Open Access

Draft genome sequence of Arthrobacter sp. strain B6 isolated from the high-arsenic sediments in Datong Basin, China

  • Linghua Xu1, 2,
  • Wanxia Shi1,
  • Xian-Chun Zeng1Email author,
  • Ye Yang1,
  • Lingli Zhou1,
  • Yao Mu1 and
  • Yichen Liu1
Standards in Genomic Sciences201712:11

DOI: 10.1186/s40793-017-0231-9

Received: 4 July 2016

Accepted: 12 January 2017

Published: 23 January 2017

Abstract

Arthrobacter sp. B6 is a Gram-positive, non-motile, facultative aerobic bacterium, isolated from the arsenic-contaminated aquifer sediment in the Datong basin, China. This strain displays high resistance to arsenic, and can dynamically transform arsenic under aerobic condition. Here, we described the high quality draft genome sequence, annotations and the features of Arthrobacter sp. B6. The G + C content of the genome is 64.67%. This strain has a genome size of 4,663,437 bp; the genome is arranged in 8 scaffolds that contain 25 contigs. From the sequences, 3956 protein-coding genes, 264 pseudo genes and 89 tRNA/rRNA-encoding genes were identified. The genome analysis of this strain helps to better understand the mechanism by which the microbe efficiently tolerates arsenic in the arsenic-contaminated environment.

Keywords

Arthrobacter sp. B6 Genome Arsenate reduction High-arsenic sediment Datong basin

Introduction

The genus Arthrobacter was first proposed in 1947 by Conn and Dimmick [1], belongs to the family of Micrococcaceae in the class of Actinobacteria . Recently, based on the intrageneric phylogeny and chemotaxonomic characteristics, the description of the genus Arthrobacter sensu lato was emended by Busse, and the genus Arthrobacter sensu stricto was restricted to A. globiformis , A. pascens , A. oryzae and A. humicola [2]. Due to their nutritional versatility and tolerance to various environmental stressors [37], Arthrobacter species are widely present in soils and the environments contaminated with chemicals and heavy metal [813], as well as extreme environments, such as Antarctic and radioactive sediments [14, 15].

Arthrobacter sp. B6 was isolated from an arsenic-contaminated sediment sample collected from the Datong Basin, China, where the uses of high arsenic groundwater for drinking and irrigation have resulted in endemic arsenic poisoning among tens of thousands of residents [16]. Strain B6 is of particular interest because it showed high level of resistance to arsenic and can dynamically transform arsenic under aerobic condition. Here, we presented a summary of the taxonomic characterization of Arthrobacter sp. B6 and its main genomic features. These data help to better understand the microbial detoxification mechanism for arsenic, and are useful for the comparisons of the genomic and physiological features between this isolate and other Arthrobacter species.

Organism information

Classification and features

Arthrobacter sp. B6 is a Gram-positive, non-motile, facultative aerobic bacterium. Cells are straight or slightly curved rods during log phase of bacterial growth (Fig. 1) and become coccoid in stationary phase. The bacteria cells formed white colonies on 0.1× Trypticase Soy Broth agar plate. Colonies are convex and circular with entire margin. The strain can grow at a wide range of temperatures from 4 to 37 °C; the optimum is 30 °C. It can proliferate in a pH range of 6.0–8.5; the optimum is 7.0. The strain tolerates high concentrations of NaCl up to approximately 7% (Table 1). It is catalase- and oxidase-positive. It hydrolyzes starch and tyrosine, but not o-nitrophenyl-β-d-galactoside, gelatin, aesculin, chitin, casein or cellulose. It is negative for nitrate reduction, H2S production, citrate utilization, indole production, arginine dihydrolase and urease activity.
Fig. 1

Images of Arthrobacter sp. B6 using scanning electron microscopy (Left) and the appearance of colony morphology on 0.1× Trypticase Soy Broth solid media (Right)

Table 1

Classification and general features of Arthrobacter sp. B6 [19]

MIGS ID

Property

Term

Evidence codea

 

Classification

Domain Bacteria

TAS [24]

  

Phylum Actinobacteria

TAS [25]

  

Class Actinobacteria

TAS [26]

  

Order Actinomycetales

TAS [27, 28]

  

Family Micrococcaceae

TAS [27, 29]

  

Genus Arthrobacter

TAS [1, 2]

  

Species undetermined

-

  

Strain: B6

IDA

 

Gram stain

Positive

IDA

 

