Summer on the Harbor

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.

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.

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.

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.

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.

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.