Understanding the Influence of Rhizosphere Microbiomes on Horticultural Crop Traits and Production

Abstract

Microbial consortia in the rhizosphere have a tremendous impact on crop traits and production but are often overlooked in agricultural research. Here, our goal was to utilize a variety of research frameworks and methodologies to develop a better understanding of the influence rhizosphere microbiomes can have on horticultural crop traits and production. Specifically, we sought to 1) search the literature for concepts and methodologies from other disciplines that may help understand rhizosphere interactions; 2) investigate group selection for enhanced plant productivity in the rhizosphere of Brassica rapa; 3) utilize plant transcriptomics to study the effects of beneficial microbial consortia derived from vermicompost on tomato foliar and fruit traits; and 4) determine the effects of intercropping on soil properties and production outcomes in horticultural cropping systems. In our group selection experiment, we showed seed yield and nitrogen agronomic use efficiency can be altered in B. rapa by repeatedly selecting for rhizosphere microbiomes associated with increased aboveground biomass production, which may be mediated by group-level microbial behaviors such as nitrogen cycling. Our greenhouse study of vermicompost microbiomes revealed microbial consortia derived from vermicompost beneficially influence tomato growth and development by altering host gene expression. Our intercropping study revealed soil chemical and biological properties can be altered in response to crop diversification, which may lead to shifts in crop production outcomes and ecosystem-level properties. Broadly, our work shows crop traits can be altered in response to microbiome manipulation, beneficial microbiomes can influence host traits via changes in plant gene expression, and aboveground management practices in horticultural systems can alter soil and plant properties relevant to production. Overall, this research demonstrates the usefulness of applying a variety of research frameworks and methodologies in developing a better understanding of the influence of rhizosphere microbiomes on crop traits.