Skip to main content
SpringerLink
Log in

Rhodococcus soli sp. nov., an actinobacterium isolated from soil using a resuscitative technique

  • Original Paper
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

A Gram-positive, aerobic, non-motile, non-spore forming strain, designated DSD51WT, was isolated using a resuscitative technique from a soil sample collected from Kyoto park, Japan, and characterized by using a polyphasic approach. The morphological and chemotaxonomic properties of the isolate were typical of those of members of the genus Rhodococcus. Strain DSD51WT was found to form a coherent cluster with Rhodococcus hoagii ATCC 7005T, Rhodococcus equi NBRC 101255T, Rhodococcus defluvii CallT and Rhodococcus kunmingensis YIM 45607T as its closest phylogenetic neighbours in 16S rRNA gene sequence analysis. However, the DNA–DNA hybridization values with the above strains were 58.2 ± 2.2, 58.4 ± 1.9, 45.1 ± 1.4 and 40.3 ± 4.7 %, respectively. In combination with differences in physiological and biochemical properties, strain DSD51WT can be concluded to represent a novel species of the genus Rhodococcus, for which the name Rhodococcus soli sp. nov. is proposed, with the type strain DSD51WT (=KCTC 29259T = JCM 19627T = DSM 46662T = KACC 17838T).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Bell KS, Philp JC, Aw DW, Christofi N (1998) The genus Rhodococcus. J Appl Microbiol 85:195–210

    Article  CAS  PubMed  Google Scholar 

  • Cerny G (1978) Studies on aminopeptidase for the distinction of Gram-negative from Gram-positive bacteria. Appl Microbiol Biotechnol 5:113–122

    Article  CAS  Google Scholar 

  • Christensen H, Angen Ø, Mutters R, Olsen JE, Bisgaard M (2000) DNA–DNA hybridization determined in micro-wells using covalent attachment of DNA. Int J Syst Evol Microbiol 50:1095–1102

    Article  CAS  PubMed  Google Scholar 

  • Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2,4-diaminobutyric acid. J Appl Bacteriol 48:459–470

  • Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in Actinomycetes and Corynebacteria. J Gen Microbiol 100:221–230

    Article  CAS  PubMed  Google Scholar 

  • Dastager SG, Mawlankar R, Tang SK, Krishnamurthi S, Ramana VV, Joseph N, Shouche YS (2014) Rhodococcus enclensis sp. nov., a novel member of the genus Rhodococcus. Int J Syst Evol Microbiol 64:2693–2699

    Article  CAS  PubMed  Google Scholar 

  • Ding LX (2004) Studies on the isolation of viable but non-culturable bacteria and the phylogenetic analysis of the genus Aquaspirillum. PhD Thesis, The University of Tokyo, Bunkyō

  • Ding LX, Su XM, Yokotal A (2011) Research progress of VBNC bacteria—a review. Acta Microbiol Sin 51:858–862

    CAS  Google Scholar 

  • Ding LX, Zhang PH, Hong HC, Lin HJ, Yokota A (2012) Cloning and expression of Micrococcus luteus IAM 14879 Rpf and its role in the recovery of the VBNC state in Rhodococcus sp. DS471. Acta Microbiol Sin 52:77–89

    CAS  Google Scholar 

  • Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229

    Article  Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  PubMed  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  • Finnerty WR (1992) The biology and genetics of the genus Rhodococcus. Annu Rev Microbiol 46:193–218

    Article  CAS  PubMed  Google Scholar 

  • Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  • Fuhrmann C, Soedarmanto I, Lämmler C (1997) Studies on the rod-coccus life cycle of Rhodococcus equi. Zentralbl Veterinarmed B 44:287–294

    CAS  PubMed  Google Scholar 

  • Garrity GM (2014) Conservation of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 and rejection of Corynebacterium hoagii (Morse 1912) Eberson 1918. Int J Syst Evol Microbiol 64:311–312

    Article  PubMed  Google Scholar 

  • Ghosh A, Paul D, Prakash D, Mayilraj S, Jain RK (2006) Rhodococcus imtechensis sp. nov., a nitrophenol-degrading actinomycete. Int J Syst Evol Microbiol 56:1965–1969

    Article  CAS  PubMed  Google Scholar 

  • Goodfellow M, Alderson G, Chun J (1998) Rhodococcal systematics: problems and developments. Antonie Van Leeuwenhoek 74:3–20

    Article  CAS  PubMed  Google Scholar 

  • Gordon RE, Barnett DA, Handerhan JE, Pang CH-N (1974) Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24:54–63

    Article  Google Scholar 

  • Groth I, Rodríguez C, Schütze B, Schmitz P, Leistner E, Goodfellow M (2004) Five novel Kitasatospora species from soil: Kitasatospora arboriphila sp. nov., K. gansuensis sp. nov., K. nipponensis sp. nov., K. paranensis sp. nov. and K. terrestris sp. nov. Int J Syst Evol Microbiol 54:2121–2129

