1887

Abstract

In this study, we isolated a novel Gram-stain-positive, aerobic, motile, rod-shaped bacterium, named GX 13764, from the rhizosphere soil of a decayed mangrove plant collected from Beihai, Guangxi, PR China, and characterized using a polyphasic taxonomic approach. The strain exhibited yellow-orange, round, convex, shiny, smooth, opaque and 2–3 mm diameter colonies on marine agar 2216 media after 3 days of incubation at 30 °C and was capable of growth at 4–45 °C (optimum, 30 °C), pH 5.0–9.0 (optimum, pH 7.0) and 0–4 % NaCl (w/v; optimum, 2 %). The strain was positive for catalase and negative for the oxidase. The main cellular fatty acid was anteiso-C, iso-C, iso-C and iso-C. The cell-wall peptidoglycan comprised -diaminopimelic acid and the main menaquinone was MK-7. The polar lipids included one diphosphatidylglycerol, one phosphatidylglycerol, two glycolipids, two unidentified phospholipids and three unidentified lipids. Based on 16S rRNA gene analysis, GX 13764 presented the highest sequence similarity to KCTC 33872 (97.04 %). The DNA G+C content of the type strain was 44.2 mol%. The average nucleotide identity values between GX 13764 and KCTC 33872, DSM 19097 and LMG 22858 were 69.39, 68.87 and 68.95 %, respectively, with digital DNA–DNA hybridization values of 19.9, 19.5 and 19.5 %, respectively. Based on the polyphasic data, strain GX 13764 should be nominated as a novel species of the genus , for which the name sp. nov. is proposed. The type strain is GX 13764 (=MCCC 1K06654=KCTC 43366).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005538
2022-08-23
2024-12-02
Loading full text...

Full text loading...

