The native seed microbiota of alpine plant species - what is transmitted to the next generation

The plant microbiota is crucial for plant health and growth. Recently, vertical transmission of a beneficial core microbiota was identified for crop seeds but for native plants, complementary mechanisms are almost completely unknown. We studied the seeds of eight native plant species growing together for centuries under the same environmental conditions in Alpine meadows (Austria) by qPCR, FISH-CLSM and amplicon sequencing targeting bacteria/archaea and fungi. Bacteria and fungi were determined with approx. 1010 gene copy numbers g-1 seed as abundant inhabitants. Archaea, which were newly discovered as seed endophytes, are less and represent only 1.1% of the signatures. The seed microbiome was highly diversified; 11 844 bacterial, 32 archaeal and 3 945 fungal OTUs were assigned. All seeds showed a species-specific, highly unique microbial signature, and shared only a negligible proportion and an exceptionally small core microbiome. The plant genotype was clearly identified as the main driver, while different life forms had less, and fruit morphology no significant impact. Bacteria were represented by many known beneficial taxa, while the fungal community comprised mainly potential plant pathogens. This finding was supported by a close, synergistic network formed by bacteria and archaea contrasting with the independent and negatively interacting fungal network. These novel insights into the native seed microbiome contribute to a deeper understanding of seed microbial diversity for plant health, and beyond that for ecosystem plasticity and diversification within plant-specific microbiota. Moreover, it allows better understanding of phytopathological processes that could be used to design a healthy plant microbiome.