Understanding soybean root microbiome assembly along its development from both plant and soil perspectives

Plants have evolved intimate partnerships with microorganisms to compensate for their sessile nature and to respond to changing biotic and abiotic environmental conditions. The plant-associated microbiome greatly expands plant functions and plasticity via improved nutrient availability/uptake, enhancing plant abiotic stress tolerance, and promoting plant defense. Understanding plant microbiome assembly is crucial for leveraging their versatile benefits to the plant host and advancing the next green movement in sustainable agriculture. In this study, we comprehensively characterized soybean root-associated microbiome assembly via the 16S rRNA gene and ITS2 (internal transcribed spacer) region amplicon sequencing. Using this technology, we examined different factors influencing the soybean rhizosphere and endosphere microbiome development. Our first study examined the impacts of both plant genotype and soil type, which revealed a predominant impact of soil background in determining soybean rhizosphere microbiome assembly, while the soybean genotype plays a minor but significant role. For the next study, we investigated the role of root exudates in structuring the microbiome, specifically focusing on strigolactones. Strigolactones are a recently discovered carotenoid-derived plant hormones that play significant roles in plant-plant and plant-microbe interactions via both in planta and ex planta activities. In this study, we built three overexpression constructs targeting one biosynthesis gene and two signaling genes involving the strigolactone signaling pathway. The overexpression of these genes in soybean roots significantly impacted rhizosphere bacterial community composition. Our final study characterized soybean root microbiome assembly at three different early development stages and evaluated the relative contribution of soil-derived and seed-carried microbiome for soybean root microbiome assembly. The results indicated that soil indigenous microbes played a more determinant role for root microbiome composition in comparison to seed microbiome. During this study, we also evaluated the impact of fungicide seed treatment for this assembly process, which turned out to be insignificant for the bacterial community but significant for the fungal community. Our findings provided a comprehensive understanding of the soybean root microbiome from a systemic perspective, incorporating plant, soil and seed aspects. It will help to pave the way for microbe-assisted sustainable agriculture by optimizing and maximizing the beneficial plant-microbe interactions.