High-throughput nanoscale culture and screening applications for microbiome research

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Uncultivated microorganisms represent the invisible majority of living things on Earth. There are an estimated 10^30 prokaryotic microorganisms on the planet, encompassing two of three domains and radiating into numerous “dark matter” divisions with no cultured representatives. Microbial abundance eclipses the number of stars in the known universe, the number of neurons in our brains and all of our synapses combined. Collectively, interconnected microbial communties drive matter and energy conversion processes that help create and sustain the conditions for life on Earth. For over 3.5 billion years microorganisms have evolved to solve complex metabolic problems at the individual, population and community levels, innovating distributed solutions to nutrient and energy conversion processes that have withstood the test of time and generated a deep reservoir of genomic potential. This potential includes countless metabolic processes as well as enzyme variants adapted to local environmental conditions. In order to access the hidden metabolic problem-solving power of this microcosmos we need new platforms and approaches that provide coherent taxonomic resolution, closed reference genomes and the potential for genetic tractability. When combined with functional screening to uncover novel enzyme functions we become poised to move beyond the known cartography of metabolic interactions into a deeper understanding of biological systems. Here we propose to combine high-throughput nanoscale culture and screening applications leveraging the capabilities of a transformative automation system called the Prospector to isolate key microbial players involved in anaerobic digestion, mine tailings remediation and lignocellulose biomass conversion. Resulting isolate collections will be used to generate closed reference genomes for metabolic pathway inference and enable the development of synthetic microbial consortia and whole-cell biocatalysts when combined with functional screening applications in both plate-based and microfluidic droplet formats. Use of the Prospector will contribute to the training of a diverse and interdisciplinary cadre of highly qualified personnel working across multiple research groups and faculties in the Life Sciences and Engineering and open up new opportunities for metabolic pathway engineering and cross-sector biotechnology innovation in support of the emerging bioeconomy in Canada.