**2. Genetic analysis of genes involved**

Examining the presence and expression of the key genes involved in bioremediation can yield more information on microbial processes than analysis of 16S rRNA sequences (Rogers and McClure. 2003). In general, there is a positive correlation between the relative abundance of the genes involved in bioremediation and the potential for contaminant degradation (Rogers and McClure. 2003., Schneegurt and Kulpa. 1998).

However, the genes for bioremediation can be present but not expressed. Therefore, there has been an increased emphasis on quantifying the levels of mRNA for key bioremediation genes. Often, increased mRNA concentrations can be, at least qualitatively, associated with higher rates of contaminant degradation (Schneegurt and Kulpa. 1998). For example, the concentra‐ tions of mRNA for *nahA* a gene involved in aerobic degradation of naphthalene were positively correlated with rates of naphthalene degradation in hydrocarbon-contaminated soil (Fleming et al. 1993).The reduction of soluble ionic mercury, Hg(II),to volatile Hg(0), is one mechanism for removing mercury from water; the concentration of mRNA for *merA* a gene involved in Hg(II) reduction was highest in mercury-contaminated waters with the highest rates of Hg (II) reduction (Nazaret et al. 1994). However, the concentration of *merA* was not always propor‐ tional to the rate of Hg (II) reduction (Nazaret et al. 1994., Jeffrey et al. 1996), illustrating that factors other than gene transcription can control the rates of bioremediation processes.

Highly sensitive methods that can detect mRNA for key bioremediation genes in single cells are now available (Bakermans and Madsen. 2002). This technique, coupled with 16S rRNA probing of the same environmental samples, could provide data on which phylogenetic groups of organisms are expressing the genes of interest. Analysis of the mRNA concentrations for genes other than those directly involved in bioremediation might yield additional insights into the factors that control the rate and extent of bioremediation. Sub-optimal nutrient levels, pH, salinity and other environmental factors can limit the growth and metabolism of organisms that are involved in bioremediation in contaminated environments. Ecological studies of phyto-plankton use molecular techniques to evaluate the stress response of photosynthetic microorganisms in the environment (Palenik and Wood. 1998). In a similar manner, evaluation of the metabolic state of bioremediating microorganisms through analysis of the mRNA concentrations for key genes that are involved in responding to stress could help to identify modifications to contaminated environments that might promote bioremediation.
