Kyle Winkler and Dr. Byron Adams, Microbiology and Molecular Biology
Soils are the basis of agriculture and the sustainability of life as we know it. Despite this fact, we know very little about soil ecosystem function and what biotic organization is required for effective nutrient cycling in soils. In this project, I attempted to better our understanding of soil food web relationships in a simple, natural ecosystem.
In order to understand the carbon-nitrogen cycle and its effect on global climate, it is important to know how trophic interactions of soil-dwelling bacteria, fungi, and invertebrates work together to provide essential recycling processes of these elements. This study was designed to allow us to see how these nutrients move through food webs. The focus of this project was to identify what species of bacteria are consumed by soil-dwelling nematodes in Antarctica.
Soil-dwelling Antarctic nematodes are used because of the simplicity of the Antarctic ecosystem. A small change anywhere in the food web can have a drastic effect throughout the environment. Once we understand ecosystem function in a simple ecosystem, we can apply that knowledge in more complex environments.
This experiment involved examining DNA from bacteria that have been consumed by nematodes and comparing them with control samples. Theoretically, by investigating the DNA sequences I could determine what species of bacteria the nematodes have been feeding on.
After nematodes were extracted from Antarctic soil samples, they were mixed with cultured e-coli bacteria and then sterilized. Sterilization was done by washing the nematodes in bleach, hydamine hydroxide, DNase, or other anti-bacterial chemicals. The e-coli is used to test the sterilization, if any e-coli DNA is found with the nematodes later on, we would know that the sterilization failed.
Once sterilized, I extracted DNA from the sample and amplified it with a Polymerase Chain Reaction (using a variety of bacterial specific primers such as 16F and 8F). I used a number of test mechanisms such as Heterorhabditis Bactiophora to refine my techniques.
These tests took place over the period of about one year. Unfortunately, good DNA template was never isolated. Contamination was the main problem, it proved extremely difficult to obtain a small amount of semi-digested bacterial gut-DNA to the exclusion of all other bacterial DNA on or around the nematode. Had good template been acquired, then it could have been sequenced and compared with databases to identify the bacterial species which have been consumed by the nematode.
I find my lack of success frustrating, but this kind of experiment has never been done successfully before. Although good DNA sequences were not acquired through our techniques, progress was made in forming good sterilization and isolation methods.
In the summer of 2004, I presented my research to that point at the Society of Nematologists. It was a fantastic experience and my presentation went very well. I got the experience of interacting with other scientists in my field and was able to see how scientific collaboration worked on an international scale. An abstract of my work was published in the Journal of Nematology*.
My own education and experience was enhanced substantially. I learned many laboratory and research skills, along with a deeper understanding of the scientific process. I am glad that I received this opportunity to further the aims of Brigham Young University. I greatly enjoyed my experience and hope to have further opportunity to increase my scientific skill.
Reference
- Winkler, K., Adams, B. The Effect of Non-Pathogenic Nematodes on Soil Ecosystems. Journal of Nematology 3(3):353.