Decoding the microbiome for sustainable agriculture

Root-associated microbiota profoundly affect crop health and productivity.Plants can selectively recruit beneficial microbes from the soil and actively balance microbe-triggered plant-growth promotion and stress tolerance enhancement.The cost associated with this is the root-mediated support of a certain number of specific microbes under nutrient limitation.Thus,it is important to consider the dynamic changes in microbial quantity when it comes to nutrient condition-induced root microbiome reassembly.Quantitative microbiome profiling(QMP)has recently emerged as a means to estimate the specific microbial load variation of a root microbiome(instead of the traditional approach quantifying relative microbial abundances)and data from the QMP approach can be more closely correlated with plant development and/or function.However,due to a lack of detailed-QMP data,how soil nutrient conditions affect quantitative changes in microbial assembly of the root-associated microbiome remains poorly understood.A recent study quantified the dynamics of the soybean root microbiome,under unbalanced fertilization,using QMP and provided data on the use of specific synthetic communities(SynComs)for sustaining crop productivity.In this editorial,we explore potential opportunities for utilizing QMP to decode the microbiome for sustainable agriculture.

Systems Biology of Plant-Microbiome Interactions

In natural environments,plants are exposed to diverse microbiota that they interact with in complex ways.While plant-pathogen interactions have been intensely studied to understand defense mechanisms in plants,many microbes and microbial communities can have substantial beneficial effects on their plant host.Such beneficial effects include improved acquisition of nutrients,accelerated growth,resilience against pathogens,and improved resistance against abiotic stress conditions such as heat,drought,and salinity.However,the beneficial effects of bacterial strains or consortia on their host are often cultivar and species specific,posing an obstacle to their general application.Remarkably,many of the signals that trigger plant immune responses are molecularly highly similar and often identical in pathogenic and beneficial microbes.Thus,it is unclear what determines the outcome of a particular microbe-host interaction and which factors enable plants to distinguish beneficials from pathogens.To unravel the complex network of genetic,microbial,and metabolic interactions,including the signaling events mediating microbe-host interactions,comprehensive quantitative systems biology approaches will be needed.

Functional assembly of root-associated microbial consortia improves nutrient efficiency and yield in soybean

Root-associated microbes are critical for plant growth and nutrient acquisition. However, scant information exists on optimizing communities of beneficial root-associated microbes or the mechanisms underlying their interactions with host plants. In this report, we demonstrate that rootassociated microbes are critical influencers of host plant growth and nutrient acquisition. Three synthetic communities(SynComs) were constructed based on functional screening of 1,893 microbial strains isolated from root-associated compartments of soybean plants. Functional assemblage of SynComs promoted significant plant growth and nutrient acquisition under both N/P nutrient deficiency and sufficiency conditions.Field trials further revealed that application of SynComs stably and significantly promoted plant growth, facilitated N and P acquisition, and subsequently increased soybean yield. Among the tested communities, SynCom1 exhibited the greatest promotion effect, with yield increases of up to 36.1% observed in two field sites. Further RNA-seq implied that SynCom application systemically regulates N and P signaling networks at the transcriptional level, which leads to increased representation of important growth pathways, especially those related to auxin responses. Overall,this study details a promising strategy for constructing SynComs based on functional screening,which are capable of enhancing nutrient acquisition and crop yield through the activities of beneficial root-associated microbes.