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

有壳变形虫（Amoebozoa）是一种古老的微生物谱系，其测试（即外壳）已被保存在可追溯到8亿年前的化石记录中。在19世纪80年代，首次通过光学显微镜观察到Arcellinida测试，并通过描述符（包括测试的大小，形状和组成）对1，000多个物种进行了分类。由于它们的可降解性，Arcellinida物种已被用作改变环境条件的生物指示剂，包括对变暖温度和污染物存在的反应。然而，这些形态种内的基因组变异表明存在着隐蔽的多样性。由于物种信息对于了解小规模分布模式和检测环境干扰引起的变化至关重要，因此必须解开这一群体中的物种界限。初步工作，包括广泛的社区采样和元代码分析的阿米巴在低pH值沼泽和沼泽横跨新英格兰，发现了新的分支，有没有在公共数据库中的参考。此外，Arcellinida基因组的变异模式表明地理上遥远的种群之间的基因流动;然而，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个多样性发现工具包，将细胞形态与基因组数据联系起来，然后在美国东北部的各个地点部署这个工具包。通过建立一个基线Arcellinida的多样性在东北部，这项研究将提供一个基础，监测关键类群的栖息地，预计会随着气候条件的波动而变化。它还将为本科生和一名博士后学者提供以最先进方法进行研究和教育的机会，“物种”的定义是根据对植物和动物的研究得出的，其基础是种群通过繁殖交换基因的能力。然而，微生物学家正在重新审视这种物种划分方法，因为：1）许多微生物谱系是不可培养的; 2）经常遇到神秘物种; 3）每个个体内微生物组的存在阻止了常规基因组工具（例如RADseq）的部署。因此，一个多方面的方法，整合了传统的形态学特征和有针对性的分子技术（即Arcellinida特定的metabarcoding和单细胞转录组学结合一个分类丰富的基因组管道）将被用来揭示神秘的谱系内Arcellinida和定义新的物种在地理和生态上不同的沼泽和沼泽在美国东北部。初步分析显示，在新英格兰存在许多潜在的形态类型，表明许多其他物种尚未被发现在这些和其他地点。这里开发的方法不仅将揭示Arcellinida内的重要生物多样性，但也将提供一个框架，为未来的研究不可培养的microeukaryotic多样性。这个奖项反映了NSF的法定使命，并已被认为是值得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的支持。

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.