Agarose-Based Model Ecosystem for Cultivating Methanotrophs in a Methane-Oxygen Counter Gradient

We wanted to design a simple, inexpensive way to grow methane-oxidizing bacteria in the lab that more closely resembles the natural environment. We wanted to do this to uncover bacterial phenotypes that are missing from standard laboratory culture conditions, and ultimately link these phenotypes to their genetic determinants. The gradient syringe is the simplified version of previously described methods to culture methanotrophs in a methane-oxygen counter gradient.

This method doesn't require continual flows of gas substrates, which allows multiple replicates to be run in parallel. We also can perform biochemical assays directly on the bacteria cultured within the agarose. Researchers have virtually unlimited access to bacterial genome sequences, but it is still difficult to put all of this information into context.

Our findings show that it is critical to consider the environment in which a bacterium evolved, to better understand the role of individual genes. We plan to use techniques like comparative metabolomics and proteomics to learn more about how methanotrophs respond to their position within the methane-oxygen counter gradient. We also have plans to culture multiple strains in the same gradient syringe to see how they interact in a spatially resolved context.