Understanding and exploiting plant beneficial microbes

Abstract

After a century of incremental research, technological advances, coupled with a need for sustainable crop yield increases, have reinvigorated the study of beneficial plant-microbe interactions with attention focused on how microbiomes alter plant phenotypes. We review recent advances in plant microbiome research, and describe potential applications for increasing crop productivity. The phylogenetic diversity of plant microbiomes is increasingly well characterized, and their functional diversity is becoming more accessible. Large culture collections are available for controlled experimentation, with more to come. Genetic resources are being brought to bear on questions of microbiome function. We expect that microbial amendments of varying complexities will expose rules governing beneficial plant-microbe interactions contributing to plant growth promotion and disease resistance, enabling more sustainable agriculture.

Insights to plant–microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes

“…Future breeding strategies to promote plant health should focus not only on multiple aspects of a plant in its given environment, including phenotypic, genotypic, and metabolomic data, but also on plant microbial communities and the potential of the plant genotypes to steer their microbial communities (Box 2; Bakker, Manter, Sheflin, Weir, & Vivanco, ; Hartmann et al, ; Hohmann & Messmer, ; Lakshmanan, ; Pérez‐Jaramillo et al, ; Smith & Goodman, ; Wissuwa, Mazzola, & Picard, ). Although much more research is needed to close major knowledge gaps and link microbial diversity with function and ecosystem services (Finkel, Castrillo, Herrera Paredes, Salas González, & Dangl, ; Hartman et al, ; Oyserman, Medema, & Raaijmakers, ), there are already certain strategies and tools breeders can consider to integrate microbiome functions in breeding programmes.

The plant genotype significantly effects the composition of the rhizosphere microbiome. Selection of plant genotypes needs to be conducted in environments that reflect the pathogen situation in the field and that are favourable for plant–microbe interactions (i.e., in the absence of pesticides and excessive fertilizers). Individual pathogenic or beneficial key players (via real‐time quantitative PCR) or whole microbiome profiles (via next‐generation sequencing) can be determined to support the selection process in target environments. Plant breeders can screen for specific root exudate compounds that are involved in microbiome‐mediated disease resistance. The heritability of plant resistance traits can be increased through the inclusion of plant genotype × environment × microbiome interactions. The identification of genomic regions associated with microbiome‐mediated disease suppression allows to design marker‐assisted selection approaches. Microbiome‐wide association studies can be used to predict plant health‐associated capacities of microbial communities.

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Ammonium excretion, auxin production and effects of maize inoculation with ethylenediamine-resistant mutants of Pseudomonas sp.

“…The identification of promising PGPB is timeconsuming, due to the lack of a reliable biomarker that allows the selection of elite PGPB strains based on biochemical or genetic analysis, leading to the need to perform inoculation trials for the screening of isolate collections (Finkel et al 2017). Nevertheless, since the in vivo screening of large microbial collections is not trivial, sequential approaches based on in vitro analysis of the expression of the interest growth-promotion traits, followed by inoculation experiments to validate PGPB strains, are the common strategy adopted even if there is no consensus on the application of such approaches to select for PGPB candidates (Smyth et al 2011;Beneduzi et al 2013;Barnett et al 2017).…”

A multifaceted approach to harness probiotics as antagonists on plant based foods, for enhanced benefits to be reaped at a global level

“…Specifically, the probiotic strains of Lactobacillus and Bifidobacterium are known to have specific pili, S‐layer proteins, and several other substances serving as effector molecules . Plants have also been noted to have an immune system of their own with such pattern‐recognition receptors . The role of effector molecules in the transition of hosts (from plant to human) will be of interest for the development of probiotic antagonists.…”

“…A molecular technique with the acronym COBRA (Constraint Based Reconstruction Analysis) enables microbial interactions with other microbes and with the host to be determined . A multitude of ecological processes governing plant‐microbe interactions provide information on how plant exudates interact with the plant microbiome . The use of exudates is a method of attracting beneficial microbes to control various plant diseases .…”