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.

浮游纤毛虫是海洋食物网的关键成员，它们在其中发挥着不同的作用，包括作为小型微生物和大型浮游生物之间的食物链联系。由于纤毛虫体积小，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比我们对鱼类和无脊椎动物等大型生物的了解要少。 该团队先前的工作测量了沿海沃茨的纤毛虫多样性，发现不同的遗传变异在时间和空间上是分开的，这种方式可能与海洋温度，盐度和深度梯度等因素有关。许多问题仍然没有答案，重要的是要了解控制浮游生物（如纤毛虫）多样性和分布的环境因素，以预测这些生物在未来几十年内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述纤毛虫物种; 2）基于DNA的所有纤毛虫和SAR进化枝的其他浮游生物成员（Stravelila，Alveolata，Rhizaria）的研究，这将提供生态背景; 3）通过单细胞和Meta转录组学进行的原位基因表达;以及4）在培养的纤毛虫物种中进行的基因表达的实验室研究。该项目包括博士后学者，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内的适当团体合作完成。该项目与史密斯学院和康州大学（包括康州大学/神秘水族馆联合REU）的本科生夏季研究经验（REU）活动相结合，这些活动特别关注代表性不足的学生。该项目还与康州大学诺伊斯学者计划合作，促进对生物多样性的理解，该计划旨在帮助职业转变的STEM专业人员成为服务水平低下的中学的教师。该项目将评估生殖隔离物种的分布，使用新方法确定纤毛虫种系基因组的特征区域。此外，它将使用基因组学的方法来确定分支特定的转录本（例如，那些spirotrich纤毛虫）从货架环境中的metatranscriptomes内，并扩大纤毛功能的知识与现场收集的细胞的单细胞转录组学。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Meta转录组学将确定性物种鉴定与功能评估相结合，有望在海洋浮游生物生态学方面取得重大进展。 本研究集中在两个广泛的问题：1）观察到的高多样性的遗传信息基因反映了生殖隔离和功能分化的浮游纤毛虫？2）不同共生种类的浮游纤毛虫是否表现出与海洋中不同生态位相对应的实质性功能差异？ 该项目评估物种边界（即生殖隔离）通过分析的模式在生殖细胞微核的亚热带纤毛虫形态种;特点的过渡密切相关的纤毛虫跨越生态梯度在海洋中;并研究物种内部和物种之间以及社区中的功能差异，该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的智力价值和更广泛的评估来支持。影响审查标准。

项目成果

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

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.

Phylogenomics of the Epigenetic Toolkit Reveals Punctate Retention of Genes across Eukaryotes

• DOI: 10.1093/gbe/evaa198
• 发表时间: 2020-12-01
• 期刊: GENOME BIOLOGY AND EVOLUTION
• 影响因子: 3.3
• 作者: Weiner, Agnes K. M.;Ceron-Romero, Mario A.;Katz, Laura A.
• 通讯作者: Katz, Laura A.