Multiple analysis of root exudates and microbiome in rice (Oryza sativa) under low P conditions

Multi-Generation Ecosystem Selection of Rhizosphere Microbial Communities Associated with Plant Genotype and Biomass in Arabidopsis thaliana

The role of the microbiome in shaping the host's phenotype has emerged as a critical area of investigation, with implications in ecology, evolution, and host health. The complex and dynamic interactions involving plants and their diverse rhizospheres' microbial communities are influenced by a multitude of factors, including but not limited to soil type, environment, and plant genotype. Understanding the impact of these factors on microbial community assembly is key to yielding host-specific and robust benefits for plants, yet it remains challenging. Here, we conducted an artificial ecosystem selection experiment for eight generations of Arabidopsis thaliana Ler and Cvi to select soil microbiomes associated with a higher or lower biomass of the host. This resulted in divergent microbial communities shaped by a complex interplay between random environmental variations, plant genotypes, and biomass selection pressures. In the initial phases of the experiment, the genotype and the biomass selection treatment had modest but significant impacts. Over time, the plant genotype and biomass treatments gained more influence, explaining ~40% of the variation in the microbial community's composition. Furthermore, a genotype-specific association of plant-growth-promoting rhizobacterial taxa, Labraceae with Ler and Rhizobiaceae with Cvi, was observed under selection for high biomass.

Dynamic metabolites: A bridge between plants and microbes

Plant metabolites have a great influence on soil microbiomes. Although few studies provided insights into plant-microbe interactions, we still know very little about how plants recruit their microbiome. Here, we discuss the dynamic progress that typical metabolites shape microbes by a variety of factors, such as physiographic factors, cultivar factors, phylogeny factors, and environmental stress. Several kinds of metabolites have been reviewed, including plant primary metabolites (PPMs), phytohormones, and plant secondary metabolites (PSMs). The microbes assembled by plant metabolites in return exert beneficial effects on plants, which have been widely applied in agriculture. What's more, we point out existing problems and future research directions, such as unclear mechanisms, few species, simple parts, and ignorance of absolute abundance. This review may inspire readers to study plant-metabolite-microbe interactions in the future.

Endophytic Phthalate-degrading Bacillus subtilis N-1-gfp colonizing in soil-crop system shifted indigenous bacterial community to remove di-n-butyl phthalate

Endophytic bacteria can degrade toxic phthalate (PAEs). Nevertheless, the colonization and function of endophytic PAE-degrader in soil-crop system and their association mechanism with indigenous bacteria in PAE removal remain unknown. Here, endophytic PAE-degrader Bacillus subtilis N-1 was marked with green fluorescent protein gene. Inoculated strain N-1-gfp could well colonize in soil and rice plant exposed to di-n-butyl phthalate (DBP) as directly confirmed by confocal laser scanning microscopy and realtime PCR. Illumina high-throughput sequencing demonstrated that inoculated N-1-gfp shifted indigenous bacterial community in rhizosphere and endosphere of rice plants with significant increasing relative abundance of its affiliating genus Bacillus than non-inoculation. Strain N-1-gfp exhibited efficient DBP degradation with 99.7% removal in culture solutions, and significantly promoted DBP removal in soil-plant system. Strain N-1-gfp colonization help plant enrich specific functional bacteria (e.g., pollutant-degrading bacteria) with significant higher relative abundances and stimulated bacterial activities (e.g., pollutant degradation) compared with non-inoculation. Furthermore, strain N-1-gfp displayed strong interaction with indigenous bacteria for accelerating DBP degradation in soil, decreasing DBP accumulation in plants and promoting plant growth. This is the first report on well colonization of endophytic DBP-degrader Bacillus subtilis in soil-plant system and its bioaugmentation with indigenous bacteria for promoting DBP removal.

Harnessing belowground processes for sustainable intensification of agricultural systems

Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant-microbe-soil interface and aim to link this knowledge with actual and potential avenues for intensifying agricultural systems, while at the same time reducing irrigation water, fertilizer inputs and pesticide use. Combining in-depth knowledge about above and belowground plant traits will not only significantly advance our mechanistic understanding of involved processes but also allow for more informed decisions regarding agricultural practices and plant breeding. Including belowground plant-soil-microbe interactions in our breeding efforts will help to select crops resilient to abiotic and biotic environmental stresses and ultimately enable us to produce sufficient food in a more sustainable agriculture in the upcoming decades.