Cell shape

Polymorphic: rod to coccus shaped

IDA

 

Motility

Non-motile

IDA

 

Sporulation

Non-sporulating

IDA

 

Temperature range

4–37 °C

IDA

 

Optimum temperature

30 °C

IDA

 

pH range; Optimum

6.0–8.5; 7

IDA

 

Carbon source

Dextrin, Tween 40, D-fructose, Gentiobiose, α-D-glucose, Lactulose, Maltotriose, D-mannose, D-mannitol, D-melezitose, Palatinose, D-psicose, D-raffinose, L-rhamnose, D-ribose, D-sorbitol, Sucrose, Turanose, α- hydroxybutyric acid, α-ketoglutaric acid, L-malic acid, Pyruvic acid, D-alanine, L-alanine, L-serine, Glycerol, Adenosine, 2-deoxy adenosine, Inosine.

IDA

MIGS-6

Habitat

Soil, sediment

IDA

MIGS-6.3

Salinity

1–7% NaCl (w/v)

IDA

MIGS-22

Oxygen requirement

Aerobic

IDA

MIGS-15

Biotic relationship

free-living

IDA

MIGS-14

Pathogenicity

Non-pathogen

NAS

MIGS-4

Geographic location

Datong basin, Shanxi, China

IDA

MIGS-5

Sample collection

August 2011

IDA

MIGS-4.1

Latitude

39.4899

IDA

MIGS-4.2

Longitude

112.915

IDA

MIGS-4.4

Altitude

Not recorded

 

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 [30]

The strain utilizes dextrin, tween 40, D-fructose, gentiobiose, α-D-glucose, lactulose, maltotriose, D-mannose, D-mannitol, D-melezitose, palatinose, D-psicose, D-raffinose, L-rhamnose, D-ribose, D-sorbitol, sucrose, turanose, α- hydroxybutyric acid, α-ketoglutaric acid, L-malic acid, pyruvic acid, D-alanine, L-alanine, L-serine, glycerol, adenosine, 2-deoxy adenosine and inosine as tested using the Biolog GP2 microplate system. The major fatty acids of strain B6 are anteiso-C15:0 (56.58%), anteiso-C17:1ω9c (8.89%), anteiso-C17:0 (8.22%), iso-C15:0 (7.63%), iso-C16:0 (5.26%), sum in feature 3 (4.31%), summed feature 3 (containing C16:1ω6c and/or C16:1ω7c) (4.31%) and iso-C16:1 H (2.32%). These data suggested that the morphological and biochemical traits and fatty acid profile of B6 are consistent with those of other described species of the genus Arthrobacter .

The 16S rRNA gene sequence of strain B6 shares 94.67–99.59% identities with those of other known species of the genus Arthrobacter . In order to evaluate the evolutionary relationships between B6 and other known strains of the genus Arthrobacter , the 16S rRNA gene sequence of all of these bacteria were aligned using ClustalW [17], and a phylogenetic tree were conducted using the maximum-likelihood and neighbor-joining algorithms implemented in MEGA 6.0, respectively [18]. The phylogeny illustrated that the strain B6 is closely associated with Arthrobacter oryzae , A. globiformis , A. pascens and A. humicola ; suggesting that B6 is affiliated with the genus Arthrobacter (Fig. 2). We also found that Arthrobacter sp. B6 showed high resistance to arsenic, with maximal inhibitory concentrations of 150.0 mM for arsenate and 5.0 mM for arsenite. A dynamic transformation of arsenic catalyzed by strain B6 was observed when it was cultured aerobically with arsenate.
Fig. 2

Phylogenetic tree based on 16S rRNA gene sequences showing the phylogenetic position of Arthrobacter sp. B6 (). Sequences were aligned with the CLUSTAL W program and were constructed using maximum-likelihood method implemented in MEGA 6.0 program [17, 18]. GenBank accession numbers are listed in parentheses. Type strains are indicated with a superscript T. Strains with published genomes are shown in bold. Bootstrap support values for 1000 replications above 50% are shown near nodes. The scale bar indicates 0.05 nucleotide substitution per nucleotide position

Genome sequencing information

Genome project history

Arthrobacter sp. strain B6 was selected for sequencing on the basis of its high resistance to arsenic and dynamic arsenic transformation capability. The Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank database under the accession number LQAP00000000. A summary of the main project information on compliance with MIGS version 2.0 is shown in Table 2 [19].
Table 2

