A microfluidic chemotaxis assay to study microbial behavior in diffusing nutrient patches

J.R. Seymour, T. Ahmed, Marcos, R. Stocker

Limnol. Oceanogr. Methods 6:477-488 (2008) | DOI: 10.4319/lom.2008.6.477

ABSTRACT: The nutrient environment experienced by planktonic microorganisms is patchy at spatiotemporal scales commensurate with their motility (µm – cm), and the efficiency with which chemotactic microbes can exploit this heterogeneous seascape influences trophodynamics and nutrient cycling rates in aquatic environments. Yet, methodological limitations have largely prevented direct examinations of microbial behavior within heterogeneous microenvironments. We used soft lithography to fabricate a microfluidic-based chemotaxis assay to study the foraging response of aquatic microbes to diffusing microscale nutrient patches. The transparency, biocompatibility, and simplicity of microfluidic devices make them ideally suited for microbial ecology studies. A microinjector was used to create a 300 µm-wide nutrient band, simulating a pulse release of solutes. The chemotactic response of microbes to the diffusing patch was measured at the population and single-cell level. In contrast to traditional chemotaxis assays, this technique permits the assessment and quantification of chemotaxis toward a potential attractant in real time, enabling rapid screening of multiple chemicals. Furthermore, detailed information on chemotactic behavior can be obtained by tracking individual organisms. Here, we applied this microassay to study the chemotactic behavior of a range of aquatic microorganisms, including three marine bacterial isolates, a species of phagotrophic flagellate, and a species of phytoplankton. Each organism exhibited a rapid chemotactic response to a variety of chemical compounds, suggesting that many marine microbes are adapted to life within patchy microenvironments. The chemotaxis assay described here was found to be a flexible platform for studying both the specific case of microbes foraging within patchy habitats and as a broadly applicable tool for rapidly assessing and quantifying microbial chemotaxis.