PurSUiT: Uncovering bacterial and archaeal diversity in Great Basin hot springs

微生物是最普遍、最古老和最有弹性的生命形式，表现出几种独特的代谢能力和对极端环境的显著适应。这些特性导致微生物在各种工业过程中的使用，从生物燃料生产和废水处理到石油泄漏的生物修复和药物生产。尽管微生物普遍存在且重要，但迄今为止，只有一小部分微生物被描述和分类，导致其工业潜力未得到充分利用，并在我们对生命的理解中存在重大差距。该项目旨在通过探索美国大盆地温泉中以前未被发现的微生物多样性来缩小这一差距，这些温泉是地球上最极端和最不了解的环境。我们瞄准大盆地温泉的理由是四方面的。首先，温泉对生物施加了强大的选择压力，从而增加了发现新物种的可能性。其次，温泉可能类似于地球上最早的一些生命栖息环境，从而使人们深入了解生命的起源。第三，已知温泉中发现的原核生物表现出很强的地方性，因此从微生物的角度来看，温泉可以被认为是“孤岛”，每个温泉都有独特的多样性。这种“岛屿”性质预计将在大部分干旱的沙漠般的大盆地特别明显。第四，大盆地有丰富的地热特征，但研究仍然很少。我们的数据将被公开，从而成为社会的宝贵资源。从大量研究不足的分类学群体中发现新物种，将有助于今后根据预测的营养需求培养新的微生物及其生理特性。增加微生物生命树的覆盖面也将有助于重建各种进化事件的时间和顺序，这些事件被认为塑造了我们星球的表面化学和气候。该项目将通过参与研究活动以及通过微生物学暑期课程，为学生提供实地工作、实验室工作和生物信息学方面的实践培训。该项目的目的是在美国大盆地的40个温泉中以全基因组分辨率恢复新的微生物（细菌和古菌）多样性，使用非培养基因组解析宏基因组学。选择温泉是为了最大限度地发掘新的微生物多样性。通过与参考数据库的比较，将对所收集的基因组进行分类学分类和功能注释。此外，将通过冷冻保存和冻干对每份样品的材料进行存档，以便于对回收的微生物多样性进行后续研究。该项目预计将导致发现1000-1500个新的原核生物物种，其中许多来自新的纲甚至门。该项目还将收集丰富的地球化学元数据，如离子浓度，pH值和温度，为恢复的基因组提供环境背景。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Microbes are the most ubiquitous, most ancient and most resilient form of life, exhibiting several unique metabolic capabilities and remarkable adaptations to extreme environments. These properties have led to the use of microbes in a variety of industrial processes, ranging from biofuel production and wastewater treatment to bioremediation of oil spills and drug production. Despite their ubiquity and importance, only a minuscule fraction of microbes has been characterized and taxonomically classified so far, resulting in a large underutilization of their industrial potential and a major gap in our understanding of life. This project aims to reduce this gap by exploring previously undiscovered microbial diversity in hot springs across the US Great Basin, which are some of Earth's most extreme and least understood environments. Our rationale for targeting Great Basin hot springs is four-fold. First, hot springs exert strong selective pressures on organisms, thus increasing the potential for discovering novel species. Second, hot springs likely resemble some of the earliest life-harboring environments on Earth, thus yielding insight into the origins of life. Third, prokaryotes found in hot springs are known to exhibit strong degrees of endemism, and hence hot springs can be considered "isolated islands" from a microbial perspective, each with unique diversity. This "island"-nature is expected to be particularly pronounced in the largely arid desert-like Great Basin. Fourth, the Great Basin is rich in geothermal features that nevertheless remain poorly studied. Our data will be made publicly available, thus serving as a valuable resource to society. The discovery of new species from a large number of poorly studied taxonomic groups will assist in the future cultivation of new microorganisms and their physiological characterization, based on predicted nutrient requirements. Increasing the coverage of the microbial tree of life will also facilitate reconstruction of the timing and order of various evolutionary events believed to have shaped our planet's surface chemistry and climate. The project will provide hands-on training to students in field work, lab work and bioinformatics, through participation in the research activities as well as through a microbiology summer course. The project aims to recover novel microbial (bacterial and archaeal) diversity in 40 hot springs across the US Great Basin at whole-genome resolution, using culture-independent genome-resolved metagenomics. The hot springs have been chosen such that the potential for discovery of new microbial diversity is maximized. Recovered genomes will be taxonomically classified and functionally annotated through comparison to reference databases. In addition, material from each sample will be archived via cryopreservation as well as lyophilization, to facilitate follow-up investigations of the recovered microbial diversity. The project is expected to lead to the discovery of 1000-1500 new prokaryotic species, many of which from new classes and even phyla. The project will also collect rich geochemical metadata, such as ion concentrations, pH and temperatures, to provide environmental context for the recovered genomes.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.