Project information

MIGS ID

Property

Term

MIGS 31

Finishing quality

High-Quality Permanent Draft

MIGS-28

Libraries used

Illumina Std. shotgun library

MIGS 29

Sequencing platforms

Illumina HiSeq 2000

MIGS 31.2

Fold coverage

161 ×

MIGS 30

Assemblers

SOAPdenovo v2.04

MIGS 32

Gene calling method

Glimmer v3.02

 

Locus Tag

AU175

 

Genbank ID

LQAP01000000

 

GenBank Date of Release

Jun 15, 2016

 

GOLD ID

Gs0118476

 

BIOPROJECT

PRJNA306410

MIGS 13

Source Material Identifier

CGMCC 1.15656

 

Project relevance

Biotechnological, Environmental

Growth conditions and genomic DNA preparation

Strain B6 was grown at 30 °C in 0.1× Trypticase Soy Broth liquid medium to mid-exponential phase. Genomic DNA was extracted from 0.5 to 1.0 g of cells using the modified method of Marmur [20]. The purity of DNA, expressed as the value of A260/A280, was assessed on a NanoDrop™ ND-1000 Spectrophotometer (Biolab).

Genome sequencing and assembly

The draft genome of Arthrobacter sp. B6 was sequenced at the Beijing Genomics Institute (BGI, Shenzhen) using the high throughout sequencing technique. A standard Illumina shotgun library was constructed and sequenced using the Illumina HiSeq 2000 platform; this generated 8,355,450 clean reads totaling 752 Mbp. These reads were assembled using the Short Oligonucleotide Analysis Package (SOAPdenovo v2.04) with all parameters set to default [21]. The final draft assembly contains 25 contigs in 8 scaffolds. Final assembly was based on all clean reads that provide an average of 161-fold coverage of the genome. The total size of the genome is 4.66 Mbp.

Genome annotation

Genes were identified using Glimmer v3.02 [22]. The predicted CDSs were translated into amino acid sequences that were used as queries to BLAST the GenBank, Swissprot, InterPro, KEGG, COG and GO databases, respectively. These data were combined to assert a product description for each predicted protein. Additional gene prediction analysis and functional annotation was performed using the Integrated Microbial Genomes-Expert Review (IMG-ER) platform [23].

Genome properties

The assembly of the draft genome sequence consists of 8 scaffolds amounting to 4,663,437 bp. The G + C content is 64.67% (Table 3). From the genome, 4309 genes were predicted, of which 3956 are protein-coding genes. Among these protein-coding genes, 154 were assigned to putative functions, and 275 were annotated as hypothetical proteins. The assignment of genes into COGs functional categories is presented in Table 4 and Fig. 3.
Table 3

Genome statistics

Attribute

Value

% of Total

Genome size (bp)

4,663,437

100.00

DNA coding (bp)

4,100,739

87.93

DNA G + C (bp)

3,015,845

64.67

DNA scaffolds

8

100.00

Total genes

4309

100.00

Protein coding genes

3956

91.81

RNA genes

89

2.07

Pseudo genes

264

6.12

Genes in internal clusters

4250

98.63

Genes with function prediction

3527

81.85

Genes assigned to COGs

2210

51.29

Genes with Pfam domains

3464

80.39

Genes with signal peptides

220

5.11

Genes with transmembrane helices

249

5.78

CRISPR repeats

125

2.90

Table 4

Number of genes associated with general COG functional categories

Code

Value

%age

Description

J

145

6.56

Translation, ribosomal structure and biogenesis

A

1

0.05

RNA processing and modification

K

162

7.33

Transcription

L

110

4.98

Replication, recombination and repair

B

1

0.05

Chromatin structure and dynamics

D

12

0.54

Cell cycle control, Cell division, chromosome partitioning

V

26

1.18

Defense mechanisms

T

58

2.62

Signal transduction mechanisms

M

72

3.26

Cell wall/membrane biogenesis

N

0

0

Cell motility

U

18

0.81

Intracellular trafficking and secretion

O

65

2.94

Posttranslational modification, protein turnover, chaperones

C

168

7.60

Energy production and conversion

G

225

10.18

Carbohydrate transport and metabolism

E

272

12.31

Amino acid transport and metabolism

F

71

3.21

Nucleotide transport and metabolism

H

111

5.02

Coenzyme transport and metabolism

I

103

4.66

Lipid transport and metabolism

P

127

5.75

Inorganic ion transport and metabolism

Q

66

2.99

Secondary metabolites biosynthesis, transport and catabolism

R

266

12.04

General function prediction only

S

131

5.93

Function unknown

-

2099

48.71

Not in COGs

The total is based on the total number of protein coding genes in the genome

Fig. 3

A graphical circular map of the genome performed with CGview comparison tool [31]. From outside to center, ring 1 and 4 show protein-coding genes oriented in the forward (colored by COG categories) and reverse (colored by COG categories) directions, respectively. ring 2 and 3 denote genes on forward/reverse strand; ring 5 shows G + C% content plot, and the inner-most ring shows GC skew, purple indicating negative values and olive, positive values

