Microbial populations in the environment are remarkably diverse, but sometimes difficult and tedious to culture and screen. We have recently obtained preliminary results suggesting that many fungi strains found in the tissue, surrounding soil, and fruit of plants may possess useful bioenergy production properties, namely, an ability to ferment xylose, the dominant five-carbon sugar of hemicellulose, to alcohol and other valuable biochemicals. Moreover, many of these plant-associated microbes are resistant to phytochemical inhibitors produced by the host. Saccharomyces cerevisiae, a common yeast used in industry for the production of bioethanol, cannot readily metabolize xylose. To date, we have used traditional bulk microbiology tools to characterize these fungi; our promising preliminary results point to the value of developing easy-to-use tools that will allow rapid screening of naturally occurring microbial populations for their potential impact on bioenergy and biochemical production from biomass. To characterize microbial populations requires high throughput methods to separate, grow, and analyze diversity in the population. Microfluidic devices have the ability to perform many of the reaction and separation operations chemical engineers are familiar with at the macroscale, but they do so in nanoliter volumes and they can be arrayed in parallel configurations to accelerate cell sorting. In this work, we describe a class of micro-eddy based microfluidic devices that can trap suspension cells in microscale continuously stirred fermenters.[1]-[3] Simulation and experiments are used to understand flow and mass transfer, as well as cell trapping, in the devices. Since microeddy-based devices have well characterized mixing, the production or consumption of chemicals within the eddies can be rapidly and quantitatively measured using optical techniques. Raman spectroscopy, fluorescence microscopy, and optical microscopy are all demonstrated. We also show that the devices can be scaled into an arrayed configuration, allowing higher throughput screening. We show how the arrayed trapping and study of single-cells from a mixed culture eliminates many of the bulk microbiology steps needed to create isolates from complex environmental samples, accelerating the screening process.

[1] B.R. Lutz, J. Chen, and D.T. Schwartz, Microfluidics without Microfabrication, PNAS (USA) 100, 4395-4398 (2003).

[2] B.R. Lutz, J. Chen, and D.T. Schwartz, Characterizing Homogeneous Chemistry Using Well-Mixed Microeddies, Anal. Chem. 78 1606-12 (2006).

[3] B.R. Lutz, J. Chen, and D.T. Schwartz, Hydrodynamic Tweezers: 1. Non-contact cell trapping in a laminar oscillating flow, Anal. Chem. 78 5429-5435 (2006).