What’s living in the sand?

Jessie Lowry, Coker College


Visible microalgae seen on the surface of wet sand at Folly Beach.

Next time you go to the beach this summer, I want you to think about the sand that you are walking on. Did you know that there are tons of microscopic photosynthetic organisms, aka microalgae, that live on the surface of sand? Before this summer, I didn’t know about these organisms either. Here is a picture of visible microalgae on the surface of the sand. Look for this next time you’re at the beach!

Microalgae communities in sand are made up of single-celled eukaryotic algae and cyanobacteria living in the top several millimeters of the sand (Miller et al., 1996). These organisms play important roles in ecosystem productivity and food chain dynamics, as well as in sediment properties, such as erodibility (Miller et al., 1996).


Dr. Craig Plante and Jessie Lowry collect samples of sediment from Folly Beach. Photo credit: Kristy Hill-Spanik.

I am studying these microalgal communities and what factors influence community structure. For example, does pH, salinity, nutrients, or grain size shape microalgal community structure? Or does geographic distance shape communities? To answer these questions, I am collecting samples from Kiawah Island, Folly Beach, Isle of Palms, and Pawley’s Island, SC. We are measuring environmental variables at each location, and using molecular tools to study microalgal community structure.

I am extracting the DNA from samples collected, amplifying specific regions from these samples using polymerase chain reaction (PCR), and then we will be getting these regions sequenced using Ion Torrent technology. We will then use QIIME to determine how similar these benthic microalgal communities are.


Jessie Lowry preparing samples for PCR, or polymerase chain reaction, which is used to make millions of copies of a piece of DNA.

Diatoms, a group of microalgae, have been proposed as bioindicators of environmental health (Desrosiers et al., 2013). Bioindicators are really cool because instead of telling a snapshot of an environmental condition, such as pH, temperature, or amount of oxygen in an environment, biological indicators reflect those changes and can give an idea of how the ecosystem is being affected. This research will further our knowledge of what factors shape benthic microalgal communities, and give a better understanding of these organisms as a potential bioindicator. In addition, this research will add to knowledge about the distribution of microorganisms, which is also not fully understood.

Learn more:




Desrosiers, C., Leflaive, J., Eulin, A., Ten-Hage, L. (2013). Bioindicators in marine waters: benthic diatoms as a tool to assess water quality from eutrophic to oligotrophic coastal ecosystems. Ecological Indicators, 32, 25-34.

Miller, D.C., Geider, R.J., MacIntyre, H.L. Microphytobethos: The ecological role of the “Secret Garden” of unvegetated, shallow-water marine habitats. Estuaries, 19(2A): 186-212.


Thank you so much to my mentors Dr. Craig Plante, and Kristy Hill-Spanik. This research is funded through the National Science Foundation and College of Charleston’s Grice Marine Lab.


Can extracellular enzymes functionalize electrodes?

Yoel Cortes-Pena, Georgia Institute of Technology

A microbial electrosynthesis cell (MEC) takes in electrical energy and converts it to chemical energy as fuels, but what supports that initial step of taking the electrons off the cathode so that they become available to the microbes? Are small redox molecules acting as intermediates between the electrode and the microbes? Or is there a more direct way?


Photo of anaerobic cultures grown in a pressurized mixture of hydrogen and carbon dioxide. The tube on the far left is a sterile control of inoculated media that has no hydrogen inside. The other three tubes are biological triplicates.

Previous studies have shown that hydrogenases, enzymes that catalyze the conversion between hydrogen cations to hydrogen gas, are able to attach themselves to an electrode and remain active (1). Additionally, a study by Deutzmann el. al. showed that extracellular hydrogenases support the production of hydrogen on a cathode in an MEC that utilizes methanogenic bacteria (2). Therefore, It is possible that active hydrogenases are able to attach themselves onto an electrode, uptake the electrons directly off the cathode, and produce hydrogen which will later be consumed by the microbes!

Over this summer internship, I took the first step to test this hypothesis by asking the question “Are active hydrogenases released from the microbes?”. Active extracellular hydrogenases in the reactor suspension would support the hypothesis that hydrogenases are also active when attached to the cathode.

