Open Access

Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2232 from Karijini National Park, Australia

  • Robert Walker1,
  • Elizabeth Watkin1,
  • Rui Tian2,
  • Lambert Bräu3,
  • Graham O’Hara2,
  • Lynne Goodwin4,
  • James Han5,
  • Tatiparthi Reddy5,
  • Marcel Huntemann5,
  • Amrita Pati5,
  • Tanja Woyke5,
  • Konstantinos Mavromatis5,
  • Victor Markowitz6,
  • Natalia Ivanova5,
  • Nikos Kyrpides5 and
  • Wayne Reeve2Email author
Standards in Genomic Sciences20149:9031168

https://doi.org/10.4056/sigs.5018795

Published: 15 June 2014

Abstract

Burkholderia sp. strain WSM2232 is an aerobic, motile, Gram-negative, non-spore-forming acid-tolerant rod that was trapped in 2001 from acidic soil collected from Karijini National Park (Australia) using Gastrolobium capitatum as a host. WSM2232 was effective in nitrogen fixation with G. capitatum but subsequently lost symbiotic competence during long-term storage. Here we describe the features of Burkholderia sp. strain WSM2232, together with genome sequence information and its annotation. The 7,208,311 bp standard-draft genome is arranged into 72 scaffolds of 72 contigs containing 6,322 protein-coding genes and 61 RNA-only encoding genes. The loss of symbiotic capability can now be attributed to the loss of nodulation and nitrogen fixation genes from the genome. This rhizobial genome is one of 100 sequenced as part of the DOE Joint Genome Institute 2010 Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) project.

Keywords

root-nodule bacterianitrogen fixationrhizobia Betaproteobacteria

Introduction

Burkholderia spp. are a diverse group of organisms capable of thriving in diverse environments with many forming mutualistic associations with organisms such as fungi and plants [1]. The development in the 1960s and 1970s of a rational classification system for Pseudomonas species resulted in proposals to give different generic names to taxonomically distinct groups. The organisms previously classified within Pseudomonas rRNA similarity Group II were transferred into the new genus Burkholderia [2]. All described Burkholderia species at that time were phytopathogenic, or opportunistic mammalian pathogens with the type species B. cepacia becoming a growing community health concern in immunocompromised and cystic fibrosis patients [35]. With the isolation of more Burkholderia spp., it has become apparent that the genus is a far more complex mix, with the isolation of numerous soil-inhabiting species capable of degrading heavy metals and environmental contaminants [6,7]. Further reports identified plant growth promoting (PGP) species and legume microsymbionts. This led to a paradigm shift in rhizobiology and resulted in numerous new novel Burkholderia spp. descriptions [810].

Most PGP, or legume microsymbiont species of Burkholderia have been isolated in South America from Mimosa spp. or South Africa from Papilionoideae legumes and until recently, B. graminis was the only described PGP bacterial species isolated from Australia in the maize rhizosphere [11]. Australian Burkholderia have been isolated as nodule occupants from some Acacia spp., [12] however none have been authenticated or tested for the nodulation of other legumes. There is little data regarding the symbiosis between Burkholderia and legumes in Australia compared to South Africa and South America. Burkholderia sp. WSM2232 was trapped from acidic soil (pHCaCl2 4.8) collected from Karijini National Park (Western Australia) using Gastrolobium capitatum as a host. Sites where the soil pH was higher (pHCaCl2 >7) did not contain any Burkholderia symbionts but did contain numerous Bradyrhizobium and Rhizobium spp. (Watkin, unpublished). Soil pH is an edaphic variable that controls microbial biogeography [13] and the acid tolerance of Burkholderia has been shown to account for the biogeographical distribution of this genus [14].

The symbiotic capacity of WSM2232 was authenticated in axenic glasshouse trials using inoculation of G. capitatum grown in nitrogen free conditions. Inoculated plants nodulated by WSM2232 produced significantly greater mass than uninoculated controls. WSM2232 was subcultured and placed in long-term storage in frozen laboratory glycerol stocks. Isolate revival and inoculation onto endemic Australian legumes failed to elicit a symbiotic response. The reason for the loss of the symbiotic phenotype has, until now, not been identified.

The genome of Burkholderia strain WSM2232 is one of two Australian Burkholderia genomes (the other being that of WSM2230 (GOLD ID Gi08831)) that have now been sequenced through the Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria (GEBA-RNB) program. Here we present a preliminary description of the general features of Burkholderia sp. WSM2232 together with its genome sequence and annotation. The absence of nodulation genes within this genome explains the nodulation minus symbiotic phenotype of the laboratory cultured strain. The genomes of WSM2232 and WSM2230 will be an important resource to identify the processes enabling such isolates to adapt to the infertile, highly acidic soils that dominate the Australian landscape.

