Open Access

Complete genome sequence of Desulfomicrobium baculatum type strain (XT)

  • Alex Copeland1,
  • Stefan Spring2,
  • Markus Göker2,
  • Susanne Schneider2,
  • Alla Lapidus1,
  • Tijana Glavina Del Rio1,
  • Hope Tice1,
  • Jan-Fang Cheng1,
  • Susan Lucas1,
  • Feng Chen1,
  • Matt Nolan1,
  • David Bruce1, 3,
  • Lynne Goodwin1, 3,
  • Sam Pitluck1,
  • Natalia Ivanova1,
  • Konstantinos Mavromatis1,
  • Galina Ovchinnikova1,
  • Amrita Pati1,
  • Amy Chen4,
  • Krishna Palaniappan4,
  • Miriam Land1, 5,
  • Loren Hauser1, 5,
  • Yun-Juan Chang1, 5,
  • Cynthia C. Jeffries1, 5,
  • Linda Meincke3,
  • David Sims3,
  • Thomas Brettin1, 3,
  • John C. Detter1, 3,
  • Cliff Han1, 3,
  • Patrick Chain1, 6,
  • Jim Bristow1,
  • Jonathan A. Eisen1, 7,
  • Victor Markowitz4,
  • Philip Hugenholtz1,
  • Nikos C. Kyrpides1 and
  • Hans-Peter Klenk2
Standards in Genomic Sciences20091:1010029

https://doi.org/10.4056/sigs.13134

Published: 20 July 2009

Abstract

Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain XT is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6% (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO2. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the GenomicEncyclopedia ofBacteria andArchaea project.

Keywords

Sulfate reducerGram-negativefree-livingnon-pathogenicfreshwateranaerobemesophile Desulfomicrobiaceae

Introduction

Strain XT (DSM 4028 = CCUG 34229 = VKM B-1378) is the type strain of the species Desulfomicrobium baculatum, which is the type species of the genus Desulfomicrobium. Strain XT was first described as Desulfovibrio baculatus by Rozanova and Nazina [1,2], and later transferred to the novel genus Desulfomicrobium (currently containing seven species) [3] (Figure 1) because several phenotypic traits were not consistent with the definition of the genus Desulfovibrio. In 1998 the species epithet was corrected to D. baculatum [4]. Three accompanying strains have been described in addition to strain XT: Strain H.L21 (DSM 2555) was isolated from anoxic intertidal sediment at the Ems-Dollard Estuary, Netherlands (16S rRNA gene accession AJ277895) [5], strain 5174 (DSM 17142) was isolated from a forest pond near Braunschweig, Germany (16S rRNA gene accession AJ277896) [6], and strain 9974 (DSM 17143) was isolated as a contaminating chemotrophic bacterium from a culture of a green sulfur bacterium designated ’ Chloropseudomonas ethylica’ N2 [6]. These strains were tentatively affiliated with the species D. baculatum based on some phenotypic traits. Although 16S rRNA gene sequence data are now available for two strains, a definitive affiliation of strains to the species Desulfomicrobium requires supplementary DNA-DNA hybridization experiments due to the observed high similarity values of 16S rRNA gene sequences among distinct species of this genus [7]. Other isolates and clones related to the species were isolated from production waters of a low-temperature biodegraded oil reservoir in Canada [8], and wastewater from penicillin G production in China (clone B19 EU234202). Screening of environmental genomic samples and surveys reported at the NCBI BLAST server indicated no closely related phylotypes that can be linked to the species. Here we present a summary classification and a set of features for D. baculatum strain XT (Table 1), together with the description of the complete genomic sequencing and annotation.
Figure 1.

Phylogenetic tree of D. baculatum strain XT and all type strains of species within members of the family Desulfomicrobiaceae, inferred from 1,457 aligned characters [22,23] of the 16S rRNA gene sequence under the maximum likelihood criterion [24]. The tree was rooted with all members from the Desulfonatronaceae, another family in the order Desulfovibrionales. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates if larger than 60%. Strains with a genome-sequencing project registered in GOLD [25] are printed in blue; published genomes in bold.

