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Volume 71, Issue 10

Proposal of fam. nov. to accommodate the genera and and reclassification of as a later heterotypic synonym of based on whole genome sequence analysis No Access

Abstract

The genus , affiliated to the class , is an important marine member that produces prodiginines. Currently, its taxonomic assignment to family level is not well presented. Phylogeny of 16S rRNA gene sequences indicated that forms a monophyletic clade with , which is neighboured by of the family and another monophyletic clade of the family . The 16S rRNA gene of S2-4-1H had sequence similarities to those of GTF13, members and members of 93.4%, 93.2–93.4  and <92.5 %, respectively. Phylogenomic analysis based on 120 bacterial conserved single-copy genes highly supported placing as a sister member of , neighboured by and members, indicating that and could be considered to belong to the same family. Thus, fam. nov. is proposed to accommodate the two genera. Colonies of and are red-pigmented, which is different from (pale-yellow pigmented). The major respiratory quinone of was ubiquinone (Q-9), similar to , but distinct from (Q-9 and Q-8). The predominant fatty acids and polar lipids of also showed a similar patterns to , but they were different from . Lastly, possessed a genome size of 6.68 Mbp and DNA G+C content of 40.1mol%, similar to , but much larger than . In addition, the 16S rRNA genes of JC2044 and JC333 possess sequence similarity of 99.79 %. Whole genome comparisons indicated that they shared 79.8 % digital DNA–DNA hybridization, 97.78 % average nucleotide identity and 97.31 % average amino acid identity values. Activities of catalase and oxidase for the two strains were positive. Hydrolysis of skimmed milk and Tweens (40, 60 and 80) was positive. Interestingly, the two strains produced different kinds of prodiginines. We propose that is a later heterotypic synonym of .

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  • Accepted:
  • Published Online:
Keyword(s): Aestuariirhabdus , phylogeny , Spartinivicinus and Zooshikella
Funding
This study was supported by the:
  • National Infrastructure of Natural Resources for Science and Technology Program of China (Award NIMR-2020-9)
    • Principle Award Recipient: ZhaobinHuang
  • National Science Foundation of Fujian Province (Award 2020J01789)
    • Principle Award Recipient: ZhaobinHuang
© 2021 The Authors
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2021-10-27
2024-04-26
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References

