Open Access

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

  • Iain J. Anderson1,
  • Hui Sun1,
  • Alla Lapidus1,
  • Alex Copeland1,
  • Tijana Glavina Del Rio1,
  • Hope Tice1,
  • Eileen Dalin1,
  • Susan Lucas1,
  • Kerrie Barry1,
  • Miriam Land1, 2,
  • Paul Richardson1,
  • Harald Huber3 and
  • Nikos C. Kyrpides1
Standards in Genomic Sciences20091:1020183

https://doi.org/10.4056/sigs.30527

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. marinusstrain F1, the type strain of the species. This is the fifth reported complete genome sequence from the order Desulfurococcales.

Keywords

Archaea Desulfurococcales sulfur-reducing hyperthermophile

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

Classification and features

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].

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

 

Current classification

Domain Archaea

TAS [7]

 

Phylum Crenarchaeota

TAS [8,9]

 

Class Thermoprotei

TAS [9,10]

 

Order Desulfurococcales

TAS [11,12]

 

Family Desulfurococcaceae

TAS [1315]

 

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

Latitude-longitude

38.4/15.0

TAS [1]

MIGS-4.2

   

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

MIGS-13

Source material identifier

DSM 3639

 

Project relevance

Tree of Life

Growth conditions and DNA isolation

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.
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 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

 
Table 4.

Numbers of genes associated with the general COG functional categories.

Code

value

%age

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.

Authors’ Affiliations

(1)
Joint Genome Institute
(2)
Bioscience Division, Oak Ridge National Laboratory
(3)
Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg

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Copyright

© The Author(s) 2009