Award: DEB-1541511

We live on a microbial planet as microbes dominate in terms of biomass, biodiversity, and evolutionary innovations. Most eukaryotes (i.e. cells with nuclei) are microbial, with the more familiar plants, animals and fungi nesting among a tremendous diversity of microscopic lineages. The work here focused on one group of  eukaryotes -- the SAR clade -- that includes stramenopiles (e.g. kelp, diatoms), alveolates (e.g. ciliates, and Plasmodium, the causative agent of malaria) and Rhizaria (e.g. many non-pathogenic amoebae and flagellates). Combining analyses of molecular data with both microscopy and field work allowed us to characterize diversity within this group, as well as to document features of life cycles and genomes. The work also generated manuscripts synthesizing the data collected with insights from past literature, and supported training of numerous scientists. Together, these efforts have illuminated further the nature of biodiversity diversity on our planet.

 

To explore the diversity within SAR, we developed tools that characterized the numbers of lineages (i.e. species) within this broad group and then among foraminifera, a type of predominantly shell building amoebae that are abundant in marine settings (e.g. mudflats, open waters, deep sea floor). Using these tools, we discovered a tremendous diversity of species and characterized their distributions across broad ecological ranges (e.g. within vernal pools, pitcher plants and sediments sampled from the Northeastern United States and from places as distant as Guam and Palau). As just one example of insights from these studies, we found a surprising diversity of freshwater foraminifera within the sediments of a single vernal pool in Massachusetts.

 

In a sharp contrast to much previous work on microbial lineages, we can now use molecular tools to characterize species that cannot be cultured in the lab. Instead of growing large numbers of individuals, we deployed "omics" tools to characterize genomes from uncultivable lineages. This opened a tremendous opportunity for research into lineages within the SAR clade and enabled us to successfully characterize thousands of genes from over 100 individuals within this group. Analyses of the resulting data allowed us to write a series of papers on ciliates, a group of microbial species in which every cell has two distinct genomes (i.e. a germline genome analogous to that in an egg or sperm, and a functional somatic genome). Our analyses show that the textbook explanations of how genomes evolve do not apply to these microbial lineages; instead, they follow rules that are distinct and that expand our understanding of biological principles on Earth.

 

The work here also supported a number of synthetic manuscripts that expanded upon hypotheses on the origins and diversification of life on Earth. For example, we have written about the nature of the first eukaryotic cells in which we speculate on the features that enable these organisms to succeed. Other manuscripts estimated the "epigenetic toolkit" (i.e. suites of genes that regulate gene expression and determine genome architectures) among eukaryotes, and synthesized information on the diversity of SAR lineages from the literature. Further, we developed tools that will be of use to other scientists, including a species-rich pipeline for estimating evolutionary trees from "omics" data.

 

The products of the work here include 25 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", a platform 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 six postdoctoral fellows, five graduate students and well over twenty-five Smith College undergraduates; of the latter, 11 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 on Earth, with a focus on our microbial neighbors. 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: 11/06/2022
Modified by: Laura A Katz