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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 73, Issue 9

sp. nov., a coral-beneficial bacterium isolated from No Access

Abstract

Coral reef ecosystems are facing decline due to climate change, overfishing, habitat destruction and pollution. Bacteria play an essential role in maintaining the stability of coral reef ecosystems, influencing the well-being and fitness of coral hosts. The exploitation of coral probiotics has become an urgent issue. A short-rod shaped aerobic bacterium, designated NTR19, was isolated in a healthy coral from Daya Bay, Shenzhen, PR China. Its cells were Gram-negative, motile with a polar flagellum. The activities of catalase and oxidase were positive. Strain NTR19 grew at 10–41 °C (optimum, 28 °C), with NaCl concentrations of 0–4 % (w/v; optimum, 0.5 %) and at pH 5.0–9.5 (optimum, pH 7.0–7.5). The predominant fatty acids (>10 %) were summed feature 8 (57.6 %), C cyclo ω8 (12.6 %) and C (12.0 %). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phospholipid and phosphatidylcholine. The major respiratory quinone was Q-10. The draft genome was 4.68 Mbp with 61.2 mol% DNA G+C content. In total, 4477 coding sequences were annotated and there were 64 RNA genes. The average nucleotide identity (ANI) and average amino acid identity (AAI) values between strain NTR19 and the related species were 78.23–79.70% and 80.26–80.50 %, respectively. This strain encoded many proteins for the activities of catalase and oxidase in the genome. Strain NTR19 was clearly distinct from its closest neighbours ACCC 05753 and ACCC 11238 with the 16S rRNA gene sequence similarity values of 96.86 and 96.36 %, respectively. The results of phylogenetic analysis, as well as ANI and AAI values, revealed that strain NTR19 belongs to and was distinct from other species of this genus. The physiological, biochemical and chemotaxonomic characteristics also supported the species novelty of strain NTR19. Thus, strain NTR19 is considered to be classified as a novel species in the genus , for which the name sp. nov. is proposed. The type strain is NTR19 (=JCM 35342=MCCC 1K07226).

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  • Accepted:
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Keyword(s): Neorhizobium turbinariae sp. nov. , scleractinian coral and Turbinaria peltata
Funding
This study was supported by the:
  • Guangdong Key Area R & D Program Project (Award 2020B1111030002)
    • Principle Award Recipient: BaohuaXiao
  • Shenzhen Science and Technology R&D Fund (Award KCXFZ20211020165547011)
    • Principle Award Recipient: BaohuaXiao
  • Shenzhen Science and Technology R&D Fund (Award JCYJ20200109144803833)
    • Principle Award Recipient: BaohuaXiao
© 2023 The Authors
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2023-09-26
2024-05-08
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References

