With sterile sample bottles at the ready, scientists in the Molecular and Environmental Microbiology Lab at NOAA’s Atlantic Oceanographic and Meteorological Laboratory (AOML) prepare to capture water samples for analysis in the lab. Invisible to the naked eye, nutrients, pollutants, and entire communities of bacteria, algae, and other microorganisms drift through these waters leaving clues in the form of pollution and DNA signatures.
The goal of AOML’s microbiologists is not only to figure out what types of pollutants and microorganisms are in this water, but to determine their origin – a process known as microbial source tracking.
With the lab’s Halozone project in the Florida Keys, they are using this technique to characterize land-based sources of pollution that have found their way into the marine environment.
“We are looking to see how these pollutants move from near-shore to off-shore and on the reef,” says Rob Bremer, a Research Associate in AOML’s Ocean Chemistry and Ecosystems Division.
With support from the Environmental Protection Agency (EPA), the Halozone Project expands AOML’s South Florida Ecosystem Restoration cruises by adding targeted sampling to investigate water-quality dynamics, connectivity, and ecological impacts within the near-shore “halo zone” of the Florida Keys. The halo zone is defined as the region within approximately 500 meters of the shoreline. As part of the project, researchers collect microbial, nutrient, and chlorophyll-a samples along four near-shore transects in Key West, Marathon Key, Key Largo, and Key Biscayne.
Along the transects, a team member deploys a niskin bottle to sample seawater, and ultimately, the microbes, nutrients, and chlorophyll found within. These samples are quickly stowed in on-board coolers chock-full of ice which helps preserve the samples and prevent DNA from degrading. Meanwhile, another researcher lowers a water quality analyzer into the water column to collect readings of temperature, salinity, dissolved oxygen, pH, and turbidity (a measurement of the amount of particulates in the water).
Then, it’s back to the lab where Bremer and other scientists pump the seawater through a fine-mesh filter that entraps the microbes and DNA. Using magnetic beads, contaminants are removed leaving behind purified DNA that is extracted for processes known as Next-Generation Sequencing and quantitative polymerase chain reaction (qPCR). During qPCR, genes specific to several key bacteria are identified and amplified.
For example, you may have heard that humans and chimpanzees share about 96% of their DNA. So, in order to differentiate whether you were looking at a sample of a human or a chimpanzee, you would need to look at specific genes or gene regions where they differ.
Scientists at AOML do the same thing looking for harmful bacteria and for other bacteria that indicate the presence of fecal pollution in water, such as enterococci and strains of fecal Bacteroides bacteria that are unique to humans. harmful bacteria in the water, like enterococci. The extracted DNA is combined with primers targeting those specific regions of the genome that are unique to each type of indicator or harmful bacteria. Then those regions are amplified until they can be detected by the qPCR machine using fluorescent dyes. From there, a known quantity of the bacteria in the water can be calculated.
They pair the results of their genetic analyses with the water quality observations, noting potential trends in the water quality measurements that could be driving differences in microbial patterns.
By pairing cutting-edge genetic tools with detailed water quality measurements, AOML scientists are uncovering where pollution begins and how it travels through the coastal environment. Ultimately, these insights simultaneously help resource managers and local communities better understand the hidden pathways connecting land, water, and reef ecosystems, and protect vital ecosystems and human health.