A reduced but stable core microbiome found in seeds of hyperaccumulators

Abstract

The seed microbiota is currently of great interest in the scientific community since seed germination is a critical stage in plant life cycle. Some seed endophytic bacteria could be commonly found in seeds of hyperaccumulating plants and may confer them an evolutionary advantage over non-hyperaccumulating plants when confronted to biotic or abiotic stress. This study focuses on the endophytic bacterial diversity of a wide diversity of metal hyperaccumulating and non-hyperaccumulating plants (93 seed samples from Mediterranean regions, Oceania, South-East Asia) to reveal the core endophyte communities specific of hyperaccumulating plants. The rather low richness of the seed bacterial communities found in all seeds suggest that a sub-population of specialized endophytic strains is able to colonize seeds and survive. The factor that shapes the diversity of those bacterial communities was first the botanical family and secondly the hyperaccumulation trait of the host plants. Based on the taxonomic affiliation, we revealed that the Brassicales had 1349 OTUs that were specific to them and the Asterales 204 OTUs, independently of their metal accumulation strategy. Nonetheless, a set of 12 OTUs were shared by the seeds of all the hyperaccumulators independently of the taxonomic order of the plants (among Asterales and Brassicales) and could be considered as a 'stable' core microbiome. Those OTUs identified as Luteibacter, Alphaproteobacteria unclassified, Sphingopyxis, Alishewanella, bacteria unclassified, Heliimonas, Aeromicrobium, Proteobacteria unclassified, Xanthomonadales unclassified and Micromonosporaceae unclassified may constitute an endophytic bacterial core with PGP traits. Further studies are needed to extend our knowledge of the possible role played by those bacteria.

Keywords: Bacterial diversity; Endophyte; High throughput sequencing; Hyperaccumulator; Seed; Trace element.