Genotype – Phenotype Relationships
Microbes play critical roles in the environment, yet their diversity 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. Accurate answers rely on meaningful species delineation. I compare genotypes (DNA sequences) and phenotypes (morphology, ecology and physiology, including gene expression) to examine species boundaries and better infer ciliate diversity, evolution and function.
Functional diversity of closely-related lineages
One intriguing finding from the projects described below and additional cooperation between the Microzooplankton lab (UConn) and the Katz lab (Smith College) is that closely-related ciliates can partition ecological niches in space and time. Lineages almost identical in morphology and common genetic markers vary with factors such as distance from shore or seasons (Refs. 17, 21, 23).
We are now working on better delimiting closely-related species and on quantifying their functional differences. We are looking for species-specific signatures identified by single-cell genomics and transcriptomics. Particularly, we are interested in knowing if such signatures correlate with ecophysiological differences tested experimentally and in situ.
Some of the better-known ciliates are the tintinnids, which have a lorica (shell). This structure has been the foundation of tintinnid taxonomy, but our comparisons of morphology and genetic markers has confirmed that loricae can show both intra-specific variability (polymorphism) and inter-specific similarity (crypticity) (Refs. 10, 17).
Our contributions to expand and curate public databases of gene sequences (GenBank, EukRef, PR2) have improved the knowledge on the diversity, taxonomy and phylogenetics of tintinnids and other ciliates (Refs. 24, 26, 28).
Tracking diversity with high-throughput sequencing
Despite the lorica limitations, tintinnids are among the few microbial groups that can be tracked in the environment by either classical microscopy or modern sequencing methods. Comparing both approaches, we have tested and set up lab and bioinformatic methods for high-throughput sequencing of ciliate assemblages (Refs. 13, 21).
Filling diversity gaps
The massive use of environmental DNA sequencing is revealing potentiality novel taxa within most microbial groups, but it is challenging to rule out technical artifacts and ultimately “put a face” to the sequences. Using single-cell DNA sequencing, we clarified the identity of two “mystery” clades. One is an abundant, known ciliate family (Leegaardiellidae) that lacked a sequenced representative in public databases (Ref. 24). But the second one resulted to be the new tintinnid genus, Dartintinnus! We recently described the genus and its type species (Ref. 27), which is named after my mentor at the University of Buenos Aires, Viviana Alder.
Photo credit: Weiwei Liu