Draft genome sequence of phenol degrading Acinetobacter sp. Strain V2, isolated from oil contaminated soil

Vikas Sharma Johnson Lin About the authors

Abstract

We report here the draft genome sequence of Acinetobacter sp. Strain V2 isolated from the oil contaminated soil collected from ENGEN, Amanzimtoti, South Africa. Degradation of phenolic compounds such as phenol, toluene, aniline etc. at 400 ppm in 24 h and oil degrading capability makes this organism an efficient multifunctional bioremediator. Genome sequencing of Acinetobacter spp. V2 was carried out on Illumina HiSeq 2000 platform (performed by the Beijing Genomics Institute [BGI], Shenzhen, China). The data obtained revealed 643 contigs with genome size of 4.0 Mb and G + C content of 38.59%.

Keywords:
Acinetobacter; Phenol degradation; Whole genome sequencing; Oil contaminated soil

Genome announcement

Acinetobacter spp. have been involved in bioremediation of various pollutants such as phenols, benzoate, crude oil, acetonitrile etc.11 Mandri T, Lin J. Isolation and characterization of engine oil degrading indigenous microorganisms in KwaZulu-Natal, South Africa. Afr J Biotechnol. 2007;6(1):23-27.,22 Tabrez S, Ahmad M. Oxidative stress mediated genotoxicity of wastewaters collected from two different stations in northern India. Mutat Res. 2011;11:15-20. and biotechnological applications like production of extra-and-intracellular lipases, proteases, bio-emulsifiers and various types of biopolymers.33 Saxena M, Gupta S, Kumar R, Kumar A. Identification and genetic characterization of phenol-degrading bacterium isolated from oil contaminated soil. Afr J Biotechnol. 2013;12:791-797.,44 Snellman EA, Colwell RR. Acinetobacter lipases: molecular biology, biochemical properties and biotechnological potential. J Ind Microbiol Biotechnol. 2004;31:391-400. Physiological and genetic characterisation of large number of phenol-degrading bacteria isolated from various sources have been done,55 Anli G, Ji LC. Proteome analysis of the adaptation of a phenol-degrading bacterium Acinetobacter sp. EDP3 to the variation of phenol loadings. Chin J Chem Eng. 2007;15:781-787.,66 Zhan Y, Yan Y, Zhang W, et al. Comparative analysis of the complete genome of an Acinetobacter calcoaceticus strain adapted to a phenol-polluted environment. Res Microbiol. 2012;163:36-43. however, little information on bacteria with a high phenol tolerance and high metabolising activity is available.77 Wang Y, Tian Y, Han B, Zhaw HB, Bi JN, Cai BL. Biodegradation of phenol by free and immobilized Acinetobacter sp. strain PD12. J Environ Sci. 2007;19:222-225. Substrate inhibition and low degradation rate are the key factors which limits their applications.88 Krastanov A, Alexieva Z, Yemendzhiev H. Microbial degradation of phenol and phenolic derivatives. Eng Life Sci. 2013;13:76-87.Acinetobacter sp. V2 strain is able to degrade 400 ppm of phenol within 24 h.99 Lin J, Sharma V, Milase R, Mbhense N. Simultaneous enhancement of phenolic compound degradations by Acinetobacter strain V2 via a step-wise continuous acclimation process. J Basic Microbiol. 2015; http://dx.doi.org/10.1002/jobm.201500263.
http://dx.doi.org/10.1002/jobm.201500263...
Presence of commercially important proteins apart from its ability to degrade diesel and engine oil makes this organism unique and thus genome sequencing.

Whole-genome sequencing was carried using Illumina HiSeq 2000 platform (Beijing Genomics Institute [BGI], Shenzhen, China) by generating paired-end libraries with an average insert size of 500 bp following the manufacturer's instructions. The reads were then aligned with the reference sequence using SOAPaligner (version 2.21) software to calculate average depth and coverage ratio (http://soap.genomics.org.cn/soapaligner.html, version 2.21).1010 Li R, Yu C, Li Y, et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009;25:1966-1967. The filtered short reads were first de novo assembled using SOAPdenovo v 2.04 according to the method described previously (http://soap.genomics.org.cn/soapdenovo.html),1111 Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics. 2008;24:713-714. and then contigs were manually connected according to their 500 bp paired-end relationships. The draft genome sequence of Acinetobacter sp. V2 strain comprised of 643 contigs and 16 scaffolds with the maximum contig size of 910,143 bp and scaffold size of 1,913,879 bp (Table 1). The genome size was 4,007,850 bp at 109.2 × coverage, with N50 of 466,223 bp and N90 of 97,271 bp and G + C content was 38.59%. A total of 3717 coding sequences (CDSs) or ORFs were predicted using Glimmer v3.02,1212 Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007;23:673-679. and homologous comparison to a non-redundant public database was performed by BLAST for function annotation. The genome annotation was performed using the (BASys) server (https://www.basys.ca/) and the output was downloaded in GenBank format resulting in 3742 (CDSs).1313 van Domselaar GH, Stothard P, Shrivastava S, et al. BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res. 2005;33:W455-W459. The genome was further annotated with Rapid Annotation using Subsystems Technology (RAST) server (http://rast.nmpdr.org/).1414 Aziz RK, Bartels D, Best AA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75. Among the predicted 3742 protein-coding genes by BASys, 79.4% (2971genes) have been assigned putative functions according to the subsystem categorization. A total of 71 tRNA genes encompassing all 20 amino acids were identified using the tRNAscan-SE program,1515 Schattner P, Brooks AN, Lowe TM. The tRNAscan-SE, snoscan and snoGPSweb servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 2005;33:W686-W689. 14 rRNA genes were identified using RNAmmer1616 Lagesen K, Hallin PF, Rødland E, Stærfeldt HH, Rognes T, Ussery DW. RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res. 2007;35:3100-3108. and the insertion sequence (IS) elements were annotated by ISsaga.1717 Varani AM, Siguier P, Gourbeyre E, Charneau V, Chandler M. ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes. Genome Biol. 2011;12:R30. All the contigs were submitted to the Gene bank and NCBI has published sequence data in April 2015. The further analysis is going on.

