Next generation microbiome applications for crop production — limitations and the need of knowledge-based solutions

Plants are associated with highly diverse microbiota, which are crucial partners for their host carrying out important functions. Essentially, they are involved in nutrient supply, pathogen antagonism and protection of their host against different types of stress. The potential of microbial inoculants has been demonstrated in numerous studies, primarily under greenhouse conditions. However, field application, for example, as biofertilizer or biocontrol agent, is still a challenge as the applied microorganisms often are not provided in sufficiently high cell numbers, are rapidly outcompeted and cannot establish or require specific conditions to mediate the desired effects. We still have limited understanding on the fate of inoculants and on holobiont interactions, that is, interactions between plants, micro-biota and macro-biota and the environment, under field conditions. A better understanding will provide the basis for establishing models predicting the behaviour of strains or consortia and will help identifying microbiome members being able to establish and to mediate desired effects under certain conditions. Such models may also inform about the best management practices modulating microbiota in a desired way. Also, smart delivery approaches of microbial inoculants as well as the selection or breeding of plant genotypes better able to interact with microbiota may represent promising avenues.

Introduction

Plants host highly diverse and dynamic microbiota, which have important functions for their host. Similar to the contribution of microbiota to human health, plant-associated microorganisms protect their host against pathogens and pests, contribute to nutrition and improve the plant stress tolerance. Although some symbionts, such as N₂-fixing rhizobia or arbuscular mycorrhizal fungi, are well known for more than a century and are components of several microbial bio-fertilizer products, (other) plant microbiota have only recently received greater attention. A high number of publications has demonstrated the huge potential of plant-associated microorganisms for improving plant nutrition, yield and tolerance towards abiotic stress and pathogens [e.g. reviewed by Backer et al. [1], Syed Ab Rahman et al. [2^•], Compant et al. [3], Berendsen et al. [4]], particularly under greenhouse conditions. Generally, the better understanding on the beneficial functions of plant microbiota and the need to develop more sustainable strategies in plant production have led to a high interest in the development of microbiome-based solutions. We are getting more and more information on the complexity of plant microbiota, their genomes and putative functions as well as mechanistic understanding of individual strains or strain combinations (synthetic communities), mostly in combination with model plants, but lack behind in ecological and mechanistic insights serving field applications. Here we address major limitations on current microbial applications and development issues and propose avenues potentially leading to the development of more efficient and reproducible ways to make use of microbial functions in crop production.