Shedding light on microbial dark matter
July 20, 2016
Technological advancements allow us to sequence the DNA of bacteria quickly and inexpensively, which has enabled us to build vast reservoirs of sequenced genomes. However, we have lagged behind in the ability to identify the functions of thousands of gene families. A big challenge facing the field of microbiology is this vast number of genes of mysterious genes, known as "microbial dark matter."
Even in incredibly well-studied organisms (like E. coli), we still do not know the function of the majority of the genes. So, how can we begin to characterize the 'unknown' genes? Many of these unknown gene families are present in many types of bacteria, offering evidence that they provide a survival benefit in some condition. So, another way to ask this question is under what circumstances do these gene families provide an advantage? My work in the Crosson lab in the Biochemistry and Molecular Biology Department in collaboration with Maureen Coleman's lab in the Department of the Geophysical Sciences aims to address this question.
While we as scientists typically study bacteria in isolation in a test tube in the lab, this is not representative of an organism's natural environment. In normal lab conditions only 10-15% of bacterial genes are required for growth. So maybe, instead of trying to determine the function of unknown genes in the lab, we should go back to the natural environments of the microbes we study. Maybe, this "microbial dark matter" is required in conditions we are just not looking in which is why we have not found the answers yet.
I use Caulobacter, a bacterium found in dilute freshwater, as a model organism to understand the impact of environmental conditions on the required genetic content of an organism. I collect water from Lake Michigan, filter it to remove the microbes present, and use it to grow Caulobacter in the lab to simulate a "natural" environment. Right now we are working to identify the genes required for growth in lake water and we predict that more genes will be required to grow in this environment than in our optimized lab conditions.
Once we identify genes of unknown function that are essential for growth in lake water, we can begin to characterize them in these conditions to identify their functions. However, this may be only a partial answer to our problem. In reality, microbes are competing with each other for available resources.
So, in addition to growing Caulobacter in filtered lake water, I am also investigating growth in a 'community' setting using unfiltered lake water, meaning that all of the microbes that Caulobacter may encounter in its natural environment are present. We predict that some genes will be required for growth and survival in these natural conditions, while others may only be required in the presence of other microbes. You could imagine a certain gene product of one organism that combats a toxin produced by another microbe would only be needed in an environment where both are present.
Studying bacteria in their natural environments is not a simple task, but it will allow me to begin to identify novel functions of gene families that are required for survival in a 'real-world' environment shedding some light on microbial dark matter.