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Volume 74, Issue 1

sp. nov., isolated from sediment of mangrove plant , and comparative genomic analyses of the genus No Access

Abstract

A Gram-negative, non-motile, strictly aerobic, rod-shaped bacterium, designated as H12, was isolated from the sediments of mangrove plant taken from Dapeng district, Shenzhen, PR China. The pairwise 16S rRNA gene sequence analysis showed that strain H12 shared high identity levels with species of the genus , with the highest similarity level of 98.5 % to SPO729, followed by 98.1 % to CN85. Phylogenetic analysis using core-genome sequences showed that strain H12 formed a cluster with type species of SPO729 and HB161719. The complete genome of strain H12 was 4 481 396 bp in size and its DNA G+C content was 56.7 mol%. The average nucleotide identity and digital DNA–DNA hybridization values among strain H12 and type species of genus were below the cut-off levels of 95–96 and 70 %, respectively. The predominant cellular fatty acids of strain H12 were iso-C (22.5 %) and C 7 (13.9 %). Ubiquinone-8 was detected as the major respiratory quinone. The polar lipids of strain H12 comprised one phosphatidylglycerol, one phosphatidylethanolamine, one unidentified aminoglycophospholipid, one unidentified glycophospholipid, three unidentified glycolipids, two unidentified aminolipids, and one unidentified lipid. Based on polyphasic evidence, strain H12 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is H12 (=KCTC 92859=MCCC 1K08451). Comparative genomic analyses of strain H12 with strains of the genus reveal its potential in degradation of pectin.

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Keyword(s): complete genome , Microbulbifer bruguierae , novel species and taxonomy
Funding
This study was supported by the:
  • Sustainable Development Project of Shenzhen Science and Technology Program (Award KCXFZ20211020165547010)
    • Principle Award Recipient: YishanLu
© 2024 The Authors
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2024-01-19
2024-12-08
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References

