Draft genome sequence of Arthrobacter sp. strain B6 isolated from the high-arsenic sediments in Datong Basin, China
© The Author(s). 2017
Received: 4 July 2016
Accepted: 12 January 2017
Published: 23 January 2017
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.
KeywordsArthrobacter sp. B6 Genome Arsenate reduction High-arsenic sediment Datong basin
The genus Arthrobacter was first proposed in 1947 by Conn and Dimmick , 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 . Due to their nutritional versatility and tolerance to various environmental stressors [3–7], Arthrobacter species are widely present in soils and the environments contaminated with chemicals and heavy metal [8–13], 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 . 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.
Classification and features
Classification and general features of Arthrobacter sp. B6 
Polymorphic: rod to coccus shaped
pH range; Optimum
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.
1–7% NaCl (w/v)
Datong basin, Shanxi, China
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 .
Genome sequencing information
Genome project history
High-Quality Permanent Draft
Illumina Std. shotgun library
Illumina HiSeq 2000
Gene calling method
GenBank Date of Release
Jun 15, 2016
Source Material Identifier
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 . 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 . 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.
Genes were identified using Glimmer v3.02 . 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 .
% of Total
Genome size (bp)
DNA coding (bp)
DNA G + C (bp)
Protein coding genes
Genes in internal clusters
Genes with function prediction
Genes assigned to COGs
Genes with Pfam domains
Genes with signal peptides
Genes with transmembrane helices
Number of genes associated with general COG functional categories
Translation, ribosomal structure and biogenesis
RNA processing and modification
Replication, recombination and repair
Chromatin structure and dynamics
Cell cycle control, Cell division, chromosome partitioning
Signal transduction mechanisms
Cell wall/membrane biogenesis
Intracellular trafficking and secretion
Posttranslational modification, protein turnover, chaperones
Energy production and conversion
Carbohydrate transport and metabolism
Amino acid transport and metabolism
Nucleotide transport and metabolism
Coenzyme transport and metabolism
Lipid transport and metabolism
Inorganic ion transport and metabolism
Secondary metabolites biosynthesis, transport and catabolism
General function prediction only
Not in COGs
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.
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.
Arsenite responsive repressor
Basic local alignment search tool
Coding DNA sequence
Clustered regularly interspaced short
Integral membrane protein
Integrated Microbial Genomes-Expert Review
Minimum information on the genome sequence
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).
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.
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.
- Conn HJ, Dimmick I. Soil Bacteria Similar in Morphology to Mycobacterium and Corynebacterium. J Bacteriol. 1947;54(3):291–303.PubMedPubMed CentralGoogle Scholar
- Busse HJ. Review of the taxonomy of the genus Arthrobacter, emendation of the genus Arthrobacter sensu lato, proposal to reclassify selected species of the genus Arthrobacter in the novel genera Glutamicibacter gen. nov., Paeniglutamicibacter gen. nov., Pseudoglutamicibacter gen. nov., Paenarthrobacter gen. nov. and Pseudarthrobacter gen. nov., and emended description of Arthrobacter rose. Int J Syst Evol Microbiol. 2016;66(1):9–37.View ArticlePubMedGoogle Scholar
- Stackebrandt E, Schumann P. Introduction to the taxonomy of Actinobacteria. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E, editors. The Prokaryotes. New York: Springer; 2006. p. 297–321.View ArticleGoogle Scholar
- Nakatsu CH, Barabote R, Thompson S, Bruce D, Detter C, Brettin T, et al. Complete genome sequence of Arthrobacter sp. strain FB24. Stand Genomic Sci. 2013;9(1):106–16.View ArticlePubMedPubMed CentralGoogle Scholar
- Arora PK, Sharma A. New metabolic pathway for degradation of 2-nitrobenzoate by Arthrobacter sp. SPG. Front Microbiol. 2015;6:551.PubMedPubMed CentralGoogle Scholar
- Ren L, Shi Y, Jia Y, Yan Y. Genome Sequence of Arthrobacter sp. YC-RL1, an Aromatic Compound-Degrading Bacterium. Genome Announc. 2015;3(4):e00749–15.View ArticlePubMedPubMed CentralGoogle Scholar
