SummarySeeds have evolved in association with diverse microbial assemblages that may influence plant growth and health. However, little is known about the composition of seed-associated microbial assemblages and the ecological processes shaping their structures. In this work, we monitored the relative influence of the host genotypes and terroir on the structure of the seed microbiota through metabarcoding analysis of different microbial assemblages associated to five different bean cultivars harvested in two distinct farms. Overall, few bacterial and fungal operational taxonomic units (OTUs) were conserved across all seed samples. The lack of shared OTUs between samples is explained by a significant effect of the farm site on the structure of microbial assemblage, which explained 12.2% and 39.7% of variance in bacterial and fungal diversity across samples. This site-specific effect is reflected by the significant enrichment of 70 OTUs in Brittany and 88 OTUs in Luxembourg that lead to differences in co-occurrence patterns. In contrast, variance in microbial assemblage structure was not explained by host genotype. Altogether, these results suggest that seed-associated microbial assemblage is determined by niche-based processes and that the terroir is a key driver of these selective forces.

Recognizing both the stakes of traditional European common bean diversity and the role farmers’ and gardeners’ networks play in maintaining this diversity, the present study examines the role that local adaptation plays for the management of common bean diversity in situ. To the purpose, four historical bean varieties and one modern control were multiplied on two organic farms for three growing seasons. The fifteen resulting populations, the initial ones and two populations of each variety obtained after the three years of multiplication, were then grown in a common garden. Twenty-two Simple Sequence Repeat (SSR) markers and 13 phenotypic traits were assessed. In total, 68.2% of tested markers were polymorphic and a total of 66 different alleles were identified. FST analysis showed that the genetic composition of two varieties multiplied in different environments changed. At the phenotypic level, differences were observed in flowering date and leaf length. Results indicate that three years of multiplication suffice for local adaptation to occur. The spatial dynamics of genetic and phenotypic bean diversity imply that the maintenance of diversity should be considered at the scale of the network, rather than individual farms and gardens. The microevolution of bean populations within networks of gardens and farms emerges as a research perspective.

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Seed germination and seedling establishment are the main factors for a successful start of a crop, determining crop health, weed suppression and overall crop performance. They are critical, but sensitive phases in crop production. High seed vigour and appropriate seed microbiota significantly contribute to the resilience of seedlings. This opinion paper is based on a review of relevant literature, two case studies with wheat and carrot and a subsequent stakeholder consultation in the framework of the European project LIVESEED. It presents a seed health strategy for organic farming systems that accounts for dynamic processes behind seed and plant health, taking advantage of the contributions of seed vigour and seed microbiota. Seed and plant health are understood as a continuum. Benefits of seed vigour and microbiota are showcased. Recommendations are given for organic seed production, seed processing and storage, as well as organic plant breeding and future research. In conclusion, organic farming systems, in particular, have the opportunity, both to develop this perspective on seed and plant health and to benefit from it. Adopting this perspective may require a shift in how crop plants and their seeds are cared for, as well as adapted regulatory frameworks.