  1. González JM, Mayer F, Moran MA, Hodson RE, Whitman WB. Microbulbifer hydrolyticus gen. nov., sp. nov., and Marinobacterium georgiense gen. nov., sp. nov., two marine bacteria from a lignin-rich pulp mill waste enrichment community. Int J Syst Bacteriol 1997; 47:369–376 [View Article] [PubMed]
     [Google Scholar]
  2. Huang H, Mo K, Hu Y, Liu M, Zhu J et al. Microbulbifer harenosus sp. nov., an alginate-degrading bacterium isolated from coastal sand. Int J Syst Evol Microbiol 2020; 70:1639–1643 [View Article] [PubMed]
     [Google Scholar]
  3. Baba A, Miyazaki M, Nagahama T, Nogi Y. Microbulbifer chitinilyticus sp. nov. and Microbulbifer okinawensis sp. nov., chitin-degrading bacteria isolated from mangrove forests. Int J Syst Evol Microbiol 2011; 61:2215–2220 [View Article] [PubMed]
     [Google Scholar]
  4. Vashist P, Nogi Y, Ghadi SC, Verma P, Shouche YS. Microbulbifer mangrovi sp. nov., a polysaccharide-degrading bacterium isolated from an Indian mangrove. Int J Syst Evol Microbiol 2013; 63:2532–2537 [View Article] [PubMed]
     [Google Scholar]
  5. Palit K, Rath S, Chatterjee S, Das S. Microbial diversity and ecological interactions of microorganisms in the mangrove ecosystem: threats, vulnerability, and adaptations. Environ Sci Pollut Res Int 2022; 29:32467–32512 [View Article] [PubMed]
     [Google Scholar]
  6. Holguin G, Vazquez P, Bashan Y. The role of sediment microorganisms in the productivity, conservation, and rehabilitation of mangrove ecosystems: an overview. Biol Fertil Soils 2001; 3:265–278 [View Article]
     [Google Scholar]
  7. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
     [Google Scholar]
  8. 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]
  9. 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]
  10. Lim HJ, Lee EH, Yoon Y, Chua B, Son A. Portable lysis apparatus for rapid single-step DNA extraction of Bacillus subtilis. J Appl Microbiol 2016; 120:379–387 [View Article] [PubMed]
     [Google Scholar]
  11. 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]
  12. 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]
  13. UniProt Consortium UniProt: a hub for protein information. Nucleic Acids Res 2015; 43:D204–D212 [View Article] [PubMed]
     [Google Scholar]
  14. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H et al. Gene ontology: tool for the unification of biology. Nat Genet 2000; 25:25–29 [View Article]
     [Google Scholar]
  15. Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 2015; 43:D261–D269 [View Article] [PubMed]
     [Google Scholar]
  16. Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 2016; 44:D457–D462 [View Article] [PubMed]
     [Google Scholar]
  17. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 2011; 39:W339–W346 [View Article] [PubMed]
     [Google Scholar]
  18. Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 2020; 48:D517–D525 [View Article] [PubMed]
     [Google Scholar]
  19. Grant JR, Stothard P. The CGView server: a comparative genomics tool for circular genomes. Nucleic Acids Res 2008; 36:W181–W184 [View Article] [PubMed]
     [Google Scholar]
  20. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article] [PubMed]
     [Google Scholar]
  21. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  22. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 2014; 42:D490–D495 [View Article] [PubMed]
     [Google Scholar]
  23. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  24. Moore WEC, Stackebrandt E, Kandler O, Colwell RR, Krichevsky MI et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37:463–464 [View Article]
     [Google Scholar]
  25. Miyazaki M, Nogi Y, Ohta Y, Hatada Y, Fujiwara Y et al. Microbulbifer agarilyticus sp. nov. and Microbulbifer thermotolerans sp. nov., agar-degrading bacteria isolated from deep-sea sediment. Int J Syst Evol Microbiol 2008; 58:1128–1133 [View Article] [PubMed]
     [Google Scholar]
  26. Yoon JH, Kim H, Kang KH, Oh TK, Park YH. Transfer of Pseudomonas elongata Humm 1946 to the genus Microbulbifer as Microbulbifer elongatus comb. nov. Int J Syst Evol Microbiol 2003; 53:1357–1361 [View Article] [PubMed]
     [Google Scholar]
  27. Yoon JH, Jung SY, Kang SJ, Oh TK. Microbulbifer celer sp. nov., isolated from a marine solar saltern of the Yellow Sea in Korea. Int J Syst Evol Microbiol 2007; 57:2365–2369 [View Article] [PubMed]
     [Google Scholar]
  28. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids MIDI Inc; 1990
     [Google Scholar]
  29. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. Microbiology 1977; 100:221–230 [View Article] [PubMed]
     [Google Scholar]
  30. Kates M. Radioisotopic techniques in lipidology. In Techniques of Lipidology, 2nd. edn Newport Somerville; 1986
     [Google Scholar]
  31. Cheng Y, Zhu S, Guo C, Xie F, Jung D et al. Microbulbifer hainanensis sp. nov., a moderately halopilic bacterium isolated from mangrove sediment. Antonie van Leeuwenhoek 2021; 114:1033–1042 [View Article] [PubMed]
     [Google Scholar]
  32. Jeong SH, Yang SH, Jin HM, Kim JM, Kwon KK. Microbulbifer gwangyangensis sp. nov. and Microbulbifer pacificus sp. nov., isolated from marine environments. Int J Syst Evol Microbiol 2013; 63:1335–1341 [View Article] [PubMed]
     [Google Scholar]
  33. Wang C-S, Wang Y, Xu X-W, Zhang D-S, Wu Y-H et al. Microbulbifer donghaiensis sp. nov., isolated from marine sediment of the East China Sea. Int J Syst Evol Microbiol 2009; 59:545–549 [View Article] [PubMed]
     [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006209
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Microbulbifer bruguierae sp. nov., isolated from sediment of mangrove plant Bruguiera sexangula, and comparative genomic analyses of the genus Microbulbifer
Int J Syst Evol Microbiol 74, 006209 (2024); https://doi.org/10.1099/ijsem.0.006209
/content/journal/ijsem/10.1099/ijsem.0.006209
/content/journal/ijsem/10.1099/ijsem.0.006209
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