Engineering Anaerobic Microbiomes for Resource Recovery

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Canada has enormous potential to recover renewable bioenergy and bioproducts from waste streams, while simultaneously reducing waste disposal impacts and our dependance on fossil fuels. Unlocking this potential will require bioengineering innovation to commoditize renewable energy and chemicals from waste streams at industrial scales. Revolutionary advances in systems and synthetic biology are positioned to make these innovations possible, as breakthroughs in DNA sequencing, mass spectrometry, and genome editing have enabled opportunities to control the metabolism of microbial communities ("microbiome"), extending from single genes to whole ecosystems. However, incorporating these developments into biotechnologies at scale has been limited by the high complexity of microbe-microbe interactions and the lack of tools to manipulate the assembly and function of microbiomes in a precise manner. The long-term goals of the research program are to 1) create novel anaerobic biotechnologies that recover valuable resources from waste streams, and 2) develop systems and synthetic biology approaches that advance microbiome engineering. This work will directly impact wastewater treatment and solid waste management practices, contributing to a circular bioeconomy in Canada. Working towards these goals, the short-term research objectives are to: 1)Assemble synthetic microbiomes that convert organic wastes into medium chain fatty acids 2)Quantify metabolic interactions in microbiomes using advanced metabolomic tools 3)Develop new genetic tools to manipulate non-model fatty acid producing bacteria If successful, the proposed program will lead to new biotechnological innovations that accelerate Canada's transition to a sustainable circular economy through resource recovery. This includes new tools to rationally manipulate, predict, and engineer microbiome metabolism, and a next-generation of bioprocesses for sustainable biomanufacturing of oleochemicals, including medium chain fatty acids, alcohols, and alkanes from low-value wastes. This will increase the diversion of waste (~18 million tonnes annually) generated in Canada away from landfills, reducing GHG production that currently accounts for 13% of national methane emissions, while producing high-value chemicals that renders resource recovery economically viable. The research will also contribute to the multi-disciplinary training of highly qualified personnel who will gain advanced skills in genomics, advanced mass spectrometry, automation, and sustainable bioprocessing applied to microbiome engineering, positioning them to be leaders in diverse areas of research and engineering practice.