Draft Genome Sequence of Burkholderia cenocepacia Strain CEIB S5-2, a Methyl Parathion- and p-Nitrophenol-Degrading Bacterium, Isolated from Agricultural Soils in Morelos, Mexico

Abstract

Burkholderia cenocepacia is an opportunistic pathogen that belongs to Burkholderia cepacia complex (BCC). Burkholderia cenocepacia strain CEIB S5-2 was isolated from agricultural soils in Morelos, Mexico, and previously has shown its abilities for bioremediation. In this study, we report the draft genome sequence of Burkholderia cenocepacia strain CEIB S5-2.

GENOME ANNOUNCEMENT

The Burkholderia cepacia complex (BCC) is a group of Gram-negative bacteria composed of at least 18 different species, including Burkholderia cenocepacia, which is common in the environment as a free form or associated with plants (1) and is also an opportunistic pathogen in patients with cystic fibrosis (2). The B. cenocepacia strain CEIB S5-2, as well as other strains of this genus (B. zhejiangensis strain CEIB S4-3 [3] and B. cenocepacia strain CEIB S5-1 [4]), was isolated from agricultural soils in Tepoztlán, Morelos, Mexico (5). Importantly, B. cenocepacia CEIB S5-2 has the capability to hydrolyze methyl parathion (MP) and use it as a carbon source, and to degrade completely p-nitrophenol (PNP) in 21 h (3). Here, we present the draft genome sequence of the organophosphorus pesticide-degrading strain B. cenocepacia CEIB S5-2.

Genomic DNA was obtained using the Ultra-Clean Microbial DNA isolation kit (Mo Bio Laboratories), and 5 µg of genomic DNA was sequenced in the HiSeq 2000 system (Illumina). We obtained a random data set of 1,842,982 paired-end reads with lengths of 300 bp. Quality-based trimming was performed with a DynamicTrim (SolexaQA++) Perl script, and genome assembly was accomplished using SPAdes version 3.1.1. The draft genome has 109 contigs with a calculated total length of 8,976,170 bp, an N₅₀ contig size of 201,068 bp, a G+C content of 65.68%, and ~62× coverage. We identified the 16S rRNA gene of B. cenocepacia CEIB S5-2 using RNAmmer version 1.2 (http://www.cbs.dtu.dk/services/RNAmmer/) and comarping the strain with 67 16S rRNA gene sequences of genus Burkholderia and two 16S rRNA genes of genus Ralstonia (outgroup). All sequences were aligned with the MUSCLE server (http://phylogeny.lirmm.fr/phylo_cgi/one_task.cgi?task_type=muscle), and a phylogenetic analysis was performed with MEGA version 6.1 with the neighbor-joining algorithm, using 1,000 replicates for bootstrapping. Phylogenetic analysis reveals that Burkholderia cenocepacia CEIB S5-2 is closely related to Burkholderia cenocepacia spp. The 16S rRNA gene of B. cenocepacia CEIB S5-2 has a length of 1,521 bp and has 99% identity and 100% alignment coverage with B. cenocepacia CEIB S5-1 (5), B. cenocepacia H111 (6), and B. cenocepacia 869T2 (7). We did not identify pathogenicity islands of B. cenocepacia CEIB S5-2 using the Pathogenicity Island Database (PAIDB) (http://paidb.sybirg.re.kr/about_paidb.php) server.

The 109 contigs were analyzed with the RAST server (http://rast.nmpdr.org), identifying 8,142 open reading frames and 8,034 coding sequences. We identified a PNP catabolic gene cluster: pnpABA’E1E2FDC, positive ranging from 79 to 100% with PnpABE1E2FDC proteins from Burkholderia sp. SJ98 (8, 9) using tBlastn program. While Burkholderia zhejiangensis CEIB S4-3 and Burkholderia cenocepacia CEIB S5-1 and S5-2 have the capability to completely degrade PNP, the strain S4-3 has two catabolic gene clusters (pnpABA’E1E2FDC and pnpE1E2FDC) (4), the strain S5-2 has one catabolic gene cluster (pnpABA’E1E2FDC) and the strain S5-1 does not has a catabolic gene cluster reported (5). Furthermore, the total genome size of Burkholderia cenocepacia CEIB S5-2 is 1,309,327 and 920,672 bp larger than that of strains S4-3 (8,976,170 bp and 154 contigs) (4) and S5-1 (7,666,843 bp and 177 contigs) (5), respectively.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number LNCR00000000. The version described in this paper is the first version, LNCR01000000.