Hydrogenase_assayPhoto of hydrogenase activity as measured spectroscopically by methyl viologen. Oxidized methyl viologen is clear and reduced methyl viologen is blue. The test involves inserting the sample that may contain hydrogenases into a reaction mixture with oxidized methyl viologen and pressurized hydrogen. Hydrogenases would proceed to oxidize hydrogen gas and reduce methyl viologen, turning the mixture blue

The main experiment I am working on involves testing hydrogenase activity in anaerobic cultures that originated from the reactor suspension. These cultures are grown in a pressurized 80:20 mixture of hydrogen and carbon dioxide, which mimics the reactor environment.

By the end of the summer I hope to have hydrogenase activity data of spent cell-free culture medium that will answer our question  “Are active hydrogenases released from the microbes?”


(1) Baffert C, Sybirna K, Ezanno P, Lautier T, Hajj V, Meynial-Salles I, Soucaille P, Bottin H, Léger C(2012). Covalent attachment of FeFe hydrogenases to carbon electrodes for direct electron transfer. Anal Chem 84(18):7999-8005. doi: 10.1021/ac301812s.

(2) Deutzmann JS, Sahin M, Spormann AM. (2015) Extracellular enzymes facilitate electron uptake in biocorrosion and bioelectrosynthesis. mBio 6(2):e00496-15. doi:10.1128/mBio.00496-15.

Hook, Line and Sinker

Sierra Duca, Goucher College

Spotted seatrout, Cynoscion nebulosus, are important recreational fish that range from the Atlantic coast to the Gulf of Mexico. They are also good indicators of environmental changes in estuarine habitats since all of their life stages are found in estuaries1. To reiterate, I am studying muscle softness in spotted seatrout induced by the parasite Kudoa inornata. Several Kudoa species are notorious for causing this muscle softening, which makes the meat of the fish go bad faster than in uninfected fish2. This is an issue with fish that are consumed by people, such as the commercially important farmed Atlantic salmon2. seatrout for blogg

Fig 1. Spotted seatrout that were caught via trammel netting (PC: Sierra Duca).

First of all, to study this I need fish. While the mode of infection of Kudoa parasites is not well understood, it is presumed that wild spotted seatrout have a higher rate of infection of Kudoa inornata; therefore, I needed some wild spotted seatrout. In addition to the traditional hook and line approach of fishing for spotted seatrout, I was able to join a group at the South Carolina Department of Natural Resources (SCDNR) as they went trammel netting. In comparison to other nets, trammel nets have three layers of netting that vary in size in order to catch fish of various sizes. trammel net for blog

Fig 2. This illustration depicts the basic function and structure of a trammel net. A similar such device is used by the SCDNR to catalogue fish in specific sites over time in order to study the changing population dynamics of various fish species.

Once I have the fish I fillet, refrigerate, and take muscle biopsies at time points between 0-6 days, which is the most likely time that the fish would be consumed. I test the firmness of these muscle biopsies, as well as the parasite density. What I am trying to accomplish is to establish whether or not there is a link between parasite density and accelerated muscle softness (which causes the meat to go bad faster in infected fish), and if the rate of muscle softening changes over the course of 6 days. Ultimately the project will help increase our understanding of the effects of Kudoa inornata on the muscle of spotted seatrout. plasmodia for blog

Fig 3. This image (under 100x magnification) displays a plasmodium structure that contains a cluster of spores (known as myxospores) of Kudoa inornata in the muscle tissue of spotted seatrout. One way that I quantify parasite density is by looking at the average area of plasmodia. I can do this because generally larger plasmodia are found in the more infected fish  (PC: Sierra Duca).

Literature Cited 1Bortone SA (ed) 2003: Biology of the Spotted Seatrout. CRC Press. Boca Raton, FL, 328 pp 2Henning SS, Hoffman LC, Manley M (2013) A review of Kudoa-induced myoliquefaction of marine fish species in South Africa and other countries. S Afr J Sci. 109: 1-5

Photo Source (Fig 2): http://thewikibible.pbworks.com/w/page/22174694/Fishing%20in%20the %2Bible%20and%20the%20Ancient%20Near%20East

Acknowledgments The Fort Johnson REU Program is funded by the National Science Foundation. This research is made possible through the mentorship of Dr. Eric McElroy and Dr. Isaure de Buron.  In addition, I would like to thank the College of Charleston and the South Carolina Department of Natural Resources for providing the help and facilities necessary for my project.

