1887

Abstract

A Gram-stain-negative, aerobic and short rod-shaped bacterial strain, designated LD6, was isolated from a forest soil sample in Suwon, Gyeonggi-do, Republic of Korea. Strain LD6 grew at 10–37 °C (optimal temperature, 28 °C), and tolerated pH 8.0 and 2 % (w/v) NaCl. Strain LD6 was related most closely to members of the genus , namely NF2-5-3 (98.2 % 16S rRNA gene sequence similarity), A3 (97.9 %), DCY85 (97.9 %) and MWAP64 (97.7 %). The strain grew well on R2A agar, tryptone soya agar, Mueller-Hinton agar and nutrient agar. The major polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and glycolipid. The major respiratory quinone was ubiquinone 8 (Q-8). The main fatty acids were C cyclo, C, C 3-OH, C cyclo ω8 and C. The DNA G+C content of the isolated strain based on the whole genome sequence was 63.4 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain LD6 and its reference type strains ranged from 80.3 to 82.4%, and from 23.7 to 33.7%, respectively. Based on phenotypic, chemotypic and genotypic evidence, strain LD6 could be differentiated phylogenetically and phenotypically from the recognized species of the genus . Therefore, strain LD6 is considered to represent a novel species, for which the name sp. nov. is proposed. The type strain is LD6 (=KACC 21387=JCM 33640).

Funding
This study was supported by the:
  • Jaisoo Kim , Kyonggi University , (Award 2018-031)
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2020-02-26
2020-06-02
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References

