Open Access

Complete genome sequence of Acetohalobium arabaticum type strain (Z-7288T)

  • Johannes Sikorski1,
  • Alla Lapidus2,
  • Olga Chertkov3,
  • Susan Lucas2,
  • Alex Copeland2,
  • Tijana Glavina Del Rio2,
  • Matt Nolan2,
  • Hope Tice2,
  • Jan-Fang Cheng2,
  • Cliff Han2, 3,
  • Evelyne Brambilla1,
  • Sam Pitluck2,
  • Konstantinos Liolios2,
  • Natalia Ivanova2,
  • Konstantinos Mavromatis2,
  • Natalia Mikhailova2,
  • Amrita Pati2,
  • David Bruce2, 3,
  • Chris Detter3,
  • Roxanne Tapia3,
  • Lynne Goodwin2, 3,
  • Amy Chen4,
  • Krishna Palaniappan4,
  • Miriam Land2, 5,
  • Loren Hauser2, 5,
  • Yun-Juan Chang2, 5,
  • Cynthia D. Jeffries2, 5,
  • Manfred Rohde6,
  • Markus Göker1,
  • Stefan Spring1,
  • Tanja Woyke2,
  • James Bristow2,
  • Jonathan A. Eisen2, 7,
  • Victor Markowitz4,
  • Philip Hugenholtz2,
  • Nikos C. Kyrpides2 and
  • Hans-Peter Klenk1
Standards in Genomic Sciences20103:3010057

DOI: 10.4056/sigs.1062906

Published: 30 August 2010

Abstract

Acetohalobium arabaticum Zhilina and Zavarzin 1990 is of special interest because of its physiology and its participation in the anaerobic C1-trophic chain in hypersaline environments. This is the first completed genome sequence of the family Halobacteroidaceae and only the second genome sequence in the order Halanaerobiales. The 2,469,596 bp long genome with its 2,353 protein-coding and 90 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Keywords

anaerobe mesophile halophile chemolithotroph methylotroph organotroph degradation of betaine consumption of trimethylamine homoacetogen Clostridia Halanaerobiales GEBA

Introduction

Strain Z-7288T (= DSM 5501 = ATCC 49924) is the type strain of the species Acetohalobium arabaticum, which is the type species of the genus Acetohalobium [1,2]. The genus name derives from the Latin word ‘acetum’, meaning vinegar, and the Greek words ‘halos’ and ‘bios’, meaning salt and life, respectively, in order to indicate an acetate-producing organism living in salt [3]. The species name derives from Arabat, a peninsula between the Sea of Azov and Sivash [3], since the strain was isolated from lagoons of the Arabat spit (East Crimea) which separates Sivash lake from the Sea of Azov [2]. Currently, this is the only known strain in the genus Acetohalobium. A. arabaticum participates together with other halophilic bacteria and the genera Methanohalophilus and Methanohalobium in the C1-trophic chain in hypersaline environments [2]. Here we present a summary classification and a set of features for A. arabaticum Z-7288T, together with the description of the complete genomic sequencing and annotation.

Classification and features

The cells of A. arabaticum are bent rods, motile by one to two subterminal flagella (Table 1) [2]. The flagella are stated in the original description [2], though they are not visible in our study (Figure 1). The cells are single, in pairs or form short chains, being 0.7–1 µm in diameter and 1–5 µm in length [2]. Other typical cell aggregates are palisades and ribbons, which are formed by adhesion of cells having intimate contact (Figure 1) [2]. The multiplication is by binary fission. The outer membrane is typical of a Gram-negative organism [2]. Growth is completely inhibited by 100 µM/ml streptomycin, benzylpenicillin, bacitracin, erythromycin, gentamycin, kanamycin, vancomycin or tetracyclin [2]. Strain Z-7288T is obligately anaerobic, tolerating up to 12 mM H2S. Neither O2, S2O32-, SO42-, nor S0 can serve as electron acceptors. Strain Z-7288T requires a salt concentration of 10–25% NaCl, the optimum is 15–18% NaCl [2]. The optimal pH is between 7.6 and 8.0 [2].
Figure 1.

Scanning electron micrograph of A. arabaticum Z-7288T

Table 1.

