Noccaea caerulescens seed endosphere: a habitat for an endophytic bacterial community preserved through generations and protected from soil influence

Background and aims While our understanding of seed microbiota has lagged far behind that of the rhizosphere and phyllosphere, many advances are now being made, particularly based on metagenomics studies. Today, our knowledge of seed microbiome assembly remains incomplete and the connections between seed and soil microbiomes are not yet fully understood, especially where hyperaccumulating plants are concerned. In this work, we assessed the structure and composition of the Noccaea caerulescens rhizosphere and endosphere-associated microbiota. Methods A pot experiment was conducted for 6 months in a growth chamber, using two populations of the hyperaccumulator Noccaea caerulescens growing on their original soil (calamine or nonmetalliferous) and vice versa. The diversity of rhizosphere soil bacteria and bacterial endophytic communities present in the different habitats (initial seed, root, stem, leaves and new seed generation) was characterized by high-throughput 16S rRNA amplicon sequencing. Results Bacterial communities from root endosphere, stem endosphere and leaf endosphere appeared to be soil-type dependent, contrary to the bacterial communities associated with seed endosphere habitats (initial seeds and new seed generation). Moreover, the seed endophytic bacterial communities of Noccaea caerulescens display a strong heritability across one plant generation. Indeed, a bacterial endophytic core-genome globally appeared to be constant between initial seeds and those obtained after the first generation. Conclusion Our results suggest that Noccaea caerulescens may carry a selected bacterial community in its seeds across generations, despite soil environment changes.