The effect of Epichloë on the microbiota of established perennial ryegrass pastures

Perennial ryegrass (Lolium perenne) is a critical agricultural plant supporting New Zealand's intensive pasture-based dairy industry. A significant breakthrough in perennial ryegrass research was the discovery of Epichloë, a genus of ascomycete fungi that form an endophytic symbiosis with grasses and reduce invertebrate pest damage. Plant breeders have incorporated several strains of Epichloë in perennial ryegrass, including AR1 and AR37, which exhibit variations in their alkaloid production to target different pasture pests. The impact of Epichloë on ryegrass production and invertebrate pests has been extensively studied; however, little attention has focussed on its effects on other associated microorganisms, particularly in established pastures. This study utilised 16S and ITS rRNA amplicon sequencing to determine the influence of two Epichloë strains, AR1, AR37, and a Nil (without Epichloë) treatment, on the bacterial and fungal communities in three-year-old perennial ryegrass swards from three locations in New Zealand. The results revealed that the ryegrass niche and farming site were the most significant factors driving microbiome variation. Epichloë strain did not consistently correlate to variation across bacterial and fungal communities across all sites, except for the shoot endosphere communities from the one Canterbury farming location sampled (Burnham). Epichloë treatment could, however, be associated with several differences in the abundance of individual fungal ASVs across the sites. This study unveils the diverse microbiota within established ryegrass pastures. The presence of core microbiota across all samples despite differences in Epichloë strain was reassuring to plant breeders in that the wide utilisation of Epichloë in New Zealand pastures could not be associated with any dramatic community differences across the microbiome of three-year-old established pastures. Any Epichloë effects on plant microbiome were subtle and site-dependent in plants surviving 3 years post-sowing. This information can assist future research on microbial solutions and plant breeding targets for mitigating soil diseases and poor ryegrass persistence across different farming regions in New Zealand.