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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 11

sp. nov., isolated from the phosphonate-amended seawater of the northwestern Pacific Ocean No Access

Abstract

A novel Gram-stain-negative, aerobic, rod-shaped bacterium, designated as HL-NP1, was isolated from the surface water of the northwestern Pacific Ocean after enrichment cultivation using the organic phosphorous compound of 2-aminoethylphosphonate. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to the genus , with the highest similarity to 40Bstr34 (98.7 %). The complete genome sequence of strain HL-NP1 comprised a circular chromosome of 5.58 Mbp and two circular plasmids of 0.15 and 0.22 Mbp. Comparison of the genome sequences between strains HL-NP1 and 40Bstr34 revealed that average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values (88.0, 86.4 and 33.9 %, respectively) were below the recommended cut-off levels for delineating bacterial species. Strain HL-NP1 showed optimal growth at 30 °C, pH 6.5–7.0, with 2.0–2.5 % (w/v) NaCl. The sole respiratory quinone was ubiquinone-10. The predominant fatty acid was summed feature 8 (C 6 and/or C 7). The polar lipids comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine, an unidentified aminolipid and four unidentified lipids. The G+C content of the genomic DNA was 65.1 %. Based on phylogenetic, genotypic, phenotypic and chemotaxonomic data, strain HL-NP1 is proposed to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is HL-NP1 (= KCCM 90499 = JCM 35838).

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  • Accepted:
  • Published Online:
Keyword(s): Jiella pelagia , new species , northwestern Pacific Ocean and phosphonate
Funding
This study was supported by the:
  • National Research Foundation (Award NRF-2021M3I6A1091272)
    • Principle Award Recipient: ChungYeon Hwang
  • Korea Institute of Marine Science and Technology promotion (Award 20210427)
    • Principle Award Recipient: ChungYeon Hwang
© 2023 The Authors
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2023-11-02
2024-05-08
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References

