Impacts of long-term organic fertilization on metabolomic and metagenomic characteristics of soils in a greenhouse vegetable production system

Organic fertilization is popular in the greenhouse vegetable farming system. This study aimed to examine the impacts of long-term fertilization of various animal and plant waste composts on chemical properties, and the characteristics of metabolomics and metagenomics of soils in a greenhouse vegetable production system. The results showed that after 20 years of continuous organic fertilization, the soil pH was reduced in all treatments except pig and chicken dung composts; the most significant reduction was in the plant waste compost-treated soils. The soil electrical conductivity value, organic matter content, and the availability of phosphorus (P), potassium (K), calcium (Ca), and magnesium (Mg) increased with organic fertilizer applications. The annual yields of leafy vegetables for all treatments were relatively stable. Among them, the yield of soybean meal compost (Soy)-treated soils was the lowest. Unique metabolomic and metagenomic profiles were noted in the five different treatments, and they were significantly different between animal and plant waste compost-treated soils. The relative abundance of nucleotide-related metabolites, such as pyrimidones, purinones, and 6-aminopurines, was higher in the high-yield treatments. The relative abundance of Bacillus and Neobacillus was negatively correlated with the total nitrogen content of the soil. In addition, Bacillus aryabhattai was a strain present in all compost-treated soils, but its relative abundance was higher in the control (unfertilized) and Soy-treated soils. This study suggests that the combination of metabolomics and metagenomics could be used to examine soil quality and function, which is a more comprehensive assessment strategy and may facilitate agricultural management.