BYGENEX

Mon, 27 Apr 2026 00:00:00 +0000

Oceanic bacterivory is the process through which marine bacteria are grazed by microbial eukaryotes. It consumes a large fraction of bacterial production, transfers bacterial biomass to upper trophic levels, and completes the inorganic nutrient recycling needed for regenerated primary production. Global estimates indicate that ~15% of the Earth’s primary production circulates through this process. Despite its central role in marine food webs, the identity of the dominant grazers is not well known, and in situ bacterivory rates are seldom measured as they require laborious techniques. Consequently, it is impossible to predict how oceanic bacterivory will react in light of the dramatic anthropogenic change we are facing. The aim of BYGENEX is to fill this gap and develop a quantitative approach to study oceanic bacterivory by using emerging omics-based tools that target marker genes for phagocytosis, the cellular mechanism behind bacterivory. We will first prepare an exhaustive collection of genomes from the main bacterivores in the global ocean. Then, we will identify highly expressed genes involved in phagocytosis in cultured and uncultured species across taxonomic lineages. We will perform in situ expression analysis of phagocytosis marker genes to quantify bacterivory rates of the community and of the dominant species, after calibration with direct activity measures. Finally, data from cruises will benchmark the present state of bacterivory in a range of oceanic regimes, and we will simulate bacterivory using a global ecosystem model to analyse ecosystem-wide effects of this process. BYGENEX will provide new tools to quantify oceanic bacterivory at unprecedented large scales and open the way to improve our current understanding of the structure and function of the microbial component and its role in the global marine system.

EPIC

Fri, 01 Sep 2023 00:00:00 +0000

Molecular surveys of microbial diversity have been transformative for the smallest unicellular eukaryotes in the ocean, revealing the existence of a substantial phylogenetic diversity within these assembles and the presence of unsuspected novel groups. In the seminal studies, there was a strong interest in finding novelty at the highest taxonomic level, accounting for new and unplaced lineages in the eukaryotic tree of life. A group of related environmental 18S rDNA sequences emerged as a novel high-rank eukaryotic taxa, and were initially named Picobiliphytes. These novel sequences appeared in distant marine regions, so they seemed new relevant ecological players, and FISH (Fluorescence In Situ Hybridization) visualizations suggested the presence of a phycobilin containing chloroplast, so they were proposed to be a new algal lineage. Due to their relevance, this group was the focus of further microbial explorations and as a result of new data it changed his name, from Picobiliphytes to Picozoa, and shifted his trophic mode, from phototrophs to heterotrophs, as the visualized chloroplast was likely an artifact. Recent data indicates that picozoans have found a robust place in the eukaryotic tree of life, an unexpected place within Archaeplastida, starting to solve the first evolutionary mystery. However, studies on picozoa so far have still failed short in providing a good description of their cell biology and ecology, to the point that even the most basic trophic mode of these novel species, how do they support their growth, is still undefined. In the project EPIC we propose a target research to advance in the knowledge of the still enigmatic picozoans. We will take advantage of existing metabarcoding datasets and new ones generated here to identify the diversity, biogeography and ecological niche of picozoan species. Then, we will design FISH probes for distinct picozoan clades to study the cell size, cell abundance and trophic mode (phagotrophy versus osmotrophy) of the dominant species, while we will also attempt to get some of them into culture. We will then asses the gene content of the main picozoan species by using single cell genomics with samples from distant marine regions. We will search in these genomes for ecologically relevant genes, which can provide critical insights on the ecological performance of picozoan species, and viral signatures, which can be seen as indicators of relevant viral-host interactions. Finally, we will use the newly generated genomes to search, in the available metagenomes, metatranscriptomes and metaviromes, for the presence and expression of picozoan genes in natural assemblages and for the co-occurrence of viral and host signatures. Even though picozoans emerged as one of the most intriguing novel protist group in seminal biodiversity surveys, they have only been studied superficially and there is still a large knowledge gap in their species diversity and biogeography, trophic modes, ecological impact in carbon fluxes, and gene repertoire. The EPIC project proposes a targeted study on this group, with the final aim to incorporate it into marine food web models.

Single Cell Genomics | Ecology of Marine Microbes

BYGENEX

EPIC