1887

Abstract

A Gram-stain-positive, aerobic, heterotrophic, non-spore-forming and rod-shaped strain, designated SJ-23, was isolated from rhizosphere soil of wheat ( L.) collected from Langfang, Hebei Province, central PR China and characterized using a polyphasic approach. Morphological and chemotaxonomic characteristics were consistent with those of members of the genus . The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, glycolipid and three unidentified lipids. The predominant menaquinones detected were MK-12, MK-11 and MK-10. Major fatty acids were identified as anteiso-C, anteiso-C and iso-C. The 16S rRNA gene sequence analysis showed that strain SJ-23 belongs to the genus with high sequence similarities to DSM 43045 (99.2 %), subsp. DSM 8595 (98.8 %) and subsp. DSM 8596 (98.6 %). Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain formed a separate branch in the genus . Furthermore, the combination of DNA–DNA hybridization results and some phenotypic characteristics demonstrated that strain SJ-23 could be distinguished from its closest relatives. Therefore, it is proposed that strain SJ-23 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is SJ-23 (=CGMCC 4.7419=DSM 105049).

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2019-10-01
2024-12-14
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References

  1. Gledhill WE, Casida LE. Predominant catalase-negative soil bacteria. III. Agromyces, gen. n., microorganisms intermediary to Actinomyces and Nocardia . Appl Microbiol 1969; 18:340–349[PubMed]
    [Google Scholar]
  2. Zgurskaya HI, Evtushenko LI, Akimov VN, Voyevoda HV, Dobrovolskaya TG et al. Emended Description of the Genus Agromyces and Description of Agromyces cerinus subsp. cerinus sp. nov., subsp. nov., Agromyces cerinus subsp. nitratus sp. nov., subsp. nov., Agromyces fucosus subsp. fucosus sp. nov., subsp. nov., and Agromyces fucosus subsp. hippuratus sp. nov., subsp. nov. Int J Syst Bacteriol 1992; 42:635–641 [View Article]
    [Google Scholar]
  3. Huang JR, Ming H, Li S, Meng XL, Zhang JX et al. Agromyces insulae sp. nov., an actinobacterium isolated from a soil sample. Int J Syst Evol Microbiol 2016; 66:2002–2007 [View Article][PubMed]
    [Google Scholar]
  4. Chen Z, Guan Y, Wang J, Li J. Agromyces binzhouensis sp. nov., an actinobacterium isolated from a coastal wetland of the Yellow River Delta. Int J Syst Evol Microbiol 2016; 66:2278–2283 [View Article][PubMed]
    [Google Scholar]
  5. Corretto E, Antonielli L, Sessitsch A, Compant S, Gorfer M et al. Agromyces aureus sp. nov., isolated from the rhizosphere of Salix caprea L. grown in a heavy-metal-contaminated soil. Int J Syst Evol Microbiol 2016; 66:3749–3754 [View Article][PubMed]
    [Google Scholar]
  6. Jurado V, Groth I, Gonzalez JM, Laiz L, Schuetze B et al. Agromyces italicus sp. nov., Agromyces humatus sp. nov. and Agromyces lapidis sp. nov., isolated from Roman catacombs. Int J Syst Evol Microbiol 2005; 55:871–875 [View Article][PubMed]
    [Google Scholar]
  7. Dorofeeva LV, Krausova VI, Evtushenko LI, Tiedje JM. Agromyces albus sp. nov., isolated from a plant (Androsace sp.). Int J Syst Evol Microbiol 2003; 53:1435–1438 [View Article][PubMed]
    [Google Scholar]
  8. Hamada M, Shibata C, Tamura T, Suzuki K. Agromyces marinus sp. nov., a novel actinobacterium isolated from sea sediment. J Antibiot 2014; 67:703–706 [View Article][PubMed]
    [Google Scholar]
  9. Park EJ, Kim MS, Jung MJ, Roh SW, Chang HW et al. Agromyces atrinae sp. nov., isolated from fermented seafood. Int J Syst Evol Microbiol 2010; 60:1056–1059 [View Article][PubMed]
    [Google Scholar]
  10. Bais HP, Weir TL, Perry LG, Gilroy S, Vivanco JM. The role of root exudates in rhizosphere interactions with plants and other organisms. Annu Rev Plant Biol 2006; 57:233–266 [View Article][PubMed]
    [Google Scholar]
