Rhodococcus is a genus of aerobic, non-sporulating, non-motile gram-positive bacteria closely related to Mycobacteria and Corynebacteria . While a few species are pathogenic, most are benign and have been found to thrive in a broad range of environments, including soil, water, and eukaryotic cells. Fully sequenced in October 2006, the genome is know to be 9.7 megabasepairs long and 67% G/C .
Strains of Rhodococcus are applicably important due to their ability to catabolize a wide range of compounds and produce bioactive steroids, acrylamide and acrylic acid and their involvement in fossil fuel biodesulfurization . This genetic and catabolic diversity is not only due to the large bacterial chromosome, but the presence of three large linear plasmids. Rhodococcus is also an experimentally advantageous system due to a relatively fast growth rate and simple developmental cycle. However, as it stands now, Rhodococcus is not well characterized .
Another important application of Rhodococcus comes from bioconversion, utilizing biological systems to convert cheap starting material into more valuable compounds. This use of Rhodococcus is born out of its ability to metabolize harmful environmental pollutants such as toluene, naphthalene, herbicides, PCBs. Rhodococci typically metabolize aromatic substrates by first oxygenating the aromatic ring to form a diol (two alcohol groups). Then, the ring is cleaved with intra/extradiol mechanisms, opening the ring and exposing the substrate to further metabolism. Since the chemistry here is very stereospecific, the diols are created with predictable chirality. While controlling the chirality of chemical reaction presents a significant challenge for synthetic chemists, biological processes can be used instead to faithfully produce chiral molecules in cases where direct chemical synthesis is infeasible or inefficient. An example of this is the use of Rhodococcus to produce indene, a precursor to the AIDS drug Crixivan(TM), a protease inhibitor, and containing two of the five chiral centers needed in the complex .
Biodegradation of Organic Pollutants
The burgeoning amount of bacterial genomic data provides unparalleled opportunities for understanding the genetic and molecular bases of the microbial biodegradation of organic pollutants. Aromatic compounds are among the most recalcitrant of these pollutants and lessons can be learned from the recent genomic studies of Rhodococcus sp. strain RHA1, one of the largest bacterial genomes completely sequenced to date. These studies have helped expand our understanding of bacterial catabolism, non-catabolic physiological adaptation to organic compounds, and the evolution of large bacterial genomes. A large number of "peripheral aromatic" pathways funnel a range of natural and xenobiotic compounds into a restricted number of "central aromatic" pathways. Some pathways are more widespread than initially thought. The Box and Paa pathways illustrate the prevalence of non-oxygenolytic ring-cleavage strategies in aerobic aromatic degradation processes. Functional genomic studies have been useful in establishing that even organisms harboring high numbers of homologous enzymes apparently contain few examples of true redundancy. For example, the multiplicity of ring-cleaving dioxygenases in certain rhodococcal isolates may be attributed to the cryptic aromatic catabolism of different terpenoids and steroids. The large gene repertoires of pollutant degraders such as Rhodococcus RHA1 have evolved principally through more ancient processes. 
- Rhodococcus aurantiacus (ex Tsukamura & Mizuno 1971) Tsukamura & Yano 1985, nom. rev.
- Rhodococcus baikonurensis Li et al. 2004
- Rhodococcus boritolerans
- Rhodococcus equi (Magnusson 1923) Goodfellow & Alderson 1977; most important species for infections of animals (horse, goat) and immunsupprimised humans (AIDS-Infected)
- Rhodococcus coprophilus Rowbotham & Cross 1979
- Rhodococcus corynebacterioides (Serrano et al. 1972) Yassin & Schaal 2005 (synonym: Nocardia corynebacterioides Serrano et al. 1972)
- Rhodococcus erythropolis (Gray & Thornton 1928) Goodfellow & Alderson 1979
- Rhodococcus globerulus Goodfellow et al. 1985
- Rhodococcus gordoniae Jones et al. 2004
- Rhodococcus jostii Takeuchi et al. 2002
- Rhodococcus koreensis Yoon et al. 2000
- Rhodococcus kroppenstedtii Mayilraj et al. 2006
- Rhodococcus luteus (ex Söhngen 1913) Nesterenko et al. 1982, nom. rev. (Synonym: R. fascians (Tilford 1936) Goodfellow 1984)
- Rhodococcus maanshanensis Zhang et al. 2002
- Rhodococcus marinonascens Helmke & Weyland 1984
- Rhodococcus opacus Klatte et al. 1995
- Rhodococcus percolatus Briglia et al. 1996
- Rhodococcus phenolicus Rehfuss & Urban 2006
- Rhodococcus polyvorum
- Rhodococcus pyridinivorans Yoon et al. 2000
- Rhodococcus rhodochrous (Zopf 1891) Tsukamura 1974
- Rhodococcus rhodnii Goodfellow & Alderson 1979 (synonym: Nocardia rhodnii)
- Rhodococcus ruber (Kruse 1896) Goodfellow & Alderson 1977 (synonym: Streptothrix rubra Kruse 1896)
- Rhodococcus triatomae Yassin 2005
- Rhodococcus tukisamuensis Matsuyama et al. 2003
- Rhodococcus wratislaviensis (Goodfellow et al. 1995) Goodfellow et al. 2002 (synonym: Tsukamurella wratislaviensis Goodfellow et al. 1995)
- Rhodococcus yunnanensis Zhang et al. 2005
- Rhodococcus zopfii Stoecker et al. 1994
- For Species and synonyms see here: National Center for Biotechnology Information (NCBI)
- van der Geize R., and L. Dijkhuizen (2004). "Harnessing the catabolic diversity of rhodococci for environmental and biotechnological applications". Microbiology. 7: 255–261.
- McLeod MP, Warren RL, Hsiao WW, Araki N, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh M, Hara H, Petrescu A, Morin RD, Yang G, Stott JM, Schein JE, Shin H, Smailus D, Siddiqui AS, Marra MA, Jones SJ, Holt R, Brinkman FS, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis LD (October 17, 2006). "The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse". PNAS. 103(42): 15582–15587.
- Treadway, S.L., K.S. Yanagimachi, E. Lankenau, P.A. Lessard, G. Stephanopoulos and A.J. Sinskey (1999). "Isolation and characterization of indene bioconversion genes from Rhodococcus strain I24". Appl. Microbiol. Biotechnol. 51(6): 786–793.
- McLeod MP and Eltis LD (2008). "Genomic Insights Into the Aerobic Pathways for Degradation of Organic Pollutants". Microbial Biodegradation: Genomics and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-17-2.