CAREER: Microbial Activity and Chemoautotrophy in the Deep Sea: Who, How, and How Much?

深海的定义是深度超过200米，是地球表面最大、开发最少的栖息地。它覆盖了近三分之二的地球表面，按体积计算包含了大约75%的海水，并且是大约55%的海洋微生物的家园。深海微生物可在塑造全球化学和气候方面发挥重要作用，例如产生和消耗温室气体(如二氧化碳和一氧化二氮)。然而，深海水域的微生物学相对于表层海洋的微生物学研究不足。最近的数据表明，在深度上有比之前认为的更多样化和更活跃的微生物群落，但还有很多事情需要了解。例如，最近的估计表明，深海中大约60%的微生物物种是新的。该项目研究深海微生物的代谢活动，重点是化学自养和碳循环。化学营养是一种利用化学能将无机碳(如二氧化碳)转化为糖和生物质的微生物代谢过程。这个项目使用了几种最先进的采样和分析技术来确定哪些物种进行化学自养(谁？)，什么类型的化学能支持它(如何？)，以及它发生的速度(多少？)在整个深海。回答这些问题提供了对深海微生物生态的洞察，以及关于深水碳源和碳汇的定量数据。结果将促进我们对海洋在长时间尺度上封存碳的能力的理解。这项工作有益于社会，因为它的发现对我们预测和缓解气候变化的能力以及它的教育使命的影响，包括通过一对一的指导、实践课程和发起以学生研究为特色的年度区域研讨会，在跨学科的气候相关科学方面培训不同的高中生、本科生和研究生。该项目调查中大洋和半大洋海洋层(200至4000米水深)中未养殖微生物的遗传潜力和活动，以确定深海微生物学的特征，并解决海洋碳循环中的一个差异，即呼吸速率始终超过对进入暗海的碳的垂直输入的估计。化学自养至少可以解释这种差异的一部分，但已知类型的化学自养(例如，与氨和亚硝酸盐氧化耦合)不足以弥合这一差距，这表明新的化学自养和不同的耦合分解代谢。最重要的假设是：(1)深海微生物比目前所认识的更活跃，(2)支持这一活动所需的有机碳至少部分是由更高的内源无机碳固定率提供的，(3)碳固定是由比目前已知的更具系统发育和代谢多样性的化学自养/混合营养生物来执行的。本研究在两次深海海洋考察中使用高压采样容器，元基因组学、元转录组学和稳定同位素实验，并通过纳米SIMS进行单细胞同位素分析，以(1)定量一般微生物的合成代谢活性，特别是在散体和单细胞水平上的化学自养、混合营养和异养，(2)表征参与化学自养和异养的基因和转录本的多样性和分布，(3)鉴定新的自养和混合营养生物，并量化它们对碳循环的贡献，以及(4)调查主要的自养深海谱系--海洋第一组--塔乌姆考古种群利用有机质的能力。这一结果有可能揭示未培养微生物的新功能，并改变我们对海洋碳循环的理解。这一奖项反映了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。

The deep sea, defined as deeper than 200 m, is the largest and least explored habitat on the surface of our planet. It covers nearly two-thirds of the Earth's surface, contains approximately 75% of marine water by volume, and is home to about 55% of all marine microorganisms. Deep-sea microorganisms can play important roles in shaping global chemistry and climate, for example producing and consuming greenhouse gases (e.g., carbon dioxide and nitrous oxide). However, the microbiology of deep-sea waters is understudied relative to that of the surface ocean. Recent data suggests a much more diverse and active microbial community at depth than previously thought, but much remains to be known. For instance, recent estimates suggest that approximately 60% of the microbial species in the deep sea are novel. This project investigates the metabolic activity of deep-sea microorganisms, focusing on chemoautotrophy and the carbon cycle. Chemoautotrophy is a microbial metabolism in which inorganic carbon (e.g., carbon dioxide) is converted to sugar and biomass using chemical energy. This project uses several state-of-the-art sampling and analyses techniques to determine which species conduct chemoautotrophy (who?), what types of chemical energy support it (how?), and at what rate it occurs (how much?) throughout the deep sea. Answering these questions provides insight into deep-sea microbial ecology and quantitative data on the sources and sinks of carbon in deep waters. Results will advance our understanding of the ability of our oceans to sequester carbon over long timescales. This work benefits society through the implications of its findings for our ability to predict and mitigate climate change, as well as its educational mission, which includes training diverse high school, undergraduate, and graduate students in interdisciplinary, climate-relevant science through one-on-one mentorship, hands-on coursework, and the initiation of an annual regional symposium featuring student research. This project investigates uncultured microorganisms' genetic potential and activity in the mesopelagic and bathypelagic oceanographic layers (200 to 4000 m water depth) to characterize deep-sea microbiology and address a discrepancy in the marine carbon cycle, namely, that respiration rates consistently exceed estimates of vertical inputs of carbon to the dark ocean. Chemoautotrophy may explain at least part of this discrepancy, but known types of chemoautotrophy (e.g., coupled to ammonia and nitrite oxidation) are insufficient to bridge the gap, suggesting novel chemoautotrophs and diverse coupled catabolisms. The overarching hypotheses are that (1) deep-sea microorganisms are more active than currently appreciated, (2) the organic carbon required to support this activity is provided, at least in part, by higher rates of endogenous inorganic carbon fixation, and (3) carbon fixation is performed by more phylogenetically and metabolically diverse chemoautotrophs/mixotrophs than currently known. This study uses high-pressure sampling containers during two deep-sea oceanographic expeditions, metagenomics, metatranscriptomics, and stable-isotope experiments coupled to single-cell isotope analyses via nanoSIMS to (1) quantify microbial anabolic activity in general and chemoautotrophy, mixotrophy, and heterotrophy specifically at bulk and single-cell levels, (2) characterize the diversity and distribution of genes and transcripts involved in chemoautotrophy and heterotrophy, (3) identify novel chemoautotrophs and mixotrophs and quantify their contribution to carbon cycling, and (4) investigate the ability of a major chemoautotrophic deep-sea lineage, the Marine Group I Thaumarchaeota, to utilize organic matter. The results have the potential to reveal novel functions in uncultured microbes and change our understanding of marine carbon cycling.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.