Our complicated relationship with chemicals

Nina Sarmiento, Binghamton University

Chemicals found all around us that have been altered, mimicked, and synthesized to be added to our products, are behind the success of our modern society. They have made our plastics strong, our crops prosperous, and our medicines effective. But I have always wondered about the toxicity of these chemicals.  When you look at their biological activity, a chemical might possess the potential to do harm, like interfere with biological processes. The safety of a potentially harmful chemical is based on exposure and dose. It is important to know if we are touching it, eating it, or breathing it in, and for what period of time. The study of evaluating the harmful effects of substances on exposed organisms is what toxicology is all about. They have such an important job because their findings influence what we know is safe and unsafe, for us and organisms all around us.

I learned early on from pursuing biology that we are exposed to many things we are unaware of. Not only are we exposed to potentially harmful chemicals, but we facilitate exposure to other living organisms that may more sensitive. Take dogs for simple example. The toxic dose of something like chocolate for humans is very high, whereas leaving a small amount of chocolate out for a dog to eat could easily kill it.  Rachel Carson is someone I greatly admire, whose work on the pesticide DDT also exemplifies this reality. Food crops were the target for DDT, but birds were indirectly ingesting it, explaining the decline in the Bald Eagle population.  She is one of the people that sparked my interest in ecotoxicology, looking at the effects of harmful substances on ecology, not just humans.

unnamedThis is an example of some of the questions ecotoxicologists ask when there is a potentially harmful substance found in the environment. Photo credit: globe.setac.org.

Here is a chemical product you may not suspect as a threat, sunscreen. In sunscreens, UV filters protect you from getting burned, but also can act as endocrine disruptors, altering hormones and growth (1). Sunscreens are only meant for human skin, however they end up in our lakes, rivers and oceans through swimming or through waste water treatment effluent (2). Unintentionally, many more organisms become exposed.


Photo credit: thesleuthjournal.com

In my project I will be using sea urchins as a model organism to study the effects sunscreens might be having on coral reefs.  I am learning how to preform toxicity tests on sea urchin sperm and embryos which involve an exposure period with sunscreen formulations and then evaluation of effects. I hope to investigate if the chemicals from sunscreens in the water can have negative impacts on coral reproduction.  My work can potentially help create understanding of how humans are contributing to coral reef decline, and influence others to take action to protect them.


This is a picture of sunscreen water accomodated fractions (WAFs) I am making. They are a mix of sunscreen and seawater and I will be exposing the sea urchin embryos to each solution!


This is me in the lab with a microscope I use to look at sea urchin sperm and embryos! Photo by Bob Podolsky

My research is funded by the National Science Foundation and College of Charleston partnered with National Oceanic and Atmospheric Administration


Works cited:

1 Krause M.,, Klit A., Jensen M., Soeborg T., Fredrickson H., Schlumpf M., Litchensteiger W., Skakkebaek N E., Drzewieck K T. 2012. Sunscreens: are they beneficial for health? An overview of endocrine disrupting properties of UV-filters. International journal of andrology. 35 424-436.

2Kyungho C., Kim  S. 2014. Occurances, toxicities, and ecological risks of benzophenone-3, a common component of organic sunscreen products: a mini review. Environment International. 70 143-157.

Let’s talk plastic

Jimena B. Pérez-Viscasillas, University of Puerto Rico


In a recent article published by The Conversation, researcher Richard Sharpe discusses his work on male reproductive efficiency and how it might be affected by phthalates. Phthalates are plasticisers, compounds added to plastic materials to make them more flexible.  “Plasticisers leach out of the plastic over time” Sharpe writes. “This is why if you use the same plastic water bottle over a long period it will eventually become brittle and break – indicating that you have drunk all of the plasticisers that leached out.”

