Award: DEB-1651908

Award Title: Biodiversity of testate (shelled) amoebae in New England bogs and fens

PI: Laura A Katz

 Award ID: 1651908

 

Though most eukaryotes (i.e. cells with nuclei) are microbial, we know far more about the ?macrobial? lineages of plants and animals. The work here focused on one group of  eukaryotes, ?shell-building? amoebae in the clade Arcellinda, a diverse clade that has been the subject of morphological analyses since the first microscopes were built. The field work here focused nearly exclusively on low pH bogs and fens (pH range 2.5-4, similar to a lemon), an example of an extreme habit type that is under threat from changing climates. We used molecular tools to characterize communities and individuals, and analyzed the resulting data with custom-built pipelines. The work provided novel insights into the diversity of these beautiful amoebae while also contributing to tools for other research groups, along with manuscripts that synthesized data from the literature. Moreover, the project contributed to the training of postdoctoral fellows, graduate students and undergraduates, many of whom come from communities that are traditionally underrepresented in science. Together, these efforts have illuminated further the nature of biodiversity diversity on our planet.

To explore the diversity within Arcellinida, we developed tools that characterized the numbers of lineages (i.e. species) sampled primarily from New England bogs and fens. Using these tools (i.e. amplicon or metabarcoding analyses), we discovered evidence for: 1) small life cycle stages (e.g. gametes/propagules) based on analyses of size fractioned communities; 2) a combination of widespread (e.g. from Massachusetts to an island off the coast of Maine) abundant species coupled with rarer species that might be specific to just one local; and 3) distinct community assemblages that vary by ecology (e.g. from open bog to forest edge to stream). We also developed protocols for studying these lineages using fluorescent microscopy, setting up for future studies that link morphology with the genetic signals that we uncovered.

The second major focus of the work was characterizing genome-scale data from individuals, with a focus on two widespread and abundant species (Hyalosphenia papilio and Hyalosphenia elegans). By analyzing the transcriptome (i.e. the genes being expressed by each amoebae), we find evidence that these amoebae have numerous cryptic species ? species that are morphologically identical but genetically distinct. Moreover, our analyses show low levels of diversity within these cryptic species, despite high population sizes (we estimated ~25 million amoebae in one local bog alone!). Finally, our analyses provide compelling evidence of genetic exchange (i.e. sex) within cryptic species, which is intriguing as sex has yet to be observed in this clade of organisms. These data provide more texture to our understanding of these amoebae, and more broadly, to our understanding of life cycles within microbial lineages.

The work here also supported a number of tools and synthetic manuscripts. One manuscript estimated the ?epigenetic toolkit? (i.e. suites of genes that regulate gene expression and determine genome architectures) among eukaryotes, including diverse amoebae. Further, we developed tools that will be of use to other scientists, including a species-rich pipeline for estimating evolutionary trees from ?omics? data (i.e. PhyloToL). Finally, the team of researchers contributed to several theoretical manuscripts that expand our understanding of the nature of microbial biodiversity. 

The products of the work here include 12 peer-reviewed manuscripts, with several more still making their way through revisions. Additional products include DNA sequencing data, images/figures, and computer programs that have been made available through open access sites (e.g. the National Center for Biotechnology Information and ?GitHub?, for computer programs/scripts). An additional study, co-authored by two Smith College undergraduates, described protocols developed for fluorescence microscopy studies of microbial lineages.

This proposal contributed to the training of two postdoctoral fellows, two graduate students and well over fifteen Smith College undergraduates; of the latter, eight contributed to peer-reviewed manuscripts. Over half of these trainees are students of color and/or first generation college students, and several have already joined graduate programs in related fields. Hence, this grant supported the diversification of participants in basic science research in the United States. The work here also transformed education through expansion of topics taught at Smith College (both in lectures and laboratory settings), and through numerous posters and talks given by the principal investigator, postdoctoral fellows, graduate students and undergraduates. 

In sum, the work conducted here contributed to our understanding of biodiversity of amoebae in New England bogs and fens. Such studies are essential given that we still know less about microbial species than we do about organisms such as plants, animals and fungi. Beyond the generation of tools and data, the broader impacts through education and outreach will continue to build our understanding of the contributions of microbial species within diverse ecosystems, which is essential in light of rapidly changing climatic conditions.

 

 

 

Last Modified: 10/29/2023
Modified by: Laura A Katz