Classification and general features of A. arabaticum Z-7288T according to the MIGS recommendations [4]

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

TAS [5]

 

Phylum Firmicutes

TAS [6,7]

 

Class Clostridia

TAS [8,9]

 

Order Halanaerobiales

TAS [1012]

 

Family Halobacteroidaceae

TAS [11,12]

 

Genus Acetohalobium

TAS [1,13]

 

Species Acetohalobium arabaticum

TAS [1,13]

 

Type strain Z-7288

TAS [2]

 

Gram stain

negative

TAS [2]

 

Cell shape

bent rod

TAS [2]

 

Motility

motile, subterminal flagella

TAS [2]

 

Sporulation

unknown; not observed

NAS

 

Temperature range

max. 47°C

TAS [2]

 

Optimum temperature

28–40°C

TAS [2]

 

Salinity

10–25% (optimal 15–18%) NaCl

TAS [2]

MIGS-22

Oxygen requirement

anaerobic

TAS [2]

 

Carbon source

CO, CO2, TMA, betaine, lactate, pyruvate

TAS [2]

 

Energy source

chemolithoautotroph, methylotroph, organotroph

TAS [2]

MIGS-6

Habitat

lagoon

TAS [2]

MIGS-15

Biotic relationship

free-living

TAS [2]

MIGS-14

Pathogenicity

not reported

 
 

Biosafety level

1

TAS [14]

 

Isolation

lagoon

TAS [2]

MIGS-4

Geographic location

Arabat Spit, Ukraine

TAS [2]

MIGS-5

Sample collection time

1990 or before

TAS [2]

MIGS-4.1

Latitude

46.26

NAS

MIGS-4.2

Longitude

34.86

 

MIGS-4.3

Depth

unknown

 

MIGS-4.4

Altitude

about 15 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 [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.

A. arabaticum exhibits three modes of nutrition [2]: It is chemolithoautotrophic using H2 together with CO2 or CO; it is methylotrophic using trimethylamine (TMA); and it is organotrophic using betaine, lactate, pyruvate or histidine. Carbohydrates are not utilized. No growth occurs on methanol, monomethylamine (MMA), dimethylamine (DMA), dimethylglycine, choline or sarcosine [2]. When grown on TMA, an equimolar amount of acetate is formed along with lesser amounts of DMA and MMA [2]. Betaine is degraded mainly to acetate and minor amounts of methylamines [2].

Carbonic anhydrase (CA; carbonate hydrolyase, EC 4.2.1.1) has been studied in strain Z-7288T and in other acetogenic bacteria [16]. This zinc-containing enzyme is found in animals, plants, bacteria and archaea and catalyzes the following reaction: CO2 + H2O ↔ HCO3- and H+ [16]. Further biochemical details of CA are described elsewhere [16]. Strain Z-7288T displayed CA activities similar to those of other CA-containing bacteria [1618]. With lactate as cultivation substrate the specific activity of CA in strain Z-7288T has been determined to be 2.1± 0.4 units per mg or protein [16]. It has been suggested that one physiological function for CA in acetogens is to increase intracellular CO2 levels [16].

The 16S rRNA genes of the other type strains in the family Halobacteroidaceae share between 85.9% (Orenia sivashensis [19]) and 95.1% (Sporohalobacter lortetii [20]) sequence identity with strain Z-7288T [21]. Uncultured clone sequences from environmental samples and metagenomic surveys do not surpass 84–86% sequence similarity to the 16S rRNA gene sequence of strain Z-7288T, indicating a lack of further members of the genus Acetohalobium in the habitats screened thus far (status June 2010).

Figure 2 shows the phylogenetic neighborhood of A. arabaticum Z-7288T in a 16S rRNA based tree. The sequences of the five 16S rRNA gene copies in the genome of Acetohalobium arabaticum Z-7288T differ from each other by up to one nucleotide, and differ by up to three nucleotides from the previously published 16S rRNA sequence generated from DSM 5501 (X89077).
Figure 2.

Phylogenetic tree highlighting the position of A. arabaticum Z-7288T relative to the type strains of the other genera within the order Halanaerobiales. The trees were inferred from 1,308 aligned characters [22,23] of the 16S rRNA gene sequence under the maximum likelihood criterion [24] and rooted in accordance with the current taxonomy [25]. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 300 bootstrap replicates [26] if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [27] are shown in blue, published genomes [28] in bold.

Chemotaxonomy

No chemotaxonomic data are currently available for the genus Acetohalobium.

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [29], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [30]. The genome project is deposited in the Genome OnLine Database [27] 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: 454 pyrosequence standard and paired ended 10kb library

MIGS-29

Sequencing platforms

454 GS Titanium, Illumina GAii

MIGS-31.2

Sequencing coverage

98.4× pyrosequence

MIGS-30

Assemblers

Newbler version 2.0.00.20-PostRelease-11-05-2008-gcc-3.4.6, phrap, Velvet

MIGS-32

Gene calling method

Prodigal 1.4, GenePRIMP

 

INSDC ID

CP002105

 

Genbank Date of Release

August 9, 2010

 

GOLD ID

Gc01329

 

NCBI project ID

32769

 

Database: IMG-GEBA

2502171194

MIGS-13

Source material identifier

DSM 5501

 

Project relevance

Tree of Life, GEBA

Growth conditions and DNA isolation

A. arabaticum Z-7288T, DSM 5501, was grown anaerobically in DSMZ medium 494 (Acetohalobium medium) [31] at 37°C. DNA was isolated from 0.5–1 g of cell paste using MasterPure Gram Positive DNA Purification Kit (Epicentre MGP04100). Two µl lysozyme and five µl mutanolysin were added to the standard lysis solution for 40min at 37°C followed by 1 hour incubation on ice after the MPC-step.

