Wait, What's in the Water? Use of qPCR to Monitor Water Quality at US Beaches

Wait, What’s in the Water?:

Use of qPCR to Monitor Water Quality at U.S. Beaches

http://cida.usgs.gov/glri/projects/nearshore_health/beach_water_quality.html with permission 

             Ah, summer!  Don’t you love to go to the beach when it’s sizzling outside?  And isn’t it more fun when no one gets diarrhea or rashes the next day from swimming in dirty water? 

            The EPA and local health authorities aim to keep it that way by monitoring at fresh water beaches for fecal (poop) contamination with techniques like microbiological culturing and qualitative polymerase chain reaction (or qPCR for short) and use of “Virtual Beach,” a computer program that helps with modeling changing conditions at the beach.

Wait, what’s in the water?

            Water at public beaches is usually clean but sometimes can be contaminated with human or wildlife fecal waste. Bacteria in the animal digestive tract help with nutrient absorption and they make up about a third of the dry weight of feces.  (That's a shipload of bacteria!)

            Health departments monitor beach water for fecal contamination by looking for bacterial indicator species, often searching for E. coli in freshwater or enterococci in salt water. These bacteria are not usually pathogenic (disease-causing) themselves, but they provide a reliable way to predict when pathogenic bacteria, viruses or protozoa that are sometimes also found in feces might be present.

            Using indicator species saves time and money because health officials search for the one indicator species instead of all possible species that might contaminate the water.  As bacterial counts of the indicator species rise, an advisory can be posted, warning swimmers of dangerous levels of bacteria,.  If they get very high over a certain level where swimmers will get sick, the beach can be closed.  

            What are the pathogenic species we’re worried about? Pathogenic bacteria include species like Salmonella, Campylobacter or even pathogenic strains of E. coli, all of which can cause gastrointestinal distress like diarrhea and vomiting. Feces might also include viruses, including those that can give you hepatitis, diarrhea, eye infections, or meningitis. And, as if that’s not enough, feces might contain pathogenic protozoa (unicellular motile eukaryotes), like Cryptosporidium or Giardia, either of which can also give you symptoms of GI distress like diarrhea. 

            That’s a pretty toxic load; so where does it come from?  I think you know the number one answer to that one; it’s waste from the digestive systems of humans and other animals! The number two answer (oh, poop jokes!), according to the EPA, is release of feces into the environment by storm water pollution, sewage overflow, direct deposition by birds, release of boating wastes, land run-off and suspension in the sands and sediments.  

Technical stuff (data dump) on acceptable bacterial levels at fresh water beaches

            The EPA recommends for fresh water beaches that “no single beach water sample exceed 235 E. coli or 61 enterococci per 100 ml.”  In Wisconsin, an advisory is posted if E. coli are at or above 235/100 mL of water and the beach is closed if E coli are at or above 1000 per 100 ml.  In case you’re wondering, the nose knows, and at this point, you’d probably notice the water was contaminated because it would smell foul and look cloudy.  

Microbiological culturing technique

            A reliable method for checking water quality at freshwater beaches is occasional testing of water by microbiological culturing, which involves filtering a sample of water through a membrane and then placing the membrane on petri plates.  The plates are incubated for 24-48 hours at about 37 C, which is body temperature, in order to allow fecal bacteria grow.  If E.coli grow, that means that E coli were present in the starting sample of water.  To remind you, the E. coli are used as an “indicator species,” indicating sewage waste is present and could contain other, potentially more serious, bacteria, viruses or other pathogens. To learn more from the EPA on this, click here.

            This traditional or “old school” method is reliable and can be made more so if used with computer modeling techniques (see below). The advantage of the microbiological culturing method is that it’s relatively inexpensive. The disadvantage is you can only get the results 1-2 days after testing, and as any grade-schooler can tell you, you’ll know if the water was dirty yesterday, but you won’t know if it’s dirty today! 

Molecular qPCR technique

            qPCR is also called real-time or quantitative polymerase chain reaction and it’s being used at some beaches to monitor for fecal indicator bacteria. In qPCR, the DNA in the sample is amplified or copied over and over again and new copies of the DNA of interest are detected using fluorescent probes as the reactions proceed.  Looking for a few E. coli in 100 mL of water is a little like searching for the proverbial needle in a haystack and qPCR lets you find that needle in just 2-3 hours! 

