Superfund Research Program

The Use of Bacterial Diversity as a Biomarker for Ecological Health Assessment

Release Date: 03/05/2000

Many estuaries and coastal regions of the United States contain a legacy of contamination from past industrial, agricultural and other activities. Chemicals including metals, organic compounds, and pesticides were discharged into some waterways for decades, resulting in a buildup of contamination in the sediments of numerous harbors and bays lining the country's coast. The ecological effects of this contamination have been devastating in some cases, resulting in a loss of aquatic life and biodiversity in areas of high contamination. As efforts continue to clean up and restore these polluted aquatic ecosystems, there is a need for tools and methods to monitor their ecological health.

Among the most useful monitors of ecological health are the biological changes produced by environmental contaminants, whether these changes occur at a biochemical, cellular, community or population level. For example, some of the proteins and enzymes that are induced in organisms upon exposure to contaminants are sensitive indicators of chemical stress. Structural alterations in the DNA of organisms are serving as biomonitors for genotoxic contaminants. While these and many other approaches are in use for ecological health assessment, there is a continuing need for alternative approaches. Moreover, in assessing the effects of aquatic pollution at the ecosystem level, it is important to have a combination of biomarkers available.

Researchers at Harvard University are exploring the use of microbial diversity as a biomarker of ecological health. The biomarker method they are developing is based on characterizing the genetic diversity between microbial communities living in sediments with varying levels of pollution. This novel approach uses molecular techniques to evaluate the relation of groups of bacteria to each other and their environment.

Bacteria tend to live in complex communities, often consisting of many different species with an overall community structure suited to survival in the local environment. Part of what makes microbial communities promising as biomarkers is their rapid adaptation to environmental changes, including chemical stress. This adaptability results in selection of organisms capable of withstanding the pressures of the environment. Changes in microbial community structure can be monitored by looking at the genetic profile or diversity of the microbes in a particular environment.

The Harvard researchers recently used a molecular technique known as 16S rRNA restriction fragment length polymorphism analysis (RFLP) to measure the genetic diversity of microbial communities living in and around New Bedford Harbor, a highly contaminated coastal marine environment in southeastern Massachusetts. Designated a Superfund site in the 1980s, the New Bedford Harbor area offers a unique opportunity to study the changing structure of microbial communities in response to pollution. There are clear gradients of PCBs and metals in the sediments, from high concentrations in the Acushnet River Estuary that feeds into the harbor, to background levels in Buzzards Bay.

Part of the cell's protein making machinery, 16S rRNA is a molecule that allows for ready determination of the relatedness of microbes. In particular, rRNA genes are well suited for diagnostic purposes because they have conserved, variable, and highly variable regions that make identification of all members of a microbial community possible, including non-culturable organisms. The sequence and number of bases in the variable regions between conserved domains of rRNA genes result in different sized fragments during RFLP analysis that provide a picture of the genetic diversity in a microbial community.

The development of this biomarker method involved extracting DNA from sediment samples collected along the gradient of decreasing contamination in New Bedford Harbor. After purifying the microbial DNA, the 16S rRNA genes were amplified by a polymerase chain reaction (PCR) method and subsequently analyzed by a 16S rRNA RFLP technique. The data set generated from the RFLP analysis was fed into a computer program that determined the bacterial diversity of each site where sediment had been collected.

Results showed that bacterial genetic diversity was consistently greater in the highly contaminated New Bedford Harbor than in Buzzards Bay where contamination was only slightly above background levels. In addition, bacterial diversity was greater in the winter than in the summer in both the harbor and the bay.

The Harvard researchers are now beginning to examine microbial isolates from New Bedford Harbor for expression of genes responsible for resistance to specific contaminants.

Few studies have addressed the issue of changing patterns of microbial communities in polluted aquatic environments. This study showed that changes in specific contaminant concentrations were correlated with changes in bacterial diversity. In addition to providing a better understanding of microbial community responses to environmental stress, this research is significant for demonstrating the potential of using genetic markers in bacteria as a tool for monitoring the ecological health of polluted environments.

For More Information Contact:

Timothy Ford
Harvard School of Public Health
665 Huntington Avenue
Environmental Science and Engineering, Room 1-G17
Boston, Massachusetts 02115
Phone: 617-432-3434

To learn more about this research, please refer to the following sources:

  • Sorci J, Paulauskis JD, Ford T. 1999. 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. Mar Pollut Bull 38(8):663-675. doi:10.1016/S0025-326X(98)90199-0
  • Ford T, Sorci J, Ika R, Shine JP. 1998. Interactions between metals and microbial communities in New Bedford Harbor, Massachusetts. Environ Health Perspect 106:1033-1039. PMID:9703489

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