  1. Mousavi SA, Österman J, Wahlberg N, Nesme X, Lavire C et al. Phylogeny of the Rhizobium-Allorhizobium-Agrobacterium clade supports the delineation of Neorhizobium gen. nov. Syst Appl Microbiol 2014; 37:208–215 [View Article] [PubMed]
     [Google Scholar]
  2. Zhang X-X, Gao J-S, Cao Y-H, Sheirdil RA, Wang X-C et al. Rhizobium oryzicola sp. nov., potential plant-growth-promoting endophytic bacteria isolated from rice roots. Int J Syst Evol Microbiol 2015; 65:2931–2936 [View Article] [PubMed]
     [Google Scholar]
  3. Kuzmanović N, Fagorzi C, Mengoni A, Lassalle F, diCenzo GC. Taxonomy of Rhizobiaceae revisited: proposal of a new framework for genus delimitation. Int J Syst Evol Microbiol 2022; 72:005243 [View Article] [PubMed]
     [Google Scholar]
  4. Zhang X, Li B, Wang H, Sui X, Ma X et al. Rhizobium petrolearium sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2012; 62:1871–1876 [View Article] [PubMed]
     [Google Scholar]
  5. Wang ET, van Berkum P, Beyene D, Sui XH, Dorado O et al. Rhizobium huautlense sp. nov., a symbiont of Sesbania herbacea that has a close phylogenetic relationship with Rhizobium galegae. Int J Syst Bacteriol 1998; 48:687–699 [View Article] [PubMed]
     [Google Scholar]
  6. Weis VM. Cellular mechanisms of cnidarian bleaching: stress causes the collapse of symbiosis. J Exp Biol 2008; 211:3059–3066 [View Article] [PubMed]
     [Google Scholar]
  7. Davy SK, Allemand D, Weis VM. Cell biology of cnidarian-dinoflagellate symbiosis. Microbiol Mol Biol Rev 2012; 76:229–261 [View Article] [PubMed]
     [Google Scholar]
  8. Tout J, Jeffries TC, Webster NS, Stocker R, Ralph PJ et al. Variability in microbial community composition and function between different niches within a coral reef. Microb Ecol 2014; 67:540–552 [View Article] [PubMed]
     [Google Scholar]
  9. Webster NS, Thomas T, Dubilier N, Collier RJ. The sponge hologenome. mBio 2016; 7:e00135-00116 [View Article] [PubMed]
     [Google Scholar]
  10. Wang Y-S, Lou Z-P, Sun C-C, Sun S. Ecological environment changes in Daya Bay, China, from 1982 to 2004. Mar Pollut Bull 2008; 56:1871–1879 [View Article] [PubMed]
     [Google Scholar]
  11. Zhang L, Xiong L, Li J, Huang X. Long-term changes of nutrients and biocenoses indicating the anthropogenic influences on ecosystem in Jiaozhou Bay and Daya Bay, China. Mar Pollut Bull 2021; 168:112406 [View Article] [PubMed]
     [Google Scholar]
  12. Yang X, Tan Y, Li K, Zhang H, Liu J et al. Long-term changes in summer phytoplankton communities and their influencing factors in Daya Bay, China (1991-2017). Mar Pollut Bull 2020; 161:111694 [View Article] [PubMed]
     [Google Scholar]
  13. Ausubel FM. Short Protocols in Molecular Biology: A Compendium of Methods from Current Protocols in Molecular Biology New York: Wiley; 1996 [View Article]
     [Google Scholar]
  14. Sun H, Hu Y, Zhou S, Zheng Y, Zhang X-H. Glycocaulis profundi sp. nov., a marine bacterium isolated from seawater of the Mariana Trench. Int J Syst Evol Microbiol 2020; 70:814–819 [View Article] [PubMed]
     [Google Scholar]
  15. 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]
  16. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
     [Google Scholar]
  17. 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]
  18. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  19. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  20. 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]
  21. 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]
  22. Wang X, Guo F, Tian P, Yu S, Xue C-X et al. Flammeovirga agarivorans sp. nov., an agar-digesting marine bacterium isolated from surface seawater. Int J Syst Evol Microbiol 2020; 70:6060–6066 [View Article] [PubMed]
     [Google Scholar]
  23. Beveridge TJ, Lawrence JR, Murray RG. Sampling and staining for light microscopy. In Methods for General and Molecular Microbiology, 3rd. edn American Society of Microbiology; 2007 pp 19–33 [View Article]
     [Google Scholar]
  24. 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]
  25. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In In Methods for General and Molecular Microbiology, 3rd. edn American Society of Microbiology; 2007 pp 330–393 [View Article]
     [Google Scholar]
  26. Yoon J-H, Lee K-C, Kho YH, Kang KH, Kim C-J et al. Halomonas alimentaria sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Int J Syst Evol Microbiol 2002; 52:123–130 [View Article] [PubMed]
     [Google Scholar]
  27. Sasser M. Technical Note 101: Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Newark, DE: MIDI; 1990
     [Google Scholar]
  28. Xie C-H, Yokota A. Phylogenetic analyses of Lampropedia hyalina based on the 16S rRNA gene sequence. J Gen Appl Microbiol 2003; 49:345–349 [View Article] [PubMed]
     [Google Scholar]
  29. 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]
  30. Collins MD, Shah HN. Fatty acid, menaquinone and polar lipid composition of Rothia dentocariosa. Arch Microbiol 1984; 137:247–249 [View Article]
     [Google Scholar]
  31. Komagata K, Suzuki K-I. 4 Lipid and cell-wall analysis in bacterial systematics. In Methods in Microbiology Elsevier; 1988 pp 161–207
     [Google Scholar]
  32. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [View Article] [PubMed]
     [Google Scholar]
  33. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007; 23:673–679 [View Article] [PubMed]
     [Google Scholar]
  34. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
     [Google Scholar]
  35. Lowe TM, Eddy SR. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article] [PubMed]
     [Google Scholar]
  36. Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL et al. Rfam: updates to the RNA families database. Nucleic Acids Res 2009; 37:D136–D140 [View Article] [PubMed]
     [Google Scholar]
  37. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article] [PubMed]
     [Google Scholar]
  38. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
     [Google Scholar]
  39. Hughes TP, Kerry JT, Álvarez-Noriega M, Álvarez-Romero JG, Anderson KD et al. Global warming and recurrent mass bleaching of corals. Nature 2017; 543:373–377 [View Article] [PubMed]
     [Google Scholar]
  40. Tchernov D, Kvitt H, Haramaty L, Bibby TS, Gorbunov MY et al. Apoptosis and the selective survival of host animals following thermal bleaching in zooxanthellate corals. Proc Natl Acad Sci U S A 2011; 108:9905–9909 [View Article] [PubMed]
     [Google Scholar]
  41. Rosenblueth M, Ormeño-Orrillo E, López-López A, Rogel MA, Reyes-Hernández BJ et al. Nitrogen fixation in cereals. Front Microbiol 2018; 9:1794 [View Article] [PubMed]
     [Google Scholar]
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Neorhizobium turbinariae sp. nov., a coral-beneficial bacterium isolated from Turbinaria peltata
Int J Syst Evol Microbiol 73, 006057 (2023); https://doi.org/10.1099/ijsem.0.006057
/content/journal/ijsem/10.1099/ijsem.0.006057
/content/journal/ijsem/10.1099/ijsem.0.006057
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