References

  1. Patel S, Gupta RS. A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov. Int J Syst Evol Microbiol 2020; 70:406–438 [View Article]
    [Google Scholar]
  2. Chen J-H, Tian X-R, Ruan Y, Yang L-L, He Z-Q et al. Bacillus crassostreae sp. nov., isolated from an oyster (Crassostrea hongkongensis). Int J Syst Evol Microbiol 2015; 65:1561–1566 [View Article] [PubMed]
    [Google Scholar]
  3. Parag B, Sasikala C, Ramana CV. Bacillus endolithicus sp. nov., isolated from pebbles. Int J Syst Evol Microbiol 2015; 65:4568–4573 [View Article] [PubMed]
    [Google Scholar]
  4. Balcázar JL, Pintado J, Planas M. Bacillus galliciensis sp. nov., isolated from faeces of wild seahorses (Hippocampus guttulatus). Int J Syst Evol Microbiol 2010; 60:892–895 [View Article] [PubMed]
    [Google Scholar]
  5. Ko KS, Oh WS, Lee MY, Lee JH, Lee H et al. Bacillus infantis sp. nov. and Bacillus idriensis sp. nov., isolated from a patient with neonatal sepsis. Int J Syst Evol Microbiol 2006; 56:2541–2544 [View Article] [PubMed]
    [Google Scholar]
  6. Mehrshad M, Amoozegar MA, Didari M, Bagheri M, Fazeli SAS et al. Bacillus halosaccharovorans sp. nov., a moderately halophilic bacterium from a hypersaline lake. Int J Syst Evol Microbiol 2013; 63:2776–2781 [View Article] [PubMed]
    [Google Scholar]
  7. Singh H, Kaur M, Kaur L, Sharma S, Mishra S et al. Bacillus lacus sp. nov., isolated from a water sample of a salt lake in India. Int J Syst Evol Microbiol 2018; 68:801–809 [View Article] [PubMed]
    [Google Scholar]
  8. Wang HL, Zhang J, Sun L. Bacillus iocasae sp. nov., isolated from Pacmanus hydrothermal field, Manus Basin. Int J Syst Evol Microbiol 2017; 67:3547–3552 [View Article] [PubMed]
    [Google Scholar]
  9. Gupta V, Singh PK, Korpole S, Tanuku NRS, Pinnaka AK. Bacillus mangrovi sp. nov., isolated from a sediment sample from a Mangrove forest. Int J Syst Evol Microbiol 2017; 67:2219–2224 [View Article] [PubMed]
    [Google Scholar]
  10. Mao H, Wei Y, Gao Y, Pei J, Zhang Y et al. Metabacillus sediminilitoris sp. nov., a marine bacterium isolated from a tidal sediment. Int J Syst Evol Microbiol 2020; 70:5211–5216 [View Article] [PubMed]
    [Google Scholar]
  11. Abbas S, Ahmed I, Kudo T, Iqbal M, Lee Y-J et al. A heavy metal tolerant novel bacterium, Bacillus malikii sp. nov., isolated from tannery effluent wastewater. Antonie van Leeuwenhoek 2015; 108:1319–1330 [View Article] [PubMed]
    [Google Scholar]
  12. Wang M, Chen L, Liu Z, Zhang Z, Qin S et al. Isolation of a novel alginate lyase-producing Bacillus litoralis strain and its potential to ferment Sargassum horneri for biofertilizer. Microbiologyopen 2016; 5:1038–1049 [View Article] [PubMed]
    [Google Scholar]
  13. Chaudhri AA, Nadeem M, Rahman AU, Alam T, Sajjad W et al. Antioxidative and radioprotective properties of glycosylated flavonoid, xanthorhamnin from radio-resistant bacterium Bacillus indicus strain TMC-6. Curr Microbiol 2020; 77:1245–1253 [View Article] [PubMed]
    [Google Scholar]
  14. Feng T, Yang X, Wang D, Hu X, Liao J et al. A practical system for high-throughput screening of mutants of Bacillus fastidiosus Uricase. Appl Biochem Biotechnol 2017; 181:667–681 [View Article] [PubMed]
    [Google Scholar]
  15. Bongaerts GP, Vogels GD. Uric acid degradation by Bacillus fastidiosus strains. J Bacteriol 1976; 125:689–697 [View Article] [PubMed]
    [Google Scholar]
  16. 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]
  17. Chun J, Goodfellow M. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 1995; 45:240–245 [View Article] [PubMed]
    [Google Scholar]
  18. Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 1989; 17:7843–7853 [View Article] [PubMed]
    [Google Scholar]
  19. 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]
  20. 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]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  22. 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]
  23. Nei M, Kumar S. Molecular Eevolution and Pphylogenetics, 1st edn. Oxford University Press; 2000
    [Google Scholar]
  24. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
    [Google Scholar]
  25. 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]
  26. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  27. Suresh K, Prabagaran SR, Sengupta S, Shivaji S. Bacillus indicus sp. nov., an arsenic-resistant bacterium isolated from an aquifer in West Bengal, India. Int J Syst Evol Microbiol 2004; 54:1369–1375 [View Article] [PubMed]
    [Google Scholar]
  28. Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 2018; 34:i884–i890 [View Article] [PubMed]
    [Google Scholar]
  29. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
    [Google Scholar]
  30. 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]
  31. 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]
  32. 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]
  33. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T et al. Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res 2017; 45:D535–D542 [View Article]
    [Google Scholar]
  34. 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]
  35. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  36. Webley DM. A simple method for producing microcultures in hanging drops with special reference to organisms utilizing oils. J Gen Microbiol 1953; 8:66–71 [View Article] [PubMed]
    [Google Scholar]
  37. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
    [Google Scholar]
  38. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using Reverse Phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
    [Google Scholar]
  39. Komagata K, Suzuki KI. 4 lipid and cell-wall analysis in bacterial systematics. Methods Microbiology 1988; 19:161–207 [View Article]
    [Google Scholar]
  40. Cai H, Shi S, Wu J, Yang L, Wang F et al. Flavimobilis rhizosphaerae sp. nov., isolated from rhizosphere soil of Spartina alterniflora. Int J Syst Evol Microbiol 1982; 71: [View Article] [PubMed]
    [Google Scholar]
  41. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
    [Google Scholar]
  42. Sasser M, Kunitsky C, Jackoway G, Ezzell JW, Teska JD et al. Identification of Bacillus anthracis from culture using gas chromatographic analysis of fatty acid methyl esters. J AOAC Int 2005; 88:178–181 [View Article] [PubMed]
    [Google Scholar]
  43. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.005538
Loading
/content/journal/ijsem/10.1099/ijsem.0.005538
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error