  11. Berendsen RL, Pieterse CM, Bakker PA. The rhizosphere microbiome and plant health. Trends Plant Sci 2012; 17:478–486 [View Article][PubMed]
    [Google Scholar]
  12. Bulgarelli D, Schlaeppi K, Spaepen S, ver Loren van Themaat E, Schulze-Lefert P. Structure and functions of the bacterial microbiota of plants. Annu Rev Plant Biol 2013; 64:807–838 [View Article][PubMed]
    [Google Scholar]
  13. Hayakawa M, Nonomura H. Humic acid-vitamin agar, a new medium for the selective isolation of soil actinomycetes. J Ferment Technol 1987; 65:501–509 [View Article]
    [Google Scholar]
  14. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  15. Jin LY, Zhao Y, Song W, Duan LP, Jiang SW et al. Streptomyces inhibens sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.). Int J Syst Evol Microbiol 2019
    [Google Scholar]
  16. Waksman SA. The Actinomycetes . A Summary of Current Knowledge New York: Ronald; 1967
    [Google Scholar]
  17. Jones KL. Fresh isolates of actinomycetes in which the presence of sporogenous aerial mycelia is a fluctuating characteristic. J Bacteriol 1949; 57:141–145[PubMed]
    [Google Scholar]
  18. Waksman SA. The Actinomycetes . Classification, Identification and Descriptions of Genera and Species vol. 2 Baltimore: Williams and Wilkins; 1961
    [Google Scholar]
  19. Kelly KL. Inter-society color council-national bureau of standards color-name charts illustrated with centroid colors published in US; 1964
  20. Fu Y, Yan R, Liu D, Jiang S, Cui L et al. Trinickia diaoshuihuensis sp. nov., a plant growth promoting bacterium isolated from soil. Int J Syst Evol Microbiol 2019; 69:291–296 [View Article][PubMed]
    [Google Scholar]
  21. Ruan Z, Wang Y, Song J, Jiang S, Wang H et al. Kurthia huakuii sp. nov., isolated from biogas slurry, and emended description of the genus Kurthia . Int J Syst Evol Microbiol 2014; 64:518–521 [View Article][PubMed]
    [Google Scholar]
  22. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 607–654
    [Google Scholar]
  23. Gordon RE, Barnett DA, Handerhan JE, Pang CH-N. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin Strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
    [Google Scholar]
  24. Yokota A, Tamura T, Hasegawa T, Huang LH. Catenuloplanes japonicus gen. nov., sp. nov., nom. rev., a new genus of the order Actinomycetales . Int J Syst Bacteriol 1993; 43:805–812 [View Article]
    [Google Scholar]
  25. Prauser H, Falta R. Phagensensibilität, Zellwand-zusammensetzung und taxonomie von actinomyceten. Zeitschrift für allgemeine Mikrobiologie 1968; 8:39–46 [View Article]
    [Google Scholar]
  26. Nakai R, Baba T, Niki H, Nishijima M, Naganuma T. Aurantimicrobium minutum gen. nov., sp. nov., a novel ultramicrobacterium of the family Microbacteriaceae, isolated from river water. Int J Syst Evol Microbiol 2015; 65:4072–4079 [View Article][PubMed]
    [Google Scholar]
  27. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
    [Google Scholar]
  28. Lechevalier MP, Lechevalier HA. The chemotaxonomy of actinomycetes. In Dietz A, Thayer DW. (editors) Actinomycete Taxonomy (Special Publication) vol. 6 Arlington: Society of Industrial Microbiology; 1980 pp. 227–291
    [Google Scholar]
  29. 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]
  30. Collins MD. Isoprenoid quinone analyses in bacterial classification and identification. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp. 267–284
    [Google Scholar]
  31. Wu C, Lu X, Qin M, Wang Y, Ruan J et al. Analysis of menaquinone compound in microbial cells by HPLC. Microbiology vol. 16 Beijing: English translation of Microbiology; 1989 pp. 176–178
    [Google Scholar]
  32. Gao R, Liu C, Zhao J, Jia F, Yu C et al. Micromonospora jinlongensis sp. nov., isolated from muddy soil in China and emended description of the genus Micromonospora . Antonie van Leeuwenhoek 2014; 105:307–315 [View Article][PubMed]
    [Google Scholar]
  33. 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 [View Article][PubMed]
