Host-Dependent Endophytes as a Resilient Biological Reservoir: Niche-Specific Expansion and Holobiont Reassembly in Grapevine.

Plants and their endophytic microbiota form a functional holobiont, wherein host-dependent endophytes (HDEs) are proposed to serve as persistent microbial components associated with host continuity. Using long-term in vitro grapevine plantlets, we investigated HDE redistribution and reassembly across successive agar-based subcultures and during the transition to soil-based cultivation. Results showed that the initial tissue niche (shoot-tip versus root-base) imprinted a persistent compositional signature on HDE communities, with distinct cultivar-dependent effects. Numerous microbial amplicon sequence variants (ASVs) remained shared across agar-based and soil-based habitats, demonstrating high persistence of HDE-associated lineages. Bacterial communities exhibited marked plasticity, with plant-associated bacterial lineages contributing substantially to soil community assembly. Notably, 204 root-enriched bacterial ASVs, comprising 10.8-14.3% of the soil community, were recovered, revealing a robust "Root-Specific Legacy". Bacterial HDEs showed higher redistribution potential (43.3%), whereas fungal transfer was significantly lower (10.4%). Functional profiling suggested habitat-associated functional patterns, with the anaerobic phenotype enriched in soil and predicted enhancements in membrane transport, nucleotide metabolism, glycan biosynthesis, and biosynthesis of secondary metabolites in roots. Cladosporium and Fusarium remained dominant in the fungal core taxa, and habitat transition altered their predicted trophic profiles. Our findings establish HDEs as a resilient biological reservoir capable of niche-specific expansion, contributing to the ecological reassembly of the plant holobiont.