Rhizosphere microbial community dynamics contribute to nitrogen fixation and forage quality in novel perennial intercrops in Rwanda

Abstract In low-fertility tropical agroecosystems, intercropping with perennial legumes has the potential to maximize biological nitrogen fixation (BNF) and improve non-legume nitrogen (N) uptake and yields. However, the microbial interactions that facilitate the beneficial effects of intercropping in perennial systems remain largely uncharacterized, particularly in the tropics. In this study, we explored the contribution of root-associated bacteria and fungi to N content and the nutritional characteristics of perennial grasses (Cenchrus purpureus and Brachiaria cv. Mulato II) and an annual cereal (Zea mays) intercropped with a perennial legume (Desmodium sp). Sampling approximately every 8 weeks at the time of forage grass anthesis, we collected biomass leaf tissue, bulk soil, and rhizosphere soil. We calculated nitrogen derived from the atmosphere (Ndfa) in Desmodium leaf tissue to estimate BNF and found that Ndfa increased in intercropping arrangements relative to single-cropped Desmodium by 91.6–147.1% on average in intercropped stands with Brachiaria and C. purpureus. Intercropping also induced positive changes in non-legume tissue quality in a species- and site-dependent manner. Furthermore, we identified microbial taxa that were significantly enriched in the rhizosphere of intercropped plants relative to monocropped plants and which correlated to multiple forage nutritive quality metrics. Fungal community structure responded more strongly to the presence of a legume intercrop than bacterial communities. We also identified species-specific trends in the degree to which monocropped and intercropped rhizosphere communities differed. Overall, this study suggests that perennial legume intercropping may recruit beneficial rhizosphere microorganisms in rainfed tropical soils to facilitate nutritional benefits in the non-legume companion crop and highlights the complexity of rhizospheric microbial interactions in intercropped systems.