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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 10

sp. nov., an alginate lyase – producing marine bacterium Free

Abstract

A Gram-stain-negative, non-motile, ellipsoid bacterium, designated HB182678, was isolated from brown alga collected from Hainan province, PR China. Growth was observed at 10–50 °C (optimum 37–40 °C), at pH 6–10 (optimum pH 8) and in the presence of 0.5–13% (w/v) NaCl (optimum, 2–4%). The predominant isoprenoid quinone was Q-10 and the major fatty acids were C ω7c, C, C and C cyclo . The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, an unidentified phospholipid, two unidentified glycolipids and three unidentified aminophospholipids. The size of the draft genome was 4.40 Mbp with G+C content 68.8 mol%. Phylogenetic analysis of 16S rRNA gene sequence indicated that strain HB182678 belonged to the genus , and the closest phylogenetically related species was T1lg56 (with the similarity of 96.3%). Whole genome average nucleotide identity (ANI) value between them was 84.3% and DNA–DNA hybridization value was 27.2%. The combined phylogenetic relatedness, phenotypic and genotypic features supported the conclusion that strain HB182678 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is HB182678 (=MCCC 1K04624=KCTC 82318).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA gene , alginate lyase , Mangrovicoccus algicolasp. nov and polyphasic taxonomy
Funding
This study was supported by the:
  • Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences (CN) (Award 19CXTD-32)
    • Principle Award Recipient: HuiqinHuang
  • Financial Fund of the Ministry of Agriculture and Rural Affairs of China (Award NHYYSWZZZYKZX2020)
    • Principle Award Recipient: ShixiangBao
  • Key Research and Development Project of Hainan Province (Award ZDYF2020182)
    • Principle Award Recipient: HuiqinHuang
© 2021 The Authors
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2021-10-18
2024-12-04
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References

  1. Yu ZL, Cao Y, Zhou GQ, Yin JH, Qiu JP. Mangrovicoccus ximenensis gen. nov., sp. nov., isolated from mangrove forest sediment. Int J Syst Evol Microbiol 2018; 68:2172
     [Google Scholar]
  2. Pujalte MJ, Lucena T, Ruvira MA, Arahal DR, Macián MC. The family Rhodobacteraceae. The Prokaryotes – Alphaproteobacteria and Betaproteobacteria Berlin: Springer Verlag; 2014 pp 439–512
     [Google Scholar]
  3. Yang Y, Sun J, Tang K, Lin D, Li C et al. Ponticoccus lacteus sp. nov. of the family Rhodobacteraceae, isolated from surface seawater. Int J Syst Evol Microbiol 2015; 65:1247–1250 [View Article] [PubMed]
     [Google Scholar]
  4. Albuquerque L, Rainey FA, Nobre MF, da Costa MS. Oceanicella actignis gen. nov., sp. nov., a halophilic slightly thermophilic member of the Alphaproteobacteria. Syst Appl Microbiol 2012; 35:385–389 [View Article] [PubMed]
     [Google Scholar]
  5. Lee K, Choo YJ, Giovannoni SJ, Cho JC. Ruegeria pelagia sp. nov., isolated from the Sargasso Sea, Atlantic Ocean. Int J Syst Evol Microbiol 2007; 57:1815–1818 [View Article] [PubMed]
     [Google Scholar]
  6. Borsodi AK, Micsinai A, Kovács G, Tóth E, Schumann P et al. Pannonibacter phragmitetus gen. nov., sp. nov., a novel alkalitolerant bacterium isolated from decomposing reed rhizomes in a Hungarian soda lake. Int J Syst Evol Microbiol 2003; 53:555–561 [View Article] [PubMed]
     [Google Scholar]
  7. Simon M, Scheuner C, Meier-Kolthoff JP, Brinkhoff T, Wagner-Döbler I. Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats. ISME J 2017; 11:1483–1499 [View Article]
     [Google Scholar]
  8. Kämpfer P, Busse HJ, McInroy JA, Criscuolo A, Clermont D et al. Xinfangfangia humi sp. nov., isolated from soil amended with humic acid. Int J Syst Evol Microbiol 2019; 69:2070–2075 [View Article] [PubMed]
     [Google Scholar]
  9. Takeshita S, Oda T, Muramatsu T. An improved plate method, in the presence of calcium chloride or sulfuric acid, for simultaneous detection of alginate lyases. Agric Biol Chem 1991; 55:2637–2638
     [Google Scholar]
  10. Lee T, Nishimura M, Yamashita T, Imanaka T, Muramatsu T et al. A simple method for determination of substrate specificity of alginate lyases. J Fermen Bioeng 1994; 2:182–184
     [Google Scholar]
  11. Weisburg WG, Barns SM, Pelletier DJ, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
     [Google Scholar]
  12. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617
     [Google Scholar]
  13. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [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. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696–704 [View Article] [PubMed]
     [Google Scholar]
  16. Rzhetsky A, Nei M. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 1992; 9:945–967
     [Google Scholar]
  17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  18. Chun J, Rainey FA. Intergrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article] [PubMed]
     [Google Scholar]
  19. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365–8370 [View Article] [PubMed]
     [Google Scholar]
  20. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinforma 2007; 6:673–679
     [Google Scholar]
  21. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic acids Res 1997; 5:955–964
     [Google Scholar]
  22. Lagesen K, Hallin P, Rødland EA, Stærfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 9:3100–3108
     [Google Scholar]
  23. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic acids Res 2013; 42:D490–D495
     [Google Scholar]
  24. Lee I, KimY O, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103
     [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; 14:60–73 [View Article] [PubMed]
     [Google Scholar]
  26. Moore L, Moore E, Murray R, Stackebrandt E, Starr M et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
     [Google Scholar]
  27. 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] [PubMed]
     [Google Scholar]
  28. Murray TS, Ledizet M, Kazmierczak BI. Swarming motility, secretion of type 3 effectors and biofilm formation phenotypes exhibited within a large cohort of Pseudomonas aeruginosa clinical isolates. J Med Microbiol 2010; 59:511–520 [View Article] [PubMed]
     [Google Scholar]
  29. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
     [Google Scholar]
  30. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241
     [Google Scholar]
  31. Ruan JS. A rapid determination method for phosphate lipids. Microbiol China 2006; 37:190–193
     [Google Scholar]
  32. Komagata K, Suzuki KI. Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  33. Kuykendall LD, Roy MA, O’Neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988; 38:358–361 [View Article]
     [Google Scholar]
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Mangrovicoccus algicola sp. nov., an alginate lyase – producing marine bacterium
Int J Syst Evol Microbiol 71, 004844 (2021); https://doi.org/10.1099/ijsem.0.004844
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