Shaping the environment for single microorganisms
Dr Vicente Fernandez, ETH Zürich, Switzerland
Variability between individual microorganisms is driven by both internal factors, such as phenotypic heterogeneity, and external factors, through spatially and temporally stochastic interactions with the environment. As new methods are developed to measure the responses of single cells, it is of equal importance to have flexible and accurate approaches to experimentally manipulate the environment at the single-cell level, in order to mimic or isolate components of their natural habitat. This involves challenges in controlling the chemical composition, temporal dynamics, and spatial distributions at the scale of individual cells. Vicente Fernandez will present new approaches combining microfluidics and image analysis for recreating interactions between bacteria and phytoplankton from aquatic environments, and for further simplifying these interactions to study the behavioural and growth responses of hundreds to thousands of single cells in parallel. These approaches unlock the possibility of understanding and quantifying fundamental marine processes from the perspective of the individual microorganisms that drive them.
Exploring deep opisthokont evolution through single-cell approaches
Dr Purificacion Lopez-Garcia, CNRS - Université Paris-Sud, France
Opisthokonts were early recognised as one of the major eukaryotic super-groups based on molecular phylogenetic analyses. They cluster in two major lineages, the Holomycota and the Holozoa, which encompass well known multicellular organisms, respectively Fungi and Metazoa, together with a cohort of unicellular relatives. Phylogenetic and functional analyses have shown that many genes typically involved in metazoan multicellularity were already present in the unicellular relatives of animals. On the holomycotan branch, the situation is complex because the boundaries defining Fungi are fuzzy and, at the same time, environmental 18S rRNA metabarcoding combined with more classical taxonomic studies have revealed a wide diversity of previously unrecognized lineages branching deeply within classical Fungi (osmotrophic lineages, including chytrids) and prior to their divergence (eg, aphelids, rozellids or cryptomycotes, microsporidians, nucleariids). Many of these lineages encompass uncultured species for which gaining information is challenging. Single-cell genomic and transcriptomic approaches offer a suitable solution to fill gaps on our knowledge about early-branching holomycotan lineages. Purificacion Lopez-Garcia will present ongoing studies of her lab to obtain phylogenomic and gene content data with the aim of unraveling hallmark evolutionary processes leading to the evolution of fungi.
Dr Adam Monier, Living Systems Institute, University of Exeter, UK
Single-cell approaches for investigating planktonic archaea
Dr Alyson Santoro, University of California, Santa Barbara, USA
Though archaea have been known in the marine water column for nearly 30 years, many questions remain about their ecology, physiology, and interactions with other members of the microbial community. In particular, the interactions between archaea and eukaryotic plankton are poorly understood. Indeed, aside from the well-known relationship between methanogenic archaea and their ciliate hosts in anaerobic environments, no archaeal symbionts of eukaryotes have been identified. To investigate this, over 400 individual protist cells were isolated using fluorescence-activated cell sorting, genome amplified, and screened for the presence of associated archaea. Despite the identification of multiple protist-bacteria associations, no archaeal-eukaryote relationships were identified. Single-cell amplified genomes (SAGs) of archaeal cells, however, have revealed interesting biogeographic differences in different oceanic regions. Further discussed is the growing availability of metagenome-assembled genomes (MAGs) for planktonic archaea and the relative utility of MAGs versus SAGs for understanding archaeal biogeography and physiology.