The Ecology of Prochlorococcus: Toward a Model System for Microbial Oceanography

一个促进我们对自然世界的理解的模型系统的力量已经在不同的科学分支学科中反复得到证明。无论是通过对特定生态系统的持续研究，还是通过对从基因组到生态系统各级组织的特定生物体的研究，这种方法对海洋微生物生态的研究同样有价值。在这个项目中，研究人员将通过一系列不同的实验室和实地研究来完成后一项工作，这些研究旨在促进对原氯球菌的了解，原氯球菌是世界海洋中数量上占主导地位的浮游植物。目的是了解是什么控制着这一重要初级生产者的分布和丰度。原氯球菌具有许多特征，使其成为一种有用的模式生物，用于理解塑造海洋微生物系统的力量，并产生将推动微生物海洋学领域的假设。它是海洋中最小、最丰富的光合作用细胞，可以分离培养，很容易计数和原位研究。此外，它拥有已知的所有光合作用细胞中最小的基因组--也就是迄今为止最小的光生生物。原氯球菌实际上是一组“生态型”，即密切相关但生理上截然不同的种群，它们沿着形成其栖息地的光、温度、营养和捕食者(包括病毒)梯度以不同的分布共存。这些分布由细胞的相对适合度决定，即沿这些梯度的生长率和死亡率的平衡。广泛的挑战是理解是什么力量在进化过程中塑造了这种微多样性，并指导这些种群在不同的选择性制度下进行自我组织。这是一个多维项目，旨在通过实验室和田间研究，了解“自下而上”(光、温度、氧气和营养物质限制生长)和“自上而下”(因病毒和放牧造成的死亡)对不同原氯球菌生态型种群增长的影响。该项目将涉及在实验室中对生态型沿环境变量梯度的生长进行高通量研究，以及在实地(在夏威夷和百慕大时间序列站、沿大西洋纵向断面以及在阿拉伯海和秘鲁上升流的最低含氧区)利用定量聚合酶链法研究生态型在空间和时间梯度上的分布，以评估其相对丰度。研究人员还将研究感染原氯球菌和生态型之间交叉感染的病毒的生命周期，以及由于放牧压力而导致的特定生态型在野外样本中的生长和死亡率。另一组分析将测量选定田间样本中共存的原氯球菌的全部多样性，并致力于了解在什么水平上遗传多样性对应于具有生态意义的多样性。最后，本研究将开发统计方法来表征和分析在实验室建立的原氯球菌生态型“适应空间”，并将它们与生态型在田间环境梯度上的分布进行比较。这将使人们能够严格分析不同的选择压力在多大程度上影响海洋中不同原氯球菌生态型的相对丰度，以及它们如何随时间和空间变化。更广泛的影响。该项目将支持(全部或部分)5名研究生和博士后(其中3名为女性)以及本科生研究人员的研究。通过与科学博物馆的正式合作，我们还将开发专注于海洋微生物学的展品。调查人员还参与了麻省理工学院的知识更新计划，该计划为专业和学生受众制作多媒体教育简报，让他们集中、快速地沉浸在新兴领域。最后，与会者将与麻省理工学院的一位人类学家合作，这位人类学家正在撰写一本书，暂定名为《绘制基因之海》，这本书将从人类学的角度审视基因组学时代的海洋探索。作者一直在与研究小组互动，以获得关于海洋微生物及其基因的纪实工作感觉。这本书将改变科学家、政策制定者和公众对海洋的理解。

The power of a model system for advancing our understanding of the natural world has been proven repeatedly in diverse sub-disciplines of science. This approach is equally valuable for the study of marine microbial ecology, either through the sustained study of a particular ecosystem, or through the study of a particular organism at all scales of organization from the genome to the ecosystem level. In this project the investigators will do the latter through a diverse set of laboratory and field studies designed to advance the understanding of Prochlorococcus, the numerically dominant phytoplankter in the world oceans. The objective is to understand what regulates the distribution and abundance of this important primary producer. Prochlorococcus has a number of features that make it a useful model organism for understanding the forces that shape marine microbial systems, and for generating hypotheses that will advance the field of Microbial Oceanography. It is the smallest and most abundant photosynthetic cell in the oceans, it can be isolated into culture, and it can be easily enumerated and studied in situ. Furthermore, it has the smallest genome of any known photosynthetic cell -- the minimal phototroph to date. Prochlorococcus is really a collection of "ecotypes", i.e., closely related but physiologically distinct populations that co-exist with different distributions along the light, temperature, nutrient, and predator (including viruses) gradients that shape their habitat. These distributions are determined by the relative fitness of the cells, i.e. the balance of growth rates and death rates along these gradients. The broad challenge is to understand the forces that have shaped this microdiversity over evolutionary time, and that guide the self-organization of these populations under different selective regimes. This is a multi-dimensional project designed to understand the "bottom up" (growth limitation by light, temperature, oxygen, and nutrients) and "top down" (mortality from viruses and grazing) influences on the population growth of different Prochlorococcus ecotypes through both laboratory and field studies. The project will involve high-throughput studies of the growth of ecotypes along gradients of environmental variables in the laboratory, as well as studies of the distribution of ecotypes along spatial and temporal gradients in the field (at the Hawaii and Bermuda Time Series Stations, along a longitudinal Atlantic transect, and in Oxygen Minimum Zones in the Arabian Sea and Peruvian Upwelling) using Q-PCR to assess their relative abundance. The investigators will also study the life cycle of viruses that infect Prochlorococcus and cross infect between ecotypes, and the growth and mortality rates of specific ecotypes in field samples due to grazing pressure. Another set of analyses will measure the full diversity of co-occurring Prochlorococcus in selected field samples, and work toward understanding at what level genetic diversity corresponds to ecologically meaningful diversity. Finally, the study will develop statistical methods for the characterization and analysis of Prochlorococcus ecotype "fitness spaces" established in the laboratory, and compare them with the distribution of ecotypes along environmental gradients in the field. This will allow a rigorously analysis of the degree to which different selective pressures shape the relative abundance of the different Prochlorococcus ecotypes in the oceans, and how they change over time and space. Broader Impacts. This project will support (in whole or in part) the research of 5 graduate students and post-docs, three of them women, as well as undergraduate researchers. Through a formal collaboration with the Museum of Science we will also develop exhibits that focus on marine microbiology. The investigators are also participating in MIT's Knowledge Update Program, which produces multi-media educational briefings designed for both professional and student audiences to provide a focused, quick immersion into emerging fields. Finally, the participants will be working with an anthropologist at MIT who is working on a book, tentatively entitled Mapping a Sea of Genes, that will offer an anthropological look at exploring the ocean in the age of genomics. The author has been interacting with the research group to get a documentary sense of work on ocean microbes and their genes. This book will transform the way scientists, policy makers and lay public understand the sea.