Diversity of endophytic bacteria and fungi in seeds of Elymus nutans growing in four locations of Qinghai Tibet Plateau, China

Seeds are involved in the transmission of microorganisms from one plant generation to the next, acting as initial inoculum for the plant microbiome, therefore provide a key source of variability in plants. This study aimed to characterize the seed bacteria and fungi communities in Elymus nutans, a dominant perennial grass growing in the Qinghai Tibet Plateau (QTP) and explore the effects of plant growth location on the seed microbiome. Seeds were collected from plants growing in four locations in the QTP. The seed microbial community was examined by Illumina MiSeq sequencing of DNA extracted from the surface sterilized seeds. The seed bacterial community was dominated by the bacteria phylum Proteobacteria (98%) and fungal phyla Ascomycota (83%) and Basidiomycota (15%). At the lower taxonomic level, the bacterial genus Pseudomonas dominated in all four locations with an average relative abundance of 83% whereas the fungal genera that dominated the seed microbiome was diverse, the most prominent being Epichloe, Pyrenophora, Mycosphaerella and Bullera. Ecologically important bacterial family Nitrosomonadaceae (nitrifiers) and fungal phylum Glomeromycota (arbuscular mycorrhizal fungi) were detected in this study for the first time as seed endophytes. The Elymus nutans seed bacterial community was not impacted by the plant growth location, in contrast, the seed fungal community varied significantly in four locations. The seeds of Elymus nutans host diverse endophytic bacteria and fungi. Unlike the bacteria, the host plant selection of seed fungal endophytes was observed to have been affected by plant growth location. Positive and negative associations in the Elymus nutans seed microbiome were observed.