Ongoing projects

From environmental metabarcoding/metatranscriptomic to a single-cell transcriptomics: evaluation of human impact on the microeukaryotic diversity of the Tietê River, Sao Paulo, Brazil.

Eukaryotic microbes (protists) play primordial roles in food webs in all ecosystems, but knowledge on their taxonomic and functional diversity is still patchy. Recent developments of high throughput sequencing (HTS) tools and especially metabarcoding make it possible to estimate the total organismal diversity from environmental DNA samples. As it is now possible to analyze simultaneously high numbers of samples we can also use HTS in fundamental and applied ecological research to determine patterns and environmental drivers of diversity, community structure and associated functions.


In this project, my aim is to assess the impact of pollution on the freshwater protistan communities of the Tietê River (São Paolo, Brazil). This river is an ideal model to study human impact on ecosystem biodiversity, as it covers, over a relatively short geographical distance, the complete range from near pristine to massively polluted (industry and domestic waste) water. My focus is on all groups of protists, building on the expertise I developed in my PhD. I will first screen the diversity of all protists lineages by using a metabarcoding approach to characterize the taxonomic composition of communities along the river and correlate them to environmental factors (nutrient content, pH and pollutant). Concurrently in collaboration with Prof. Matthew Brown from Mississippi State University, I will use a metatranscriptomic approach to evaluate overall gene expression within the community. Finally, I will isolate, describe, and culture a selection of the most interesting candidate bioindicating taxa. I will expose these organisms to different conditions (e.g., pollutants and temperature) to determine genes expression patterns using single-cell transcriptomic approaches developed by Prof. Brown and Prof. Lahr at the University of São Paolo.


























The combination of these observational and experimental methods will expand my range of expertise and allow me to develop an integrative approach for the study of microeukaryotic diversity, a prerequisite needed for both fundamental (e.g. diversity and physiology) and applied (bioindication and water resource management) research on protists.