Open Access

Genome sequence of the moderately thermophilic, amino-acid-degrading and sulfur-reducing bacterium Thermovirga lienii type strain (Cas60314T)

  • Markus Göker1,
  • Elisabeth Saunders2, 3,
  • Alla Lapidus2,
  • Matt Nolan2,
  • Susan Lucas2,
  • Nancy Hammon2,
  • Shweta Deshpande2,
  • Jan-Fang Cheng2,
  • Cliff Han2, 3,
  • Roxanne Tapia2, 3,
  • Lynne A. Goodwin2, 3,
  • Sam Pitluck2,
  • Konstantinos Liolios2,
  • Konstantinos Mavromatis2,
  • Ioanna Pagani2,
  • Natalia Ivanova2,
  • Natalia Mikhailova2,
  • Amrita Pati2,
  • Amy Chen4,
  • Krishna Palaniappan4,
  • Miriam Land2, 5,
  • Yun-juan Chang2, 5,
  • Cynthia D. Jeffries2, 5,
  • Evelyne-Marie Brambilla1,
  • Manfred Rohde6,
  • Stefan Spring1,
  • John C. Detter2, 3,
  • Tanja Woyke2,
  • James Bristow2,
  • Jonathan A. Eisen2, 7,
  • Victor Markowitz4,
  • Philip Hugenholtz2, 8,
  • Nikos C. Kyrpides2 and
  • Hans-Peter Klenk1
Standards in Genomic Sciences20126:6020230

DOI: 10.4056/sigs.2726028

Published: 25 May 2012

Abstract

Thermovirga lienii Dahle and Birkeland 2006 is a member of the genus Thermovirga in the genomically moderately well characterized phylum ‘Synergistetes’. Members of this relatively recently proposed phylum ‘Synergistetes’ are of interest because of their isolated phylogenetic position and their diverse habitats, e.g. from humans to oil wells. The genome of T. lienii Cas60314T is the fifth genome sequence (third completed) from this phylum to be published. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,999,646 bp long genome (including one plasmid) with its 1,914 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords

anaerobic chemoorganotrophic Gram-negative motile thermophilic marine oil well Synergistaceae GEBA

Introduction

Strain Cas60314T (= DSM 17291 = ATCC BA-1197) is the type strain of the species Thermovirga lienii [1] of the monospecific genus Thermovirga [1]. The strain was originally isolated from 68°C hot oil-well production water from an oil reservoir in the North Sea (Norway) [1]. The genus name Thermovirga was derived from the Greek word for thermê, heat, and the Latin word virga, rod, meaning the hot rod [1]; the species epithet was derived of Lien, in honor of the Norwegian microbiologist Professor Torleiv Lien, for his important contribution in the study of anaerobes from petroleum reservoirs [1]. Whether or not strain Cas60314T occurs naturally in the oil reservoir is not clear, but is likely because the oil well was not injected with seawater (which eliminates a common source of contamination) [1]. Here we present a summary classification and a set of features for T. lienii Cas60314T, together with the description of the genomic sequencing and annotation.

Classification and features

A representative genomic 16S rRNA sequence of T. lienii Cas60314T was compared using NCBI BLAST [2,3] 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 [4] and the relative frequencies of taxa and keywords (reduced to their stem [5]) were determined, weighted by BLAST scores. The most frequently occurring genera were Dethiosulfovibrio (45.6%), Thermanaerovibrio (30.2%), Aminobacterium (12.5%) and Thermovirga (11.7%) (16 hits in total). Regarding the single hit to sequences from members of the species, the average identity within HSPs was 100.0%, whereas the average coverage by HSPs was 92.2%. Among all other species, the one yielding the highest score was Thermanaerovibrio velox (FR733707), which corresponded to an identity of 90.1% and an HSP coverage of 85.5%. (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 HM041945 (‘aggregate-forming and crude-oil-adhering microbial biodegraded -temperature petroleum reservoir produced fluid Niiboli oilfield clone NRB28’), which showed an identity of 99.7% and an HSP coverage of 98.3%. The most frequently occurring keywords within the labels of all environmental samples which yielded hits were ‘digest’ (10.9%), ‘anaerob’ (7.4%), ‘sludg’ (5.8%), ‘mesophil’ (5.6%) and ‘wastewat’ (5.6%) (234 hits in total). The most frequently occurring keywords within the labels of those environmental samples which yielded hits of a higher score than the highest scoring species were ‘microbi’ (6.3%), ‘temperatur’ (4.4%), ‘oil’ (3.6%), ‘water’ (3.6%) and ‘anaerob’ (3.2%) (43 hits in total). Although these keywords are not in conflict with the habitat from which strain Cas60314T was isolated, they do not reveal new insights into the largely unknown natural habitat for members of the species.

