Field Samples: Exploring the Aquatic Microbiome

Welcome to our weekly Q&A asking researchers what they’ve been up to and what they’ve learned. Today, Mike Braus, a graduate student at the UW-Madison’s Nelson Institute talks about lakes, rivers, climate change, and the tiny little microbes running the show.
Who are you, where are you from, and how did you get here?

Mike Braus takes a ride on a sculpture of micrasterias.
Mike Braus takes a ride on a sculpture of Micrasterias.

I was born and raised in Madison, but I spent a few years in my college years on the west coast and a semester abroad in Costa Rica, where I specialized in tropical ecology as part of my BA in Zoology from the UW-Madison. After graduating, I did an internship on Fire Island on the Long Island Sound with the Student Conservation Assocation, and later I discovered the Nelson Institute for Environmental Studies in my hometown. Surprised and delighted, I applied, got in, and got to know the people in botany, zoology, limnology, bacteriology, and history of science, settling into the interdisciplinary sort of work the Nelson Institute is known for.
Pretend we just boarded an elevator and you only have a one-minute ride to tell me about your work….3, 2, 1, go!

I study aquatic microbes that live on green filamentous algae in lakes and rivers, and these lakes and rivers are known for emitting greenhouse gases. We all know that a lot of microbes live on our bodies, in the soil, and in the water. What if those tiny microbes in the water collectively do more than we know to deal with enormous problems for us like climate change? Where and how do they thrive, and how can we study them when they’re so darn small and look so darn similar to one another? I want to make useful emerging molecular techniques and computational resources more widely available to researchers (especially limnologists and climate scientists) whose projects involve microbes, whether or not they realize it.
What question did you ask and answer or do you hope to answer? What other questions might your work lead scientists to ask?

How does the diversity and function of algal microbial associates changer over a growth season? My work should lead scientists to question whether algae are just a nuisance (it’s quite the opposite in fact) and how they and their microbial associates could be important to maintaining the conditions that make life possible on Earth.

The alga Cladophora under the microscope.

Not to sound harsh, but why should someone NOT in the field of freshwater sciences care about your work? What’s a bigger picture implication?

Filamentous algae, teeming with microbes.
Filamentous algae, teeming with microbes.

Well, you have to first ask yourself a few simple questions: Why do you brush your teeth? How did you manage to digest that big Thanksgiving dinner? Where does over half the oxygen you breathe come from? And the answer is microbes. Microbes permeate all the environments we know and love, especially the biochemical pathways and cycles in those environments. My work can be applied to a public health official wondering what is living on those metal rails in city buses, a farmer wondering what is in the soil to help a crop get nitrogen, or a cheese-maker wondering what microbes might be in a particularly delicious wheel of cheese. I just happen to study the microbes living on the beautiful, harmless little green filaments of algae found in Lake Mendota and most lakes around the world.

What do you love about your work? What do you love, well, not-so-much?
My favorite part of my work is the interface of the computer science culture and the physical science culture. There is a lot we can learn from one another, like physical scientists doing more automation and computer scientists doing more open-ended exploration. We can work together, but this is also the thing I love not-so-much. Getting researchers and technologists to speak the language of the other is a really big challenge, and you get quite a few raised eyebrows when you (perhaps like me being thoroughly a non-expert) walk into a lab and ask a researcher or technologist to explain the gritty details of their work.
Tell me about one funny, memorable, exciting or awesome moment from this project (either in the field or in the lab).
A tiny vial, with a whole lot of data.
A tiny vial, with a whole lot of data.

To be honest, I sort of ran before I could walk. Things like DNA extractions and PCR were completely foreign to me, but they still remain the most awesome part of this technique and technology. You make a tiny solution of DNA and from it blooms enormous data sets with tens of millions of bits of data.
The moment I got the genetic data back from the sequencing center, looked at the summary of their work, and pulled out a calculator, my jaw dropped at how rich the data was. [And that was[ after collecting just a single molecule shared by all organisms.
Where do you hope to go from here? New research questions? Continuing with this work?
The overarching goal is to scale these methods up. I hope to work with folks like those at the Earth Microbiome Project, streamlining and standardizing the process so as to later mesh these microbial ecological data with global measurements of biotic and abiotic aspects of freshwater, marine, and terrestrial environments. If we want to make accurate models of big aggregate global impacts like climate change, we need to find out if and how microbes are participating.
All images courtesy of Mike Braus