1887

Abstract

A Gram-stain-negative, non-spore-forming, motile, aerobic, rod-shaped bacteria strain, designated LCB8, was isolated from the insect captured from a deserted cropland in Shuangliu district, Chengdu, PR China. Phylogenetic analysis on the basis of 16S rRNA gene sequence indicated that the strain represented a member of the genus , family , class CCUG 60088 (97.9 %) and CCUG 38531 (98.8 %) were identified as the most closely related phylogenetic neighbours of strain LCB8. The novel strain was able to grow at salt concentrations of 0–4.5 % (w/v), pH 5–9 and temperatures of 20–42 °C. The major quinone system was ubiquinone Q-10, the major fatty acids were Cω7, C and C. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmonomethylethanolamine, diphosphatidylglycerol and four undefined aminolipids. The major polyamines were putrescine and spermidine. Genome sequencing revealed a genome size of 4.76 Mbp and a DNA G+C content of 57.1 mol%. These phenotypic, genotypic and chemotaxonomic traits excellently supported the affiliation of LCB8 to the genus . Pairwise determined whole-genome average nucleotide identity (ANI) values indicated that strain LCB8 represents a novel species, for which we propose the name sp. nov. with the type strain LCB8 (=KCTC 72031=CGMCC 1.13984).

Funding
This study was supported by the:
  • Yongqiang Tian , the National Key Research and Development Program of China , (Award 2018YFC1802201)
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2020-02-25
2020-06-04
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References

