In situ microbial ecology for quantitative appraisal, monitoring, and risk assessment of pollution remediation in soils, the subsurface, the rhizosphere and in biofilms

Numerous studies have established a relationship between soil, sediment, surface biofilm and subsurface contaminant pollution and a marked impact on the in situ microbial community in both microcosms and in the field. The impact of pollution on the in situ microbial community can now be quantitatively measured by molecular `fingerprinting' using `signature' biomarkers. Such molecular fingerprinting methods can replace classical microbiological techniques that relied on isolation and subsequent growth of specific microbes from the in situ microbial community. Classical methods often revealed less than 1% of the extant microbial communities. Molecular fingerprinting provides a quantitative measure of the in situ viable microbial biomass, community composition, nutritional status, relative frequency of specific functional genes, nucleic acid polymers of specific microbes, and, in some cases, the community metabolic activity can be inferred. Current research is directed at establishing correlations between contaminant disappearance, diminution in toxicity, and the return of the viable biomass, community composition, nutritional status, gene patterns of the in situ microbial community towards that of the uncontaminated soil, sediment or subsurface material with the original uncontaminated microniche environments. Compared to the current reliance on disappearance of pollutants and associated potentially toxic products for detection of effective and quantitative bioremediation, assessment of the in situ microbial community will be an additional and possibly more convincing risk assessment tool. The living community tends to accumulate and replicate toxic insults through multiple interactions within the community, which may then effect viable biomass, community composition, nutritional status, community metabolic activities, and specific nucleic acid polymer patterns.