Institute of Marine and Environmental Technology

Summer on the Harbor

Hutton Scholar explores biodiversity beneath Baltimore's Inner Harbor

Hutton Scholar Alexandra Grayson shares insights from her summer fellowship at the Institute of Marine and Environmental Technology.

In the beginning

June 18, 2018

Ten years ago, planting flowers in front of my elementary school on Earth Day was, in my eyes, the pinnacle of environmental education. This somehow developed into three years worth of AP and IB level environmental courses in high school. I can now say in confidence that the development of my newfound interest in environmental problems and their solutions has become the highlight of my environmental education.

For a two-year long research assignment in my favorite class, IB Environmental Systems and Societies, I explored the impact of land use and impervious cover on water quality in various bodies of water in the Baltimore area. However, at the end of the two years, unanswered questions remained, and I was interested in learning more about the impact of urbanization on local water systems.

The teacher of this class, Ms. Frye, who spent the summer of 2016 working with Dr. Eric Schott at the Institute of Marine and Environmental Technology (IMET), recommended I apply for The American Fisheries Society’s Hutton Junior Fisheries Biology Program.

The Hutton Program is geared toward students within demographics that are underrepresented in the fisheries industry. The goal of the program is to increase diversity in fisheries science and management by stimulating interest in the industry through a summer internship. After answering questions about personal experiences that incited interest in the fisheries profession, accepted applicants are assigned a mentor.

When I was accepted as a 2018 Hutton Scholar, I was assigned to work under the mentorship of University of Maryland Center for Environmental Science (UMCES) researcher Dr. Eric Schott at IMET this summer. My mentor works alongside Dr. Tsvetan Bachvaroff, a researcher at IMET, and together they, in partnership with the National Aquarium and Maryland Sea Grant, have been studying the water quality and biodiversity of the Inner Harbor since 2016 in a very layered biodiversity project.

Now, I do understand that biodiversity and the Inner Harbor seem like two words that should not be found together, as there is a false notion that Baltimore’s Inner Harbor is too dirty to be anything but a lifeless entity. The biodiversity project is seeking to change this narrative using four different methods:

  • By restoring ecosystem services: The biodiversity project partners have placed “biohut habitats” and aerated floating islands in the harbor. These structures attract a great deal of biodiversity and ultimately serve as a means to filter and clean the water.
  • By identifying and quantifying organisms in the harbor: The partners are quantifying the organisms during biohut counts and by watching biofilms. We use a method called DNA barcoding to identify the exact species of animals that we observe living in the harbor.
  • By monitoring the water quality: We are taking measurements of water quality indicators in order to see how urban abiotic and environmental factors influence the water quality and the life in the harbor.
  • By educating people: Launched educational programs and resources that present the Harbor’s biodiversity data to the public and assist in the understanding of quantifying biodiversity.


Throughout the course of my summer as a Hutton Scholar in Dr. Schott’s lab, I will have a chance to participate in each aspect of the project. This blog will go into further depth about each one and my involvement in it each summer, as well as serve as a chronicle of the life in the harbor. I will have the opportunity to witness first-hand in hopes that readers will be able to see that there is an abundance of life within urban estuaries, such as the Baltimore Harbor, that need protection, and stakeholders within the greater Baltimore community should be encouraged to assist the greater Baltimore community in improving the environmental conditions and minimizing coastal ecosystem impacts.

DNA Barcoding

Friday, June 29, 2018

Forever. Last week myself alongside two undergraduate interns, Langston and Chima, were in Dr. Danara Krupatkin ’s lab scraping whip mudworms (Polydora cornuta) off of an oyster shell for an amount of time that honestly felt like forever. Unbeknownst to us three, one of the six mudworms we were able to collect was not even a mudworm. After an analysis of its sequencing data, we discovered that it was actually fly larvae.

This particular moment shed light on the fact that while visual assessments to identify a species are necessary, it is important to use the sequencing data in conjunction with a visual assessment in order for a completely accurate understanding of what life is in the harbor. After conducting meta-DNA barcoding on a community from one of the biodisks, UMCES scientists discovered that there were water molds, or oomycetes, in the harbor. Many animals, like the water mole, cannot be identified—or can be misidentified, like in the case of the fly larvae—when solely using a visual assessment of the species (i.e. biofilms).

