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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 71, Issue 9

sp. nov., isolated from soil of Pu-erh tea cellar Free

Abstract

A Gram-reaction-negative, yellow-pigmented, non-spore-forming rod, aerobic, motile bacterium, designated SJY3, was isolated from soil samples collected from a Pu-erh tea cellar in Bolian Pu-erh tea estate Co. Ltd. in Pu'er city, Yunnan, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belonged to the genus . The closest phylogenetic relative was CICC 24458 (99.5 %), followed by CCUG45783 (97.9 %), CCUG43427A (97.8 %), and DSM 18055 (97.8 %). The major fatty acids were C and C 7 and/or C 6. The major respiratory quinone was ubiquinone Q-8 and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. Genome sequencing revealed a genome size of 5.97 M bp and a G+C content of 65.4 mol%. Pairwise determined whole genome average nucleotide identity (gANI) values and digital DNA–DNA hybridization (dDDH) values were all below the threshold. Although the 16S rRNA gene similarity of stain SJY3 and CICC 24458 was more than 99 %, the gANI, dDDH values and genomic tree clearly indicated that they were not of the same species. In summary, strain SJY3 represents a new species, for which we propose the name sp. nov. with the type strain SJY3 (=CGMCC 1.17158=KCTC 82193).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): genome , Massilia , novel species , polyphasic taxonomy and Pu-erh tea Cellar
Funding
This study was supported by the:
  • Applied Basic Research Key Project of Yunnan (Award 2019ZG00909-02)
    • Principle Award Recipient: LiangYan
© 2021 The Authors
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2021-09-09
2025-02-10
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References

