Multi-Omics Approaches in Plant–Microbe Interactions Hold Enormous Promise for Sustainable Agriculture

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Abstract

Plants do not grow in isolation; they interact with diverse microorganisms in their habitat. The development of techniques to identify and quantify the microbial diversity associated with plants contributes to our understanding of the complexity of environmental influences to which plants are exposed. Identifying interactions which are beneficial to plants can enable us to promote healthy growth with the minimal application of agrochemicals. Beneficial plant–microbial interactions assist plants in acquiring inaccessible nutrients to promote plant growth and help them to cope with various stresses and pathogens. An increased knowledge of plant–microbial diversity can be applied to meet the growing demand for biofertilizers for use in organic agriculture. This review highlights the beneficial effects of soil–microbiota and biofertilizers on improving plant health and crop yields. We propose that a multi–omics approach is appropriate to evaluate viability in the context of sustainable agriculture.

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Plant-microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture.

Gabriele Berg (2009)

Plant-associated microorganisms fulfill important functions for plant growth and health. Direct plant growth promotion by microbes is based on improved nutrient acquisition and hormonal stimulation. Diverse mechanisms are involved in the suppression of plant pathogens, which is often indirectly connected with plant growth. Whereas members of the bacterial genera Azospirillum and Rhizobium are well-studied examples for plant growth promotion, Bacillus, Pseudomonas, Serratia, Stenotrophomonas, and Streptomyces and the fungal genera Ampelomyces, Coniothyrium, and Trichoderma are model organisms to demonstrate influence on plant health. Based on these beneficial plant-microbe interactions, it is possible to develop microbial inoculants for use in agricultural biotechnology. Dependent on their mode of action and effects, these products can be used as biofertilizers, plant strengtheners, phytostimulators, and biopesticides. There is a strong growing market for microbial inoculants worldwide with an annual growth rate of approximately 10%. The use of genomic technologies leads to products with more predictable and consistent effects. The future success of the biological control industry will benefit from interdisciplinary research, e.g., on mass production, formulation, interactions, and signaling with the environment, as well as on innovative business management, product marketing, and education. Altogether, the use of microorganisms and the exploitation of beneficial plant-microbe interactions offer promising and environmentally friendly strategies for conventional and organic agriculture worldwide.

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Competition for light causes plant biodiversity loss after eutrophication.

Y Hautier, P. A. Niklaus, A. Hector (2009)

Human activities have increased the availability of nutrients in terrestrial and aquatic ecosystems. In grasslands, this eutrophication causes loss of plant species diversity, but the mechanism of this loss has been difficult to determine. Using experimental grassland plant communities, we found that addition of light to the grassland understory prevented the loss of biodiversity caused by eutrophication. There was no detectable role for competition for soil resources in diversity loss. Thus, competition for light is a major mechanism of plant diversity loss after eutrophication and explains the particular threat of eutrophication to plant diversity. Our conclusions have implications for grassland management and conservation policy and underscore the need to control nutrient enrichment if plant diversity is to be preserved.

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Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

Víctor Carrión, Juan Pérez-Jaramillo, Viviane Cordovez … (2019)

Microorganisms living inside plants can promote plant growth and health, but their genomic and functional diversity remain largely elusive. Here, metagenomics and network inference show that fungal infection of plant roots enriched for Chitinophagaceae and Flavobacteriaceae in the root endosphere and for chitinase genes and various unknown biosynthetic gene clusters encoding the production of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs). After strain-level genome reconstruction, a consortium of Chitinophaga and Flavobacterium was designed that consistently suppressed fungal root disease. Site-directed mutagenesis then revealed that a previously unidentified NRPS-PKS gene cluster from Flavobacterium was essential for disease suppression by the endophytic consortium. Our results highlight that endophytic root microbiomes harbor a wealth of as yet unknown functional traits that, in concert, can protect the plant inside out.