1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 6

sp. nov., isolated from rhizosphere soil of Free

Abstract

A Gram-negative, strictly aerobic, gliding motility, none-spore forming, yellow, rods bacterial strain, designated XS-5, was isolated from rhizosphere soil of , in Tumd Right Banner, Inner Mongolia, PR China. A phylogenetic tree based on the 16S rRNA gene sequences and the phylogenomic tree both showed that strain XS-5 clustered with F44-8 (shared 97.2 % of 16S rRNA gene similarity) and FCS-5 (97.6 %), and shared <96.0 % of 16S rRNA gene similarities with all other type strains. Strain XS-5 contained MK-6 as the major respiratory quinone. Its major polar lipids were phosphatidylethanolamine, an unidentified aminolipid and an unidentified lipid; and the major fatty acids were iso-C, iso-C 3-OH, C, iso-C 3-OH, Summed feature 3 (iso-C 2-OH and/or C ω), and Summed feature 9 (iso-C 9 and/or C 10-methyl). The genome consisted of a 3 985 855 bp circular chromosome, with a G+C content of 37.9 mol%, predicting 3616 coding sequences genes, 45 tRNA genes and three rRNA operons. The average nucleotide identity, amino acid identity and digital DNA–DNA hybridization values of strain XS-5 to F44-8 and FCS-5 were 79.2 and 79.2 %, 81.7 and 81.6 %, 22.3 and 22.2 %, respectively. The results of phylogenetic, physiological and biochemical tests allowed the discrimination of strain XS-5 from its phylogenetic relatives. sp. nov. is therefore proposed with strain XS-5 (=CGMCC 1.17077=KCTC 72459) as the type strain.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Bacteroidetes , Flavobacterium , rhizosphere and taxonomy
Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 31960020)
    • Principle Award Recipient: Ji-Quan Sun
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004255
2020-06-04
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/6/3888.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004255&mimeType=html&fmt=ahah

