SCUBA Mentor Led Research
Coral reefs are a diverse and complex ecosystem that impact the world’s macro environment. It is estimated that 50% of the planet’s oxygen is generated via photosynthesis within phytoplankton in the ocean. A large part of phytoplankton is within the coastal reef areas. In addition, coral reefs provide safe environments for juvenile fish to grow and other fish to reproduce. Without these environments, a large portion of the food-chain for human consumption would be disrupted. Coral themselves are the integral part of building and maintaining the reef ecosystem.
In recent decades, coral reef ecosystems have become stressed or endangered via myriad of inter-related threats: natural processes such as El Nino events and hurricanes; and man-made stresses such as industrial induced climate change, overfishing of coastal waters, and land based discharge of fertilizers & waste.
The UT System LSAMP STEM Pathways group is engaged in a marine science research program to study many aspects of the reef environment in a holistic fashion (Figure 1 below).
Figure 1: Venn Diagram of the Midland College Marine Science Research Effort
Research mentors at Midland College and UT-Arlington offer students from a wide scope of STEM majors the opportunity to expand their knowledge in their respective field of study as it is applied to the coral reef ecosystem. STEM areas of study include; Chemistry, Engineering/Physics, Computer Science, Environmental Science, Biology, Genetics, and Microbiology. Students will have access to multiple data sets to examine possible cross-correlations, so interdisciplinary interactions will occur. Please visit the pages below to see which project best suits your research interests!
Laura Mydlarz (Ph.D.) – University of Texas at Arlington / coral disease
(for extensive information, see the web-site: http://www.themydlarzlab.com/ )
Corals and other invertebrates must be able to defend themselves against infection, predation, competition and abiotic stressors to maintain homeostasis. Much advancement has been made on the elucidation of pathways and phenotypes involved in both resistance to, and active response to infection in corals and other reef inhabitants. We are interested in immunorecognition, signaling pathways, effector responses as well as putting immunity in the context of organismal studies, such as life-history tradeoffs and effects of the environment on immunity. See our page (link above) dedicated to Cnidarian Immunity for more information.
Specific projects under Dr. Mydlarz - - - -
Effects of temperature on coral immunity
The Caribbean has suffered from two unprecedented bleaching events, one in 2005 and one in 2010. We have worked on these naturally bleached corals to assess the effects of bleaching and oxidative stress on coral immunity and disease outbreaks. We have also experimentally stressed corals with temperature and pathogens recognition molecules and found supression of immunity.
Coral immunity and life history - why do corals differ in disease susceptibility?
We are looking at how immunocompetence varies between species with different morphology, growth rates, reproduction and susceptibility to disease and bleaching.
Symbiodinium recognition and coral immunity
Corals rely on a symbiotic relationship with an immotile dinoflagellate known as Symbiodinium. Using Symbiodinium cultures we are comparing the response of several types of Symbiodinium to temperature and pathogen stress. We are measuring growth rates, production and release of reactive oxygen and antioxidants as well as proteomics to look at responses.
Thomas Ready (Ph.D.) – Midland College / Marine Chemistry
Coral & phytoplankton (algae) both depend on dissolved nutrients (i.e. Nitrate NO3-, Nitrite NO2-, Phosphate PO4-3, Bicarbonate HCO3-, Carbonate CO3-2, and others) to maintain growth and sustainability. There are complex interplays between coral and phytoplankton. On the one hand, symbiodinium algae imbed themselves in the coral tissue and assist coral acquisition and metabolism of nutrients via photosynthesis. On the other hand, phytoplankton in the ocean compete with coral for dissolved nutrients. Likewise, mature plant-like algae also compete with coral for space. In broad terms, high concentrations of nutrients tend to favor the growth of phytoplankton / algae while low concentrations tend to favor healthy coral. The concentration of these nutrients vary with depth. Students will measure the concentrations of the dissolved nutrients at different depths & within coral mucus and attempt to develop correlations between nutrient concentrations and coral health /phytoplankton biomass / coral mucus microbiota / water quality. Students will practice assay protocols during the academic year prior to the Caribbean trip on samples acquired from fresh water lakes in Texas and New Mexico as well as the Texas Coast.
