1887

Abstract

A novel Gram-stain-negative, rod-shaped, non-motile, yellowish bacterium, designated strain 1.3611, was isolated from the wormcast of . The strain grew optimally at 30–37 ℃, at pH 7.0 and with 0–1.0 % (w/v) NaCl. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, strain 1.3611 showed the highest degree of 16S rRNA gene sequence similarity to HAL-9 (97.0 %), followed by Y3L14 (95.8 %). The respiratory quinone of strain 1.3611 was menaquinone-7 (MK-7) and its major cellular fatty acids were iso-C (41.3 %), summed feature 3 (C 7 and/or C 6, 22.1 %) and iso-C 3-OH (16.2 %). The major polar lipids were sphingophospholipid, phosphatidylethanolamine, four unidentified glycolipids, two unidentified phospholipids and five unidentified polar lipids. The genomic DNA G+C content was 39.0 mol%. The digital DNA–DNA hybridization and average nucleotide identity values between the genomes of strain 1.3611 and HAL-9 were 37.9 and 88.9 %, respectively. According to the phenotypic and chemotaxonomic phylogenetic results, strain 1.3611 should represent a novel species of the genus , for which the name sp. nov. is proposed, with strain 1.3611 (=KCTC 62980=CCTCC AB 2018349) as the type strain.

Funding
This study was supported by the:
  • the Ten-thousand Talents Program in Yunnan Province (Award YNWR-CYJS-2019-042)
    • Principle Award Recipient: MingHe Mo
  • the Department of Science and Technology of Yunnan Province (Award 202001BB050072)
    • Principle Award Recipient: MingHe Mo
  • the Department of Science and Technology of Yunnan Province (Award 2019ZG00901)
    • Principle Award Recipient: MingHe Mo
  • the Program of Guizhou Provincial Tobacco Company (Award 2021XM12)
    • Principle Award Recipient: MingHe Mo
  • the National Natural Science Foundation Program of China (Award 31660544)
    • Principle Award Recipient: MingHe Mo
  • the National Natural Science Foundation Program of China (Award 31870091)
    • Principle Award Recipient: MingHe Mo
  • the National Natural Science Foundation Program of China (Award 31960022)
    • Principle Award Recipient: MingHe Mo
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2021-05-28
2022-01-24
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References

