check out the latest


Can Habitat Restoration Improve Water Quality in Urban Estuaries?  September 2016 BOP-CCERS Colloquium

By Heather Flanagan
September 27, 2016

Aniline Amoguis, right, of The Young Women’s Leadership School of Astoria, collects oyster biodeposits in the hands-on portion of the BOP-CCERS September Colloquium.

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.

This September we were excited to welcome back our BOP-CCERS teacher fellows for our September Colloquium featuring guest lecturer Professor Chester Zarnoch of Baruch College and Graduate Center, City University of New York.  Professor Zarnoch’s work focuses on “the physiological ecology of bivalves to address questions related to restoration and aquaculture.”  His presentation for our group looked at the impact of sewage pollution on New York Harbor- and what we can do about it.

For the BOP-CCERS September Colloquium, Professor Chester Zarnoch of Baruch College and Graduate Center, City University of New York presented on habitat restoration in urban estuaries.

For the BOP-CCERS September Colloquium, Professor Chester Zarnoch of Baruch College and Graduate Center, City University of New York presented on habitat restoration in urban estuaries.

We’ve covered sewage pollution before- in their field trainings and at our May Colloquium, fellows learned that more than 25 BILLION GALLONS of raw sewage and polluted stormwater discharge into New York Harbor each year 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.  (You can check it out in the video of the Gowanus Canal below!)

A CSO event in the Gowanus Canal.

In earlier sessions, teachers learned how to test for the presence of fecal pathogens from scientists and partners involved in citizen science water quality testing.  But microbial contamination is not the only threat CSOs present to our waterways.  Professor Zarnoch explained that “the Hudson River is the most nitrogen loaded estuary in the world” and that “more than half of that nitrogen is coming from wastewater, so we know it’s human derived nitrogen.”  Unfortunately, as the fellows learned in the June Colloquium, all of that nitrogen triggers a phenomenon known as “algal blooms,” which lead to “dead zones,” or the condition known as “eutrophication.”  Nitrogen is a nutrient that stimulates an explosion of phytoplankton growth, and with it a corresponding increase in waste from the organisms that consume it.  When the supply runs out, the phytoplankton die and are consumed by bacteria, who use up a tremendous amount of oxygen in the process, causing “hypoxia.”  The marine life that depends on oxygen either dies or leaves, essentially becoming “biological deserts.”  NOAA has a good visualization of this:

NOAA visualization of dead zones.

The Hudson River Estuary is resilient because it gets extensive ocean flushing- but that doesn’t mean there aren’t consequences from the nitrogen overload.  Professor Zarnoch pointed to massive soft shell clam die-offs, the loss of New York City’s oyster fishery by the 1920s, and the destabilization of salt marshes in Jamaica Bay- we’re “losing hectares per year, even now.”  This has lead to efforts to reduce nitrogen loading in New York City, but he noted that to fix it we’d need to spend $200 million a year to continue to upgrade our wastewater treatment system, and it’s a challenge to convince people that it’s important.  He’s hoping that through programs like BOP-CCERS, we can reconnect New Yorkers to our water and get them to “think of the environment as a resource.”

In the meantime, his research focuses on removing nitrogen, which only happens “through a process microbes mediate- denitrification.”  His work asks, “Can we enhance it? Can we ramp it up so we get more nitrogen removal?”  To help the group examine this, he needed to start with an explanation of the nitrogen cycle.  (I’ve added some additional explanation and context to clarify the process for readers less familiar with the nitrogen cycle.)

Nitrogen gas, which makes up 79% of air, is inert, meaning it won’t readily combine with other elements without a tremendous amount of energy input.  Historically, nitrogen molecules (N2) mainly combined with other atoms, which is called “nitrogen fixation,” through lightning (nitrogen + oxygen) and biological processes carried out by bacteria (yielding ammonia [NH3], a combination of nitrogen + hydrogen).  However, at the beginning of the 20th century, German chemists invented an industrial process (called the Haber-Bosch process after its inventors) to produce ammonia, which can fertilize plants- or create bombs.  Smithsonian (in an article about Fritz Haber, a true embodiment of the ambivalence of 20th century science who would later go on to become the “father of chemical warfare”) calls the Haber-Bosch process “likely the most important technological innovation of the 20th century. It sustains the food base for the equivalent of half the world’s population today.”  This triggered, among other unintended consequences, a global population boom.

As we mentioned earlier, an increasing population means that without adequate wastewater treatment, more and more human waste bypasses our overtaxed sewer system- and that human waste is full of organic nitrogen.  Once this organic nitrogen enters the water, certain bacteria convert it to inorganic nitrogen in the form of ammonium (NH4).  Other bacteria then convert that ammonium to nitrites, and still more bacteria convert the nitrites into nitrates.  I really like this YouTube video for explaining this process- here’s their diagram explaining the conversion of ammonium to nitrites (the little anthropomorphic figure in the middle represents bacteria):


  …and the conversion of nitrites to nitrates:


Finally, another type of bacteria, called “denitrifiers,” convert the nitrates back into nitrogen gas (N2), allowing it to harmlessly bubble out of the waterway and into the air.  But it’s important to note that unlike the process of creating nitrates, denitrification only happens when there’s no oxygen, referred to as “anoxic” conditions.


