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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 71, Issue 10

gen. nov., sp. nov., a novel member of the family isolated from the Pearl River No Access

Abstract

A novel actinobacterium, designated strain SYSU M44304, was isolated from freshwater samples in the Pearl River Estuary. The isolate was Gram-stain-positive, aerobic, coccus-shaped, oxidase-positive and motile. The cell wall contained -diaminopimelic acid as its diagnostic diamino acid. The predominant menaquinone was MK-8. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylethanolamine and seven unidentified phospholipids. The major fatty acids were C and C. The G+C content based on genomic DNA was 73.2 mol %. The nearest phylogenetic neighbours to the novel strain were NBRC 104925 and YIM 101593. On the basis of chemotaxonomic and physiological characteristics and phylogenetic analysis, strain SYSU M44304 should be considered to represent a novel species of a new genus in the family , for which we propose the name gen. nov., sp. nov. The type strain of is SYSU M44304 (=NBRC 114808=CGMCC 1.18608).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Agilicoccus flavus gen. nov., sp.nov , Dermatophilaceae and Pearl River
Funding
This study was supported by the:
  • Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) (Award 311021004)
    • Principle Award Recipient: Jia-LingLi
  • Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) (Award 311021006)
    • Principle Award Recipient: Wen-JunLi
  • guangdong basic and applied basic research foundation, china (Award 2020A1515011139)
    • Principle Award Recipient: Jia-LingLi
  • postdoctoral research foundation of china (Award 2018M643294)
    • Principle Award Recipient: Jia-LingLi
  • national natural science foundation of china (Award 31850410475)
    • Principle Award Recipient: Jia-LingLi
© 2021 The Authors
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2021-10-07
2024-04-20
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References

  1. Austwick PKC. Cutaneous streptotrichosis, mycotic dermatitis and strawberry foot rot and the genus Dermato-philus van sacEghem. VetRevAnnot 1958; 4:33–38
     [Google Scholar]
  2. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria. Front Microbiol 2018; 9:2007 [View Article] [PubMed]
     [Google Scholar]
  3. Salam N, Jiao J-Y, Zhang X-T, Li W-J. Update on the classification of higher ranks in the phylum actinobacteria. Int J Syst Evol Microbiol 2020; 70:1331–1355 [View Article] [PubMed]
     [Google Scholar]
  4. Hamada M, Iino T, Iwami T, Harayama S, Tamura T et al. Mobilicoccus pelagius gen. nov., sp. nov. and Piscicoccus intestinalis gen. nov., sp. nov., two new members of the family Dermatophilaceae, and reclassification of Dermatophilus chelonae (Masters et al. 1995) as Austwickia chelonae gen. nov., comb. nov. J Gen Appl Microbiol 2010; 56:427–436 [View Article] [PubMed]
     [Google Scholar]
  5. Liu W-T, Hanada S, Marsh TL, Kamagata Y, Nakamura K. Kineosphaera limosa gen. Nov., sp. Nov., a novel gram-positive polyhydroxyalkanoate-accumulating coccus isolated from activated sludge. Int J Syst Evol Microbiol 2002; 52:1845–1849 [View Article] [PubMed]
     [Google Scholar]
  6. Azuma R, Ung-Bok B, Murakami S, Ishiwata H, Osaki M et al. Tonsilliphilus suis gen. Nov., sp. Nov., causing tonsil infections in pigs. Int J Syst Evol Microbiol 2013; 63:2545–2552 [View Article] [PubMed]
     [Google Scholar]
  7. Dionne JC. Towards a more adequate definition of the ST. Lawrence estuary Zeitschrift für Geomorphologie 1963; 7:36–44
     [Google Scholar]
  8. Mai Y-Z, Lai Z-N, Li X-H, Peng S-Y, Wang C. Structural and functional shifts of bacterioplanktonic communities associated with spatiotemporal gradients in river outlets of the subtropical Pearl River Estuary, South China. Mar Pollut Bull 2018; 136:309–321 [View Article] [PubMed]
     [Google Scholar]
  9. Buck JD. Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 1982; 44:992–993 [View Article] [PubMed]
     [Google Scholar]
  10. Leifson E. Atlas of Bacterial Flagellation London: Academic Press; 1960
     [Google Scholar]
  11. Kovacs N. Identification of Pseudomonas pyocyanea by the oxidase reaction. Nature 1956; 178:703–704 [View Article] [PubMed]
     [Google Scholar]
  12. Nie GX, Ming H, Li S, Zhou EM, Cheng J. Amycolatopsis dongchuanensis sp. nov., an actinobacterium isolated from soil. Int J Syst Evol Microbiol 2012; 62:2650–2656 [View Article] [PubMed]
     [Google Scholar]
  13. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov., an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article] [PubMed]
     [Google Scholar]
  14. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. In. Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM. eds In Methods for general and molecular microbiology, third edition Washington, DC: American Society of Microbiology; 2007
     [Google Scholar]
  15. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
     [Google Scholar]
  16. Liu Y-H, Guo J-W, Salam N, Li L, Zhang Y-G et al. Culturable endophytic bacteria associated with medicinal plant Ferula songorica: molecular phylogeny, distribution and screening for industrially important traits. 3 Biotech 2016; 6:209 [View Article] [PubMed]
     [Google Scholar]
  17. Yang Z-W, Salam N, Hua Z-S, Liu B-B, Han M-X et al. Siccirubricoccus deserti gen. nov., sp. nov., a proteobacterium isolated from a desert sample. Int J Syst Evol Microbiol 2017; 67:4862–4867 [View Article] [PubMed]
     [Google Scholar]
  18. 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 [View Article] [PubMed]
     [Google Scholar]
  19. 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]
  20. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  21. 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]
  22. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
     [Google Scholar]
  23. 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]
  24. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  25. Harrison P, Strulo B. SPADES - a process algebra for discrete event simulation. Journal of Logic and Computation 2000; 10:3–42 [View Article]
     [Google Scholar]
  26. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article] [PubMed]
     [Google Scholar]
  27. Li R, Li Y, Kristiansen K, Wang J. Soap: Short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
     [Google Scholar]
  28. 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]
  29. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012; 28:1033 [View Article] [PubMed]
     [Google Scholar]
  30. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  31. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article] [PubMed]
     [Google Scholar]
  32. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688–2690 [View Article] [PubMed]
     [Google Scholar]
  33. 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]
  34. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54:31–36 [View Article]
     [Google Scholar]
  35. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
  36. Minnikin DE, Collins MD, Goodfellow M. Fatty Acid and Polar Lipid Composition in the Classification of Cellulomonas, Oerskovia and Related Taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
     [Google Scholar]
  37. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101 Newark: Microbial ID, Inc; 1990
     [Google Scholar]
  38. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
     [Google Scholar]
  39. Chen X, Li Q-Y, Li G-D, Xu F-J, Jiang C-L et al. Mobilicoccus caccae sp. nov., isolated from the faeces of the primate Rhinopithecus roxellanae. Int J Syst Evol Microbiol 2017; 67:2253–2257 [View Article] [PubMed]
     [Google Scholar]
  40. Gordon MA. The genus Dermatophilus. J Bacteriol 1964; 88:509–522 [View Article] [PubMed]
     [Google Scholar]
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Agilicoccus flavus gen. nov., sp. nov., a novel member of the family Dermatophilaceae isolated from the Pearl River
Int J Syst Evol Microbiol 71, 005076 (2021); https://doi.org/10.1099/ijsem.0.005076
/content/journal/ijsem/10.1099/ijsem.0.005076
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