1887

Abstract

A taxonomic study was carried out on strain BGMRC 0090, which was isolated from seawater. The isolate was a Gram-negative, aerobic, flagellated, rod-shaped bacterium with algicidal activity. Optimal growth was observed at 30 °C, pH 6.0 and with 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain BGMRC 0090 belonged to the genus , with highest sequence similarity to CC-MMS-1 (98.4 %). Average nucleotide identity, amino acid identity and digital DNA–DNA hybridization values between strain BGMRC 0090 and five strains of the genus with publicly available genomes were below 84.0, 69.2 and 21.4 %, respectively. The genome of strain BGMRC 0090 was 3.2 Mb with 64.8 mol% DNA G+C content and encoded 2905 predicted proteins, three rRNA, 42 tRNA and four ncRNA genes. Some algicidal biosynthesis-associated genes were detected in the genome. Strain BGMRC 0090 contained Q-10 as the major quinone. The predominant fatty acids were identified as summed feature 8 (Cω7/ω6) and C. Based on the polyphasic evidence presented in this paper, strain BGMRC 0090 is concluded to represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is BGMRC 0090 (= KCTC 92591=MCCC 1K08100).

Funding
This study was supported by the:
  • Science and Technology Major Project of Guangxi Autonomous Region (Award AA18242047)
    • Principle Award Recipient: FeiLi
  • Science and Technology Major Project of Guangxi Autonomous Region (Award ZY21195027)
    • Principle Award Recipient: Jun-XiangLai
  • This research was supported by the National Natural Science Foundation of China (Award 42066002)
    • Principle Award Recipient: Xian-LingQin
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2023-04-06
2024-06-19
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References

  1. Edvardsen B, Imai I. The ecology of harmful flagellates within Prymnesiophyceae and Rapidophyceae. In Grane´li E, Turner JT. eds Ecology of Harmful Algae Berlin: Springer; 2006 pp 67–79
    [Google Scholar]
  2. Nishibori N, Niitsu M, Fujihara S, Sagara T, Nishio S et al. Occurrence of the polyamines caldopentamine and homocaldopentamine in axenic cultures of the red tide flagellates Chattonella antiqua and Heterosigma akashiwo (Raphidophyceae). FEMS Microbiol Lett 2009; 298:74–78 [View Article]
    [Google Scholar]
  3. Cho JC, Giovannoni SJ. Parvularcula bermudensis gen. nov., sp. nov., a marine bacterium that forms a deep branch in the alpha-Proteobacteria. Int J Syst Evol Microbiol 2003; 53:1031–1036 [View Article]
    [Google Scholar]
  4. Arun AB, Chen W-M, Lai W-A, Chou J-H, Rekha PD et al. Parvularcula lutaonensis sp. nov., a moderately thermotolerant marine bacterium isolated from a coastal hot spring. Int J Syst Evol Microbiol 2009; 59:998–1001 [View Article]
    [Google Scholar]
  5. Sun L-L, Dang Y-R, Li Y, Qin Q-L, Su H-N et al. Parvularcula marina sp. nov., isolated from surface water of the South China Sea, and emended description of the genus Parvularcula. Int J Syst Evol Microbiol 2019; 69:2571–2576 [View Article]
    [Google Scholar]
  6. Al-Omari J, Szabó I, Szerdahelyi GS, Radó J, Kaszab E et al. Parvularcula mediterranea sp. nov., isolated from marine plastic debris from Zakynthos Island, Greece. Int J Syst Evol Microbiol 2021; 71:004608 [View Article] [PubMed]
    [Google Scholar]
  7. Yu ZW, Lai QL, Li GZ, Shao ZZ. Parvularcula dongshanensis sp. nov., isolated from soft coral. Int J Syst Evol Microbiol 2013; 63:2114–2117 [View Article]
    [Google Scholar]
  8. Guillard RRL. Culture of phytoplankton for feeding marine invertebrates. In Smith WL, Canley MH. eds Culture of Marine Invertebrate Animals New York: Plenum Press; 1975 pp 29–60
    [Google Scholar]
  9. de Lamballerie X, Zandotti C, Vignoli C, Bollet C, de Micco P. A one-step microbial DNA extraction method using “Chelex 100” suitable for gene amplification. Res Microbiol 1992; 143:785–790 [View Article] [PubMed]
    [Google Scholar]
  10. Li W-J, Xu P, Schumann P, Zhang Y-Q, Pukall R et al. Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China), and emended description of the genus Georgenia. Int J Syst Evol Microbiol 2007; 57:1424–1428 [View Article]
    [Google Scholar]
  11. 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]
  12. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article]
    [Google Scholar]
  13. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
    [Google Scholar]
  14. 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]
  15. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  16. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406 [View Article]
    [Google Scholar]
  17. 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]
  18. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article]
    [Google Scholar]
  19. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
    [Google Scholar]
  20. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
    [Google Scholar]
  21. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article] [PubMed]
    [Google Scholar]
  22. 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]
  23. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276–W282 [View Article] [PubMed]
    [Google Scholar]
  24. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
  25. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  26. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
    [Google Scholar]
  27. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004; 32:D277–80 [View Article] [PubMed]
    [Google Scholar]
  28. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V et al. The carbohydrate-active enzymes database (CAZY): an expert resource for glycogenomics. Nucleic Acids Res 2009; 37:D233–8 [View Article]
    [Google Scholar]
  29. Salomon PS, Imai I. Pathogens of harmful alga. In Grane′ li E, Turner JT. eds Ecology of Harmful Algae Berlin Heidelberg: Springer-Verlag; 2006 pp 271–282
    [Google Scholar]
  30. Xian QM, Chen HD, Liu HL, Zou HX, Yin DQ. Isolation and identification of antialgal compounds from the leaves of Vallisneria spiralis L. by activity-guided fractionation. Environ Sci Pollut Res Int 2006; 13:233–237 [View Article]
    [Google Scholar]
  31. Zhang B-H, Chen W, Li H-Q, Yang J-Y, Zha D-M et al. l-Valine, an antialgal amino acid from Streptomyces jiujiangensis JXJ 0074(T). Appl Microbiol Biotechnol 2016; 100:4627–4636 [View Article]
    [Google Scholar]
  32. Kelly KL. Inter-Society Color Council-National Bureau of Standards Color-Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
    [Google Scholar]
  33. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family “Oxalobacteraceae” isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article]
    [Google Scholar]
  34. Gordon RE, Barnett DA, Handerhan JE, Pang C-N. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
    [Google Scholar]
  35. Graham PH, Parker CA. Diagnostic features in the characterisation of the root-nodule bacteria of legumes. Plant Soil 1964; 20:383–396 [View Article]
    [Google Scholar]
  36. Yokota A, Tamura T, Hasegawa T, Huang LH. Catenuloplanes japonicus gen. nov., sp. nov., nom. rev., a new genus of the order Actinomycetales. Int J Syst Bacteriol 1993; 43:805–812 [View Article]
    [Google Scholar]
  37. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newslett 1990; 20:1–6
    [Google Scholar]
  38. Collins MD. Isoprenoid quinones. In Goodfellow M, O’Donnell AG. eds Chemical Methods in Prokaryotic Systematics Chichester: John Wiley &Sons; 1994 pp 345–401
    [Google Scholar]
  39. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
  40. 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]
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