In order to gain more information about the biodiversity of the harbor, Institute of Marine and Environmental Technology scientists Dr. Eric Schott and Dr. Tsetso Bachvaroff use DNA barcoding to get genetic information about animals collected in the harbor, which is then compared to a database consisting of the genomes of thousands of marine animals. Since my most advanced academic exposure to biology took place in my ninth grade GT biology class, I had to learn take some time familiarize myself a bit with the process of DNA barcoding. After repetition and plenty of reading so that I can completely understand the purpose of each step in the procedure, I think I am now somewhat qualified to explain DNA barcoding—and if nothing else, I am now at least far more qualified than I was prior to the start of my internship.

DNA barcoding is a method that uses a short standardized section in the mitochondrial cytochrome of an organism’s genome—the Cyclooxygenase 1, or Cox-1, gene—to identify an animal. This particular gene is used in DNA barcoding because it is present in most eukaryotic species and because it is the perfect length for such a procedure, or as Dr. Tsetso likes to say, it is the ‘Goldilocks’ gene; the 648 base-pair region is short enough to be accessible and quick to sequence but long enough that it is possible to differentiate between species.

Once Chima, Langston, and I collected the six mudworms, we conducted an individual barcoding assessment on each of them. The whole body of the mudworm was used to extract DNA due to the small size of the individual worms. From the extracted DNA, the region we are barcoding is then separated from the rest of its fellow genes. Isolated, a singular gene cannot be sequenced in a timely manner. So we then use an amplification process called Polymerase Chain Reaction, or PCR, to turn this single COX1 gene into billions of copies of the particular sequence. The sequence, now amplified, is then transferred to computer programming that expresses it in a series of Cs, cytosine, As, adenine, Ts, thymine, and Gs, guanine.

We then copy this series of letters into a database called BLAST, which stands for Basic Local Alignment Search Tool, and, sort of like the way Google Search orders its results from most to least similar to your search, BLAST presents a list of species names recorded in the database by other scientists that have sequences most similar to the one we copied into the search engine, along with the percent similarity of each.

The analyzation of DNA sequencing has uncovered more of the mystery about what exactly is living beneath the surface of urban estuaries.

Sex (and death) in the city: The last night on earth for Baltimore’s clam worm

July 13, 2018

If today you feel particularly refreshed, perhaps renewed, or as if today were the start to a new beginning, feel free to blame it on the “moistness” of your brain.

Greek philosopher Aristotle believed that similar to tides, the human brain, made up of 75% water, is also impacted by the moon’s phase shifts. And today, Friday the 13th, a new moon is upon us—and a new moon is significant to many organisms, not only humans and not only on an Aristotelian level, but on a biological one as well.

Our mentor, Eric Schott, took the three of us outside to the water in front of IMET to search for clam worms. There, we found a lot more than what was necessary for our genetic experiment. Not only did we find the six clam worms we needed, but, as the picture shows, we also caught an abundance of female mud crabs and a baby Atlantic eel -- just from sticking net in the water.

Clam worm, Atlantic eel, and mud crab research was divided between the three of us. I took on the task of researching mud crabs, Langston was to learn some more about eels, and Chima - the clam worm. What we learned from each other the next day was quite interesting, like that the Atlantic eel we found probably came from the Sargasso Sea, but I found particular interest Chima’s comments regarding the reproductive system of the species that was the focus of our genetic research.

Clam worm, Atlantic eel, and mud crab research was divided between the three of us. I took on the task of researching mud crabs, Langston was to learn some more about eels, and Chima - the clam worm. What we learned from each other the next day was quite interesting, like that the Atlantic eel we found probably came from the Sargasso Sea, but I found particular interest Chima’s comments regarding the reproductive system of the species that was the focus of our genetic research.


One of these organisms is a native of the Baltimore Inner Harbor: the Neanthes succinea, a pink, lilac, and brown toned marine polychaete, usually resting at about an inch long, which we here at the Institute of Marine and Environmental Technology (IMET) often refer to as the “clam worm”.

