Open Access

Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1

  • Iain J. Anderson
  • , Hui Sun
  • , Alla Lapidus
  • , Alex Copeland
  • , Tijana Glavina Del Rio
  • , Hope Tice
  • , Eileen Dalin
  • , Susan Lucas
  • , Kerrie Barry
  • , Miriam Land,
  • , Paul Richardson
  • , Harald Huber
  • and Nikos C. Kyrpides
Corresponding author

DOI: 10.4056/sigs.30527

Received: 25 September 2009

Published: 29 September 2009

Abstract

Staphylothermus marinus Fiala and Stetter 1986 belongs to the order Desulfurococcales within the archaeal phylum Crenarchaeota. S. marinus is a hyperthermophilic, sulfur-dependent, anaerobic heterotroph. Strain F1 was isolated from geothermally heated sediments at Vulcano, Italy, but S. marinus has also been isolated from a hydrothermal vent on the East Pacific Rise. We report the complete genome of S. marinus strain F1, the type strain of the species. This is the fifth reported complete genome sequence from the order Desulfurococcales.

Keywords:

ArchaeaDesulfurococcalessulfur-reducinghyperthermophile

Introduction

Strain F1 is the type strain of the species Staphylothermus marinus. It was isolated from geothermally heated sediments at Vulcano, Italy [1], and was the strain sequenced. S. marinus was also isolated from a hydrothermal vent on the East Pacific Rise. There is one other species within the genus, Staphylothermus hellenicus, which was isolated from a hydrothermal vent at Milos, Greece [2]. Four other complete genomes from the order Desulfurococcales have been published, but S. marinus is not closely related to any of these organisms (Figure 1).

Figure 1

Phylogenetic tree of 16S ribosomal RNA of members of the order Desulfurococcales with completely sequenced genomes. Sulfolobus metallicus is the outgroup. The tree was generated with weighbor through the Ribosomal Database Project [3] and viewed with njplot [4].

S. marinus is a nonmotile coccus with a diameter of 0.5-1.0 μm. At low nutrient concentrations it forms clumps of up to 100 cells, while at higher nutrient concentrations single cells or pairs of cells are observed. At high concentrations of yeast extract, giant cells with a diameter of up to 15μm are formed [1]. The optimum and maximum growth temperatures also depend on the nutrient concentration. At low nutrient concentration the optimum growth temperature is 85°C and the maximum is 92°C, while at higher nutrient concentration the optimum growth temperature is 92°C and the maximum is 98°C [1]. The optimum pH for growth is 6.5, but growth is observed within a range of 4.5 to 8.5.

S. marinus is a heterotroph, growing on complex media but not on simple carbohydrates or amino acids. Elemental sulfur is required for growth, and it can not be substituted by other sulfur compounds [1]. In the absence of sulfur, cells can survive while producing hydrogen [5]. Metabolic products are CO2, H2S, acetate, and isovalerate, suggesting a metabolism similar to that of Pyrococcus species [1].

We describe here the properties of the complete genome sequence of S. marinus strain F1 (DSM 3639, ATCC 43588).

Classification and features

Several features suggest that S. marinus is a typical member of the Archaea. Its growth was not inhibited by vancomycin, kanamycin, streptomycin, or chloramphenicol, but it is sensitive to diphtheria toxin [1]. Its cell wall lacks murein, and it contains typical archaeal membrane lipids [1]. Other features of the organism are presented in Table 1.

Table 1

Classification and general features of S. marinus F1 according to the MIGS recommendations [6].

