Overview

Background & motivation

• There has been a step change in Microbiomics in the last few years but plant holobiome and particularly soil metagenomics is still a challenge
• Healthy soil is a hot topic in agriculture and the soil microbiome is a significant contributor to soil heath.
• Now is a good time to review the Agri-Microbiomics landscape to get a clearer understanding of current state of the science, and in particular relative to industry challenges

Scope

The workshop will focus on soil health in the context of understanding how soil microbiomes relate to soil health status, as determined for example by impact on plant health and/or crop productivity as proxies for healthy/unhealthy soils. Climate and agronomic practice are expected to impact soil microbiomes and this will also be considered during the workshop. Key to developing actionable hypotheses will be the collection of the “correct” data sets at the different scales (landscape to rhizosphere) and the choices will be use case driven. The workshop therefore offers a good opportunity at this early phase in the development of soil microbiomics methods, for industry to consider how they can collaborate to develop core pre-competitive data sets and the best approaches to encourage the use of common data standards in public repositories. In summary, the workshop aims to:

• explore relationships between soil health and soil microbiomes
• learn how climate and agronomic practices impact soil microbiomes and the associated consequences for soil health
• begin to develop a pre-competitive data strategy for soil (agri) microbiomics   

Anticipated outcomes

• Bring together key opinion leaders from Agri Industry, biotech, and academia
• Share key knowledge and experiences:
  • Peer to peer learning – industry use case presentations/interactive discussions
  • Cutting edge technologies – academic presentations
  • Data sources, tools, platforms & computational methods
  • Identify high priority issues and challenges
• Provide opportunities for networking and collaborations between industry members and academic partners

Organising committee

Mike Csukai, Syngenta (proposer) | Vanessa King, Unilever | Mark Ott, Bayer (proposer) | Ben Oyserman, Syngenta | Lauren Ray, Syngenta | Marc-Sven Roell, Bayer | Christopher Sweeney, Syngenta | Katherine Karberg, Bayer | Irina Shilova, Bayer

EMBL-EBI organisers

Effie Mutasa-Gottgens

Senior Scientific Officer

Industry Partnerships

effie@ebi.ac.uk

Matt Hall

Senior Scientific Officer

Industry Partnerships

matth@ebi.ac.uk

Speakers

Confirmed speakers

• Noah Fierer, Professor at the University of Colorado Boulder and Director of the Centre for Microbial Exploration
• Duncan Cameron, Chair in Environmental Sustainability at the University of Manchester, UK
• Santiago Fragoso, Software Developer- Machine Learning, Microbiome Informatics, EMBL-EBI
• Katie Field, Professor of Plant-Soil Processses at the University of Sheffield, UK
• Marcek van der Heijden, Professor for Agroecology and Plant-Microbiome Interactions at the university of Zurich and Head of the Plant Soil Interactions Group at the Swiss Federal Research Institute Agroscope
• Nicola Holden, Professor in Food Safety at Scotland’s Rural College, UK
• Matthew Ryan, Lead for Biological Resources at CABI and project Manager for UK BBSRC Crop Microbiome Biobank
• Andy Neal, Microbiologist – Soil Systems Research Scientist at Rothamsted Research, UK
• Dimitrios Karpouzas, Professor in Environmental Microbiology and Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Greece
• Christopher Sweeney, Soil Microbiologist, Technical Expert at Syngenta
• Marc-Sven Roell, Research Ecotoxicologist Early Environmental Safety at Bayer

Outputs

Outputs

Content will be added after the workshop, if permissions are granted.

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