Before mid-June, when I began my internship with the American Fisheries Society’s Hutton Junior Fisheries Biology Program, I was quite frankly unaware of the immense amount of life in Baltimore’s Inner Harbor.

I was introduced to the clam worm, the first of many organisms I would have the chance to experience this summer, when I began working with two fellow interns, Chima, a rising senior at Coppin State University, and Langston, a rising senior at Stevenson University, on DNA extraction, sampling, and barcoding of clam worms in the Inner Harbor. Our goal was to learn more about the genetic diversity within the species. Though before we could get to the sampling and barcoding, which I explain further in this article, we had to go out to the harbor to collect a few clam worms.

The Lunar Cycle and Clam Worm Reproduction

Synchronized spawning is what the new moon means for the clam worm. On nights like tonight, though the moon is not visible, one is able to see sexually mature clam worms swimming to the surface and reproducing in mass.

Though the new moon is also the mark to an unfortunate end for many clam worms; similar to salmon, octopus and squid, many clam worms die after mating, on nights like tonight, there is an undebatable, non-hypothetical “fresh start” in the life cycle of the clam worm. And though nobody completely understands why the clam worm mates according to the phases of the moon, our Inner Harbor’s connection to the lunar cycle was quite fascinating to explore. Which is why we’ve placed a net underneath of the biohut

The more I learned about the genetic biodiversity of the clam worm, the more I was able to appreciate the Inner Harbor as a natural habitat to lots of really cool species I had no clue were there. So maybe Aristotle was right in a sense -- the lunar cycle does impact more than the tides. The new moon is symbolic of new beginnings for many species, including the birth of one who calls the Inner Harbor its home, the clam worm.


Will the harbor’s whip mudworm population be wiped-out by 2020?

 July 20, 2018

Beneath the waters of Baltimore’s Inner Harbor lives yet another worm species. One that is found globally but with origins that are unknown. This is the whip mudworm, known scientifically as the Polydora cornuta, and unlike the clam worm, the whip mudworm is microscopic.

Whip mudworms are typically found close together in loose communities. Their notable tentacles, which they use to transport food into their mouth, makes them relatively easy to spot when looking through a microscope. Whip mudworms are more often than not hiding under burrows, which is why it can take so long to get a whole mudworm, and not just the tentacles, off of a biodisk.

And, trust me, I know worms in general do not seem like the most compelling creatures, but past the surface, the presence of the whip mudworm is actually very interesting in the sense that its presence says a lot about the ecology of the Inner Harbor. In particular, one important fact regarding the mudworm is that it is widely regarded as an ‘indicator species’. This term refers to animals that are able to serve as an indicator of water pollution.

The population of whip mudworms is particularly high in the Inner Harbor as they are able to rapidly increase and thrive in estuaries that are eutrophic and/or receiving toxic substances. Due to its ability to reproduce at high rates in polluted estuaries where most other marine polychaetes are unable to survive, the whip mudworm tends to become the dominant species in many marine estuaries at various parts of the year. For example, after counting the animals on biofilm disks with the National Aquarium, it was found that the whip mudworm is most abundant during the summer months which is probably due to the fact that the Inner Harbor is most eutrophic during this time.

The Waterfront Partnership has a goal of making the Inner Harbor both fishable and swimmable by the year 2020. This clearly conflicts with this pollution indicator species. What the fate of the whip mudworm will be as we continue to restore the ecosystem services in the Baltimore Inner Harbor, is unknown. All we can do is continue to study the population dynamics of this marine polychaete as well as many others that are able to survive the pollutants and eutrophic conditions of the Inner Harbor and see if they will in fact exist in a harbor that is cleaner and healthier in, hopefully, the near future.

Restoring ecosystem services

We often hear the phrase “Save the Ocean” or, for those of us who reside in close proximity to the Chesapeake: “Save Our Bay”. One facet of the biodiversity project I am spending my summer on is working to develop innovative ways to save our bay, or, in other words, to restore ecosystem services. We have done so by placing “biohut habitats” and aerated floating islands in the harbor. These attract a great deal of biodiversity and ultimately serve as a means to filter and clean the water.

