Tailoring plant-associated microbial inoculants in agriculture: a roadmap for successful application

Abstract

Plants are now recognized as metaorganisms which are composed of a host plant associated with a multitude of microbes that provide the host plant with a variety of essential functions to adapt to the local environment. Recent research showed the remarkable importance and range of microbial partners for enhancing the growth and health of plants. However, plant-microbe holobionts are influenced by many different factors, generating complex interactive systems. In this review, we summarize insights from this emerging field, highlighting the factors that contribute to the recruitment, selection, enrichment, and dynamic interactions of plant-associated microbiota. We then propose a roadmap for synthetic community application with the aim of establishing sustainable agricultural systems that use microbial communities to enhance the productivity and health of plants independently of chemical fertilizers and pesticides. Considering global warming and climate change, we suggest that desert plants can serve as a suitable pool of potentially beneficial microbes to maintain plant growth under abiotic stress conditions. Finally, we propose a framework for advancing the application of microbial inoculants in agriculture.

Keywords: Abiotic and biotic stress; DARWIN21; desert bacteria; endophytes; plant growth-promoting rhizobacteria (PGPRs); plant microbiome; plant–microbe interaction; soil microbial community; synthetic community (SynCom).

Fig. 1.

Microbial communities are shaped by several factors that must be considered in agricultural applications. Seasonal and climatic factors alter soil physicochemical properties and plant physiology. Microbial communities in the soil are affected by seasonal and climatic factors and soil factors. Plant factors alter microbial communities in the phyllosphere, endosphere, and rhizosphere, with the latter being via root exudates. Agricultural management practices can cause changes in the microbial communities in the soil either directly or via altering soil properties. Microbes associated with plants, in either the rhizosphere or the endosphere, are capable of promoting plant growth by making nutrients available or producing/modulating phytohormones.

Fig. 2.

Proposed framework for the successful application of microbial inoculants in agriculture. A framework in which the farmers/farming industry, scientific community, and research and agricultural technology companies collectively contribute to reach the goal of successful microbial inoculant applications. Microbial inoculants must be customized for the target crop, climate, and soil properties (left panel). An increase in scientific research of plant microbiomes, culture collections, and functional characterization of potential microbial inoculants paves the way for meeting farmers’ requirements (right panel). The integration of available microbial inoculants with farmers’ requirements and the large-scale production and formulation (especially for SynComs) is performed by agricultural technology companies (center panel). Collaboration and constant feedback between all three entities is required for the success of field application.