A high-throughput phenotyping platform for genome and microbiome evolution

我们使用大规模的平行实验来研究基因组和微生物群如何在不同的环境中进化。为此，我们使用多孔板在顶针大小的微型宇宙或更小的微型宇宙中种植了一些世界上最小的动植物，浮萍(Lemna)和线虫(Canowhabditis)，然后在高度重复的多因素实验中对表型和适应性进行了数千次测量。我们操纵它们的基因类型、物种组成和非生物环境；测量它们的特征和生长速度，通常伴随着基因组或微生物组测序。为了使我们的实验真正高通量，我们迫切需要新的设备来实现平板填充、数据收集和分析的自动化。拟议的NSERC RTI资金将使我们能够购买一个集成系统，包括用于填充平板的液体处理机器人，用于自动测量种群增长率和其他特征的平板阅读器，用于对复杂微生物群落中不同细菌的细胞进行计数的流式细胞仪，用于培养细菌的摇床，用于获取和处理大量井板的数字图像的图像分析系统，以及用于为转基因和其他实验操作制造微注射针的抽针器。*这种由RTI支持的基础设施将使我们能够大幅加快我们由NSERC Discovery资助的研究项目的进展。有可能推动我们对基因组和微生物组进化的理解取得重大突破。我们将能够进行有史以来最大的微生物群实验操作，并通过实验进化我们的研究生物体，以更好地了解环境污染物和气候变化背景下的物种形成和适应。有了RTI资助的设备，我们的总部将使用尖端技术来丰富他们的培训计划，为他们在工业、学术界和政府的职业生涯做好准备。我们的实验对于进化和生态学中基础的、发现驱动的研究都很重要，它们也具有应用价值；例如，朝着为环境应用设计微生物群的目标。这一NSERC RTI将使一个独特的高通量平台得以实施，以测试物种间和宿主-微生物组关联。

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.