Deciphering the rhizosphere microbiota composition of nature farming soybean (Glycine max L.) with different nodulation phenotypes

Background Nature farming, a sustainable agricultural method which avoids agrochemicals and untreated organic amendments, promotes both agricultural productivity and ecological conservation. This system may foster unique plant-microbiota interactions for growth and fitness; however the microbiota of nature-farmed plants remains largely unexplored. Second, root nodule symbiosis (RNS) is crucial for nitrogen fixation in legumes; however, its broader impact on rhizosphere microbiota assembly is not well understood. This study examined the dynamics between impaired nodule symbiosis, soil management, and the rhizosphere microbiota composition and growth of soybean (Glycine max L.). Results We evaluated the growth and characterized the rhizosphere bacterial and fungal communities of soybean by comparing wildtype soybeans (Enrei) with the non-nodulating mutants (En1282) across four soils under conventional and nature farming, including fumigated and unfumigated conditions. We found that the non-nodulating soybean mutants (En1282) exhibited reduced growth compared with wild-type (Enrei) plants, especially in untreated soils. Soil fumigation decreased microbial diversity and reshaped rhizosphere community composition with a significant reduction in plant growth and nodulation in all soils. Restriction in RNS increased bacterial diversity in untreated soils, possibly as a compensatory mechanism for nitrogen acquisition, whereas fungal diversity remained relatively stable. Nature farming promoted beneficial microbes like Rhizobium, Trichoderma, and Chloridium, whereas conventional soil plants favored Bacillus and Aspergillus. Notably, differential enrichment analysis identified distinct associations for each nodulation phenotype, with Enrei predominantly enriched for Pseudomonas, and En1282 associated primarily with oligotrophic microbes. Conclusion Our study sheds light on the complex interplay between legume symbiosis and rhizosphere microbiota assembly and highlights the significance of eco-friendly farming methods like nature farming in cultivating a healthy rhizosphere for plant growth. The results paves way for future strategies to manipulate rhizosphere microbiota, ultimately promoting robust and sustainable farming systems that reduce reliance on chemical inputs.