Classification and features

Burkholderia sp. strain WSM2232 is a motile, non-sporulating, non-encapsulated, Gram-negative rod in the order Burkholderiales of the class Betaproteobacteria. The rod-shaped form varies in size with dimensions of 0.25–0.5 µm for width and 0.5–2.0 µm for length (Figure 1A and 1B).
Figure 1.

Images of Burkholderia sp. strain WSM2232using scanning (A) and transmission (B) electron microscopy.

It is fast growing, forming colonies within 1–2 days when grown on LB agar [15] devoid of NaCl and within 3–4 days when grown on half strength Lupin Agar (½LA) [16], tryptone-yeast extract agar (TY) [17] or a modified yeast-mannitol agar (YMA) [18] at 28°C. Colonies on ½LA are opaque, slightly domed and moderately mucoid with smooth margins.

Burkholderia sp. WSM2232 falls into a large clade containing PGP, bioremediation and legume microsymbiont species, and WSM2232 demonstrates PGP phenotypes including phosphate solubilization and hydroxamate-like siderophore production and is acid tolerant with growth in the pH range of 4.5–9.0 (Walker, unpublished).

Minimum Information about the Genome Sequence (MIGS) is provided in Table 1. Figure 2 shows the phylogenetic neighborhood of Burkholderia sp. strain WSM2232 in a 16S rRNA sequence based tree. This strain shares 99% (1352/1364 bp) sequence identity to the 16S rRNA gene of the sequenced strain Burkholderia sp. WSM2230 (Gi08831).
Figure 2.

Phylogenetic tree showing the relationship of Burkholderia sp. strain WSM2232 (shown in bold print) to other members of the order Burkholderiales based on aligned sequences of the 16S rRNA gene (1,242 bp internal region). All sites were informative and there were no gap-containing sites. Phylogenetic analyses were performed using MEGA [29], version 5. The tree was built using the Maximum-Likelihood method with the General Time Reversible model [30]. Bootstrap analysis [31] with 500 replicates was performed to assess the support for the clusters. Type strains are indicated with a superscript T. Brackets after the strain name contain a DNA database accession number and/or a GOLD ID (beginning with the prefix G) for a sequencing project registered in GOLD [32]. Published genomes are indicated with an asterisk.

Table 1.

Classification and general features of Burkholderia sp. strain WSM2232 according to the MIGS recommendations [19]

MIGS ID

Property

Term

Evidence codea

 

Current classification

Domain Bacteria

TAS [20]

 

Phylum Proteobacteria

TAS [21]

 

Class Betaproteobacteria

TAS [22,23]

 

Order Burkholderiales

TAS [23,24]

 

Family Burkholderiaceae

TAS [23,25]

 

Genus Burkholderia

TAS [2,26,27]

 

Species Burkholderia sp.

IDA

 

Strain WSM2232

IDA

 

Gram stain

Negative

IDA

 

Cell shape

Rod

IDA

 

Motility

Motile

IDA

 

Sporulation

Non-sporulating

NAS

 

Temperature range

Mesophile

IDA

 

Optimum temperature

30°C

IDA

 

Salinity

Non-halophile

IDA

MIGS-22

Oxygen requirement

Aerobic

IDA

 

Carbon source

Varied

IDA

 

Energy source

Chemoorganotroph

NAS

MIGS-6

Habitat

Soil, root nodule, on host

IDA

MIGS-15

Biotic relationship

Free living, symbiotic

IDA

MIGS-14

Pathogenicity

Non-pathogenic

IDA

 

Biosafety level

1

TAS

 

Isolation

Root nodule of Gastrolobium capitatum

IDA

MIGS-4

Geographic location

Karijini National Park, Australia

IDA

MIGS-5

Soil collection date

September, 2001

IDA

MIGS-4.1

Latitude

117.99

IDA

MIGS-4.2

Longitude

−22.45

IDA

MIGS-4.3

Depth

0-10 cm

IDA

MIGS-4.4

Altitude

Not recorded

IDA

aEvidence codes - IDA: Inferred from Direct Assay; 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 [28].

Symbiotaxonomy

Burkholderia sp. WSM2232 formed nodules (Nod+) and fixed N2 (Fix+) with G. capitatum when first isolated and was Nod- on various other Australian legumes and Mimosa pudica (Table 2). However, after long-term storage and subsequent culture, it failed to effectively nodulate G. capitatum.
Table 2.

Compatibility of Burkholderia sp. WSM2232 with nine legume species for nodulation (Nod) and N2-Fixation (Fix).

