A Vavilovian approach to discovering crop-associated microbes with potential to enhance plant immunity

Iago L Hale,Gloria Iriarte,Kirk Broders

doi:10.3389/fpls.2014.00492

Abstract

Through active associations with a diverse community of largely non-pathogenic microbes, a plant may be thought of as possessing an “extended genotype,” an interactive cross-organismal genome with potential, exploitable implications for plant immunity. The successful enrichment of plant microbiomes with beneficial species has led to numerous commercial applications, and the hunt for new biocontrol organisms continues. Increasingly flexible and affordable sequencing technologies, supported by increasingly comprehensive taxonomic databases, make the characterization of non-model crop-associated microbiomes a widely accessible research method toward this end; and such studies are becoming more frequent. A summary of this emerging literature reveals, however, the need for a more systematic research lens in the face of what is already a metagenomics data deluge. Considering the processes and consequences of crop evolution and domestication, we assert that the judicious integration of in situ crop wild relatives into phytobiome research efforts presents a singularly powerful tool for separating signal from noise, thereby facilitating a more efficient means of identifying candidate plant-associated microbes with the potential for enhancing the immunity and fitness of crop species.

Highlights

The two basic crop improvement strategies available to agricultural scientists are traditionally understood to be: (1) assembling/developing plant genetic diversity and selecting for superior plant genotypes; and (2) modifying growing conditions, primarily via cultural practices, to optimize the desired performance of those superior genotypes
A second potential means of modifying the crop phytobiome may lie in selecting host genotypes better able to recruit a superior community of microorganisms from the ambient microbiome (Figure 1)
We argue that the practical advancement of either of these potential strategies, ambient microbiome enrichment or host genotype modification, could benefit from the adoption of a research framework which takes into account the processes and consequences of crop evolution and domestication

Summary

Introduction

The two basic crop improvement strategies available to agricultural scientists are traditionally understood to be: (1) assembling/developing plant genetic diversity and selecting for superior plant genotypes; and (2) modifying growing conditions, primarily via cultural practices, to optimize the desired performance of those superior genotypes. A second potential means of modifying the crop phytobiome may lie in selecting host genotypes better able to recruit a superior community of microorganisms from the ambient microbiome (i.e., to assemble a superior “extended genotype”) (Figure 1).

Results

Conclusion