    Article  CAS  PubMed  Google Scholar 

  • Hasegawa T, Takizawa M, Tanida S (1983) A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Microbiol 29:319–322

    Article  CAS  Google Scholar 

  • Hwang CY, Lee I, Cho Y, Lee YM, Baek K, Jung YJ, Yang YY, Lee T, Rhee TS, Lee HK (2014) Rhodococcus aerolatus sp. nov., isolated from rainwater on the subarctic Bering Sea. Int J Syst Evol Microbiol. doi:10.1099/ijs.0.070086-0

    Google Scholar 

  • Jones AL, Sutcliffe IC, Goodfellow M (2013a) Prescottia equi gen. nov., comb. nov.: a new home for an old pathogen. Antonie Van Leeuwenhoek 103:655–671

    Article  PubMed  Google Scholar 

  • Jones AL, Sutcliffe IC, Goodfellow M (2013b) Proposal to replace the illegitimate genus name Prescottia Jones et al. 2013 with the genus name Prescottella gen. nov. and to replace the illegitimate combination Prescottia equi Jones et al. 2013 with Prescottella equi comb. nov. Antonie van Leeuwenhoek 103:1405–1407

  • Kämpfer P, Dott W, Martin K, Glaeser SP (2014) Rhodococcus defluvii sp. nov., isolated from wastewater of a bioreactor and formal proposal to reclassify [Corynebacterium hoagii] and Rhodococcus equi as Rhodococcus hoagii comb. nov. Int J Syst Evol Microbiol 64:755–761

    Article  PubMed  Google Scholar 

  • Kelly KL (1964) Inter-society color council-National Bureau of Standards Color-name charts illustrated with centroid colors. US Government Printing Office, Washington

    Google Scholar 

  • Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon Y, Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    Article  CAS  PubMed  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  PubMed  Google Scholar 

  • Kovacs N (1956) Identification of Pseudomonas pyocyanea by oxidase reaction. Nature 178:703–704

    Article  CAS  PubMed  Google Scholar 

  • Larkin MJ, Kulakov LA, Allen CCR (2005) Biodegradation and Rhodococcus-masters of catabolic versatility. Curr Opin Biotechnol 16:282–290

    Article  CAS  PubMed  Google Scholar 

  • Lechevalier MP, Lechevalier HA (1970) Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20:435–443

    Article  CAS  Google Scholar 

  • Leifson E (1960) Atlas of bacterial flagellation. Atlas of bacterial flagellation

  • Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R, Xu LH, Stackebrandt E, Jiang CL (2007) Georgenia ruanii sp.nov., a novel actinobacterium isolated from forest soil in Yunnan (China) and emended description of the genus Georgenia. Int J Syst Evol Microbiol 57:1424–1428

    Article  PubMed  Google Scholar 

  • Li SH, Jin Y, Cheng J, Park DJ, Kim CJ, Hozzein WN, Wadaan MAM, Shu WS, Ding LX, Li WJ (2014) Gordonia jinhuaensis sp. nov., a novel actinobacterium, isolated from a VBNC (viable but non-culturable) state in pharmaceutical wastewater. Antonie Van Leeuwenhoek 106:347–356

    Article  CAS  PubMed  Google Scholar 

  • Liu H, Zhang YJ, Liu CX, Fang BZ, Li C, Guan XJ, Li LJ, Wang XJ, Xiang WS (2014) Rhodococcus kronopolitis sp. nov., a novel actinobacterium isolated from a millipede (Kronopolites svenhedind Verhoeff). Antonie van Leeuwenhoek (in press, doi:10.1007/s10482-014-0290-5)

  • Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    Article  CAS  Google Scholar 

  • Ming H, Nie GX, Jiang HC, Yu TT, Zhou EM, Feng HG, Tang SK, Li WJ (2012) Paenibacillus frigoriresistens sp. nov., a novel psychrotroph isolated from a peat bog in Heilongjiang, Northern China. Antonie van Leeuwenhoek 102:297–305

    Article  CAS  PubMed  Google Scholar 

  • Minnikin DE, Collins MD, Goodfellow M (1979) Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 47:87–95

    Article  CAS  Google Scholar 

  • Minnikin DE, Hutchinson IG, Caldicott AB, Goodfellow M (1980) Thin layer chromatography of methanolysates of mycolic acid-containing bacteria. J Chromatogr A 188:221–233

    Article  CAS  Google Scholar 

  • Mukamolova GV, Kaprelyants AS, Young DI, Young M, Kell DB (1998) A bacterial cytokine. Proc Natl Acad Sci USA 95:8916–8921

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 20:16

    Google Scholar 

  • Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340

    Article  Google Scholar 

  • Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849

    Article  CAS  Google Scholar 

  • Stackebrandt E, Rainey FA, Ward-Rainey NL (1997) Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47:479–491

