As a part of our Microbiome Awards winners interview series, we spoke with Dr. Andrea M. Tarnecki, a Postdoctoral Research Fellow at Mote Marine Laboratory in Sarasota, Florida. Dr. Tarnecki received her Ph.D. from Auburn University, and her research interests include probiotics for use in aquaculture and deciphering beneficial host-microbe interactions. She is a recipient of the 2016 Microbiome Award. We interviewed Dr. Tarnecki, to discuss the impact of oil spills on fish microbiomes and how researching bacteria can help us learn more about the impact of stressor events on fish health
Give us some idea about your background and how you got interested in science? Was it always your first choice to work as a scientist?
As I child, I was always outside. Our house in Ohio was next to a corn field, and our house in Tennessee had a creek and woods just behind it, and I was happy in either place getting dirty and catching whatever animals I happened to come across. So, I guess I always knew I loved science and I’ve always been particularly drawn to aquatic science because of my love for fish. But, the way I got into microbiome research wasn’t so obvious. I never really liked microbiology, I guess because I didn’t understand it and I thought of all microbes as disease-causing organisms. When it came time for graduate school, I was offered the opportunity to take on microbiome research, and the real selling point at the time was that I could research the microbial communities of fish. Now that I’ve been in the fish microbiome field for a little over 6 years, I can’t imagine doing anything else. I’ve gained a whole new understanding and respect for microorganisms, not just for their ability to cause disease, but also for their ability to prevent it.
Can you give a summary of the project that won the Microbiome Award and any updates on the work since the award was issued?
During disease, the microbiome shifts to a community exhibiting lower species diversity coupled with increased abundances of potential pathogens. The bacterial assemblages return to the original, healthy state during recovery, suggesting that members of the bacterial community could act as biomarkers for fish health status. Monitoring of fish health via bacterial biomarkers presents a minimally invasive, non-lethal alternative to current techniques including blood draw and biopsies. This project will use oil exposure as a stressor in order to determine which bacterial taxonomic groups are altered in abundance, and those groups will be tied to a wide suite of measured health parameters, in order to identify bacterial biomarkers that can be used to indicate exposure during oil spill events, such as that of [the] Deepwater Horizon.
Since the award was issued, exposure trials have been concluded and all samples have been collected. Samples to be analyzed include the adherent and non-adherent microbiome of red drum Scianops ocellatus exposed to oil through feed, as well as the external skin-associated microbiome of Florida pompano Trachinotus carolinus exposed through the water. Samples are currently being prepped for sequencing.
Are you working on any other new projects in the field of microbiome research? If so can you tell us a little about these?
One project currently underway, funded by Florida Sea Grant, is investigating the impacts of site acclimation on the microbiome and innate immune function in juvenile common snook, a popular sport fish species in Florida. Mote Marine Lab has a research group dedicated to development of responsible stock enhancement protocols and previous studies indicate[d] that a 48-hour acclimation in enclosed cages prior to release nearly doubles fish recapture rates. We are attempting to find a physiological mechanism behind this acclimation, including looking at innate immune activity and microbiome structure, as these two parameters are tightly linked and it is known that wild fish harbor different microbes than captive ones.
Research in our group is also focused on identifying beneficial bacterial species in fishes that can be developed as probiotics. Probiotics are live bacterial supplements that provide a benefit to the host, including everything from improving water quality, increasing digestion, enhancing nutrient absorption and competing against pathogens. Our research focuses on the early life stages of marine fishes, as mortality of larvae in aquaculture systems can often reach 99%. We are working to determine what bacterial groups are present in the microbiome of healthy fish larvae, to investigate the possibility of a microbial component to these mortalities, and to identify bacterial species that can be used to prevent establishment of pathogenic bacteria in these systems.
What do you find most interesting about your project/what is the most interesting or surprising result you have found?
I don’t yet have results from this project. We just finished sampling, and I’m set to send the samples off for sequencing next week. However, the most interesting thing to me is that this study is the first to relate microbiome structure to such a wide suite of health parameters. Tying together microbiome structure and host physiology is the ultimate goal of my research efforts, and it requires collaboration between scientists of all expertise including aquaculture, immunology and reproductive physiology. Without the funds from the Microbiome Award, I would have missed this unique opportunity.
What are the important benefits of your research to science/human or animal health?
As most of my research focuses on fish, the obvious impacts are related to aquaculture and fisheries. My research on probiotics aims to reduce the larval bottleneck of fish production both for food fish and stock enhancement. I want fish that are produced to be healthy, disease-free and safe and nutritious for human consumption. Improper use of antibiotics is of global concern because of the increase in antibiotic-resistant microbes and probiotics offer a promising alternative, but there is still a lot to understand about how probiotics work. However, an aspect of my research that is often overlooked is its applicability to human health. Humans are also associated with complex microbiomes that can be altered through the use of probiotics to provide health benefits. Many of the interactions between fish and their microbes are mirrored in humans, so studying the fish microbiome can also help elucidate the role of microorganisms in humans.
When you are not doing experiments in the lab, what keeps you busy in your free time?
Apart from my regular hobbies like listening to music and traveling, my favorite hobby is fishing which occupies most of my free time.
What are the top challenges you face during extraction of RNA/DNA from a wide variety of samples?
Characterizing microbes can be challenging due to the difficulty of isolating or culturing them in the lab, which limits our knowledge of the vast microbial world. Understanding the microbial community is important because studies have shown that it plays an important role in health and the environment.
The top challenges are:
1) The limited amounts of RNA/DNA from a few precious samples
2) [The] presence of natural inhibitors in the microbiome samples which may interfere with the RNA/DNA isolation
3) Obtaining high-quality nucleic acids that can be used for sensitive downstream applications such as qPCR and NGS
Which QIAGEN products do you use/have you used in the past and what did you like about the products?
I have used: vortex adapter[s] for 1.7 ml tubes, bead tubes, the QIAamp BiOstic Bacteremia DNA Kit, [the] DNeasy Blood and Tissue Kit, RNAlater, [the] DNeasy PowerSoil Kit, [and the] QIAamp DNA Microbiome Kit.
I really like the reasonable cost of the products and the ease of use of all the DNA extraction kits. However, my favorite so far is the DNeasy PowerSoil Kit because it is effective at DNA extraction and inhibitor removal and the entire protocol can be completed fairly quickly. I have used this kit the most for my microbiome studies.