Insights from the genome sequence

Genome comparison using the RAST Prokaryotic Genome Annotation Server revealed that the genome sequence of Arthrobacter sp. B6 is most similar to that of Arthrobacter sp. FB24 (comparison score: 536), but less similar to those of other Arthrobacter strains. Arthrobacter sp. B6 shares 2035, 2011, 1958, 1930, 1850 and 1829 genes with the strains A. globiformis NBRC 12137, Arthrobacter sp. FB24, A. enclensis NIO-1008, A. nitrophenolicus SJCon, A. castelli DSM 16402 and A. crystallopoietes BAB-32, respectively.

A three-gene (arsR-acr3-arsC) operon involved in the regulation of arsenate tolerance and reduction was identified from the genome of Arthrobacter sp. B6. The putative arsenate reductase (ArsC) of strain B6 shows 96% and 95% sequence identities to those of Arthrobacter sp. Leaf137 and Pseudarthrobacter phenanthrenivorans Sphe3, respectively. It also shows 89% identities to those of A. globiformis NBRC 12137, A. nitrophenolicus SJCon, A. enclensis NIO-1008 and Arthrobacter sp. FB24, respectively. The amino acid sequence of ACR3 displays 85% identity to that of the arsenic transporter from Arthrobacter sp. FB24. Numerous genes responsible for tolerance or detoxification of metals were identified from the genome of Arthrobacter sp. B6, including copper resistance protein CopC and CopD, copper chaperone, copper-translocating P-type ATPase, cobalt-zinc-cadmium resistance protein CzcD, mercuric reductase, DNA gyrase subunit A and B involved in fluoroquinolones resistance, various polyols ABC transporter and DedA protein involved in the uptake of selenate and selenite. In addition, there are some genes in the genome responsible for osmotic stress. The high tolerance of salt (7% NaCl) of strain B6 may be explained by the presence of glycine betaine ABC transport system permease protein in the genome.

Conclusions

In the present study, we characterized the genome of Arthrobacter sp. B6 that was isolated from the arsenic-contaminated aquifer sediment in the Datong Basin, China. It contains numerous genes involved in heavy metal tolerance and detoxification. The knowledge of the genome sequence of Arthrobacter sp. B6 lays foundation for better understanding of the special metabolic abilities of the strain and for elucidation of the metabolic diversity of bacteria inhabiting in the high-arsenic environment. Further functional analyses of the identified genes may gain insights into the detailed molecular mechanisms by which the microbes tolerate and transform arsenic in the arsenic-contaminated environments.

Abbreviations

ABC: 

ATP-binding cassette

ACR3: 

Arsenite transporter

ArsC: 

Arsenate reductase

ArsR: 

Arsenite responsive repressor

BLAST: 

Basic local alignment search tool

CDS: 

Coding DNA sequence

CRISPR: 

Clustered regularly interspaced short

DedA: 

Integral membrane protein

IMG-ER: 

Integrated Microbial Genomes-Expert Review

MIGS: 

Minimum information on the genome sequence

Declarations

Acknowledgements

This work was financially supported by the National Natural Science Foundation of China (grants nos. 41272257, 41472219, 41072181 and 41521001), and the Research Projects of the Educational Commission of Hubei Province of China (grant no. Q20154401).

Authors’ contributions

LHX performed laboratory experiments, analyzed the data and wrote the draft manuscript. YY and YM cultured the bacterial cells. WXS, LLZ and YCL analyzed the data and revised the manuscript. XCZ revised the manuscript and provided financial supports. All authors read and approved the final manuscript.

Competing interests

The authors declare that they have no competing interests.

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

Authors’ Affiliations

(1)
State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan)
(2)
School of Chemistry and Chemical Engineering, Hubei Polytechnic University

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Copyright

© The Author(s). 2017