Simultaneous profiling of seed‐associated bacteria and fungi reveals antagonistic interactions between microorganisms within a shared epiphytic microbiome on Triticum and Brassica seeds

Abstract

In order to address the hypothesis that seeds from ecologically and geographically diverse plants harbor characteristic epiphytic microbiota, we characterized the bacterial and fungal microbiota associated with Triticum and Brassica seed surfaces.The total microbial complement was determined by amplification and sequencing of a fragment of chaperonin 60 (cpn60). Specific microorganisms were quantified by qPCR. Bacteria and fungi corresponding to operational taxonomic units (OTU) that were identified in the sequencing study were isolated and their interactions examined.A total of 5477 OTU were observed from seed washes. Neither total epiphytic bacterial load nor community richness/evenness was significantly different between the seed types; 578 OTU were shared among all samples at a variety of abundances. Hierarchical clustering revealed that 203 were significantly different in abundance on Triticum seeds compared with Brassica. Microorganisms isolated from seeds showed 99–100% identity between the cpn60 sequences of the isolates and the OTU sequences from this shared microbiome. Bacterial strains identified as Pantoea agglomerans had antagonistic properties toward one of the fungal isolates (Alternaria sp.), providing a possible explanation for their reciprocal abundances on both Triticum and Brassica seeds.cpn60 enabled the simultaneous profiling of bacterial and fungal microbiota and revealed a core seed-associated microbiota shared between diverse plant genera.

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

“…These core OTUs were affiliated to bacterial (e.g. Pantoea agglomerans or Pseudomonas viridiflava) and fungal taxa (Alternaria or Cladosporium) that are frequently associated with seeds of various plant species (Barret et al 2015;Hodgson et al 2014;Links et al 2014;Rezki et al 2016;Truyens et al 2015). Altogether, these results suggest a low heritability of the seed microbiota across plant generations.…”

“…All fungal OTUs were related to the Alternaria genus, more precisely to the section Alternata and Infectoria (Woudenberg et al 2013). Although these fungal taxa are usually described as plant pathogens (Woudenberg et al 2013), their prevalence in symptomless seeds (Links et al 2014;Barret et al 2015) and their potential selection by the host plant may indicate plantbeneficial traits.…”

“…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.…”

“…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).…”

Emergence Shapes the Structure of the Seed Microbiota

“…However, the vast majority of these results have been obtained with surface-disinfected seeds, thus ignoring the influence of seed epiphytes as a source of inoculum. More recently, the composition of the seed-associated epiphytic microbiota of Brassica and Triticum has been investigated by sequencing a portion of cpn60 (18). Although this molecular marker has provided interesting information on bacterial and fungal taxa present at the seed surface, the lack of 16S rRNA gene and internal transcribed spacer (ITS) sequence data impaired comparison of these results with those of studies performed on other plant compartments.…”