Single cell ecology

09:05-09:30 Cooperative growth and community assembly at the microbe scale

Professor Otto X Cordero, MIT, USA

Abstract

Bacterial cooperation, whereby cells secrete compounds that can facilitate the growth of neighbouring cells, has been extensively studied through the lens of evolutionary biology. However, the environmental implications of cooperation and the ecological scenarios under which it takes place remain much less understood. In this talk Otto Cordero will discuss the conditions under which cooperation emerges in microbial populations that degrade complex organic particles in the ocean. Otto will show that organisms that privatise their enzymes by tethering them to their membranes are more likely to engage in cooperative interactions by forming cell-aggregates that enables them to efficiently uptake of the solubilised organic matter. By contrast, when organisms secrete highly active enzymes dynamics quickly turn competitive, and the efficiency of carbon uptake drops. Otto will back up this results with theory, data from individual based models and experiments. Finally, he will discuss the genomic underpinnings and potential role of social cheaters in the natural environment, based on a study with hundreds of micro-scale particle colonisation experiments in natural seawater.

09:45-10:15 A single cell view on host-virus interactions in the ocean

Professor Assaf Vardi, Weizmann Institute of Science, Israel

Abstract

Investigating host-pathogen interactions at the whole-population level tends to mask cell-to-cell variability, hampering the ability to discern between diverse phenotypes. To overcome this limitation, the Vardi group applied single-cell dual RNA-seq to study the dynamic transcriptomes of a cosmopolitan bloom-forming alga, Emiliania huxleyi, and its specific large DNA virus EhV. Gene expression was profiled for multiple genomes (nuclear, plastid, mitochondrial and viral) using the massively parallel RNA single-cell sequencing method for cells sorted from infected cultures during a time course. Striking heterogeneity in the overall viral transcription was observed among individual cells from all samples, with cells exhibiting either high or very low viral transcript numbers, but very few at intermediate levels. The cells with high viral expression formed subpopulations characterised by clusters of strongly co-expressed viral genes. By re-ordering cells based on their transcriptional pattern, the group defined a continuum infection states along a pseudo-temporal scale. As the infection progressed, the viral genes were successively expressed in five partially overlapping kinetic classes that end with constitutive expression of the virion structural protein genes. Majority of cells with high viral gene expression showed a selective shutoff of host nucleus-encoded genes and minor fraction exhibited differential gene expression relate to cell fate regulation, lipid biosynthesis, and flagellated resistant phenotype. Vardi’s group further applied this scRNAseq approach to track viral infection dynamics during natural bloom of E. huxleyi which enabled a first single cell view on host and virus arms race at sea.

10:30-11:00 Coffee

11:00-11:30 Single cell genomics

Professor Stephen Quake, Stanford University, USA

Abstract

An exciting emerging area revolves around the use of microfluidic tools for single-cell genomic analysis. Stephen Quake’s group has been using microfluidic devices for both gene expression analysis and for genome sequencing from single cells. In the case of gene expression analysis, it has become routine to analyse hundreds of genes per cell on hundreds to thousands of single cells per experiment. This has led to many new insights into the heterogeneity of cell populations in human tissues, especially in the areas of cancer and stem cell biology. These devices make it possible to perform “reverse tissue engineering” by dissecting complex tissues into their component cell populations, and they are also used to analyse rare cells such as circulating tumour cells or minor populations within a tissue. The group has also used single-cell genome sequencing to analyse the genetic properties of microbes that cannot be grown in culture – the largest component of biological diversity on the planet – as well as to study the recombination potential of humans by characterising the diversity of novel genomes found in the sperm of an individual. Stephen expects that single cell genome sequencing will become a valuable tool in understanding genetic diversity in many different contexts.

11:45-12:15 Single cell analysis with droplet microfluidics

Professor David Weitz, Harvard University, USA

13:30-14:00 The Malaria Cell Atlas and using scRNA-seq to examine developmental decisions made by single-celled parasites

Dr Mara Lawniczak, Wellcome Sanger Institute, UK

Abstract

Single-cell RNA sequencing is revolutionising our understanding of malaria parasites. The Lawniczak group has used a combination of Smart-seq2 and 10X to characterise the transcriptional networks underpinning the developmental trajectories of parasites. Here Mara presents thousands of single-cell transcriptomes covering the entire life cycle of the rodent malaria parasite Plasmodium berghei, both in the mosquito and in the mammalian host. The group uses these data to identify how modules of genes are used throughout the life cycle, the variability in their expression, and how they are putatively regulated. They have developed an open-access interactive interface to view the complete dataset, enabling researchers to explore the behaviour of any gene within single parasites across the entire lifecycle. Finally, Mara will present work that uses both multiplexed gene knock-out screens and scRNA-seq to examine one of the most critical decisions a parasite makes: whether or not to become sexually committed. This work demonstrates how scRNA-seq can be used to profile the entire life-cycle of a single-celled organism, revealing novel insights into its genome.

14:15-14:45 Cell Atlas Technologies and the maternal-foetal interface

Dr Sarah Teichmann FMedSci, Wellcome Sanger Institute, UK

Abstract

Genomics has undergone a resolution revolution, such that the nucleic acid content of individual cells is now sequenced routinely in high-throughput mode. Thus we can define the cellular composition of tissues in an unbiased and comprehensive way using single cell transcriptomics, revealing the molecular fingerprint of cell states and their predicted signalling circuits in tissues across development and disease. Sarah Teichmann will illustrate this with the maternal-foetal interface in the first trimester placenta/decidua.

