[Paper Review] Microbiomes and pathogen survival in crop residues, an ecotone between plant and soil

Lydie Kerdraon, Valérie Laval+1 more|arXiv (Cornell University)|Mar 6, 2019

Plant Disease Resistance and Genetics117 references90 citations

TL;DR

A review linking residue microbiomes with the survival of residue-borne fungal pathogens to inform microbially informed disease management in cereal systems.

ABSTRACT

This review focuses on microbiomes associated with residues within the context of other microbial habitats in cereal-producing agroecosystems such as phyllosphere or rhizosphere. We connect residue microbiome with the survival of residue-borne fungal plant pathogens, thus combining knowledge in microbial ecology and epidemiology, two disciplines still not sufficiently connected. We provide an overview of the impact of residues on cereal disease epidemics and how dynamic interactions between microbial communities of non-buried residues during their degradation, along with soil and multitude of abiotic factors, can contribute to innovative disease management strategies, including next-generation microbiome-based biocontrol strategies. Starting from the classical but still relevant view of crop residues as a source of pathogen inoculum, we first consider possibilities for limiting the amount of residues on the soil surface to reduce the pathogen pressure. We then describe residues as a transient half-plant/half-soil compartment constituting a key fully fledged microbial ecosystem: in other words, an ecotone which deserves special attention. We focus on microbial communities, the changes in these communities over time and the factors influencing them. Finally, we discuss how the interactions between the microbial communities and the pathogens present on residues could be used: identification of keystone taxa and beneficial assemblages, then preservation of these taxa by adapted agronomic practices or development of synthetic communities, rather than the introduction of a single exogenous biocontrol species designed as a 'treatment product'.

Motivation & Objective

• Synthesize how residue-associated microbial communities influence pathogen survival and cereal disease epidemics.
• Connect residue microbiology with broader microbial habitats (phyllosphere, rhizosphere) and epidemiology.
• Identify keystone taxa and microbial assemblages that could support biocontrol strategies.
• Discuss agronomic practices that preserve beneficial residue microbiomes to mitigate disease pressure.

Proposed method

• Literature synthesis across microbial ecology and plant pathology perspectives.
• Conceptual framework describing residues as a transient, half-plant/half-soil ecotone.
• Evaluation of factors shaping residue microbiomes over time, including abiotic influences and degradation dynamics.
• Discussion of how interactions between residue microbes and pathogens could guide biocontrol strategies beyond single-species introductions.

Experimental results

Research questions

• RQ1 How do microbial communities in crop residues change during degradation and what factors shape these dynamics?
• RQ2 What is the relationship between residue-associated microbiomes and the survival or suppression of residue-borne fungal pathogens?
• RQ3 Can identification of keystone taxa and beneficial assemblages inform durable, microbiome-based disease management in cereals?
• RQ4 What agronomic practices best preserve beneficial residue microbiomes to reduce pathogen pressure?

Key findings

• Residue microbiomes interact with soil and abiotic factors to influence pathogen survival during residue degradation.
• Residues function as a distinct ecotone with unique microbial dynamics separating plant and soil habitats.
• Understanding microbial interactions in residues could enable development of synthetic communities or conservation of keystone taxa for biocontrol.
• A shift from single-biocontrol agents to ecosystem-based strategies may improve disease management.
• The review highlights the potential for integrating microbiome knowledge into innovative, sustainable cereal disease control.