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HAL
open science

# Biological control methods against plant diseases at the Plant Pathology research unit

Marc Bardin

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## To cite this version:

Marc Bardin. Biological control methods against plant diseases at the Plant Pathology research unit. CSIRO meeting, Nov 2023, Canberra (AU), Australia. hal-04288338

HAL Id: hal-04288338

https://hal.inrae.fr/hal-04288338

Submitted on 16 Nov 2023

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

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Distributed under a Creative Commons Attribution 4.0 International License
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marc.bardin@inrae.fr

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Key facts and figures

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Our missions

Producing and disseminating **knowledge** to address societal issues

Use this knowledge for **innovation**, expertise and support for public policies

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Our major topics

- Climate change and risk

- Agroecology

- Biodiversity

- Food, global health

- Bioeconomy

- Society and Regions

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<figure><img src="image_9.png" /><figcaption>Départements d'Outre-mer</figcaption></figure>

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18 centers

1 billion €
budget

10,000 hectares
of Experimental Terrain.

14
Research
Departments

268 Research,
Service and
Experimental units

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**Plant Health and Environment**
**Research Department**

* **Aim of the department** : protect the health of crops while respecting the environment, from the plant to the landscape.

* ✓ Explore a wide variety of questions, focusing on understanding the biology of deleterious and beneficial interactions between plants and associated organisms (pests, microbiota, pollinators, symbionts).

* ✓ Questions addressed at different scales : from the study of molecular interactions to community ecology, epidemiology and population biology.

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INRA
science for people, life & earth

# Plant Health and Environment
## Research Department

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2022

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724 permanent staff

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214 researchers (permanent)

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22 research units
6 experimental units (extension services)

Plant Pathology research unit
Avignon,
Provence-Alpes-Côte d'Azur
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Research focused on issues specific to the **Mediterranean region** : agroecology and adaptation of agriculture and forests to climate change, water resources, natural risks, human nutrition

A local scientific context very favorable to research on plant health

Very active research community in ecology, biostatistics and modeling

INRAO

tersys

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l'intelligence du vivant
structure federative de recherche

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AVIGNON

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INRAO

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IMPLANTEUS

SUSTAINABLE MEDITERRANEAN
AGRICULTURE FOR HEALTH

GRADUATE
SCHOOL

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INRAO
## General scientific objective :

Contribute to the development of rational, efficient and durable protection against plant diseases

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<figure><img src="image_30.png" /><figcaption>Bacteria</figcaption></figure>

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## Fruits and vegetables produced in the Mediterranean basin

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<figure><img src="image_33.png" /><figcaption>Oilseed rape</figcaption></figure>

Ornamentals and plane tree

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## Research conducted:

**1. Etiology-diagnostics :**
to identify emerging threats to crops

**2. Ecology of pathogens :**
to expand knowledge on the ecology and life history of plant pathogens

**3. Epidemiology of diseases :**
to identify the main drivers of prevalence, diversity and spatial structure of plant pathogens

**4. Plant protection :**
to deploy this knowledge to conceive novel, environment-friendly and durable means for protecting plant health

including biocontrol

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# Main plant pathogens studied

## Viruses of vegetable and flower crops

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CMV, WMV, ZYMV, CABYV, ENMV...

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## Large collection of isolates

<figure><img src="image_43.png" /><figcaption>**Pseudomonas syringae**
*Clavibacter michiganensis*
*Erwinia amylovora*</figcaption></figure>

<figure><img src="image_44.png" /><figcaption>Botrytis cinerea</figcaption></figure>

<figure><img src="image_45.png" /><figcaption>Powdery mildew fungi</figcaption></figure>

<figure><img src="image_46.png" /><figcaption>Sclerotinia sclerotiorum</figcaption></figure>

<figure><img src="image_47.png" /><figcaption>Fusarium proliferatum</figcaption></figure>
# Plant Pathology Research Unit