- Overhage J, Sielker S, Homburg S, Parschat K, Fetzner S. Identification of large linear plasmids in Arthrobacter spp. encoding the degradation of quinaldine to anthranilate. Microbiology. 2005;151:491–500.View ArticlePubMedGoogle Scholar
- Isbella C, Daniela L. Arthrobacters: successful arid soil bacteria: a review. Arid Land Res Manag. 1987;1:1–30.Google Scholar
- Crocker FH, Fredrickson JK, White DC, Ringelberg DB, Balkwill DL. Phylogenetic and physiological diversity of Arthrobacter strains isolated from unconsolidated subsurface sediments. Microbiology. 2000;146:1295–310.View ArticlePubMedGoogle Scholar
- Hanbo Z, Changqun D, Qiyong S, Weimin R, Tao S, Lizhong C, et al. Genetic and physiological diversity of phylogenetically and geographically distinct groups of Arthrobacter isolated from lead-zinc mine tailings. FEMS Microbiol Ecol. 2004;49:333–41.View ArticlePubMedGoogle Scholar
- Macur RE, Jackson CR, Botero LM, McDermott TR, Inskeep WP. Bacterial populations associated with the oxidation and reduction of arsenic in an unsaturated soil. Environ Sci Technol. 2004;38:104–11.View ArticlePubMedGoogle Scholar
- Li H, Zeng XC, He Z, Chen X, Guo-ji E, Han Y, et al. Long-term performance of rapid oxidation of arsenite in simulated groundwater using a population of arsenite-oxidizing microorganisms in a bioreactor. Water Res. 2016;101:393–401.View ArticlePubMedGoogle Scholar
- Zhang WH, Huang Z, He LY, Sheng XF. Assessment of bacterial communities and characterization of lead-resistant bacteria in the rhizosphere soils of metal-tolerant Chenopodium ambrosioides grown on lead-zinc mine tailings. Chemosphere. 2012;87:1171–8.View ArticlePubMedGoogle Scholar
- Dsouza M, Taylor MW, Turner SJ, Aislabie J. Genomic and phenotypic insights into the ecology of Arthrobacter from Antarctic soils. BMC Genomics. 2015;16:36.View ArticlePubMedPubMed CentralGoogle Scholar
- Fredrickson JK, Zachara JM, Balkwill DL, Kennedy D, Li SM, Kostandarithes HM, et al. Geomicrobiology of high-level nuclear waste-contaminated vadose sediments at the Hanford site, Washington state. Appl Environ Microbiol. 2004;70:4230–41.View ArticlePubMedPubMed CentralGoogle Scholar
- He J, Charlet L. A review of arsenic presence in China drinking water. J Hydrol (Amst). 2013;492(10):79–88.View ArticleGoogle Scholar
- Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23(21):2947–8.View ArticlePubMedGoogle Scholar
- Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 2013;30(12):2725–9.View ArticlePubMedPubMed CentralGoogle Scholar
- Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26(5):541–7.View ArticlePubMedPubMed CentralGoogle Scholar
- Marmur J, Doty P. Thermal Renaturation of Deoxyribonucleic Acids. J Mol Biol. 1961;3(5):585–94.View ArticlePubMedGoogle Scholar
- Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience. 2012;1:18.View ArticlePubMedPubMed CentralGoogle Scholar
- Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23(6):673–9.View ArticlePubMedPubMed CentralGoogle Scholar
- Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E, Grechkin Y, et al. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res. 2012;40:D115–22.View ArticlePubMedGoogle Scholar
- Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990;87(12):4576–9.View ArticlePubMedPubMed CentralGoogle Scholar
- Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW, editors. Bergey’s Manual of Systematic Bacteriology, vol. 1. Secondth ed. New York: Springer; 2001. p. 119–69.View ArticleGoogle Scholar
- Stackebrandt E, Rainey F, Ward-Rainey N. Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol. 1997;47:479–91.View ArticleGoogle Scholar
- Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Am Soc Microbiol. 1980;30(1):225–420.Google Scholar
- Buchanan RE. Studies in the nomenclature and classification of bacteria: II. The primary subdivisions of the Schizomycetes. J Bacteriol. 1917;2(2):155–64.PubMedPubMed CentralGoogle Scholar
- Pribram E. A contribution to the classification of microorganisms. J Bacteriol. 1929;18(6):361–94.PubMedPubMed CentralGoogle Scholar
- Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene Ontology: tool for the unification of biology. Nat Genet. 2000;25:25–9.View ArticlePubMedPubMed CentralGoogle Scholar
- Grant JR, Arantes AS, Stothard P. Comparing thousands of circular genomes using the CGView Comparison Tool. BMC Genomics. 2012;13:202.