Comparative metagenomic and metabolomic characterization of conventionally and nitrogen-only fertilized maize soils...

Long-term nitrogen-only fertilization can alter soil physicochemical properties and microbial community structure in maize fields. In this study, nitrogen-only fertilized soil (S) and conventionally fertilized soil (B) were collected from a four-year maize field trial in Anshun City, Guizhou Province, China. Meanwhile, a forest-derived microbial enrichment system (T) was prepared through fermentation using forest soil, rice bran, and molasses. Metagenomic sequencing and untargeted metabolomics were used to compare microbial, functional gene, and metabolite differences between S and B soils within the agricultural field system, and to describe the microbial community composition, functional gene profiles, and metabolite features of T as an independent reference system. The results showed that Pseudomonadota accounted for 44.33% of the microbial community in T, compared with 20.63% in S and 22.31% in B. Carbon and nitrogen metabolism-related genes, including ackA, gltB, and ureC, showed higher relative abundances in T than in S. Pathway-level annotation indicated higher representation of genes or modules related to glycolysis and nitrogen metabolism in T. Metabolomic profiling revealed distinct metabolite patterns in T, including differences in amino acids, carbohydrates, and metabolites annotated to phenylpropanoid-related pathways. Candidatus Rokubacteria also showed high relative abundance among nitrogen-metabolism-associated taxa in T. Overall, this study provides descriptive multi-omics evidence of the microbial composition, functional gene profiles, and metabolite features of a forest-derived fermentation-enriched microbial community. Because T was an artificially enriched system and was not introduced into agricultural soil, these results should be interpreted as baseline data for future controlled validation rather than direct evidence of soil remediation or functional compensation.