## A stimulating environment

* 38 permanent staff

* 15-30 non-permanent/year

Scientific expertise in plant pathology, microbial ecology, epidemiology, biological control

Technical skills from gene to landscape

**Specific facilities and equipment**
(mycology, bacteriology, virology laboratories)

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**Shared experimental facilities**
dedicated to plant production,
including a prototyping workshop

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Experimental platforms
located nearby

## Organised in 2 research teams

### Virology

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### MISTRAL

(Microbiology of agroeco-Systems : TRAnslational research from pathogen Life histories)

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### Plant health research department

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### Microscopy

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### Molecular biology

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### Metabolomics

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# Biological control methods against plant diseases

## Context

* **Microbial biocontrol:** an essential lever for reducing dependence on chemical pesticides **against plant diseases**
[31 registered products in France, https://ephy.anses.fr/]

* Diverse and often poorly understood **modes of action**
[Köhl et al, 2018; Legein et al. 2020]

* Protection tools based on **natural regulations**: more complex **positioning** than chemical pesticides.
Success of protection depends on **biotic and abiotic** variables

* System in constant **evolution** :
  * ✓ Increasing complexity of farming practices
  * ✓ Global changes

→ A situation that promotes variability in their efficacy and hinders their adoption

Towards effective microbial
biocontrol of pathogens

ÉCOPHYTO

RÉDUIRE ET AMÉLIORER
L'UTILISATION DES PHYTOS

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## 1. Gain better understanding of complex interactions taking place at plant level

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**Conditions for survival, installation, colonization ?**

Develop models to predict population fluctuations according to main external environmental factors

**Conditions for the activation of the mode(s) of action ?**

Models to predict the activation of mechanisms of action according to main external environmental factors

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Turc et al, 2023. CABI.
**2. Take into account the durability of protection efficacy**

**Risk for biocontrol protection to be overcome by plant pathogens?**

1. Demonstrated diversity in the susceptibility to biocontrol agents in populations of several plant pathogens

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2. Demonstrated adaptation potential of certain pathogens to the action of biocontrol agents

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* Probability of resistance outbreak according to the mode(s) of action of the biocontrol agent and the targeted pathogen ?

* Link between lack of consistency in field efficacy of biocontrol and the diversity in susceptibility within populations of the pathogen ?
## 3. Combine biocontrol with other protection methods

Plant
resistance

X

Biocontrol
agent

X

Flashes of UV-C

X

Nitrogen
fertilization

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Plant pathogens

* Botrytis cinerea

* Oidium neolycopersici

* Phytophthora infestans

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* Efficacy of biocontrol modulated by other protection methods ?

* Genes (QTL) implicated in plant response to biocontrol agents ?

* Mechanisms implicated in plant defense induction (transcriptomic and metabolomic analyses)

* Is it possible to rely on indigenous plant microbiota ?

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GAFL

PSH
UR 1115

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lae

AVIGNON
UNIVERSITE

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4. Translate complex scientific knowledge into practical and operational information for farmers

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* The protective effect of biocontrol agents is modulated by multiple interconnected factors

* Farmers need advice to use biocontrol agents most effectively for disease management

Develop Decision Support tools for better implementation of biocontrol by farmers in the field

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DeciControl
Ephytia

Consortium Biocontrôle DECCONTROL+,
HORIZON-EU ADOPT-IPM, CASDAR Bioc'App

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EU-China joint action
to increase the development
and adoption of IPM tools

2022-2026

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Funded by
the European Union

ADOPT-IPM

Overall structure
& WP interaction

WP6

Coordination and project management

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Optimisation
Loops

Assessment criteria
Options for **optimisation**

WP1

Optimisation of existing IPM tools
to fulfill end-users expectations

Optimised IPM tools
Data on combinations

Field trial protocols
Data for training

Feedback on
**optimised IPM tools**

Novel IPM tools
for combinations

WP5

Communication,
dissemination,
and exploitation
support

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End-users
needs /
problems

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WP3

Assessment and support systems
for IPM tools and packages

Assessment criteria
Options for **innovation**

Novel IPM tools

Field trial protocols
Data for training

Feedback on **novel**
IPM tools

End-users
uptake

Activity types:

