Superfund Research Program

Assessment of Biological Responses to Organic and Metal Contaminants in New Bedford: Methods for Monitoring

Project Leader: Timothy Ford
Grant Number: P42ES005947
Funding Period: 2000 - 2006

Project-Specific Links

Final Progress Reports

Year:   2005 

While genes involved in anaerobic degradation of PCBs from New Bedford harbor sediments remain elusive, Dr. Tim Ford leads a research project that has lead to considerable advances examining genes involved in degradation of metal-contaminated sediments from the Clark Fork River, Montana.  The researchers are examining microbial diversity, stress gene prevalence/ expression and geochemical parameters in order to develop microbial ecotoxicological biomarkers.  These biomarkers can then be used to determine anthropogenic impacts on agriculturally, commercially and recreationally important waterways.  Work in 2005 focused on optimization of techniques necessary for the extraction of high quality nucleic acids from sediments - vital for the application of microbial biomarkers that function on the basis of specificity of response.  Targeted genes encode a number of metal detoxification functions (relating to the redox of arsenic and the efflux of copper, cadmium and zinc) and general stress proteins (heat shock proteins, bacterial metallothionein and oxidative stress proteins) related to cellular homeostasis following metal-induced perturbation.

Sites chosen for the initial application of microbial biomarkers were adjacent to and downstream of the Anaconda Smelter, MT.  For 125 years, this facility engaged in smelting operations at the southern end of the Deerlodge Valley, and has been identified by EPA reports as a significant source of trace metal pollution.  Initial amplification of metal detoxification and general stress genes demonstrated strong correlations between site-specific metal loads and the presence, quantity and type of genes that can be amplified. 

For example, the highest prevalence of both general stress genes and metal detoxification genes was observed at all sampling times (7.6 / 9 genes tested) in samples from the most contaminated site immediately downstream of the smelter (average metal concentrations: Cu 747 mg/kg, Zn 510 mg/kg, As 47 mg/kg).  By contrast, an off river reference site had the lowest number of amplifiable genes (2/ 9 genes tested) and the lowest metal concentrations of all sites examined, indicating that low levels of metal contamination may result in low copy numbers of stress genes, below the detection sensitivity of the PCR amplification assay.  Closer examination of the amplified genes noted that at all sites genes related to oxidative stress (superoxide dismutase) were amplified, while metal detoxification genes were amplifiable only at highly contaminated sites.

The application of a novel real-time PCR assay was able to quantitatively amplify specific genes directly from the sites along the Clark Fork River.  Copy numbers of three selected genes (superoxide dismutase, catalase and metallothinein) showed significantly higher levels within the most polluted sites when compared to sites with ambient metal levels.  The application and development of this assay represents a significant advance within the field of ecotoxicology.