1887

Abstract

The genus contains several species with agricultural, biotechnological and ecological importance. Within this genus, many phyllosphere, rhizosphere and endosphere strains are plant growth promoting bacteria, whereas strains designated as are plant pathogens. In this study, we isolated 47 strains from a range of herbaceous and woody plant species. Phylogenetic analysis based on 16S rDNA, B and B genes was used to compare our strains with type strains of . For most of our strains, sequence similarity of the 16S rDNA, B and B regions to type strains ranged from 98–100 %. Results of the concatenated gene sequence comparisons identified 18 strains of and three strains of . The remaining strains were unclassified, and may represent novel species of . Phylogenetic analysis based on B sequences provided a more precise classification of our strains to species level than 16S rDNA sequences, whereas analysis of B sequences was unable to identify strains with orange-coloured colonies to species level.

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2020-10-23
2024-04-18
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References

  1. Kuyukina MS, Ivshina IB. Application of Rhodococcus in bioremediation of contaminated environments. In Alvarez H. editor Biology of Rhodococcus 2010; Microbiology Monographs 16 Berlin, Heidelberg: Springer; 2010
    [Google Scholar]
  2. Larkin M, Kulakov L, Allen C. Biodegradation by members of the genus Rhodococcus: Biochemistry, physiology, and genetic adaptation. Adv Appl Microbiol 2006; 59:1–29
    [Google Scholar]
  3. Larkin MJ, Kulakov LA, Allen CCR. Biodegradation and Rhodococcus-masters of catabolic versatility. Curr Opin Biotechnol 2005; 16:282–290 [View Article][PubMed]
    [Google Scholar]
  4. Mara DD, Oragui JI. Occurrence of Rhodococcus coprophilus and associated actinomycetes in feces, sewage, and freshwater. Appl Environ Microbiol 1981; 42:1037–1042 [View Article]
    [Google Scholar]
  5. Ivshina IB, Oborin AA, Nesterenko OA, Kasumova SA. Bacteria of the Rhodococcus genus from the ground water of oil-bearing deposits in the Perm region near the Urals. Mikrobiolgiya 1981; 50:709–717
    [Google Scholar]
  6. Valo R, Haggblom M, SalkinojaSalonen M. Bioremediation of chlorophenol containing simulated ground water by immobilized bacteria. Water Res 1990; 24:253–258 [View Article]
    [Google Scholar]
  7. Miteva VI, Sheridan PP, Brenchley JE. Phylogenetic and physiological diversity of microorganisms isolated from a deep Greenland glacier ice core. Appl Environ Microbiol 2004; 70:202–213 [View Article]
    [Google Scholar]
  8. Goodfellow M, Minnikin DE. The genera Nocardia and Rhodococcus . In Starr MP, Stolp H, Trüper HG, Balows A, Schlegel HGpp. (editors) The Prokaryotes 2, 2nd ed. Berlin: Springer-Verlag; 1981 pp 2016–2026
    [Google Scholar]
  9. Ko KS, Kim Y, Seong CN, Lee SD. Rhodococcus antrifimi sp. nov., isolated from dried bat dung of a cave. Int J Syst Evol Microbiol 2015; 65:4043–4048 [View Article][PubMed]
    [Google Scholar]
  10. Ben-Yakir D. Growth retardation of Rhodnius prolixus symbionts by immunizing host against Nocardia (Rhodococcus) rhodnii . J Insect Physiol 1987; 33:379–383 [View Article]
    [Google Scholar]
  11. Bell KS, Philp JC, Aw DW, Christofi N. The genus Rhodococcus . J Appl Microbiol 1998; 85:195–210 [View Article][PubMed]
    [Google Scholar]
  12. Francis IM, Vereecke D. Plant-associated Rhodococcus species, for better and for worse. In Alvarez HM. editor Biology of Rhodococcus, (Microbiology Monographs, 16), 2nd ed. Cham: Springer International Publishing; 2019 pp 359–377
    [Google Scholar]
  13. Sangal V, Goodfellow M, Jones AL, Seviour RJ, Sutcliffe IC. Refined systematics of the genus Rhodococcus based on whole genome analyses. In Alvarez HM. editor Biology of Rhodococcus, (Microbiology Monographs, 16), 2nd ed. Cham: Springer International Publishing; 2019 pp 1–21
    [Google Scholar]
  14. Dhaouadi S, A. H M, Rhouma A. The plant pathogen Rhodococcus fascians. History, disease symptomatology, host range, pathogenesis and plant–pathogen interaction. Ann Appl Biol 2020; 177:4–15 [View Article]
