1887

Abstract

Two novel filamentous bacteria, designated as IB182353 and IB182357, were isolated from stony coral of the South China Sea. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains IB182353 and IB182357 were closely related to DSM 45707 (with 93.4 and 93.5% similarity, respectively). The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization results showed that the pairwise similarities between isolate IB182353 and the other recognized species were less than 68.9, 60.5 and 21.1 %, respectively. Both strains produced aerial and substrate mycelia, grew optimally at 25–30 °C, pH 8.0–9.0 and with 2–3 % (w/v) NaCl. The cell-wall peptidoglycan type was -DAP and the whole-cell hydrolysates contained ribose. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminophospholipid and three unidentified phospholipids. The genomic DNA G+C content was 39.5 mol%. Strain IB182353 was distinguishable from its related type strains by the contents of two fatty acids, iso-C and iso-C 10. Based on polyphasic taxonomic characterization, we propose that strains IB182353 and IB182357 represent a novel genus and species within the family , for which the name gen. nov. sp. nov. is proposed. The type strain is IB182353 (=MCCC 1K04631=JCM 34206).

Funding
This study was supported by the:
  • Special Fund for Agro-scientific Research in the Public Interest (Award 1630052019014)
    • Principle Award Recipient: Yonghua Hu
  • Department of Agriculture and Rural Affairs of Zhejiang Province (Award NHYYSWZZZYKZX2020)
    • Principle Award Recipient: Yonghua Hu
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2023-10-04
2024-05-08
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References

