Field Samples: Cracking (Genetic) Code to Understand Microbe Diversity

Field Samples is a Q&A with aquatic researchers. Today graduate student, Sarah Stevens, talks computer programming and microbes in lakes. Sarah will give a public lecture on her work today at noon in the Water Science & Engineering Lab as part of the Center for Limnology’s weekly Wednesday seminar.

Who are you, where are you from, and how did you get here?
Sarah StevnesI’m Sarah Stevens, and I’m a graduate student in Trina McMahon’s Lab.  This will be my fourth year in the Microbiology Doctoral Training Program.  I am from the corn and soybean fields of rural Illinois.  I did my undergraduate degree in Molecular and Cellular Biology at the University of Illinois Urbana –  Champaign. I joined Trina’s lab to study microbial ecology and evolution.
Pretend we just boarded an elevator and you only have one-minute to tell me what it is you’re presenting on at seminar….3,2,1 go!
Microbes have incredible genetic diversity in the environment and it is hard to define microbial species because each cell can reproduce on its own. My work uses the similarity between genomes from environmental samples to define bacterial populations.  Using this definition and our time-series of samples from the lakes, we can test predictions about how microbes diversify.
Why should someone not in the field of freshwater sciences care about your work?

For such tiny organisms, it takes a lot of equipment to unravel the microbial genome. Image courtesy of Sarah Stevens.
For such tiny organisms, it takes a lot of equipment to unravel the microbial genome. Image courtesy of Sarah Stevens.

Microbes are are responsible for most of the nutrient cycling and decomposition in lakes. (Editor’s note: nutrient cycling and decomposition are kind of a big deal for everything that lives in a lake!)
From the genome of an individual microbe, we can predict what it eats, breathes, and poops.  Defining a relevant ecological unit allows us to scale up from single cells to populations.  This will enable us to better model the nutrient transformations carried out by the microbial community.
What do you love about your work? What do you not love so much?
I love writing computer programs to analyze data.  It amazes me how a little creativity and some computer code can pull out the answers to questions I have.  It is really fun to learn new ways to code and problem solve with the computer.  This is also one of the most frustrating parts of my work.  I will spend hours thinking, searching the internet, and struggling to get my program to work.  However, I generally find my frustration with a program and my joy when I get it working to be directly proportional.
Where do you hope to go from here?
I’d really like to stay in the overlap between microbiology and computation.  I’m also really enjoying learning more about open science and teaching Software Carpentry workshops to help researchers get started writing software.  I hope to continue these two themes [in my work] wherever I go.

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