Table 1.

Classification and general features of D. baculatum XT in accordance to the MIGS recommendations [28]

MIGS ID

Property

Term

Evidence code

 

Current classification

Domain Bacteria

 
 

Phylum Proteoobacteria

 
 

Class Deltaproteobacteria

TAS [29]

 

Order Desulfovibrionales

TAS [29]

 

Family Desulfomicrobiaceae

TAS [29]

 

Genus Desulfomicrobium

TAS [1]

 

Species Desulfomicrobium baculatum

TAS [1]

 

Type strain X

TAS [1]

 

Gram stain

negative

TAS [1]

 

Cell shape

rod-shaped

TAS [1]

 

Motility

motile, single polar flagellum

TAS [1]

 

Sporulation

non-sporulating

TAS [1]

 

Temperature range

mesophilic

TAS [1]

 

Optimum temperature

28–37°C

TAS [1]

 

Salinity

10 g NaCl/I

TAS [1]

MIGS-22

Oxygen requirement

strictly anerobic

TAS [1]

 

Carbon source

lactate, pyruvate, malate, fumarate

TAS [1,8]

 

Energy source

formate, H2

TAS [1]

MIGS-6

Habitat

freshwater to brackish anoxic sediments

TAS [1]

MIGS-15

Biotic relationship

free-living

NAS

MIGS-14

Pathogenicity

none

NAS

 

Biosafety level

1

TAS [30]

 

Isolation

water-saturated manganese carbonate ore

TAS [1]

MIGS-4

Geographic location

not reported

 

MIGS-5

Sample collection time

1975 or earlier

IDA

MIGS-4.1

Latitude - Longitude

not reported

 

MIGS-4.2

 

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

Classification and features

Cells of D. baculatum strain XT are short rods with rounded ends of 0.6 × 1–2 µm (Figure 2). Cells stain Gram-negative, are motile by a single polar flagellum, and do not form endospores. The metabolism is strictly anaerobic and can be respiratory or fermentative [3,9]. Temperature range for growth is 2–41°C (optimum 28–37°C) and NaCl concentrations of 0–6% (w/v) are tolerated (optimum 1% w/v). Sulfate, sulfite and thiosulfate are used as electron acceptors and are reduced to H2S. Nitrate is not reduced. Simple organic compounds are incompletely oxidized to acetate [3]. Malate, fumarate and pyruvate can be fermented with succinate and acetate as end products. Carbohydrates are not fermented. Vitamins are not required for growth [3]. D. baculatum strain 9974 (DSM 1743) is also able to use ethanol as a substrate [10] and sulfur as an electron acceptor [6]. The use of ethanol as an electron donor for sulfate respiration depends on supplementing the medium with the trace elements tungstate or molybdate [10]. Sulfate uptake in symport with sodium ions has been shown in strain 9974, unlike in other fresh water sulfate reducers which use protons [11]. Distinctive features of D. baculatum strain XT are: (i) NaCl is not required for growth [3], (ii) fermentation of fumarate and malate to succinate and acetate is preferred against utilization of these substrates as electron donors for sulfate reduction [9], (iii) sulfur is not used as an electron acceptor and (IV) molecular nitrogen can be assimilated [3].
Figure 2.

Scanning electron micrograph of D. baculatum XT (Manfred Rohde, Helmholtz Centre for Infection Biology, Braunschweig)

A desulfoviridin-type dissimilatory sulfite reductase, which is a hallmark feature of the genus Desulfovibrio, is absent in strain XT, however a sulfite reductase of the desulforubidin-type was reported for strain 9974 [12]. Cells of D. baculatum strain XT contain c- and b-type cytochromes [3]. The tetraheme cytochrome c3 of strain 9974, which is thought to play a role in sulfur reduction and the coupling of electron transfer to hydrogenases, has been analyzed in some detail using advanced biophysical methods [1315]. Strain 9974 also contains several distinct [NiFeSe] hydrogenases that are located in different cellular compartments [16]. The crystal structure of the periplasmic [NiFeSe] hydrogenase of this strain has been determined [17] and it is proposed that the selenium ion in the active center plays a role in the oxygen-tolerant hydrogen production of this enzyme, which distinguishes it from most [NiFe] hydrogenases [18]. An active selenocysteine system for usage of the 21st amino acid has been studied in detail for D. baculatum strain 9974 [1921]. Pyridoxal-5′-phosphate, the prosthetic group of selenocysteine synthases, is bound to a distinct lysine residue (Lys295) within the active site of the enzyme of this strain [20].