Fig. 1  Plastics aren’t the only products with phthalates. These compounds can also be found in fragrances, personal care products, etc. (Taken from University of Michigan Formative Children’s Environmental Health and Disease Prevention Center


What could this mean for our health? Many different studies have been conducted to find out how these compounds might be affecting our bodies. Sharpe specifically focuses on how they might affect the male reproductive system. He argues that, because the available data on the subject is so variable, it is not yet completely conclusive whether phthalates are indeed the cause of lower male fertility.

What we do know, however, is that phthalates have been found to disrupt the production of some hormones in the body. Because hormones are the body’s chemical messengers, not having them able to deliver their messages to tissues properly could mean trouble for one’s health. One such case is that of prostaglandins, the hormone I’m looking at in this summer’s research. Prostaglandins are hormones that regulate inflammatory responses in the body. When you prick your finger and see it swell up, part of what you’re observing is due to prostaglandins doing their job, allowing more blood and immune cells into your tissue. Prostaglandins play major roles in the immune and reproductive systems. Therefore, it is hypothesized that if a pregnant woman suffers from hormonal inhibition because of exposure to phthalates, this could have long-term health effects on her baby too.

Fig 2. Human embryo. (Image taken from BBC)

Sharpe asks this research question in his article as well. However, part of the reason why effects of contaminants on human health are so difficult to research is precisely because exposure to them is so common among human populations. As he points out, “this means we don’t really have an unexposed group (“control”) against which to compare.” Luckily, we humans aren’t the only organisms around. Studying other species (such as, say, gators and chickens…) allows us to better understand these possible hazards.  Finding evolutionary relationships between us and sentinel species is an essential step towards understanding just what these phthalates and many other contaminants are up to in our bodies.

To learn more about phthalates, click here. For more about my research, stay tuned. Later, gators!


This research is made possible thanks to the Hollings Marine Laboratory, the Medical University of South Carolina, the College of Charleston and funding by NSF through the Fort Johnson REU program.

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Kristensen, David M. (2011). Many Putative Endocrine Disruptors Inhibit Prostaglandin Synthesis.  ENVIRONMENTAL HEALTH PERSPECTIVES. Vol.119 No. 4: 534 – 541.

Milnes MR, Guillette LJ Jr. Alligator Tales: New Lessons about Environmental Contaminants from a Sentinel Species; BioScience 2008; Vol. 58 No.11 doi:10.1641/B581106

Sharpe, Richard. “Are plastics making men infertile?” The Conversation 25 Jun. 2015. Web 29 Jun. 2015.

I’m on a Boat

Bryce Penta, University of Notre Dame

When you think of scientists, you usually picture someone in a white lab coat holding a beaker full of chemicals. While that’s part of being a scientist, field work is our way of getting messy and calling it work. Going out into the field, we give up the comfort and stability of the lab and its carefully controlled conditions. Sometimes this work involves a real field, other times its an ocean.


For seven days, the lab and I cruised through the Atlantic Ocean collecting hundreds of samples. Over the course of the first five days we shifted from the greenish waters near the coast to the crystal clear waters of the deep ocean.

I spent most of the week running the samples through a flourometer to measure their photosynthetic efficiency. As we moved from station to station, I observed the shift in the productivity of the phytoplankton. Along with these stations, I measured the effect on photosynthetic efficiency by variations in nutrient levels of vitamin B12 and nitrate in a controlled experiment.

IMG_5989Fig 1. Setting up the experiment for nutrient limitation.

Though science was the main objective of the research cruise, I think that the trip provided a great way for the entire lab to bond, especially when Peter caught a 55 inch wahoo! Science isn’t all lab coats and fume hoods. Sometimes its a boat in the middle of the ocean.


This project is possible due to funding from the NSF College of Charleston Summer REU program and the Grice Marine Laboratory. Project ideation and collaboration with Dr. Peter Lee and the Di Tullio lab from the College of Charleston. Lab space and facilities provided by the Hollings Marine Laboratory.


What’s that pointy shrub thing?

Kaelyn Lemon, Macalester College/ Dr. Bob Podolsky at Grice Marine Lab

Arbacia punctulata is.. a shrub? Right? Arbacia sounds like some kind of plant, maybe.

