CAREER: Targeted Environmental Genomics: Stable Isotope Probing of Non-cultivated Diazotrophs in Soil

固氮是一种古老的微生物过程，在我们星球的历史早期就已经进化，对生物圈至关重要。所有生物都需要固定的氮素来进行生物合成，土壤中的固氮微生物为许多陆地生态系统提供了主要的自然氮源。尽管它们具有古老而持久的生态重要性，但人们对这些微生物和一般土壤微生物的生态学和进化知之甚少。这项研究工作将实施一种新的方法，将稳定的同位素探测与环境基因组学相结合，以定位非培养的重氮菌的基因组。这种方法将允许从这些非培养微生物中获取基因组DNA，提供了一个极好的机会来促进我们对环境和基因组机制的理解，这些机制调节着对全球N循环至关重要的微生物过程的多样性和活性。获得的基因组序列将通过揭示以前未描述的微生物中固氮酶超操纵子的复杂结构，有助于阐明固氮的进化和基因组进化。此外，通过以该微生物群落为模型，本研究将揭示与微生物多样性的功能意义有关的基本原理，以及调控土壤中微生物过程的机制。因此，该项目将产生具体和深远的影响，将提高对土壤中微生物过程的了解，并提高有效管理陆地生态系统的能力。作为该项目的一部分，将制定一个由三个部分组成的教育计划，旨在提高科学素养，提高对微生物学的认识，并培训下一代环境基因组学研究人员。第一个组成部分是“微生物地球”暑期讲习班，该讲习班将为高中科学教师提供模块，使他们能够在课程中实施开放式实验室练习，并将提供设备和援助，帮助他们实现教学目标。第二个部分是康奈尔大学数码塔网站的一个名为“微生物前沿的生物勘探”的网络模块。这个多媒体单元将突出环境基因组学在发现新的生命模式和有价值的新酶方面的作用。最后一个组成部分是环境基因组学高级本科课程，以测试利用基因组学合作社的本科生来实现双重目标的想法，即为学生提供初步研究经验，同时为原始基因组数据的分析和注释做出贡献。

Nitrogen (N) fixation is an ancient microbial process which evolved early in the history of our planet and is of central importance to the biosphere. All living things require fixed N for biosynthesis and N-fixing microbes in soils provide the dominant natural source of N in many terrestrial ecosystems. Despite their ancient and enduring ecological importance remarkably littleis known about the ecology and evolution of these microorganisms and of soil microbes in general. This research effort will implement a novel approach that combines stable isotope probing in concert with environmental genomics to target the genomes of non-cultivated diazotrophs. This approach will allow access to genomic DNA from these non-cultivated microbes, providing a remarkable opportunity to advance our understanding of the environmental and genomic mechanisms that regulate the diversity and activity of a microbial process of central importance to the global N-cycle. The genome sequences obtained will help shed light on the evolution of N-fixation and on genome evolution in general by revealing the complex structure of nitrogenase supraoperons in previously uncharacterized microorganisms. In addition, by using this microbial community as a model, this research will reveal basic principles pertaining to the functional significance of microbial diversity and the mechanisms that regulate microbial process in soils. Thus, this project will have both specific and far reaching effects that will improve understanding of microbial processes in the soil, and the ability to effectively manage terrestrial ecosystems. As part of this project an educational program will be developed that is composed of three components designed to increase science literacy, to improve awareness of microbiology, and to train the next generation of environmental genomics researchers. The first component is a summer workshop "The Microbial Earth" that will provide high school science teachers with modules allowing them to implement open ended laboratory exercises in their curricula and will provide equipment and assistance to help them achieve their teaching goals. The second component is a web module called "Bioprospecting on the Frontiers of Microbiology" for the Cornell CyberTower site. This multimedia module will highlight the role of environmental genomics in discovering novel modes of life and valuable new enzymes. The last component is an advanced undergraduate course in environmental genomics to test the idea of using undergraduates in genomics cooperatives to achieve the dual goals of providing students with primary research experience while contributing to the analysis and annotation of raw genome data.