  1. Lv HP, Zhong QS, Lin Z, Wang L, Tan JF et al. Aroma characterization of Pu-erh tea using headspace-solid phase microextraction combined with GC/MS and GC–olfactometry. Food Chem 2012; 130:1074–1081
     [Google Scholar]
  2. Song TT. The Study on the Change of Green Tea’ Quality During Storage[D] Hangzhou: Zhejiang university; 2010
     [Google Scholar]
  3. Lee LK, Foo KY. Recent advances on the beneficial use and health implications of Pu-Erh tea. Food Res Int 2013; 53:619–628
     [Google Scholar]
  4. La Scola B, Birtles RJ, Mallet MN, Raoult D. Massilia timonae gen.nov., sp. nov., isolated from blood of an immunocompromised patient with cerebellar lesions. J Clin Microbiol 1998; 36:2847–2852 [View Article] [PubMed]
     [Google Scholar]
  5. Gallego V, Sánchez-Porro C, García MT, Ventosa A. Massilia aurea sp. nov., isolated from drinking water. Int J Syst Evol Microbiol 2006; 56:2449–2453 [View Article]
     [Google Scholar]
  6. Weon HY, Kim BY, Hong SB, Jeon YA, Koo BS et al. Massilia niabensis sp. nov. and Massilia niastensis sp. nov., isolated from air samples. Int J Syst Evol Microbiol 2009; 59:1656–1660 [View Article] [PubMed]
     [Google Scholar]
  7. Wang J, Zhang J, Pang H, Zhang Y, Li Y et al. Massilia flava sp. nov., isolated from soil. Int J Syst Evol Microbiol 2012; 62:580–585 [View Article] [PubMed]
     [Google Scholar]
  8. Kämpfer P, Lodders N, Martin K, Falsen E. Revision of the genus Massilia La Scola et al. 2000, with an emended description of the genus and inclusion of all species of the genus Naxibacter as new combinations, and proposal of Massilia consociata sp. nov. Int J Syst Evol Microbiol 2011; 61:1528–1533 [View Article] [PubMed]
     [Google Scholar]
  9. Altankhuu K, Kim J. Massilia pinisoli sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2016; 66:3669–3674 [View Article] [PubMed]
     [Google Scholar]
  10. Zhang Y-Q, Li W-J, Zhang K-Y, Tian X-P, Jiang Y et al. Massilia dura sp. nov., Massilia albidiflava sp. nov., Massilia plicata sp. nov. and Massilia lutea sp. nov., isolated from soils in China. Int J Syst Evol Microbiol 2006; 56:459–463 [View Article] [PubMed]
     [Google Scholar]
  11. Kämpfer P, Lodders N, Martin K, Falsen E. Massilia oculi sp. nov., isolated from a human clinical specimen. Int J Syst Evol Microbiol 2012; 62:364–369 [View Article] [PubMed]
     [Google Scholar]
  12. Luo X, Xie Q, Wang J, Pang H, Fan J et al. Massilia lurida sp. nov., isolated from soil. Int J Syst Evol Microbiol 2013; 63:2118–2123 [View Article] [PubMed]
     [Google Scholar]
  13. Rodríguez-Díaz M, Cerrone F, Sánchez-Peinado M, SantaCruz- Calvo L, Pozo C et al. Massilia umbonata sp. nov., able to accumulate poly-β-hydroxybutyrate, isolated from a sewage sludge compost-soil microcosm. Int J Syst Evol Microbiol 2014; 64:131–137 [View Article] [PubMed]
     [Google Scholar]
  14. Shen L, Liu Y, Gu Z, Xu B, Wang N et al. Massilia eurypsychrophila sp. nov. a facultatively psychrophilic bacteria isolated from ice core. Int J Syst Evol Microbiol 2015; 65:2124–2129 [View Article] [PubMed]
     [Google Scholar]
  15. Ren M, Li X, Zhang Y, Jin Y, Li S et al. Massilia armeniaca sp. nov., isolated from desert soil. Int J Syst Evol Microbiol 2018; 68:2319–2324 [View Article] [PubMed]
     [Google Scholar]
  16. Wang H, Zhang X, Wang S, Zhao B, Lou K et al. Massilia violaceinigra sp. nov., a novel purple-pigmented bacterium isolated from glacier permafrost. Int J Syst Evol Microbiol 2018; 68:2271–2278
     [Google Scholar]
  17. Lindquist D, Murrill D, Burran WP, Winans G, Janda JM et al. Characteristics of Massilia timonae and Massilia timonae-like isolates from human patients, with an emended description of the species. J Clin Microbiol 2003; 41:192–196 [View Article] [PubMed]
     [Google Scholar]
  18. Lane DJ. 16S/23S rRNA sequencing. Stackebrandt E, Goodfellow M. eds In Nucleic Acid Techniques in Bacterial Systematics Chichester: Wiley: 1991 pp 115–175
     [Google Scholar]
  19. 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] [PubMed]
     [Google Scholar]
  20. Ludwig W, Strunk O, Westram R, Richter L Y. Arb: a software environment for sequence data. Nucleic Acids Res 2004; 32:1363–1371 [View Article] [PubMed]
     [Google Scholar]
  21. Yarza P, Peplies J, Euzeby J, Schleifer KH. The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008; 31:241–250 [View Article] [PubMed]
     [Google Scholar]
  22. 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]
  23. Kishino H, Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from dna sequence data, and the branching order in hominoidea. J Mol Evol 1989; 29:170–179 [View Article] [PubMed]
     [Google Scholar]
  24. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  25. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. mega6: molecular evolutionary genetics analysis version 6.0. Mol biol Evol 2013; 30:2725–2729 [View Article] [PubMed]
     [Google Scholar]
  26. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  27. 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]
  28. Rintala H, Pitkäranta M, Toivola M, Paulin L, Nevalainen A. Diversity and seasonal dynamics of bacterial community in indoor environment. BMC Microbiol 2008; 8:56 [View Article] [PubMed]
     [Google Scholar]
  29. 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]
  30. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article] [PubMed]
     [Google Scholar]
  31. 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]
  32. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ et al. ABySS: a parallel assembler for short read sequence data. Genome Res 2009; 19:1117 [View Article] [PubMed]
     [Google Scholar]
  33. Lin SH, Liao YC. CISA: contig integrator for sequence assembly of bacterial genomes. PloS one 2013; 8:e60843 [View Article] [PubMed]
     [Google Scholar]
  34. Galperin MY, Makarova KS, Wolf YI, Koonin EV. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Research 2015; 43:261–269
     [Google Scholar]
  35. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  36. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
     [Google Scholar]
  37. Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 2015; 16:157 [View Article] [PubMed]
     [Google Scholar]
  38. Sievers F, Wilm A, Dineen D, Gibson Toby J, Karplus K et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 2011; 7:539 [View Article] [PubMed]
     [Google Scholar]
  39. 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]
  40. 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]
  41. 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 [View Article] [PubMed]
     [Google Scholar]
  42. Murray R, Doetsch RN, Robinow CF. Determinative and cytological light microscopy. Gerhardt P, Murray R, Wood W, Krieg N. eds In Meth Gen Mol Bacteriol Washington, DC: American Society for Microbiology; 1994 pp 21–41
     [Google Scholar]
  43. Smibert RM, Krieg NR. Phenotypic characterization. Gerhardt P, Murray R, Wood W, Krieg N. eds In Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
     [Google Scholar]
  44. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070
     [Google Scholar]
  45. Piao AL, Feng XM, Nogi Y, Han L, Lv J. Sphingomonas qilianensis sp. nov., isolated from surface soil in the permafrost region of Qilian Mountains, China. Curr Microbiol 2016; 72:363–369 [View Article] [PubMed]
     [Google Scholar]
  46. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Netwark, DE: MIDI Inc; 1990
     [Google Scholar]
  47. 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. J Microbiol Methods 1984; 2:233–241
     [Google Scholar]
  48. Da Costa MS, Albuquerque L, Nobre MF, Wait R. The extraction and identification of respiratory lipoquinones of prokaryotes and their use in taxonomy. Methods Microbiol 2011; 38:197–206
     [Google Scholar]
  49. Da Costa MS, Albuquerque L, Nobre MF, Wait R. The identification of polar lipids in prokaryotes. Method Microbiol 2011; 38:165–181
     [Google Scholar]
  50. Zhang B, Yang R, Zhang G, Zhang D, Zhang W et al. Massilia arenae sp. nov., isolated from sand soil in the Qinghai-Tibetan Plateau. Int J Syst Evol Microbiol 2020; 70:2435–2439 [View Article] [PubMed]
     [Google Scholar]
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Massilia puerhi sp. nov., isolated from soil of Pu-erh tea cellar
Int J Syst Evol Microbiol 71, 004992 (2021); https://doi.org/10.1099/ijsem.0.004992
/content/journal/ijsem/10.1099/ijsem.0.004992
/content/journal/ijsem/10.1099/ijsem.0.004992
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