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Collaborative Research: Combining single-cell and community 'omics' to test hypotheses about diversity and function of planktonic ciliates

合作研究：结合单细胞和群落“组学”来检验有关浮游纤毛虫多样性和功能的假设

基本信息

批准号：
1924527
负责人：
George McManus
金额：
$ 54.02万
依托单位：
University of Connecticut
依托单位国家：
美国
项目类别：
Standard Grant
财政年份：
2019
资助国家：
美国
起止时间：
2019-09-01 至 2023-08-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1924527&HistoricalAwards=false
关键词：
Collaborative Research Combining single cell

项目摘要

Planktonic ciliates are key members of marine food webs where they serve diverse roles, including as food chain links between smaller microbes and larger plankton. Due to their small size and difficulties in identifying and cultivating them, we know less about ciliate diversity and distributions in the ocean than we do about larger organisms such as fish and invertebrates. Previous work from this team measured ciliate diversity in coastal waters and found that distinct genetic variants were separated in time and space in a way that could be related to factors such as ocean temperature, salinity, and depth gradients. Many questions remained unanswered, and it is important to understand the environmental factors that control the diversity and distribution of plankton such as ciliates to predict how these organisms may respond to a changing enviroment in the coming decades. This project focuses on: 1) how ciliate species are delineated using single-cell genomics and transcriptomics; 2) DNA-based studies of all ciliates and other planktonic members of the SAR clade (Stramenopila, Alveolata, Rhizaria), which will provide ecological context; 3) in situ gene expression by single-cell and meta- transcriptomics; and 4) laboratory studies of gene expression in cultivated ciliate species. This project involves training of postdoctoral scholars, graduate students, and undergraduates. The researchers are committed to creating diverse and inclusive research labs; recruitment of participants will be done through partnership with appropriate groups on our campuses. The project integrates with summer Research Experiences for Undergraduates (REU) activities at both Smith College and UCONN (including the UCONN/Mystic Aquarium joint REU), which are especially focused on underrepresented students. This project also enhances efforts to broaden understanding of biodiversity in partnership with the UCONN Noyce Scholars Program, which facilitates career-changing STEM professionals to become teachers in underserved secondary schools.This project will assess distributions of reproductively-isolated species, determined using a new method to characterize regions of the ciliate germline genome. Furthermore, it will use phylogenomic methods to identify clade-specific transcripts (e.g. those of spirotrich ciliates) within metatranscriptomes from the shelf environment and to expand knowledge of ciliate function with single-cell transcriptomics of field-collected cells. These approaches will be a substantial improvement over the culture-based methods that are potentially biased towards "weedy" species in the ocean. The combination of definitive species identification with assessment of function via single-cell and meta- transcriptomics promises to provide significant advances in marine plankton ecology. The research focuses on two broad questions: 1) does the observed high diversity in phylogenetically-informative genes reflect reproductive isolation and functional differentiation in planktonic ciliates? and 2) do different co-occurring species of planktonic ciliates show substantial functional differences that correspond to different niches in the ocean? The project assesses species boundaries (i.e. reproductive isolation) through analyses of patterns in the germline micronuclei of planktonic ciliate morphospecies; characterizes transitions of closely-related ciliates across ecological gradients in the ocean; and examines functional differences within and between species, and in communities, through analyses of transcriptomics.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

浮游纤毛虫是海洋食物网的关键成员，它们发挥着多种作用，包括作为较小微生物和较大浮游生物之间的食物链纽带。由于纤毛虫体型小，识别和培养困难，我们对海洋中纤毛虫的多样性和分布的了解少于对鱼类和无脊椎动物等较大生物的了解。该团队之前的工作测量了沿海水域的纤毛虫多样性，发现不同的遗传变异在时间和空间上分离，其方式可能与海洋温度、盐度和深度梯度等因素有关。许多问题仍未得到解答，重要的是了解控制纤毛虫等浮游生物多样性和分布的环境因素，以预测这些生物体在未来几十年如何应对不断变化的环境。该项目重点关注：1）如何利用单细胞基因组学和转录组学来描述纤毛虫物种； 2) 对所有纤毛虫和 SAR 进化枝的其他浮游成员（Stramenopila、Alveolata、Rhizaria）进行基于 DNA 的研究，这将提供生态背景； 3）通过单细胞和宏转录组学进行原位基因表达； 4) 栽培纤毛虫基因表达的实验室研究。该项目涉及博士后学者、研究生和本科生的培训。研究人员致力于创建多元化、包容性的研究实验室；参与者的招募将通过与我们校园内的适当团体合作来完成。该项目与史密斯学院和康涅狄格大学（包括康涅狄格大学/神秘水族馆联合 REU）的本科生夏季研究体验 (REU) 活动相结合，这些活动特别关注代表性不足的学生。该项目还与康涅狄格大学诺伊斯学者计划合作，加强对生物多样性的理解，该计划促进改变职业的 STEM 专业人员成为服务不足的中学的教师。该项目将评估生殖隔离物种的分布，并使用一种新方法来表征纤毛虫种系基因组区域。此外，它将使用系统发育学方法来识别来自架子环境的宏转录组中的进化枝特异性转录本（例如螺旋毛纤毛虫的转录本），并通过现场收集的细胞的单细胞转录组学来扩展纤毛虫功能的知识。这些方法将是对基于培养的方法的重大改进，这些方法可能偏向于海洋中的“杂草”物种。通过单细胞和宏转录组学将明确的物种鉴定与功能评估相结合，有望为海洋浮游生物生态学带来重大进展。该研究重点关注两个广泛的问题：1）观察到的系统发育信息基因的高度多样性是否反映了浮游纤毛虫的生殖隔离和功能分化？ 2）不同共生的浮游纤毛虫物种是否表现出与海洋中不同生态位相对应的显着功能差异？该项目通过分析浮游纤毛虫形态种的种系微核模式来评估物种边界（即生殖隔离）；描述了密切相关的纤毛虫在海洋生态梯度上的转变；该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。