Microbial Alliances: Unveiling the Effects of a Bacterial and Fungal Cross-Kingdom SynCom on Bacterial Dynamics, Rhizosphere Metabolites, and Soybean Resilience in Acidic Soils

Acidic soils, covering 40 to 50% of arable land, hinder
productivity
due to phosphorus limitation and aluminum toxicity. Using a synthetic
community (SynCom) approach, we tested a native Rhizobium (Rh) and a non-native Ensifer fredii (Ef) strain, both combined with the mycorrhizal fungus Rhizophagus intraradices (Ri), on soybean growth
in acidic soil. The native RhRi SynCom outperformed EfRi, significantly
improving soybean growth, yield, and soil health. Metagenomics and
metabolomics revealed that RhRi significantly enhanced beneficial
microorganisms (AD3, Gemmataceae) and metabolites
(putrescine, stearic acid), hence improving nutrient cycling, stress
tolerance, and membrane integrity. RhRi also enhanced soil enzyme
activity (urease, phosphatases), which resulted in an increase in
nitrogen and phosphorus availability and a decrease in rhizosphere
toxicity. These alterations enhanced plant resilience, soil structure,
and microbial diversity. RhRi activated metabolic pathways (amino
acids, lipids, ABC transporters, and secondary metabolites) that are
involved in nutrient acquisition and stress response. Conversely,
EfRi provided minimal advantages, emphasizing the significance of
native microbial compatibility. Our findings show that native SynComs
boost crop resilience and production in acidic soils through synergistic
microbial interactions and metabolic reprogramming, thereby offering
a sustainable agricultural strategy in harsh environments.