Greg Larson (M.S.) – Midland College / Marine Environmental Science
Water quality parameters include: temperature, pH, dissolved oxygen concentration, Reduction/oxidation potential, conductivity (salinity), turbidity, current flow rate, nitrate concentration, phytoplankton biomass. Changes from the norm in any of these parameters can adversely affect both coral health and phytoplankton populations. Climate change is presumed to be actively affecting these parameters. Students will measure these water quality parameters by deploying a submersible autonomous sonde as well as custom-built sensor packages. Students will compare these measurements to the historical values in an attempt to determine trends as well as correlations between each parameter and changes in coral health / changes in phytoplankton populations / changes in dissolved or coral mucus nutrients / coral mucus microbiota.
Ethel Matthews (M.S.) – Midland College / Marine Microbiology
Marlana Mertens (M.S.) – Midland College / Marine Microbiology
In many higher life forms, including humans, there is a microbiota community that populates the host. The native microbiota often plays a role in the host’s ability to maintain health (ie. Human gut microbiota). Disturbances in the native microbiota or invasion of non-native bacteria can cause infection or disease. This is also the case for coral. There is a microbiota community that dwell within the mucous that is normally secreted by coral. This microbiota community is different for each species of coral and in many cases not well characterized.
Coral disease has been credited as a cause of the decline of coral reef health. Stressed coral releases mucus as a protective measure against many threats to coral health. They also secrete mucus under normal conditions to capture bacteria and other small zooplankton as food. White Plague Disease (WPD), Black Band Disease (BBD), and others have been linked to the decimation of corals in many coastal reef systems. Though the causative agent of these diseases has not been elucidated due to the variety of microbes identified in association with these diseases, Cyanobacteria has been strongly linked to BBD. It is not known if the Cyanobacteria are part of the normal flora and opportunistic, or if they are causative in the disease process. Cyanobacteria mats are found to be increased in areas where coral is on the decline. Many benthic Cyanobacteria mats (BCM) contain only Cyanobacteria where other BCM contain diverse consortia of microbes.
This particular part of the SCUBA program will use molecular techniques to show the presence of Cyanobacteria in the water surrounding the coral reef and in the mucus on diseased and healthy coral. The water, at depths of 20m, 40m, and 60m above the coral reef, were tested with Cyanobacteria specific primers for the presence of planktonic Cyanobacteria. Mucus samples collected from diseased and healthy coral, as well as visually diseased and visually healthy areas of a single coral species, will be evaluated for Cyanobacteria species.
PCR reactions using five primer sets for the 16S rDNA of Cyanobacteria have been selected from currently available literature, will possibly confirm the presence of Cyanobacteria mats in coral communities. PCR reactions using two primer sets targeting the microcystin synthase gene have selected to evaluate the possibility of microcystin toxin in the area of the coral reef.
Aside from Cyanobacteria, there is a plethora of other species of bacteria in coral mucus. It is estimated that less than 1% of the coral mucus microbiota has been able to be cultured in a laboratory setting. In this ambitious part of the science, Mathews / Mertens will lead an effort to elucidate aspects of coral microbiota populations. Students will participate in the acquisition of coral mucous from select coral species. In the Roatan Institute of Marine Science (RIMS) laboratory, the coral mucous will be 1.) inoculated onto growth media, attempting to isolate specific colonies of bacteria, 2.) isolated bacteria strains will be subjected to standard protocols to determine are gram-positive or gram-negative, 3.) Attempts will be made to extract DNA from isolated bacteria strains so that it can be sent to the U.S. for sequencing and gene bar-coding.