Genome sequencing and assembly

The genome of A. arabaticum Z-7288T was sequenced at using a combination of Illumina and 454 technologies. An Illumina GAii shotgun library with reads of 483 Mb a 454 Titanium draft library with average read length of 341 bases, and a paired end 454 library with average insert size of 10 kb were generated for this genome. All general aspects of library construction and sequencing can be found at http://www.jgi.doe.gov/. Illumina sequencing data was assembled with VELVET and the consensus sequences were shredded into 1.5 kb overlapped fake reads and assembled together with the 454 data. Draft assemblies were based on 241 Mb 454 draft data, and 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20. The initial assembly contained 72 contigs in one scaffold. The initial 454 assembly was converted into a phrap assembly by making fake reads from the consensus, collecting the read pairs in the 454 paired end library. The Phred/Phrap/Consed software package was used for sequence assembly and quality assessment in the following finishing process [32]. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with gapResolution (http://www.jgi.doe.gov/), Dupfinisher [32], or sequencing cloned bridging PCR fragments with subcloning or transposon bombing (Epicentre Biotechnologies, Madison, WI). Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F. Cheng, unpublished). A total of 292 additional reactions were necessary to close gaps and to raise the quality of the finished sequence. Illumina reads were used to improve the final consensus quality using an in-house developed tool (the Polisher [33],). The completed genome sequences have an error rate of less than 1 in 100,000 bp.

Genome annotation

Genes were identified using Prodigal [34] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMPpipeline [35]. 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 [36].

Genome properties

The genome consists of a 2,469,596 bp long chromosome with a 36.6% GC content (Table 3 and Figure 3). Of the 2,443 genes predicted, 2,353 were protein-coding genes, and 90 RNAs; Seventy-one pseudogenes were also identified. The majority of the protein-coding genes (76.4%) 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 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)

2,469,596

100.00%

DNA coding region (bp)

2,147,537

86.96%

DNA G+C content (bp)

904,645

36.63%

Number of replicons

1

 

Extrachromosomal elements

0

 

Total genes

2,443

100.00%

RNA genes

90

3.67%

rRNA operons

5

 

Protein-coding genes

2,353

96.33%

Pseudo genes

71

3.30%

Genes with function prediction

1,873

76.36%

Genes in paralog clusters

505

20.58%

Genes assigned to COGs

1,861

75.87%

Genes assigned Pfam domains

2,022

82.43%

Genes with signal peptides

378

15.41%

Genes with transmembrane helices

303

12.35%

CRISPR repeats

1

 
Table 4.

Number of genes associated with the general COG functional categories

Code

value

%age

Description

J

133

6.5

Translation, ribosomal structure and biogenesis

A

0

0.0

RNA processing and modification

K

119

5.8

Transcription

L

139

6.8

Replication, recombination and repair

B

2

0.1

Chromatin structure and dynamics

D

26

1.3

Cell cycle control, cell division, chromosome partitioning

Y

0

0.0

Nuclear structure

V

21

1.0

Defense mechanisms

T

88

4.3

Signal transduction mechanisms

M

123

6.0

Cell wall/membrane/envelope biogenesis

N

66

3.2

Cell motility

Z

0

0.0

Cytoskeleton

W

0

0.0

Extracellular structures

U

56

2.8

Intracellular trafficking, secretion, and vesicular transport

O

85

4.2

Posttranslational modification, protein turnover, chaperones

C

150

7.4

Energy production and conversion

G

62

3.0

Carbohydrate transport and metabolism

E

187

9.2

Amino acid transport and metabolism

F

61

30

Nucleotide transport and metabolism

H

144

7.1

Coenzyme transport and metabolism

I

43

2.1

Lipid transport and metabolism

P

106

5.2

Inorganic ion transport and metabolism

Q

19

0.9

Secondary metabolites biosynthesis, transport and catabolism

R

224

11.0

General function prediction only

S

183

9.0

Function unknown

-

582

24.1

Not in COGs

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Maren Schröder (DSMZ) for growing cultures of A. arabaticum. 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 and SI 1352/1-2.

Authors’ Affiliations

(1)
DSMZ - German Collection of Microorganisms and Cell Cultures GmbH
(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

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Copyright

© The Author(s) 2010