  1. Liang J, Liu J, Zhang X-H. Jiella aquimaris gen. nov., sp. nov., isolated from offshore surface seawater. Int J Syst Evol Microbiol 2015; 65:1127–1132 [View Article] [PubMed]
     [Google Scholar]
  2. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
     [Google Scholar]
  3. Tuo L, Yan XR, Xiao JH. Jiella endophytica sp. nov., a novel endophytic bacterium isolated from root of Ficus microcarpa Linn. f. Antonie van Leeuwenhoek 2019; 112:1457–1463 [View Article] [PubMed]
     [Google Scholar]
  4. Xue Z, Zhu S, Chen X, Chen T, Ren N et al. Jiella pacifica sp. nov., isolated from the West Pacific Ocean. Int J Syst Evol Microbiol 2020; 70:4345–4350 [View Article] [PubMed]
     [Google Scholar]
  5. Chen M-S, Li F-N, Chen X-H, Huang Z-H, Yan X-R et al. Jiella mangrovi sp. nov., a novel endophytic bacterium isolated from leaf of Rhizophora stylosa. Antonie van Leeuwenhoek 2021; 114:1633–1645 [View Article]
     [Google Scholar]
  6. Chen M-S, Pu X-L, Weng M-D, Chen L, Zhu L-Y et al. Description and genomic characterization of Jiella flava sp. nov., isolated from Acrostichum aureum. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  7. Chen M-S, Yi H-B, Huang Z-H, Yan X-R, Chen X-H et al. Jiella sonneratiae sp. nov., a novel endophytic bacterium isolated from bark of Sonneratia apetala. Int J Syst Evol Microbiol 2022; 72: [View Article]
     [Google Scholar]
  8. Zhang Y, Liu F, Li F-N, Chen M-S, Ma X et al. Jiella avicenniae sp. nov., a novel endophytic bacterium isolated from bark of Avicennia marina. Arch Microbiol 2022; 204:700 [View Article] [PubMed]
     [Google Scholar]
  9. Villarreal-Chiu JF, Quinn JP, McGrath JW. The genes and enzymes of phosphonate metabolism by bacteria, and their distribution in the marine environment. Front Microbiol 2012; 3:19 [View Article] [PubMed]
     [Google Scholar]
  10. G.Ternan N, Mc Grath JW, Mc Mullan G, Quinn JP. Organophosphonates: occurrence, synthesis and biodegradation by microorganisms. World J Microbiol Biotechnol 1998; 14:635–647 [View Article]
     [Google Scholar]
  11. Cook AM, Daughton CG, Alexander M. Phosphonate utilization by bacteria. J Bacteriol 1978; 133:85–90 [View Article] [PubMed]
     [Google Scholar]
  12. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Good-fellow M. eds Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley; 1991
     [Google Scholar]
  13. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
     [Google Scholar]
  14. Jeon Y-S, Lee K, Park S-C, Kim B-S, Cho Y-J et al. EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes. Int J Syst Evol Microbiol 2014; 64:689–691 [View Article] [PubMed]
     [Google Scholar]
  15. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  16. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  17. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  18. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [Google Scholar]
  19. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  20. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540–546 [View Article] [PubMed]
     [Google Scholar]
  21. Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V et al. Twelve years of SAMtools and BCFtools. Gigascience 2021; 10:giab008 [View Article] [PubMed]
     [Google Scholar]
  22. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  23. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016 [View Article]
     [Google Scholar]
  24. Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH, Hancock J. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 2020; 36:1925–1927 [View Article]
     [Google Scholar]
  25. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992; 8:275–282 [View Article] [PubMed]
     [Google Scholar]
  26. Manav MC, Sofos N, Hove‐Jensen B, Brodersen DE. The Abc of phosphonate breakdown: a mechanism for bacterial survival. BioEssays 2018; 40: [View Article]
     [Google Scholar]
  27. Liu D, Zhang Y, Fan G, Sun D, Zhang X et al. IPGA: a handy integrated prokaryotes genome and pan‐genome analysis web service. iMeta 2022; 1: [View Article]
     [Google Scholar]
  28. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
     [Google Scholar]
  29. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:913 [View Article] [PubMed]
     [Google Scholar]
  30. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
     [Google Scholar]
  31. Bernardet J-F, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article] [PubMed]
     [Google Scholar]
  32. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In Reddy CA, Beveridge TJ, B JA, Marzluf G. eds Methods for General and Molecular Microbiology American Society of Microbiology; 2007 pp 330–393 [View Article]
     [Google Scholar]
  33. Smibert R, Krieg N, Gerhardt P, Murray R, Wood W. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1993 pp 607–654
     [Google Scholar]
  34. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria Cambridge University Press; 1965
     [Google Scholar]
  35. Lányi B. Classical and rapid identification methods for medically important bacteria. Method Microbiol 1987; 19:1–67
     [Google Scholar]
  36. Jang GI, Lee I, Ha TT, Yoon SJ, Hwang YJ et al. Pseudomonas neustonica sp. nov., isolated from the sea surface microlayer of the Ross Sea (Antarctica). Int J Syst Evol Microbiol 2020; 70:3832–3838 [View Article] [PubMed]
     [Google Scholar]
  37. Gosink JJ, Woese CR, Staley JT. Polaribacter gen. nov., with three new species, P. irgensii sp. nov., P. franzmannii sp. nov. and P. filamentus sp. nov., gas vacuolate polar marine bacteria of the Cytophaga-Flavobacterium-Bacteroides group and reclassification of “Flectobacillus glomeratus” as Polaribacter glomeratus comb. nov. Int J Syst Bacteriol 1998; 48 Pt 1:223–235 [View Article] [PubMed]
     [Google Scholar]
  38. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  39. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Inc 1990
     [Google Scholar]
  40. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
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Jiella pelagia sp. nov., isolated from the phosphonate-amended seawater of the northwestern Pacific Ocean
Int J Syst Evol Microbiol 73, 006139 (2023); https://doi.org/10.1099/ijsem.0.006139
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