Dimensions: Ordering the microbial world into natural genetic, ecological, and functional units

我们星球上生物多样性的绝大多数是微生物，由于DNA测序技术的进步，这种多样性正在以前所未有的速度被发现。然而，我们对微生物多样性的程度、微生物多样性是如何产生、维持和被进化塑造的，以及它在地球生态系统中的作用的无知，极大地阻碍了我们对这些有机体的作用的理解。了解微生物世界的这些方面对于社会的几个关键问题是基本的，例如“新出现的疾病是新物种，还是现有疾病的变种？”以及“微生物种群将如何应对气候变化？”该项目有一个雄心勃勃的目标，即开发方法，首次允许以具有生物学意义的方式对所有微生物物种进行分类，并将揭示产生新物种的因素。这项研究是四个实验室之间的合作，这些实验室在微生物生物学、基因组分析、进化遗传学和统计学方面具有互补的科学优势。除了促进科学家对微生物的基本了解外，该项目还将为培养本科生、研究生和即将成为独立科学家的博士后学者提供一个重要平台。这项研究计划本身涉及三个主要目标。第一个主要目标是在生物物种概念(BSC)提供的框架下识别细菌物种，该概念将物种定义为遗传和生殖隔离的单位。应用这一框架将统一细菌和真核生物的系统发育组织，使研究人员能够确定物种之间的功能和生态差异，并量化它们之间的遗传交换的速度和数量。第二个主要目标是区分“生态型”，这些“生态型”代表物种内生态、功能或地理上孤立的种群。这一目标将基于一个在真核系统发育学中已经确立的名为“融合”的遗传框架。这项工作将揭示微生物多样性的新维度，并开发新的统计工具，供其他科学家使用。第三个主要目标是确定细菌物种形成的过程是如何发生的，以及它是否模仿了在真核生物中观察到的模式。这一目标将通过检查与宿主物种(包括人类)共同多样化的细菌基因组中的基因交换模式来实现，结果将提供新细菌物种出现所需时间的第一次测量。这一奖项反映了NSF的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

The vast majority of our planet's biological diversity is microbial, and this diversity is being discovered at unprecedented rates due to advances in DNA sequencing technologies. Understanding the roles of these organisms, however, has been greatly hindered by our ignorance of the extent of microbial diversity, how it is generated, maintained, and shaped by evolution, and how it functions in the Earth's ecosystems. Understanding these aspects of the microbial world are fundamental to several questions critical to society, such as "Are emerging diseases new species, or variants of existing ones?", and "How will microbial populations respond to changing climates?". This project has the ambitious goals of developing methods that will for the first time allow all microbial species to be classified in a biologically meaningful way, and it will reveal the factors that give rise to new species. The research is a collaboration between four laboratories that have complementary scientific strengths in microbial biology, genome analysis, evolutionary genetics, and statistics. In addition to advancing scientists' fundamental understanding of microbes, the project will provide an important platform for training undergraduates, graduate students, and the postdoctoral scholars that will soon become independent scientists. This research program itself involves three major aims. The first major aim is to identify bacterial species under the framework provided by the Biological Species Concept (BSC), which defines species as genetically and reproductively isolated units. Applying this framework will unify the phylogenetic organization of bacteria with that of eukaryotes, and allow the researchers to determine the functional and ecological differences among species, and to quantify the rates and amounts of genetic exchange between them. The second major aim is to distinguish "ecotypes" that represent ecologically, functionally, or geographically isolated populations within species. This aim will be based on a genetic framework called "coalescence" that is well-established in eukaryotic phylogenetics. This work will both uncover new dimensions of microbial diversity and develop new statistical tools for other scientists to use. The third major aim is to determine how the process of bacterial speciation occurs and whether it mimics the patterns observed in eukaryotes. This aim will be accomplished by examining the patterns of gene exchange in the genomes of bacteria that have co-diversified with their host species (including humans), and the results will provide the first measurement of the amount of time required for the emergence of new bacterial species.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.