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Overview

Satellite meeting organised by Professor Thomas Richards, Dr Ramon Massana and Professor Neil Hall

Single cell approaches are changing how we study many biological problems. This meeting will bring together biophysicists, molecular biologists and microbial ecologists who are using these technologies to understand the natural world. The aim of this satellite meeting is to report progress, identify areas for synergy and lay down the foundations for further developing this interdisciplinary science.

The speaker biographies and abstracts are below. Recorded audio of the presentations will be available on this page after the meeting has taken place.  

Enquires: Contact the Scientific Programmes team.

Organisers

Schedule


Chair

09:05-09:30
Bacterial grazers in the oceans

Abstract

The perception that marine microbial life is extremely diverse is well grounded based upon molecular diversity surveys and the existence of a wide variety of cultured forms. This also applies to the smallest colourless eukaryotes in planktonic systems, the heterotrophic flagellates, which are important agents in bacterial mortality through grazing. The use of extensive sampling datasets and high-throughput sequencing tools allows to identify the dominant species and better define their ecological relevance in the marine environment. In particular, Ramon Massana’s group focuses here in two model groups that represent contrasted ecological strategies in terms of growth and grazing dynamics and oceanic distribution. One of these two groups still remains uncultured, so single cell genomics is the only way to access to its genome content, which can then be used to analyse gene expression in natural communities. Opening the black box of microbial functional guilds is a necessity to really understand ecosystemic processes.

Speakers


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09:45-10:15
Are single-cell approaches useful for evolutionary questions?

Abstract

Single-cell genomics is a powerful method to get genomic data from uncultured organisms. However, the genome data generated for eukaryotes are usually less than 50% of the genome. The question is then whether this is useful for evolutionary questions. By obtaining single-cell genomic data from three choanoflagellates, Iñaki Ruiz-Trillo investigated whether this methodology can provide valuable data for evolutionary questions. In particular, and given the phylogenetic position of choanoflagellates as the sister-group to animals, the authors analysed the use of these data to address the origin of animals. The potential and the challenges will be discussed.

Speakers


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10:30-11:00
Coffee
11:00-11:30
Power and challenges of single cell experimentation for the study of the smallest photosynthetic eukaryotes

Abstract

Bacterial-sized unicellular eukaryotes of the class Mamiellophyceae are ubiquitous in the marine environment, where they significantly contribute to the primary production. Their ease of manipulation and compact genomes make them ideal models for benchmarking single cell approaches for phytoplanktonic micro-organisms. During this talk, Gwenaël Piganeau will explain how single cell experimentations enable to address two fundamental issues about the mode and tempo of evolution in these microalgae. First, how the set up of mutation accumulation experiment assays in liquid medium allows the segregation of deleterious and slightly deleterious mutations in individual microalgae cells. Whole genome re-sequencing of these lineages in five phytoplanktonic species enabled the estimation of the genome wide spontaneous mutation rate, the ultimate source of genetic diversity in the fate of environmental change. Second, single cell manipulation is required to estimate the phenotypic diversity within isogenic cells. This is particularly important to understand the mechanisms involved in the resistance of microalga to viruses infecting them, and how this impacts the microalga virus ratio, which influences the carbon flux in the sunlit ocean.

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11:45-12:15
Dissecting trophic interactions among microbes in the ocean

Abstract

Predatory protists have long been recognised for their role in aquatic food webs, often exerting control on microbial abundance and community structure. Nevertheless, little is known about the relative importance and activity of different predatory groups, let alone the specific predator-prey interactions that drive population dynamics of individual taxa in the ocean. Resolving such interactions is complicated by the extreme diversity of the predators involved, both in terms of their distant evolutionary histories spanning the eukaryotic tree of life, as well as their functional diversity that includes the combination of photosynthetic with predatory nutrition in a mixotrophic lifestyle. Here, single-cell and population level cell sorting based on the presence of acidic food vacuoles were used to identify actively feeding microbes in the NE Pacific Ocean. Prey assimilation by predators feeding on the most abundant photosynthetic microbe Prochlorococcus was further verified by RNA-stable isotope probing. Both of these approaches suggested the quantitative importance of choanoflagellates as microbial predators in both productive coastal and nutrient-poor oceanic waters. Finally, the suitability of transcriptional patterns to indicate a predatory, phagotrophic nutrition will be discussed. Collectively, these approaches help to dissect the diverse trophic roles of microbial eukaryotes that shape the marine carbon cycle.