Close. A. punctulata is short and round, like a shrub, but it lives in the ocean. And instead of branches sticking out from its center, it has spines. You may be more familiar with one of its nicknames: Purple-spined sea urchin, or Brown rock urchin (1). So A. punctulata is an animal, not a plant. Rather than a shrub, a better analogy would be the initial English meaning of sea urchin: sea hedgehog (2).

Purple-spined sea urchins, somewhat obviously, have purple spines. The second common name of A. punctulata, though, gives a clue that these urchins are not always purple. They can actually vary in color from a range of purple hues to brown or black and even red (1). While some urchins have both long and short spines, a unique feature of A. punctulata is having only long spines. The spines are the easiest body part of an urchin to identify- they are the sometimes incredibly sharp protrusions that are also the reason Taylor Swift has an irrational fear of sea urchins (see: https://www.youtube.com/watch?v=yPGrJCbaKB4). Spines can break off, but they can re-grow (2). However, sea urchins are not immobile pincushions waiting to stab things. Their spines can move around in joints where they connect to the test. The test is main shell-like skeleton of the urchin, the part in the center that can make urchins look like rocks rather than animals. For sand dollars, the closest relatives of sea urchins, the test is the white shell-like structure that you collect dried on the beach.

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The two most basic parts of a sea urchin, shown on A. punctulata. Photo credit: Aaron Baumgardner

Sea urchins have radial symmetry and are symmetrical in five parts. Their mouths are on the bottom, where they have five plate-like “teeth” that scrape against rocks or whatever they are on top of, even other urchins (2). Sea urchins release both their poop and their gametes (sperm or eggs) from the top of the test (though out of different locations!). Finally, while urchins pretty obviously have tons of spines, what you can’t see unless you look closely are the tons of tube feet. Tube feet look like extremely thin fleshy strings with little suctions cups at the ends. They come out of pores in the test and can extend beyond the length of the spines. They are controlled by increasing and decreasing the amount of water inside them, and are how sea urchins move (yes, they do move, sometimes surprisingly rapidly).

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Sea urchins can be broken into five parts that are symmetrical to each other. Photo credit: Aaron Baumgardner


This is a view looking from a bottom angle at A. punctulata. If you look where the urchin meets the side of the bin, you can see tiny tube feet, like little strings with suction cups at the ends, holding on to the wall. Three white spots near the top of the dark underside view are teeth plates that surround the mouth. Photo credit: Kaelyn  Lemon

There are male and female sea urchins, which release sperm and eggs, respectively, into the water where they hope to meet, fertilize, and create an embryo that will develop into a larva. Unlike humans, where usually one egg is released at a time (into the uterus rather than out of the body), urchin females will release millions of eggs at once (2). Sea urchin larvae are bilaterally symmetrical, just like dogs, fish, and people. Unlike adult urchins, which are less mobile and stick to the ground, urchin larvae are free swimming in the ocean water.

A. punctulata is found along the entire Atlantic coast of the US and west to Texas, as well as in the Caribbean around Cuba and Panama. These urchins are usually found in water that is less than 164 feet deep (1). A. punctulata is mainly an herbivore, eating mostly algae, though it can also eat animals such as sponges, corals, and sand dollars, as well as other urchins, even those of its own species.

Sea urchins, besides being incredibly beautiful feats of nature, are important to people in two main ways. Nearly every species of sea urchin is eaten by people- either the meat inside the test, or the urchin’s eggs (2). Second, urchins are incredibly important to science because they are used as a model organism to study reproduction and development.

A. punctulata specifically will be contributing greatly to my research by providing gametes that I fertilize and develop into larvae while being exposed to normal or high carbon dioxide levels. I greatly admire the incredible, and somewhat variable, body structure and coloration of these purple animals.


While this individual may look very different from the urchins in previous photos, it is actually still the same species. Photo credit: Aaron Baumgardner

Cited References:

1. Smithsonian Marine Station at Fort Pierce: http://www.sms.si.edu/irlspec/Arbaci_punctu.htm

2. Animal Diversity Web: http://animaldiversity.org/accounts/Arbacia_punctulata/

Funding and support for my research is provided by the National Science Foundation and the College of Charleston

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