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

• 批准号: 1924570
• 负责人: Laura Katz
• 金额: $ 44.32万
• 依托单位: Smith College
• 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 2025-02-28
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1924570&HistoricalAwards=false
• 关键词: Collaborative; Research; Combining; single; cell

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.

浮游生物纤毛是海洋食品网的关键成员，它们在其中发挥了各种作用，包括作为较小的微生物和较大浮游生物之间的食物链联系。由于它们在识别和培养它们方面的尺寸小和困难，我们对海洋中纤毛的多样性和分布了解少于我们对鱼类和无脊椎动物等较大生物的了解。 该团队的先前工作测量了沿海水域的纤毛多样性，发现不同的遗传变异在时间和空间中以可能与海洋温度，盐度和深度梯度等因素有关的方式分开。许多问题尚未解决，重要的是要了解控制浮游生物（例如纤毛）的多样性和分布的环境因素，以预测这些生物在未来几十年中如何应对不断变化的环境。 该项目的重点是：1）如何使用单细胞基因组学和转录组学描绘纤毛物种； 2）基于DNA的SAR进化枝的所有纤毛和其他浮游成员（Stramenopila，Alveolata，Rhizaria），它将提供生态环境； 3）单细胞和元转录组学原位基因表达； 4）培养纤毛物种中基因表达的实验室研究。该项目涉及培训博士后学者，研究生和本科生。研究人员致力于创建多样化和包容性的研究实验室；参与者的招募将通过与我们校园中适当的团体的合作伙伴关系来完成。该项目与史密斯学院和UConn的本科生（REU）活动（包括UConn/Mystic Aquarium Joint REU）的夏季研究经验相结合，这些活动尤其专注于代表性不足的学生。该项目还加强了与UConn Noyce Scholars计划合作扩大对生物多样性的努力，该计划促进了改变职业的STEM专业人员，以成为服务不足的中学的教师。该项目将评估生殖分离的物种的分布，该项目使用一种新方法来确定纤毛生殖基因组的新方法。此外，它将使用系统基因组方法来识别从货架环境中的元转录组中识别进化枝特异性的转录本（例如，螺旋形纤毛的成绩单（例如，螺旋形纤毛），并通过现场收集细胞的单细胞转录组学对纤毛功能的知识进行扩展。这些方法将对基于文化的方法有很大的改进，这些方法可能偏向海洋中的“杂草”物种。通过单细胞和元记录组学评估确定的物种鉴定与功能评估的结合有望在海洋浮游生物生态学方面取得重大进展。 该研究重点介绍了两个广泛的问题：1）观察到的系统发育信息基因的高多样性是否反映了浮游纤毛的生殖分离和功能分化？ 2）不同的同时发生物种的浮游纤毛物种是否显示出与海洋中不同生态位相对应的实质功能差异？ 该项目通过分析浮游纤毛形成型的种系微核中的模式来评估物种边界（即生殖隔离）；表征了海洋生态梯度紧密相关的纤毛的过渡；并通过转录组学的分析来检查物种内部和社区之间的功能差异。该奖项反映了NSF的法定任务，并被认为是值得通过基金会的知识分子优点和更广泛的影响评估标准通过评估来支持的。

项目成果

Single-cell transcriptomics supports presence of cryptic species and reveals low levels of population genetic diversity in two testate amoebae morphospecies with large population sizes

• DOI: 10.1093/evolut/qpad158
• 发表时间: 2023-09-06
• 期刊: EVOLUTION
• 影响因子: 3.3
• 作者: Weiner，Agnes K. M.;Sehein，Taylor;Katz，Laura A.
• 通讯作者: Katz，Laura A.

Genome architecture used to supplement species delineation in two cryptic marine ciliates

• DOI: 10.1111/1755-0998.13664
• 发表时间: 2022-06-26
• 期刊: MOLECULAR ECOLOGY RESOURCES
• 影响因子: 7.7
• 作者: Smith，Susan A.;Santoferrara，Luciana F.;McManus，George B.
• 通讯作者: McManus，George B.

Exploring the diversity of microeukaryotic communities in New England tide pools

• DOI: 10.3354/ame02003
• 发表时间: 2023-10-12
• 期刊: AQUATIC MICROBIAL ECOLOGY
• 影响因子: 1.4
• 作者: Grow，Adri K.;Sleith，Robin S.;Katz，Laura A.
• 通讯作者: Katz，Laura A.

Illuminating the first bacteria

• DOI: 10.1126/science.abh2814
• 发表时间: 2021-05-07
• 期刊: SCIENCE
• 影响因子: 56.9
• 作者: Katz, Laura A.

Top-Down and Bottom-Up Controls on Microeukaryotic Diversity (i.e., Amplicon Analyses of SAR Lineages) and Function (i.e., Metatranscriptome Analyses) Assessed in Microcosm Experiments

• DOI: 10.3389/fmars.2019.00818
• 发表时间: 2020-01
• 作者: Jean-David Grattepanche;L. Katz