1887

Abstract

A novel endophytic bacterium, designated strain SX2RGS8, was isolated from the surface-sterilized roots of an endangered medicinal plant ( K. M. Shen) collected from Xinjiang, north-western PR China. The taxonomic position of the candidate was investigated using a polyphasic approach. Strain SX2RGS8 was found to be aerobic, Gram-stain-negative, oxidase-negative, catalase-positive and axiolitic-shaped. Strain SX2RGS8 grew at 4–45 °C (optimum, 28 °C), pH 4.0–10.0 (pH 7.0) and in the presence of 0–5 % (w/v) NaCl. The polar lipids detected for strain SX2RGS8 were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, unidentified phosphoglycolipids, an unidentified phospholipid and unidentified lipids. The major respiratory quinone of strain SX2RGS8 was ubiquinone 10 and the major fatty acid was summed feature 8 (Cω7 and/or Cω6). The DNA G+C content was determined to be 66.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the isolate belonged to the family and showed 99.2 % (), 95.5 % () and 95.4 % () similarities to its closest relatives. The isolate contained carotenoids, but no bacteriochlorophyll . On the basis of phenotypic, genotypic and phylogenetic data, strain SX2RGS8 represents a novel species of a novel genus in the family , for which the name gen. nov., sp. nov. is proposed. The type strain is SX2RGS8 (=CGMCC 1.16402=KCTC 62090). In addition, Coil . 2016 is proposed to be transferred to this new genus as comb. nov.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003540
2019-08-01
2019-08-19
Loading full text...

Full text loading...