Species Name

Common Name

Growth Type

Nod

Fix

Reference

Gastrolobium capitatum a

Bitter Pea

Perennial

+1

+1

IDAc

Gastrolobium capitatum b

Bitter Pea

Perennial

IDA

Kennedia coccinea

Coral Vine

Perennial

IDA

Swainsona formosa

Sturts Desert Pea

Annual

IDA

Indigofera trita

Annual

IDA

Oxylobium robustum

Shaggy Pea

Perennial

IDA

Acacia acuminata

Jam Wattle

Perennial

IDA

Acacia paraneura

Weeping Mulga

Perennial

IDA

Acacia stenophylla

Perennial

IDA

Mimosa pudica

Sensitive Plant

Perennial

IDA

aresult obtained from trapping experiment b authentication result following long-term storage. cEvidence codes - IDA: Inferred from Direct Assay from www.geneontology.org/GO.evidence.shtml of the Gene Ontology project [28].

Phenotype Microarray

Strain WSM2232 was assayed using the Biolog Phenotype Microarray® plates (PM1 to 3) system testing 190 carbon and 95 nitrogen compounds. Plates were purchased from Biolog and tests were carried out per manufacturer’s instructions. The irreversible reduction of tetrazolium dye to formazan is used in this system to report on active metabolism [33]. The results obtained from the colorimetric assay are shown in Table 3.
Table 3.

Reduction of tetrazolium dye by NADH produced by respiring cells of Burkholderia sp. WSM2232 in the Biolog Phenotype Microarray

PM1 plate Compound

 

PM2 plate Compound

 

PM3 plate Compound

 

