One Fish, Two Fish…

Ana Silverio, The University of Texas at Austin

The Approach: In my previous post, I explained how important small fishes are to the food web and how their new found interaction with Gracilaria vermiculophylla came about. Now, measuring something such as diversity and abundance may sound confusing but it’s as simple as one, two, three!

Abundance is the number of individuals per species in an ecosystem and relative abundance is the overall evenness of those individuals. Diversity is more of a measurement of variation or how many different species are counted in a designated area/habitat.

Fine mesh seine net being dragged over the 15-meter transect to capture our fish.
Photo Credit: Norma Salcedo

Now that we understand what we are measuring… what’s next? As mentioned before, the Charleston harbor has been introduced with an invasive species of seaweed, but it has served as a home for the juvenile fish. To measure diversity and abundance we have to take samples from two different sites affected by this invasive species. Luckily, it’s a short stroll over to Grice Beach behind our marine lab to find a section of Gracilaria with 20% coverage for our sparse site and one with 80% coverage for our dense site. After establishing our sample sites, we take a 15-meter transect which we will pull our fine-mesh seine net through at about knee-deep water. We quickly but gently pull the net up to the beach and start sorting through our samples placing the fish in a half-gallon jar while discarding any invertebrates. We repeat this at our second site and voilà we have our samples!

Initial sorting process for our samples
Photo Credit: Norma Salcedo

Are we done yet? Of course not! Once we collect both of our samples from the different patches of Gracilaria, we take them back to the lab to set in preservatives for about a week and begin the sorting process. While we sort each jar, we try to identify each fish down to the lowest classification if possible (in a perfect world we would have all of our critters down to species). After identification is complete, we start our measurements of diversity and abundance by counting our fish. When we are finished counting, we organize our data and use statistical analyses to see if there is a significant difference in diversity and abundance in our two sample sites. We have followed procedures from the past two summers and each time we have sampled this summer to make sure we can compare our data at the end.

And now for the big reveal… Drumroll please! Will we find a difference in diversity? In abundance? In neither or both? Will we finally win a battle against the dreadful pluff mud? Although the last part seems unfortunately unlikely, join me next time to finally find out what secrets Gracilaria has tangled up in the Charleston Harbor!

Special thanks to my mentor, Dr. Harold for his support and guidance throughout this project. Also, to Dr. Podolsky and Grice Marine Lab for giving me the opportunity to conduct this research. This project is supported by the Fort Johnson REU program, NSF DBI-1757899.

Counting Corals

Jordan Penn, Millersville University

The Approach: In my last post, I discussed that the consequences of habitat-degrading practices (e.g., bottom trawling, dumping of waste, drilling) include the loss of species such as gorgonian corals, which provide structural habitat for other species.

My research seeks to understand the relationship between soft corals and their geological substrate. In other words, our lab want to understand whether or not soft corals are more likely to be present on rocky or sandy sea floors. We are also looking for relationships between the abundance of soft corals at different depths. We are investigating these relationships in order to gain some understanding of where soft corals are most likely to be found. 

Example of a transect with three segments. Image credit: Science X.

In order to assess these potential relationships, first we need to divide the video footage of dives from the ROV (remotely-operated vehicle) Beagle into 15-minute transects containing 3 5-minute segments. We take this step in order to determine the density (number of individuals per square meter of area) of corals at each site as accurately as possible.

Next, I will analyze the video footage, counting each Leptogorgia, Acanthogorgia, Eugorgia, Adelogorgia, and sea pen (these are good model organisms because they are conspicuous in our study site). Along with the number of corals, I will denote the type of substrate that was dominant throughout the 5-minute segment (e.g., rocky bottom, sandy bottom, mixed/coarse bottom).

Finally, I will be able to run statistical analyses on these data to determine average density, the average deviation from the determined average density, and potential drivers of diversity at each site (e.g., does depth/bottom type/something else affect how many corals are present in an area?).

Thank you to the members of the Etnoyer Lab for their guidance and assistance as well as the Grice Lab and College of Charleston for funding this project. This project is supported by the Fort Johnson REU Program, NSF DBI-1757899.


NOAA. (2012, April 17). NOAA releases new views of Earth’s ocean floor. Retrieved June 17, 2019, from NOAA

This Is How We Do It ♫

Julianna Duran, Virginia Tech


First and foremost, if you didn’t get the reference in the title please click here!

Now that I have educated you on the topic of music, let’s switch to science.

 The Approach: In my previous post I mentioned that I am studying the lipids of Nile Crocodile and Mozambique Tilapia. So the first thing I did is wrestle the reptile like Steve Irwin and hand catch my fish – just kidding, but imagine how cool that would be! My samples were collected from Lake Loskop, South Africa in 2014. Once they were in my possession, here is what I did.

