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

变形虫属于变形纲(变形纲)，是一个古老的微生物谱系，其测试(即贝壳)已保存在8亿年前的化石记录中。在19世纪80年代的S，通过光学显微镜首次观察到天牛的测试，并通过描述包括测试的大小、形状和组成在内的描述对1,000多种进行了分类。由于它们的保存性，Arcellinida物种已被用作环境条件变化的生物指示器，包括对变暖的温度和污染物的存在的反应。然而，这些形态种内的基因组变异表明存在隐蔽的多样性。由于有关物种的信息对于理解小规模分布模式和检测对环境干扰的响应变化至关重要，因此拆解这一群体中的物种边界是至关重要的。初步工作，包括对新英格兰各地低pH沼泽和沼泽中的阿米巴进行广泛的群落采样和变形码分析，发现了公共数据库中没有参考资料的新支系。此外，Arcellinida基因组的变异模式表明，地理上相距遥远的种群之间存在基因流动；然而，细胞之间的遗传交换机制尚不清楚。这个项目的目标是开发一个将细胞形态与基因组数据联系起来的多样性发现工具包，然后在美国东北部的各个地点部署这个工具包。通过为东北地区的Arcellinida多样性建立基线，这项研究将为监测生境中的关键类群提供基础，这些生境预计将随着气候条件的变化而变化。它还将为本科生和博士后提供最新方法的研究和教育机会。物种的定义是基于种群通过繁殖交换基因的能力，这一定义源于对植物和动物的研究。然而，微生物学家正在重新检查这种物种划分的方法，因为：1)许多微生物谱系是不可培养的；2)经常遇到神秘的物种；3)每个个体中存在一个微生物组，阻碍了传统基因组工具的部署(例如RADseq)。因此，将使用一种多方面的方法，结合传统的形态特征和有针对性的分子技术(即Arcellinida特定的元组编码和单细胞转录与丰富的分类群系统基因组管道相结合)来揭示Arcellinida内隐秘的谱系，并在美国东北部地理和生态上截然不同的沼泽和沼泽中定义新物种。初步分析显示，在新英格兰存在许多隐藏在地貌类型下的神秘物种，这表明在这些和其他地点还没有发现更多的物种。这里开发的方法不仅将发现Arcellinida内显著的生物多样性，还将为未来对不可培养的微真核生物多样性的研究提供一个框架。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.