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。氧气消耗、有害藻华和其他海洋疾病都可归因于这些最小的浮游生物。然而，它们对有机物质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。由于它们的体积小，评估微生物的生物多样性比评估大型生物（如海洋的鱼类和哺乳动物种群）更困难，然而，由于它们的高丰度和海洋代谢的主导地位，我们能够测量微生物多样性并了解其如何随环境变化而随不同时间和空间尺度变化是至关重要的。这个项目将在帮助我们了解微生物多样性方面迈出重要的一步，并为未来几十年预期的变化设定基线。在开展这项研究的过程中，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的微生物多样性，采用深度测序技术同时对数十万种微生物进行采样。为了实现尽可能深入的采样，它将专注于一组微生物，纤毛虫，将它们作为类似微生物的模型。以前使用这种方法已经揭示了一种共同的模式，在这种模式中，一小群常见的纤毛虫物种伴随着一大群罕见的纤毛虫。由于新的测序技术从每个样本中提供了如此多的微生物群落信息，该项目将能够评估群落的常见和稀有部分（后者通常被称为“稀有生物圈”）如何随着季节、距离海岸的距离、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，以测试关于多样性与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.