MIGS ID

Property

Term

Evidence code

Domain Archaea

TAS [7]

Phylum Crenarchaeota

TAS [8,9]

Class Thermoprotei

TAS [9,10]

Current classification

Order Desulfurococcales

TAS [11,12]

Family Desulfurococcaceae

TAS [13-15]

Genus Staphylothermus

TAS [1]

Species Staphylothermus marinus

TAS [1]

Gram stain

negative

TAS [1]

Cell shape

coccus

TAS [1]

Motility

nonmotile

TAS [1]

Sporulation

nonsporulating

NAS

Temperature range

65-98°C

TAS [1]

Optimum temperature

85-92°C

TAS [1]

MIGS-6.3

Salinity

1-3.5% NaCl

TAS [1]

MIGS-22

Oxygen requirement

anaerobe

TAS [1]

Carbon source

peptides

TAS [1]

Energy source

peptides

TAS [1]

MIGS-6

Habitat

marine geothemally heated areas

TAS [1]

MIGS-15

Biotic relationship

free-living

TAS [1]

MIGS-14

Pathogenicity

none

NAS

Biosafety level

1

NAS

Isolation

geothermally heated sediment

TAS [1]

MIGS-4

Geographic location

Vulcano, Italy

TAS [1]

MIGS-5

Isolation time

1984

TAS [1]

MIGS-4.1 MIGS-4.2

Latitude-longitude

38.4/15.0

TAS [1]

MIGS-4.3

Depth

0.5 m

TAS [1]

MIGS-4.4

Altitude

not applicable

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 the Gene Ontology project [16]. If the evidence code is IDA, then the property was observed for a living isolate by one of the authors or an expert mentioned in the acknowledgements.

Genome sequencing and annotation

Genome project history

S. marinus was selected for sequencing based upon its phylogenetic position relative to other sequenced archaeal genomes. It is part of a 2006 Joint Genome Institute Community Sequencing Program (CSP) project that included six diverse archaeal genomes. The complete genome sequence was finished in February, 2007. The GenBank accession number for the chromosome is CP000575. The genome project is listed in the Genomes OnLine Database (GOLD) [17] as project Gc00511. 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-28

Libraries used

3kb, 6kb and 40kb (fosmid)

MIGS-29

Sequencing platform

ABI3730

MIGS-31.2

Sequencing coverage

13.3×

MIGS-31

Finishing quality

Finished

Sequencing quality

less than one error per 50kb

MIGS-30

Assembler

Phrap

MIGS-32

Gene calling method

CRITICA, Glimmer

GenBank ID

CP000575

GenBank date of release

February 2007

GOLD ID

Gc00511

NCBI project ID

17449

IMG Taxon ID

640069332

Project relevance

Tree of Life

DNA isolation, genome sequencing and assembly

The methods for DNA isolation, genome sequencing and assembly for this genome have previously been published [18].

Genome annotation

Protein-coding genes were identified using a combination of Critica [19] and Glimmer [20] followed by a round of manual curation using the JGI GenePRIMP pipeline [21]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. The tRNAScan-SE tool [22] was used to find tRNA genes. Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes Expert Review (IMG-ER) platform [23].

Genome properties

The genome of S. marinus F1 consists of a single circular chromosome (Table 3 and Figure 2). The genome size of 1.57 Mbp is smaller than most Crenarchaeota, although Desulfurococcus kamchatkensis and Ignicoccus hospitalis have smaller genomes. The G+C percentage is 35.7%, lower than that of most Crenarchaeota. Among Crenarchaeota with sequenced genomes, only Sulfolobus tokodaii has a lower G+C percentage (32.8%). The total number of genes is 1,659, with 1,610 protein-coding genes and 49 RNA genes. There are 40 pseudogenes, constituting 2.4% of the total genes. The percentage of the genome encoding genes (89.1%) is close to the average for Crenarchaeota. About 59% of predicted genes begin with an AUG codon, 33% begin with UUG, and only 8% begin with GUG. There is one copy of each ribosomal RNA. The properties and statistics of the genome are shown in Table 3, and the distribution of proteins in COG categories is shown in Table 4.

Table 3

Genome statistics

Attribute

Value

% of total

Genome size (bp)

1,570,485

100.00%

DNA coding region (bp)

1,399,620

89.1%

DNA G+C content (bp)

561,080

35.7%

Number of replicons

1

Extrachromosomal elements

0

Total genes

1659

100.00%

RNA genes

49

3.0%

rRNA operons

1

Protein-coding genes

1610

97.0%

Pseudogenes

40

2.4%

Genes with function prediction

974

60.5%

Genes in paralog clusters

542

33.7%

Genes assigned to COGs

1109

68.9%

Genes assigned Pfam domains

1089

67.6%

Genes with signal peptides

317

19.7%

Genes with transmembrane helices

348

21.6%

CRISPR repeats

12

Figure 2

Graphical circular map of the chromosome. From outside to the center: Genes on forward strand (colored by COG categories), Genes on reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Table 4

Numbers of genes associated with the 25 general COG functional categories.

