Comparative analysis of microbial communities during enrichment and isolation of DDT-degrading bacteria by culture-dependent and -independent methods.

Microcosms for enrichment of DDT degrading microorganisms were monitored using culture-dependent and -independent methods. Culture dependent methods isolated several strains with DDT degradation potential, Pseudomonas species being the most frequent. One isolate, Streptomyces sp. strain D3, had a degradation rate of 77% with 20mgL-1 of DDT after 7days incubation, D3 also had degradation rates of 75% and 30% for PCB77 (3,3',4,4'-tetrachloro biphenyl) and PCNB (pentachloronitrobenzene) respectively. Culture-independent high-throughput sequencing identified a different subset of the microbial community within the enrichment microcosms to the culture dependent method. Pseudomonas, the most frequently isolated strain, only represented the 12th most abundant operational taxonomic unit in the sequencing dataset (relative abundance 0.9%). The most frequently observed bacterial genus in the culture-independent analysis did not correspond with those recovered by culture-dependent methods. These results suggested that deep sequencing followed by a targeted isolation approach might provide an advantageous route to bioremediation studies.