Sucrose and pipecolic acid-mediated enrichment of rhizosphere Rhizobiale Burkholderiale bacteria improve soybean growth under low light conditions.

Abstract

Low light (LL) is a major constraint on the productivity of intercropped legumes and dense planting crops, and also affects the root-associated microbial communities. However, how LL reshapes the root-microbe interactions and whether the root microbiota can mitigate LL-induced damage in legumes remain unclear. Here, a meta-analysis based on field observations revealed that negative effects predominated (>70%) in intercropped and dense planting legume systems, with the light intensity emerging as the primary determinant of yield variation. Using soybean as a model, we found that LL suppressed photosynthesis, biomass accumulation and nodulation, and these effects were further aggravated in sterile soil. Furthermore, soil-transplantation experiments showed that soils conditioned by LL-grown plants reduced subsequent plant biomass. Compared to normal light (NL), LL shifted rhizosphere microbial assembly toward a more deterministic process, reducing bacterial diversity and simplifying bacterial co-occurrence networks, with Rhizobiales and Burkholderiales being the significantly reduced taxa. Metabolomic analysis identified sucrose and pipecolic acid as LL-responsive metabolites that were strongly correlated with these taxa. Chemotaxis and growth assays demonstrated that sucrose functions as both a carbon source and a chemoattractant, whereas pipecolic acid acts as a chemoattractant. Reintroduction of representative isolates or simplified SynCom alleviated LL-induced growth inhibition by enhancing photosynthetic performance, modulating redox status, and reprogramming host transcriptional responses. Together, our findings provide evidence of a belowground regulatory mechanism linking root exudates, rhizosphere microbiota, and plant performance under LL, and highlight the potential of microbiome-based strategies to improve crop production in low-light environments.