ABSTRACT
Here, we report the draft genome sequence of Stenotrophomonas daejeonensis strain NLF4-10, isolated from a livestock wastewater treatment plant in Nonsan, Republic of Korea. The whole-genome sequence of S. daejeonensis strain NLF4-10 was analyzed using the Pacific Biosciences Sequel and Illumina NovaSeq sequencing platforms. The genome comprises a 3,655,148 bp chromosome with a GC content of 68%, 3,274 coding DNA sequences (CDSs), 59 transfer RNAs (tRNAs), and 4 noncoding RNAs (ncRNAs).
ANNOUNCEMENT
Wastewater treatment plants emit various kinds of odor pollutants, like ammonia, hydrogen sulfide, volatile fatty acids, acetic acid, styrene, and other organic compounds (1–3). These malodorous gases in livestock manure adversely affect human beings, such as causing irritation to the nose, headache, dizziness, hyperemia, asphyxiation, nausea, and unconsciousness (4, 5). Recently, strain NLF4-10 was isolated during the investigation of the odor reducing bacteria.
The species S. daejeonensis MJ03T, which is Gram-stain-negative, motile, and rod shaped, was isolated from sewage treatment plants (6). Here, we describe the draft genome sequence and annotation of S. daejeonensis Strain NLF4-10 that was isolated from a livestock wastewater treatment plant in Nonsan, Republic of Korea. The biofilterfunctions as a livestock odor removal system. A liquid sample from the biofilter was immediately placed in a 4°C refrigerated room. The sample was 10-fold serially diluted in saline solution, and 100 μl of each dilution was spread on sulfur oxidation bacteria medium. The composition of sulfur oxidation bacteria medium was as follows: 8.0 g Na2S2O3·5H2O, 2.0 g K2HPO4, 2.0 g KH2PO4, 0.4 g NH4Cl, 0.2 g MgCl2·7H2O, 0.01 g FeSO4·7H2O, 15.0 g agar, 1L Distilled water at pH 7.0. After 5 to 10 days of incubation at 30°C, single colonies were selected.
The Strain NLF4-10 was grown in Trypticase soy agar (Difco, USA) for 5 days at 30°C. The genomic DNA was obtained from the cultivated cells on Trypticase soy agar (Difco, USA) using the Maxwell 16 DNA purification kit (Promega, USA). The extracted DNA was sequenced at Theragen Bio Institute (Republic of Korea) with a PacBio sequel using a 15 kb SMRTbell template library and Illumina Nova Seq platform (2 × 151-bp). A size selection cutoff of 7,000 bp was used. The size-selected SMRTbell library was annealed and bound according to the SMRT Link setup and sequenced on a Sequel II instrument. SMRTbell template prep kit 2.0 (PacBio) and TruSeq nano DNA library prep kit (Illumina) were used to prepare sequencing libraries. The 101,469 total reads (read N50, 11,224 bp) produced by the PacBio RS II platform were assembled, whereas the Illumina platform produced 15,357,866 total reads (read N50, 13,549 bp). Then, de novo genome assembly, error correction, and annotation were performed by Canu (v1.7) (7), Pilon (v1.22) (8), and Prokka (v1.1.0) (9) software, respectively. Aragon (v1.2.36) was used to predict tRNAs, and Barrnap software (v0.6) was used to predict rRNAs (5S rRNAs, 16S rRNAs, and 23S rRNAs) (10). To confirm species, the average nucleotide identity (ANI) was calculated using OrthoANI (11). Default parameters were used for all software unless otherwise specified.
The draft genome of strain NLF4-10 consisted of 4 contigs with a total length of 3,655,148 bp (read N50, 3, 578, 136). The sequencing depth of coverage was 236.0x and the genomic DNA GC content was 68.0 mol%. A total of 3,274 protein coding genes, 9 rRNA genes (3 of 5S rRNA, 3 of 16S rRNA, and 3 of 23S rRNA), 59 tRNA genes, 4 non-coding RNA, and 50 pseudo genes were predicted. Based on the 16S rRNA gene sequence similarity and average nucleotide identity, the strain NLF4-10 is most closely related to S. daejeonensis MJ03T with values of 99.11% and 97.85%, respectively.
