Tuber Inoculation Drives Rhizosphere Microbiome Assembly and Metabolic Reprogramming in Corylus

TL;DR

This study shows how Tuber fungi change the soil microbes and plant metabolism in Corylus, promoting a mutualistic ecosystem.

Contribution

The novel use of integrated multi-omics reveals how Tuber inoculation reshapes rhizosphere microbiomes and plant metabolism.

Findings

Tuber inoculation establishes a dominant fungal guild and suppresses pathogenic fungi in the rhizosphere.

Root metabolism shifts toward strigolactone upregulation and gibberellin downregulation, indicating a symbiosis-priority strategy.

Microbial community and root metabolite correlations suggest Tuber as a core regulator of a mutualistic micro-ecosystem.

Abstract

To elucidate the potential of integrated multi-omics approaches for studying systemic mechanisms of mycorrhizal fungi in mediating plant-microbe interactions, this study employed the Tuber-inoculated Corylus system as a model to demonstrate how high-throughput profiling can investigate how fungal inoculation reshapes the rhizosphere microbial community and correlates with host metabolism. A pot experiment was conducted comparing inoculated (CTG) and non-inoculated (CK) plants, followed by integrated multi-omics analysis involving high-throughput sequencing (16S/ITS), functional prediction (PICRUSt2/FUNGuild), and metabolomics (UPLC-MS/MS). The results demonstrated that inoculation significantly restructured the fungal community, establishing Tuber as a dominant symbiotic guild and effectively suppressing pathogenic fungi. Although bacterial alpha diversity remained stable, the functional profile shifted markedly toward symbiotic support, including antibiotic biosynthesis and environmental adaptation. Concurrently, root metabolic reprogramming occurred, characterized by upregulation of strigolactones and downregulation of gibberellin A5, suggesting a potential “symbiosis-priority” strategy wherein carbon allocation shifted from structural growth to energy storage, and plant defense transitioned from broad-spectrum resistance to targeted regulation. Multi-omics correlation analysis further revealed notable associations between microbial communities and root metabolites, proposing a model in which Tuber acts as a core regulator that collaborates with the host to assemble a complementary micro-ecosystem. In summary, the integrated approach successfully captured multi-level changes, suggesting that Tuber-Corylus symbiosis constitutes a fungus-driven process that transforms the rhizosphere from a competitive state into a mutualistic state, thereby illustrating the role of mycorrhizal fungi as “ecosystem engineers” and providing a methodological framework for green agriculture research.

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