    [Google Scholar]
  34. Kim SB, Brown R, Oldfield C, Gilbert SC, Iliarionov S et al. Gordonia amicalis sp. nov., a novel dibenzothiophene-desulphurizing actinomycete. Int J Syst Evol Microbiol 2000; 50:2031–2036 [View Article][PubMed]
    [Google Scholar]
  35. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22:4673–4680 [View Article][PubMed]
    [Google Scholar]
  36. 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]
  37. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  38. 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]
  39. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
    [Google Scholar]
  40. 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]
  41. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article][PubMed]
    [Google Scholar]
  42. 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 [View Article][PubMed]
    [Google Scholar]
  43. de Ley J, Cattoir H, Reynaerts A. The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 1970; 12:133–142 [View Article][PubMed]
    [Google Scholar]
  44. Huss VA, Festl H, Schleifer KH. Studies on the spectrophotometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 1983; 4:184–192 [View Article][PubMed]
    [Google Scholar]
  45. Thomas EA, Alvarez CE, Sutcliffe JG. Evolutionarily distinct classes of S27 ribosomal proteins with differential mRNA expression in rat hypothalamus. J Neurochem 2000; 74:2259–2267 [View Article][PubMed]
    [Google Scholar]
  46. Yoon SH, 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 [View Article][PubMed]
    [Google Scholar]
  47. 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 [View Article][PubMed]
    [Google Scholar]
  48. Jacques MA, Durand K, Orgeur G, Balidas S, Fricot C et al. Phylogenetic analysis and polyphasic characterization of Clavibacter michiganensis strains isolated from tomato seeds reveal that nonpathogenic strains are distinct from C. michiganensis subsp. michiganensis . Appl Environ Microbiol 2012; 78:8388–8402 [View Article][PubMed]
    [Google Scholar]
  49. Rong X, Huang Y. Taxonomic evaluation of the Streptomyces hygroscopicus clade using multilocus sequence analysis and DNA-DNA hybridization, validating the MLSA scheme for systematics of the whole genus. Syst Appl Microbiol 2012; 35:7–18 [View Article][PubMed]
    [Google Scholar]
  50. Chen XY, Zhou YK, Zheng FC. Comparison of two extracting methods for soil microbial total DNA.. Chin J Trop Agric 2008; 28:41–43
    [Google Scholar]
  51. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article][PubMed]
    [Google Scholar]
  52. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
    [Google Scholar]
  53. Bai Y, Müller DB, Srinivas G, Garrido-Oter R, Potthoff E et al. Functional overlap of the arabidopsis leaf and root microbiota. Nature 2015; 528:364–369 [View Article][PubMed]
    [Google Scholar]
  54. Ramachandran VK, East AK, Karunakaran R, Downie JA, Poole PS. Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics. Genome Biol 2011; 12:(10) [View Article][PubMed]
    [Google Scholar]
  55. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
    [Google Scholar]
  56. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  57. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014; 64:316–324 [View Article][PubMed]
    [Google Scholar]
  58. Jurado V, Groth I, Gonzalez JM, Laiz L, Saiz-Jimenez C. Agromyces subbeticus sp. nov., isolated from a cave in southern Spain. Int J Syst Evol Microbiol 2005; 55:1897–1901 [View Article][PubMed]
    [Google Scholar]
  59. Ortiz-Martinez A, Gonzalez JM, Evtushenko LI, Jurado V, Laiz L et al. Reclassification of Agromyces fucosus subsp. hippuratus as Agromyces hippuratus sp. nov., comb. nov. and emended description of Agromyces fucosus . Int J Syst Evol Microbiol 2004; 54:1553–1556 [View Article][PubMed]
    [Google Scholar]
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