Emergence Shapes the Structure of the Seed Microbiota

Abstract

Seeds carry complex microbial communities, which may exert beneficial or deleterious effects on plant growth and plant health. To date, the composition of microbial communities associated with seeds has been explored mainly through culture-based diversity studies and therefore remains largely unknown. In this work, we analyzed the structures of the seed microbiotas of different plants from the family Brassicaceae and their dynamics during germination and emergence through sequencing of three molecular markers: the ITS1 region of the fungal internal transcribed spacer, the V4 region of 16S rRNA gene, and a species-specific bacterial marker based on a fragment of gyrB. Sequence analyses revealed important variations in microbial community composition between seed samples. Moreover, we found that emergence strongly influences the structure of the microbiota, with a marked reduction of bacterial and fungal diversity. This shift in the microbial community composition is mostly due to an increase in the relative abundance of some bacterial and fungal taxa possessing fast-growing abilities. Altogether, our results provide an estimation of the role of the seed as a source of inoculum for the seedling, which is crucial for practical applications in developing new strategies of inoculation for disease prevention.

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

“…The gyrB database is composed of 30,525 sequences retrieved from 30,175 genomic sequences available in the IMG database v4 (Markowitz et al 2012). According to the gANI cliques defined previously by Varghese and collaborators (Varghese et al 2015), the gyrB marker has the best precision (0.964) and sensitivity (0.955) at a genetic distance of 0.02 (Barret et al 2015).…”

“…The choice of gyrB as a bacterial molecular marker was dictated by its lowest taxonomic resolution (species-level) in comparison to classic molecular markers based on the hypervariable regions of the 16S rRNA gene (Barret et al 2015). The gyrB database is composed of 30,525 sequences retrieved from 30,175 genomic sequences available in the IMG database v4 (Markowitz et al 2012).…”

“…Amplifications of one bacterial marker (gyrB) and one fungal marker (ITS1) were performed with the primer sets gyrB_aF64/gyrB_aR353 (Barret et al 2015) and ITS1F/ITS2 (Buée et al 2009) following procedures described earlier (Barret et al 2015). Amplicon libraries were mixed with 5% PhiX control according to Illumina's protocols.…”

“…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).…”