Collaborative Research: Diversity and Biogeography of Marine Oligotrich and Choreotrich Ciliates Assessed by Morphological and Molecular Markers

海洋中的微型浮游动物组合通常以少食和多食纤毛虫为主。纤毛虫群落具有多样性和动态性，其丰度和物种组成在短时间内变化迅速。如果我们要将一个纤毛虫群落或几个培养物种获得的测量结果（例如放牧、生长）外推到区域或全球食物网模型，了解纤毛虫群落多样性的性质和含义是至关重要的。此外，这些纤毛虫在空间和时间尺度上的种间和种内遗传变异程度是未知的。最后，形态学标记的单独分析在认为所有纤毛虫都是世界性的研究者和认为在地理上孤立的纤毛虫种群之间存在有限的基因流动的研究者之间引起了相当大的争论。解决所有这些问题的一个关键是量化群体内部和群体之间分子标记和形态之间的对应关系。然而，目前，这些重要的生态群体的分子数据很少。本项目结合分子和形态学方法，阐明了海纤毛亚纲（毛毛亚纲）和少毛亚纲（螺毛亚纲）的多样性。这一大群浮游食草动物在浮游植物、细菌生产和高级消费者之间构成了重要的营养联系。本研究的主要重点是收集舞毛虫和寡毛虫自然种群的DNA序列数据，并将这些序列与传统方法确定的形态种联系起来。通过对新英格兰南部海岸和英国西海岸的纤毛虫进行密集采样，将技术组合应用于从自然组合中精心挑选的细胞，以评估从米到数千公里范围内的多样性。种内遗传变异也将被量化为种群内在短时间和空间尺度上的变化。该研究有两个目标：1)利用形态学和分子标记量化从近岸环境中取样的海洋寡食和舞食纤毛虫物种的多样性；2)评估少数丰富的寡食和舞食纤毛虫物种在短时空尺度上的种内变异模式。为了这两个目的，单个细胞将被挑选出来进行遗传分析，并保存下来用于物种鉴定。目的一是比较小亚基核糖体基因序列。第二个目标，将分析更多的可变标记，包括核糖体基因的内部转录间隔区（ITS1和ITS2）和组蛋白H3和H4之间的中间序列（H3H4IS）。本研究将结合分子和形态学方法，对寡毛菌和舞毛菌群体的遗传多样性进行全面的研究。这些数据是将跨越时间和空间采样的单个物种丰度信息与整个纤毛虫群落联系起来的重要的第一步。此外，这项工作将提供首次使用分子数据对海洋纤毛虫特有进行测试，并将在相关形态学和分子技术方面培养研究生。所得到的数据将对全球原生生物多样性和生物地理学问题产生更广泛的影响，并将对充分探索纤毛虫在海洋系统能量流动和营养循环中的作用是必要的。

Microzooplankton assemblages in the sea are often dominated by oligotrich and choretrich ciliates. Ciliate communities are diverse and dynamic, with rapid changes in abundance and species composition over short time scales. Understanding the nature and implications of diversity in ciliate communities is critical if we are to extrapolate measurements (e.g. grazing, growth) obtained with one ciliate community or a few species in culture to regional or global models of food webs. In addition, the degree of inter- and intraspecific genetic variability across spatial and temporal scales is unknown for these ciliates. Finally, analysis of morphological markers alone has generated considerable debate between researchers who argue that all ciliates are cosmopolitan versus those who believe that there is limited gene flow between geographically isolated ciliate populations. One key to addressing all of these issues is to quantify the correspondence between molecular markers and morphology within and between populations. At present, however, molecular data are sparse for these ecologically important groups. This project combines molecular and morphological methods to elucidate the diversity of marine ciliates in the subclasses Choreotrichia and Oligotrichia (Cl: Spirotrichea). This large group of planktonic grazers comprises an important trophic link between phytoplankton and bacterial production and higher consumers. The main focus of the study is to collect DNA sequence data from natural populations of choreotrichs and oligotrichs, and to relate these sequences to morphospecies determined by traditional methods. A combination of techniques will be applied to handpicked cells from natural assemblages to evaluate diversity across a range of scales from meters to thousands of kilometers, with intensive sampling of ciliates along the southern coast of New England and the western coast of the United Kingdom. Intraspecific genetic variability will also be quantified as changes within populations over short temporal and spatial scales. The study has two objectives: 1) to quantify diversity within a subset of marine oligotrich and choreotrich species sampled from nearshore environments using both morphology and molecular markers, and 2) to assess patterns of intraspecific variation on short spatial and temporal scales in a few abundant species of oligotrich and choreotrich ciliates. For both objectives, individual cells will be picked for genetic analysis and preserved for species identification. For objective one, small subunit ribosomal gene sequences will be compared. For the second objective, more variable markers will be analyzed, including the internally transcribed spacer regions (ITS1 and ITS2) of the ribosomal genes and an intervening sequence between histones H3 and H4 (H3H4IS). Combining molecular and morphological approaches, this study will produce comprehensive data on genetic diversity of populations of oligotrichs and choreotrichs. These data are an essential first step for connecting information on individual species abundances sampled across time and space to whole communities of ciliates. In addition, this work will provide the first test using molecular data on marine ciliate endemism and will train graduate students in relevant morphological and molecular techniques. The resulting data will have broader implications for questions regarding global protist diversity and biogeography and will be necessary to fully explore the role of ciliates in energy flow and nutrient cycling in marine systems.