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Dev. & Application

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Research

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Mgt. & Support

Innovation
Loops

WP2

Development of innovative IPM
tools and practices

WP4

Field demonstrations and implementation
of IPM tools and packages by end-users

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<figure><img src="image_95.png" /><figcaption>tomato</figcaption></figure>

<figure><img src="image_96.png" /><figcaption>leafy vegetables</figcaption></figure>

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EU-China joint action
to increase the development
and adoption of IPM tools

2022-2026

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TOPIC:

HORIZON-CL6-2021-FARM2FORK-01-19 - EU-China international cooperation on integrated pest management in agriculture

Coordinated by Nicolas DESNEUX, INRAE

19 partners from

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Belgium

Denmark

France

Italy

Spain

The Netherlands

UK

13 partners from

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Beijing

Anhui

Guizhou

Shandong

Sichuan

Yunnan

Zhejiang

Partners from academia, companies, growers' associations + other key stakeholders
# SCLEROZA

2022-2026

Develop and test a unique biocontrol solution for rapeseed on
a pre-industrial scale

4 partners

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Capsulae
Innovative microencapsulation

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Agroécologie
Dijon

Unité de Recherche

INRAE

UQO agro

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AVIGNON PATHOLOGIE VEGETALE

ADEME

AGENCE DE LA
TRANSITION
ECOLOGIQUE

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RÉPUBLIQUE
FRANÇAISE

Liberté
Égalité
Fraternité

INRAE
la science pour la vie, l'humain, la terre

Identify the modes of action of selected micro-organisms

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# Why are we at CSIRO this week?

* Expression of Interest for INRAE-CSIRO linkage proposals 2022

* Proposal: Exploring biocontrol traits to optimise the resilience and durability of crop protection

@INRAE

## Evaluation of the durability of biocontrol agents

Screening of a genetically diverse subset of the INRAE collections of *Sclerotinia sclerotiorum* (100 strains) and *Botrytis cinerea* (50 strains) against a CSIRO biofungicide

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INRAE,
October 2023

@CSIRO

## Use of metabolomics tools for biocontrol mode of action studies.

Sharing of CSIRO biochemistry/metabolomics analysis for functional biocontrol MOA studies of 2 bacteria.

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CSIRO,
November 2023
Thank you !

INRAO

AVIGNON PATHOLOGIE VEGETALE

Plant Pathology research unit

Avignon,
Provence-Alpes-Côte d'Azur

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LEPINAY</figcaption></figure>

<figure><img src="image_118.png" /><figcaption>Philippe
NICOT</figcaption></figure>

<figure><img src="image_119.png" /><figcaption>Jean-François
BOURGEAY</figcaption></figure>

<figure><img src="image_120.png" /><figcaption>Magali
DUFFAUD</figcaption></figure>

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PRESSECQ</figcaption></figure>

<figure><img src="image_122.png" /><figcaption>Margot
GRIMONPONT</figcaption></figure>

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SANGARE</figcaption></figure>

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JACQUIN</figcaption></figure>

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IOBC-WPRS

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ADOPT
IPM

EU-China joint action
to increase the development
and adoption of IPM tools

AGENCE NATIONALE DE LA RECHERCHE
ANR

Cap

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Phyto

ADEME

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Agence de l'Environnement
et de la Matière de l'Énergie

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RÉGION
SUD

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biocontrôle

ÉCOPHYTO
RÉDUIRE ET AMÉLIORER
L'UTILISATION DES PHYTOS

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Liberté • Egalité • Fraternité
RÉPUBLIQUE FRANÇAISE

MINISTÈRE
DE LA TRANSITION
ÉCOLOGIQUE ET SOLIDAIRE

MINISTÈRE
DE L'AGRICULTURE
ET DE L'ALIMENTATION