L-Arabinose

+

Chondroitin Sulfate C

Ammonia

+

N-Acetyl-D Glucosamine

+

α-Cyclodextrin

Nitrite

+

D-Saccharic Acid

+

β-Cyclodextrin

Nitrate

+

Succinic Acid

+

γ-Cyclodextrin

Urea

+

D-Galactose

+

Dextrin

+

Biuret

L-Aspartic Acid

+

Gelatin

L-Alanine

+

L-Proline

+

Glycogen

L-Arginine

+

D-Alanine

+

Inulin

L-Asparagine

+

D-Trehalose

+

Laminarin

L-Aspartic Acid

+

D-Mannose

+

Mannan

L-Cysteine

+

Dulcitol

+

Pectin

L-Glutamic Acid

+

D-Serine

N-Acetyl-D-Galactosamine

+

L-Glutamine

+

D-Sorbitol

+

N-Acetyl-Neuraminic Acid

Glycine

+

Glycerol

+

β-D-Allose

L-Histidine

+

L-Fucose

+

Amygdalin

L-Isoleucine

+

D-Glucuronic Acid

+

D-Arabinose

+

L-Leucine

+

D-Gluconic Acid

+

D-Arabitol

+

L-Lysine

+

D,L-α-Glycerol-Phosphate

+

L-Arabitol

+

L-Methionine

+

D-Xylose

+

Arbutin

L-Phenylalanine

+

L-Lactic Acid

+

2-Deoxy-D-Ribose

+

L-Proline

+

Formic Acid

+

I-Erythritol

L-Serine

+

D-Mannitol

+

D-Fucose

+

L-Threonine

+

L-Glutamic Acid

+

3-0-β-D-Galacto-pyranosyl-DArabinose

L-Tryptophan

+

D-Glucose-6-Phosphate

+

Gentiobiose

L-Tyrosine

+

D-Galactonic Acid-γ-Lactone

+

L-Glucose

L-Valine

+

D,L-Malic Acid

+

Lactitol

D-Alanine

+

D-Ribose

+

D-Melezitose

D-Asparagine

+

Tween 20

+

Maltitol

D-Aspartic Acid

+

L-Rhamnose

+

α-Methyl-D-Glucoside

D-Glutamic Acid

+

D-Fructose

+

β-Methyl-D-Galactoside

+

D-Lysine

+

Acetic Acid

+

3-Methyl Glucose

D-Serine

+

α-D-Glucose

+

β-Methyl-D-Glucuronic Acid

D-Valine

+

Maltose

α-Methyl-D-Mannoside

L-Citrulline

+

D-Melibiose

β-Methyl-D-Xyloside

L-Homoserine

+

Thymidine

Palatinose

L-Ornithine

+

L-Asparagine

+

D-Raffinose

N-Acetyl-D,L-Glutamic Acid

+

D-Aspartic Acid

Salicin

N-Phthaloyl-L-Glutamic Acid

D-Glucosaminic Acid

+

Sedoheptulosan

L-Pyroglutamic Acid

+

1,2-Propanediol

L-Sorbose

Hydroxylamine

+

Tween 40

+

Stachyose

Methylamine

+

α-Keto-Glutaric Acid

+

D-Tagatose

+

N-Amylamine

+

α-Keto-Butyric Acid

+

Turanose

+

N-Butylamine

+

α-Methyl-D-Galactoside

Xylitol

+

Ethylamine

α-D-Lactose

N-Acetyl-D-Glucosaminitol

+

Ethanolamine

+

Lactulose

+

γ-Amino Butyric Acid

+

Ethylenediamine

Sucrose

δ-Amino Valeric Acid

+

Putrescine

+

Uridine

+

Butyric Acid

+

Agmatine

L-Glutamine

+

Capric Acid

Histamine

M-Tartaric Acid

+

Caproic Acid

+

β-Phenylethylamine

+

D-Glucose-1-Phosphate

+

Citraconic Acid

+

Tyramine

D-Fructose-6-Phosphate

+

Citramalic Acid

+

Acetamide

+

Tween 80

+

D-Glucosamine

+

Formamide

+

α-Hydroxy Glutaric Acid-γ-Lactone

2-Hydroxy Benzoic Acid

Glucuronamide

+

α-Hydroxy Butyric Acid

+

4-Hydroxy Benzoic Acid

+

D,L-Lactamide

+

β-Methyl-D-Glucoside

β-Hydroxy Butyric Acid

+

D-Glucosamine

+

Adonitol

+

γ-Hydroxy Butyric Acid

+

DGalactosamine

+

Maltotriose

α-Keto Valeric Acid

DMannosamine

+

2-Deoxy Adenosine

Itaconic Acid

N-Acetyl-D-Glucosamine

+

Adenosine

+

5-Keto-D-Gluconic Acid

N-Acetyl-D-Galactosamine

Glycy-L-Aspartic Acid

+

D-Lactic Acid Methyl Ester

+

N-Acetyl-D-Mannosamine

Citric Acid

+

Malonic Acid

+

Adenine

+

M-Inositol

+

Melibionic Acid

+

Adenosine

+

D-Threonine

Oxalic Acid

+

Cytidine

+

Fumaric Acid

+

Oxalomalic Acid

+

Cytosine

+

Bromo Succinic Acid

+

Quinic Acid

+

Guanine

Propionic Acid

+

D-Ribono-1,4-Lactone

Guanosine

+

Mucic Acid

+

Sebacic Acid

+

Thymine

+

Glycolic Acid

Sorbic Acid

+

Thymidine

Glyoxylic Acid

+

Succinamic Acid

+

Uracil

+

D-Cellobiose

D-Tartaric Acid

+

Uridine

+

Inosine

+

L-Tartari c Acid

+

Inosine

+

Glycyl-L-Glutamic Acid

+

Acetamide

Xanthine

+

Tricarballylic Acid

+

L-Alaninamide

+

Xanthosine

+

L-Serine

+

N-Acetyl-L-Glutamic Acid

+

Uric Acid

+

L-Threonine

+

L-Arginine

+

Alloxan

+

L-Alanine

+

Glycine

Allantoin

+

L-Allnyl-Glycine

+

L-Histidine

+

Parabanic Acid

+

Acetoacetic Acid

+

L-Homoserine

+

D,L-α-Amino-N-Butyric Acid

+

N-Acetyl-β-D-Mannosamine

Hydroxy-L-Proline

+

γ-Amino-N-Butyric Acid

+

Mono Methyl Succinate

+

L-Isoleucine

+

ε-Amino-N-Caproic Acid

Methyl Pyruvate

+

L-Leucine

+

D,L-α-Amino-Caprylic Acid

D-Malic Acid

+

L-Lysine

+

δ-Amino-N-Valeric Acid

+

L-Malic Acid

+

L-Methionine

α-Amino-N-Valeric Acid

+

Glycyl-L-Proline

+

L-Ornithine

+

Ala-Asp

+

p-Hydroxy Phenyl Acetic Acid

+

L-Phenylalanine

+

Ala-Gln

+

m-Hydroxy Phenyl Acetic Acid

L-Pyroglutamic Acid

+

Ala-Glu

+

Tyramine

L-Valine

+

Ala-Gly

+

D-Psicose

D,L-Carnitine

+

Ala-His

+

L-Lyxose

+

Sec-Butylamine

Ala-Leu

