Draft genome sequence data and analysis of Shinella sp. strain JR1-6 isolated from nitrate- and radionuclide-contaminated groundwater in Russia

Shinella sp. strain JR1-6 is a Gram-negative, facultatively anaerobic, non-spore-forming, motile, rod-shaped bacterium isolated from radionuclide- and nitrate-contaminated groundwater. This bacterium reduces nitrate to N2. Strain JR1-6 has potential for removal of nitrate contamination, which is the main reason for the interest in sequencing its genome. Here, we present a set of features of Shinella sp. strain JR1-6, together with the description of its genomic sequencing and annotation. The draft genome of strain JR1-6 has a size of ∼7.09 Mb and contains 6,945 genes, including 62 RNA genes. In the genome of strain JR1-6, the genes were revealed encoding nitrate reduction to N2, as well as the genes associated with metal resistance, showing its adaptation to the conditions of the environment and possible role in nitrate removal from contaminated groundwater. The draft genome sequence of Shinella sp. strain JR1-6 is available at DDBJ/EMBL/GenBank under the accession no. SHMI00000000.

sp. strain JR1-6 is available at DDBJ/EMBL/GenBank under the accession no. SHMI00000000. © 2019 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4.0/).

Data
In the present work, we report the draft genome sequence data and genome annotation of a denitrifying bacterial strain JR1-6 (¼VKM B-3307) isolated from a groundwater sample collected near the surface reservoir for liquid radioactive waste (Ozyorsk, South Urals, Russia) (55 38 0 N 60 47 0 E) [1]. Strain JR1-6 was chosen for genome sequencing in order to identify the genetic determinants providing for its occurrence in the environment contaminated with nitrate and radionuclides and to elucidate its possible application in wastewater treatment biotechnologies for nitrate and nitrous oxide removal. The cells of the strain JR1-6 grown in liquid TEG medium with bacto-trypton, yeast extract, and glucose were non-spore-forming rods 0.65e0.96 Â 1.3e3.5 mm, motile at the early stage of incubation (Fig. 1).
The strain grew optimally at 23e28 C, pH 7e8, and 1e1.5% NaCl (Table 1). In the medium with acetate and nitrate the strain reduced nitrate to nitrite and then to dinitrogen gas. Strain JR1-6 was a member of the genus Shinella within the family Rhizobiaceae of the class Alphaproteobacteria (Table 1) [2e7]. Its 16S rRNA gene sequence (GenBank accession number MG205606) showed the highest similarity with respective sequence of Shinella yambaruensis MS4 T (98.8%) (Fig. 2)

Value of the data
The data obtained might increase the molecular information on bacteria inhabiting groundwater highly contaminated with nitrate and radionuclides. The draft genome sequence of Shinella sp. strain JR1-6 will provide insights into the genetic determinants involved in heavy metal and antibiotic resistance in bacteria of the genus Shinella. Data of genome sequencing of Shinella sp. JR1-6 can be used for further understanding of the genomic potential of the strain and elucidation of its possible biotechnological application for nitrate removal from contaminated water. and S. pollutisoli [7e10]. Members of this genus are aerobic organotrophs, which have been isolated from an anaerobic sludge blanket reactor and a sewage treatment system, from domestic waste compost, root nodules, and from polluted soil. Nitrate is reduced and supports anaerobic growth of S. fusca and S. daejeonensis. Since the genome of the S. yambaruensis type strain is not represented in the  NCBI database, unequivocal determination of the species position of the new strain JR1-6 was impossible. The features for the draft genome sequence of Shinella sp. JR1-6 are summarized in Table 2.
The draft genome sequence of Shinella sp. strain JR1-6 contained 6,945 genes, of which 6,701 were protein-coding sequences, 182 were pseudo genes, and 58 coded RNAs (tRNAs, 5S, 16S, and 23S) and 4 ncRNAs. Most of the annotated genes determined the synthesis of amino acids and derivatives (558), carbohydrate metabolism (493), protein metabolism (227), membrane transport (214), and synthesis of cofactors, vitamins, prosthetic groups and pigments (176) (Fig. 3). The genome of Shinella sp. JR1-6 contained at least 7 plasmids, since 7 different repABC gene clusters located on 7 different contigs were detected. In the genome of Shinella sp. strain JR1-6 the genes were revealed encoding nitrate reduction to N 2 , as well as the genes responsible for utilization of various monosaccharides and proteins. Several genes responsible for cobalt, zinc, cadmium, and mercury resistance were also observed. Phenotypic  and genomic data set of Shinella sp. strain JR1-6 indicates its adaptation to the conditions of the environment and its possible role in nitrate removal from contaminated groundwater. The Whole Genome Shotgun project of Shinella sp. JR1-6 has been deposited at DDBJ/EMBL/GenBank under the accession no. SHMI00000000 and the release date of its GenBank Data is February 26, 2019. The raw FASTQ reads have been deposited in the NCBI SRA database under the accession no. SRR9587904.