Figure 1 shows the phylogenetic neighborhood of D. baculatum strain XT in a 16S rRNA based tree. Analysis of the two 16S rRNA gene sequences in the genome of strain XT indicated that the two genes are almost identical (1 bp difference), and that both genes differed by one nucleotide from the previously published 16S rRNA sequence generated from DSM 4028 (AJ277894).

Chemotaxonomy

The cellular fatty acid patterns of D. baculatum strain XT and the accompanying strains 5174, 9974 and H.L21 [26] were found to be dominated by anteiso- (ai) and iso-methyl branched unsaturated and saturated fatty acids. The most abundant fatty acid is iso-17:1 cis7 (24.2-28.6%), followed by 18:1 cis11 (6.4-12.2%), iso-15:0 (8.2-11.6%), ai-17:0 (4.5-8.3%), ai-15:0 (5.2-7.7%), 18:0 (3.9-7.1%) and 16:0 (3.6-5.7%). Less abundant fatty acids are iso-15:1 (3.1–4.0%), 16:1 cis7 (2.2–5.0%), ai-17:1 (2.4–4.1%), 18:1 cis9 (2.6–4.3%), iso-16:1 (0.5–2.2%), and 17:0 (0.2-0.3%). Branched chain, hydroxylated fatty acids are also present, 3-OH iso-15:0 (1.4–2.4%), 3-OH ai-15:0 (0.7–1.2%), and 3-OH iso-17:0 (1.2–2.2%), which may be derived from a lipopolysaccharide. The polar lipid composition of D. baculatum strain XT has not been investigated. The respiratory quinone composition of D. baculatum strain XT has also not been investigated, but the presence of MK-6 has been reported in D. macestii and D. norvegicum [7,27].

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position, and is part of the Genomic Encyclopedia of Bacteria and Archaea project. The genome project is deposited in the Genomes OnLine Database [25] and the complete genome sequence (CP001629) 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 8 kb Sanger pMCL200 library and

one 454 pyrosequence standard library

MIGS-29

Sequencing platforms

ABI3730, 454 GS FLX

MIGS-31.2

Sequencing coverage

6.8x Sanger; 30.4x pyrosequence

MIGS-20

Assemblers

Newbler version 1.1.02.15, phrap

MIGS-32

Gene calling method

Prodigal

 

INSDC / Genbank ID

CP001629

 

Genbank Date of Release

not yet

 

GOLD ID

Gc01026

 

NCBI project ID

29527

 

Database: IMG-GEBA

2501416908

MIGS-13

Source material identifier

DSM 4028

 

Project relevance

Tree of Life, GEBA

Growth conditions and DNA isolation

D. baculatum strain XT (DSM 4028) was grown in DSMZ medium 63 at 30°C. DNA was isolated from 1–1.5 g of cell paste using Qiagen Genomic 500 DNA Kit (Qiagen, Hilden, Germany) with a modified protocol for cell lysis, adding 100 µl lysozyme; 500 µl achromopeptidase, lysostaphin, mutanolysin, each, to standard lysis solution, but reducing proteinase K to 160µl, only. Incubation over night at 35°C.