+

Glucuronamide

D,L-Octopamine

Ala-Thr

+

Pyruvic Acid

+

Putrescine

Gly-Asn

+

L-Galactonic Acid-γ-Lactone

+

Dihydroxy Acetone

Gly-Gln

+

D-Galacturonic Acid

+

2,3-Butanediol

+

Gly-Glu

+

Phenylethylamine

+

2,3-Butanone

+

Gly-Met

+

2-Aminoethanol

+

3-Hydrox y-2-Butanone

Met-Ala

+

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its environmental and agricultural relevance to issues in global carbon cycling, alternative energy production, and biogeochemical importance, and is part of the Community Sequencing Program at the U.S. Department of Energy, Joint Genome Institute (JGI) for projects of relevance to agency missions. The genome project is deposited in the Genomes OnLine Database [32] and a standard-draft genome sequence in IMG. Sequencing, finishing and annotation were performed by the JGI. A summary of the project information is shown in Table 4.
Table 4.

Genome sequencing project information for Burkholderia sp. WSM2232.

MIGS ID

Property

Term

MIGS-31

Finishing quality

Standard draft

MIGS-28

Libraries used

One Illumina fragment library

MIGS-29

Sequencing platforms

Illumina HiSeq 2000

MIGS-31.2

Sequencing coverage

Illumina: 255×

MIGS-30

Assemblers

Velvet version 1.1.04; Allpaths-LG version r37348

MIGS-32

Gene calling methods

Prodigal 1.4

 

GOLD ID

Gi08832a

 

NCBI project ID

182741

 

Database: IMG

2508501125b

 

Project relevance

Symbiotic N2 fixation, agriculture

Growth conditions and DNA isolation

Burkholderia sp. strain WSM2232 was cultured to mid logarithmic phase in 60 ml of TY rich medium on a gyratory shaker at 28°C [34]. DNA was isolated from the cells using a CTAB (Cetyl trimethyl ammonium bromide) bacterial genomic DNA isolation method (http://my.jgi.doe.gov/general/index.html).

Genome sequencing and assembly

The genome of Burkholderia sp. strain WSM2232 was sequenced at the Joint Genome Institute (JGI) using Illumina technology [35]. An Illumina standard shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform, which generated 12,244,888, reads totaling 1,837 Mbp.

All general aspects of library construction and sequencing performed at the JGI can be found at http://my.jgi.doe.gov/general/index.html. All raw Illumina sequence data was passed through DUK, a filtering program developed at JGI, which removes known Illumina sequencing and library preparation artifacts (Mingkun, L., Copeland, A. and Han, J., unpublished). The following steps were then performed for assembly:
  1. (1)

    Filtered Illumina reads were assembled using Velvet [36] (version 1.1.04)

     
  2. (2)

    1–3 Kbp simulated paired end reads were created from Velvet contigs using wgsim (https://github.com/lh3/wgsim)

     
  3. (3)

    Illumina reads were assembled with simulated read pairs using Allpaths-LG [37] (version r37348).

     
Parameters for assembly steps were:
  1. 1)

    Velvet —v —s 51 —e 71 —i 2 —t 1 —f “-shortPaired -fastq $FASTQ” —o “-ins_length 250 -min_contig_lgth 500”)

     
  2. 2)

    wgsim (-e 0 -1 76 -2 76 -r 0 -R 0 -X 0)

     
  3. 3)

    Allpaths-LG (STD_1, project, assembly, fragment, 1,200,35,,,inward,0,0 SIMREADS, project,assembly,jumping,1,,,3000,300,inward,0,0).

     

The final draft assembly contained 72 contigs in 72 scaffolds. The total size of the genome is 7.2 Mbp and the final assembly is based on 1,837 Mbp of Illumina data, which provides an average 255× coverage of the genome.

Genome annotation

Genes were identified using Prodigal [38] as part of the DOE-JGI annotation pipeline [39], followed by a round of manual curation using the JGI GenePrimp pipeline [40]. 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 tRNAScanSE tool [41] was used to find tRNA genes, whereas ribosomal RNA genes were found by searches against models of the ribosomal RNA genes built from SILVA [42]. Other non-coding RNAs such as the RNA components of the protein secretion complex and the RNase P were identified by searching the genome for the corresponding Rfam profiles using INFERNAL (http://infernal.janelia.org). Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes (IMG-ER) platform [43].

Genome properties

The genome is 7,208,311 nucleotides 63.11% GC content (Table 5) and comprised of 72 scaffolds (Figure 3) of 72 contigs. From a total of 6,383 genes, 6,322 were protein encoding and 61 RNA only encoding genes. The majority of genes (80.90%) were assigned a putative function whilst the remaining genes were annotated as hypothetical. The distribution of genes into COGs functional categories is presented in Table 6.
Figure 3.

