Investigation of viruses and microbes circulating deep in the seafloor

海洋的尽头并不在海底。海水深入大洋地壳，形成巨大的海底地下含水层。海水、岩石和微生物之间的相互作用改变了海水通过该含水层时的性质。改变后的流体从玄武岩流出并回到海洋的流量相当于地球上所有河流的流量，这种深海流体的交换影响着海洋的化学平衡。获取这些流体的样本一直是了解海底含水层内发生的生物过程的主要障碍，但现在在海底的钻孔中开发和安装称为软木塞的特殊井口，为探索地球上最偏远的栖息地的生物学提供了机会。最近对从软木上采集的流体进行的分析表明，海洋基底中的微生物群落与上面海水中的微生物群落非常不同，但人们对它们的生态知之甚少。特别是，关于病毒如何与这个栖息地的细胞相互作用，我们一无所知。当裂解病毒感染细胞时，它会裂解并杀死细胞，但温带病毒通常会与宿主细胞建立稳定的共生关系，从而改变细胞的功能。由于这些重要作用，病毒对微生物群落的大小、组成和活动产生重大影响。因此，研究海洋基底中裂解病毒和温带病毒的作用，对于了解基底中微生物的活动是如何调节的至关重要。在这个项目中，研究人员将从大西洋中部的洋底采集流体样本，以进行病毒在缓慢扩散的地壳系统中的重要性的首次调查。除了在科学期刊上发表详细的研究结果外，研究人员还将出版一本针对小学高年级到中学生的书，书中捕捉到了深海探索的兴奋和挑战，并介绍了在地球深处发现的生命形式的奥秘-S地壳。这本书将与国家海洋素养原则和共同核心标准保持一致。分发将集中在夏威夷少数族裔服务的学校，目标是培养在STEM领域传统上代表性较低的群体对海洋、地球和生命科学的兴趣。为了收集流体中的病毒和微生物，研究人员将在远程操作工具的帮助下使用被动和主动收集方法。对于被动收集，微过滤器和超过滤器将串联到井口，流体将通过含水层和底层海水之间的压差驱动通过过滤器。对于主动采样，将使用机械泵将基底液或底层海水引导到样本袋中，以便在船上提取和处理。从液体中收获的微生物和病毒将被分成不同的种群。这些病毒和细胞将通过电子显微镜进行检查，以量化形态多样性并确定感染细胞的比例。来自细胞和病毒的核酸将被测序，以1)表征病毒的遗传多样性，2)确定整合了病毒基因组的细胞的比例，3)确定病毒对细胞贡献的功能基因，以及4)基于CRISPR元件的分析将特定病毒与其可能的宿主联系起来。研究人员假设，基底病毒将与底层海水中的病毒不同，与细胞更丰富的表层海水相比，基底中活跃的裂解感染将较低，但温带病毒的感染将异常常见。该项目的数据将有助于限制病毒在海洋基底有机碳循环中的重要性，并阐明病毒基因可能正在如何改变影响海洋化学的微生物活动。

The ocean does not end at the seafloor. Seawater penetrates deep into the ocean crust forming an enormous subseafloor aquifer. Interactions among seawater, rocks, and microorganisms alter the properties of seawater as it passes through this aquifer. The flux of the altered fluid out of the basaltic rocks and back into the sea is equivalent to the flux of all the rivers on the planet and this exchange of deep-sea fluids influences the chemical balance of the ocean. Obtaining samples of these fluids has been a major obstacle to understanding the biological processes that occur within the ocean basement aquifer, but the development and installation of special wellheads, called CORKs, into boreholes on the seafloor now provides opportunities to probe the biology of the most remote habitat on earth. Recent analyses of fluids sampled from CORKs have shown that the microbial communities in the ocean basement are very different from those of the overlying seawater, but little is known of their ecology. In particular, nothing is known about how viruses interact with the cells in this habitat. When a lytic virus infects a cell, it will lyse and kill the cell, but temperate viruses often establish a stable, symbiotic relationship with the host cell that changes how the cell functions. Because of these important roles, viruses exert a major influence on the size, composition, and activity of microbial communities. Investigating the contributions of lytic and temperate viruses in the ocean basement is therefore central to understanding how activities of microbes in the basement are regulated. For this project, the researchers will sample fluids from the ocean basement in the central Atlantic Ocean to conduct the first investigation of the importance of viruses in a slow spreading crustal system. In addition to publishing the detailed results in scientific journals, the researchers will produce a book (in English and Hawaiian) targeting upper elementary to middle schoolchildren that captures the excitement and challenges of deep-sea exploration and introduces the mysteries of the life forms being discovered deep in the earth?s crust. The book will align with National Ocean Literacy Principles and Common Core Standards. Distribution will be focused on the minority-serving schools in Hawaii with the goal of fostering interest in the ocean, earth, and life sciences in groups traditionally underrepresented in STEM fields.To collect the viruses and microorganisms in the fluids, the researchers will use both passive and active collection methods with the help of a remotely operated vehicle. For passive collection, micro- and ultrafilters will be connected in series to the wellhead and fluids will be driven through the filters by the pressure differential between aquifer and bottom seawater. For active sampling, mechanical pumps will be used to direct either basement fluids or bottom seawater into sample bags for retrieval and processing aboard ship. Microorganisms and viruses harvested from the fluids will be fractionated to separate populations. The viruses and cells will be examined by electron microscopy to quantify morphological diversity and to determine the proportion of infected cells. Nucleic acids from the cells and viruses will be sequenced to 1) characterize the genetic diversity of the viruses, 2) determine the proportion of cells with integrated viral genomes, 3) identify the functional genes contributed to the cells by the viruses, and 4) link specific viruses to their likely hosts based on analysis of CRISPR elements. The researchers hypothesize that the basement viruses will be distinct from those of bottom seawater and that, compared to surface seawater where cells are more abundant, active lytic infections in the basement will be low, but infections by temperate viruses will be exceptionally common. The data from this project will help to constrain the importance of viruses in recycling of organic carbon in the ocean basement and shed light on how viral genes may be altering the microbial activities that influence ocean chemistry.