Beyond Plant Microbiome Composition: Exploiting Microbial Functions and Plant Traits via Integrated Approaches

Abstract

Plants recruit specific microorganisms to live inside and outside their roots that provide essential functions for plant growth and health. The study of the microbial communities living in close association with plants helps in understanding the mechanisms involved in these beneficial interactions. Currently, most of the research in this field has been focusing on the description of the taxonomic composition of the microbiome. Therefore, a focus on the plant-associated microbiome functions is pivotal for the development of novel agricultural practices which, in turn, will increase plant fitness. Recent advances in microbiome research using model plant species started to shed light on the functions of specific microorganisms and the underlying mechanisms of plant-microbial interaction. Here, we review (1) microbiome-mediated functions associated with plant growth and protection, (2) insights from native and agricultural habitats that can be used to improve soil health and crop productivity, (3) current-omics and new approaches for studying the plant microbiome, and (4) challenges and future perspectives for exploiting the plant microbiome for beneficial outcomes. We posit that integrated approaches will help in translating fundamental knowledge into agricultural practices.

Potentials, Utilization, and Bioengineering of Plant Growth-Promoting Methylobacterium for Sustainable Agriculture

“…carry these functions and play an important role in microbiomes [15,51,55,63]. Different plants grow in different environments and possess tolerance to different stresses which might depend on microbiomes to some degree [64]. Then, the transfer of these capacities to plants that lack them is important.…”

Tackling the Context-Dependency of Microbial-Induced Resistance

“…Whether or not successful establishment of the beneficial microbes in the rhizosphere results in activation of ISR is strongly dependent on the genetic background of the plant and microbe. The plant genetic background is a crucial factor since plants from different species or cultivars often show differences in the extent to which they express ISR in response to a single microbial strain [49]. For example, Pseudomonas fluorescens WCS374r has been shown to induce resistance in radish (Rhaphanus sativus) [50] but not in Arabidopsis thaliana [51] while Pseudomonas putida strain WCS358r can elicit ISR in Arabidopsis but not in radish [51].…”

Insights into the soil microbiome and prospects for its manipulation for improved pasture resilience

“…In the context of agricultural ecosystems, it is difficult to consider the soil microbiome without some reference to plants and their associated microbiomes (Cordovez et al 2019;Song et al 2020). Plants are key drivers of the structure and function of soil microbial communities with the root-soil interface -known as the rhizosphere-considered a hotspot of soil microbial activity (Kuzyakov & Blagodatskaya 2015).…”