Research

Biodiversity

Ciliates play critical roles in the environment, yet their biodiversity is poorly known at the taxonomic (how many and which taxa are there?), phylogenetic (how are they related?), and functional (what do they do?) levels. 

We have compared genotypes (DNA sequences) and phenotypes (morphology) to tackle various goals, from questioning species delineation to exploring distribution patterns, biogeography and phylogeny. We have also contributed to expand and curate public databases of ciliate gene sequences (GenBank, EukRef, PR2) and to describe new taxa. 

Closely-related ciliates partition ecological niches in time and space. Lineages almost identical in morphology and common genetic markers (ribosomal RNA genes) vary with factors such as seasons or distance from shore. We are looking for species-specific signatures using single-cell genomics and transcriptomics, as well as ecophysiological differences tested experimentally and in situ.

Relationships with the environment

Where and when a species thrives is determined by its evolutionary history as well as contemporary biological interactions (for example, with prey, predators and parasites) and abiotic conditions (such as water temperature, pH and oxygenation). Quantifying microbial distributions informs us about plankton trophic links and the influence of environmental changes on aquatic ecosystems.

In Long Island Sound, we are studying impacts of summer hypoxia (low oxygen in the water) on the structure and function of microbial communities (bacteria, archaea, protists), with emphasis on ciliates and other consumers. This relatively new research line is now funded by the NSF and we will be hiring a postdoc and several students soon. Stay tuned!