  1. Sample Preparation
    • The muscle tissue samples I received looked like chicken breasts you buy from the grocery store – except the size of a fat bean. These solid chunks need to be turned into a fine powder for me to analyze them. This was done by freezing the sample in the cryomill machine – where the samples were shaken extremely fast and broken up



  2. Extraction
    • Think of what happens when you pour oil in water. They go to different ends and don’t mix, right? (Yes) That is exactly what I’m doing with my samples. We are adding lots of chemicals to break down fats into their building blocks: Fatty Acids! The muscle layer (organic layer) hates touching the chemicals, so I take that out and can use it for my next step!
    • Check out a video I made of one of my extractions
  3. Gas Chromatography
    • This instrument is how I will measure the amount of each fatty acid in my samples.
    • How does it work?
      • The sample is injected into the system and enters a narrow glass column. The sample separates in this column based on its weight and boiling point. The particle encounters a flame at the end of the glass, which detects what specific fatty acid it is. The computer then gets this signal and generates a graph showing a fatty acid profile. Each peak on the graph is a different fatty acid, and the height of the peak indicates how much of it there is in the sample.
      • For help envisioning this process, take a look at this video (I used it when I learned about this instrument!)




I will be physically and chemically breaking down my samples, then getting fatty acid profiles for each of my individual species. This is all to see if there is a difference between healthy and diseased species and what lipids are most affected by Pansteatitis!

Supported by the Fort Johnson REU Program (NSF DBI-1757899), Dr. Mike Napolitano, Dr. John Bowden, The College of Charleston, NOAA, and NIST. 


CryoMill. (accessed Jun 18, 2019).

Pinniped Problems: Domoic Acid Diatom Denotes Death

Jackson Eberwein, Sonoma State University

The Problem: Imagine a new disease spreading through your community, and it is deadly. It injures the kidneys, affects heart muscles, and causes parts of the brain to wither away. Scientists and doctors know that it is caused by a toxin made by a microscopic organism that loves to suddenly appear with force in unpredictable restaurants across the country. Despite this knowledge, doctors have no good way of knowing that a person has the disease until it is too late.
This is the reality for California sea lions. Along the west coast, large blooms of algae have been producing a toxin called domoic acid, and sea lions have been getting stomachs full of it through their diet of alga-eating fish. According to California Marine Mammal Stranding Network records from 1998 to 2006, around one out of every four California sea lion beach strandings or deaths along most of the California coast were due to exposure to the biotoxin. Since 2006, blooms of the algae have increased, with stranding numbers rising along with them.

California Sea Lion (Zalophus californianus) spooked about eating bad fish.
Photograph by Pixiabay

No good blood test exists for Domoic Acid Toxicosis, as the biotoxin that causes it rapidly clears from the body of sea lions. This means veterinarians can’t see if a sea lion has it unless they use outdated or expensive tests, or guess based on how an animal acts. Since veterinarians don’t have a good way to measure how bad the disease is, they don’t really know for sure if what they do helps a sick sea lion. If they wait to use the behavior of the animal to judge, then it is already too late because the disease has done permanent damage.
So how do we get a viable blood test? Can something be measured in blood when it is simply not there? In this case, we think it can, though not directly. While the domoic acid is in the body, it will be doing what toxins do best: messing with a lot of things that should not be messed with. This will cause changes in the body, such as more or less of a protein being made than it usually is. An unusual change in production of a protein could be measured instead of the toxin that caused that change. In this situation, the protein is called a “biomarker”, or a proxy for measuring the real target. By finding a biomarker protein in sea lion blood, it will actually be possible to make a cheap and effective blood test for the impacts of domoic acid!


I would like to thank Dr. Michael Janech, Dr. Benjamin Neely, Alison Bland, The Marine Mammal Center, & College of Charleston. Supported in part by the Fort Johnson REU Program, NSF DBI-1757899.

Neely BA, Ferrante JA, Chaves JM, Soper JL, Almeida JS, Arthur JM, et al. (2015) Proteomic Analysis of Plasma from California Sea Lions (Zalophus californianus) Reveals Apolipoprotein E as a Candidate Biomarker of Chronic Domoic Acid Toxicosis. PLoScONE 10(4): e0123295. doi:10.1371/ journal.pone.0123295

Bejarano, A.C., Gulland, F.M., Goldstein, T., Leger, J.S., Hunter, M.S., Schwacke, L.H., VanDolah, F.M., & Rowles, T.K. (2008). Demographics and Spatio-Temporal Signature of the Biotoxin Domoic Acid in California Sea Lion ( Zalophus californianus ) Stranding Records.

Laake JL, Lowry MS, DeLong RL, Melin SR, Carretta JV (2018) Populationgrowth and status of California sea lions.J Wildl Manage82: 583–595 .

