The composition of microbial communities in polycyclic aromatic hydrocarbon contaminated bottom waters of the Delaware Estuary

Denaturing gradient gel electrophoresis (DGGE) and fluorescence in situ hybridization (FISH) with oligonucleotide probes were used to investigate the effects of polycyclic aromatic hydrocarbons (PAHs) on microbial community composition in estuarine waters. I systematically compared the results of these two independent methods to determine if they implied the same general picture of community composition. In most cases, the phylotypes represented in DGGE gels were members of the most dominant groups according to FISH. One notable exception were the β-proteobacteria, which were the dominant phylotype in several samples according to FISH, but were often absent in DGGE gels. Both of these methods were used to investigate the effects of naphthalene additions on microbial communities in enrichment experiments using estuarine bottom water. Enhanced naphthalene mineralization and bacterial production rates and changes in microbial community composition were observed within three days after adding naphthalene. FISH data revealed that naphthalene-amended treatments contained fewer of the phylogenetic groups investigated (α,β,γ-proteobacteria, Cytophaga-Flavobacteria cluster) than controls.{09}Sequence analysis of bands recovered from DGGE gels indicated that three bacteria similar to known hydrocarbon degraders had grown up only in naphthalene-amended treatments. Similarly, in a survey of the Delaware Estuary and its tributary, the Schuylkill River, I observed the presence of bacteria similar to known hydrocarbon degraders most often at stations with high PAH concentrations. Oligonucleotide probes designed from PCR-DGGE derived sequences confirmed the presence of bacteria similar to known hydrocarbon degraders at PAH-contaminated sites. The detection of these bacteria in DGGE and with specific oligonucleotide probes suggests they are abundant in the environment. I demonstrated that microbial community composition was affected by naphthalene in laboratory experiments and also found a unique microbial community in the Schuylkill River where PAH concentrations were highest. In both the experiments and the survey, I was able to recover sequences of bacteria similar to known hydrocarbon degraders, suggesting that PAH-degrading bacteria are abundant even when PAH concentrations are low relative to natural organic components.