Hello, I’m Kelly! This year, I participated in the New Visions - Life Sciences program through the Tompkins-Seneca-Tioga Boards of Cooperative Education Services (TST BOCES) and Cornell University. New Visions gave me the opportunity to explore ecology and conservation through immersion in the Cornell research environment. I connected with research groups spanning topical areas from manure management to forest spatial ecology, before joining the Schmidt Aquatic Microbiology Lab as an intern.
My year in the lab
I read a lot. My favorite paper was “The Microbial Loop” (Pomeroy, et al., 2007). I learned R- and bash-scripting and helped with the Schmidt Lab’s January Software Carpentries Workshop. This was a great introduction to data visualization and analysis for aquatic microbial communities, as Gus (lab mate) had modified the lesson to use sample data collected by our lab on Lake Ontario. I went to departmental seminar presentations from scientists visiting the Cornell Department of Microbiology and also sat in on discussions and coding labs for Mar’s class, “BIOMI 4300/6300: Computational Approaches to Microbial Systems.” Sophia taught me how to run PCR and qPCR. I wrote a literature review for my project on oyster bed sediment microbiota, and then I analyzed beta diversity in the project dataset and made functional predictions using PICRUSt2. In May, I presented findings at the New Visions - Life Sciences research symposium in poster and slideshow format and wrote a research paper.
Thank you to the Schmidt Lab for their guidance and encouragement and for connecting me with so many cool opportunities to grow my knowledge of microbial ecology, bioinformatics/statistics, and the research scene.
Highlights of the year
Sophia and Gus helping me work through buggy code, listening to our rotation student (Kailyn Hanke) present on microbial dormancy at “Limno Lab,” daily NYT Crossword Club with the Microbiology graduate students, making illustrations for my research presentation (see below), coding labs in Mar’s spring class: “Computational Approaches to Microbial Systems,” celebrating Gus passing his A-Exam with a lab nail painting party, postdoc Eric teaching us about giant clams, and eating sweet treats brought in by the talented bakers in our lab.
My Research Project
I studied the microbial community make-up of oyster bed sediments and predicted these microbes’ capacity for performing the denitrification pathway (NO~3~ -> N~2~).
Microbial Community Make-Up
Oysters fertilize marine sediments with organic material, carbon, phosphorus, nitrogen, and trace minerals. According to existing scientific work, this promotes a biodiverse and functionally diverse microbial community. In our samples from the Rhode Island/southern Massachusetts coast, we found that the effect of oyster presence on microbial community composition was on par with the effect of seasonal change. Consider the difference between Summer and Fall in New England… That’s a pretty significant change!
Denitrification Capacity
Denitrification is a metabolic pathway that occurs at higher rates in the presence of oysters. It results in the stable storage of nitrogen as atmospheric dinitrogen (N~2~). However, prior to N2, denitrifying microbes produce nitrous oxide (N~2~O), a greenhouse gas three hundred times the potency of carbon dioxide. As denitrification is often a pathway performed commensally by microbes, this begs the question of how much nitrous oxide escapes into the atmosphere due to unequal presence of early-stage and late-stage denitrifying microbes. We found that at 2/4 examined sample sites, microbial communities had lower capacity for late-stage denitrification (nitrous oxide reduction) than their control site counterparts. In other words, sometimes oyster bed sediments release more nitrous oxide into the water column–where it then bubbles up into the atmosphere–than bare sediments.
See my poster below for more information:
A caveat
I read Ray et al., 2019, which displayed the figure to the right. This figure shows that oyster aquaculture does produce nitrous oxide, but compared to nitrous oxide emissions from terrestrial food production, oyster emissions are negligible. Looking at greenhouse gas emissions holistically, oysters are the clear choice for a low-footprint protein source (excluding external factors like transport).
A case for accessible science
Scientific work is more impactful when it is digestible by a diverse audience. It was satisfying to wrap up the New England oyster bed microbe project into a slideshow to present to a crowd of mixed academic backgrounds. Using Canva, I made illustrations about microbiology concepts and the nitrogen cycle.
- Nitrogen Fixation: Dinitrogen is the form in which most oxygen in our atmosphere exists. Due to the triple bond between atoms, it is very stable. Only one enzyme, nitrogenase, can break this bond. This is the process of nitrogen fixation.
- Microbial Dormancy: Metabolic potential is the reaction-catalyzing capacity of all DNA in a sample. This can include dormant microbes.
- Gene Expression: Even if a microbe has the gene for a particular enzyme, the gene is not always expressed and the microbe may not perform the function associated with that gene and enzyme.
- Microbial Cross-Feeding: Denitrification is performed collectively by marine oyster bed sediment microbes through metabolic cross-feeding. The microbe performing nitric oxide reduction may be different from the microbe performing nitrous oxide reduction. If the intermediate in this situation, nitrous oxide, is sitting in the environment, it will escape into the atmosphere from oyster bed sediments.
