Grantee Research Project Results
2000 Progress Report: Phylogenetic Analysis of Microbial Communities in Contaminated Nearshore Marine Sediments
EPA Grant Number: R826108Title: Phylogenetic Analysis of Microbial Communities in Contaminated Nearshore Marine Sediments
Investigators: Herwig, Russell P.
Institution: University of Washington
EPA Project Officer: Hahn, Intaek
Project Period: September 1, 1997 through August 31, 2000 (Extended to September 30, 2001)
Project Period Covered by this Report: September 1, 1999 through August 31, 2000
Project Amount: $370,446
RFA: Exploratory Research - Environmental Biology (1997) RFA Text | Recipients Lists
Research Category: Biology/Life Sciences , Aquatic Ecosystems
Objective:
Little is known about the composition of microbial communities that live in contaminated nearshore marine sediments and how the composition in contaminated sediments compares to that found in clean reference sites. Environmental pollutants not only impact the composition and health of animals and plants that live in or on marine sediments, but also may influence the composition of the microbial communities. In many areas of the United States, urbanized or industrialized estuaries and marine sites are contaminated with polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and heavy metals. Because microorganisms that live in sediments are largely responsible for the transformation and bioremediation of environmental pollutants and play a significant role in geochemical cycling, it is important to understand the composition of the microorganisms that live in contaminated sites. Our laboratory has developed molecular protocols for the analysis of the microbial communities in marine sediments. With support from the EPA, we continue to develop our protocols and examine the microbial composition of: (1) intertidal and subtidal marine sediments contaminated with creosote, a contaminant composed largely of PAHs; and (2) clean intertidal and subtidal reference marine sites. Samples for our investigation were retrieved from Eagle Harbor and Blakely Harbor, Washington. Both of these harbors are located on the western shores of Puget Sound in an environment that has a relatively high marine salinity. Eagle Harbor is the site of a former wood treatment facility that was the source of creosote found in the nearby marine sediments. This location is formally known as the Wyckoff Eagle Harbor Superfund site. Both the upland terrestrial and intertidal areas have been under intensive remedial investigation. The primary objective of our research is to develop and test protocols for performing large-scale analyses on the composition of the microbial communities in nearshore marine sediments from Puget Sound using 16S rRNA phylogenetic techniques.Progress Summary:
Determining the composition of the microorganisms that live in contaminated areas traditionally has been performed using broth or solid bacteriological media that supports the growth of microorganisms in the laboratory. Only a very small fraction of the microorganisms that exist in an environmental sample can be cultivated using such methods. In other words, only those organisms that were capable of multiplying on the bacteriological media were enumerated, isolated, and characterized in previous studies. To avoid the requirement to culture microorganisms, scientists have attempted to identify the microbial species that are present in an environmental sample by extracting and characterizing distinctive fragments of DNA, such as the genes for the 16S ribosomal RNA (16S rDNA). The 16S rDNA can be used to identify different species of bacteria and to explore the evolutionary or phylogenetic relationship between diverse species of organisms. During this past year, we continued to successfully develop the required steps of a molecular protocol that enables us to perform the analysis of microbial communities in contaminated marine sediments.The basic steps of our protocol include: (1) extracting and purifying high-molecular weight DNA from the sediments; (2) amplifying and cloning of 16S rDNA; (3) screening of cloned 16S rDNA by performing a restriction fragment length analysis with three restriction enzymes; (4) sequencing the 16S rDNA from representative clones; and (5) performing a phylogenetic analysis of the representative 16S rDNA. Completion of these steps results in the characterization of microbial populations in the sediment samples that were collected.
Future Activities:
During the remaining period of EPA grant support, we will focus our efforts on completing manuscripts for publication in peer-reviewed scientific journals. In addition, we plan to evaluate some modifications to our protocols using samples retrieved from Eagle Harbor. The modifications are a result of recent experiments that we have performed in the laboratory and recent advances in molecular biology protocols that should allow for easier and more efficient cloning of the 16S rDNA that is amplified from the environmental samples. We also modified our DNA extraction procedure so that it is simpler to perform than the protocol we developed for our project a couple of years ago. During the remaining grant period, we also may have the opportunity to examine samples from new remediation activity that is being pursued at Wyckoff Eagle Harbor. The Army Corps of Engineers will be using a thermal extraction method to remove creosote from subsurface soils in the upland area. It would be interesting to characterize the microbial populations before and after the thermal treatment. We would like to gather preliminary information about the microbial populations associated with the new remedial activity.Supplemental Keywords:
sediments, marine, estuary, PAHs, bacteria, bioremediation, biology, monitoring, pacific coast, pacific northwest, Washington, WA, EPA Region 10., Scientific Discipline, Toxics, Geographic Area, Waste, Water, Contaminated Sediments, HAPS, State, Environmental Microbiology, Ecological Risk Assessment, Ecology and Ecosystems, Biology, contaminated marine sediment, contaminant transport, contaminated sediment, Washington (WA), microbial pollution, aquatic ecosystems, phylogenic analysis, ecology assessment models, indicator species, marine ecosytemsRelevant Websites:
http://faculty.washington.edu/herwig/![Exit EPA icon](https://www.epa.gov/ncer/images/exit.gif)
Progress and Final Reports:
Original AbstractThe perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.