Figure 1 shows the phylogenetic neighborhood of T. lienii in a 16S rRNA based tree. The sequences of the three 16S rRNA gene copies in the genome differ from each other by up to three nucleotides, and differ by up to three nucleotides from the previously published 16S rRNA sequence (DQ071273).
Figure 1.

Phylogenetic tree highlighting the position of T. lienii relative to the type strains of the other species within the phylum Synergistetes. The tree was inferred from 1,385 aligned characters [6,7] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [8]. Rooting was done initially using the midpoint method [9] 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 1,000 ML bootstrap replicates [10] (left) and from 1,000 maximum parsimony bootstrap replicates [11] (right) if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [12] are labeled with one asterisk, those also listed as ‘Complete and Published’ with two asterisks [13,14]. Dethiosulfovibrio peptidovorans [15] and Aminomonas paucivorans [16] are without a second asterisk, because these publications were based on ‘non-complete’ permanent draft sequences.

Cells of T. lienii Cas60314T are Gram-negative staining, motile (only in the early exponential growth phase), straight rods of 0.4 to 0.8 εm diameter and 2 to 3 εm length (Figure 2) [1]. Cells appeared to be singly, or in chains of 2 to 5 cells, but can also form aggregates of several hundred cells [1]. The growth range of strain Cas60314T spans from 37–68°C, with an optimum at 58°C, and pH 6.2–8.5, with an optimum at 6.5–7 [1]. Strain Cas60314T grow best in medium containing 2–3% NaCl [1]. Physiological characteristics such as growth substrates and products formed are described in great detail by Dahle and Birkeland [1]; the organism has a fermentative metabolism and utilizes amino acids, proteinaceous substrates and selected organic acids, but no sugars, fatty acids or alcohols [1]. Strain Cas60314T reduces cysteine and elemental sulfur to sulfide, but not thiosulfate [1]. The strain could not grow in unreduced medium under an N2/air (20:1, v/v) gas phase, but was able to grow with 100% H2 in the headspace, with peptone as substrate [1].
Figure 2.

Scanning electron micrograph of T. lienii Cas60314T

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [22], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [23]. The genome project is deposited in the Genomes On Line Database [12] 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 1.

Classification and general features of T. lienii Cas60314T according to the MIGS recommendations [17].

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [18]

 

Phylum “Synergistetes

TAS [19]

 

Class Synergistia

TAS [19]

 

Order Synergistales

TAS [19]

 

Family Synergistaceae

TAS [19]

 

Genus Thermovirga

TAS [1]

 

Species Thermovirga lienii

TAS [1]

 

Type strain Cas60314

TAS [1]

 

Gram stain

negative

TAS [1]

 

Cell shape

rod-shaped

TAS [1]

 

Motility

motile

TAS [1]

 

Sporulation

none

TAS [1]

 

Temperature range

thermophilic

TAS [1]

 

Optimum temperature

58°C

TAS [1]

 

Salinity

optimum 2–3% (w/v) NaCl

TAS [1]

MIGS-22

Oxygen requirement

obligate anaerobic

TAS [1]

 

Carbon source

amino acids, proteinous substrates, organic acids

TAS [1]

 

Energy metabolism

chemoorganotrophic

TAS [1]

MIGS-6

Habitat

fresh water, oil fields

TAS [1]

MIGS-15

Biotic relationship

free living

TAS [1]

MIGS-14

Pathogenicity

none

NAS

 

Biosafety level

1

TAS [20]

MIGS-23.1

Isolation

production water from oil well

TAS [1]

MIGS-4

Geographic location

Troll C Reservoir, North Sea, Norway

TAS [1]

MIGS-5

Sample collection time

September 2003

NAS

MIGS-4.1

Latitude

60.886

TAS [1]

MIGS-4.2

Longitude

3.612

TAS [1]

MIGS-4.3

Depth

not reported

 

MIGS-4.4

Altitude

not reported

 

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

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 (8 kb insert size), one Illumina library

MIGS-29

Sequencing platforms

Illumina GAii, 454 GS FLX Titanium

MIGS-31.2

Sequencing coverage

223.9 × Illumina; 78.8 × pyrosequence

MIGS-30

Assemblers

Newbler version 2.0.00.20-PostRelease-11-05-2008, Velvet version 1.0.13, phrap version SPS - 4.24

MIGS-32

Gene calling method

Prodigal

 

