Collaborative research: Patterns of diversity in planktonic ciliates ? spatio-temporal scales and community assembly in the coastal ocean

海洋中的大部分生物量、生产力和整体新陈代谢都是由微生物造成的，包括细菌、单细胞藻类和原生动物。氧气耗尽、有害水华和其他海洋疾病都可以归因于这些最小的浮游生物成员。然而，它们对有机物的生产和加工构成了海洋食物网的基础，从而决定了人类可以从海洋中收获的食物数量。由于微生物体型较小，评估微生物的生物多样性比评估海洋鱼类和哺乳动物种群等较大的生物更困难，但由于微生物的高度丰富性和海洋新陈代谢的主导地位，我们能够测量微生物多样性并了解其如何随环境变化而在不同的时间和空间尺度上变化是至关重要的。该项目将在帮助我们了解微生物生物多样性和为未来几十年预期的变化设定基线方面向前迈出重要的一步。在进行这项研究时，本科生和研究生以及博士后学者将获得最新测序和数据处理技术方面的培训，这是保持美国在生物技术领域领先地位的重要目标。该项目将使用基于DNA的方法来测量沿海海洋中的微生物多样性，使用深度测序技术同时对数十万种微生物进行采样。为了能够进行尽可能深的采样，它将专注于一组微生物，即纤毛虫，将它们用作类似微生物的模型。以前对这种方法的使用揭示了一个共同的模式，即一小群常见的纤毛虫伴随着一大群稀有的纤毛虫。由于新的测序技术提供了关于每个样本微生物群落的大量信息，该项目将能够评估群落的常见部分和稀有部分(后者通常被称为“稀有生物圈”)如何随季节、距海岸的距离、气候带等而变化。该项目的技术目标是评估海洋中纤毛虫多样性如何随时间和空间变化，评估驱动这种变化的环境因素，包括非生物和生物因素，并在受控条件下进行实验，以检验关于多样性和这些因素之间关系的假设。

Most of the biomass, productivity, and overall metabolism in the ocean are due to microbes, including bacteria, single-celled algae and protozoa. Oxygen depletion, harmful blooms, and other ocean ills are all attributable to these smallest members of the plankton. Their production and processing of organic matter, however, form the basis of the ocean's food web and thus determine the amount of food humans can harvest from the sea. Due to their small size, it is more difficult to assess the biological diversity of microbes than it is for larger organisms, such as the ocean's fish and mammal populations, yet because of their high abundance and dominance of ocean metabolism it is critical that we are able to measure microbial diversity and to understand how it changes over different time and space scales in response to changes in the environment. This project will make an important step forward in helping us to understand microbial biodiversity and set a baseline for changes that are expected in coming decades. In carrying out this research, undergraduate and graduate students as well as post-doctoral scholars will obtain training in the latest sequencing and data-processing technologies, an important goal for maintaining US leadership in biotechnology. This project will use DNA-based methods to measure microbial diversity in the coastal ocean, employing the deep-sequencing technology to sample hundreds of thousands of microbial species simultaneously. To enable the deepest possible sampling, it will focus on a single group of microbes, the ciliates, using them as a model for similar microbes. Previous use of such methods has revealed a common pattern in which a small group of common ciliate species is accompanied by a very large group of rare ones. Because the new sequencing technologies provide so much information about microbial communities from each sample, this project will be able to evaluate how both the common and rare parts of the community (the latter is often referred to as the "rare biosphere") change with seasons, distance from shore, climate zone, etc. The technical goals for this project are to evaluate how ciliate diversity varies over time and space in the ocean, to evaluate environmental factors, both abiotic and biotic, that drive this variation, and to perform experiments under controlled conditions to test hypotheses about the relationship between diversity and these factors.