Isolation of the strain JR1-6
Strain JR1-6 was isolated from a groundwater sample contaminated with nitrate, sulfate, acetate, and radionuclides. At the time of sampling, pH and Eh of the groundwater were 7.9 and þ 200 mV, respectively. The sample was collected at the observation well 1/69 from the depth of 44 m at a distance 3.2 km from the Karachai Lake (Ozyorsk town, South Urals, Russia) [1]. The strain was purified by successive transfers from the liquid TEG medium containing bacto-trypton (5.0 g L À1 ), yeast extract (1.0 g L À1 ), glucose (5.0 g L À1 ), and distilled water (1 L, pH 7.0) to solid TEG medium with agar-agar (15.0 g L À1 ). Bacteria were incubated at 22e28 C. Strain JR1-6 was deposited in the All-Russian Collection of Microorganisms as VKM В-3307.

DNA isolation and sequencing
Biomass of the strain JR1-6 was grown in TEG liquid medium for 72 h at 28 C. The cells were harvested by centrifugation. Integrity of the cells was accessed by transmission electron microscopy (JEOL JEM-1010, Japan) of bacteria negatively stained with 1% phosphotungstic acid (Fig. 1B). Genomic DNA was extracted according to the method of Wilson [11], with minor modifications. The cell pellet was resuspended in 400 ml of TE-buffer. Thereafter, 25 mL of 10% SDS and 20 mL of proteinase K solution were added and the mixture was incubated at 37 C for 60 min. After incubation, 125 mL of 4 M NaCl, 160 mL of 5% CTAB and 20 mL of RNase (10 mg/mL) were added. The mixture was then incubated for 10 min at 65 C and cooled to room temperature; thereafter, the mixture was treated with chloroform followed by centrifugation for 10 min at 9000 Â g. DNA was extracted from the supernatant by adding 0.6 volume of isopropanol. The dried DNA sample was dissolved in 50 mL of MQ. The libraries were constructed with the NEBNext DNA library prep reagent set for Illumina, according to the protocol for the kit. Next-generation shotgun-sequencing of the genomic DNA was carried out using the Illumina HiSeq 1500 platform (Illumina Inc., USA) with 250-bp single-end reads.

Genome assembly and annotation
A total of 1,734,433 reads were obtained from JR1-6. Raw sequence reads were quality-checked with FastQC v.11.7 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and low-quality reads were trimmed using Trimmomatic v. 0.36 [12]. Subsequently, the quality-filtered reads were de novo assembled with SPAdes version 3.11.0 using the default settings [13]. The final assembled 7,093,386-bplong genome comprised of 131 scaffolds, with an N 50 value of 237,993 bp and an average coverage of 41 Â . Identification of protein-coding sequences and primary annotation was performed using the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP) [14]. Additional gene prediction and functional annotation were performed in the Rapid Annotation using Subsystems Technology (RAST) server [15].