Graphical map of the four largest scaffolds genome for the genome of Burkholderia sp. strain WSM2232. From bottom to the top of each scaffold: Genes on forward strand (color by COG categories as denoted by the IMG platform), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, sRNAs red, other RNAs black), GC content, GC skew.

Table 5.

Genome Statistics for Burkholderia sp. strain WSM2232

Attribute

Value

% of Totala

Genome size (bp)

7,208,311

100.00

DNA coding region (bp)

6,203,174

86.06

DNA G+C content (bp)

4,548,885

63.11

Number of scaffolds

72

 

Number of contigs

72

 

Total gene

6,383

100.00

RNA genes

61

0.96

rRNA operonsb

1

0.02

Protein-coding genes

6,322

99.04

Genes with function prediction

5,164

80.90

Genes assigned to COGs

5,151

80.70

Genes assigned Pfam domains

5,425

84.99

Genes with signal peptides

645

10.10

Genes with transmembrane helices

1,497

23.45

CRISPR repeats

1

 

a4 copies of 5S, 2 copies of 16S and 1 copy of 23S rRNA.

Table 6.

Number of protein coding genes of Burkholderia sp. strain WSM2232 associated with the general COG functional categories.

Code

Value

%agea

Description

J

474

8.15

Carbohydrate transport and metabolism

A

3

0.05

RNA processing and modification

K

151

2.60

Replication, recombination and repair

L

559

9.61

Transcription

B

1

0.0

Chromatin structure and dynamics

D

42

0.72

Cell cycle control, cell division and chromosome partioning

Y

0

0.0

Nuclear structure

V

0

0.0

Defense mechcanism

T

318

5.47

Signal transduction mechanisms

M

371

6.38

Cell wall/membrane/envelope biogenesis

N

125

2.15

Cell motility

Z

0

0.00

Cytoskeleton

W

2

0.03

Extracellular structures

U

154

2.65

Intracellular trafficking, secretion, and vesicular transport

O

183

3.15

Posttranslational modification, protein turnover, chaperones

C

384

6.60

Energy production conversion

G

194

3.34

Translation, ribosomal structure and biogenesis

E

569

9.79

Amino acid transport and metabolism

F

100

1.72

Nucleotide transport and metabolism

H

213

3.66

Coenzyme transport and metabolism

I

277

4.76

Lipid transport and metabolism

P

269

4.63

Inorganic ion transport and metabolism

Q

199

3.42

Secondary metabolite biosynthesis, transport and catabolism

R

673

11.58

General function prediction only

S

500

8.60

Function unknown

-

1,232

19.30

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.

Authors’ Affiliations

(1)
School of Biomedical Sciences, Faculty of Health Sciences, Curtin University
(2)
Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University
(3)
School of Life and Environmental Sciences, Deakin University
(4)
Los Alamos National Laboratory
(5)
DOE Joint Genome Institute
(6)
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory

