Integrated microbiome and metabolomics analysis reveal a closer relationship between soil metabolites and bacterial community than fungal community in pecan plantations

Abstract Understanding soil metabolic diversity and the chemical signals that shape rhizosphere microbial activity is important for protecting plants and improving forest productivity. At present, little information is known about the metabolites in the rhizosphere soil of pecan ( Carya illinoinensis ) plantation. Based on technologies of untargeted metabolomics and high‐throughput sequencing, we investigated differences in the metabolic profiles of rhizosphere and bulk soils and the relationship between metabolites and microorganisms in pecan plantations. The results showed that the abundance of metabolites in rhizosphere soil was significantly higher than that in bulk soil ( p < 0.05), especially reflected in plant secondary metabolites and lipids. Orientaloside and marmesin rutinoside were significantly enriched in rhizosphere soil metabolites of pecan at three pecan ages (VIP >1, p < 0.05). The linoleic acid and α‐linolenic acid metabolic pathways were significantly enriched in the differential metabolic set ( p < 0.01). In addition, tryptophan metabolism, starch and sucrose metabolism, and galactose metabolism were also important factors affecting the rhizosphere metabolic spectrum. Differential metabolites between bulk and rhizosphere soils were more closely associated with bacteria than with fungal communities, particularly in young pecans. With the increasing age of pecans, new significant enrichment of plant secondary metabolites such as cyanidin, 3‐trans‐caffeoyltormentic acid, N‐(1‐Deoxy‐1‐fructosyl) serine and piperdia emerged in the rhizosphere soil. 3‐trans‐caffeoyltormentic acid was positively related to Saitozyma and Protoglossum . Phenylacetaldehyde was positively correlated with Gaiellaceae , Tausonia , and Tuber . This study provides new insights into the mechanisms of interaction between pecans and microorganisms.