  1. Sawana A, Adeolu M, Gupta RS. Molecular signatures and phylogenomic analysis of the genus Burkholderia: Proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species. Front Genet 2014; 5:1–22 [CrossRef]
    [Google Scholar]
  2. Dobritsa AP, Samadpour M. Transfer of eleven species of the genus Burkholderia to the genus Paraburkholderia and proposal of Caballeronia gen. nov. to accommodate twelve species of the genera Burkholderia and Paraburkholderia . Int J Syst Evol Microbiol 2016; 66:2836–2846 [CrossRef]
    [Google Scholar]
  3. Lopes-Santos L, Castro DBA, Ferreira-Tonin M, Corrêa DBA, Weir BS et al. Reassessment of the taxonomic position of Burkholderia andropogonis and description of Robbsia andropogonis gen. nov., comb. nov. Antonie van Leeuwenhoek 2017; 110:727–736 [CrossRef]
    [Google Scholar]
  4. Estrada-de Los Santos P, Palmer M, Chávez-Ramírez B, Beukes C, Steenkamp ET et al. Whole genome analyses suggests that Burkholderia sensu lato contains two additional novel genera (Mycetohabitans gen. nov., and Trinickia gen. nov.): implications for the evolution of diazotrophy and nodulation in the Burkholderiaceae . Genes 2018; 9:389 [CrossRef]
    [Google Scholar]
  5. Suárez-Moreno ZR, Caballero-Mellado J, Coutinho BG, Mendonça-Previato L, James EK et al. Common features of environmental and potentially beneficial plant-associated Burkholderia. Microb Ecol 2012; 63:249–266 [CrossRef]
    [Google Scholar]
  6. Paulitsch F, Dall'Agnol RF, Delamuta JRM, Ribeiro RA, da Silva Batista JS et al. Paraburkholderia guartelaensis sp. nov., a nitrogen-fixing species isolated from nodules of Mimosa gymnas in an ecotone considered as a hotspot of biodiversity in Brazil. Arch Microbiol 2019; 201:14351446 [CrossRef]
    [Google Scholar]
  7. Bournaud C, Moulin L, Cnockaert M, Faria Sde, Prin Y et al. Paraburkholderia piptadeniae sp. nov. and Paraburkholderia ribeironis sp. nov., two root-nodulating symbiotic species of Piptadenia gonoacantha in Brazil. Int J Syst Evol Microbiol 2017; 67:432–440 [CrossRef]
    [Google Scholar]
  8. Lim JH, Baek SH, Lee ST. Burkholderia sediminicola sp. nov., isolated from freshwater sediment. Int J Syst Evol Microbiol 2008; 58:565–569 [CrossRef]
    [Google Scholar]
  9. Lee Y, Jeon CO. Paraburkholderia aromaticivorans sp. nov., an aromatic hydrocarbon-degrading bacterium, isolated from gasoline-contaminated soil. Int J Syst Evol Microbiol 2018; 68:1251–1257 [CrossRef]
    [Google Scholar]
  10. Yoo SH, Kim BY, Weon HY, Kwon SW, Go S-J et al. Burkholderia soli sp. nov., isolated from soil cultivated with Korean ginseng. Int J Syst Evol Microbiol 2007; 57:122–125 [CrossRef]
    [Google Scholar]
  11. Gao Z, Yuan Y, Xu L, Liu R, Chen M et al. Paraburkholderia caffeinilytica sp. nov., isolated from the soil of a tea plantation. Int J Syst Evol Microbiol 2016; 66:4185–4190 [CrossRef]
    [Google Scholar]
  12. Weber CF, King GM. Volcanic soils as sources of novel co-oxidizing Paraburkholderia and Burkholderia: Paraburkholderia hiiakae sp. nov., Paraburkholderia metrosideri sp. nov., Paraburkholderia paradisi sp. nov., Paraburkholderia peleae sp. nov., and Burkholderia alpina sp. nov. a member of the Burkholderia cepacia complex. Front Microbiol 2017; 8:1–10 [CrossRef]
    [Google Scholar]
  13. Choi GM, Im WT. Paraburkholderia azotifigens sp. nov., a nitrogen-fixing bacterium isolated from paddy soil. Int J Syst Evol Microbiol 2018; 68:310–316 [CrossRef]
    [Google Scholar]
  14. Gao ZH, Zhong SF, Lu ZE, Xiao SY, Qiu LH. Paraburkholderia caseinilytica sp. nov., isolated from the pine and broad-leaf mixed forest soil. Int J Syst Evol Microbiol 2018; 68:1963–1968 [CrossRef]
    [Google Scholar]
  15. Fu JC, Lv YY, You J, Gao ZH, Wang BF et al. Paraburkholderia dinghuensis sp. nov., isolated from soil. Int J Syst Evol Microbiol 2019; 69:1613–1620 [CrossRef]
    [Google Scholar]
  16. Xiao SY, Gao ZH, Lin QH, Qiu LH. Paraburkholderia pallida sp. nov. and Paraburkholderia silviterrae sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 2019; 69:37773785 [CrossRef]
    [Google Scholar]
  17. Lv YY, Chen MH, Xia F, Wang J, Qiu LH. Paraburkholderiapallidirosea sp. nov., isolated from a monsoon evergreen broad-leaved forest soil. Int J Syst Evol Microbiol 2016; 66:4537–4542 [CrossRef]
    [Google Scholar]
  18. Pham VHT, Kim J. Cultivation of unculturable soil bacteria. Trends Biotechnol 2012; 30:475–484 [CrossRef]
    [Google Scholar]
  19. Tindall BJ, Garrity GM. Proposals to clarify how type strains are deposited and made available to the scientific community for the purpose of systematic research. Int J Syst Evol Microbiol 2008; 58:1987–1990 [CrossRef]
    [Google Scholar]
  20. Cheng H-R, Jiang N. Extremely rapid extraction of DNA from bacteria and yeasts. Biotechnol Lett 2006; 28:55–59 [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. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [CrossRef]
    [Google Scholar]
  23. 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]
  24. 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]
  25. Felsenstein J. Confidence limits on phylogenies : An approach using the bootstrap. Soc Study Evol 1985; 39:783–791
    [Google Scholar]
  26. 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]
  27. Bertels F, Silander OK, Pachkov M, Rainey PB, van Nimwegen E. Automated reconstruction of whole-genome phylogenies from short-sequence reads. Mol Biol Evol 2014; 31:1077–1088 [CrossRef]
    [Google Scholar]
  28. Yoon S-H, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [CrossRef]
    [Google Scholar]
  29. 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 [CrossRef]
    [Google Scholar]
  30. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75–15 [CrossRef]
    [Google Scholar]
  31. Grant JR, Stothard P. The CGView server: a comparative genomics tool for circular genomes. Nucleic Acids Res 2008; 36:W181–W184 [CrossRef]
    [Google Scholar]
  32. Adamek M, Spohn M, Stegmann E, Ziemert N. Mining Bacterial Genomes for Secondary Metabolite Gene Clusters. In Sass P. editor Antibiotics Method and Protocols Humana Press; 2017 pp 23–49
    [Google Scholar]
  33. Blin K, Shaw S, Steinke K, Villebro R, Ziemert N et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res 2019; 47:W81–W87 [CrossRef]
    [Google Scholar]
  34. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 2011; 39:W339–W346 [CrossRef]
    [Google Scholar]
  35. Lanyi B. Classical and Rapid Identification Method for Medically Important Bacteria. In Cowell R. editor Method in Microbiology 19 Academic Press; 1987 pp 1–65
    [Google Scholar]
  36. Moyes RB, Reynolds J, Breakwell DP. Differential staining of bacteria: gram stain. Curr Protoc Microbiol 2009; Appendix 3:1–8 [CrossRef]
    [Google Scholar]
  37. Krieg NR, Padgett PJ. Phenotype and Physiological Characterization Methods. In Rainey F. editor Methods in microbiology 38 Academic Press; 2011 pp 15–60
    [Google Scholar]
  38. Mcllvaine TC. A buffer solution for colorimetric comparison. J Biol Chem 1921; 49:183–186
    [Google Scholar]
  39. Delory GE, King EJ. A sodium carbonate-bicarbonate buffer for alkaline phosphatases. Biochem J 1945; 39:245 [CrossRef]
    [Google Scholar]
  40. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic Characterization and the Principles of Comparative Systematics. In Reddy CA. editor Methods for General and Molecular Microbiology ASM Press; 2007 pp 330–393
    [Google Scholar]
  41. Sierra G. A simple method for the detection of lipolytic activity of micro-organisms and some observations on the influence of the contact between cells and fatty substrates. Antonie Van Leeuwenhoek 1957; 23:15–22 [CrossRef]
    [Google Scholar]
  42. 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 [CrossRef]
    [Google Scholar]
  43. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [CrossRef]
    [Google Scholar]
  44. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. Tech Note 2001; 101:1–6
    [Google Scholar]
  45. Vandamme P, Opelt K, Knochel N, Berg C, Schonmann S et al. Burkholderia bryophila sp. nov. and Burkholderia megapolitana sp. nov., moss-associated species with antifungal and plant-growth-promoting properties. Int J Syst Evol Microbiol 2007; 57:2228–2235
    [Google Scholar]
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