References

  1. Lee KB et al. The hierarchical system of the 'Alphaproteobacteria': description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov. Int J Syst Evol Microbiol 2005;55:1907–1919 [CrossRef]
    [Google Scholar]
  2. Kwon KK, Woo JH, Yang SH, Kang JH, Kang SG et al. Altererythrobacter epoxidivorans gen. nov., sp. nov., an epoxide hydrolase-active, mesophilic marine bacterium isolated from cold-seep sediment, and reclassification of Erythrobacter luteolus Yoon et al. 2005 as Altererythrobacter luteolus comb. nov. Int J Syst Evol Microbiol 2007;57:2207–2211 [CrossRef]
    [Google Scholar]
  3. Xu XW, Wu YH, Wang CS, Wang XG, Oren A et al. Croceicoccus marinus gen. nov., sp. nov., a yellow-pigmented bacterium from deep-sea sediment, and emended description of the family Erythrobacteraceae. Int J Syst Evol Microbiol 2009;59:2247–2253 [CrossRef][PubMed]
    [Google Scholar]
  4. Huang Y, Zeng Y, Feng H, Wu Y, Xu X. Croceicoccus naphthovorans sp. nov., a polycyclic aromatic hydrocarbons-degrading and acylhomoserine-lactone-producing bacterium isolated from marine biofilm, and emended description of the genus Croceicoccus. Int J Syst Evol Microbiol 2015;65:1531–1536 [CrossRef]
    [Google Scholar]
  5. Shiba T, Simidu U. Erythrobacter longus gen. nov., sp. nov., an aerobic bacterium which contains bacteriochlorophyll a. Int J Syst Bacteriol 1982;32:211–217 [CrossRef]
    [Google Scholar]
  6. Yurkov V, Stackebrandt E, Holmes A, Fuerst JA, Hugenholtz P et al. Phylogenetic positions of novel aerobic, bacteriochlorophyll a-containing bacteria and description of Roseococcus thiosulfatophilus gen. nov., sp. nov., Erythromicrobium ramosum gen. nov., sp. nov., and Erythrobacter litoralis sp. nov. Int J Syst Bacteriol 1994;44:427–434 [CrossRef]
    [Google Scholar]
  7. Fuerst JA, Hawkins JA, Holmes A, Sly LI, Moore CJ et al. Porphyrobacter neustonensis gen. nov., sp. nov., an aerobic bacteriochlorophyll-synthesizing budding bacterium from fresh water. Int J Syst Bacteriol 1993;43:125–134 [CrossRef]
    [Google Scholar]
  8. Feng XM, Mo YX, Han L, Nogi Y, Zhu YH et al. Qipengyuania sediminis gen. nov., sp. nov., a member of the family Erythrobacteraceae isolated from subterrestrial sediment. Int J Syst Evol Microbiol 2015;65:3658–3665 [CrossRef][PubMed]
    [Google Scholar]
  9. Xue X, Zhang K, Cai F, Dai J, Wang Y et al. Altererythrobacter xinjiangensis sp. nov., isolated from desert sand, and emended description of the genus Altererythrobacter. Int J Syst Evol Microbiol 2012;62:28–32 [CrossRef]
    [Google Scholar]
  10. Subhash Y, Tushar L, Sasikala C, Ramana C. Erythrobacter odishensis sp. nov. and Pontibacter odishensis sp. nov. isolated from dry soil of a solar saltern. Int J Syst Evol Microbiol 2013;63:4524–4532 [CrossRef][PubMed]
    [Google Scholar]
  11. Coil DA, Flanagan JC, Stump A, Alexiev A, Lang JM et al. Porphyrobacter mercurialis sp. nov., isolated from a stadium seat and emended description of the genus Porphyrobacter. PeerJ 2016;3:e1400 [CrossRef]
    [Google Scholar]
  12. Furuhata K, Edagawa A, Miyamoto H, Kawakami Y, Fukuyama M. Porphyrobacter colymbi sp. nov. isolated from swimming pool water in Tokyo, Japan. J Gen Appl Microbiol 2013;59:245–250 [CrossRef]
    [Google Scholar]
  13. Kikuzaki H, Hisamoto M, Hirose K, Akiyama K, Taniguchi H. Antioxidant properties of ferulic acid and its related compounds. J Agric Food Chem 2002;50:2161–2168 [CrossRef]
    [Google Scholar]
  14. Iranshahi M, Arfa P, Ramezani M, Jaafari MR, Sadeghian H et al. Sesquiterpene coumarins from Ferula szowitsiana and in vitro antileishmanial activity of 7-prenyloxycoumarins against promastigotes. Phytochemistry 2007;68:554–561 [CrossRef]
    [Google Scholar]
  15. Qin S, Wang HB, Chen HH, Zhang YQ, Jiang CL et al. Glycomyces endophyticus sp. nov., an endophytic actinomycete isolated from the root of Carex baccans Nees. Int J Syst Evol Microbiol 2008;58:2525–2528 [CrossRef]
    [Google Scholar]
  16. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966;16:313–340 [CrossRef]
    [Google Scholar]
  17. Atlas RM In: Parks LC. editor Handbook of Microbiological Media, 4th ed. Boca Raton, FL: CRC Press; 2010; pp.719
    [Google Scholar]
  18. Waksman SA. The Actinomycetes. A Summary of Current Knowledge New York: RonaldPress; 1967
    [Google Scholar]
  19. Kelly KL. Inter-Society Color Council-National Bureau of Standards Color-Name Charts Illustrated with Centroid Colors Washington: US Government Printing Office; 1964
    [Google Scholar]
  20. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ 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 [CrossRef][PubMed]
    [Google Scholar]
  21. Gordon RE, Barnett DA, Handerhan JE, Pang CHN. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974;24:54–63 [CrossRef]
    [Google Scholar]
  22. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL. In Williams ST, Sharpe ME, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriologyvol. 4 Baltimore: Williams & Willkins; 1989; pp.2453–2492
    [Google Scholar]
  23. Gaisin VA, Kalashnikov AM, Grouzdev DS, Sukhacheva M V, Kuznetsov BB et al. Chloroflexus islandicus sp. nov. a thermophilic filamentous anoxygenic phototrophic bacterium from geyser Strokkur (Iceland). Int J Syst Evol Microbiol 2017;67:1381–1386
    [Google Scholar]
  24. Li J, Zhao GZ, Long LJ, Wang FZ, Tian XP et al. Rhodococcus nanhaiensis sp. nov., an actinobacterium isolated from marine sediment. Int J Syst Evol Microbiol 2012;62:2517–2521 [CrossRef]
    [Google Scholar]
  25. Yoon SH, Ha SM, 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][PubMed]
    [Google Scholar]
  26. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403–410 [CrossRef]
    [Google Scholar]
  27. Thompson J, 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 [CrossRef]
    [Google Scholar]
  28. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4:406–425
    [Google Scholar]
  29. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969;18:1–32 [CrossRef]
    [Google Scholar]
  30. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971;20:406–416 [CrossRef]
    [Google Scholar]
  31. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981;17:368–376 [CrossRef]
    [Google Scholar]
  32. Kumar S, Stecher G, Tamura K. mega7.0: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef]
    [Google Scholar]
  33. 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]
  34. Kimura M. The Neutral Theory of Molecular Evolution Cambridge University Press; 1985
    [Google Scholar]
  35. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39:783–791 [CrossRef]
    [Google Scholar]
  36. Harrison P. SPADES - a process algebra for discrete event simulation. J Logic Comput 2000;10:3–42 [CrossRef]
    [Google Scholar]
  37. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010;11:119 [CrossRef]
    [Google Scholar]
  38. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 2012;28:1033–1034 [CrossRef]
    [Google Scholar]
  39. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32:1792–1797 [CrossRef]
    [Google Scholar]
  40. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000;17:540–552 [CrossRef]
    [Google Scholar]
  41. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014;30:1312–1313 [CrossRef]
    [Google Scholar]
  42. Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 2016;44:W242–W245 [CrossRef]
    [Google Scholar]
  43. Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014;196:2210–2215 [CrossRef]
    [Google Scholar]
  44. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977;100:221–230 [CrossRef]
    [Google Scholar]
  45. 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]
  46. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982;5:2359–2367 [CrossRef]
    [Google Scholar]
  47. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983;54:31–36 [CrossRef]
    [Google Scholar]
  48. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: MicrobialID, Inc; 1990
    [Google Scholar]
  49. Goris J, Klappenbach JA, Vandamme P, Coenye T, Konstantinidis KT et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007;57:81–91 [CrossRef]
    [Google Scholar]
  50. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106:19126–19131 [CrossRef]
    [Google Scholar]
  51. 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 [CrossRef]
    [Google Scholar]
  52. 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]
  53. Yurkov VV, Krieger S, Stackebrandt E, Beatty JT. Citromicrobium bathyomarinum, a novel aerobic bacterium isolated from deep-sea hydrothermal vent plume waters that contains photosynthetic pigment-protein complexes. J Bacteriol 1999;181:4517–4525
    [Google Scholar]
  54. Rainey FA, Silva J, Nobre MF, Silva MT, da Costa MS. Porphyrobacter cryptus sp. nov., a novel slightly thermophilic, aerobic, bacteriochlorophyll a-containing species. Int J Syst Evol Microbiol 2003;53:35–41 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003540
Loading
/content/journal/ijsem/10.1099/ijsem.0.003540
Loading

Data & Media loading...

Supplementary File 1

PDF

Most Cited This Month

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