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.


References

NOAA. (2012, April 17). NOAA releases new views of Earth’s ocean floor. Retrieved June 17, 2019, from https://phys.org/news/2012-04-noaa-views-earth-ocean-floor.html NOAA

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This Is How We Do It ♫

Julianna Duran, Virginia Tech

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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

      Cryomill

      Cryomill

  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!)

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        Chromatogram

Summary:

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. 


References:

CryoMill. https://www.retsch.com/products/milling/ball-mills/mixer-mill-cryomill/function-features/ (accessed Jun 18, 2019).

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.


References:

Marine Applied Research and Exploration. (n.d.). ROV Beagle. Retrieved June 17, 2019, from https://www.maregroup.org/rov-beagle.html

NOAA Southwest Fisheries Science Center, Advanced Survey Technologies Group. (2015, June 10). Southern California Bight. Retrieved June 27, 2019, from https://deepseacoraldata.noaa.gov/gallery/southern-california-bight

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.


References

 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.

Crikey! What’s in the Water?

Julianna Duran, Virginia Tech

1B7047D7-DD01-4D65-B081-9D809AC07271The Problem: South Africa is home to some of the most extraordinary wildlife and culture. This diverse ecotourism plays a major role in their economy and conservation efforts.

Crocodile

Nile Crocodile (Photo credit: Darren Poke)

The Olifants River System in the Mpumalanga Province is a large source of water that provides a habitat for several species. Over the last 30 years in this region, there have been dramatic declines of Nile Crocodile (Crocodylus niloticus), fish, and waterfowl.

The cause of this is a disease called Pansteatitis. It is hypothesized that contaminants from coal mining and agriculture contributed to the emergence of the disease. Invasive species and the stagnant water may also be enhancing the intensity of its effects.

Pansteatitis is an inflammatory disease that affects the lipids, or fats, of an animal. The fats become tough which cause pain and a reduction in mobility that can make the species easier prey or unable to hunt for food.

Mozambique Tilapia (Oreochromis mossambicus) have been frequently diagnosed with pansteatitis and maintain a large population size. These characteristics make them a perfect model organism to use for researching pansteatitis – which is why they were selected for my project. I will be analyzing muscle tissue samples of these fish to compare the fatty acid profiles between healthy and diseased specimen; infected Nile Crocodile muscle will also be key in understanding how pansteatitis affects different organisms.

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Mozambique Tilapia – Photo taken from John Snow

It is important that we study Mozambique Tilapia to influence management efforts for top predators like Nile Crocodile, whose presence and actions impact the food web. In addition, tilapia and other fish are harvested and I want to ensure that any diseased fish caught are safe to eat. Although there have been no studies that have found whether or not this disease can directly affect humans, I hope that my study can give us an indication of the indirect human health risks.

Research Questions

  1. What is the difference in Fatty Acid Profiles between healthy and diseased Mozambique Tilapia?
  2. What is the difference between diseased Mozambique Tilapia and Nile Crocodile?
  3. What lipids are most affected by Pansteatitis?

This Summer, I will be investigating these questions and reporting back my findings. To find more information on the topics check out these links:

Blood Chemistry of Pansteatitis-Affected Tilapia

Life History of Mozambique Tilapia

Life History of Nile Crocodile


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


References:

Bowden, J., Cantu, T., Chapman, R., Somerville, S., Guillette, M., Botha, H., Hoffman, A., Luus-Powell, W., Smit, W., Lebepe, J., Myburgh, J., Govender, D., Tucker, J., Boggs, A. and Guillette, L. (2016). Predictive Blood Chemistry Parameters for Pansteatitis-Affected Mozambique Tilapia (Oreochromis mossambicus). PLOS ONE, 11(4), p.e0153874.

Poke, D. 5 Interesting Facts About Nile Crocodiles. https://haydensanimalfacts.com/2015/03/04/5-interesting-facts-about-nile-crocodiles/ (accessed Jun 27, 2019).

Snow, J. Mozambique Tilapia. https://www.mexican-fish.com/mozambique-tilapia/ (accessed Jun 17, 2019).

Saving Samples for the Sea Turtles

lil turt and me

Photo Cred: Kaylie Anne Costa

Kelly Townsend, Elmhurst College

Findings: What an amazing summer this has been! I have been working to discover the quality and stability of RNA and plasma proteins from loggerhead sea turtle blood in different storage conditions. The results have showed that plasma proteins are quite stable while RNA degrades at a much higher rate. Therefore, we were able to conclude that samples that have been stored for many years are still viable for plasma protein analysis but not RNA analysis.

