Abstract
Achromobacter xylosoxidans ADAF13, isolated from farmland soil, possesses a large number of putative degradation genes and pathways that break down a wide variety of aromatic hydrocarbons, pesticides, endocrine disruptors, and other high-impact xenobiotics. These properties make this strain an excellent candidate for further development as a broad-spectrum bioremediation agent.
GENOME ANNOUNCEMENT
Achromobacter xylosoxidans ADAF13 is a Gram-negative, oxidase- and catalase-positive bacterium from the genus Achromobacter. A. xylosoxidans is well known for its opportunistic pathogenicity and infection of pulmonary tissue in immunocompromised individuals. These infections are particularly common in cystic fibrosis patients (1). However, A. xylosoxidans is a metabolically versatile microorganism and has significant potential value in environmental bioremediation applications (1). We have isolated and identified a new strain of A. xylosoxidans from farmland soil taken from Cypress, TX, as part of an undergraduate environmental sampling research module that collects samples from across the state of Texas and screens them for bacteria with the capacity to degrade organophosphate insecticides (2). In comparison to other Achromobacter genome projects, genomic analysis showed that ADAF13 is most closely related to Achromobacter arsenitoxydans SY8, and then Achromobacter piechaudii HLE, Achromobacter sp. strain DH1f, and A. xylosoxidans C54, in order of decreasing similarity. While lacking the extensive arsenite gene islands that define A. arsenitoxydans SY8 (3), we report here the genome sequence of a broad-spectrum xenobiotic degrader of polycyclic aromatic hydrocarbons and organophosphate insecticides with the added capacity to putatively target both bisphenol A and trinitrotoluene. The genome sequencing of ADAF13 was performed through Illumina MiSeq paired-end sequencing (total reads, 3,363,665; 35 to 250 bp in each read), with a final sequencing coverage of 194.86×. Sequence reads were checked for quality using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and filtered using BBTools (https://sourceforge.net/projects/bbmap/), with a minimum Phred score of 20. Paired-end reads were assembled into 120 contigs with the SPAdes 3.6.2 program (4). Preliminary reference-based annotation using PATRIC (5) Web resources was carried out to identify conserved pathways. Final de novo annotation was performed with Prokka (6) and the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html). The metabolic pathways of aromatic and heterocyclic compounds were examined using the KEGG databases (7). ADAF13 has a G+C content of 65.84% and contains 5,184 putative coding sequences (CDSs; 984 bp average length), of which 4,021 CDSs are functional. The project accession also contains sequences for 6 rRNA, 54 tRNA, and 4 noncoding RNA (ncRNA) loci.
Nucleotide sequence accession numbers.
The A. xylosoxidans ADAF13 whole-genome shotgun (WGS) project has the project accession no. LSMI00000000. This version of the project (01) has the accession no. LSMI01000000 and consists of sequences LSMI01000001 to LSMI01000120.
ACKNOWLEDGMENT
The authors acknowledge efforts of Brian Iken in sample preparation.
Funding Statement
Funding for this work was provided for by the National Science Foundation (award no. 1505403). The NSF had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Footnotes
Citation Iyer R, Damania A. 2016. Draft genome sequence of the broad-spectrum xenobiotic degrader Achromobacter xylosoxidans ADAF13. Genome Announc 4(2):e00203-16. doi:10.1128/genomeA.00203-16.
REFERENCES
- 1.Jeukens J, Freschi L, Kukavica-Ibrulj I, Nguyen D, Levesque RC. 2015. Draft genome sequence of triclosan-resistant cystic fibrosis isolate Achromobacter xylosoxidans CF304. Genome Announc 3(4):e00865-15. doi: 10.1128/genomeA.00865-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 2.Iyer R, Smith K, Kudrle B, Leon A. 2015. Detection and location of OP-degrading activity: a model to integrate education and research. New Biotechnol 32:403–411. doi: 10.1016/j.nbt.2015.03.010. [DOI] [PubMed] [Google Scholar]
- 3.Li X, Hu Y, Gong J, Lin Y, Johnstone L, Rensing C, Wang G. 2012. Genome sequence of the highly efficient arsenite-oxidizing bacterium Achromobacter arsenitoxydans SY8. J Bacteriol 194:1243–1244. doi: 10.1128/JB.06667-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. doi: 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R, Machi D, Mao C, Nordberg EK, Olson R, Overbeek R, Pusch GD, Shukla M, Schulman J, Stevens RL, Sullivan DE, Vonstein V, Warren A, Will R, Wilson MJC, Seung YH, Zhang C, Zhang Y, Sobral BW. 2014. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res 42:D581–D591. doi: 10.1093/nar/gkt1099. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. doi: 10.1093/bioinformatics/btu153. [DOI] [PubMed] [Google Scholar]
- 7.Kanehisa M, Goto S. 2000. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28:27–30. doi: 10.1093/nar/28.1.27. [DOI] [PMC free article] [PubMed] [Google Scholar]