Speakers


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Chair

13:30-14:00

Speakers

14:15-14:45
Single-cell mitogenomics of heterotrophic flagellates

Abstract

Most eukaryotic microbial diversity is uncultivated, under-studied, and lacks nuclear genome data. Mitochondrial sampling is more comprehensive, yet still groups that occupy important phylogenetic positions remain unexplored. Using photopigment exclusion and tubulin-specific fluorescence staining, the group sorted single-cell ‘heterotrophic’ flagellates directly from eastern North Pacific waters for genome sequencing. They recovered 206 single amplified genomes (SAGs) predominantly from under-represented protistan branches on the tree of life. 69 SAGs contained mitochondrial contigs including 21 unique complete, or near-complete, mitochondrial genomes from cryptic phylogenetic branches including telonemids, katablepharids and marine stramenopiles (MASTs). Collectively, these data point to a dynamic history of mitochondrial genome evolution including intron gain/loss, extensive patterns of genetic code variation, and complex patterns of convergent gene loss and endosymbiotic gene transfer. Surprisingly, mitochondrial coding content variation in heterotrophic stramenopiles resembles patterns previously only observed in plants.

Speakers


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15:00-15:30
Tea
15:30-16:00
Understanding microbial interactions with eukaryotes at a single cell level

Abstract

The Darby lab currently has a good understanding of how bacteria form partnerships with arthropods, but very little is known about eukaryotic microbes and their roles in arthropod biology. There are obviously exceptions as some parasites have been extensively studied, such as Plasmodium and Trypanosomes. However, these examples only represent the tip of the iceberg in terms of the possible diversity and interactions between microeukaryotes and arthropods. The main reason that we still don’t understand much about this microeukaryote diversity is that they are non-culture viable and are extremely rare in arthropod populations. Therefore, there is a need to develop high-throughput tools targeting microeukaryotes to describe their diversity in arthropods and to sequence their genomes so we can understand their functions. In this talk Alistair Darby will give examples of how harassing cell generics can be used to describe diversity and function, but also highlight some of the challenges still to be solved in studying these systems.

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16:15-18:00
Poster session

Chair

09:00-09:30
Shaping the environment for single microorganisms

Abstract

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.

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09:45-10:15
Exploring deep opisthokont evolution through single-cell approaches

Abstract

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.

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10:30-11:00
Coffee
11:00-11:30

Speakers


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11:45-12:15
Single-cell approaches for investigating planktonic archaea

Abstract

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.

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Chair

13:30-14:00
Improving the read accuracy of Oxford Nanopore Technology sequencers to enable the high-throughput analysis of isoform-level single cell transcriptomes

Abstract

Christopher Vollmers has previously shown that Oxford Nanopore Technology (ONT) cDNA sequencing can uncover transcript isoform diversity in single cells in unprecedented detail. Now, his group has developed a new method to increase the accuracy of cDNA reads generated by the ONT MinION. These more accurate reads can be used to demultiplex high-throughput single cell cDNA libraries and identify base-accurate full-length transcript isoforms. Further, his group has benchmarked this new method by analysing a cDNA pool of 96 B cells and found isoform diversity with potential implications for cancer treatment.

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14:15-14:45
Early metazoan cell type diversity and regulation by single-cell RNA-seq analysis

Abstract

A fundamental characteristic of animals is their ability to form large cell populations that are capable of cooperating through interaction between different archetypical functional programs, which are sometimes called cell types. The deployment and maintenance of these cell type-specific transcriptional programs is coordinated by transcription factor regulatory networks. However, the phylogenetic relationships and evolutionary dynamics underlying cell type hierarchies and their regulation are poorly understood. To gain insights into this question Arnau’s group profiled thousands of single-cell transcriptomes in the cnidarian Nematostella vectensis and other early-branching animals. The resulting whole-organism cell type classification atlases reveal an unanticipated high diversity of cell types in some of these species, particularly neuronal types. Moreover, the group identifies the gene modules specific to these cell behaviours, as well as the master transcription factors regulating them at different levels of the cell type hierarchy. These results provide the first glimpses to early-multicellular cell type complexity and the regulatory principles that orchestrate it.

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15:00-15:30
Tea
15:30-16:00
Single cell multi-omics: multiple measurements from single cells

Abstract

The ability to analyse the genomes, epigenomes and transcriptomes of individual cells has offered a new way in which to explore cellular heterogeneity in a diverse array of living systems. The Macaulay group has focussed on the development of technologies that enable us to explore, in parallel, multiple omic parameters of single cells – enabling combined gene expression and genome sequencing from the same cell. Another major focus of the group's work in this area is the understanding of alternative splicing in individual cells using long-read sequencing. In this talk Iain Macaulay will give an overview of the group’s approaches, how they aim to apply them in a wide array of applications across mammalian, plant and microbial biology.

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16:15-17:00
Panel discussion/overview

Related Events

Scientific meeting

Single cell ecology

10 - 11 December 2018

Scientific discussion meeting organised by Professor Thomas Richards, Dr Ramon Massana and Professor Neil Hall