Genetic diversity among members of the genus Rhodococcus

Advances in technology have provided an opportunity for microbiologists to investigate microbial evolution and species diversity at a level of detail that had been unapproachable previously. Conventional methodologies analyzed metabolic and morphological characters eschewing then undeveloped genetic techniques. Analysis of a collection comprising strains classified as the genus Rhodococcus, isolated from widely distributed locales, displaying metabolic and morphological diversity presents an opportunity to investigate microbial diversity in an informative way. In this work, the global genomic organization of R. erythropolis strain D-1 is described. The size of the D-1 genome, 5.1 Mb, agrees with measurements of other R. erythropolis strains. Also, analysis of sequence diversity among an operon that encodes a rare catabolic phenotype demonstrates sequence conservation of the operon shared by six R. erythropolis strains. Restriction Fragment Length Polymorphism analysis of a 9.6 Kb amplicon equivalent to the operon demonstrates that the sequence is monomorphic. Sequence simlarities relationships among fourteen Rhodococcus strains are demonstrated through ClustaIX alignment of 16S rDNA sequences. A 1.3 Kb region of the 16S rRNA genes was amplified by PCR. Construction of composite 16S sequences was possible by sequencing both DNA strands. Neighbor-Joining analysis of the 16S rDNA sequences was used to produce dendograms that illustrate relationships among strains. Sequence analysis of 16S rDNA typically assumes that, in strains possessing multiple rDNA operons, all 16S sequences are identical. To test this assumption, a 849 by region within the 16S rDNA of each of the five rrn of R. erythropolis was amplified by PCR and sequenced. 53968 16S rDNA sequence comparisons reveal that the genes are effectively identical. Sequence conservation among 16S rDNA sequences may render them ineffectual for inferring relationships among closely related strains. Therefore, the more variable 16S--23S Internal Transcribed Spacer (ITS) region has been used to infer relationships. Individual ITS regions were amplified by PCR and sequenced. ClustaIX sequence alignments exhibited the sequence diversity among the five rrn operons of a given strain as well as among the operons of four closely related strains. All told, Rhodococcus display simultaneously conservation of genome size and GC skew concurrent with sequence diversity.