Wait, What’s in the Water?:
Use of qPCR to Monitor Water Quality at U.S. Beaches
 |
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!
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.
