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Complete genome sequence of Vulcanisaeta distributa type strain (IC-017T)

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Standards in Genomic Sciences20103:3020117

https://doi.org/10.4056/sigs.1113067

©  The Author(s) 2010

  • Published:

Abstract

Vulcanisaeta distributa Itoh et al. 2002 belongs to the family Thermoproteaceae in the phylum Crenarchaeota. The genus Vulcanisaeta is characterized by a global distribution in hot and acidic springs. This is the first genome sequence from a member of the genus Vulcanisaeta and seventh genome sequence in the family Thermoproteaceae. The 2,374,137 bp long genome with its 2,544 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords

  • hyperthermophilic
  • acidophilic
  • non-motile
  • microaerotolerant anaerobe
  • Thermoproteaceae
  • Crenarchaeota
  • GEBA

Introduction

Strain IC-017T (= DSM 14429 = JCM 11212) is the type strain of the species Vulcanisaeta distributa, which is the type species of its genus Vulcanisaeta [1]. The only other species in the genus is V. souniana [1,2]. The genus name derives from the Latin words ‘vulcanicus’ meaning volcanic, and ‘saeta’ meaning stiff hair, to indicate a rigid rod inhabiting volcanic hot springs [1]. The species epithet derives from the Latin ‘distributa’, referring to the wide distribution of strains belonging to this species [1]. The type strain IC-017T was isolated from a hot spring in Ohwakudani, Kanagawa, Japan [1]. Fourteen additional strains [IC-019, IC-029 (= JCM 11213), IC-030, IC-032, IC-051, IC-052, IC-058, IC-064 (= JCM 11214), IC-065 (= JCM 11215), IC-124 (= JCM 11216), IC-135 (= JCM 11217), IC-136, IC-140 and IC-141 (= JCM 11218)] are included in this species [1]. At the time of the species description, the terminus ‘distributa’ referred simply to a wide distribution within Japan [1]. However, 16S rRNA sequences which probably belong to the genus Vulcanisaeta (≥95% sequence similarity to V. distributa) have been obtained from 117°C hot deep-sea hydrothermal fluid in the south Mariana area [3]. Clone sequences that are highly similar to the 16S rRNA gene sequence of strain IC-017T were obtained from an acidic hot spring water at the Tatung Volcano area in Northern Taiwan (99%, FJ797325), the hot Sylvan Spring in Yellowstone National Park (=YNP, USA, 98%, DQ243774), at the Cistern Hot Spring at Norris Geyser Basin in YNP (98%, DQ924709) and also at other springs in YNP (98%, DQ833773). Metagenomic sequences from uncultured clones in YNP (94%, ADKH01000984) also support these observations. The 16S rRNA gene similarity values to non-hot-spring metagenomes, e.g., from marine, soil, or human gut, were all below 83%, indicating that Vulcanisaeta is probably not found in these habitats (status July 2010).

Although it is not the case for the type strain IC-017T, V. distributa recently received further interest, as it was found that strain IC-065 contained a 691 bp large intron within its 16S rRNA sequence [4]. Novel 16S rRNA introns have been found in several members of the family Thermoproteaceae [4]. Here we present a summary classification and a set of features for V. distributa strain IC-017T, together with the description of the complete genomic sequencing and annotation.

Classification and features

The cells of strain IC-017T are rigid, straight to slightly curved rods (Figure 1 and Table 1)[4]. Occasionally, they bend, branch out, or bear spherical bodies at the terminae (not seen in Figure 1), which have been termed as ‘golf clubs’. Most cells are 0.4–0.6 µm in width and 3–7 µm long [4]. Pili have been observed to rise terminally or laterally; motility has not been observed [4]. Usually, strain IC-017T grows anaerobically. However, when cultured in media in which sulfur is replaced by sodium thiosulfate (1.0 g/l), strain IC-017T showed weak growth in a low-oxygen atmosphere (1%), but not in air [4].
Figure 1.
Figure 1.

Scanning electron micrograph of V. distributa IC-017T

Table 1.