Paul Mangum (Ph.D.) – Midland College / Plant Genetics near marine environments
The coast-lines along coral reefs have a huge diversity of plant life. These plants play a role in absorbing & re-cycling nutrients that run-off of land into the waters above coral reefs. Not all of these plants have been fully characterized.
Students who participate in this project will 1.) isolate DNA from plant leaf material, 2.) use PCR on the DNA to amplify part of the ribulose-bisphosphate carboxylate gene (rbcL), Send the PCR product to GeneWiz for sequencing.
Philip Lee (Ph.D.) – Midland College / Marine Genetics/Biology (specializing in algae & phytoplankton)
Phytoplankton populations are integrally connected to the overall health of the coral reef environment. Because phytoplankton use photosynthesis to process nutrients for growth, these populations decrease with depth. Students will participate in the characterization of phytoplankton in terms of overall total biomass as well as individual species populations (when possible). Species identification may involve extraction/amplification of algal DNA for transport to U.S. laboratories for sequencing and gene bar-coding and/or flow cytometry and other microscopic evaluations. Students will attempt to draw correlations with both water quality parameters / nutrient concentrations and coral health.
Additionally, since phytoplankton are primary producers at the bottom of the food chain many organisms prey on them. These organisms include viruses, bacteria, and fungi that infect or parasitize phytoplankton. Others are consumers of phytoplankton such as single celled protozoa and multicellular zooplankton. These interactions are vital in the reef environment to maintain balance in the ecosystem, but are also industrially important to understand for commercial growers of algae. Thus, populations of phytoplankton predators will also be identified microscopically and by DNA sequencing.
Brian Flowers (Ph.D.) – Midland College / Marine Engineering / Physics / Computer Science
Michael Gibbons (Ph.D.) – Midland College / Marine Engineering / Physics / Computer Science
Midland College is active in developing low cost, autonomous, in situ sensor arrays to measure a variety of water quality parameters; temperature, pH, dissolved oxygen concentration, Reduction/oxidation potential, conductivity (salinity), turbidity, current flow rate, nitrate concentration, phytoplankton biomass. Other measurements are also in the design phase. These sensors must produce both high quality data and withstand a high external hydrodynamic pressure, and a corrosive aqueous environment. Students will participate in the design/fabrication/testing of their own sensor package. This may include (Arduino / Raspberry Pi) computer programming. Testing of sensor package prototypes will take place during the academic year at fresh-water lakes in Texas and New Mexico.
The most commonly utilized method for assessing coral health is to photograph sections of the coral reef (called a transect line) and assess the health by reviewing the photographs manually. This can be laborious. There are computer programs which can assess the photographs digitally and make assessments based on mathematical algorithms. Most of these programs have deficiencies. Midland College would like to develop its own program/algorithm for assessing coral health from digital photographs. Students involved with this project would acquire the transect line data and construct computer code to interpret the photographic data.
A separate engineering project related to the transect line analysis involves the design/fabrication/testing of novel photo-grid quadrants to be utilized for the assessment of overall coral health. Current technologies (transect lines and or small photo-grids) have limitations either in dimensions of the grid or the inherent biases in grid placement. The ultimate goal for this project is to build a light-weight, collapsible, 8-meter x 8-meter grid framework that will be used in making a photographic record of reef sites. This is a daunting engineering challenge as the collapsible grid must fit on the dive boat, be transportable underwater by divers to the study site, be expandable to 64 m2 by divers underwater, float 3 feet above the reef so as not to damage the coral underneath, be retracted and delivered back to the dive boat in 40 minutes of total dive time. Testing of grid prototypes will take place during the academic year at fresh-water lakes in Texas and New Mexico.
The UT System LSAMP program is funded by the National Science Foundation grant number HRD-1202008 and HRD-1826745. Funding for the Bridge to the Doctorate projects is provided by NSF grant numbers HRD-0832951 (BD 2008-2010), HRD-0929727 (BD 2009-2011), HRD-1139929 (BD 2011-2013), HRD-1301858 (BD 2013-2015), and HRD-1810898 (BD 2018-2020).