  1. Matsuo Y, Katsuta A, Matsuda S, Shizuri Y, Yokota A et al. Mechercharimyces mesophilus gen. nov., sp. nov. and Mechercharimyces asporophorigenens sp. nov., antitumour substance-producing marine bacteria, and description of Thermoactinomycetaceae fam. nov. Int J Syst Evol Microbiol 2006; 56:2837–2842 [View Article] [PubMed]
    [Google Scholar]
  2. Guan X, Liu C, Fang B, Zhao J, Jin P et al. Baia soyae gen. nov., sp. nov., a mesophilic representative of the family Thermoactinomycetaceae, isolated from soybean root [Glycine max (L.) Merr]. Int J Syst Evol Microbiol 2015; 65:3754–3760 [View Article] [PubMed]
    [Google Scholar]
  3. Yu T-T, Zhang B-H, Yao J-C, Tang S-K, Zhou E-M et al. Lihuaxuella thermophila gen. nov., sp. nov., isolated from a geothermal soil sample in Tengchong, Yunnan, south-west China. Antonie van Leeuwenhoek 2012; 102:711–718 [View Article] [PubMed]
    [Google Scholar]
  4. Hatayama K, Shoun H, Ueda Y, Nakamura A. Planifilum fimeticola gen. nov., sp. nov. and Planifilum fulgidum sp. nov., novel members of the family “Thermoactinomycetaceae” isolated from compost. Int J Syst Evol Microbiol 2005; 55:2101–2104 [View Article] [PubMed]
    [Google Scholar]
  5. Li J, Zhang G-T, Yang J, Tian X-P, Wang F-Z et al. Marininema mesophilum gen. nov., sp. nov., a thermoactinomycete isolated from deep sea sediment, and emended description of the family Thermoactinomycetaceae. Int J Syst Evol Microbiol 2012; 62:1383–1388 [View Article] [PubMed]
    [Google Scholar]
  6. Buss SN, Cole JA, Hannett GE, Nazarian EJ, Nazarian L et al. Hazenella coriacea gen. nov., sp. nov., isolated from clinical specimens. Int J Syst Evol Microbiol 2013; 63:4087–4093 [View Article] [PubMed]
    [Google Scholar]
  7. Zhou E-M, Yu T-T, Liu L, Ming H, Yin Y-R et al. Geothermomicrobium terrae gen. nov., sp. nov., a novel member of the family Thermoactinomycetaceae. Int J Syst Evol Microbiol 2014; 64:2998–3004 [View Article] [PubMed]
    [Google Scholar]
  8. Hatayama K, Kuno T. Croceifilum oryzae gen. nov., sp. nov., isolated from rice paddy soil. Int J Syst Evol Microbiol 2015; 65:4061–4065 [View Article] [PubMed]
    [Google Scholar]
  9. Gontang EA, Fenical W, Jensen PR. Phylogenetic diversity of gram-positive bacteria cultured from marine sediments. Appl Environ Microbiol 2007; 73:3272–3282 [View Article] [PubMed]
    [Google Scholar]
  10. Tsubouchi T, Shimane Y, Mori K, Usui K, Hiraki T et al. Polycladomyces abyssicola gen.nov., sp. nov., a thermophilic filamentous bacterium isolated from hemipelagic sediment. Int J Syst Evol Microbiol 2013; 63:1972–1981
    [Google Scholar]
  11. Yang G, Chen J, Zhou S. Novibacillus thermophilus gen. nov., sp. nov., a gram-staining-negative and moderately thermophilic member of the family Thermoactinomycetaceae. Int J Syst Evol Microbiol 2015; 65:2591–2597 [View Article] [PubMed]
    [Google Scholar]
  12. Yassin AF, Hupfer H, Klenk H-P, Siering C. Desmospora activa gen. nov., sp. nov., a thermoactinomycete isolated from sputum of a patient with suspected pulmonary tuberculosis, and emended description of the family Thermoactinomycetaceae Matsuo et al. 2006. Int J Syst Evol Microbiol 2009; 59:454–459 [View Article] [PubMed]
    [Google Scholar]
  13. Mo k, Wang L, Wu Q, Ye L, Liu X. Pontibacter mangrovi sp. nov., isolated from mangrove sediment. Int J Syst Evol Microbiol 2020; 70:4245–4249 [View Article] [PubMed]
    [Google Scholar]
  14. 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]
  15. 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]
  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. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  18. 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]
  19. 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]
  20. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  21. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 2014; 42:D206–D214 [View Article] [PubMed]
    [Google Scholar]
  22. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJe1900v1 2016; 4: [View Article]
    [Google Scholar]
  23. Yoon S-H, Ha S-M, 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] [PubMed]
    [Google Scholar]
  24. 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; 14:60 [View Article] [PubMed]
    [Google Scholar]
  25. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article] [PubMed]
    [Google Scholar]
  26. 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]
  27. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
    [Google Scholar]
  28. Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 2023; 51:W46–W50 [View Article] [PubMed]
    [Google Scholar]
  29. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
    [Google Scholar]
  30. Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME et al. Division of the genus Chryseobacterium: observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020; 70:4432–4450 [View Article] [PubMed]
    [Google Scholar]
  31. Cerny G. Studies on the aminopeptidase test for the distinction of gram-negative from gram-positive bacteria. J Appl Microbiol Biotechnol 1978; 5:113–122 [View Article]
    [Google Scholar]
  32. Chen Y, Ye L, Huang H, Jiang M, Hu Y et al. Paenibacillus oceani sp. nov., isolated from surface seawater. Int J Syst Evol Microbiol 2021; 71:5024 [View Article] [PubMed]
    [Google Scholar]
  33. Lacey J. Thermoactinomyces sacchari sp. nov., a thermophilic actinomycete causing bagassosis. J Gen Microbiol 1971; 66:327–338 [View Article] [PubMed]
    [Google Scholar]
  34. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 2001
    [Google Scholar]
  35. Komagata K, Suzuki K. Lipids and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207
    [Google Scholar]
  36. 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. Microbiol in Methods 1984; 2:233–241 [View Article]
    [Google Scholar]
  37. Schumann P. Peptidoglycan structure. Methods Microbiol 2011; 38:101–129
    [Google Scholar]
  38. Lechevalier MP, Lechevalier HA. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
    [Google Scholar]
  39. Yoon JH, Kim IG, Shin YK, Park YH. Proposal of the genus Thermoactinomyces sensu stricto and three new genera, Laceyella, Thermoflavimicrobium and Seinonella, on the basis of phenotypic, phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 2005; 55:395–400 [View Article] [PubMed]
    [Google Scholar]
  40. Wu H, Liu B, Pan S. Thermoactinomyces guangxiensis sp. nov., a thermophilic actinomycete isolated from mushroom compost. Int J Syst Evol Microbiol 2015; 65:2859–2864 [View Article] [PubMed]
    [Google Scholar]
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