Data availability.
The genome sequence and raw sequencing reads for strain NLF4-10 were deposited under GenBank accession numbers JAKSEE000000000, BioProject accession number PRJNA807444, BioSample accession number SAMN25981972, and Sequence Read Archive (SRA) accession number SRX15804104. The version described in this paper is the first version, JAKSEE010000000. S. daejeonensis strain NLF4-10 has been deposited in the Korean Collection for Type Cultures under accession number KCTC 14796BP.
ACKNOWLEDGMENTS
This work was carried out with the support of a grant (project number NNIBR202202111) from the Nakdonggang National Institute of Biological Resources, funded by the Ministry of Environment, Republic of Korea.
Contributor Information
Mi-Hwa Lee, Email: blume96@nnibr.re.kr.
Frank J. Stewart, Montana State University
REFERENCES
- 1.Lebrero R, Bouchy L, Stuetz R, Muñoz R. 2011. Odor assessment and management in wastewater treatment plants: a review. Critical Rev Environ Sci Technol 41:915–950. doi: 10.1080/10643380903300000. [DOI] [Google Scholar]
- 2.Lebrero R, Rangel MGL, Muñoz R. 2013. Characterization and biofiltration of a real odorous emission from wastewater treatment plant sludge. J Environ Manage 116:50–57. doi: 10.1016/j.jenvman.2012.11.038. [DOI] [PubMed] [Google Scholar]
- 3.Godayol A, Besalú E, Anticó E, Sanchez JM. 2015. Monitoring of sixteen fragrance allergens and two polycyclic musks in wastewater treatment plants by solid phase microextraction coupled to gas chromatography. Chemosphere 119:363–370. doi: 10.1016/j.chemosphere.2014.06.072. [DOI] [PubMed] [Google Scholar]
- 4.Costantini M, Bacenetti J, Coppola G, Orsi L, Ganzaroli A, Guarino M. 2020. Improvement of human health and environmental costs in the European Union by air scrubbers in intensive pig farming. J Clean Prod 275:1–11. doi: 10.1016/j.jclepro.2020.124007. [DOI] [Google Scholar]
- 5.Wang Y-C, Han M-F, Jia T-P, Hu X-R, Zhu H-Q, Tong Z, Lin Y-T, Wang C, Liu D-Z, Peng Y-Z, Wang G, Meng J, Zhai Z-X, Zhang Y, Deng J-G, Hsi H-C. 2021. Emissions, measurement, and control of odor in livestock farms: a review. Sci Total Environ 776:1–16. doi: 10.1016/j.scitotenv.2021.145735. [DOI] [PubMed] [Google Scholar]
- 6.Lee M, Woo SG, Chae M, Shin MC, Jung HM, Ten LN. 2011. Stenotrophomonas daejeonensis sp. nov., isolated from sewage. Int J Syst Evol Microbiol 61:598–604. doi: 10.1099/ijs.0.017780-0. [DOI] [PubMed] [Google Scholar]
- 7.Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 27:722–736. doi: 10.1101/gr.215087.116. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, Earl AM. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9:e112963. doi: 10.1371/journal.pone.0112963. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 9.Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. doi: 10.1093/bioinformatics/btu153. [DOI] [PubMed] [Google Scholar]
- 10.Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108. doi: 10.1093/nar/gkm160. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Yoon SH, Ha SM, Lim J, Kwon S, Chun J. 2017. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110:1281–1286. doi: 10.1007/s10482-017-0844-4. [DOI] [PubMed] [Google Scholar]
Associated Data
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Data Availability Statement
The genome sequence and raw sequencing reads for strain NLF4-10 were deposited under GenBank accession numbers JAKSEE000000000, BioProject accession number PRJNA807444, BioSample accession number SAMN25981972, and Sequence Read Archive (SRA) accession number SRX15804104. The version described in this paper is the first version, JAKSEE010000000. S. daejeonensis strain NLF4-10 has been deposited in the Korean Collection for Type Cultures under accession number KCTC 14796BP.