Draft Genome Sequence of Bacillus sp. Strain CDB3, an Arsenic-Resistant Soil Bacterium Isolated from Cattle Dip Sites

Abstract

ABSTRACT

Bacillus sp. strain CDB3, isolated from cattle dip sites in Australia, is highly resistant to arsenic. It contains 22 arsenic resistance (ars) genes, of which 17 are organized in 3 ars clusters. Here, we report the draft genome sequence of CDB3, which will assist us in understanding the overall ars mechanism.

GENOME ANNOUNCEMENT

Arsenic contamination in soil and water is a global issue. Microbes that possess high arsenic resistance (ars) can provide insights into the resistance mechanism and may assist with treating arsenic poisoning. Bacillus sp. strain CDB3 was isolated from arsenic-contaminated cattle tick dip sites in Australia and was previously identified based on its 16S classification and fatty acid composition profile (1). It demonstrated a significantly high tolerance toward arsenic (1), and two ars clusters were already identified (2). Bacillus sp. CDB3 serves a good system for ars study, possessing not only novel ars genes but also, interestingly, a rare ars cluster (2).

Genomic DNA library construction, pyrosequencing, data assembly, and annotation were carried out as previously described (3). Draft genome sequences were also submitted to PHASTER for prophage identification (4).

The draft genome size of Bacillus sp. CDB3 comprises approximately 6,000 kb, with a coverage of about 45-fold. The assembled genome contained 148 contigs (N₅₀ value, 104,943 bp) arranged into 19 scaffolds (N₅₀ value, 4,125,929 bp), with a G+C content of 35.3%. There were 6,236 coding sequences (CDSs; length >100 bp) and 115 RNAs found in the genome, while the closest neighbor based on genome comparison was Bacillus cereus BAG1X1-3 (accession no. GCA_000291055.1). An intact prophage (phIS3501, accession no. NC_019502) was also found in the genome.

Genome analysis of CDB3 confirmed the 2 ars gene clusters found in our previous study (2). The long 8-gene operon, ars1 (arsRYCDATorf7orf8), possesses an interesting posttranscriptional regulation mechanism (5) and 2 novel genes, orf7 and orf8, coding for proteins homologous to HesB and dual-specificity protein phosphatase, respectively (6). The second operon, ars2, is highly homologous to other arsRorf2YC operons which are present in the skin element (7). However, as an intact sigK was found, ars2 was suggested not to be part of the skin element in our strain. Note that an orf2 homologue has been found to be responsible for MAs(III) demethylation and was denoted arsI (8). Furthermore, an additional ars cluster (ars3) was revealed upstream of ars1, harboring 5 genes that were related to arsenic resistance (arsR₃TO₁O₂N). Although ars1 and ars3 were found located relatively close (apart by 7,046 bp) on a 24,354-bp mobile genomic island, our previous study based on resistance screening did not isolate ars3 (2), suggesting that this cluster alone may not confer significant arsenic resistance.

Furthermore, several individually located ars gene homologues were also found in the CDB3 genome, including 4 additional arsenite transporters (ArsY3 and 3 ArsBs) and one other ATPase (ArsA2). The draft genome sequence of CDB3 provides further information for understanding arsenic resistance in bacteria.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. ALBR00000000. The version described in this paper is the first version, ALBR01000000.