Long-term partial substitution of chemical fertilizer by organic amendments influences soil microbial functional diversity of phosphorus cycling and improves phosphorus availability in greenhouse vegetable production

Substitution of chemical fertilizers with organic amendments is an important practice for promoting soil phosphorus (P) transformation and alleviating excessive P accumulation in greenhouse vegetable production, yet little research has comprehensively investigated the effects on functional traits of P cycling microorganisms. Here, we integrated metagenomics and genome binning to explore 24 soil microbial P cycling traits in a 10-year field experiment including four treatments (equal NPK input): chemical fertilizer (CC), half of chemical N substituted with manure (CM), straw (CS), or manure plus straw (CMS). Compared with the CC treatment, organic substitution fertilization (CM, CS, and CMS) increased microbial taxonomic and functional diversity. Among P cycling-related genes, organic substitution fertilization significantly reduced the relative abundance of the phoU and increased the absolute abundance of gcd, ppx, and phoD (fluorescence quantitative PCR). Among microbial taxa containing gcd and phoD genes, organic substitution fertilization significantly increased the abundance of Alphaproteobacteria and Gammaproteobacteria, which were the most important predictors of soil Olsen P. Long-term organic substitution fertilization increased the microbial P solubilization and mineralization capacity by increasing soil C:P and N:P ratios and decreasing the pH. The gcd, ppx and phoD genes were positively correlated with labile P and Olsen P. The 12 reconstructed bacterial genomes harbored P solubilization genes, and the abundances of most genomes were higher under organic substitution fertilization than under CC treatment. Overall, organic substitution fertilization mainly increased the microbial P solubilization and mineralization capacity for P availability and also promoted microbial P immobilization, reducing losses to the environment in greenhouse vegetable production.