Microbial Ecology Of Aromatic Compound Degradation In A Coal Tar Waste Contaminated Aquifer
Microbial ecology links community structure, phenotypic potential, community function and interactions of microorganisms within communities and with their environments. Native microbial populations are responsible for biodegradation of naphthalene and other organic pollutants in a shallow coal tar waste-contaminated aquifer in South Glens Falls, NY. Though many details of the biochemistry and genetics of bacterial naphthalene degradation are known from studies in pure culture, molecular methods of analysis applied in situ can signi?cantly advance understanding of microbial degradation processes in an ecological context. PCR-based molecular characterization of 16S and 18S rRNA genes was used to signi?cantly extend previous work characterizing the microbial communities in site groundwater, and to establish the temporally dynamic nature of native microbial communities. Long term natural attenuation of pollutants was documented, and the presence of members of a potentially intricate microbial food web was linked to organic contamination in the subsurface waters. A broadrange PCR assay was used to uncover a diverse suite of Rieske dioxygenase genes, including 32 previously uncharacterized clone groups, in 2 contaminated wells within the aquifer. A quantitative competitive PCR assay detecting nah and nag genes, encoding naphthalene dioxygenase, showed that these biochemically divergent pathways (associated with aerobic naphthalene con- version to either catechol or gentisate, via salicylate) were prevalent at the site. RT-PCR results showed that both genes were transcribed in situ, at micromolar concentrations of ambient naphthalene, in proportions corresponding with structural gene abundance. Aerobic but not anaerobic naphthalene metabolism was observed in site water incubation experiments. However, metabolites of anaerobic naphthalene metabolism and expressed anaerobic degradation pathway mRNA transcripts (bssA) were detected in situ showing that anerobic metabolism of contaminants occurred on site. Cytochrome c nitrite reductase and ammonia monooxygenase gene expression in situ provided evidence of a complete nitrogen cycle via dissimilatory nitrate reduction to ammonia (DNRA) and nitri?cation carried out by native microbial communities. These data suggest that conditions in the contaminated aquifer had progressed from heterotrophic (carbon-oxidizing) to accumulation of reduced metabolic end products (ammonia, sul?de, methane) supporting lithotrophic and otherwise absent microbial populations. Genome analysis of the aromatic hydrocarbon-degrading, facultatively chemolithotrophic, contaminated sediment-dwelling ?-proteobacterium, Polaromonas naphthalenivorans strain CJ2, revealed a mosaic chromosome and 8 extrachromosomal elements. Comparisons with the closest sequenced relative, Polaromonas JS666, and related ?-proteobacteria revealed both substantial homology and ?uidity of genetic content. The genomic context and lateral transfer origins of the chromosomally encoded nag-like naphthalene catabolic operon were analyzed. Mobile genetic elements, signal transduction pathways, central and peripheral metabolic pathways, energy metabolism, transport systems, inorganic nutrient scavenging mechanisms, carbon and energy storage functions, and oxidative stress tolerance mechanisms were investigated in detail.
dissertation or thesis