A high-throughput phenotyping platform for genome and microbiome evolution

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We use massively parallel experiments to study how genomes and microbiomes evolve in different environments. To do this, we grow some of the world's smallest plants and animals, duckweeds (Lemna) and nematodes (Caenorhabditis), in thimble-sized microcosms or smaller using multi-well plates, and then take thousands of measurements of phenotypes and fitness in highly replicated, multi-factor experiments. We manipulate their genotypes, species compositions, and abiotic environments; and measure their traits and growth rates, often accompanied by genomic or microbiome sequencing. To make our experiments truly high-throughput, we urgently require new equipment that will automate plate-filling, data collection, and analysis. The proposed NSERC RTI funds will enable us to purchase an integrated system comprised of liquid-handling robots to fill plates, a plate reader to automate measurements of population growth rates and other traits, a flow cytometer to count cells of different bacteria in complex microbial communities, a shaking incubator to culture bacteria, an image analysis system to acquire and process digital images of large numbers of well plates, and a needle-puller to make micro-injection needles for transgenic and other experimental manipulations.******This RTI-supported infrastructure will allow us to substantially accelerate the progress of our NSERC Discovery-funded research programs, with the potential to drive major breakthroughs in our understanding of genome and microbiome evolution. We will be able to undertake the largest-ever experimental manipulations of microbiomes, and to experimentally evolve our study organisms to better understand speciation and adaptation in the context of environmental pollutants and climate change. With the RTI-funded equipment, our HQP will use leading-edge technologies to enrich their training programs, preparing them for careers in industry, academia, and government. Our experiments are important for both basic, discovery-driven research in evolution and ecology, and they also have applied value; for example, toward goals to engineer microbiomes for environmental applications. This NSERC RTI will enable the implementation of a unique high-throughput platform for testing inter-species and host-microbiome associations.