Draft Genome Sequence of Nitrincola sp. Strain A-D6, an Arsenic-Resistant Gammaproteobacterium Isolated from a Salt Flat

Abstract

We report Nitrincola sp. strain A-D6, which was characterized as an arsenic-resistant bacterium isolated from the Ascotán Salt Flat in northern Chile. The size of the genome is 3,795,776 bp, with a G+C content of 49.96%. Genes for the arsenic-resistant Ars system and arsenic oxidation have been encoded.

GENOME ANNOUNCEMENT

Arsenic (As) is a ubiquitous element present in the environment in different forms (1). Inorganic arsenic, most often in trivalent or pentavalent form, is the most abundant species of As in nature and is commonly present in soil, water, and food (2). This metalloid is extremely toxic to living organisms and its toxicity is primarily based on its chemical speciation. However, some microorganisms cope with arsenic toxicity in a variety of different ways (1, 3, 4). Such microorganisms therefore play an important role in the arsenic geocycle (5).

Nitrincola sp. strain A-D6 was isolated from Salar de Ascotán, a circum-neutral and arsenic-containing salt flat environment in northern Chile. The Nitrincola genus comprises aerobic and Gram-negative bacteria belonging to the Gammaproteobacteria subdivision (6). This report can shed light on the molecular mechanisms involved in arsenic metabolism in this bacterium and its role in the biogeochemical cycle of arsenic in this extreme environment.

The genome of strain A-D6 was sequenced using the Ion Torrent PGM platform and single-end libraries. The low-quality sequences were examined by FastQC (version 0.10.1; Babraham Institute [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/]) and then trimmed by Trimmomatic version 0.32 (7) before assembly. The trimmed sequence were assembled de novo using a coverage assembled of 40×, with Mira assembler version 4.0.2 (8) and the CAP3 (9) program. This resulted in 117 contigs. Contig sizes range from 850 to 121,978 bp (N₅₀, 52,683 bp). The length of the total draft genome of Nitrincola sp. strain A-D6 is 3,795,776 bp, with a G+C content of 49.96%.

The annotation of the assembled genome was submitted to the RAST (Rapid Annotation using Subsystem Technology) server (10). The tRNA genes were detected by tRNAscan-SE version 1.23 (11) and the rRNA with RNAmmer (12). The draft genome was shown to encode 43 tRNA sequences, one complete 5S-16S-23S operon, and 4,401 protein-coding genes, 22.27% of which were assigned hypothetical functions. This hypothetical set was assigned to 4 clusters of orthologous groups that comprise a metabolic cluster with 662 genes, a genetic information processing cluster with 187 genes, an environmental information processing cluster with 272 genes, and a cellular process cluster with 99 genes.

The genes responsible for arsenic metabolism include arsenite oxidase small subunit (aioA) and large subunit (aioB), and an azu gene encoding for the physiological electron acceptor azurin (13). The genes responsible for arsenic resistance include an Ars system (arsRDACH). ArsC from the Ars system is a cytoplasmic arsenate reductase that reduces As(V) to As(III) (1). ArsD represses upper expression levels of the ars operon in the absence of As(III). ArsA is an ATPase that converts membrane potential to ATP, which is usually hydrolyzed by ArsB, making As(III) efflux more efficient. ArsB is an integral membrane protein that pumps As(III) out of the cell (1), however a canonical arsB gene is not encoded in the genome of this bacterium. Interestingly, Nitrincola sp. has a gene that encodes for the Acr3 extrusion pump (14). Thus, Nitrincola sp. strain A-D6 possesses a complete set of genes for dissimilatory oxidation and a system for reducing and extruding arsenic.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number JRLB00000000. The version described in this paper is version JRLB01000000.