Throughout the summer, I have participated in many amazing opportunities to explore different field work and sampling techniques. I was fortunate enough to go on a four day cruise to do a health assessment of juvenile and adult loggerheads, volunteer on a turtle nesting beach to survey the loggerhead nests, and have a behind the scenes tour of the turtle hospital located at the Charleston aquarium. Even though my research pertained to turtles, I was also able to go shark lil turttagging for a day. Each experience has taught me something new and I have loved every minute of it.

During this project, I have also acquired new lab techniques and life skills that will make me a better scientist. Working alongside my mentors who are a part of the National Institute of Standards and Technology (NIST), I learned meaningful organizational and professional skills that I will be able to apply in any lab I work in. I have also learned new techniques in the lab involving new instruments that I have never used before this summer. All this new knowledge will greatly help me throughout my career. Overall, I had an awesome experience conducting research this summer and I have acquired so much new knowledge to apply in my life.

A huge thank you to Dr. Jennifer Lynch, Jennifer Trevillian, and Jennifer Ness with the National Institute of Standards and Technology for being my supportive and fantastic mentors. I would not have been able to complete this project and have amazing opportunities without them. This project was made possible by the samples collected by Dr. Michael Arendt and the funding from the National Science Foundation (NSF DBI-1757899) supported by the Fort Johnson REU program.

Methods for the Manatees

Kaylie Anne Costa, University of Miami

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The Approach: In my previous post, I described cold stress syndrome (CSS) in Florida manatees and the major threat it poses to the survival of this integral species. To expand the current scientific knowledge of CSS, I will be analyzing the lipids (aka fats) and metabolites, which are the products remaining after biological processes such as digestion, respiration, and maintenance of homeostasis, in 12 healthy and 21 CSS-affected manatee plasma samples in hopes of learning more about the metabolism of this condition and potential avenues for therapeutic applications.

In order to study the lipids and metabolites in manatee blood, I will be using liquid chromatography and mass spectrometry (LC/MS) with an electrospray ionization source. Metabolomics and lipidomics will be separately analyzed. After a chemical extraction is performed to selectively separate either the lipids or metabolites in the plasma, each extract will be individually injected into the chromatographic column to separate the chemical compounds present so that only similar compounds are analyzed in any moment of time (methodology proposed by Bligh & Dyer, 1959 and Cambridge Isotope Laboratories, Inc.). Once the separated compounds reach the end of the column, they are

css manatee

Rescued manatee showing signs of cold stress syndrome. (Photo from: https://savethemanateenewtech.weebly.com/endangerment.html)

transferred to the electrospray ion source where a high temperature and voltage will be applied to evaporate the solvent and give the compounds a charge to form ions that are then directed into the mass spectrometer. Within the mass spectrometer, the ions will first be filtered by electric fields to remove anything other than either lipids or metabolites and then detected by mass to charge ratio. The most abundant ions will be fragmented and the mass to charge ration of the fragments will also be detected using an MS/MS scan. To see an animation of the flow of ions through the mass spectrometer, please click the following hyperlink: https://www.youtube.com/watch?v=_A6NBBBcdts

As a result of the above processes, retention times for each ion are displayed in a graphical form called a chromatogram and the mass spectrum is recorded. Since the masses and retention times will not change between scans, these parameters for each ion can be matched to known databases of known lipids and metabolites. By applying multivariate statistics, we can determine if there is a difference in the lipids and/or metabolites in the plasma of manatees with CSS compared to healthy manatees.

flow chart

The top left graph shows a chromatogram. The highlighted peak is then shown on the mass spectrum below with a mass to charge ratio (m/z) of 760.58607. By locating this m/z and the m/z of its fragments in the mass spectrum of a MS/MS scan and matching the values with a database, we know the original peak represents Phosphatidylcholine (16:0_18:1).                                        (Graphic by Dr. Mike Napolitano)

The goal of my project is to see if CSS alters the lipid and metabolite contents of manatee plasma. If differences exist, I will study them to learn more about the progression of cold stress syndrome in manatees and the particular systems and metabolic pathways that are affected. It is our hope that this information leads to developing both diagnostic and treatment options for these animals thereby reducing the impacts of this syndrome.


A huge thank you goes to my mentor Dr. John Bowden and co-mentor Dr. Mike Napolitano as well as everyone at NIST, HML, and Fort Johnson for all of their help and guidance. I would also like to thank the National Science Foundation for funding and the Fort Johnson REU program for making this research possible (NSF DBI-1757899).


References:

Bligh, E. G., & Dyer, W. J. (1959). A rapid method of total lipid extraction and

purification.Canadian journal of biochemistry and physiology, 37(8), 911-917.

Cambridge Isotope Laboratories, Inc. Metabolomics QC Kit For Untargeted/Targeted Mass

Spectrometry: User’s Manual. Tewksbury, MA: Author.