  1. Yabuuchi E, Kaneko T, Yano I, Moss CW, Miyoshi N. Sphingobacterium gen. nov., Sphingobacterium spiritivorum comb. nov., Sphingobacterium multivorum comb. nov., Sphingobacterium mizutae sp. nov., and Flavobacterium indologenes sp. nov.: glucose-nonfermenting gram-negative rods in CDC groups IIk-2 and IIb. Int J Syst Bacteriol 1983; 33:580–598 [View Article]
    [Google Scholar]
  2. Choi H-A, Lee S-S. Sphingobacterium kyonggiense sp. nov., isolated from chloroethene-contaminated soil, and emended descriptions of Sphingobacterium daejeonense and Sphingobacterium mizutaii . Int J Syst Evol Microbiol 2012; 62:2559–2564 [View Article][PubMed]
    [Google Scholar]
  3. Wauters G, Janssens M, De Baere T, Vaneechoutte M, Deschaght P. Isolates belonging to CDC group II-i belong predominantly to Sphingobacterium mizutaii Yabuuchi et al. 1983: emended descriptions of S. mizutaii and of the genus Sphingobacterium . Int J Syst Evol Microbiol 2012; 62:2598–2601 [View Article][PubMed]
    [Google Scholar]
  4. Chaudhary DK, Kim J. Sphingobacterium terrae sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2018; 68:609–615 [View Article][PubMed]
    [Google Scholar]
  5. Kaur M, Singh H, Sharma S, Mishra S, Tanuku NRS et al. Sphingobacterium bovisgrunnientis sp. nov., isolated from yak milk. Int J Syst Evol Microbiol 2018; 68:636642 [View Article][PubMed]
    [Google Scholar]
  6. Zhou X-K, Li Q-Q, Mo M-H, Zhang Y-G, Dong L-M et al. Sphingobacterium tabacisoli sp. nov., isolated from a tobacco field soil sample. Int J Syst Evol Microbiol 2017; 67:4808–4813 [View Article][PubMed]
    [Google Scholar]
  7. Niu X, Cui W, Cui M, Zhang X, Zhang S et al. Sphingobacterium solani sp. nov., isolated from potato stems. Int J Syst Evol Microbiol 2018; 68:1012–1017 [View Article][PubMed]
    [Google Scholar]
  8. Yoo S-H, Weon H-Y, Jang H-B, Kim B-Y, Kwon S-W et al. Sphingobacterium composti sp. nov., isolated from cotton-waste composts. Int J Syst Evol Microbiol 2007; 57:1590–1593 [View Article][PubMed]
    [Google Scholar]
  9. Huys G, Purohit P, Tan CH, Snauwaert C, Vos PD et al. Sphingobacterium cellulitidis sp. nov., isolated from clinical and environmental sources. Int J Syst Evol Microbiol 2017; 67:1415–1421 [View Article][PubMed]
    [Google Scholar]
  10. Peng S, Hong DD, Xin YB, Jun LM, Hong WG. Sphingobacterium yanglingense sp. nov., isolated from the nodule surface of soybean. Int J Syst Evol Microbiol 2014; 64:3862–3866 [View Article][PubMed]
    [Google Scholar]
  11. Sun J-Q, Liu M, Wang X-Y, Xu L, Wu X-L. Sphingobacterium suaedae sp. nov., isolated from the rhizosphere soil of Suaeda corniculata. Int J Syst Evol Microbiol 2015; 65:4508–4513 [View Article][PubMed]
    [Google Scholar]
  12. Sun L-N, Zhang J, Chen Q, He J, Li S-P. Sphingobacterium caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2013; 63:2260–2264 [View Article][PubMed]
    [Google Scholar]
  13. Li Y, Guo L-M, Chang J-P, Yang X-Q, Xie S-J et al. Sphingobacterium corticibacter sp. nov., isolated from bark of Populus × euramericana. Int J Syst Evol Microbiol 2019; 69:1870–1874 [View Article][PubMed]
    [Google Scholar]
  14. Liu B, Yang X, Sheng M, Yang Z, Qiu J et al. Sphingobacterium olei sp. nov., isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2020; 70:1931–1939 [View Article][PubMed]
    [Google Scholar]
  15. Song J, Joung Y, Li S-H, Hwang J, Cho J-C. Sphingobacterium chungjuense sp. nov., isolated from a freshwater lake. Int J Syst Evol Microbiol 2020; 70:6126-6132 [View Article][PubMed]
    [Google Scholar]
  16. Zhou X-K, Huang Y, Li M, Zhang X-F, Wei Y-Q et al. Sphingobacterium cavernae sp. nov., a novel bacterium isolated from soil sampled at Tiandong Cave. Int J Syst Evol Microbiol 2020; 70:2348–2354 [View Article][PubMed]
    [Google Scholar]
  17. Artursson V, Jansson JK. Use of bromodeoxyuridine immunocapture to identify active bacteria associated with arbuscular mycorrhizal hyphae. Appl Environ Microbiol 2003; 69:6208–6215 [View Article][PubMed]
    [Google Scholar]
  18. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
    [Google Scholar]
  19. 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]
  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. 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]
  22. 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]
  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. Xu L, Sun J-Q, Wang L-J, Gao Z-W, Sun L-Z et al. Sphingobacterium alkalisoli sp. nov., isolated from a saline-alkaline soil. Int J Syst Evol Microbiol 2017; 67:1943–1948 [View Article][PubMed]
    [Google Scholar]
  26. Xi L, Zhang Z, Qiao N, Zhang Y, Li J et al. Complete genome sequence of the novel thermophilic polyhydroxyalkanoates producer Aneurinibacillus sp. XH2 isolated from Gudao oilfield in China. J Biotechnol 2016; 227:54–55 [View Article][PubMed]
    [Google Scholar]
  27. 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]
  28. 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]
  29. 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]
  30. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler OK. International Committee on systematic bacteriology. Report of the ad hoc Committee on reconciliation of approaches to bacterial Systematics. Int J Syst Bacterio 1987; 137:463–464
    [Google Scholar]
  31. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
    [Google Scholar]
  32. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  33. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007; 35:W182–W185 [View Article][PubMed]
    [Google Scholar]
  34. Skerman VBD. A Guide to the Identification of the Genera of Bacteria, 2nd ed. Baltimore: Williams & Wilkins; 1967
    [Google Scholar]
  35. Gregersen T. Rapid method for distinction of Gram-negative from Gram-positive bacteria. Eur J Appl Microbiol Biotechnol 1978; 5:123–127 [View Article]
    [Google Scholar]
  36. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article][PubMed]
    [Google Scholar]
  37. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington: American Society for Microbiology; 1994 pp 607–655
    [Google Scholar]
  38. Luo X, Wang J, Zeng X-C, Wang Y, Zhou L et al. Mycetocola manganoxydans sp. nov., an actinobacterium isolated from the Taklamakan desert. Int J Syst Evol Microbiol 2012; 62:2967–2970 [View Article][PubMed]
    [Google Scholar]
  39. Fraser SL, Jorgensen JH. Reappraisal of the antimicrobial susceptibilities of Chryseobacterium and Flavobacterium species and methods for reliable susceptibility testing. Antimicrob Agents Chemother 1997; 41:2738–2741 [View Article][PubMed]
    [Google Scholar]
  40. 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]
  41. 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 [View Article]
    [Google Scholar]
  42. Komagata K, Suzuki K. Lipid and cell-wall analysis in bacterialsystematics. Methods Microbiol 1987; 19:161–207
    [Google Scholar]
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