Complete Genome Sequence of Achromobacter denitrificans PR1

ABSTRACT 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.

A chromobacter 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)(4)(5)(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 ϫ 300 bp), two libraries were independently prepared from 1 g 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 g 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 (ϾQ20) with the BBDuk tool (https://sourceforge.net/projects/bbmap). MinION sequencing generated 12,591 2D reads (10) (ϾQ9) 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 Ͻ1ϫ 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% GϩC content.
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.
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).