INSDC ID

CP003096 (chromosome)

 

CP003097 (plasmid)

 

GenBank Date of Release

November 03, 2011

 

GOLD ID

Gc02016

 

NCBI project ID

33163

 

Database: IMG

2505119043

MIGS-13

Source material identifier

DSM 17291

 

Project relevance

Bioenergy and phylogenetic diversity

Growth conditions and DNA isolation

T. lienii strain Cas60314T, DSM 17291, was grown anaerobically in DSMZ medium 383 (Desulfobacterium medium) [24] at 55°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 the following modification for cell lysis: 1µl lysozyme and 5 µl mutanolysin added to the standard lysis solution for 40 min at 37°C; after the MPC-step the lysis solution was incubated for one hour on ice. DNA is available through the DNA Bank Network [25].

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 [26]. Pyrosequencing reads were assembled using the Newbler assembler (Roche). The initial Newbler assembly consisting of 127 contigs in one scaffold was converted into a phrap [27] assembly by making fake reads from the consensus, to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (379.0 Mb) was assembled with Velvet [28] 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 156.8 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 [27] 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 [26], Dupfinisher [29], 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 811 additional reactions and 23 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 [30]. 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 302.7 × coverage of the genome. The final assembly contained 569,599 pyrosequence and 12,441,8 Illumina reads.

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) non-redundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. These data sources were combined to assert a product description for each predicted protein. Non-coding genes and miscellaneous features were predicted using tRNAscan-SE [33], RNAMMer [34], Rfam [35], TMHMM [36], and signalP [37].

Genome properties

The genome consists of a 1,967,774 bp long chromosome and a 31,872 bp long circular plasmid with a 47.1% G+C content (Table 3 and Figure 3). Of the 1,973 genes predicted, 1,914 were protein-coding genes, and 59 RNAs; 38 pseudogenes were also identified. The majority of the protein-coding genes (79.0%) 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.

Graphical map of the chromosome (plasmid not shown, but accessible through the img/er pages on the JGI web pages [26]). 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)

1,999,646

100.00%

DNA coding region (bp)

1,838,210

91.93%

DNA G+C content (bp)

941,059

47.06%

Number of replicons

2

 

Extrachromosomal elements

1

 

Total genes

1,973

100.00%

RNA genes

59

2.99%

rRNA operons

3

 

tRNA genes

47

2.38%

Protein-coding genes

1,914

97.01%

Pseudo genes

38

1.93%

Genes with function prediction (proteins)

1,558

78.97%

Genes in paralog clusters

833

42.22%

Genes assigned to COGs

1,685

85.40%

Genes assigned Pfam domains

1,695

85.91%

Genes with signal peptides

285

14.45%

Genes with transmembrane helices

486

24.63%

CRISPR repeats

0

 
Table 4.

Number of genes associated with the general COG functional categories

Code

value

%age

Description

J

149

8.1

Translation, ribosomal structure and biogenesis

A

0

0.0

RNA processing and modification

K

98

5.3

Transcription

L

147

7.9

Replication, recombination and repair

B

2

0.1

Chromatin structure and dynamics

D

31

1.7

Cell cycle control, cell division, chromosome partitioning

Y

0

0.0

Nuclear structure

V

14

0.8

Defense mechanisms

T

77

4.2

Signal transduction mechanisms

M

99

5.4

Cell wall/membrane biogenesis

N

61

3.3

Cell motility

Z

0

0.0

Cytoskeleton

W

0

0.0

Extracellular structures

U

50

2.7

Intracellular trafficking and secretion, and vesicular transport

O

60

3.2

Posttranslational modification, protein turnover, chaperones

C

160

8.6

Energy production and conversion

G

91

4.9

Carbohydrate transport and metabolism

E

229

12.4

Amino acid transport and metabolism

F

56

3.0

Nucleotide transport and metabolism

H

77

4.2

Coenzyme transport and metabolism

I

40

2.2

Lipid transport and metabolism

P

73

3.9

Inorganic ion transport and metabolism

Q

31

1.7

Secondary metabolites biosynthesis, transport and catabolism

R

189

10.2

General function prediction only

S

117

6.3

Function unknown

-

288

14.6

Not in COGs

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Maren Schröder (DSMZ) for growing T. lienii cultures. 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, 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)
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures
(2)
DOE Joint Genome Institute
(3)
Bioscience Division, Los Alamos National Laboratory
(4)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(5)
Oak Ridge National Laboratory
(6)
HZI - Helmholtz Centre for Infection Research
(7)
University of California Davis Genome Center
(8)
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland

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