    [Google Scholar]
  15. Creason AL, Vandeputte OM, Savory EA, Davis EW, Putnam ML et al. Analysis of genome sequences from plant pathogenic Rhodococcus reveals genetic novelties in virulence Loci. PLoS One 2014; 9:e101996 [View Article]
    [Google Scholar]
  16. Kämpfer P, Wellner S, Lohse K, Lodders N, Martin K. Rhodococcus cerastii sp. nov. and Rhodococcus trifolii sp. nov., two novel species isolated from leaf surfaces. Int J Syst Evol Microbiol 2013; 63:1024–1029 [View Article]
    [Google Scholar]
  17. Li J, Zhao GZ, Chen HH, Qin S, Xu LH et al. Rhodococcus cercidiphylli sp. nov., a new endophytic actinobacterium isolated from a Cercidiphyllum japonicum leaf. Syst Appl Microbiol 2008; 31:108–113 [View Article][PubMed]
    [Google Scholar]
  18. Zhao GZ, Li J, Zhu WY, Tian SZ, Zhao LX et al. Rhodococcus artemisiae sp. nov., an endophytic actinobacterium isolated from the pharmaceutical plant Artemisia annua L. Int J Syst Evol Microbiol 2012; 62:900–905 [View Article]
    [Google Scholar]
  19. Ma J, Zhang L, Wang G, Zhang S, Zhang X et al. Rhodococcus gannanensis sp. nov., a novel endophytic actinobacterium isolated from root of sunflower (Helianthus annuus L.). Antonie van Leeuwenhoek 2017; 110:1113–1120 [View Article]
    [Google Scholar]
  20. Wang YX, Wang HB, Zhang YQ, Xu LH, Jiang CL et al. Rhodococcus kunmingensis sp. nov., an actinobacterium isolated from a rhizosphere soil. Int J Syst Evol Microbiol 2008; 58:1467–1471 [View Article]
    [Google Scholar]
  21. Silva LJ, Souza DT, Genuario DB, Hoyos HAV, Santos SN et al. Rhodococcus psychrotolerans sp. nov., isolated from rhizosphere of Deschampsia antarctica . Antonie van Leeuwenhoek 2018; 111:629–636 [View Article]
    [Google Scholar]
  22. Bafana A. Diversity and metabolic potential of culturable root-associated bacteria from Origanum vulgare in sub-Himalayan region. World J Microbiol Biotechnol 2013; 29:63–74 [View Article]
    [Google Scholar]
  23. 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]
    [Google Scholar]
  24. Ritpitakphong U, Falquet L, Vimoltust A, Berger A, Métraux JP et al. The microbiome of the leaf surface of Arabidopsis protects against a fungal pathogen. New Phytol 2016; 210:1033–1043 [View Article]
    [Google Scholar]
  25. Dhaouadi S, Mougou AH, Bahri BA, Rhouma A, Fichtner EJ. First report of Rhodococcus spp. isolates causing stunting and lateral stem proliferation of Iresine herbstii ‘Aureo-Reticulata’ in Tunisia. Phytopathologia Mediterranea 2019; 58:391–394
    [Google Scholar]
  26. Dhaouadi S, Mougou AH, Gleason ML, Rhouma A, Fichtner EJ. First report of bushy stunt of Japanese spindle caused by Rhodococcus spp. in Tunisia. Plant Dis 2020; 104:1250 [View Article]
    [Google Scholar]
  27. Dhaouadi S, Win J, Mougou AH, Harant A, Kamoun S et al. Genome Sequences of Plant-Associated Rhodococcus sp. Isolates from Tunisia. Microbiol Resour Announc 2020; 9:e00293–20 [View Article]
    [Google Scholar]
  28. Goodfellow M, Alderson G, Chun J. Rhodococcal systematics: problems and developments. Antonie van Leeuwenhoek 1998; 74:3–20 [View Article]
    [Google Scholar]
  29. Gürtler V, Mayall BC, Seviour R. Can whole genome analysis refine the taxonomy of the genus Rhodococcus ?. FEMS Microbiol Rev 2004; 28:377–403 [View Article]
    [Google Scholar]
  30. Jones AL, Goodfellow ML. Genus IV. Rhodococcus (Zopf 1891) emend Goodfellow, Alderson and Chun 1998a. In Goodfellow M, Kampfer P, Busee HJ, Trujillo ME, Suzuki K. (editors) Bergey’s Manual of Systematic Bacteriology. The Actinobacteria, Part A 5, 2nd ed. New York, NY: Springer; 2012 pp 437–477
    [Google Scholar]
  31. Gürtler V, Seviour R. Systematics of members of the genus Rhodococcus (Zopf 1891) emend Goodfellow, et al. 1998. The past, present and future. In Alvarez HM. editor Biology of Rhodococcus, Microbiology Monographs 16 Springer-Verlag Berlin Heidelber.; 2010
    [Google Scholar]
