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Single cell ecology

Discussion meeting

Location

The Royal Society, London, 6-9 Carlton House Terrace, London, SW1Y 5AG

Overview

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

Bacteria (false coloured blue) living on the surface of a large protist in the hindgut of a termite. © K Carpenter and P Keeling (University of British Columbia).

Interdisciplinary meeting to explore the use of single cell technologies to understand the function, diversity and interactions of microbes. By bringing together physicists who manipulate cells, microbiologists who seek to understand the nature of microbial communities and genomicists who are developing new approaches to study individual cells we will achieve a greater understanding of the potential of this new field.

The schedule of talks and speaker biographies are below. Speaker abstracts will be available closer to the meeting. Recorded audio of the presentations will be available on this page after the meeting has taken place. Meeting papers will be published in a future issue of Philosophical Transactions B.

Poster session

There will be a poster session at 16:15 on Monday 10 December. If you would like to apply to present a poster please submit your proposed title, abstract (not more than 200 words and in third person), author list, name of the proposed presenter and institution to the Scientific Programmes team with the subject heading "Single cell ecology: poster abstract" no later than Monday 22 October 2018. Please note that places are limited and posters are selected at the scientific organiser's discretion. Poster abstracts will only be considered if the presenter is registered to attend the meeting.

Attending the event

This meeting is intended for researchers in relevant fields.

  • Free to attend
  • Limited places, advanced registration is essential
  • An optional lunch can be purchased during registration

Enquiries: Contact the Scientific Programmes team.

Event organisers

Select an organiser for more information

Schedule of talks

10 December

09:00-12:30

Getting a handle on single cells

4 talks Show detail Hide detail

Chairs

Professor Tom Richards, University of Exeter, UK

09:05-09:30

Professor Otto X Cordero, MIT, USA

Show speakers

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

Professor Assaf Vardi, Weizmann Institute of Science, Israel

Show speakers

10:30-11:00 Coffee

11:00-11:30

Professor Stephen Quake, Stanford University, USA

Show speakers

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

Professor David Weitz, Harvard University, USA

Show speakers

12:30-13:30

Lunch

13:30-17:00

Diverse cells in diverse interactions

4 talks Show detail Hide detail

Chairs

Professor Neil Hall, Earlham Institute, UK

13:30-14:00

Dr Mara Lawniczak, Wellcome Sanger Institute, UK

Show speakers

14:15-14:45 Immunogenomics one cell at a time

Dr Sarah Teichmann FMedSci, Wellcome Sanger Institute, UK

Show speakers

15:00-15:30 Tea

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

Dr Stefano Pagliara, University of Exeter, UK

Show speakers

16:15-18:00 Poster session

11 December

09:00-12:30

Cells in the environment

4 talks Show detail Hide detail

Chairs

Dr Alyson Santoro, University of California, Santa Barbara, USA

09:00-09:30 The spatial self-organization of multicellular microbial groups

Professor Martin Ackermann, ETH Zurich and Eawag, Switzerland

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09:45-10:15 Virtual microfluidic channels – from single cell to tissue mechanics

Dr Oliver Otto, University of Greifswald, Germany

Show speakers

10:30-11:00 Coffee

11:00-10:30 Studying uncultivated diversity via single-cell approaches

Dr Tanja Woyke, DOE Joint Genome Institute, USA

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11:45-12:15 Interrogating marine microbes for their degree of activity and growth: an overview and recent developments

Dr Josep M Gasol, Institut de Ciències del Mar, CSIC, Spain

Show speakers

12:30-13:30

Lunch

13:30-17:00

Single cell analysis to unlock microbial diversity

4 talks Show detail Hide detail

Chairs

Dr Ramon Massana Institute of Marine Sciences, CSIC, Spain

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.

Show speakers

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.

Show speakers

15:00-15:30 Tea

15:30-16:00 Identifying physical co-associations between biological entities in the marine environment

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

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16:15-17:00 Panel discussion/overview

Related events

Single cell ecology

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

The Royal Society, London 6-9 Carlton House Terrace London SW1Y 5AG UK
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