  1. Huang Z, Dong L, Lai Q, Liu J. Spartinivicinus ruber gen. nov., sp. nov., a novel marine gammaproteobacterium producing heptylprodigiosin and cycloheptylprodigiosin as major red pigments. Front Microbiol 2020; 11:2056 [View Article] [PubMed]
     [Google Scholar]
  2. Oren A, Garrity GM. List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication. Int J Syst Evol Microbiol 2021; 71: [View Article]
     [Google Scholar]
  3. Yi H, Chang Y-H, Oh HW, Bae KS, Chun J. Zooshikella ganghwensis gen. nov., sp. nov., isolated from tidal flat sediments. Int J Syst Evol Microbiol 2003; 53:1013–1018 [View Article] [PubMed]
     [Google Scholar]
  4. Ramaprasad EV, Bharti D, Sasikala C. Zooshikella marina sp. nov. a cycloprodigiosin- and prodigiosin-producing marine bacterium isolated from beach sand. Int J Syst Evol Microbiol 2015; 65:4669–4673 [View Article] [PubMed]
     [Google Scholar]
  5. Khan SA, Jung HS, Kim HM, Oh J, Lee SS et al. Aestuariirhabdus litorea gen. nov., sp. nov., isolated from a sea tidal flat and proposal of Aestuariirhabdaceae fam. nov. Int J Syst Evol Microbiol 2020; 70:2239–2246 [View Article] [PubMed]
     [Google Scholar]
  6. Parks DH, Chuvochina M, Chaumeil PA, Rinke C, Mussig AJ et al. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat Biotechnol 2020; 38:1079–1086 [View Article] [PubMed]
     [Google Scholar]
  7. Liao H, Lin X, Li Y, Qu M, Tian Y. Reclassification of the taxonomic framework of orders Cellvibrionales, Oceanospirillales, Pseudomonadales, and Alteromonadales in class Gammaproteobacteria through phylogenomic tree analysis. mSystems 2020; 5:e00543-20 [View Article] [PubMed]
     [Google Scholar]
  8. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  9. Lanoot B, Vancanneyt M, Dawyndt P, Cnockaert M, Zhang J et al. BOX-pCR fingerprinting as a powerful tool to reveal synonymous names in the genus Streptomyces. Emended descriptions are proposed for the species Streptomyces cinereorectus, S. fradiae, S. tricolor, S. colombiensis, S. filamentosus, S. vinaceus and S. phaeopurpureus. Syst Appl Microbiol 2004; 27:84–92 [View Article] [PubMed]
     [Google Scholar]
  10. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:1–14 [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]
     [Google Scholar]
  12. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118 [View Article]
     [Google Scholar]
  13. Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
     [Google Scholar]
  14. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
     [Google Scholar]
  15. 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]
  16. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article] [PubMed]
     [Google Scholar]
  17. Letunic I, Bork P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 2007; 23:127–128 [View Article] [PubMed]
     [Google Scholar]
  18. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterial systematics. Methods in Microbiology 1987; 19:161–207
     [Google Scholar]
  19. 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]
  20. Bartz JO, Blom J, Busse HJ, Mvie JB, Hardt M et al. Parendozoicomonas haliclonae gen. nov. sp. nov. isolated from a marine sponge of the genus Haliclona and description of the family Endozoicomonadaceae fam. nov. comprising the genera Endozoicomonas, Parendozoicomonas, and Kistimonas. Syst Appl Microbiol 2018; 41:73–84 [View Article] [PubMed]
     [Google Scholar]
  21. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:913 [View Article] [PubMed]
     [Google Scholar]
  22. Lee JS, Kim YS, Park S, Kim J, Kang SJ et al. Exceptional production of both prodigiosin and cycloprodigiosin as major metabolic constituents by a novel marine bacterium, Zooshikella rubidus S1-1. Appl Environ Microbiol 2011; 77:4967–4973 [View Article] [PubMed]
     [Google Scholar]
  23. Kurahashi M, Yokota A. Endozoicomonas elysicola gen. nov., sp. nov., a gamma-proteobacterium isolated from the sea slug Elysia ornata. Syst Appl Microbiol 2007; 30:202–206 [View Article] [PubMed]
     [Google Scholar]
  24. Choi EJ, Kwon HC, Sohn YC, Yang HO. Kistimonas asteriae gen. nov., sp. nov., a gammaproteobacterium isolated from Asterias amurensis. Int J Syst Evol Microbiol 2010; 60:938–943 [View Article] [PubMed]
     [Google Scholar]
  25. Glaeser SP, Kämpfer P. Endozoicomonadaceae. In Bergey’s Manual of Systematics of Archaea and Bacteria 2020 pp 1–4
     [Google Scholar]
  26. Goldberg SR, Haltli BA, Correa H, Kerr RG. Description of Sansalvadorimonas verongulae gen. nov., sp. nov., a gammaproteobacterium isolated from the marine sponge Verongula gigantea. Int J Syst Evol Microbiol 2018; 68:2006–2014 [View Article] [PubMed]
     [Google Scholar]
  27. Sheu SY, Lin KR, Hsu MY, Sheu DS, Tang SL et al. Endozoicomonas acroporae sp. nov., isolated from Acropora coral. Int J Syst Evol Microbiol 2017; 67:3791–3797 [View Article] [PubMed]
     [Google Scholar]
  28. Chen WM, Lin KR, Sheu SY. Endozoicomonas coralli sp. nov., isolated from the coral Acropora sp. Arch Microbiol 2019; 201:531–538 [View Article] [PubMed]
     [Google Scholar]
  29. Hyun DW, Shin NR, Kim MS, Oh SJ, Kim PS et al. Endozoicomonas atrinae sp. nov., isolated from the intestine of a comb pen shell Atrina pectinata. Int J Syst Evol Microbiol 2014; 64:2312–2318 [View Article] [PubMed]
     [Google Scholar]
  30. Lee J, Shin NR, Lee HW, Roh SW, Kim MS et al. Kistimonas scapharcae sp. nov., isolated from a dead ark clam (Scapharca broughtonii), and emended description of the genus Kistimonas. Int J Syst Evol Microbiol 2012; 62:2865–2869 [View Article] [PubMed]
     [Google Scholar]
  31. Appolinario LR, Tschoeke DA, Rua CP, Venas T, Campeao ME et al. Description of Endozoicomonas arenosclerae sp. nov. using a genomic taxonomy approach. Antonie vVan Leeuwenhoek 2016; 109:431–438 [View Article] [PubMed]
     [Google Scholar]
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Proposal of Zooshikellaceae fam. nov. to accommodate the genera Zooshikella and Spartinivicinus and reclassification of Zooshikella marina as a later heterotypic synonym of Zooshikella ganghwensis based on whole genome sequence analysis
Int J Syst Evol Microbiol 71, 005055 (2021); https://doi.org/10.1099/ijsem.0.005055
/content/journal/ijsem/10.1099/ijsem.0.005055
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