Collaborative Research: Illuminating microbes and their viruses within the dark ocean crust through strain-level approaches

我们星球的海底主要由玄武岩基底上的沉积层组成。每隔5万到10万年，相当于整个全球海洋的海水就会通过海底下的裂缝和裂缝循环，形成地球上最大的微生物储存库之一。虽然在大洋中脊标志性的热液喷口排放的高温流体在视觉上引人注目，但流入和流出这些脊的侧翼的流体大约大三个数量级，与所有河流向海洋的排放相媲美。当它穿过深海海底时，这种流体会因水和岩石的相互作用以及微生物的代谢活动而发生显着变化，这些微生物被认为最终有助于塑造全球海洋的营养和能量预算。然而，我们对这一系统的知识和理解在很大程度上受到了后勤困难的影响，无法进入这一系统进行科学研究。最初的证据表明，具有参与关键代谢途径的酶的古老同系物的未表征微生物被认为对地球早期微生物居民很重要，它们居住在这个生物群系中，并被新型病毒感染。在这项研究中，研究人员正在进行一系列综合的观察，实验和分析，旨在通过提供新的，基本的见解来促进我们对深海海底微生物及其病毒的理解，这些生物和代谢在这种环境中是活跃的，它们的进化历史和遗传特征，以及它们的相互作用。该项目有助于发展多样化的STEM教育的劳动力，并将一名博士后科学家，两名研究生和约29名本科生的培训纳入实地研究，湿实验室实验和生物信息学。该项目还促进了科学家和夏威夷大学创意媒体学院之间的独特合作，支持学院的本科实习生与项目人员合作，制作创意视频和图形，向不同的受众传达我们研究的各个方面。最后，该项目支持两名早期职业女性科学家，他们于2017年开始担任教职。该项目利用现有的采样基础设施，能源部联合基因组研究所的DNA测序，以及对美国华盛顿海岸附近胡安德富卡岭（JdFR）侧翼的研究考察，该研究已经得到NSF的支持。在这里，海底观测站以前已经安装，以帮助探索活跃流动的海底地壳流体。这些流体将从不同的取样深度收集，用于一套综合的地球化学、基因组和培养研究。该项目的具体目标是（i）使用基因组学来表征JdFR侧翼地壳流体中的微生物和病毒种群，（ii）使用转录组学来识别与JdFR侧翼微生物内元素循环相关的活性代谢途径，以及识别这些微生物中的活性病毒感染，和（iii）从JdFR侧翼的地壳流体产生微生物和病毒纯培养物或有限多样性富集物。它结合了生物信息学分析，受控实验室实验和现场采样，以追求假设驱动和基于发现的培养实验，病毒检测以及菌株水平的生态基因组学和元转录组学分析。重要的是，研究人员打算培养新的微生物和病毒，作为研究深海地壳生命特征的模型系统。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。

Our planet's seafloor consists primarily of sediment layered over a basement of basalt rock. Every 50,000 to 100,000 years, a volume of seawater equivalent to the entire global ocean circulates through cracks and fissures of this basement beneath the seafloor, forming one of the largest reservoirs for microscopic life on Earth. While high temperature fluids discharging at iconic hydrothermal vents at mid-ocean ridges are visually striking, the fluid flowing in and out of the flanks of these ridges is around three orders of magnitude greater and rivals the discharge of all rivers to the ocean. As it travels through the deep subseafloor, this fluid is significantly altered by water and rock interaction and the metabolic activity of microorganisms that are thought to ultimately help shape nutrient and energy budgets of the global ocean. However, our knowledge and understanding of this system suffer greatly from logistical difficulties in accessing it for scientific inquiry. Initial evidence suggests uncharacterized microbes that possess ancient homologs of enzymes involved in key metabolic pathways thought to be important to Earth's early microbial inhabitants populate this biome and are infected by novel viruses. In this study, the investigators are performing an integrated set of observations, experiments, and analyses aimed to advance our understanding of deep subseafloor microbes and their viruses by providing new, fundamental insights into which organisms and metabolisms are active in this environment, their evolutionary history and genetic characteristics, and their interactions. This project contributes to the development of a diverse STEM-educated workforce, and incorporate the training of one postdoctoral scientist, two graduate students, and ~29 undergraduate students in field-based research, wet-lab experimentation, and bioinformatics. This project also fosters a unique collaboration between scientists and the University of Hawaii Academy for Creative Media that supports undergraduate interns from the Academy to work with project personnel and produce creative videos and graphics to communicate aspects of our research to diverse audiences. Finally, this project supports two early career female scientists who started faculty positions in 2017.This project leverages existing sampling infrastructure, DNA sequencing by the Department of Energy Joint Genome Institute, and a research expedition to the Juan de Fuca Ridge (JdFR) flank off the coast of Washington, USA, that is already supported by NSF. Here, subseafloor observatories have been previously installed to aid in exploring actively flowing subseafloor crustal fluids. These fluids will be collected from different sampling depths for an integrated set of geochemical, genomic, and cultivation studies. The project's specific objectives are to (i) use genomics to characterize microbial and viral populations inhabiting crustal fluids of the JdFR flank, (ii) use transcriptomics to identify the active metabolic pathways that are performing transformations relevant to elemental cycling within microorganisms of the JdFR flank, as well as identify active viral infections in these microbes, and (iii) generate microbial and viral pure cultures or limited diversity enrichments from crustal fluids of the JdFR flank. It combines bioinformatic analyses, controlled laboratory experiments, and field sampling to pursue both hypothesis-driven and discovery-based cultivation experiments, viral assays, and strain-level ecogenomic and metatranscriptomic analyses. Importantly, the investigators intend to generate new cultivated microbes and viruses to serve as model systems for investigating the characteristics of life in the deep ocean crust.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.