16S rRNA restriction fragment length polymorphism analysis of bacterial diversity as a biomarker of ecological health in polluted sediments from New Bedford Harbor, Massachusetts, USA

A polymerase chain reaction (PCR)-based method was developed to compare bac terial diversity among environmental sites with varying degrees of anthropo genic impact. New Bedford Harbor, MA, a US Environmental Protection Agency- designated Superfund hazardous waste site, was studied to assess changes in bacterial diversity resulting from long-term inputs of organic and inorgan ic pollutants. Total DNA was extracted from surficial sediments sampled fro m four sites along a transect of decreasing contamination (Upper and Lower Acushnet Estuary, New Bedford Harbor, and Buzzards Bay, respectively). Olig onnucleotide primers specific to conserved regions of the 16S rRNA gene wer e used to PCR-amplify sequences from DNA extracts. Restriction fragment len gth polymorphism (RFLP) analysis resulted in generation of a number of uniq ue operational taxonomic units (OTUs), Cluster analysis of fragment pattern data using the computer program RESTSITE allowed for bacterial diversity e stimations, which, in agreement with standard culture techniques, showed hi gher bacterial diversity in New Bedford Harbor sediments, relative to Buzza rds Bay. By employing bacterial diversity as a sensitive indicator of envir onmental stress, the method has wide applicability to many environments for the assessment of anthropogenic impact on aquatic ecosystems. (C) 1999 Pub lished by Elsevier Science Ltd. All rights reserved.