  32. Goodfellow M, Jones AL, Order V. Corynebacteriales ord. nov. In Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K-I et al. (editors) Bergey’s manual of systematic bacteriology New York: Springer; 2012
    [Google Scholar]
  33. Creason AL, Davis EW, Putnam ML, Vandeputte OM, Chang JH. Use of whole genome sequences to develop a molecular phylogenetic framework for Rhodococcus fascians and the Rhodococcus genus. Front Plant Sci 2014; 5:406 [View Article]
    [Google Scholar]
  34. Táncsics A, Benedek T, Szoboszlay S, Veres PG, Farkas M et al. The detection and phylogenetic analysis of the alkane 1-monooxygenase gene of members of the genus Rhodococcus . Syst Appl Microbiol 2015; 38:1–7 [View Article]
    [Google Scholar]
  35. Táncsics A, Máthé I, Benedek T, Tóth EM, Atasayar E et al. Rhodococcus sovatensis sp. nov., an actinomycete isolated from the hypersaline and heliothermal Lake Ursu. Int J Syst Evol Microbiol 2017; 67:190–196 [View Article][PubMed]
    [Google Scholar]
  36. Kasai H, Watanabe K, Gasteiger E, Bairoch A, Isono K et al. Construction of the gyrB Database for the identification and classification of bacteria. Genome Inform Ser Workshop Genome Inform 1998; 9:13–21
    [Google Scholar]
  37. Kasai H, Ezaki T, Harayama S. Differentiation of phylogenetically related slowly growing mycobacteria by their gyrB sequences. J Clin Microbiol 2000; 38:301–308
    [Google Scholar]
  38. Richert K, Brambilla E, Stackebrandt E. Development of PCR primers specific for the amplification and direct sequencing of gyrB genes from microbacteria, order Actinomycetales. J Microbiol Methods 2005; 60:115–123 [View Article]
    [Google Scholar]
  39. Kasai H, Tamura T, Harayama S. Intrageneric relationships among Micromonospora species deduced from gyrB-based phylogeny and DNA relatedness. Int J Syst Evol Microbiol 2000; 50:127–134 [View Article]
    [Google Scholar]
  40. Yamamoto S, Harayama S, Arnold DL, Jackson RW, Kasai H et al. Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 2000; 146:2385–2394
    [Google Scholar]
  41. Coenye T, LiPuma JJ. Use of the gyrB gene for the identification of Pandoraea species. FEMS Microbiol Lett 2002; 208:15–19 [View Article]
    [Google Scholar]
  42. Táncsics A, Benedek T, Farkas M, Máthé I, Márialigeti K et al. Sequence analysis of 16S rRNA, gyrB and catA genes and DNA–DNA hybridization reveal that Rhodococcus jialingiae is a later synonym of Rhodococcus qingshengii . Int J Syst Evol Microbiol 2014; 64:298–301 [View Article]
    [Google Scholar]
  43. Kado CI, Heskett MG. Selective media for isolation of Agrobacterium, Corynebacterium, Erwinia, Pseudomonas, and Xanthomonas . Phytopathology 1970; 60:969–976 [View Article]
    [Google Scholar]
  44. Pei Z, Bini EJ, Yang L, Zhou M, Francois F et al. Bacterial biota in the human distal esophagus. Proc Natl Acad Sci U S A 2004; 101:4250–4255 [View Article]
    [Google Scholar]
  45. Shen FT, Lu HL, Lin JL, Huang WS, Arun AB et al. Phylogenetic analysis of members of the metabolically diverse genus Gordonia based on proteins encoding the gyrB gene. Res Microbiol 2006; 157:367–375 [View Article]
    [Google Scholar]
  46. 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]
    [Google Scholar]
  47. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688–2690 [View Article]
    [Google Scholar]
  48. Garrido-Sanz D, Redondo-Nieto M, Martín M, Rivilla R. Comparative genomics of the Rhodococcus genus shows wide distribution of biodegradation traits. Microorganisms 2020; 8:774 [View Article]
    [Google Scholar]
  49. Stamler RA, Kilcrease J, Kallsen C, Fichtner EJ, Cooke P et al. First report of Rhodococcus isolates causing pistachio bushy top syndrome on ‘UCB-1’ rootstock in California and Arizona. Plant Disease 2015; 99:1468–1476 [View Article]
    [Google Scholar]
  50. Vereecke D, Zhang Y, Francis IM, Lambert PQ, Venneman J et al. Functional genomics insights into the pathogenicity, habitat fitness, and mechanisms modifying plant development of Rhodococcus sp. PBTS1 and PBTS2. Front Microbiol 2020; 11:14 [View Article]
    [Google Scholar]
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