Host Species Mediate Distinct Seed Microbiome Responses to Restoration

Abstract Microbial diversity is a key driver of ecosystem function, yet it remains poorly integrated into ecological restoration frameworks. While seeds are the primary dispersal unit of plants and the foundation of most restoration programs, the microbial communities they carry are rarely considered. Here, we assess whether sites that have undergone restoration have altered seed-associated microbial communities. We do this by comparing bacterial and fungal seed microbiomes across natural and restored landscapes. Using a landscape-scale sampling design, seeds were collected from multiple plant host species and populations across 41 sites spanning a broad latitudinal gradient. High-throughput sequencing of the 16S rRNA gene and ITS2 region was used to characterise bacterial and fungal communities, respectively, and differences in diversity, composition, and network structure were assessed using multivariate and network-based approaches. Seed microbiomes differed between natural and restored sites, but the magnitude and nature of these changes varied among host species. Restored sites were associated with shifts in microbial diversity, community composition, and network structure, including changes in the retention of putative keystone taxa. In some species, restoration was linked to pronounced restructuring of seed-associated microbial communities, whereas in others, microbiomes remained comparatively stable. Together, these results demonstrate that restoration can alter seed microbial communities in ways that are not consistently predicted by soil-focused restoration outcomes and that host identity mediates these responses. Incorporating seed microbiome data into restoration monitoring may therefore provide a complementary and previously overlooked indicator of restoration success, with implications for improving plant germination and health.