Classification and general features of V. distributa IC-017T according to the MIGS recommendations [5]

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Archaea

TAS [6]

 

Phylum Crenarchaeota

TAS [7,8]

 

Class Thermoprotei

TAS [8,9]

 

Order Thermoproteales

TAS [10–13]

 

Family Thermoproteaceae

TAS [10,12,13]

 

Genus Vulcanisaeta

TAS [1]

 

Species Vulcanisaeta distributa

TAS [1]

 

Type strain IC-017

TAS [1]

 

Gram stain

not reported

TAS [1]

 

Cell shape

rigid, straight to slightly curved rods

TAS [1]

 

Motility

non-motile

TAS [1]

 

Sporulation

not reported

TAS [1]

 

Temperature range

70–92°C

TAS [1]

 

Optimum temperature

90°C

TAS [1]

 

Salinity

1% NaCl or below

TAS [1]

MIGS-22

Oxygen requirement

microaerotolerant anaerobe

TAS [1]

 

Carbon source

yeast extract, peptone, beef extract, casamino acids, gelatin, maltose, starch, malate, galactose, mannose

TAS [1]

 

Energy source

heterotrophic

TAS [1]

MIGS-6

Habitat

acidic hot environments (water, soil, mud)

TAS [1]

MIGS-15

Biotic relationship

free living

TAS [1]

MIGS-14

Pathogenicity

not pathogenic

NAS

 

Biosafety level

1

TAS [14]

 

Isolation

acidic hot water

TAS [1]

MIGS-4

Geographic location

Ohwakudani, Japan

TAS [1]

MIGS-5

Sample collection time

September 1993

TAS [1]

MIGS-4.1

Latitude

35.447

NAS

MIGS-4.2

Longitude

139.642

 

MIGS-4.3

Depth

unknown

 

MIGS-4.4

Altitude

unknown

 

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

In contrast to Thermocladium or Caldivirga strains, V. distributa grows well even in the absence of a vitamin mixture or archaeal cell-extract solution in the medium [4]. All seven tested strains of V. distributa were shown to be resistant to chloramphenicol, kanamycin, oleandomycin, streptomycin and vancomycin, but sensitive to erythromycin, novobiocin and rifampicin (all at 100 µg per ml) [4]. V. distributa needs acidic conditions to grow (pH 3.5 to 5.6). Under optimal growth conditions, the doubling time is 5.5 to 6.5 hours [4]. Sulfur or thiosulfate is required as an electron acceptor. Strain IC-017T does not utilize d-arabinose, d-fructose, lactose, sucrose, d-xylose, acetate, butyrate, formate, fumarate, propionate, pyruvate, succinate, methanol, formamide, methylamine or trimethylamine as carbon sources and does not utilize fumarate, malate or nitrate as electron acceptors [4].

Figure 2 shows the phylogenetic neighborhood of V. distributa IC-017T in a 16S rRNA based tree. The sequence of the single 16S rRNA gene copy in the genome of strain IC-017T does not differ from the previously published 16S rRNA sequence (AB063630).
Figure 2.
Figure 2.

Phylogenetic tree highlighting the position of V. distributa IC-017T relative to the other type strains within the genus Vulcanisaeta and the type strains of the other genera within Thermoproteales. The tree was inferred from 1,356 aligned characters [16,17] of the 16S rRNA gene sequence under the maximum likelihood criterion [18] and rooted with the type strains of the genera of Desulfurococcales and Acidilobales. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 150 bootstrap replicates [19] if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [20] are shown in blue, published genomes [21–24] and INSDC accessions CP000504 and CP00852 in bold.

Chemotaxonomy

Strain IC-017T possesses cyclic and acyclic tetraether core lipids [4]. The major cellular polyamines are norspermidine (1.25), spermidine (0.55), agmatine (0.15), norspermine (0.1) and cadaverine (0.1) (values are in µmol/g wet weight of the cell) [25]. Further chemotaxonomic data are not available.

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [26], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [27]. The genome project is deposited in the Genome OnLine Database [20] 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

Two genomic libraries: one 454 pyrosequence standard library, one 454 PE library (22.9kb insert size)

MIGS-29

Sequencing platforms

454 GS FLX Titanium

MIGS-31.2

Sequencing coverage

106.3 × pyrosequence

MIGS-30

Assemblers

Newbler version 2.0.0-PostRelease-09/05/2008, phrap

MIGS-32

Gene calling method

Prodigal 1.4, GenePRIMP

 

INSDC ID

CP002100

 

Genbank Date of Release

September 23, 2010

 

GOLD ID

Gc01374

 

NCBI project ID

32589

 

Database: IMG-GEBA

2502790013

MIGS-13

Source material identifier

DSM 14429

 

Project relevance

Tree of Life, GEBA

Growth conditions and DNA isolation

V. distributa IC-017T, DSM 14429, was grown anaerobically in DSMZ medium 88 (Sulfolobus medium) [28] at 90°C. DNA was isolated from 0.5–1 g of cell paste using Qiagen Genomic 500 DNA Kit (Qiagen, Hilden, Germany) following the standard protocol as recommended by the manufacturer.

