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

模型系统的力量促进了我们对自然世界的理解，这在不同的科学分支学科中得到了反复的证明。这种方法对于海洋微生物生态学的研究同样有价值，无论是通过对特定生态系统的持续研究，还是通过从基因组到生态系统水平的所有组织尺度上对特定生物体的研究。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进行后者，这些研究旨在增进对原绿球藻的了解，原绿球藻是世界海洋中数量占主导地位的浮游植物。目的是了解是什么调节了这一重要初级生产者的分布和丰度。原绿球藻具有许多特征，使其成为一种有用的模式生物，可以用来理解形成海洋微生物系统的力量，并产生将推动微生物海洋学领域发展的假设。它是海洋中最小和最丰富的光合细胞，它可以被分离到培养中，并且可以很容易地在原位枚举和研究。此外，它的基因组是所有已知光合细胞中最小的——是迄今为止最小的光营养细胞。原绿球藻实际上是“生态型”的集合，即密切相关但生理上不同的种群，它们在形成其栖息地的光线、温度、营养和捕食者（包括病毒）梯度的不同分布中共存。这些分布是由细胞的相对适合度决定的，即沿这些梯度的生长速率和死亡率的平衡。广泛的挑战是了解在进化过程中形成这种微多样性的力量，以及在不同选择制度下指导这些种群自我组织的力量。这是一个多维度的项目，旨在通过实验室和实地研究，了解“自下而上”（光、温度、氧气和营养对生长的限制）和“自上而下”（病毒和放牧造成的死亡率）对不同原绿球藻生态型种群增长的影响。该项目将涉及在实验室沿环境变量梯度对生态型生长的高通量研究，以及在实地（在夏威夷和百慕大时间序列站，沿大西洋纵向样带，以及在阿拉伯海和秘鲁上升流的最低氧区）使用Q-PCR方法沿空间和时间梯度研究生态型的分布，以评估它们的相对丰度。研究人员还将研究感染原绿球藻和不同生态型交叉感染的病毒的生命周期，以及特定生态型在放牧压力下在野外样品中的生长和死亡率。另一组分析将测量在选定的野外样本中共同发生的原绿球藻的全部多样性，并努力了解在何种水平上遗传多样性对应于有生态意义的多样性。最后，本研究将采用统计方法对实验室建立的原绿球藻生态型“适合度空间”进行表征和分析，并与野外生态型沿环境梯度的分布进行比较。这将允许严格分析不同选择压力在多大程度上塑造海洋中不同原绿球藻生态类型的相对丰度，以及它们如何随时间和空间变化。更广泛的影响。本项目将支持（全部或部分）5名研究生和博士后（其中3名女性）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，我们还将开发以海洋微生物学为重点的展览。研究人员还参与了麻省理工学院的知识更新计划，该计划为专业人士和学生观众设计了多媒体教育简报，以提供一个专注的、快速沉浸在新兴领域的机会。最后，参与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名为《绘制基因之海》（Mapping a Sea of Genes）的书，该书将从人类学的角度探索基因组时代的海洋。作者一直在与研究小组进行互动，以获得对海洋微生物及其基因工作的纪实性。这本书将改变科学家、政策制定者和普通公众对海洋的理解。

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.