Terroir is a key driver of seed‐associated microbial assemblages

Abstract

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.

Assembly of seed-associated microbial communities within and across successive plant generations

“…While generation-specific variation was observed within seed-associated microbiota, the highest variation was found between seed samples collected within the same year but on different individual plants. As most diversity surveys of seed-associated microbial communities are performed on seed samples consisting of multiple plant entities (Barret et al 2015;Links et al 2014: Klaedtke et al 2016, this source of variation is usually ignored. The fluctuations in microbial community composition observed between seed samples collected on different individual plants were partly explained by neutral processes.…”

“…These two features are frequently encountered in seedassociated bacterial communities. Indeed, the overall composition of seed-associated bacterial communities is not shaped by the host genotype (Barret et al 2015;Klaedtke et al 2016). Moreover, seed-associated microbial communities are composed of few abundant entities and a multitude of low-abundance members (Rezki et al 2016) that may be prone to local extinction.…”

“…Based on these previous studies, it seems that selection by the host plant is not a major driver of seed community assembly (Barret et al 2015;Klaedtke et al 2016). In contrast, selection by the environment has been shown to shape the structure of seed-associated fungal microbiota but not seed-associated bacterial microbiota (Klaedtke et al 2016). Hence variation in microbiota composition observed across seed samples could be due to other ecological forces such as dispersal, diversification or ecological drift.…”

“…Moreover seedassociated micro-organisms contribute to seed preservation (Chee-Sanford et al 2006) and the release of seeds from dormancy (Goggin et al 2015); they also have been associated with decreased germination rates (Nelson 2004;Munkvold 2009) and enhancement of ear emergence (Mitter et al 2017). Recent diversity surveys of the seed microbiota revealed a high level of variation in microbial assemblages composition (LopezVelasco et al 2013;Links et al 2014;Barret et al 2015;Klaedtke et al 2016;Rezki et al 2016). Based on these previous studies, it seems that selection by the host plant is not a major driver of seed community assembly (Barret et al 2015;Klaedtke et al 2016).…”

“…Recent diversity surveys of the seed microbiota revealed a high level of variation in microbial assemblages composition (LopezVelasco et al 2013;Links et al 2014;Barret et al 2015;Klaedtke et al 2016;Rezki et al 2016). Based on these previous studies, it seems that selection by the host plant is not a major driver of seed community assembly (Barret et al 2015;Klaedtke et al 2016). In contrast, selection by the environment has been shown to shape the structure of seed-associated fungal microbiota but not seed-associated bacterial microbiota (Klaedtke et al 2016).…”