            For those who know a little bit about DNA and the process of DNA replication, here is the procedure in more detail. 1) Technicians start by collecting water in sterile containers at specified collecting sites.  2) Any bacteria present are concentrated by filtration and bacteria are collected on a filter membrane.  3) Cells on the filter membrane are disrupted (broken open) using glass beads in order to release the DNA that’s in the cells.  4)  qPCR is performed using thermal cycling, where the samples are repeatedly moved to different temperatures. First, the DNA is made single-stranded or “un-zipped.” At the next temperature, a single-stranded primer specific to the indicator species is allowed to anneal or “stick to” the single stranded DNA.   At the final temperature, a DNA polymerase enzyme is used for primer extension reactions to replicate or “copy” the starting strand. Thermal cycling amplifies DNA according to the power law, with one target DNA becoming two after one round of qPCR, then four after two rounds, then eight after three rounds, and so on. If there aren’t any target bacteria present, there will be no replication of target DNA.  Fluorescent dyes are used to label or “identify” the target double-stranded DNA produced during thermal cycling.  The accumulation of fluorescence over time relative to controls is used to quantify amounts of DNA present in the starting sample.

qPCR from http://oh.water.usgs.gov/micro_qpcr_method.htm

            To learn more, you can check out the excellent site at Michigan State University including background and training videos.

            Using qPCR for the application of water quality monitoring means you have to be a bit of an early bird. If you have a qPCR machine in a facility at your beach, you need to get your water sample by 7 AM so you can get your results and act on them by 10 AM when the beach opens! 
 

Computer modeling techniques:

            Computer modeling with use of real-time data from either method described above adds to the accuracy of predictions.  Health officials monitoring either freshwater or marine recreational beaches can use the program “Virtual Beach,” by the EPA to make better predictions about changing conditions.  The program allows beach managers to see how variables like wind or current speed and direction will affect indicator bacterial concentrations.  They can then make better decisions about potential beach closings. Click here to learn more about Virtual Beach.  

Results and Remediation

            Results from beach monitoring are reported on state or province websites. Beach managers may put up an advisory sign on the beach or even close a beach if certain contamination levels are reached.  Again, in Wisconsin, an advisory is posted if E. coli are at or above 235/100 mL of water and the beach is closed if E coli are at or above 1000 per 100 ml. (3)

            In the Great Lakes, results are reported at the following websites (click on the link to follow the link): Michigan BeachGuard, Ohio BeachGuard, IndianaBeachGuard, Illinois BeachGuard, Wisconsin Beach Health and OntarioBeaches You can also get a handy BeachGuard app (for MI, IN, IN and OH) for your droid phone here   and the app will apparently soon be available for iPhones, too.

            You can also find results on other freshwater or saltwater beaches, at the website of the National Resources Defense Council.  You can type in the state of the beach you want to visit and then scroll down for the name of the beach and to get the testing results, if there are any.

            Results are also used to change the beach landscape to have fewer beach advisories.  Interviews with Dr. Julie Kinselman in Wisconsin, Meredith Nevers in Indiana and Dr. Sharon Briggs in Michigan revealed a surprise. Although you’d expect sewage overflow is the most worrisome problem, it’s not very common.  Instead, pooping by geese and gulls on the shore and parking lots is the ongoing, serious problem that requires remediation.  When economically feasible, beach managers try to manage water flow over the shore and parking lot areas by building birms, redirecting stormwater, using porous pavement for the parking lot, deterring bird landings, using storm drains, etc…Who knew that flock of geese landing on the beach today could close the beach tomorrow?

            It’s cool you that, before you visit, you can check out the health status of almost any beach.  Dedicated workers like Drs. Kinselman, Nevers and Briggs in the U.S. and Canada use a number of techniques and computer programs to make good decisions about whether or not it’s safe for you to swim. So this summer, after you find your beach is clean and open for business, grab a towel and sunglasses and enjoy your natural resources!  Time for some fun in the sun because the surf’s up!

Additional References:

1. http://www.usgs.gov/solutions/docs/Beaches_USGS_factsh.pdf

2. Phone interview with Dr. Julie Kinzelman, City of Racine Health Department, University of Suffolk Visiting Fellow and University of Wisconsin School of Freshwater Sciences affiliate.

3. Phone interview with Dr. Shannon Briggs, Michigan Department of Environmental Quality.

4. Phone interview with Meredith Nevers, USGS Lake Michigan Ecological Station.

This blogpost was written for the benefit of students at Washtenaw Community College and the community as part of my sabbatical activities for winter 2015.  I am solely responsible for the content and hold the copyright for the work. Feel free to use the information in this blog; just credit me with a link back to my blog! -Emily Thompson, Ph.D.