High-Throughput Screening and Selection of High Lipid Producers for Biofuels

As researchers strive to develop the next generation of renewable fuels, they often need to screen through thousands or even millions of microbial clones to find the best ones for further development. However, manual selection and further downstream functional screening is time consuming and prone to error. In addition, protocols and methods may need to be adjusted to accommodate one or more microbial species that are not widely used.  Here we present a method for identifying high-lipid producing clones of Rhodococcus opacus using Nile Red, a lipophilic fluorescent dye. This method can be easily generalized to other species and other indicators. We cultured a high-lipid accumulating strain of R. opacus with Nile Red and used a QPix 420 to select and pick colonies based on morphology and fluorescence intensity.  The lipid content of the picked colonies was confirmed by staining with BODIPY 505/515, a lipophilic fluorescent dye, and using a SpectraMax M5 for fluorescence measurement.  By selecting only colonies with high fluorescence intensity, we were able to find desired colonies in an initial primary screen, limiting downstream functional assays to only the most promising candidates, or even eliminating the need for additional secondary screening, saving significant time and resources.