RUI: PurSUiT: Biodiversity discovery of shell-building amoebae (Arcellinida: Amoebozoa) in low pH bogs and fens

RUI：追求：低 pH 沼泽和沼泽中造壳变形虫（Arcellinida：Amoebozoa）的生物多样性发现

• 批准号: 2230391
• 负责人: Laura Katz
• 金额: $ 47.79万
• 依托单位: Smith College
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-05-01 至 2026-04-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2230391&HistoricalAwards=false
• 关键词: RUI; PurSUiT; Biodiversity; discovery; shell

Testate amoebae in the order Arcellinida (Amoebozoa) are an ancient lineage of microbes whose tests (i.e. shells) have been preserved in the fossil record dating back to 800 million years ago. Arcellinida tests were first observed by light microscopy in the 1880’s and over 1,000 species were classified by descriptors including the size, shape, and composition of the tests. Because of their preservability, Arcellinida species have been used as bioindicators for changing environmental conditions, including responses to warming temperatures and the presence of pollutants. However, genomic variation within these morphospecies suggests that cryptic diversity exists. Because information on species is critical to understanding small-scale distribution patterns and detecting changes in response to environmental disturbances, unraveling species boundaries in this group is essential. Preliminary work, including broad community sampling and metabarcode analyses of amoebae in low-pH bogs and fens across New England, has uncovered novel clades for which there are no references in public databases. Moreover, patterns of variation in Arcellinida genomes suggest gene flow between geographically distant populations; however, the mechanisms of genetic exchange between cells are unknown. The goals of this project are to develop a toolkit for diversity discovery that links cell morphology to genomic data, and then deploy this toolkit across sites in the Northeastern United States. By establishing a baseline for Arcellinida diversity across the Northeast, this research will provide a foundation for monitoring key taxa in habitats that are predicted to change with fluctuating climatic conditions. It will also provide research and educational opportunities in state-of-the-art methods for undergraduates and a postdoctoral scholar.The definition of “species” based on the ability of populations to exchange genes through reproduction emerged from studies of plants and animals. Microbiologists, however, are re-examining this approach to species delineation given that: 1) many microbial lineages are uncultivable; 2) cryptic species are frequently encountered; and 3) the presence of a microbiome within each individual prevents deployment of conventional genomic tools (e.g. RADseq). Hence, a multifaceted approach that integrates traditional morphological characterization and targeted molecular techniques (i.e. Arcellinida-specific metabarcoding and single-cell transcriptomics combined with a taxon-rich phylogenomic pipeline) will be used to uncover cryptic lineages within the Arcellinida and define new species across geographically and ecologically distinct bogs and fens in the Northeastern United States. Preliminary analyses reveal the presence of numerous cryptic species underlying morphotypes in New England, indicating that many additional species are yet to be discovered at these and other locations. Approaches developed here will not only uncover significant biodiversity within the Arcellinida but will also provide a framework for future studies of uncultivable microeukaryotic diversity.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.

Arcellinida（Amoebozoa）中的遗嘱变形虫是一种古老的微生物谱系，其测试（即贝壳）的历史记录可以追溯到8亿年前。首先通过光学显微镜在1880年代观察到了Arcellinida的测试，并通过描述符分类，包括测试的大小，形状和组成。由于它们的保留性，Arcellinida物种已被用作改变环境条件的生物指导者，包括对温暖温度和污染物的存在的反应。然而，这些形态疗法中的基因组变异表明存在加密多样性。由于有关物种的信息对于理解小规模的分布模式并检测到响应环境灾难的变化至关重要，因此该组中的物种边界至关重要。初步工作，包括广泛的社区抽样和新英格兰低ph沼泽和芬斯的变形虫分析，已经揭示了公共数据库中没有参考文献的新颖进化枝。此外，Arcellinida基因组的变异模式表明，地理距离种群之间的基因流动。但是，细胞之间的遗传交换机制尚不清楚。该项目的目标是开发一种将细胞形态与基因组数据联系起来的多样性发现工具包，然后将此工具包部署在美国东北部的站点。通过建立整个东北地区Arcellinida多样性的基线，这项研究将为监测栖息地中的关键分类群提供基础，这些栖息地预计会随着杂交状况的波动而变化。它还将在本科生和博士后科学的最先进方法中提供研究和教育机会。基于种群通过对动植物研究的繁殖能力来交换基因的能力，“物种”的定义。然而，微生物学家正在重新检查这种物种描述的方法：1）许多微生物谱系是无法养殖的； 2）经常遇到加密物种； 3）每个个体内的微生物组的存在可防止传统基因组工具的部署（例如RadSeq）。因此，一种多方面的方法将传统的形态特征和有针对性的分子技术（即Arcellinida特定的特定于特定的元法编码和单细胞转录组学结合结合了富含类型的系统基因组管道），将用于跨地球群中的密码和范围内的新地域范围，并在遍布新的物种中，并在遍布新的物种中，将其构成新的范围。初步分析表明，新英格兰的形态型潜在的许多加密物种存在，表明在这些位置和其他位置尚待发现许多其他物种。此处开发的方法不仅将在Arcellinida中揭示重要的生物多样性，而且还将为未来的不可言式微核动物多样性的研究提供一个框架。该奖项反映了NSF的法定任务，并被认为是通过基金会的知识分子优点和更广泛影响的审查标准来通过评估来获得的支持。

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.