Genome sequencing and assembly

The genome was sequenced using a 454 sequencing platform. All general aspects of library construction and sequencing can be found at the JGI website. Pyrosequencing reads were assembled using the Newbler assembler version 2.0.0-PostRelease-09/05/2008 (Roche). The initial Newbler assembly consisted of 147 contigs in 13 scaffolds and was converted into a phrap assembly by making fake reads from the consensus, and collecting the read pairs in the 454 paired end library. Draft assemblies were based on 252.4 Mb 454 draft 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 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, Dupfinisher [29], or sequencing cloned bridging PCR fragments with subcloning or transposon bombing (Epicentre Biotechnologies, Madison, WI) [30].

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. The error rate of the completed genome sequence is less than 1 in 100,000. The final assembly contains 0.8 million pyrosequencing reads that provide 106.3× coverage of the genome.

Genome annotation

Genes were identified using Prodigal [31] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [32]. 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. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes - Expert Review (IMG-ER) platform [33].

Genome properties

The genome consists of a 2,374,137 bp long chromosome with a 45.4% GC content (Table 3 and Figure 3). Of the 2,593 genes predicted, 2,544 were protein-coding genes, and 49 RNAs; fifty one pseudogenes were also identified. The majority of the protein-coding genes (57.2%) were assigned 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.
Figure 3.

Graphical circular map of the genome. 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)

2,374,137

100.00%

DNA coding region (bp)

2,136,210

98.11%

DNA G+C content (bp)

1,078,516

45.43%

Number of replicons

1

 

Extrachromosomal elements

0

 

Total genes

2,593

100.00%

RNA genes

49

1.89%

rRNA operons

1

 

Protein-coding genes

2,544

98.11%

Pseudo genes

51

1.97%

Genes with function prediction

1,483

57.19%

Genes in paralog clusters

327

12.61%

Genes assigned to COGs

1,548

59.70%

Genes assigned Pfam domains

1,665

64.21%

Genes with signal peptides

205

7.91%

Genes with transmembrane helices

591

22.79%

CRISPR repeats

18

 
Table 4.

Number of genes associated with the general COG functional categories

Code

Value

%age

Description

J

161

9.6

Translation, ribosomal structure and biogenesis

A

4

0.2

RNA processing and modification

K

65

3.9

Transcription

L

67

4.0

Replication, recombination and repair

B

4

0.2

Chromatin structure and dynamics

D

18

1.1

Cell cycle control, cell division, chromosome partitioning

Y

0

0.0

Nuclear structure

V

13

0.8

Defense mechanisms

T

25

1.5

Signal transduction mechanisms

M

61

3.6

Cell wall/membrane/envelope biogenesis

N

8

0.5

Cell motility

Z

1

0.1

Cytoskeleton

W

0

0.0

Extracellular structures

U

20

1.2

Intracellular trafficking and secretion, and vesicular transport

O

64

3.8

Posttranslational modification, protein turnover, chaperones

C

167

10.0

Energy production and conversion

G

96

5.7

Carbohydrate transport and metabolism

E

160

9.5

Amino acid transport and metabolism

F

55

3.3

Nucleotide transport and metabolism

H

64

3.8

Coenzyme transport and metabolism

I

69

4.1

Lipid transport and metabolism

P

59

3.5

Inorganic ion transport and metabolism

Q

29

1.7

Secondary metabolites biosynthesis, transport and catabolism

R

263

15.7

General function prediction only

S

160

9.5

Function unknown

-

1,045

40.3

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 599/1-1 and SI 1352/1-2.

Authors’ Affiliations

(1)
DOE Joint Genome Institute, Walnut Creek, California, USA
(2)
DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
(3)
Microbiology - Archaeenzentrum, University of Regensburg, Regensburg, Germany
(4)
Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico, USA
(5)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
(6)
Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
(7)
HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
(8)
University of California Davis Genome Center, Davis, California, USA

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