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发挥着重要作用，并对粮食安全、极端天气和海岸线变化具有重大影响。许多活着的生物体，包括细菌和古菌等微小细胞，都通过在自然界中生产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高度丰富，包括在覆盖大部分行星表面的深海生态系统中。因此，Rubisco可能代表了海洋微生物帮助缓解气候变化的一种重要方式。为了充分量化这一潜力，迫切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使用Rubisco识别细菌和古菌，并全面描述它们的多样性、生态和分布，来解决科学理解中的这些关键差距。这一知识还将有助于描述具有Rubisco的生物体在向该栖息地的其他成员提供必要的碳方面可能发挥的作用。在陆地上，植物利用Rubisco蛋白质生长和生产生物质。通过提供具有潜在新的生化特征的新的Rubisco序列，我们的研究还可以帮助正在进行的努力，设计陆地植物，以更有效地吸收碳，并最终提高作物产量。更广泛地说，该项目在很大程度上借鉴了编程原则，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。该项目还将为对微生物学和海洋科学感兴趣的本科生提供指导和建议，重点是那些来自历史上被排除在外的群体的学生。具体地说，拟议的项目将建立一个关于深海Rubisco多样性的全面图景，并为利用它来固定二氧化碳的生物的生态提供新的认识。首先，将汇集一大套公开可用的全球中上层和深海微生物群的元基因组数据，以研究Rubisco编码生物(REO)的系统发育和酶多样性。下一步，将通过测试REO主动结合同位素标记的碳酸氢盐的能力来对碳固定潜力的元基因组预测进行实验评估。第三，这些孵化的结果将被用来识别和表征活跃的REO，并随后探索能量支持自养发生的成对分解代谢(S)。最后，这些合并的发现将被用来研究Rubisco的进化起源，以及整个生命树上塑造其序列和功能多样性的过程。这些分析将解决有关碳固定的起源以及影响其在细菌和古生物领域分布的过程的重要悬而未决的问题。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.