Synthetic Microbial Communities Regulate Rhizosphere Microorganisms to Ameliorate Arid Farmland Soil and Improve Onion Growth across Growth Stages

Abstract Although microbial inoculants exhibit plant-growth-promoting potential, their regulatory mechanisms remain unclear. Using absolute quantitative sequencing, we explored how the fermentation broth of synthetic microbial communities (SynComs) built from six strains modulated onion rhizosphere microecology throughout the growth period. SynComs broth elevated soil enzyme activities and available nutrients at specific growth stages. Absolute abundances of beneficial bacteria Nitrospira and Nocardioides increased in all stages, whereas pathogenic fungi Cladosporium and Alternaria decreased. Stochastic assembly dominated bacterial community construction, whereas fungal communities were governed mainly by homogeneous selection. Methylotrophic bacteria and saprotrophic predatory fungi were enriched. At harvest, bulb soluble protein, total sugar, and single-bulb fresh weight increased by 73.36%, 33.46%, and 21.91%, respectively. Fungal functional group mediated correlations between environmental factors and bulb nutritional traits. Collectively, SynComs coordinately enhanced onion quality via optimizing soil conditions and reshaping microbial assemblages, providing theoretical support for the microbial restoration of arid agricultural soils.