References

  1. Compant S, Nowak J, Coenye T, Clement C, Barka EA. Diversity and occurrence of Burkholderia spp. in the natural environment. FEMS Microbiol Rev 2008; 32:607–626. http://dx.doi.org/10.1111/j.1574-6976.2008.00113.x PubMedView ArticlePubMedGoogle Scholar
  2. Yabuuchi E, Kosako Y, Oyaizu H, Yano I, Hotta H, Hashimoto Y, Ezaki T, Arakawa M. Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov. Microbiol Immunol 1992; 36:1251–1275. PubMedView ArticlePubMedGoogle Scholar
  3. Vial L, Chapalain A, Groleau MC, Deziel E. The various lifestyles of the Burkholderia cepacia complex species: a tribute to adaptation. Environ Microbiol 2011; 13:1–12. http://dx.doi.org/10.1111/j.1462-2920.2010.02343.x PubMedView ArticlePubMedGoogle Scholar
  4. Govan JR, Hughes JE, Vandamme P. Burkholderia cepacia: medical, taxonomic and ecological issues. J Med Microbiol 1996; 45:395–407. http://dx.doi.org/10.1099/00222615-45-6-395 PubMedView ArticlePubMedGoogle Scholar
  5. Vandamme P, Holmes B, Vancanneyt M, Coenye T, Hoste B, Coopman R, Revets H, Lauwers S, Gillis M, Kersters K, et al. Occurrence of multiple genomovars of Burkholderia cepacia in cystic fibrosis patients and proposal of Burkholderia multivorans sp. nov. Int J Syst Bacteriol 1997; 47:1188–1200. http://dx.doi.org/10.1099/00207713-47-4-1188View ArticlePubMedGoogle Scholar
  6. Chain PS, Denef VJ, Konstantinidis KT, Vergez LM, Agullo L, Reyes VL, Hauser L, Cordova M, Gomez L, Gonzalez M, et al. Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc Natl Acad Sci USA 2006; 103:15280–15287. http://dx.doi.org/10.1073/pnas.0606924103 PubMedPubMed CentralView ArticlePubMedGoogle Scholar
  7. Achouak W, Christen R, Barakat M, Martel MH, Heulin T. Burkholderia caribensis sp. nov., an exopolysaccharide-producing bacterium isolated from vertisol microaggregates in Martinique. Int J Syst Bacteriol 1999; 49:787–794. http://dx.doi.org/10.1099/00207713-49-2-787 PubMedView ArticlePubMedGoogle Scholar
  8. Angus AA, Hirsch AM. Insights into the history of the legume-betaproteobacterial symbiosis. Mol Ecol 2010; 19:28–30. http://dx.doi.org/10.1111/j.1462-2920.2010.02343.x PubMedView ArticlePubMedGoogle Scholar
  9. Chen WM, de Faria SM, Straliotto R, Pitard RM, Simões-Araùjo JL, Chou J, Chou Y, Barrios E, Prescott AR, Elliott GN, et al. Proof that Burkholderia strains form effective symbioses with legumes: a study of novel Mimosa-nodulating strains from South America. Appl Environ Microbiol 2005; 71:7461–7471. http://dx.doi.org/10.1128/AEM.71.11.7461-7471.2005 PubMedPubMed CentralView ArticlePubMedGoogle Scholar
  10. Suárez-Moreno ZR, Caballero-Mellado J, Coutinho BG, Mendonca-Previato L, James EK, Venturi V. Common features of environmental and potentially beneficial plant-associated Burkholderia. Microb Ecol 2012; 63:249–266. http://dx.doi.org/10.1007/s00248-011-9929-1 PubMedView ArticlePubMedGoogle Scholar
  11. Viallard V, Poirier I, Cournoyer B, Haurat J, Wiebkin S, Ophel-Keller K, Balandreau J. Burkholderia graminis sp. nov., a rhizospheric Burkholderia species, and reassessment of Pseudomonas phenazinium, Pseudomonas pyrrocinia and Pseudomonas glathei as Burkholderia. Int J Syst Bacteriol 1998; 48:549–563. http://dx.doi.org/10.1099/00207713-48-2-549 PubMedView ArticlePubMedGoogle Scholar
  12. Hoque MS, Broadhurst LM, Thrall PH. Genetic characterisation of root nodule bacteria associated with Acacia salicina and A. stenophylla (Mimosaceae) across south-eastern Australia. Int J Syst Evol Microbiol 2011; :299–309. http://dx.doi.org/10.1099/ijs.0.021014-0 PubMedView ArticleGoogle Scholar
  13. Fierer N, Jackson RB. The diversity and biogeography of soil bacterial communities. Proc Natl Acad Sci USA 2006; 103:626–631. http://dx.doi.org/10.1073/pnas.0507535103 PubMedPubMed CentralView ArticlePubMedGoogle Scholar
  14. Stopnisek N, Bodenhausen N, Frey B, Fierer N, Eberl L, Weisskopf L. Genus-wide acid tolerance accounts for the biogeographical distribution of soil Burkholderia populations. Environ Microbiol 2013. http://dx.doi.org/10.1111/1462-2920.12211 PubMed
  15. Miller JH. Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; 1972.Google Scholar
  16. Howieson JG, Ewing MA, D’antuono MF. Selection for acid tolerance in Rhizobium meliloti. Plant Soil 1988; 105:179–188. http://dx.doi.org/10.1007/BF02376781View ArticleGoogle Scholar
  17. Beringer JE. R factor transfer in Rhizobium leguminosarum. J Gen Microbiol 1974; 84:188–198. http://dx.doi.org/10.1099/00221287-84-1-188 PubMedPubMedGoogle Scholar
  18. Terpolilli JJ. Why are the symbioses between some genotypes of Sinorhizobium and Medicago suboptimal for N2 fixation? Perth: Murdoch University; 2009. 223 p.Google Scholar