    Article  Google Scholar 

  • Su XM, Liu YD, Hashmi MZ, Hu JX, Ding LX, Wu M, Shen CF (2014) Rhodococcus biphenylivorans sp. nov., a polychlorinated biphenyl-degrading bacterium. Antonie van Leeuwenhoek (in press, doi:10.1007/s10482-014-0303-4)

  • Tamaoka J, Katayama-Fujimura Y, Kuraishi H (1983) Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54:31–36

    Article  CAS  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Táncsics A, Benedek T, Farkas M, Máthe I, Márialigeti K, Szoboszlay S, Kukolya J, Kriszt B (2014) 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 64:298–301

    Article  PubMed  Google Scholar 

  • Tang SK, Wang Y, Chen Y, Lou K, Cao LL, Xu LH, Li WJ (2009) Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella. Int J Syst Evol Microbiol 59:2025–2032

    Article  CAS  PubMed  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Tindall BJ (2014a) The correct name of the taxon that contains the type strain of Rhodococcus equi. Int J Syst Evol Microbiol 64:302–308

    Article  CAS  PubMed  Google Scholar 

  • Tindall BJ (2014b) A note on the genus name Rhodococcus Zopf 1891 and its homonyms. Int J Syst Evol Microbiol 64:1062–1064

    Article  CAS  PubMed  Google Scholar 

  • Wang YX, Wang HB, Zhang YQ, Xu LH, Jiang CL, Li WJ (2008) Rhodococcus kunmingensis sp. nov., an actinobacterium isolated from a rhizosphere soil. Int J Syst Evol Microbiol 58:1467–1471

    Article  CAS  PubMed  Google Scholar 

  • Warhurst AM, Fewson CA (1994) Biotransformations catalyzed by the genus Rhodococcus. Crit Rev Biotechnol 14:29–73

    Article  CAS  PubMed  Google Scholar 

  • Williams S (1989) Genus Streptomyces Waksman and Henrici 1943. Bergey’s Man Syst Bacteriol 4:2452–2492

    Google Scholar 

  • Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ, Chen HH, Xu LH, Jiang CL (2005) Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evol Microbiol 55:1149–1153

    Article  CAS  PubMed  Google Scholar 

  • Yassin AF (2005) Rhodococcus triatomae sp. nov., isolated from a blood-sucking bug. Int J Syst Evol Microbiol 55:1575–1579

    Article  CAS  PubMed  Google Scholar 

  • Zopf W (1891) Über Ausscheidung von Fettfarbstoffen (Lipochromen) seitens gewisser Spaltpilze. Ber Dtsch Bot Ges 9:22–28

    Google Scholar 

Download references

Acknowledgments

The authors are grateful to Prof. Hans-Peter Klenk (DSMZ, Germany) and Dr. Tomohiko Tamura (NBRC, Japan) for their kind providing the reference type strains, and Prof. Peter Kämpfer (Justus-Liebig-Universität, Germany) for his kind providing the genomic DNA of strain Rhodococcus defluvii CallT. This research was supported by the Deanship of Scientific Research, College of Sciences Research Center, King Saud University, the National Natural Science Foundation of China (31340071) and a grant NRF-2006-08790 funded by Ministry of Science, ICT and Future Planning of Korean government. W-J Li was also supported by Guangdong Province Higher Vocational Colleges & Schools Pearl River Scholar Funded Scheme (2014).

Author information

Authors and Affiliations

  1. Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, People’s Republic of China

    Shan-Hui Li & Wen-Jun Li

  2. College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, 321004, People’s Republic of China

    Xiao-Yun Yu & Lin-Xian Ding

  3. College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, People’s Republic of China

    Xiao-Yun Yu & Lin-Xian Ding

  4. Microbial Resource Center, KRIBB, Daejeon, 305-806, Republic of Korea

    Dong-Jin Park & Chang-Jin Kim

  5. Bioproducts Research Chair (BRC), College of Science, King Saud University, Riyadh, 11451, Kingdom of Saudi Arabia

    Wael N. Hozzein & Mohammed A. M. Wadaan

  6. State Key Laboratory of Biocontrol, Key Laboratory of Biodiversity Dynamics and Conservation of Guangdong Higher Education Institutes, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, 510275, People’s Republic of China

    Wen-Sheng Shu & Wen-Jun Li

Authors
  1. Shan-Hui Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xiao-Yun Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Dong-Jin Park
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Wael N. Hozzein
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Chang-Jin Kim
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Wen-Sheng Shu
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Mohammed A. M. Wadaan
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Lin-Xian Ding
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Wen-Jun Li
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Lin-Xian Ding or Wen-Jun Li.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 932 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Li, SH., Yu, XY., Park, DJ. et al. Rhodococcus soli sp. nov., an actinobacterium isolated from soil using a resuscitative technique. Antonie van Leeuwenhoek 107, 357–366 (2015). https://doi.org/10.1007/s10482-014-0334-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10482-014-0334-x

Keywords

Search

Navigation