Genome sequencing and assembly

The genome was sequenced using a combination of Sanger and 454 sequencing platforms. All general aspects of library construction and sequencing performed at the JGI can be found at the JGI website. 454 Pyrosequencing reads were assembled using the Newbler assembler version 1.1.02.15 (Roche). Large Newbler contigs were broken into 4,375 overlapping fragments of 1,000 bp and entered into assembly as pseudo-reads. The sequences were assigned quality scores based on Newbler consensus q-scores with modifications to account for overlap redundancy and to adjust inflated q-scores. A hybrid 454/Sanger assembly was made using the parallel phrap assembler (High Performance Software, LLC). Possible mis-assemblies were corrected with Dupfinisher or transposon bombing of bridging clones [32]. Gaps between contigs were closed by editing in Consed, custom primer walk or PCR amplification. 731 Sanger finishing reads were produced to close gaps, to resolve repetitive regions, and to raise the quality of the finished sequence. The error rate of the completed genome sequence is less than 1 in 100,000. Together all sequence types provided 37.2 x coverage of the genome.

Genome annotation

Genes were identified using Prodigal [33] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using JGI’s GenePRIMP pipeline [34]. 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 were performed within the Integrated Microbial Genomes (IMG-ER) platform. [35]

Genome properties

The genome is 3,942,657 bp long and comprises one circular chromosome with a 58.7% GC content (Table 3 and Figure 3). Of the 3,565 genes predicted, 3,494 were protein coding genes, and 71 RNAs; 58 pseudogenes were also identified. 74.9% of the genes were assigned a putative function while the remaining ones were annotated as hypothetical proteins. The properties and the statistics of the genome are summarized in Table 3. 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)

3,942,657

 

DNA Coding region (bp)

3,572,336

90.61%

DNA G+C content (bp)

2,312,250

58.65%

Number of replicons

1

 

Extrachromosomal elements

0

 

Total genes

3565

 

RNA genes

71

2.02%

rRNA operons

2

 

Protein-coding genes

3494

97.98%

Pseudo genes

58

1.63%

Genes with function prediction

2675

75.01%

Genes in paralog clusters

357

12.82%

Genes assigned to COGs

2689

75.41%

Genes assigned Pfam domains

2688

75.38%

Genes with signal peptides

723

20.27%

Genes with transmembrane helices

897

25.15%

CRISPR repeats

0

 
Table 4.

Number of genes associated with the 21 general COG functional categories

Code

Value

%

Description

J

166

4.8

Translation, ribosomal structure and biogenesis

A

0

0.0

RNA processing and modification

K

154

4.4

Transcription

L

116

3.3

Replication, recombination and repair

B

3

0.1

Chromatin structure and dynamics

D

35

1.0

Cell cycle control, mitosis and meiosis

Y

0

0.0

Nuclear structure

V

38

1.1

Defense mechanisms

T

325

9.3

Signal transduction mechanisms

M

221

6.3

Cell wall/membrane biogenesis

N

108

3.1

Cell motility

Z

0

0.0

Cytoskeleton

W

0

0.0

Extracellular structures

U

82

2.3

Intracellular trafficking and secretion

O

122

3.5

Posttranslational modification, protein turnover, chaperones

C

241

6.9

Energy production and conversion

G

126

3.6

Carbohydrate transport and metabolism

E

266

7.6

Amino acid transport and metabolism

F

68

1.9

Nucleotide transport and metabolism

H

135

3.9

Coenzyme transport and metabolism

I

52

1.5

Lipid transport and metabolism

P

137

3.9

Inorganic ion transport and metabolism

Q

34

1.0

Secondary metabolites biosynthesis, transport and catabolism

R

319

9.1

General function prediction only

S

221

6.3

Function unknown

-

805

23.0

Not in COGs

Declarations

Acknowledgements

We would like to gratefully acknowledge the help of Maren Schroeder (DSMZ) for growing D. baculatum cultures. 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 as well as German Research Foundation (DFG) INST 599/1-1.

Authors’ Affiliations

(1)
DOE Joint Genome Institute
(2)
DSMZ - German Collection of Microorganisms and Cell Cultures GmbH
(3)
Bioscience Division, Los Alamos National Laboratory
(4)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory
(5)
Oak Ridge National Laboratory
(6)
Lawrence Livermore National Laboratory
(7)
University of California Davis Genome Center

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Copyright

© The Author(s) 2009