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Health and Environmental Effects Research

AED scientists developing genomic test to assess small seabed organisms

Sediments are sinks for our waste. Material from cities, farms, and factories ultimately end up in sediments (soil including sand, silt, and gravel under water). As we become better at controlling the amount of waste that’s dumped into our rivers, lakes, and oceans, sediments themselves can become sources of pollution. Contaminants can desorb from sediments to the cleaner water column.

Scientists study micro-,meio-, and macrobenthic organisms—small organisms that live in or on the seabed—to learn more about what’s in our sediments. This can guide environmental managers in identifying what water bodies represent the greatest risk to our health and ecosystems. Benthic communities often are impacted most by contaminants that accumulate in sediments. As such, they can act as indicators of whether certain areas are polluted or not.

However, these organisms are very small, so the method used to identify them requires significant amounts of time, labor, and expertise. Traditionally, researchers preserve sediment samples in formaldehyde, and then sift out the organisms prior to viewing them under a microscope. EPA scientists in Narragansett, RI, are developing a novel, more efficient method for identifying micro- or meiobenthos: Extracting DNA from a small plug of sediment and then comparing the DNA with an existing DNA library to see what organisms are present.

“We’re now comparing this genomic method with the traditional counting method to see if they agree,” said Kay Ho, an EPA chemical oceanographer who is the leader of this project.

Dr. Ho’s team also is adapting a test method that will enable scientists to assess intact benthic communities while controlling for factors that can interfere with results. Benthic community assessments typically are done either in the field (where experiments are difficult to control because of environmental influences such as storms, freshwater surges, and cold fronts) or the laboratory (where usually only select species rather than an entire community assemblage are studied). Using this test, scientists will collect intact sediment cores, bring them to the laboratory, and then layer them with sediments spiked with a contaminant. The layering will force oxygen-dependent organisms to migrate through and into the contaminated layer. Because genomic testing does not distinguish between living and dead DNA, researchers also will add a layer of DNA-free sediment on top of the contaminated layer after 3 weeks of exposure, once again forcing any living benthos to move up. They will then extract DNA from the topmost layer to see what, if any, organisms survived the contaminant.

“The success of this project will greatly enhance the ability of environmental researchers and managers to assess intact benthic communities under different ecological conditions in controlled environments and identify species critical to community structure,” said Dr. Ho. “In addition, the development of a rapid genomic end point will revolutionize the benthic ecology field. Laborious sorting and counting methods requiring significant expertise in identifying and naming species, and using samples preserved with toxic formaldehyde, will be replaced with relatively simple DNA extraction and sequencing.”

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