207713-47-2-590View ArticlePubMedGoogle Scholar
  4. Nunoura T, Akihara S, Takai K, Sako Y. Thermaerobacter nagasakiensis sp. nov., a novel aerobic and extremely thermophilic marine bacterium. Arch Microbiol 2002; 177:339–344. PubMed doi:https://doi.org/10.1007/s00203-002-0398-2View ArticlePubMedGoogle Scholar
  5. Spanevello MD, Yamamoto H, Patel BK. Thermaerobacter subterraneus sp. nov., a novel aerobic bacterium from the Great Artesian Basin of Australia, and emendation of the genus Thermaerobacter. Int J Syst Evol Microbiol 2002; 52:795–800. PubMed doi:https://doi.org/10.1099/ijs.0.01959-0PubMedGoogle Scholar
  6. Tanaka R, Kawaichi S, Nishimura H, Sako Y. Thermaerobacter litoralis sp. nov., a strictly aerobic and thermophilic bacterium isolated from a coastal hydrothermal field. Int J Syst Evol Microbiol 2006; 56:1531–1534. PubMed doi:https://doi.org/10.1099/ijs.0.64203-0View ArticlePubMedGoogle Scholar
  7. Yabe S, Kato A, Hazaka M, Yokota A. Thermaerobacter composti sp. nov., a novel extremely thermophilic bacterium isolated from compost. J Gen Appl Microbiol 2009; 55:323–328. PubMed doi:https://doi.org/10.2323/jgam.55.323View ArticlePubMedGoogle Scholar
  8. Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK, Lim YW. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259–2261. PubMed doi:https://doi.org/10.1099/ijs.0.64915-0View ArticlePubMedGoogle Scholar
  9. Moriya T, Hikota T, Yumoto I, Ito T, Terui Y, Yamagishi A, Oshima T. Calditerricola satsumensis gen. nov., sp. nov. and C. yamamurae sp. nov., extreme thermophiles isolated from a high temperature compost. Int J Syst Bacteriol 2010 [Epub ahead of print] April 16 2010.Google Scholar
  10. Collins MD, Lawson PA, Willems A, Cordoba JJ, Fernandez-Garayzabal J, Garcia P, Cai J, Hippe H, Farrow JAE. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 1994; 44:812–826. PubMed doi:https://doi.org/10.1099/00207713-44-4-812View ArticlePubMedGoogle Scholar
  11. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, et al. The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol 2007; 5:e77. PubMed doi:https://doi.org/10.1371/journal.pbio.0050077PubMed CentralView ArticlePubMedGoogle Scholar
  12. 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:https://doi.org/10.1128/AEM.03006-05PubMed CentralView ArticlePubMedGoogle Scholar
  13. 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
  14. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452–464. PubMed doi:https://doi.org/10.1093/bioinformatics/18.3.452View ArticlePubMedGoogle Scholar
  15. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 2008; 57:758–771. PubMed doi:https://doi.org/10.1080/10635150802429642View ArticlePubMedGoogle Scholar
  16. 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:https://doi.org/10.1007/978-3-642-02008-7_13View ArticleGoogle Scholar
  17. 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 2009; 38:D346–D354. PubMed doi:https://doi.org/10.1093/nar/gkp848PubMed CentralView ArticlePubMedGoogle Scholar
  18. 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:https://doi.org/10.1038/nbt1360PubMed CentralView ArticlePubMedGoogle Scholar
  19. 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:https://doi.org/10.1073/pnas.87.12.4576PubMed CentralView ArticlePubMedGoogle Scholar
  20. Ludwig W, Schleifer KH, Whitman WB. Taxonomic outline of the phylum Firmicutes, p.15–17. In P. de Vos, G.M. Garity, D. Jones, N.R. Krieg, W. Ludwig, F.A. Rainey, K.-H. Schleifer, W.B. Whitman (eds.). Bergey’s Manual of Systematic bacteriology, 2nd ed, vol.3. Springer, New York.Google Scholar
  21. Gibbons NE, Murray RGE. Proposals Concerning the Higher Taxa of Bacteria. Int J Syst Bacteriol 1978; 28:1–6. doi:https://doi.org/10.1099/00207713-28-1-1View ArticleGoogle Scholar
  22. Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 119–169.View ArticleGoogle Scholar
  23. List Editor. List of new names and new combinations previously effectively, but not validly, published. List no. 132. Int J Syst Evol Microbiol 2010; 60:469–472. doi:https://doi.org/10.1099/ijs.0.022855-0
  24. Rainey FA. Class II. Clostridia class nov. In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 3, Springer-Verlag, New York, 2009, p. 736.Google Scholar
  25. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225–420. doi:https://doi.org/10.1099/00207713-30-1-225View ArticleGoogle Scholar
  26. Prévot AR. In: Hauderoy P, Ehringer G, Guillot G, Magrou. J., Prévot AR, Rosset D, Urbain A (eds), Dictionnaire des Bactéries Pathogènes, Second Edition, Masson et Cie, Paris, 1953, p. 1–692.Google Scholar
  27. Notification List. Notification that new names and new combinations have appeared in volume 49, part 2, of the IJSB. Int J Syst Bacteriol 1999; 49:937–939. doi:https://doi.org/10.1099/00207713-49-3-937
  28. Classification of Bacteria and Archaea in risk groups. www.baua.de TRBA 466
  29. 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:https://doi.org/10.1038/75556PubMed CentralView ArticlePubMedGoogle Scholar
  30. Hamana K, Niitsu M, Samejima K, Itoh T. Polyamines of the thermophilic eubacteria belonging to the genera Thermosipho, Thermaerobacter and Caldicellulosiruptor. Microbios 2001; 104:177–185. PubMedPubMedGoogle Scholar
  31. Hosoya R, Hamana K, Niitsu M, Itoh T. Polyamine analysis for chemotaxonomy of thermophilic eubacteria: Polyamine distribution profiles within the orders Aquificales, Thermotogales, Thermodesulfobacteriales, Thermales, Thermoanaerobacteriales, Clostridiales and Bacillales. J Gen Appl Microbiol 2004; 50:271–287. PubMed doi:https://doi.org/10.2323/jgam.50.271View ArticlePubMedGoogle Scholar
  32. Klenk HP, Goeker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175–182. PubMed doi:https://doi.org/10.1016/j.syapm.2010.03.003View ArticlePubMedGoogle Scholar
  33. 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:https://doi.org/10.1038/nature08656PubMed CentralView ArticlePubMedGoogle Scholar
  34. Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2008; 36:D475–D479. PubMed doi:https://doi.org/10.1093/nar/gkm884PubMed CentralView ArticlePubMedGoogle Scholar
  35. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php.
  36. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829. PubMed doi:https://doi.org/10.1101/gr.074492.107PubMed CentralView ArticlePubMedGoogle Scholar
  37. 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. doi:https://doi.org/10.4056/sigs.761PubMed CentralView ArticlePubMedGoogle Scholar
  38. 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
  39. 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:https://doi.org/10.1186/1471-2105-11-119PubMed CentralView ArticlePubMedGoogle Scholar
  40. 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:https://doi.org/10.1038/nmeth.1457View ArticlePubMedGoogle Scholar
  41. 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:https://doi.org/10.1093/bioinformatics/btp393View ArticlePubMedGoogle Scholar
  42. DOE Joint Genome Institute. http://www.jgi.doe.gov.
  43. The Pred/Phrap/Consed software package. http://www.phrap.com.

Copyright

© The Author(s) 2010