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Genome Announc. 2017 August; 5(31): e00762-17.
Published online 2017 August 3. doi:  10.1128/genomeA.00762-17
PMCID: PMC5543652

Complete Genome Sequence of Achromobacter denitrificans PR1


Achromobacter denitrificans strain PR1 was isolated from an enrichment culture able to use sulfamethoxazole as an energy source. Here, we describe the complete genome of this strain sequenced by Illumina MiSeq and Oxford Nanopore MinION.


Achromobacter denitrificans is a Gram-negative rod-shaped bacterium commonly found in soil and occasionally in human infections (1, 2). Members of this species have previously been linked to the degradation of xenobiotics (3,6), highlighting their potential for bioremediation. Here, we describe the complete genome sequence of A. denitrificans strain PR1, originally obtained from enriched activated sludge and able to use sulfamethoxazole (SMX) as an energy source (7).

Strain PR1 was incubated overnight at 30°C in mineral medium B (8) with ammonium sulfate (0.54 g/liter), succinate (0.83 g/liter), yeast extract (0.2 g/liter), and SMX (0.15 g/liter). Genomic DNA extraction was performed with GenElute bacterial genomic DNA kit (Sigma) and sequenced using MiSeq (Illumina) and MinION (Oxford Nanopore). For MiSeq paired-end sequencing (2 × 300 bp), two libraries were independently prepared from 1 µg of DNA with the TruSeq DNA LT sample prep kit (library 1 [lib1]) from Illumina or the Kapa HyperPrep kit (library 2 [lib2]) from Kapa Biosystems. The MinION library was prepared from 1 µg of DNA, sheared into 5-kb fragments with a g-TUBE (Covaris), prepared with the genomic DNA sequencing kit (SQK-MAP-103), and sequenced using a flow cell with R7 chemistry (Oxford Nanopore). The library was loaded in the beginning and after 24 h to coincide with the g1-to-g2 pore switch (9).

MiSeq sequencing generated 2.5 million (lib1) and 0.3 million (lib2) paired-end raw reads. All reads were screened for PhiX contamination and adapter and quality trimmed (>Q20) with the BBDuk tool ( MinION sequencing generated 12,591 2D reads (10) (>Q9) that were converted to fastq format with Poretools version 0.5.1 (11). Hybrid de novo assembly was done with SPAdes version 3.10.0 (12) with the options -careful and -nanopore. Contigs with <1× coverage were removed from the assembly, resulting in a single scaffold. Circularization was performed with PCR and Sanger sequencing, generating a single circular chromosome of 6,929,205 bp with 46-fold average coverage and 67.4% G+C content.

Analysis with the Rapid Annotations using Subsystems Technology (RAST) server version 2.0 (13) predicted 6,425 protein-coding sequences (CDSs), 4 copies of the rRNA operon, and 59 tRNAs. Functional prediction of the CDSs was further refined by aligning protein sequences against the Gene Ontology (GO) database (14) with InterProScan (15) and BLASTp (16) in Blast2GO version 4.1 (17). Of the total CDSs, 5,210 (81.1%) had a functional prediction, and, from these, 2,939 (45.7%) had catalytic activity (891 hydrolases and 746 oxidoreductases). ResFinder (18) analysis identified multiple antibiotic resistance genes (sul1, sul2, and tetC), with some (cmlA1h and aadA2) within the new class I integron In1410 (19). Average nucleotide identity (ANI) analysis (20) and in silico DNA-DNA hybridization (DDH) analysis (21, 22) with the A. denitrificans type strain genome (GenBank accession number BCTQ00000000) showed that strain PR1 belongs to the same species (ANI, 99.33%; DDH, 94.60%; difference in %G+C content, 0.19).

The genome of strain PR1 will provide further insights into sulfamethoxazole metabolism in this microbial consortium and into the species versatility and potential for xenobiotic degradation.

Accession number(s).

This complete genome sequence has been deposited in GenBank under the accession no. CP020917. The version described in this paper is the first version.


Ana Reis is recipient of a Ph.D. scholarship from the Portuguese Foundation for Science and Technology (FCT, grant reference SFRH/BD/95814/2013). This work was financially supported by projects (i) “Beyond pollutant removal—understanding the biochemical mechanism of sulfonamide degradation in wastewater and the role of ipso-substitution” (Swiss National Science Foundation grant no. 160332), (ii) POCI-01-0145-FEDER-006939 (Laboratory for Process Engineering, Environment, Biotechnology and Energy; grant UID/EQU/00511/2013) funded by the European Regional Development Fund (ERDF), through COMPETE2020-Programa Operacional Competitividade e Internacionalização (POCI) and by national funds, through FCT, (iii) NORTE-01-0145-FEDER-000005-LEPABE-2-ECO-Innovation, supported by North Portugal Regional Operational Program (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the ERDF.

Illumina and MinION sequencing were both performed in the School of Life Sciences (HLS) of the University of Applied Sciences and Arts Northwestern Switzerland (FHNW).


Citation Reis AC, Kroll K, Gomila M, Kolvenbach BA, Corvini PFX, Nunes OC. 2017. Complete genome sequence of Achromobacter denitrificans PR1. Genome Announc 5:e00762-17.