Invisible Neighbors: How Gracilaria Changes Bacterial Communities

Lilia Garcia, Illinois Wesleyan University

The Problem: It only takes a walk along the mudflats to notice large patches of wiry, red seaweed. The seaweed is called Gracilaria vermiculophylla, an invasive organisms that is native to East Asia (SERC, 2019)  The seaweed is hard to miss, but its effects on the ecosystem are not easily seen. This summer I will be studying how Gracilaria affects a bacterial community invisible to the naked eye.

Mudflat with Gracilaria, taken by L. Garcia

According to previous studies, Gracilaria is found to increase the amount of a bacteria called Vibrio (Gonzalez, et al., 2014). This may not mean much at first, since most of us don’t think about microscopic interactions. Bacteria, however, are important in maintaining the health of complex environments like estuaries. They cycle and break down nutrients and organic matter, influencing oxygen, carbon, and nitrogen levels. An increase in one group of bacteria, such as Vibrio, can change these patterns. And like most of us know, bacteria tends to spread easily. There are a few strains, or types, of Vibrio, such as V. vulnificus, V. parahaemolyticus, and V. cholera, that are dangerous to human health. An increase in these strains may cause an increase in disease from swimming or eating infected food.†

Vibrio growing on petri dish, taken by L. Garcia

We known Vibrio levels increase with Gracilaria, but we do not know how this happens. We also don’t know if all Vibrio strains increase together, or if only a few strains grow. To understanding the relationship between Gracilaria and Vibrio, I will record how much total Vibrio and how many strains of Vibrio grow in and away from patches of Gracilaria. In order to preserve its own health, Gracilaria produces compounds that promote or stop organisms from growing around it (Assaw et al., 2018). These are compounds I will test against different strains to study the mechanism Gracilaria uses affect specific Vibrio levels. I want to see how the growth of each strain is affected by different extracts. Will the strains further away from the Gracilaria be unable to grow when exposed to a certain type of extract? Will other strains grow better with the extract?

We tend to think about invasive species on a large scale, assessing the damage it causes to other familiar animals and plants. The ecosystem relies on tiny, cellular organism and studying how bacteria changes leads to a deeper understanding of environmental health. An invisible community is changing as Gracilaria flourishes, and there is a lot left to learn about it. 


Thank you to my mentor Dr. Erik Sotka, and our collaborator Dr. Erin Lipp. I would also like to thank Dr. Alan Strand and Kristy Hill-Spanik for their supporting guidance. Lastly, thank you to Dr. Loralyn Cozy (IWU) for preparing me to succeed in the lab. All research is funded by Grice Marine Lab and College of Charleston through the Fort Johnson REU Program, NSF DBI-1757899


Assaw S, Rosli N, Adilah N, Azmi M, Mazlan N, Ismail N. 2018. Antioxidant and Antibacterial Activities of Polysaccharides and Methanolic Crude Extracts of Local Edible Red Seaweed Gracilaria sp. Malays Appl Biol. 47(4): 135-144. 

Fofonoff PW, Ruiz GM, Steves B, Simkanin C, & Carlton JT. 2019. National Exotic Marine and Estuarine Species Information System. 

Gonzalez D, Gonzalez R, Froelich B, Oliver J, Noble R, McGlathery K. 2014. Non-native macroalga may increase concentrations of Vibrio bacteria on intertidal mudflats. Mar Ecol Prog Ser. 505: 29-36.

Calling All Corals

Jordan Penn, Millersville University

The Problem: On average, light cannot penetrate ocean waters beyond a depth of 200m. This region of the world ocean is commonly named the “deep sea.” These depths are characterized by enormous pressure and frigid temperatures. However, the deep sea has become an area of increasing interest as we have come to learn about the unique habitat it provides as well as the abundance and diversity of species it supports. Researchers estimate that the deep sea may be home to as many as 100 million species, most of which are still unrecorded.

Adelogorgia phyllosclera, one of my five corals of interest. Image credit: NOAA Southwest Fisheries Science Center, Advanced Survey Technologies Group

Although corals are most commonly known to be found in shallow tropical waters, many exist in the deep sea. Because of the lack of photosynthesis in the deep sea, survival of the corals in the deep is dependent upon “marine snow,” the rain of phytoplankton and other organic material from the ocean’s surface to the sea floor. Dense clusters of corals are termed “coral gardens,” and these gardens provide refuge for many bottom-dwelling species.

Cold water corals are vulnerable to habitat destruction by human influence because their locations are generally undocumented. We’re working to identify and protect these slow-growing aggregations of coral and the communities that they support!

ROV Beagle, remotely-operated vehicle used to collect samples in the Channel Islands, CA. Image credit: MARE Group.