  19. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen M, Angiuoli SV, et al. Towards a richer description of our complete collection of genomes and metagenomes “Minimum Information about a Genome Sequence” (MIGS) specification. Nat Biotechnol 2008; 26:541–547. http://dx.doi.org/10.1038/nbt1360 PubMedPubMed CentralView ArticlePubMedGoogle Scholar
  20. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576–4579. http://dx.doi.org/10.1073/pnas.87.12.4576 PubMedPubMed CentralView ArticlePubMedGoogle Scholar
  21. Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 1.View ArticleGoogle Scholar
  22. Garrity GM, Bell JA, Lilburn T. Class II. Betaproteobacteria class. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 2, Part C, Springer, New York, 2005, p. 575.View ArticleGoogle Scholar
  23. Validation List No. 107. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2006; 56:1–6. http://dx.doi.org/10.1099/ijs.0.64188-0 PubMed
  24. Garrity GM, Bell JA, Lilburn T. Order I. Burkholderiales ord. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 2, Part C, Springer, New York, 2005, p. 575.View ArticleGoogle Scholar
  25. Garrity GM, Bell JA, Lilburn T. Family I. Burkholderiaceae fam. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey’s Manual of Systematic Bacteriology, Second Edition, Volume 2, Part C, Springer, New York, 2005, p. 575.View ArticleGoogle Scholar
  26. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. List No. 45. Int J Syst Bacteriol 1993; 43:398–399. http://dx.doi.org/10.1099/00207713-43-2-398
  27. Gillis M, Van TV, Bardin R, Goor M, Hebbar P, Willems A, Segers P, Kersters K, Heulin T, Fernandez MP. Polyphasic taxonomy in the genus Burkholderia leading to an emended description of the genus and proposition of Burkholderia vietnamiensis sp. nov. for N2-fixing isolates from rice in Vietnam. Int J Syst Bacteriol 1995; 45:274–289. http://dx.doi.org/10.1099/00207713-45-2-274View ArticleGoogle Scholar
  28. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25–29. http://dx.doi.org/10.1038/75556 PubMedPubMed CentralView ArticlePubMedGoogle Scholar
  29. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 2011; 28:2731–2739. http://dx.doi.org/10.1093/molbev/msr121 PubMedPubMed CentralView ArticlePubMedGoogle Scholar
  30. Nei M, Kumar S. Molecular Evolution and Phylogenetics. New York: Oxford University Press; 2000.Google Scholar
  31. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791. http://dx.doi.org/10.2307/2408678View ArticleGoogle Scholar
  32. Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2008; 36:D475–D479. PubMed http://dx.doi.org/10.1093/nar/gkm884PubMed CentralView ArticlePubMedGoogle Scholar
  33. Barry RB, Peter G, Eugenia P. Phenotype microarrays for high-throughput phenotypic testing and assay of gene function. Genome Res 2001; 11:1246–1255. http://dx.doi.org/10.1101/gr.186501 PubMedView ArticleGoogle Scholar
  34. Reeve WG, Tiwari RP, Worsley PS, Dilworth MJ, Glenn AR, Howieson JG. Constructs for insertional mutagenesis, transcriptional signal localization and gene regulation studies in root nodule and other bacteria. Microbiology 1999; 145:1307–1316. http://dx.doi.org/10.1099/13500872-145-6-1307 PubMedView ArticlePubMedGoogle Scholar
  35. Bennett S. Solexa Ltd. Pharmacogenomics 2004; 5:433–438. http://dx.doi.org/10.1517/14622416.5.4.433 PubMedView ArticlePubMedGoogle Scholar
  36. Zerbino DR. Using the Velvet de novo assembler for short-read sequencing technologies. Current Protocols in Bioinformatics 2010;Chapter 11:Unit 11 5.Google Scholar
  37. Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci USA 2011; 108:1513–1518. http://dx.doi.org/10.1073/pnas.1017351108 PubMedPubMed CentralView ArticlePubMedGoogle Scholar
  38. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. http://dx.doi.org/10.1186/1471-2105-11-119 PubMedPubMed CentralView ArticlePubMedGoogle Scholar
  39. Mavromatis K, Ivanova NN, Chen IM, Szeto E, Markowitz VM, Kyrpides NC. The DOE-JGI Standard operating procedure for the annotations of microbial genomes. Stand Genomic Sci 2009; 1:63–67. http://dx.doi.org/10.4056/sigs.632 PubMedPubMed CentralView ArticlePubMedGoogle Scholar
  40. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455–457. http://dx.doi.org/10.1038/nmeth.1457 PubMedView ArticlePubMedGoogle Scholar
  41. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964. PubMedPubMed CentralView ArticlePubMedGoogle Scholar
  42. Pruesse E, Quast C, Knittel K. Fuchs BdM, Ludwig W, Peplies J, Glöckner FO. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 2007; 35:7188–7196. http://dx.doi.org/10.1093/nar/gkm864 PubMedPubMed CentralView ArticlePubMedGoogle Scholar
  43. Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271–2278. http://dx.doi.org/10.1093/bioinformatics/btp393 PubMedView ArticlePubMedGoogle Scholar

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© The Author(s) 2014