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Organic fertilization reshapes core microbial taxa to enhance soil health and plant performance
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DOI：10.1007/s11104-026-08910-z.png)
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Abstract
En 中文
Soil health is essential for crop production and plays a crucial role in agricultural sustainability by supporting vital ecosystem services. Beneficial microorganisms are increasingly recognized as drivers of soil health in agroecosystems. However, it remains unclear whether microbial enrichment induced by organic fertilization can causally enhance soil health and plant performance. This study employed amplicon sequencing and shotgun metagenomics to characterize the fertilizer-induced shifts in soil microbial communities and metabolism-related genes, and their link with soil health (assessed through chemical and biological properties). Six strains were isolated from fertilizer-enriched taxa and their growth-promoting and soil health-improving abilities were experimentally verified. Organic fertilization increased soil health by 119% and was associated with shifts in microbial functional gene composition. Nitrogen-cycling genes, particularly those involved in nitrogen assimilation (nasB, gdh, and nirA), were the strongest predictors of the soil health index, explaining a substantially greater proportion of variance (63.78%) than genes associated with phosphorus (38.73%) or carbon (32.33%) cycling. Furthermore, a synthetic community composed of five Pseudomonas spp. and one Microbacterium sp. increased soil health index by 36.1% relative to non-inoculated controls and significantly enhanced plant height and biomass, providing evidence for the functional potential of fertilization-enriched taxa to soil health and plant growth. Our findings demonstrate that organic fertilization reshapes the soil microbiome toward functionally important taxa, particularly those involved in nitrogen cycling, thereby improving soil health and plant performance. This provides a mechanistic basis for leveraging beneficial microbiota to support sustainable agriculture.
Keywords:
Nutrient genes
Organic fertilization
Plant growth
Pseudomonas
Soil health
Synthetic community
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