Offshore drilling, commercial bottom trawling (a form of fishing that severely degrades bottom habitats), and dumping of waste are the greatest threats to deep sea corals and the species that take advantage of the habitat that they provide. The deep sea has become a popular fishery and drilling prospect, so it has become increasingly important to protect these habitats so that any profitable resources there may be harvested sustainably. My project this summer focuses on sea pens as well as an order of cold water corals called gorgonians in the Channel Islands, CA. I will be analyzing video data from an ROV (remotely-operate vehicle) in order to record the locations and quantify the abundance of my study organisms. The results of this research should provide the scientific community and commercial managers with information on how to protect these vulnerable habitats.

Thank you to the members of the Etnoyer Lab for their guidance and assistance as well as the Grice Lab and College of Charleston for funding this project. This project is supported by the Fort Johnson REU Program, NSF DBI-1757899.


Marine Applied Research and Exploration. (n.d.). ROV Beagle. Retrieved June 17, 2019, from

NOAA Southwest Fisheries Science Center, Advanced Survey Technologies Group. (2015, June 10). Southern California Bight. Retrieved June 27, 2019, from

Gracilaria: New Intruder Weeding Through Charleston

Ana Silverio, The University of Texas at Austin

The Problem: Invasive species are animals that enter a new habitat away from their own home and are known for usually bringing about negative effects on natives in the area. Invasive species thrive in new environments when they can adapt to local conditions, and cause troubles in the way it works. With their usual predators not around, chaos can erupt, as they take away from some resources from the animals who call this habitat home (Albins et al 2015). Gracilaria vermiculophylla is a type of seaweed but also an invasive species from Asia and first seen on the Virginia coast. Although it is an invasive species, this seaweed seems to be singing a different song than usual (Nyberg et al 2009). Since it was first seen on the beaches of North America, it has taken a different role by providing a new habitat to local fishes. Gracilaria vermiculophylla is a dark brownish red seaweed with tangled strands that brush up against anything wading through the shallow water. Perfect for smaller fish to hide in. Although this seaweed seems to be bringing good things to the fishes not much is understood about what life was like for them under the waters of Charleston before our new stranger came about so we can’t comment on that part of the story. On the other hand, an interaction is indeed unfolding before our eyes and the story behind our new visitor is a bit fishier than one may think.

Example of a sample site: sparse patch of Gracilaria vermiculophylla on Grice Beach.
Photo taken by: Norma Salcedo

Gracilaria vermiculophylla is hard to miss on the shorelines of Charleston, it can be found in patches when the tide dwindles or on the seafloor. Its branches provide an ideal habitat along with a hiding space for juvenile fish during their vital first years of life and increases their numbers (Munari et al 2015). The preservation of these fishes during their early life stages is important to maintaining a healthy food web that keeps marine life afloat. Food is energy and energy is moved up to some of the biggest fisheries in this country from the very bottom of the smallest animals. It is important to know how the bigger fish’s food source is interacting with its habitat to make sure it’s healthy. Understanding how the interaction is working is a key factor in creating conservation plans and maintaining the ecosystem in good health.

Dense patch of Gracilaria vermiculophylla.
Photo taken by: Norma Salcedo

This summer, my research focus is on untangling Gracilaria vermiculophylla’s ecological relationships with these small fishes for a better understanding how diverse life is underwater. Replicating a design from the past two summers, I am curious to see the differences in diversity and abundances based on different patches of seaweed and if body size plays a significant role. Will more seaweed correlate with more diversity? The past two summers revealed some common patterns between fish diversity and patterns of seaweed patches but also some surprising differences between the two field seasons. Will we have a tie breaker this summer? Stay tuned to find out!

Special thanks to my mentor, Dr. Harold for his support and guidance throughout this project. Also, to Dr. Podolsky and Grice Marine Lab for giving me the opportunity to conduct this research. This project is supported by the Fort Johnson REU program, NSF DBI-1757899.


 Albins MA (2015) Invasive Pacific lionfish Pterois volitans reduce abundance and species richness of native Bahamian coral-reef fishes. Mar Ecol Prog Ser 522:231-243. 

Munari, C., N. Bocchi, and M. Mistri. “Epifauna associated to the introducedGracilaria vermiculophylla (Rhodophyta; Florideophyceae: Gracilariales) and comparison with the nativeUlva rigida(Chlorophyta; Ulvophyceae: Ulvales) in an Adriatic lagoon.” Italian Journal of Zoology 82.3 (2015): 436-445.

Nyberg, C. D., M. S. Thomsen, and I. Wallentinus. “Flora and fauna associated with the introduced red algaGracilaria vermiculophylla.” European Journal of Phycology 44.3 (2009): 395-403.