Different fertilizers regulated the microbiome and metabolism of Pinus koraiensis to promote nutrient cycling

Pinus koraiensis is a commercially important tree species that provides high-quality wood and a highly nutritious fruit. Plant roots absorb soil nutrients, but the effects of different nutrients on root metabolism are imperfectly known. We examine microbial communities, gene expression, metabolites, and nutrient contents in P. koraiensis roots using multiple omics and biochemistry to determine how different fertilizers (N, P, K, and compound fertilizer) affect root metabolism. Microbial composition changes with fertilizer type. Nutrient input promotes plant nutrient cycling and reprograms primary metabolism, specifically pyruvate metabolism, the tricarboxylic acid cycle, and ribosome and protein processing in the endoplasmic reticulum, to provide substances and energy for fatty and amino acid metabolism. Root secondary metabolism is also activated, with phenylpropanoid, flavonoid, flavone, and flavonol biosynthesis changing successively, increasing phenylpropanoids and polyketides. We report the application of fertilizers to influence the metabolic function of roots, and for mechanisms to be similar. Recombination of the main metabolic pathways is demonstrated. New perspectives on how environment affects plant metabolism are discussed. • Nutrient input changes the bacterial and fungal communities in the roots. • Nutrient input accelerates some primary metabolisms of the roots. • Phenylpropanoids and polyketides of the roots is increased by fertilizers. • Fertilizers promote the absorption and cycling of nutrients by Pinus koraiensis .