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

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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.