OCE-PRF Beyond the light: ecological and evolutionary insights into RuBisCO from the dark ocean

大气中二氧化碳等温室气体的积累在气候变化中起着重要作用，并对粮食安全、极端天气和不断变化的海岸线产生重大影响。许多生物体，包括细菌和古细菌等微观细胞，通过在自然界中产生和消耗温室气体来影响温室气体的积累。例如，在许多微生物中，一种名为RuBisCO的蛋白质可以从大气中去除二氧化碳，并将其转化为碳源或生长所需的能量。这种蛋白质被认为在地球上非常丰富，包括覆盖大部分行星表面的深海生态系统。因此，RuBisCO可能代表了海洋微生物帮助减缓气候变化的一种重要方式。为了充分量化这一潜力，非常需要更好地了解深海中哪些生物使用RuBisCO，它们有多常见以及它们在哪里被发现。在这个项目中，我们将通过在深海中用RuBisCO识别细菌和古菌，并全面表征它们的多样性、生态和分布，来解决科学认识中的这些关键差距。这些知识也将有助于描述生物体与RuBisCO可能发挥的作用，在提供必要的碳，这个栖息地的其他成员。在陆地上，RuBisCO蛋白被植物用来生长和生产生物质。通过提供具有潜在新生化特征的新RuBisCO序列，我们的研究还可以帮助正在进行的工程陆地植物更有效地吸收碳并最终提高作物产量的努力。更广泛地说，该项目大量借鉴了编程原则，并将其应用于海洋微生物学领域。这些技能将通过为来自服务不足社区的高中生开设的计算机科学入门课程与更广泛的公众分享。该项目的外联工作还将包括为对微生物学和海洋科学感兴趣的本科生提供指导和咨询，重点关注那些来自历史上被排斥的群体，具体而言，拟议的项目将全面了解深海的RuBisCO多样性，并为利用其固定二氧化碳的生物生态学提供新的认识。首先，将收集大量来自全球中层和深海微生物的公开宏基因组数据，以研究RuBisCO编码生物（REO）的系统发育和酶多样性。接下来，碳固定潜力的宏基因组预测将通过测试REO主动掺入同位素标记的碳酸氢盐的能力进行实验评估。第三，这些孵育的结果将用于鉴定和表征活性REO，并随后探索在其发生的地方大力支持自养的成对催化剂。最后，综合研究结果将用于研究RuBisCO的进化起源以及在生命树中塑造其序列和功能多样性的过程。这些分析将解决围绕碳固定起源的重要未决问题，以及影响其在细菌和微生物领域分布的过程。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。

Atmospheric accumulation of greenhouse gasses like carbon dioxide plays an important role in climate change and has major implications for food security, extreme weather, and changing coastlines. Many living organisms, including microscopic cells like bacteria and archaea, impact the accumulation of greenhouse gasses by both producing and consuming them in nature. For example, in many microorganisms, a protein called RuBisCO removes carbon dioxide from the atmosphere and converts it into a source of carbon or energy for growth. This protein is thought to be highly abundant on Earth, including in deep ocean ecosystems that cover much of the planetary surface. Thus, RuBisCO may represent an important way ocean microbes could help mitigate climate change. To fully quantify this potential, a better understanding of which organisms use RuBisCO in the deep sea, how common they are, and where they are found is highly needed. In this project, we will address these key gaps in scientific understanding by identifying bacteria and archaea with RuBisCO in the deep sea and comprehensively characterizing their diversity, ecology, and distribution. This knowledge will also help to describe the roles that organisms with RuBisCO might play in supplying necessary carbon to other members of this habitat. On land, the RuBisCO protein is used by plants to grow and produce biomass. By providing new RuBisCO sequences with potentially novel biochemical features, our research could also aid ongoing efforts to engineer land plants to more efficiently uptake carbon and ultimately increase crop yields. More broadly, this project draws heavily on principles of programming and applies them to the field of marine microbiology. These skills will be shared with the broader public through an introductory computer science course for high school students from underserved communities. Outreach for this project will also include mentorship and advising of undergraduate students interested in microbiology and marine science, with a focus on those from historically excluded groups.Specifically, the proposed project will build a comprehensive picture of RuBisCO diversity in the deep sea and shed new light on the ecology of organisms that use it to fix carbon dioxide. First, a large set of publicly-available metagenomic data from global mesopelagic and bathypelagic microbiomes will be assembled to examine the phylogenetic and enzymatic diversity of RuBisCO-encoding organisms (REOs). Next, metagenomic predictions of carbon fixation potential will be experimentally assessed by testing the ability of REOs to actively incorporate isotopically labelled bicarbonate. Third, the results of these incubations will be used to identify and characterize active REOs and subsequently explore the paired catabolism(s) energetically supporting autotrophy, where it is occurring. Finally, the combined findings will be used to examine the evolutionary origins of RuBisCO and the processes shaping its sequence and functional diversity across the tree of life. These analyses will address important outstanding questions around the origin of carbon fixation and the processes shaping its distribution in the domains Bacteria and Archaea.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.