References

  1. Bergey DH, Harrison FC, Breed RS, Hammer BW, Huntoon FM. Bergey’s Manual of Determinative Bacteriology Baltimore: Williams & Wilkins; 1923
     [Google Scholar]
  2. Bernardet J-F, Segers P, Vancanneyt M, BErthe F, Kersters K et al. Cutting a gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis Strohl and Tait 1978). Int J Syst Bacteriol 1996; 46:128–148 [View Article]
     [Google Scholar]
  3. Montero-Calasanz MdelC, Göker M, Rohde M, Spröer C, Schumann P et al. Chryseobacterium oleae sp. nov., an efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea L.) cuttings and emended descriptions of the genus Chryseobacterium, C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense . Syst Appl Microbiol 2014; 37:342–350 [View Article][PubMed]
     [Google Scholar]
  4. Sun J-Q, Xu L, Liu M, Wang X-Y, Wu X-L. Flavobacterium suaedae sp. nov., an endophyte isolated from the root of Suaeda corniculata . Int J Syst Evol Microbiol 2016; 66:1943–1949 [View Article][PubMed]
     [Google Scholar]
  5. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][PubMed]
     [Google Scholar]
  6. Kim I, Kim J, Chhetri G, Seo T. Flavobacterium humi sp. nov., a flexirubin-type pigment producing bacterium, isolated from soil. J Microbiol 2019; 57:1079–1085 [View Article][PubMed]
     [Google Scholar]
  7. Kim H, Heo S-Y, Kim J-H, Chae J-C, Yu SM. Flavobacterium sangjuense sp. nov. isolated from sediment. Antonie van Leeuwenhoek 2019; 112:1699–1704 [View Article][PubMed]
     [Google Scholar]
  8. Choi H, Park S, Heo M. Flavobacterium jocheonensis sp. nov., Isolated from Marine Green Alga Ulva pertusa . J Microbiol Biotechnol 2019; 29:1266–1272 [View Article][PubMed]
     [Google Scholar]
  9. Sheu S-Y, Guo Y-P, Chen W-M. Flavobacterium amnicola sp. nov., isolated from a sub-tropical stream. Int J Syst Evol Microbiol 2019; 69:2283–2291 [View Article][PubMed]
     [Google Scholar]
  10. Chen W-M, Guo Y-P, Kwon S-W, Sheu C, Sheu S-Y. Flavobacterium stagni sp. nov., isolated from a freshwater reservoir. Int J Syst Evol Microbiol 2019; 69:2372–2379 [View Article][PubMed]
     [Google Scholar]
  11. Li G, Chen X, Li Y, Shi S, Jiang L et al. Flavobacterium viscosus sp. nov. and Flavobacterium tangerina sp. nov., from Primates Feces. Curr Microbiol 2019; 76:818–823 [View Article][PubMed]
     [Google Scholar]
  12. Larsbrink J, Zhu Y, Kharade SS, Kwiatkowski KJ, Eijsink VGH et al. A polysaccharide utilization locus from Flavobacterium johnsoniae enables conversion of recalcitrant chitin. Biotechnol Biofuels 2016; 9:260 [View Article][PubMed]
     [Google Scholar]
  13. Nedashkovskaya OI, Balabanova LA, Zhukova NV, Kim S-J, Bakunina IY et al. Flavobacterium ahnfeltiae sp. nov., a new marine polysaccharide-degrading bacterium isolated from a Pacific red alga. Arch Microbiol 2014; 196:745–752 [View Article][PubMed]
     [Google Scholar]
  14. Chaudhary DK, Kim D-U, Kim D, Kim J. Flavobacterium petrolei sp. nov., a novel psychrophilic, diesel-degrading bacterium isolated from oil-contaminated Arctic soil. Sci Rep 2019; 9:4134 [View Article][PubMed]
     [Google Scholar]
  15. Nayarisseri A, Suppahia A, Nadh AG, Nair AS. Identification and characterization of a pesticide degrading Flavobacterium species EMBS0145 by 16S rRNA gene sequencing. Interdiscip Sci 2015; 7:93–99 [View Article][PubMed]
     [Google Scholar]
  16. Jeong J-J, Sajidah S, Oh JY, Sang MK, Kim K-S et al. Complete genome sequence data of Flavobacterium anhuiense strain GSE09, a volatile-producing biocontrol bacterium isolated from cucumber (Cucumis sativus) root. Data Brief 2019; 25:104270 [View Article][PubMed]
     [Google Scholar]
  17. J-P M, Wang Z, Lu P, Wang H-J, Ali SW et al. Biodegradation of the sulfonylurea herbicide chlorimuron-ethyl by the strain Pseudomonas sp. LW3. FEMS Microbiol Lett 2010; 296:203–209
     [Google Scholar]
  18. 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]
  19. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876–4882 [View Article][PubMed]
     [Google Scholar]
  20. 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]
  21. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  22. 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]
  23. Xu L, Zhang H, Xing Y-T, Li N, Wang S et al. Complete genome sequence of Sphingobacterium psychroaquaticum strain SJ-25, an aerobic bacterium capable of suppressing fungal pathogens. Curr Microbiol 2020; 77:115–122 [View Article][PubMed]
     [Google Scholar]
  24. Hyatt D, Chen G-L, 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]
  25. Qi J, Wang B, Hao B-I. Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach. J Mol Evol 2004; 58:1–11 [View Article][PubMed]
     [Google Scholar]
  26. Zuo G, Hao B. CVTree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genom Proteom Bioinf 2015; 13:321–331 [View Article][PubMed]
     [Google Scholar]
  27. 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]
  28. Rodriguez-R LM, KK T. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PEER J 2016e1900
     [Google Scholar]
  29. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117134 [View Article][PubMed]
     [Google Scholar]
  30. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  31. Kates M. Techniques of Lipidology, 2nd ed. Amsterdam: Elsevier; 1986
     [Google Scholar]
  32. Komagata K, Suzuki K. Lipid and cell wall analysis in bacterial Systematics. Methods Microbiol 1987; 19:161–207
     [Google Scholar]
  33. Fautz E, Reichenbach H. A simple test for flexirubin-type pigments. FEMS Microbiol Lett 1980; 8:87–91 [View Article]
     [Google Scholar]
  34. Oren A. Characterization of pigments of prokaryotes and their use in taxonomy and classification. Methods Microbiol 38:261–282
     [Google Scholar]
  35. Akhwale JK, Göker M, Rohde M, Schumann P, Klenk H-P et al. Belliella kenyensis sp. nov., isolated from an alkaline lake. Int J Syst Evol Microbiol 2015; 65:457–462 [View Article][PubMed]
     [Google Scholar]
  36. Kaur I, Kaur C, Khan F, Mayilraj S. Flavobacterium rakeshii sp. nov., isolated from marine sediment, and emended description of Flavobacterium beibuense Fu et al. 2011. Int J Syst Evol Microbiol 2012; 62:2897–2902 [View Article][PubMed]
     [Google Scholar]
  37. Fu Y, Tang X, Lai Q, Zhang C, Zhong H et al. Flavobacterium beibuense sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2011; 61:205–209 [View Article][PubMed]
     [Google Scholar]
  38. Smibert RM, Krieg NR. Phenotypic Characterization. In Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
     [Google Scholar]
  39. Dong XZ, Cai MY. Determinative Manual for Routine Bacteriology Beijing: Scientific Press; 2001
     [Google Scholar]
  40. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000; 50:1861–1868 [View Article][PubMed]
     [Google Scholar]
  41. Kim B-C, Jeong W-J, Kim DY, Oh H-W, Kim H et al. Paenibacillus pueri sp. nov., isolated from Pu'er tea. Int J Syst Evol Microbiol 2009; 59:1002–1006 [View Article][PubMed]
     [Google Scholar]
  42. 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]
  43. Kuo I, Saw J, Kapan DD, Christensen S, Kaneshiro KY et al. Flavobacterium akiainvivens sp. nov., from decaying wood of Wikstroemia oahuensis, Hawai'i, and emended description of the genus Flavobacterium . Int J Syst Evol Microbiol 2013; 63:3280–3286 [View Article][PubMed]
     [Google Scholar]
  44. Ali Z, Cousin S, Frühling A, Brambilla E, Schumann P et al. Flavobacterium rivuli sp. nov., Flavobacterium subsaxonicum sp. nov., Flavobacterium swingsii sp. nov. and Flavobacterium reichenbachii sp. nov., isolated from a hard water rivulet. Int J Syst Evol Microbiol 2009; 59:2610–2617 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004255
Loading
Flavobacterium alkalisoli sp. nov., isolated from rhizosphere soil of Suaeda salsa
Int J Syst Evol Microbiol 70, 3888 (2020); https://doi.org/10.1099/ijsem.0.004255
/content/journal/ijsem/10.1099/ijsem.0.004255
/content/journal/ijsem/10.1099/ijsem.0.004255
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error