1. Coenye T, Vancanneyt M, Cnockaert MC, Falsen E, Swings J, Vandamme P 2003. Kerstersia gyiorum gen. nov., sp. nov., a novel Alcaligenes faecalis-like organism isolated from human clinical samples, and reclassification of Alcaligenes denitrificans Ruger and Tan 1983 as Achromobacter denitrificans comb. nov. Int J Syst Evol Microbiol 53:1825–1831. doi:.10.1099/ijs.0.02609-0 [PubMed] [Cross Ref]
2. Kersters K, De Ley J 1984. Genus Alcaligenes Castellani and Chalmers 1919, 936AL, p 361–373. In Krieg NR, Holt JG (ed), Bergey’s manual of systematic bacteriology. Williams & Wilkins, Baltimore, MD.
3. Benjamin S, Kamimura N, Takahashi K, Masai E 2016. Achromobacter denitrificans SP1 efficiently utilizes 16 phthalate diesters and their downstream products through protocatechuate 3,4-cleavage pathway. Ecotoxicol Environ Saf 134:172–178. doi:.10.1016/j.ecoenv.2016.08.028 [PubMed] [Cross Ref]
4. Mawad AMM, Hesham AE-l, Mostafa YM, Shoriet A 2016. Pyrene degrading Achromobacter denitrificans ASU-035: growth rate, enzymes activity, and cell surface properties. Rend Fis Acc Lincei 27:557–563. doi:.10.1007/s12210-016-0521-y [Cross Ref]
5. Pradeep S, Josh MK, Binod P, Devi RS, Balachandran S, Anderson RC, Benjamin S 2015. Achromobacter denitrificans strain SP1 efficiently remediates di(2-ethylhexyl)phthalate. Ecotoxicol Environ Saf 112:114–121. doi:.10.1016/j.ecoenv.2014.10.035 [PubMed] [Cross Ref]
6. Sałek K, Zgoła-Grześkowiak A, Kaczorek E 2013. Modification of surface and enzymatic properties of Achromobacter denitrificans and Stenotrophomonas maltophilia in association with diesel oil biodegradation enhanced with alkyl polyglucosides. Colloids Surf B Biointerfaces 111:36–42. doi:.10.1016/j.colsurfb.2013.05.021 [PubMed] [Cross Ref]
7. Reis PJM, Reis AC, Ricken B, Kolvenbach BA, Manaia CM, Corvini PFX, Nunes OC 2014. Biodegradation of sulfamethoxazole and other sulfonamides by Achromobacter denitrificans PR1. J Hazard Mater 280:741–749. doi:.10.1016/j.jhazmat.2014.08.039 [PubMed] [Cross Ref]
8. Barreiros L, Nogales B, Manaia CM, Ferreira AC, Pieper DH, Reis MA, Nunes OC 2003. A novel pathway for mineralization of the thiocarbamate herbicide molinate by a defined bacterial mixed culture. Environ Microbiol 5:944–953. doi:.10.1046/j.1462-2920.2003.00492.x [PubMed] [Cross Ref]
9. Ip CLC, Loose M, Tyson JR, de Cesare M, Brown BL, Jain M, Leggett RM, Eccles DA, Zalunin V, Urban JM, Piazza P, Bowden RJ, Paten B, Mwaigwisya S, Batty EM, Simpson JT, Snutch TP, Birney E, Buck D, Goodwin S, Jansen HJ, O’Grady J, Olsen HE, MinION Analysis and Reference Consortium 2015. Phase 1 data release and analysis [version 1; referees: 2 approved]. F1000Res 4:1075. doi:.10.12688/f1000research.7201.1 [PMC free article] [PubMed] [Cross Ref]
10. Lu H, Giordano F, Ning Z 2016. Oxford Nanopore MinION sequencing and genome assembly. Genomics Proteomics Bioinformatics 14:265–279. doi:.10.1016/j.gpb.2016.05.004 [PMC free article] [PubMed] [Cross Ref]
11. Loman NJ, Quinlan AR 2014. Poretools: a toolkit for analyzing nanopore sequence data. Bioinformatics 30:3399–3401. doi:.10.1093/bioinformatics/btu555 [PMC free article] [PubMed] [Cross Ref]
12. 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 [PMC free article] [PubMed] [Cross Ref]
13. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. doi:.10.1186/1471-2164-9-75 [PMC free article] [PubMed] [Cross Ref]
14. The Gene Ontology Consortium 2015. Gene Ontology Consortium: going forward. Nucleic Acids Res 43:D1049–D1056. doi:.10.1093/nar/gku1179 [PMC free article] [PubMed] [Cross Ref]
15. Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R 2005. InterProScan: protein domains identifier. Nucleic Acids Res 33:W116–W120. doi:.10.1093/nar/gki442 [PMC free article] [PubMed] [Cross Ref]
16. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402. doi:.10.1093/nar/25.17.3389 [PMC free article] [PubMed] [Cross Ref]
17. Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676. doi:.10.1093/bioinformatics/bti610 [PubMed] [Cross Ref]
18. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV 2012. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67:2640–2644. doi:.10.1093/jac/dks261 [PMC free article] [PubMed] [Cross Ref]
19. Moura A, Soares M, Pereira C, Leitao N, Henriques I, Correia A 2009. INTEGRALL: a database and search engine for integrons, integrases and gene cassettes. Bioinformatics 25:1096–1098. doi:.10.1093/bioinformatics/btp105 [PubMed] [Cross Ref]
20. Rodriguez-R LM, Konstantinidis KT 2016. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ 4:e1900v1 [PubMed]
21. Clarke GDP, Beiko RG, Ragan MA, Charlebois RL 2002. Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J Bacteriol 184:2072–2080. doi:.10.1128/JB.184.8.2072-2080.2002 [PMC free article] [PubMed] [Cross Ref]
22. Meier-Kolthoff JP, Klenk HP, Göker M 2014. Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age. Int J Syst Evol Microbiol 64:352–356. doi:.10.1099/ijs.0.056994-0 [PubMed] [Cross Ref]

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