Code

value

%

Description

E

74

4.6

Amino acid transport and metabolism

G

72

4.5

Carbohydrate transport and metabolism

D

8

0.5

Cell cycle control, cell division, chromosome partitioning

N

4

0.2

Cell motility

M

23

1.4

Cell wall/membrane/envelope biogenesis

B

2

0.1

Chromatin structure and dynamics

H

53

3.3

Coenzyme transport and metabolism

Z

0

0.0

Cytoskeleton

V

17

1.1

Defense mechanisms

C

92

5.7

Energy production and conversion

W

0

0.0

Extracellular structures

S

116

7.2

Function unknown

R

199

12.4

General function prediction only

P

85

5.3

Inorganic ion transport and metabolism

U

12

0.7

Intracellular trafficking, secretion, and vesicular transport

I

15

0.9

Lipid transport and metabolism

Y

0

0.0

Nuclear structure

F

39

2.4

Nucleotide transport and metabolism

O

53

3.3

Posttranslational modification, protein turnover, chaperones

A

2

0.1

RNA processing and modification

L

71

4.4

Replication, recombination and repair

Q

5

0.3

Secondary metabolites biosynthesis, transport and catabolism

T

18

1.1

Signal transduction mechanisms

K

60

3.7

Transcription

J

164

10.2

Translation, ribosomal structure and biogenesis

-

426

26.5

Not in COGs

Insights from genome sequence

The genome of S. marinus has several novel features compared to other Crenarchaeota. It is the first crenarchaeote found to have a sodium ion-translocating decarboxylase, which is probably involved in energy generation from amino acid degradation [18]. In addition it is the first crenarchaeote found to have proteins related to multisubunit cation/proton antiporters, although the S. marinus proteins probably do not function as antiporters. These antiporter-related proteins belong to larger operons similar to the mbh and mbx operons of Pyrococcus furiosus [24,25], therefore, they may play a role in sulfur reduction or hydrogen production. S. marinus appears to use different proteins for sulfur reduction than the other anaerobic, sulfur-reducing Crenarchaeota. Both Thermofilum pendens and Hyperthermus butylicus appear to have molybdenum-containing sulfur/polysulfide reductases and NADPH:sulfur oxidoreductases, but these are not present in S. marinus [18]

Declarations

Acknowledgements

This work was performed under the auspices of the US Department of Energy's 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. M. L. was supported by the Department of Energy under contract DE-AC05-000R22725.