In an effort to not only change people’s perception of the Inner Harbor, this project also seeks to actually change the ecosystem of the harbor in order to make it more liveable.

Striped bass in the Inner Harbor

July 19

Aside from the blue crab, there is another Maryland marine staple that lives in the Baltimore Harbor: our state fish, the striped bass (Morone saxatilis). I first learned of the presence of striped sea bass in Baltimore’s Inner Harbor when I was sitting in the National Aquarium’s Animal Care and Rescue Center and heard Jack Cover from the National Aquarium say he witnessed someone fish a pretty big striped bass from the diagonal bridge between Pier 3 and Pier 4 at the Inner Harbor.

Earlier in the summer, Dr. David Secor gave a presentation to myself and the Institute of Marine and Environmental Technology (IMET) undergraduate interns that Dr. Rosemary Jagus hosts each summer. Dr. Secor informed us that a moratorium was placed on the striped sea bass in 1979 in an Emergency Striped Bass Act passed by Congress due to the mortality of striped bass reaching 80-99.9% in the 1970s. According to the U.S. Fish and Wildlife Service, the increased mortality rate was an effect of overfishing, which also made the population more susceptible to natural stresses, like pollution and fluctuation of water temperature. Knowing this about the striped bass population, it was difficult to wrap my head around the Inner Harbor being an ideal estuary for striped bass. I was proven wrong today.

Today was the first time I was able to see Atlantic striped sea bass in the Inner Harbor myself. Today was also the first day of the aeration study being conducted by UMCES scientists Dr. Schott and Dr. Bachvaroff, in conjunction with the National Aquarium, in the Inner Harbor to see if aeration pumps were having their intended impact on the water quality. The aeration pumps were installed in the harbor by the National Aquarium in order to not only add oxygen, but to remove dissolved gases (such as carbon dioxide) and oxidize dissolved metals such as iron, hydrogen sulfide, and volatile organic chemicals (VOCs), the chemicals responsible for smog in urban areas. The aeration study consisted of a team of about 15 people reaching various transect points in the Harbor either by foot, or by a boat kept on the transect using a rope extending between the Pier 3 and Pier 4.

Map of aeration transects for striped bass

At each of these points, dissolved oxygen, temperature, salinity, and chlorophyll are measured and recorded. The aeration was kept at 80% capacity today and will be cut off during our later dates for the study.

After a 3 ½ hour day assisting with the aeration study, the results showed that there was not a significant difference in the water quality indicators in the aerated zones. This was probably due to the fact that there was a low dissolved oxygen (DO) event in the harbor yesterday. This also explains why the striped sea bass, among other harbor animals, were seen swimming at the top layer of the water in an attempt to get oxygen that the bottom portion of the water lacked. Their gravitation toward the floating island, to me, seemed like an indication of some influence the aeration has on the harbor.

Though there are Maryland Department of Natural Resrouces Eyes on the Bay stations in the Baltimore Harbor, constantly monitoring the water quality at the biodiversity project study sites, spending 3 ½ hours recording water quality data during a low DO event really helped me understand the impact of outside factors connected to urbanization, hardened shorelines, and weather have on the water quality.

I also learned about the effectiveness of the aeration and floating island in attracting biodiversity, to the physical structure, currents, and low levels of chemicals in the water as a result of their presence. And, moreover, I saw the potential of floating island structures as a means to effectively restore ecosystem services and the populations of marine animals like the striped bass.

Check out a video by Blue Water Baltimore’s Healthy Harbor Initiative and Maryland Sea Grant with footage of several fish species, including the striped bass, in Baltimore’s Inner Harbor:

Crabby thoughts on our iconic crustacean

Few places are associated with a marine species the way Maryland is with the blue crab.

As a Marylander, I do not think I would be doing my home state any justice if I neglected to chronicle my experiences with the blue crab while studying the biodiversity of the Baltimore Harbor. That’s right. Blue crabs live in the Inner Harbor. They swim there. They hide there. And yes, they do sometimes die there.

