Engineering Anaerobic Microbiomes for Resource Recovery

加拿大在从废物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。释放这一潜力将需要生物工程创新，将可再生能源和化学品从工业规模的废物流中商品化。系统和合成生物学方面的革命性进展将使这些创新成为可能，因为DNA测序、质谱学和基因组编辑方面的突破使控制微生物群落(微生物组)的新陈代谢成为可能，从单基因延伸到整个生态系统。然而，由于微生物-微生物相互作用的高度复杂性，以及缺乏以精确方式操纵微生物群的组装和功能的工具，将这些发展大规模地纳入生物技术受到了限制。该研究计划的长期目标是1)创造从废物中回收宝贵资源的新型厌氧生物技术，2)开发促进微生物组工程的系统和合成生物学方法。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)组装将有机废物转化为中链脂肪酸的合成微生物群2)使用先进的代谢组学工具量化微生物群中的代谢相互作用3)开发新的遗传工具来操纵非模式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。这包括合理操作、预测和设计微生物组代谢的新工具，以及可持续生物生产油脂化学品的下一代生物工艺，包括从低价值废物中提取中链脂肪酸、醇和烷烃。这将增加加拿大产生的废物(每年约1800万吨)从垃圾填埋场转移出去，减少目前占全国甲烷排放量13%的温室气体排放，同时生产使资源回收在经济上可行的高价值化学品。这项研究还将有助于对高素质人才的多学科培训，他们将获得应用于微生物组工程的基因组学、先进质谱学、自动化和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.