This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

References

  1. Fiala G, Stetter KO, Jannasch HW, Langworthy TA and Madon J. Staphylothermus marinus sp. nov. represents a novel genus of extremely thermophilic submarine heterotrophic archaebacteria growing up to 98°C. Syst Appl Microbiol. 1986; 8:106-113
  2. Arab H, Völker H and Thomm M. Thermococcus aegaeicus sp. nov. and Staphylothermus hellenicus sp. nov., two novel hyperthermophilic archaea isolated from geothermally heated vents off Palaeochori Bay, Milos, Greece. Int J Syst Evol Microbiol. 2000; 50:2101-2108PubMed
  3. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T and Garrity GM. The ribosomal database project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res. 2009; 37:D141-D145 View ArticlePubMed
  4. Perrière G and Gouy M. WWW-Query: an on-line retrieval system for biological sequence banks. Biochimie. 1996; 78:364-369 View ArticlePubMed
  5. Hao X and Ma K. Minimal sulfur requirement for growth and sulfur-dependent metabolism of the hyperthermophilic archaeon Staphylothermus marinus. Archaea. 2003; 1:191-197 View ArticlePubMed
  6. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ and Angiuoli SV. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008; 26:541-547 View ArticlePubMed
  7. Woese CR, Kandler O and 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 View ArticlePubMed
  8. Garrity GM, Holt JG. Phylum AI. Crenarchaeota phy. nov. In Bergey's Manual of Systematic Bacteriology, vol. 1. 2nd ed. Edited by: Garrity, GM, Boone, DR and Castenholz, RW. Springer, New York; 2001: 169-210.
  9. . Validation of publication of new names and new combinations previously effectively published outside the IJSEM. Validation List no. 85. Int J Syst Evol Microbiol. 2002; 52: 685-690 View ArticlePubMed
  10. Reysenbach AL. Class I. Thermoprotei class. nov. In Bergey's Manual of Systematic Bacteriology, vol. 1. 2nd ed. Edited by: Garrity, GM, Boone, DR and Castenholz, RW. Springer, New York; 2001: 169.
  11. Huber H, Stetter O. Order II. Desulfurococcales ord. nov. In Bergey's Manual of Systematic Bacteriology, vol. 1. 2nd ed. Edited by: Garrity, GM, Boone, DR and Castenholz, RW. Springer, New York; 2001: 169.
  12. . Validation List no. 22. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Bacteriol. 1986; 36: 573-576
  13. Burggraf S, Huber H and Stetter KO. Reclassification of the crenarchael orders and families in accordance with 16S rRNA sequence data. Int J Syst Bacteriol. 1997; 47: 657-660PubMed
  14. Zillig W, Stetter KO, Prangishvilli D, Schäfer W, Wunderl S, Janekovic D, Holz I and Palm P. Desulfurococcaceae, the second family of the extremely thermophilic, anaerobic, sulfur-respiring Thermoproteales. Zentralbl Bakteriol Parasitenkd Infektionskr Hyg Abt 1 Orig. 1982; 3:304-317
  15. . Validation List no. 10. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Bacteriol. 1983; 33: 438-440
  16. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS and Eppig JT. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25:25-29 View ArticlePubMed
  17. Liolios K, Mavromatis K, Tavernarakis N and Kyrpides NC. The Genomes OnLine Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2008; 36:D475-D479 View ArticlePubMed
  18. Anderson IJ, Dharmarajan L, Rodriguez J, Hooper S, Porat I, Ulrich LE, Elkins JG, Mavromatis K, Sun H and Land M. The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota. BMC Genomics. 2009; 10:145 View ArticlePubMed
  19. Badger JH and Olsen GJ. CRITICA: coding region identification tool invoking comparative analysis. Mol Biol Evol. 1999; 16:512-524PubMed
  20. Delcher AL, Harmon D, Kasif S, White O and Salzberg SL. Improved microbial gene identification with GLIMMER. Nucleic Acids Res. 1999; 27:4636-4641 View ArticlePubMed
  21. Pati A., et al. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes. (Submitted).
  22. Lowe TM and Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997; 25:955-964 View ArticlePubMed
  23. Markowitz VM, Mavromatis K, Ivanova NN, Chen IMA, Chu K and Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009; 25:2271-2278.. View ArticlePubMed
  24. Sapra R, Verhagen MFJM and Adams MWW. Purification and characterization of a membrane-bound hydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol. 2000; 182:3423-3428 View ArticlePubMed
  25. Schut GJ, Bridger SL and Adams MWW. Insights into the metabolism of elemental sulfur by the hyperthermophilic archaeon Pyrococcus furiosus: characterization of a coenzyme A-dependent NAD(P)H sulfur oxidoreductase. J Bacteriol. 2007; 189:4431-4441 View ArticlePubMed
  26. Garrity GM, Lilburn TG, Cole JR, Harrison SH, Euzeby J, and Tindall BJ. “Part 1- The Archaea, Phyla Crenarchaeota and Euryarchaeota” Taxonomic Outline of the Bacteria and Archaea 2007. Web Site
  27. Burggraf S, Huber H and Stetter KO. Reclassification of the crenarchaeal orders and families in accordance with 16S rRNA sequence data. Int J Syst Bacteriol. 1997; 47:657-660PubMed