Callinectes sapidus. Blue crab. Those red claws signifying a female crab being pulled out of the water adjacent to my grandfather’s house in Annapolis, my first encounter with the Maryland staple. It was was not my first encounter with the waters of Annapolis, and in the mind of the then single-digit aged Alexandra, the familiar blue waters near my grandfather’s house were exactly what my first-grade reading teacher was referring to when we discussed the Chesapeake Bay. Single-digit aged Alexandra had yet to make the connection between the Chesapeake Bay, Annapolis, and what I saw at Baltimore’s Inner Harbor. Though I would eventually make this connection a few months later, my recent witnessing of a blue crab in the Baltimore Harbor during my second week at IMET really solidified my understanding of the Inner Harbor as a place that is not .

I’m going to be completely transparent, though. While I was in fact connecting the dots between the Harbor’s relationship with the Chesapeake, the overwhelming emotion I felt in that moment was shock. Though I will confess that, at the time, I was not the most well-versed in my understanding of the staple crustacean, I by no means would have thought that a blue crab would find the Inner Harbor suitable habitat. Under the impression that this was a rare sight, as I had never seen a blue crab in the harbor before, I was looking forward to getting home and telling my parents about what I had seen.

I by no means would have thought that a blue crab would find the Inner Harbor suitable habitat. I was under the impression that this was a rare sight, as I had never seen a blue crab in the harbor before on all my previous visits there.

I was looking forward to getting home and telling my parents about what I had seen.

They did not react how I expected. To me, spotting the crab was exciting. To them, it was quite the anticlimactic anecdote. They informed me that they saw blue crabs in the harbor “all the time” growing up in the ‘70s.

Blue Crabs in the Chesapeake Bay

I then made it a goal to become a bit more well-versed in my understanding of the blue crab. In this pursuit, I learned a bit about the life cycle of the blue crab, which also explained my confusion and shock directed toward the blue crab in the Inner Harbor.

I learned that it is now mating season for the blue crab as blue crabs mate between May and October in estuaries in the mid-Chesapeake area.

Once the crabs mate, the two part ways as the female crab makes her way to the lower Chesapeake Bay and the male goes on a search for another female crab to mate with.

During her time in the lower Chesapeake, the female blue crab will develop an almost fluorescent orange colored external egg mass beneath her abdomen with anywhere between 750,000 and eight million eggs depending on her size. The crab larvae, called zoea, are then released near the Atlantic Ocean.

After being pushed into the waters of the Atlantic Ocean by currents, the zoea, now more developed after having gone through several molts in the Atlantic, return to the Bay and other estuaries. During their last larval molt, zoea metamorphose into megalops, which is the stage right before they begin to look like the tiny adult crabs that I was so taken aback by during my second week interning at IMET.

I’ve grown to understand that our relatively high regard of the blue crab and low regard of the Baltimore Inner Harbor can be cause for some confusion, disbelief, and maybe even internal conflict when one makes the connection between the Baltimore Inner Harbor and the blue crab.

For me, understanding the pattern of the blue crab also meant making the connection between the Inner Harbor in my hometown of Baltimore, the familiar waters of Annapolis I experienced in my youth at my grandfather’s house, the Chesapeake Bay we learn about in school, and the Atlantic Ocean that connects us here in Baltimore to every coastal region in the east coast of North America, the Western border of the continent of Africa, Western Europe, and the rest of the globe.

It hardly seems fair to our iconic crustacean to write it off in this way, to think, because of our perception of the harbor as a trash and debris-ridden entity, that there is no way our beloved creatures could live here. In fact, they can, but imagine how many more crabs we would see if we as a city made an effort to make this connection and keep our water cleaner.

Alexandra Grayson is a 2018 Hutton Scholar summer intern working under the mentorship of Dr. Eric Schott at the University of Maryland Center for Environmental Science’s Institute of Marine and Environmental Technology. The American Fisheries Society sponsors the Hutton Junior Fisheries Biology Program to increase diversity in fisheries science. She is learning about the harbor’s diversity through conducting DNA extraction, sampling, and barcoding of different marine animals and learning about ways to effectively communicating the scientific work done in Dr. Schott’s lab.