Table 1
General features of the Acinetobacter sp. Strain V2 genome.

Nucleotide sequence accession numbers: This WGS project has been deposited at DDBJ/EMBL/GenBank under the accession JZFB00000000. The version described in this paper is version JZFB01000000. Bioproject registered under accession: PRJNA275383 ID: 275383. The Acinetobacter sp. V2 isolate was deposited at the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures and is available under the Accession No. DSM 101893.

References

  • 1
    Mandri T, Lin J. Isolation and characterization of engine oil degrading indigenous microorganisms in KwaZulu-Natal, South Africa. Afr J Biotechnol. 2007;6(1):23-27.
  • 2
    Tabrez S, Ahmad M. Oxidative stress mediated genotoxicity of wastewaters collected from two different stations in northern India. Mutat Res. 2011;11:15-20.
  • 3
    Saxena M, Gupta S, Kumar R, Kumar A. Identification and genetic characterization of phenol-degrading bacterium isolated from oil contaminated soil. Afr J Biotechnol 2013;12:791-797.
  • 4
    Snellman EA, Colwell RR. Acinetobacter lipases: molecular biology, biochemical properties and biotechnological potential. J Ind Microbiol Biotechnol 2004;31:391-400.
  • 5
    Anli G, Ji LC. Proteome analysis of the adaptation of a phenol-degrading bacterium Acinetobacter sp. EDP3 to the variation of phenol loadings. Chin J Chem Eng. 2007;15:781-787.
  • 6
    Zhan Y, Yan Y, Zhang W, et al. Comparative analysis of the complete genome of an Acinetobacter calcoaceticus strain adapted to a phenol-polluted environment. Res Microbiol. 2012;163:36-43.
  • 7
    Wang Y, Tian Y, Han B, Zhaw HB, Bi JN, Cai BL. Biodegradation of phenol by free and immobilized Acinetobacter sp. strain PD12. J Environ Sci. 2007;19:222-225.
  • 8
    Krastanov A, Alexieva Z, Yemendzhiev H. Microbial degradation of phenol and phenolic derivatives. Eng Life Sci 2013;13:76-87.
  • 9
    Lin J, Sharma V, Milase R, Mbhense N. Simultaneous enhancement of phenolic compound degradations by Acinetobacter strain V2 via a step-wise continuous acclimation process. J Basic Microbiol 2015; http://dx.doi.org/10.1002/jobm.201500263
    » http://dx.doi.org/10.1002/jobm.201500263
  • 10
    Li R, Yu C, Li Y, et al. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009;25:1966-1967.
  • 11
    Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008;24:713-714.
  • 12
    Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007;23:673-679.
  • 13
    van Domselaar GH, Stothard P, Shrivastava S, et al. BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res. 2005;33:W455-W459.
  • 14
    Aziz RK, Bartels D, Best AA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008;9:75.
  • 15
    Schattner P, Brooks AN, Lowe TM. The tRNAscan-SE, snoscan and snoGPSweb servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res. 2005;33:W686-W689.
  • 16
    Lagesen K, Hallin PF, Rødland E, Stærfeldt HH, Rognes T, Ussery DW. RNammer: consistent annotation of rRNA genes in genomic sequences. Nucleic Acids Res. 2007;35:3100-3108.
  • 17
    Varani AM, Siguier P, Gourbeyre E, Charneau V, Chandler M. ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes. Genome Biol. 2011;12:R30.

Publication Dates

  • Publication in this collection
    Apr-Jun 2017
Sociedade Brasileira de Microbiologia USP - ICB III - Dep. de Microbiologia, Sociedade Brasileira de Microbiologia, Av. Prof. Lineu Prestes, 2415, Cidade Universitária, 05508-900 São Paulo, SP - Brasil, Ramal USP 7979, Tel. / Fax: (55 11) 3813-9647 ou 3037-7095 - São Paulo - SP - Brazil
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