ABSTRACT
Cupriavidus sp. strain IK-TO18 was isolated from antimony-contaminated sediment. The draft genome sequence of the isolate contains 6,605 predicted protein-coding sequences, including genes associated with heavy metal resistance and the aerobic degradation of aromatic hydrocarbons. This sequence will provide valuable information regarding the functional versatility of the genus Cupriavidus.
ANNOUNCEMENT
Species in the genus Cupriavidus are well characterized for their ability to tolerate numerous heavy metals and degrade aromatic compounds (1–3). The versatile metabolisms of Cupriavidus species have gained interest as model organisms in bioremediation and geochemical studies. Here, we present the draft genome sequence of Cupriavidus sp. strain IK-TO18, which was isolated from antimony-contaminated sediment.
Enrichment culturing was conducted in anaerobically prepared basal salts medium (4) amended with lactate (2 mM) and anthraquinone-2,6-disulfonate (AQDS; 1 mM) and inoculated with antimony-contaminated sediment (containing 12.0 mg kg−1 Sb) collected from a former mine site (Ehime, Japan). The cultures were incubated at 25°C, and positive AQDS reduction was visually identified by the production of orange anthrahydroquinone-2,6-disulfonate (AHQDS) (5). Serially diluted positive enrichments were inoculated onto Luria broth plates and incubated aerobically. The colonies were restreaked for isolation, and the obtained pure culture was identified as a Gram-negative Cupriavidus sp. by sequencing the 16S rRNA gene and designated strain IK-TO18.
Strain IK-TO18 was grown in basal salts medium with lactate under anaerobic conditions, as described above. Genomic DNA was extracted using the MoBio PowerSoil DNA isolation kit (Qiagen) and fragmented into an average size of 350 bp using an M220 sonicator (Covaris Inc., MA). A paired-end library (insert size, ∼350 bp) was prepared using the NEBNext Ultra DNA library prep kit for Illumina (New England BioLabs). Genome sequencing was performed on the HiSeq X sequencing platform (Illumina, San Diego, CA) at the National Institute for Environmental Studies. A total of 11,668,203 raw paired-end reads were generated (2 × 150 bp), and low-quality sequences (Q ≤ 13) were removed using the Trim_Reads tool implemented in CLC Genomic Workbench 20.0.2 (GW; Qiagen). The sequences were assembled by de novo assembly in slow mode in GW with default parameters, except for the minimum contig length (500) and word size (30). The resulting 109 contigs had an N50 value of 230,767 bp and a maximum contig length of 531,585 bp. The draft genome sequence of strain IK-TO18 was 7,423,042 bp long, with 231.0× genome coverage and a G+C content of 66.1%. Annotation was conducted using the NCBI Prokaryotic Genome Annotation Pipeline (6), resulting in 6,605 predicted protein-coding sequences, 63 tRNAs, and 3 complete rRNAs (1 copy each of 5S, 16S, and 23S). BLASTn analysis of the 16S rRNA gene showed that this strain is closely related to other Cupriavidus strains (sequence identity, >98%), such as the copper-resistant bacterium Cupriavidus necator strain N-1 (GenBank accession number NR_102851.1) (3).
The genome annotation identified a variety of genes responsible for heavy metal resistance, including the ars operon (arsenic resistance), mer operon (mercury resistance), cobalt/zinc/cadmium resistance protein, copper resistance proteins, and ATPases for transport of lead/cadmium, zinc, and mercury. In addition, genes were found encoding enzymes involved in the aerobic degradation of aromatic hydrocarbons, including phenol degradation (phenol hydroxylase), catechol degradation via the meta- and ortho-cleavage pathways (catechol 2,3-dioxygenase and catechol 1,2-dioxygenase, respectively), and benzoate degradation (benzoate 1,2-dioxyganase). The draft genome sequence of Cupriavidus sp. strain IK-TO18 provides valuable information regarding the functional versatility of the genus Cupriavidus.
Data availability.
The draft genome sequence was deposited in GenBank under accession number JADGMP000000000, BioProject accession number PRJNA622630, BioSample accession number SAMN16491722, and SRA accession number SRX9374696.
ACKNOWLEDGMENTS
This work was supported by the Japan Society for the Promotion of Science (JSPS) KAKENHI (grant numbers 19KK0270, 19H04302, and 18K19879 to N.H.) and the Environmental Genomics Promotion Project of the National Institute for Environmental Studies.
We thank Yuri Sakai, Yurie Matsuda, and Kumiko Chatani for technical assistance.
Contributor Information
Natsuko Hamamura, Email: hamamura.natsuko.256@m.kyushu-u.ac.jp.
Irene L. G. Newton, Indiana University, Bloomington
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Associated Data
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Data Availability Statement
The draft genome sequence was deposited in GenBank under accession number JADGMP000000000, BioProject accession number PRJNA622630, BioSample accession number SAMN16491722, and SRA accession number SRX9374696.