15:00-15:30 Tea

15:30-16:00 Single-cell responses to environmental cues

Dr Stefano Pagliara, University of Exeter, UK

Abstract

Clonal microbial populations feature cell-to-cell differences in physiological parameters such as gene expression, growth rate, and resistance to stress. This phenotypic heterogeneity is at the basis of fundamental biological processes such as membrane transport, stem cell differentiation, and tolerance to antimicrobial compounds. Therefore, it is paramount understanding how changes in the environment affect the phenotypic heterogeneity within a clonal microbial population. Stefano will illustrate how embryonic stem cells respond to physical environmental cues such as transient confinement into narrow grooves. He will show that this mechanical response is heterogeneous. Remarkably, the nuclei of some embryonic stem cells display a unique material property that is they are auxetic; exhibiting a cross-sectional expansion when stretched and a cross-sectional contraction when compressed. He will then talk about the different strategies that individual bacteria can exploit to escape antibiotics and illustrate current efforts to understand how the environment predetermines the outcome of antibiotic treatment.

16:15-18:00 Poster session

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.

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.

10:30-11:00 Coffee

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.

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.

13:30-14:00 Ocean microbiome datafication

Dr Ramunas Stepanauskas, Bigelow Laboratory for Ocean Sciences, USA

Abstract

Data-rich, molecular analyses are becoming important sources of knowledge about the composition and activities of microorganisms in diverse environments. Yet, today only a small fraction of these meta-omics data (short DNA, RNA and peptide sequences) can be accurately assigned to specific lineages and metabolic pathways, due to the lack of adequate reference genome databases. To address this challenge, the Stepanauskas group sequenced 20,000 individual bacteria, archaea and viral particles from the tropical and subtropical epipelagic using an unbiased, Big Data approach. This GORG-Tropics database provides some of the first insights into the global pangenomes, infections, biogeography and sizes of many of the bacterial and archaeal lineages that dominate surface ocean. The group shows that GORG-Tropics enables accurate taxonomic and functional assignments of the majority of meta-omics data from this global environment. Intriguingly, the group found that every sequenced cell was genomically unique, and that a large fraction of the global bacterioplankton coding potential was present in a single drop of seawater. GORG-Tropics expands the capacity of oceanography’s cyber-infrastructure and enhances the interpretation of diverse marine omics studies. It also demonstrates that relevant genomic representation of complex microbiomes is an achievable goal and may be applied in other environments.

14:15-14:45 How do we define the role of eukaryotic cells in complex microbial ecosystems?

Professor Patrick Keeling, University of British Columbia, Canada

Abstract

One challenge associated with developing a functional understanding of microbial ecosystems is the magnitude of the diversity encompassed by the word “microbial”. Most ecology is biased towards a few macroscopic plants and animals. In contrast, microbial ecosystems are made up of more than ten-times the diversity of eukaryotes alone, in addition to bacteria, archaea, and viruses. Microbial ecology is also heavily biased, towards bacteria (and sometimes archaea). So we are faced with a need to develop a fuller picture of these networks, but to do so both a quantitative and qualitative problem, because the diversity is so great that neither the technical approaches nor the basic biology required to understand one group is readily translatable to others. For microbial eukaryotes there are paths forward to solving many technical challenges though single cell methods, and advances in both genomics and transcriptomics will be discussed. But this still leaves a thornier conceptual problem of how such data will (or will not) reveal ecological roles of microbial eukaryotes because translating genomics to ecological function is largely restricted to metabolism. For most microbial eukaryotes, complex cellular structures and resulting behaviours are much more significant, but we lack strong conceptual frameworks to derive these traits from genomic data alone.

15:00-15:30 Tea

15:30-16:00 Exposing uncultured marine eukaryotes and their ecological interactions through single cell genomics

Professor Alexandra Worden, Monterey Bay Aquarium Research Institute (MBARI), USA

Abstract

For decades and longer scientists have described diverse unicellular eukaryotic organisms in aquatic ecosystems. The introduction of molecular approaches to ocean ecology has expanded our view of the diversity of marine protists and their importance in these ecosystems, yet many key taxa remain uncultured. Hence it has been difficult to examine their evolutionary relationships beyond what is possible with marker gene analyses. Likewise, it has not been possible to characterise their nuclear and organellar genomes. Moreover, lack of cultures has obviated deeper exploration of their interactions with other biological entities in the sea. In 2005 the Worden group began using at-sea flow cytometry to sort wild protists in order to generate both targeted (population) metagenomes and eukaryotic single-cell metagenomes. In addition to providing insights into the evolution and distribution of wild phytoplankton species these studies are increasingly revealing co-associations between the targeted eukaryote and other entities. Here, Alexandra will discuss a suite of findings from studies in the tropical Atlantic and eastern North Pacific Oceans. Her long term goal is to use these approaches to facilitate research that goes deeper into the biology of key uncultured groups and their ecological interactions. Collectively, these types of studies are critical for establishing a baseline against which future changes in microbial community structure can be assessed and for understanding the diversity and evolution of marine protists.

16:15-17:00 Panel discussion/overview