Molecular analysis of Mycobacterium community shifts in soil during the biodegradation of polycyclic aromatic hydrocarbons

Polycyclic aromatic hydrocarbons (PAHs) are organic compounds with two or more fused benzene rings. They are ubiquitous organic pollutants produced and released into the environment during fossil fuel combustion or as by-products of many industrial processes such as coal gasification, waste incineration, and manufacturing of petroleum-derived products. High-molecular-weight PAHs are recalcitrant and some of them are known carcinogens and/or mutagens. Several fast-growing species of Mycobacterium have the potential for PAH degradation. However, little is known about the ecology, diversity, and community structure of indigenous soil mycobacteria, either in PAH-contaminated or pristine soils. It is likely that many other Mycobacterium species, including as-yet-uncultured strains, also possess the ability to degrade the pollutants. In this study, total bacterial DNA was extracted from pristine and PAH-contaminated soils. Culture-independent molecular techniques including polymerase chain reaction (PCR), temperature gradient gel electrophoresis (TGGE), sequencing, and phylogenetic analysis of 16S rRNA genes were employed to determine the community composition of fast-growing mycobacteria in these soils. The effects of introducing exogenous PAH-degraders, nutrient- and surfactant-amendments, and acclimation of soil microorganisms to PAHs, on PAH mineralization patterns and the degradative potential of the community were measured and correlated with Mycobacterium population dynamics. Results indicated that inoculation of soil with exogenous PAH-degrader had both positive and negative effects on PAH degradation, probably due to competition with indigenous microorganisms. Both nutrients and surfactants enhanced the rate and level of PAH degradation in contaminated soils, but the soil that had the highest level of mineralization had the least changes in Mycobacterium community structure. Pre-exposure of soil microorganisms to a PAH decreased the acclimation period and increased the initial rates for subsequent degradation of the same or a different PAH, in some soils. Contamination of soil samples with PAHs all resulted in Mycobacterium community shifts, as revealed by PCR-TGGE. The results obtained provided insight into understanding the ecological limitations to effective bioremediation of contaminated environmental sites.