Daniele Giannoti
Single-cell Transcriptomics Elucidates the Evolution of Retaria
Single-cell transcriptomics has allowed us to uncover the phylogenetic placement of an increasing number of hard-to-cultivate protist lineages, while also providing a scaffold for the reconstruction of the evolutionary history of their traits. Retarians (foraminifera and radiolarians) are mostly marine rhizarian amoebae which are infamously difficult to cultivate and represent one of the least studied groups of eukaryotes; consequently, little is known about their biology, ecology, and evolution. While previous phylogenetic and phylogenomic analyses have incorporated retarian lineages, there has been little consensus over the relationships between their major groups, and two conflicting topological hypotheses persist: (i) Acantharea as the sister group of Foraminifera & Polycystinea; (ii) Foraminifera as the sister group of Acantharea & Polycystinea. Moreover, the branching position of Sticholonchea remains unresolved. Previous attempts have been hindered by limited taxon sampling and poor data coverage, especially concerning radiolarians, and potentially by modelling artefacts. To address this and better represent retarian diversity, radiolarian and planktonic foraminiferan cells were individually collected from marine environmental samples; each cell was processed to obtain cDNA libraries, which were further used for high-throughput sequencing. Seventy-four new transcriptomes from as many retarian cells (17 foraminifera + 57 radiolarians) have been included in phylogenomic analyses along with publicly available data from an additional 41 taxa (28 foraminifera + 13 radiolarians), more than doubling the overall coverage. Preliminary results indicate that Foraminifera likely differentiated from a radiolarian ancestor, making radiolarians non-monophyletic with Acantharea as a sister group to all other retarians. However, the placement of Sticholonchea continues to be weakly supported. While additional analyses are required, the framework provided thus far already elucidates our understanding of the evolution of Retaria and can be used as a more reliable foundation for further studies.

Marie Leleu
Combining Transcriptomic, Microscopy and Phylogenomics to study Foraminifera
Foraminifera, single-celled protists with complex life cycles have long presented challenges for integrating molecular data. To address this, we developed a suite of methods to visualize and analyze the genome architecture and gene expression of Foraminifera. We adapted a workflow to isolate individual Allogromia laticolaris cells from the confocal and perform single-cell transcriptomics, enabling gene expression analysis directly from imaged cells. Furthermore, we present PhyloToL, a modular, user-friendly pipeline with taxon-rich databases that allow for effective data curation and phylogenomic analysis. With the increasing availability of ‘omics-scale data from diverse microeukaryotes, studies of eukaryotic evolution and symbiotic interactions, grapple with the difficulties inherent in integrating data of various types into taxon-rich studies. This is particularly challenging for analyses of uncultivable lineages for which single-cell approaches generate a mixture of sequence data from hosts, associated microbiomes, and contaminants. PhyloToL enhances phylogenomic reconstructions, facilitating the curation of transcriptomic data and the interpretation of evolution and diversity. Together, these methods establish a novel framework for providing key insights into Foraminifera biology and evolutionary history.

Manon Laget
Siliceous Rhizaria and ocean biogeochemistry: an overview
Siliceous Rhizaria are diverse both in morphology and ecology. Their size range spans a few tens of µm to several mm, and their skeleton made of biogenic silica makes them important contributors of the ocean silicon cycle. In particular, they constitute a unique source of biogenic silica production and stock in the mesopelagic layer, where no other silicifiers are found. They can be either heterotrophic or mixotrophic, and thus have different ecological niches and roles in the carbon cycles. Mixotrophic taxa, belonging to Radiolaria, are predominant in surface oceans and contribute to carbon uptake particularly in oligotrophic regions. Heterotrophic taxa, mostly belonging to Phaeodaria, are often found in the mesopelagic layer of productive areas, where they feed upon sinking particles. Upon death, these organisms sink, carrying organic and mineral material to the deep ocean. While Radiolaria are correlated to large flux events, Phaeodaria have the ability to aggregate particles around them, which are then ballasted by their silica skeleton. Yet, recently, it was estimated that large mesopelagic Phaeodaria could intercept up to 9% of the gravitational particle flux. This leaves an open question: are Rhizaria contributing to carbon fluxes or do they act as gatekeepers of the biological carbon pump?

Nielja S. Knecht
The impact of foraminifera on the marine carbon cycle - using species distribution models to estimate global patterns and predictors
Planktic foraminifers are calcifying zooplankton that contribute to the biological carbon pump via the sinking of their calcareous shells. However, their importance for regional and global plankton biomass and carbon fluxes is not well understood. Here, we modeled global annual patterns of foraminifer total carbon (TC) biomass and total inorganic carbon (TIC) export fluxes over the top 200 m using five statistical species distribution models (SDMs). An extended version of the MARine Ecosystem DATa (MAREDAT) of zooplankton abundance observations was used to estimate the biomass.