Award: OCE-1924570

Award Title: Collaborative Research: Combining single-cell and community 'omics' to test hypotheses about diversity and function of planktonic ciliates

PI: Laura A Katz

Federal Award ID: 1924570

We live on a microbial planet as microbial species dominate in terms of biomass, biodiversity and evolutionary innovation. Even among eukaryotes (i.e. organisms made up of cells with nuclei, like ourselves) most species are microbial; yet we know far more about the ‘macrobial’ lineages of plants and animals. The work here focused on one group of  eukaryotes, ciliates, that are defined by the presence of both cilia (small hair-like projections that support motility) and two distinct nuclei in every cell (i.e. a germline micronucleus and a somatic (i.e. body, functional) macronucleus). Ciliates are abundant in the oceans where they play crucial roles in marine food webs – ciliate feed on smaller bacteria and algae, and in turn are fed upon by zooplankton. Despite their importance, many basic questions about ciliates remain unanswered including understanding their diversity and the nature of species in this diverse clade.

For the work here, a team of researchers based at UConn and Smith College, combined molecular tools and microscopy to study ciliate species in nearshore environments off the coast of New England. Using samples from a research cruise combined with frequent collections from waters near UConn Avery Point, we addressed a major challenge in studying ciliates by collecting both community ‘amplicon’ and single-cell ‘omics data (i.e. transcriptomics, or the study of expressed genes) for analysis of species boundaries. This work is important as relying on microscopy alone can miss important differences among ciliates, which can make it challenging to categorize ecological roles of these abundant microorganisms. 

We focused on generating over 100 samples of molecular data, representing a combination of both community samples and single-cell transcriptome data, and all the resulting sequences are now publicly available on GenBank. These data will serve as a resource for scientists interested in the diversity and ecology of ciliates, and particularly Spirotrichea. We also developed bioinformatic pipelines for analyzing the resulting from ciliates, including a focus on removing contamination and determining species boundaries. This work is particularly important because it reveals "cryptic species"—organisms that look the same but are genetically distinct and may have different ecological roles.

 

A considerable amount of time was invested in the generation of EukPhylo, an open source taxon-rich pipeline that enables study of gene families and evolutionary history of diverse microbial eukaryotes. Among the unique aspects of EukPhylo are: 1) the focus on phylogenetically-informed removal of contaminants; 2) the inclusion of data from 500 gene families sampled in 1000 species, which can be used by scientists interested in placing their species on the eukaryotic tree of life; 3) the ability to either use the EukPhylo Hook Database (a total of 15,000 gene families) or to substitute in a set of gene families of interest to the user; and 4) the inclusion of numerous tools (i.e. for managing phylogenies and analyzing sequence statistics), which can be deployed within EukPhylo or as stand alone tools. We are optimistic that EukPhylo will be of use by many in the communities of ecologists, evolutionary biologists and microbiologists. 

The products of the work here include 19 peer-reviewed manuscripts, with several more still making their way through revisions. These papers include fundamental insights into the biodiversity of ciliates off the coast of New England, and provide protocols and pipelines for researchers interested in expanding this work to other groups of microbial eukaryotes. 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, GitHub)

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 at regional and national meetings. The project contributed to the training of postdoctoral fellows, graduate students and undergraduates, with the aim of increasing the workforce of scientists in the USA. Together, these efforts have illuminated further the nature of biodiversity diversity on our planet.

In sum, the work conducted here contributed to our understanding of biodiversity of ciliates in New England waters. 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 on Earth. 

Last Modified: 07/07/2025
Modified by: Laura A Katz