Abstract
The taxonomic position of Rhodococcus strain RHA1, an effective degrader of polychlorinated biphenyls with a large linear chromosome, was established using a polyphasic approach. The morphological and chemotaxonomic properties of the strain were typical of members of the genus Rhodococcus. The strain shared a high level of 16S rRNA sequence similarity (99.9 %) with the type strain of Rhodococcus jostii, a member of the Rhodococcus erythropolis subclade. The two strains shared a DNA:DNA relatedness value well above the cut-off point recommended for the circumscription of genomic species and had a broad range of phenotypic properties in common. The combination of genomic and phenotypic data show strain RHA1 to be a bona fide member of the species Rhodococcus jostii.
References
Collins MD (1994) Isoprenoid quinones. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 265–309
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376
Felsenstein J (1985) Confidence limits on phylogenics: an approach using the bootstrap. Evolution 39:783–791
Gonzalez JM, Saiz-Jimenez C (2005) A simple fluorimetric method for the estimation of DNA–DNA relatedness between closely related microorganisms by thermal denaturation temperatures. Extremophiles 9:75–79
Goodfellow M, Jones AL (2012) Order V. Corynebacteriales ord. nov. In: Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K-I, Ludwig W, Whitman WB (eds) Bergey’s manual of systematic bacteriology, vol 5, 2nd edn. The Actinobacteria part A, New York, pp 235–243
Goodfellow M, Thomas EG, Ward AC, Jones AL (1990) Classification and identification of rhodococci. Zentralbl Bakteriol 274:299–315
Gordon RE, Mihm JM (1962) Identification of Nocardia caviae (Erikson) comb. nov. Ann NY Acad Sci 98:628–636
Jones AL, Goodfellow M (2012) Genus Rhodococcus (Zopf 1891) emend Goodfellow, Alderson and Chun. In: Goodfellow M, Kämpfer P, Busse H-J, Trujillo ME, Suzuki K-I, Ludwig W, Whitman WB (eds) Bergey’s manual of systematic bacteriology, vol 5, 2nd edn., The Actinobacteria part ASpringer, New York, pp 437–464
Jones AL, Brown JM, Mishra V, Perry JD, Steigerwalt A, Goodfellow M (2004) Rhodococcus gordoniae sp. nov., an actinomycete isolated from clinical material and phenol contaminated soil. Int J Syst Evol Microbiol 54:407–411
Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism, vol 3. Academic Press, New York, pp 21–132
Kim D, Chun J, Sahin N, Hah YC, Goodfellow M (1996) Analysis of thermophilic clades within the genus Streptomyces in 16S rRNA ribosomal DNA sequence comparisons. Int J Syst Evol Bacteriol 46:581–587
Kimbara K, Hashimoto T, Fukuda M, Koana T, Takagi M, Oshi M, Yano K (1989) Cloning and sequencing of two tandem genes involved in degradation of 2.3 dihydroxybiphenyl to benzoic acid in the polychlorinated biphenyl-degrading soil bacterium Pseudomonas sp. strain KKS 102. J Bacteriol 171:2740–2747
Kluge AG, Farris FS (1969) Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32
Kroppenstedt RM (1985) Fatty acid and menaquinone analysis of actinomycetes and related organisms. In: Goodfellow M, Minnikin DE (eds) Chemical methods in bacterial systematics. Academic Press, London pp, pp 173–199
Lechevalier MP, Lechevalier H (1970) Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 20:435–443
Lechevalier MP, De Biévre C, Lechevalier HA (1977) Chemotaxonomy of aerobic actinomycetes: phospholipid composition. Biochem Syst Ecol 5:249–260
Masai E, Yamada A, Healy JM, Hatta T, Kimbara K, Fukuda M, Yano K (1995) Characterization of biphenyl catabolic genes of Gram-positive polychlorinated biphenyl degrader Rhodococcus sp. strain RHA1. Appl Environ Microbiol 61:2079–2085
McFarland J (1907) The nephelometer: an instrument for estimating the number of bacteria in suspensions used for calculating the opsonic index and for vaccines. J Am Med Assoc 14:1176–1178
McLeod MP, Warren RL, Hsiao WW, Araki N, Myhre M et al (2006) The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci USA 103:15582–15587
Minnikin DE, Hutchinson JG, Caldicott AB, Goodfellow M (1980) Thin-layer chromatography of methanolysates of mycolic-acid containing bacteria. J Chromatogr A188:221–233
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241
Saitou N, Nei M (1987) The Neighbour-joining method: a new method for constructing phylogenetic trees. Mol Biol Evol 4:406–425
Schaal KP (1985) Identification of clinically significant actinomycetes and related bacteria using chemical techniques. In: Goodfellow M, Minnikin DE (eds) Chemical methods in bacterial systematics. Wiley, Chichester, pp 359–381
Seto M, Kimbara K, Shimura M, Hatta T, Tukuda M, Yano K (1995) A novel transformation of polychlorinated biphenyls by Rhodococcus sp. strain RHA1. Appl Environ Microbiol 61:3353–3358
Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231
Sutcliffe IC (2000) Characterisation of a lipomannan lipoglycan from the mycolic acid containing actinomycete Dietzia maris. Antonie Van Leeuwenhoek 78:195–201
Takeuchi M, Hatano K, Sedlácek I, Pácová Z (2002) Rhodococcus jostii sp. nov., isolated from a medieval grave. Int J Syst Evol Microbiol 52:409–413
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA 5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum-parsimony methods. Mol Biol Ecol 28:2731–2739
Uchida K, Kudo T, Suzuki KI, Nakase T (1999) A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram. J Gen Appl Microbiol 45:49–56
Wayne LG, Brenner DJ, Colwell RR et al (1987) International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464
Whitman WB (2011) Intent of the nomenclatural code and recommendations about naming new species based on genomic sequences. The Bulletin of BISMiS 2:135–139
Yam KC, Okamoto S, Roberts JN, Ellis LD (2011) Adventures in Rhodococcus: from steroids to explosives. Can J Microbiol 57:155–168
Acknowledgments
The authors are indebted to Lindsay Eltis and Bill Mohn of the University of British Columbia; Vancouver, for their helpful input into this study.
Author information
Authors and Affiliations
Corresponding author
Additional information
The GenBank accession number for the 16S rRNA gene sequence of Rhodococcus jostii RHA1 is CP 000431.
Rights and permissions
About this article
Cite this article
Jones, A.L., Davies, J., Fukuda, M. et al. Rhodococcus jostii: a home for Rhodococcus strain RHA1. Antonie van Leeuwenhoek 104, 435–440 (2013). https://doi.org/10.1007/s10482-013-9958-5
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10482-013-9958-5