  1. Holmes B, Popoff M, Kiredjian M, Kersters K. Ochrobactrum anthropi gen. nov., sp. nov. from human clinical specimens and previously known as group Vd. Int J Syst Bacteriol 1988; 38:406–416 [CrossRef]
    [Google Scholar]
  2. Li Y-Q, Li L, Chen W, Duan Y-Q, Nimaichand S et al. Novosphingobium endophyticum sp. nov. isolated from roots of Glycyrrhiza uralensis . Arch Microbiol 2015; 197:911–918 [CrossRef]
    [Google Scholar]
  3. Lebuhn M, Achouak W, Schloter M, Berge O, Meier H et al. Taxonomic characterization of Ochrobactrum sp. isolates from soil samples and wheat roots, and description of Ochrobactrum tritici sp. nov. and Ochrobactrum grignonense sp. nov. Int J Syst Evol Microbiol 2000; 50 Pt 6:2207–2223 [CrossRef]
    [Google Scholar]
  4. Tripathi AK, Verma SC, Chowdhury SP, Lebuhn M, Gattinger A et al. Ochrobactrum oryzae sp. nov., an endophytic bacterial species isolated from deep-water rice in India. Int J Syst Evol Microbiol 2006; 56:1677–1680 [CrossRef]
    [Google Scholar]
  5. Zurdo-Piñeiro JL, Rivas R, Trujillo ME, Vizcaíno N, Carrasco JA et al. Ochrobactrum cytisi sp. nov., isolated from nodules of Cytisus scoparius in Spain. Int J Syst Evol Microbiol 2007; 57:784–788 [CrossRef]
    [Google Scholar]
  6. Kämpfer P, Sessitsch A, Schloter M, Huber B, Busse H-J et al. Ochrobactrum rhizosphaerae sp. nov. and Ochrobactrum thiophenivorans sp. nov., isolated from the environment. Int J Syst Evol Microbiol 2008; 58:1426–1431 [CrossRef]
    [Google Scholar]
  7. Imran A, Hafeez FY, Frühling A, Schumann P, Malik KA et al. Ochrobactrum ciceri sp. nov., isolated from nodules of Cicer arietinum . Int J Syst Evol Microbiol 2010; 60:1548–1553 [CrossRef]
    [Google Scholar]
  8. Huber B, Scholz HC, Kämpfer P, Falsen E, Langer S et al. Ochrobactrum pituitosum sp. nov., isolated from an industrial environment. Int J Syst Evol Microbiol 2010; 60:321–326 [CrossRef]
    [Google Scholar]
  9. Woo S-G, Ten LN, Park J, Lee M. Ochrobactrum daejeonense sp. nov., a nitrate-reducing bacterium isolated from sludge of a leachate treatment plant. Int J Syst Evol Microbiol 2011; 61:2690–2696 [CrossRef]
    [Google Scholar]
  10. Kämpfer P, Buczolits S, Albrecht A, Busse H-J, Stackebrandt E. Towards a standardized format for the description of a novel species (of an established genus): Ochrobactrum gallinifaecis sp. nov. Int J Syst Evol Microbiol 2003b; 53:893–896 [CrossRef]
    [Google Scholar]
  11. Kämpfer P, Huber B, Busse H-J, Scholz HC, Tomaso H et al. Ochrobactrum pecoris sp. nov., isolated from farm animals. Int J Syst Evol Microbiol 2011; 61:2278–2283 [CrossRef]
    [Google Scholar]
  12. Velasco J, Romero C, López-Goñi I, Leiva J, Díaz R et al. Evaluation of the relatedness of Brucella spp. and Ochrobactrum anthropi and description of Ochrobactrum intermedium sp. nov., a new species with a closer relationship to Brucella spp. Int J Syst Bacteriol 1998; 48 Pt 3:759–768 [CrossRef]
    [Google Scholar]
  13. Teyssier C, Marchandin H, Jean-Pierre H, Masnou A, Dusart G et al. Ochrobactrum pseudintermedium sp. nov., a novel member of the family Brucellaceae, isolated from human clinical samples. Int J Syst Evol Microbiol 2007; 57:1007–1013 [CrossRef]
    [Google Scholar]
  14. Kämpfer P, Scholz HC, Huber B, Falsen E, Busse H-J. Ochrobactrum haematophilum sp. nov. and Ochrobactrum pseudogrignonense sp. nov., isolated from human clinical specimens. Int J Syst Evol Microbiol 2007; 57:2513–2518 [CrossRef]
    [Google Scholar]
  15. Sultan S, Hasnain S. Reduction of toxic hexavalent chromium by Ochrobactrum intermedium strain SDCr-5 stimulated by heavy metals. Bioresour Technol 2007; 98:340–344 [CrossRef]
    [Google Scholar]
  16. Arulazhagan P, Vasudevan N. Biodegradation of polycyclic aromatic hydrocarbons by a halotolerant bacterial strain Ochrobactrum sp. Va1. Mar Pollut Bull 2011; 62:388–394 [CrossRef]
    [Google Scholar]
  17. Kikuchi Y, Hayatsu M, Hosokawa T, Nagayama A, Tago K et al. Symbiont-mediated insecticide resistance. Proc Natl Acad Sci U S A 2012; 109:8618–8622 [CrossRef]
    [Google Scholar]
  18. Spiteller D, Dettner K, Bolan W. Gut bacteria may be involved in interactions between plants, herbivores and their predators: microbial biosynthesis of N-acylglutamine surfactants as elicitors of plant volatiles. Biol Chem 2000; 381:755–762 [CrossRef]
    [Google Scholar]
  19. Bansal R, Hulbert S, Schemerhorn B, Reese JC, Whitworth RJ et al. Hessian fly-associated bacteria: transmission, essentiality, and composition. PLoS One 2011; 6:e23170 [CrossRef]
    [Google Scholar]
  20. Chun J, Goodfellow M. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 1995; 45:240–245 [CrossRef]
    [Google Scholar]
  21. 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 [CrossRef]
    [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 [CrossRef]
    [Google Scholar]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [CrossRef]
    [Google Scholar]
  24. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [CrossRef]
    [Google Scholar]
  25. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–967
    [Google Scholar]
  26. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [CrossRef]
    [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 [CrossRef]
    [Google Scholar]
  28. Kimura M. The Neutral Theory of Molecular Evolution New York: Cambridge University Press; 1983
    [Google Scholar]
  29. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012; 1:18 [CrossRef]
    [Google Scholar]
  30. Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 2015; 31:587–589 [CrossRef]
    [Google Scholar]
  31. Gan L, Zhang Y, Tang R, Liu B, Wang S et al. Genomic characterization of a potentially novel Streptococcus species producing exopolysaccharide. 3 Biotech 2019; 9: [CrossRef]
    [Google Scholar]
  32. Gan L, Zhang Y, Zhang L, Li X, Wang Z et al. Planococcus halotolerans sp. nov., isolated from a saline soil sample in China. Int J Syst Evol Microbiol 2018; 68:3500–3505 [CrossRef]
    [Google Scholar]
  33. Haddock JD, Horton JR, Gibson DT. Dihydroxylation and dechlorination of chlorinated biphenyls by purified biphenyl 2,3-dioxygenase from Pseudomonas sp. strain LB400. J Bacteriol 1995; 177:20–26 [CrossRef]
    [Google Scholar]
  34. Lin C-jiao, Yang L-rong, Xu G, Wu J-ping, Lin C et al. Enhancement of haloacetate dehalogenase production by strain mutation and condition optimization. Biotechnology and Bioprocess Engineering 2011; 16:923–929 [CrossRef]
    [Google Scholar]
  35. Zhang R, Cui Z, Jiang J, He J, Gu X et al. Diversity of organophosphorus pesticide-degrading bacteria in a polluted soil and conservation of their organophosphorus hydrolase genes. Can J Microbiol 2005; 51:337–343 [CrossRef]
    [Google Scholar]
  36. 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 [CrossRef]
    [Google Scholar]
  37. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Manual of Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  38. Gerhardt P, Murray RGE, Costilow RN, Nester EW, Wood WA et al. Manual of Methods for General Bacteriology Washington, DC: American Society for Microbiology; 1981
    [Google Scholar]
  39. Cappuccino JG, Sherman N. Microbiology: a Laboratory Manual, 8th ed. San Francisco, CA: Pearson/Benjamin Cummings; 2008
    [Google Scholar]
  40. Barrow GI, Feltham RKA. Cowan and Steel’s Manual for the Identification of Medical Bacteria Cambridge: Cambridge University Press; 2004
    [Google Scholar]
  41. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  42. Xiang W, Liu C, Wang X, Du J, Xi L et al. Actinoalloteichus nanshanensis sp. nov., isolated from the rhizosphere of a fig tree (Ficus religiosa). Int J Syst Evol Microbiol 2011; 61:1165–1169 [CrossRef]
    [Google Scholar]
  43. Kates M. Techniques of lipidology: isolation, analysis and identification of lipids. In Work TS, Work E. (editors) Laboratory Techniques in Biochemistry and Molecular Biology 3 Amsterdam: Elsevier; 1972 pp 269–610
    [Google Scholar]
  44. Raj PS, Ramaprasad EVV, Vaseef S, Sasikala C, Ramana CV. Rhodobacter viridis sp. nov., a phototrophic bacterium isolated from mud of a stream. Int J Syst Evol Microbiol 2013; 63:181–186 [CrossRef]
    [Google Scholar]
  45. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [CrossRef]
    [Google Scholar]
  46. Scherer P, Kneifel H. Distribution of polyamines in methanogenic bacteria. J Bacteriol 1983; 154:1315–1322 [CrossRef]
    [Google Scholar]
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