Expanding the frontiers of microbial diversity and function

微生物群落控制着碳和养分的生物地球化学循环，影响土壤和水环境的肥力，维持人体的健康功能，在食品工业中发挥着重要作用，并在生物技术方面提供了无数的应用。微生物对人类生活和全球气候的深刻影响突显了研究环境中微生物的生物地理学、探索与未培养的微生物生命相关的大量基因资源以及扩大我们对地球上大多数微生物物种的知识的价值：这些微生物的相对丰度较低。尽管技术限制阻碍了微生物生态学家量化微生物多样性和充分描述微生物群落的能力，但情况已经不再是这样了。我的研究计划利用下一代测序和计算生物学的进步来探索陆地和水环境中的微生物生物地理学。通过这样做，我们瞄准并回收新的微生物物种，这些微生物物种将扩大我们对生命树的知识，并使我们能够挖掘基因组，以实现科学突破和工业利益。我的研究计划的长期目标是确定影响微生物群落组成和多样性的因素，将特定的微生物群体与环境参数联系起来，发现陆地和水生环境中低丰度的新微生物，并调查参与碳和氮的生产和衰减的关键微生物。我的研究计划将继续提供对土壤和淡水微生物生态学原理的洞察，产生预测性数据集，这些数据集将指导发现新的生物和酶，在未来许多年对研究和工业有价值。我的具体短期目标包括：1)描述微生物生物地理学和稀有慈善研究保护区(安大略省剑桥)的稀有生物圈，2)生成大河流域的全面微生物地图，3)探索氨氧化古菌(AOA；我们的模型稀有生物圈成员)在工程淡水环境中的新陈代谢和生态意义。这项建议包括一项关于高度新颖的AOA的基因组和代谢特征的计划，在过去的两年里，我们已经将其浓缩到接近纯度：念珠菌、亚硝酸假丝酵母和水产假丝酵母。总之，拟议的研究计划将开发群落结构的量化模型，并揭示尚未发现的稀有微生物。确定控制微生物多样性的模式能够为土壤和水管理实践提供强有力的预测性方法，并有助于集中培养和基于元基因组学发现与生物地球化学循环和潜在工业应用两者相关的生物体。

Microbial communities govern biogeochemical cycling of carbon and nutrients, impact the fertility of soils and aquatic environments, maintain the healthy function of human bodies, play an important role in the food industry, and offer countless applications in biotechnology. The profound influence of microorganisms on human life and the global climate underlines the value of studying the biogeography of microorganisms in the environment, exploring the vast resource of genes associated with uncultured microbial life, and expanding our knowledge of most microbial species on earth: those present at low relative abundance. Although technical limitations have hindered the ability of microbial ecologists to quantify microbial diversity and adequately characterize microbial communities, this is no longer the case. My research program leverages advances in next-generation sequencing and computational biology to explore microbial biogeography in terrestrial and aquatic environments. In doing so, we target and recover novel microbial species that will expand our knowledge of the tree of life and enable us to mine genomes for scientific breakthroughs and industrial benefit.The long-term goals of my research program are to identify factors that influence microbial community composition and diversity, link specific microbial groups to environmental parameters, discover novel microorganisms present at low abundance in terrestrial and aquatic environments, and investigate key microorganisms involved in the production and attenuation of carbon and nitrogen. My research program will continue to offer insight into the principles of soil and freshwater microbial ecology, producing predictive datasets that will guide the discovery of new organisms and enzymes of value to research and industry for many years to come.My specific short-term objectives include: 1) Characterise microbial biogeography and the rare biosphere of the rare Charitable Research Reserve (Cambridge, Ontario), 2) Generate a comprehensive microbial map of the Grand River watershed, and 3) Explore the metabolism and ecological significance of ammonia-oxidizing archaea (AOA; our model rare biosphere members) within engineered freshwater environments. This proposal includes a plan for genomic and metabolic characterization of highly novel AOA that we have enriched to near purity over the past two years: Candidatus Nitrosofontus exaquare and Candidatus Nitrosopura aquariensis. Together, the proposed research program will develop quantitative models of community structure and reveal rare microorganisms that have not yet been discovered. Identifying patterns governing microbial diversity enables strong predictive approaches for soil and water management practices and assists in focused cultivation- and metagenomics-based discovery of organisms of relevance for both biogeochemical cycling and potential industrial applications.