Chairs
Dr Alyson Santoro, University of California, Santa Barbara, USA
Dr Alyson Santoro, University of California, Santa Barbara, USA
Dr Alyson Santoro is an Assistant Professor in the Department of Ecology, Evolution and Marine Biology at the University of California, Santa Barbara. Alyson’s research focuses on microbes involved in nutrient cycling in the ocean, especially of the element nitrogen. She is interested in cultivating new microbes and discovering novel ways of tracking their activity. This research combines laboratory experiments with field observations, and to date has used genomics, transcriptomics, proteomics and stable isotope geochemistry as tools to uncover the activity of microbes in the mesopelagic ocean. A particular focus of the lab is the marine archaea, a largely uncultured group of microbes. Findings from their recent research include the discovery that archaea in the ocean can make the greenhouse gas nitrous oxide, and that some marine archaea have exceptionally small genomes. Alyson received her PhD in Environmental Engineering at Stanford University and completed a postdoctoral fellowship at Woods Hole Oceanographic Institution.
09:00-09:30
Short-range interactions govern cellular dynamics in microbial multi-genotype systems
Professor Martin Ackermann, ETH Zurich and Eawag, Switzerland
Abstract
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.
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Professor Martin Ackermann, ETH Zurich and Eawag, Switzerland
Professor Martin Ackermann, ETH Zurich and Eawag, Switzerland
Martin Ackermann is a Professor at ETH Zürich. His group consists of about 15 PhD students and postdocs with backgrounds in microbiology, evolutionary biology, physics and computer science. The goal of the group is to work on general principles of how bacteria interact with each other and with their environment. A first interest of the group is bacterial individuality, that is, differences in behaviour and properties between genetically identical cells. The group works on how individual cells that specialise in different tasks can interact with each other and engage in the division of labour. A second interest is how bacteria cope with dynamic environments — how cellular decisions of individual bacteria are influenced by past events as well as by stochastic processes. A third interest is on biological systems that are composed of several interacting genotypes; the group is interested in how new functionality at the level of microbial consortia emerges based on the properties of individuals and their interactions.
09:45-10:15
Virtual fluidic channels: from functional single cell rheology to tissue mechanics
Dr Oliver Otto, University of Greifswald, Germany
Abstract
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.
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Dr Oliver Otto, University of Greifswald, Germany
Dr Oliver Otto, University of Greifswald, Germany
The research group of Oliver Otto develops and applies microfluidic technologies for the label-free characterization of suspended and adherent cells. Specifically, he is interested in the role of mechanical properties for homeostasis in the cardiovascular system. Oliver received his PhD in Physics from the University of Cambridge, UK, where he investigated single molecule dynamics at the Cavendish Laboratory. In 2012, he joined the Technical University of Dresden, Germany, as a postdoctoral researcher where he was working on the translation of high-throughput screening into the field of cell mechanics. His method, real-time deformability cytometry, allows for the first time the measurement of cell mechanical properties with the throughput of a flow cytometer. Since 2016 Oliver has been an independent group leader at the Centre of Innovation Competence – Humoral Immune Reactions in Cardiovascular Diseases at the University of Greifswald, Germany. He leads a group of interdisciplinary researchers combining expertise in Biology, Engineering as well as Physics.
11:00-10:30
Studying uncultivated diversity via single-cell approaches – from microorganisms to viruses
Dr Tanja Woyke, DOE Joint Genome Institute, USA
Abstract
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.
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Dr Tanja Woyke, DOE Joint Genome Institute, USA
Dr Tanja Woyke, DOE Joint Genome Institute, USA
After studying the mechanism of action of antifungal natural products and their derivatives during her PhD in Microbiology at the Eberhard Karls University of Tübingen, Germany, Dr Tanja Woyke pursued her postdoctoral research at the JGI in 2004. The main objective of her research was the symbiont community of a gutless oligochaete for which she deciphered function and host-symbiont interplay using metagenomics. Taking on a Research Scientist position in 2007, she switched gears from metagenomics to single-cell genomics, which is now her primary interest and passion. Tanja stepped into the microbial genomics program lead position in 2009. She now holds a Staff Scientist position at the JGI, an Adjust Scientist position at the Bigelow Laboratory for Ocean Sciences and an Adjunct Associate Professor at the UC Merced School of Natural Sciences.
11:45-12:15
Interrogating marine microbes for their activity and growth: an overview and recent developments
Dr Josep M Gasol, Institut de Ciències del Mar, CSIC, Spain
Abstract
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.
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Dr Josep M Gasol, Institut de Ciències del Mar, CSIC, Spain
Dr Josep M Gasol, Institut de Ciències del Mar, CSIC, Spain
Dr Josep M Gasol is a Research Professor in Barcelona, interested in planktonic microbe abundance and activity, and their ecosystem effects, with emphasis on microorganism community structure (size, functional and taxonomical structure), and how the physical and biological factors shape it. He approaches these question by empirical analysis of data bases, oceanographic cruise, mesocosm and microcosm experiments, and by the combined use of image analysis and flow cytometry and metabolic fluorescent probes. Josep started his career working on the microbes of one of the most interesting lakes in the world, Lake Cisó. He was then a postdoc in Montreal where instead of focussing on one lake, he tried to study as many lakes as possible, and then started to focus on the Ocean. Josep is very involved with the Microbial Observatory of Blanes Bay, where he coordinates the long term research, was the Microbiology coordinator of the Malaspina-2010 circumnavigation, and he has recently edited the last edition of the Microbial Ecology of the Ocean book.