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BOP-CCERS May Colloquium Recap: The Microbiology of New York Harbor

By Heather Flanagan
June 6, 2016

Professor Greg O’Mullan pops a New York Harbor water sample into a heat sealer, part of the process of testing for fecal indicator bacteria in his work with Riverkeeper, a Hudson River watchdog organization. As little as 1/10 of an inch of rain can send raw sewage and polluted stormwater into New York’s waterways. By engaging citizen scientists in water quality testing efforts, organizations like Riverkeeper help communities develop local solutions to local problems- learn how below!

The CCERS Fellowship at Pace is a two‐year professional development program that trains teachers to engage their students in hands‐on environmental STEM and restoration ecology in New York Harbor.  The Fellowship is open to NYC Department of Education middle school teachers working in Title I funded schools.  Classes and trainings are taught by guest experts, scientists from Columbia’s Lamont Doherty Earth Observatory, curriculum specialists from New York Harbor Foundation, and partner organizations such as The River Project and BioBus/BioBase.

More than 25 BILLION GALLONS of raw sewage and polluted stormwater discharge into New York Harbor each year.  Massive numbers of pathogens enter our waterways whenever this happens, creating human health risks and damaging marine habitats.  For the BOP-CCERS May Colloquium, we explored this phenomenon and the microbiology of New York Harbor with guest expert Professor Gregory O’Mullan, an environmental microbiologist from CUNY Queens College.  Professor O’Mullan works with Riverkeeper, an organization that engages citizen scientists in water quality testing to help protect the Hudson River Estuary, so for the night’s hands-on activity teachers were able to culture a bacteria sample and interpret data for themselves.

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Professor O’Mullan started the night out with a question he hears a lot: “How’s the water?”  He noted, “Primarily, [people] want to know, ‘Can my kid go in the water?  What information do I need?’” but that “the more I dug into ‘How’s the water?’, the more concerned I was that info was misleading or inadequate.”  To better answer this question, he connected with Riverkeeper about ten years ago, and since then they’ve set up 74 testing locations along the Hudson River Estuary, from The Battery up past Albany up into the Mohawk River (the Hudson River’s largest tributary) north of Troy.  Riverkeeper’s program “applies the United States Environmental Protection Agency (EPA) method 1600 to quantify the abundance of Enterococcus bacteria, a reliable indicator of fecal-contamination.”  (Click here for more information.)  According to Professor O’Mullan, since Enterococci don’t live in pristine environments, when they’re found in a water sample they represent “a connection between our (and warm-blooded animals’) guts and the waterway.”

This connection is through the city’s 460 Combined Sewer Overflow (CSO) outfalls.  Although New York Harbor’s water quality has improved dramatically over the last forty years because of legislation like 1972’s Clean Water Act and improvements in wastewater treatment plants, the city’s sewer system is over 100 years old and wasn’t designed to handle the sheer volume of water we put into it.  Whenever there is too much water for either the sewage pipes or the wastewater treatment plants to handle, a CSO event occurs, meaning raw sewage and untreated stormwater discharges into the waterways through the outfalls (the 25 billion gallon a year figure mentioned earlier).

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Professor O’Mullan discusses how raw sewage and polluted stormwater contaminates waterways through CSOs.

Enterococci themselves actually aren’t terribly hazardous, and they only account for about 1% of the total microbial community that humans excrete.  But as Professor O’Mullan explained, “Enterococci are signaling that broader suite of organisms”- including possible pathogens- which is why Enterococci are known as “fecal indicator bacteria.”  Consequently, the EPA guidelines state that more than 60 entero cells per 100 mL of water represents conditions that are dangerous for human health.

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To test water samples for the presence of Enterococci, Riverkeeper uses IDEXX water sample trays like this:


A cultured water sample tray from the May Colloquium fluorescing under a blacklight. Photo courtesy of Gregory O’Mullan.

Each tray contains a mixture of harbor water and a nutrient solution that fluoresces when it’s metabolized by the bacteria.  After the trays are heat sealed and incubated, it’s possible to determine the Most Probable Number (MPN) of Enterococci based on the number of large and small wells that fluoresce.  While the fellows had previous experience interpreting MPN tables from Field Training #2, the hands-on portion of the night presented a new challenge: preparing these IDEXX water sample trays themselves.

The gear, including empty IDEXX trays, sterile containers, tiny containers of nutrient solution, bottles of sterile water, and graduated pipettes. The large bottle in the center contains a harbor water sample from Flushing Bay.

The gear, including empty IDEXX trays, sterile containers, tiny containers of nutrient solution, bottles of sterile water, and graduated pipettes. The large bottle in the center contains a harbor water sample from Flushing Bay.

Since the salt in New York Harbor water can inhibit bacterial growth, the fellows first had to dilute the sample with 90 mL of sterile water:

Then, as Professor O’Mullan demonstrates here, they added the fluorescent nutrient solution to the diluted water:

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Next, they used the graduated pipette to add a 10 mL harbor water sample to the sterile water and nutrient mix:

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Once the fellows finished mixing the solutions, they labeled the IDEXX trays and poured the solution into the tray.  Professor O’Mullan emphasized that it’s very important to make sure that tray stays upright!

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The fellows then carefully fit the tray into a mold so it could go into the heat sealer:

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Because the heat-sealed trays would still need to incubate for 24 hours to get a result, Professor O’Mullan joked that they’d “pretend like it’s 24 hours later like a baking show” and practice interpreting data using pre-incubated trays:

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But he was kind enough to send us the results the next day (all photos below courtesy of Gregory O’Mullan):


Professor O’Mullan shared his experience that water quality varies at small spatial scales, meaning nearby areas can have very different water quality, so “If you find local pollution sources and local solutions, you’re going to be able to improve their water quality.”  It was a great reminder that the data collection work of citizen scientists, like the ones at Riverkeeper and BOP, can help communities advocate for themselves and make change.

To wrap up the night, two fellows from Cohort One, Jack Wasylyk (M.S. 88) and Jyoti Dhar (M.S. 188) presented on restoration-based curriculum they’ve used in their classrooms.  Jack prepared a slideshow on keeping an in-class oyster aquarium and shared a video he’d made on M.S. 88’s oyster restoration work.  Jyoti shared student work, including these awesome 3D oyster reefs!

Coming up next- we’re looking forward to seeing ALL of the fellows on June 10th for our BOP-CCERS culminating event, the Billion Oyster Project Research Symposium!  The Symposium will bring together a diverse community of schools, scientists, and partner organizations from across New York Harbor for a day of networking, co-learning, and celebration.  The goals for the day are to open up new educational and career opportunities for NYC students and advance the collective knowledge we need to restore the Harbor and our City’s relationship to it. We’d love for you to be a part of it!  Click here to learn more!

Interested in reading more about BOP-CCERS and how we’re bringing hands-on restoration science to classrooms all over the city?  Sign up for our newsletter and click here to read all BOP-CCERS posts!