Engineering Anaerobic Microbiomes for Resource Recovery

加拿大在从废物流中回收可再生生物能源和生物产品方面具有巨大潜力，同时减少废物处理的影响和我们对化石燃料的依赖。释放这一潜力需要生物工程创新，将可再生能源和工业规模的废物流中的化学品商品化。随着DNA测序、质谱分析和基因组编辑技术的突破，系统生物学和合成生物学的革命性进步使这些创新成为可能，从而有机会控制微生物群落（“微生物组”）的代谢，从单个基因扩展到整个生态系统。然而，将这些发展大规模地纳入生物技术受到微生物-微生物相互作用的高度复杂性和缺乏以精确方式操纵微生物组的组装和功能的工具的限制。该研究项目的长期目标是：1)创造新的厌氧生物技术，从废物流中回收有价值的资源；2)开发系统和合成生物学方法，推进微生物组工程。这项工作将直接影响废水处理和固体废物管理实践，为加拿大的循环生物经济做出贡献。为了实现这些目标，短期研究目标是：1)组装合成微生物组，将有机废物转化为中链脂肪酸2)使用先进的代谢组学工具量化微生物组中的代谢相互作用3)开发新的遗传工具来操纵非模型脂肪酸产生细菌如果成功，拟议的计划将导致新的生物技术创新，通过资源回收加速加拿大向可持续循环经济的过渡。这包括合理操纵、预测和设计微生物组代谢的新工具，以及从低价值废物中可持续生产油脂化学品（包括中链脂肪酸、醇和烷烃）的下一代生物工艺。这将增加加拿大从垃圾填埋场产生的废物（每年约1800万吨）的转移，减少目前占全国甲烷排放量13%的温室气体排放，同时生产高价值化学品，使资源回收在经济上可行。该研究还将有助于培养多学科的高素质人才，他们将获得基因组学、先进质谱、自动化和应用于微生物组工程的可持续生物处理方面的高级技能，使他们成为不同研究和工程实践领域的领导者。

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.