Short-range interactions govern cellular dynamics in microbial multi-genotype systems
Professor Martin Ackermann, ETH Zurich and Eawag, Switzerland
Many microorganisms live in communities that are spatially structured, for example in biofilms. Such communities exhibit activities and functions that are shaped by metabolic interactions between the community member. Interactions are expected to mainly occur between cells that are close in space. As a consequence, the nature and strength of the interactions that will occur will depend on the spatial arrangement of different types of microbial cells. In turn, the spatial arrangement is expected to be shaped by metabolic interactions, which determine regions where a given cell type grows well. The Ackermann group’s goal here is to better understand this interplay between the spatial arrangement of different types of microbial cells and the interactions that arise between them. Working with synthetic consortia of different E. coli strains with well-defined metabolic interactions, Martin can quantify the spatial range over which interactions occur and understand the consequences for the spatial self-organisation of these multi-genotype systems. The goal of this work is to contribute to identifying general principles that govern how different types of microorganisms organise in space, and how this spatial self-organisation shapes the activities and functions of microbial systems.
Virtual fluidic channels: from functional single cell rheology to tissue mechanics
Dr Oliver Otto, University of Greifswald, Germany
The mechanical properties of cells have long been established as a sensitive and label-free biomarker. While mechanical cell assays have been traditionally limited to low throughput or small sample size, the introduction of real-time deformability cytometry (RT-DC) increased analysis rates to up to 1,000 cells per second. RT-DC has demonstrated its relevance in basic and fundamental life science research, e.g. by observing the activation of immune cells and describing the membrane dynamics of Malaria pathogenesis. However, linking immune cell activation to underlying tissue alterations has not been possible so far. Here, the concept of virtual fluidic channels is introduced to bridge the gap between single cell rheology and tissue mechanics. Virtual channels can be created in almost any microfluidic geometry and can be tailored dynamically towards hydrodynamic stress distributions sufficient to probe the rheology of arbitrary cell sizes. Using spheroids as a tissue model, results from virtual channel measurements indicate that the Young’s modulus of single cells exceeds the one of spheroids and that their elasticity increases with size. The availability of a high-throughput assay for mechanical spheroid characterization might lead to a better understanding of tissue rheology and help to study the interplay of virus infiltration and tissue regeneration.
Studying uncultivated diversity via single-cell approaches – from microorganisms to viruses
Dr Tanja Woyke, DOE Joint Genome Institute, USA
The bacterial and archaeal tree of life has undergone significant expansion, chiefly from candidate phyla obtained through genome-resolved metagenomics and, at smaller scale, via single-cell sequencing efforts. Following this path, viral diversity is being uncovered at a rapid pace. Tanja Woyke discusses how the combination of flow cytometry followed by genome amplification and sequencing can provide a means to cataloguing uncultivated microbial and viral diversity. Focusing on Nanoarchaeota symbionts attached to their hosts, she illustrates that this approach further allows the assignment of novel putative host associations, facilitating the exploration of cell-cell interactions and fine-scale genomic diversity.
Interrogating marine microbes for their activity and growth: an overview and recent developments
Dr Josep M Gasol, Institut de Ciències del Mar, CSIC, Spain
Recent developments in community and single-cell genomic approaches have provided an unprecedented amount of information on the ecology of microbes in the aquatic environment. However, linkages between each specific microbe’s identity and their in situ level of activity (be it growth, division, or just metabolic activity) are much more difficult to obtain. One of the ultimate goals of marine microbial ecology would be integrate three levels: the genomic (including identity) one, the activity/growth one, and the morphology/visualisation, and all this for as many individual cells as possible, as a means to understand how each environmental characteristic determines the types of different microbes in nature and their activity or growth, alongside with information on morphology and cell-to-cell associations. Recent reviews have stressed ways for capturing the activity level of different genomic entities, but often one of the three legs, that of visualization, has not been well covered by the available methods. A review of current methodologies that have been applied to marine microbes, particularly prokaryotes, will be presented combined with a discussion of the difficulties in identifying and categorizing activity and growth, in doing so at with the minimal manipulation of the environment, and the level of within-population single-cell variability in activity that occurs in natural marine environments.