Now, back to the central question of the lecture- can habitat restoration improve water quality in urban estuaries?  


According to Professor Zarnoch, an important 2011 paper measured denitrification in multiple habitats in different seasons, and found that “three dimensional habitats had much higher levels of denitrification than the two dimensional habitats…[these habitats] provide conditions that are ideal for enhanced denitrification.”  One such three dimensional habitat is the root structure of salt marshes- the oxygen released from the plants’ roots make nitrate more available for denitrifiers (who carry out their work in anoxic pockets nearby).  Since a lack of either carbon or nitrates limits denitrification and salt marshes provide both (the plants’ roots also release carbon), they’ve been the focus of a lot of denitrification attention.  


In New York City where natural salt marshes have largely degraded, 25 restoration sites have been created since 2002.  Researchers wanted to understand, starting from pure sand, how long it would take a restored marsh to provide ecosystem services- or whether it would ever provide the services of a normal marsh at all.  To test this, they used four sites clustered together in Jamaica Bay that had been restored at different times, plus a degraded reference site and a healthy site:


They found that as time goes on, salt marshes increase below ground biomass, and start to approach what a natural marsh would look like.  Correspondingly, an older restored marsh provides more denitrification than a younger marsh. They also found that denitrification was limited in the summer by nitrogen (phytoplankton and seaweed blooms suck up lots of nitrogen in the summer) and in the fall by carbon, which can help explain why an older marsh, which produces more carbon, is more successful.


It’s tempting here at BOP to assume that another three dimensional habitat, the oyster reef, would readily prove to be a successful denitrifier.  However, it’s a challenge to study the denitrification efficacy of a healthy oyster reef in New York Harbor, where the natural reefs have long since degraded.  To test denitrification in this environment, Professor Zarnoch conducted an experiment in 2010 in Jamaica Bay using live oysters in trays above sediment, as in the photos below:



Unfortunately, “oysters themselves didn’t enhance denitrification” except when nutrients were limited, which didn’t happen that often during the experiment.  (You can read a summary of this experiment on page 13 of this National Parks Service PDF here.  In it, he concludes that “[o]ur initial results show that the desirable impacts of oyster restoration may not be attained under eutrophic conditions occurring seasonally in Jamaica Bay. Continued analysis will help elucidate the environmental drivers of these ecological processes and guide future management actions.”)  

But the experimental scenario wasn’t the same as a reef, so Professor Zarnoch decided to test the newly restored Soundview Reef in the Bronx.  Here too, denitrification rates were virtually the same both near and away from the reef.  However, as a young reef with relatively few live oysters, Soundview isn’t necessarily an indicator of the denitrification capabilities of an older, healthier reef with lots of live oysters.  Other studies, like one in Virginia, have demonstrated  that in ideal conditions, one acre of reefs could remove 500 pounds of nitrogen from the water per year.  And as BOP curriculum specialist Annie Lederberg pointed out, there’s been some research that suggests that an oyster’s gut is an environment that’s primed for anaerobic activity, meaning that living oysters might enhance denitrification in a way oyster shells in a reef do not.

For the hands-on portion of the evening, the fellows had the chance to try collecting oysters’ “biodeposits”- that is, their feces and pseudofeces (inorganic materials that oysters filter in that they can’t digest, which they then cover in mucous and eject).  Professor Zarnoch set up five trays with circulating New York Harbor water, then added live oysters:


The teachers then collected the feces and pseudofeces and placed them on a filter, similar to how researchers would collect these materials in the field to determine what organic and inorganic materials the oysters were filtering and how fast:


Next, BOP-CCERS Program Manager Sam Janis walked the teachers through the BOP-CCERS digital platform.  The platform is a learning management tool that allows teachers to assign students protocols to complete during trips to their oyster restoration stations, and where students can upload their expedition data.  The platform also features a library of curriculum created by BOP’s curriculum specialists- as Ann and Annie noted, there are 36 lesson plans available to date, with more coming soon.

For the final portion of the meeting, two fellows from the first BOP-CCERS cohort returned for “microteaching”- a demo of a restoration education-related lesson plan they’d developed and used with their classes.  First, Lui Yi of the International School for Liberal Arts in the Bronx engaged teachers in a lesson on hypotheses vs. questions vs. conclusions.  Working in groups, using mini whiteboards Yi had made himself, the fellows worked on turning questions into hypotheses and finally into experiments, an example of “making thinking visible.”

Finally, Lou Lahana of M.S. 188 on the Lower East Side described one of his lessons that “use[s] low and high tech tools to solve social problems.”  Lahana addressed the teachers as though they were middle schoolers being introduced to the issues of CSOs and sewage pollution using images and video from his website,  Lahana’s teaching practice encourages students to be makers, and his CSO lesson (which is on his website here) guides students to use “SketchUp, Scratch, Lego or any other Maker tool to teach others about wastewater treatment.”  Unfortunately a fire drill cut his microteaching session short, but his website features a fantastic collection of teaching resources for any educators looking to tackle social and environmental justice issues with their students- check out the list here.

We can’t wait to see how Cohort Two’s teachers bring restoration education into their classrooms this school year- keep checking back on the Billion Oyster Project blog for more posts, follow the BOP-CCERS Tumblr, and sign up for our newsletter to learn more!