Composition of estuarine bacterial communities assessed by denaturing gradient gel electrophoresis and fluorescence in situ hybridization

We compared the results from two culture-independent techniques commonly used to investigate microbial community composition in aquatic ecosystems: fluorescence in situ hybridization ( FISH) with oligonucleotide probes and denaturing gradient gel electrophoresis (DGGE). These two techniques were used with samples from the Delaware Estuary and from experiments in the estuary and Chesapeake Bay. Most of the ribotypes identified by DGGE were members of the phylogenetic groups identified by FISH (alpha, beta, and gamma proteobacteria and the Cytophaga-like bacteria). DGGE and FISH usually (64% of all comparisons) identified the same phylogenetic group as being dominant, and both methods revealed systematic changes in bacterial community structure along the estuarine gradient. Cytophaga-like bacteria appeared to be sampled adequately by DGGE, even though bacteria from this cluster are often underrepresented in clone libraries of 16S rRNA genes. However, there were notable instances when DGGE and FISH failed to identify the same phylogenetic group as being most abundant. In several cases, the dominant group was beta-proteobacteria according to FISH but these bacteria were absent in DGGE gels.