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Draft genome sequence of Enterobacter hormaechei DVZ29, an iodide-oxidizing bacterium isolated from the Hanford site
1
Robert L. Smith,
1
M. Hope Howard,
2
Danielle L. Saunders,
2
and Brady D. Lee
3
Associated Data
ABSTRACT
Enterobacter hormaechei DVZ29 was isolated from a sediment trap incubated in an 129I plume at the Hanford Site (Washington State, USA). A whole genome sequencing of the strain resulted in 32 contigs and revealed that the genome is 4.90 Mb, with a G + C content of 55.61%.
ANNOUNCEMENT
From 1943 to 1987, plutonium was produced at the Hanford Site (Washington State, USA) resulting in the generation of more than 1,000,000,000 m3 of liquid wastes, including radioactive materials, which have contaminated the local ecosystems (1). Isolate DVZ29 was among several bacteria we cultured from a sediment trap incubated for 50 days in a groundwater monitoring well located within a plume containing the radioisotope 129I at the Hanford Site (2). Its identity was determined using full-length 16S rRNA gene sequencing with the closest match being Enterobacter hormaechei strain 0992–77 (NR_042154.1) (2). E. hormaechei DVZ29 was identified as an iodide oxidizer, though less efficient than most other bacteria tested, in a study to explore the potential for native bacteria in the soil ecosystem to contribute to bioremediation efforts at the site (2). Here, we report the draft genome of E. hormaechei DVZ29 to contribute to the understanding of the genetics of bacterial iodine transformation and bioremediation efforts at the Hanford Site.
E. hormaechei DVZ29 was grown from a −80°C freezer stock in tryptic soy broth with shaking for 48 h at 28°C before DNA extraction with the Invitrogen PureLink Genomic DNA Mini Kit. DNA sequencing was performed at SeqCenter (https://www.seqcenter.com). Briefly, the Illumina DNA Prep kit and IDT 10 bp UDI indices were used to generate sample libraries, which were then sequenced on an Illumina NextSeq 2000, resulting in 2 × 151 bp paired-end reads. Demultiplexing, quality control, and adapter trimming were performed with bcl-convert v3.9.3 (https://emea.support.illumina.com/sequencing/sequencing_software/bcl-convert.html). The Bacterial and Viral Bioinformatics Resource Center (BV-BRC; https://www.bv-brc.org/) genome assembly pipeline using Unicycler v0.4.8 assembled reads into contigs (3, 4). CheckM was used to determine the completeness and contamination of the genome, which was then annotated using the Prokaryotic Genome Annotation Pipeline v.6.5 from the National Center for Biotechnology Information (5, 6). In addition to the NCBI average nucleotide identity (ANI) process at genome submission to confirm the identity of DVZ29, the genome sequence data were also uploaded to the Type (Strain) Genome Server (TYGS; https://tygs.dsmz.de) for digital DNA-DNA hybridization (dDDH) analysis (7, 8). Default parameters were used except where otherwise noted.
The E. hormaechei DVZ29 genome is 4,903,890 bp in length, with a G + C content of 55.61%, 69 tRNAs, and 4 rRNAs. CheckM analysis indicated that the genome was 99.73% complete, with 0.16% contamination. See Table 1 for additional assembly and sequencing information. The species designation was confirmed with a dDDH (formula d4) value of 91.3% (95% CI, 89.2–93.1) and an ANI of >99% when compared to Enterobacter hormaechei subsp. steigerwaltii DSM 16691 NZ_CP017179.
TABLE 1
Information for E. hormaechei DVZ29
| Parameters | Genome data |
|---|---|
| Bioproject | PRJNA855226 |
| SRA (Sequence Read Archive) accession | SRR23366688 |
| Genome assembly accession | GCA_030238495.1 |
| Total no. of reads | 10,204,820 |
| Total read length (bp) | 2,630,013,875 |
| Avg read length (bp) | 128 |
| N50 (bp) | 511,208 |
| Genome size (bp) | 4,903,890 |
| No. of contigs | 32 |
| Mean coverage (x) | 531 |
| % GC content | 55.61 |
| No. of protein coding sequences | 4,627 |
| No. of tRNAs | 69 |
| No. of rRNAs | 4 |
ACKNOWLEDGMENTS
We thank Ahlam Akmel and Glory B. Bassey for technical assistance.
This work was funded by a National Science Foundation grant to C.J.R. (DEB 1832140).
DATA AVAILABILITY
This Whole Genome Shotgun project has been deposited in GenBank under the accession number JASSUV000000000. The version described in this paper is JASSUV000000000.1. The raw reads are available under SRA accession number SRR23366688. Additional information is available in Table 1.