Influence of Epichloë on the Microbiota of Established Lolium perenne Pastures in Aotearoa, New Zealand

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Perennial ryegrass (Lolium perenne) is a critical species supporting New Zealand's intensive pasture-based agricultural industries. Perennial ryegrass forms a symbiotic, mutualistic association with asexual Epichloë, an endophytic fungus known to increase invertebrate pest resistance. 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 been given to its effects on other associated microorganisms, particularly in established pastures. This study utilised 16S and ITS amplicon sequencing to explore the bacterial and fungal communities of established perennial ryegrass swards from three prominent New Zealand farming locations infected with different Epichloë strains. The value of this study was its replication of real-life farming pastures with different environmental and management variables. The results revealed that plant niche (rhizosphere, root/shoot endosphere) and farming site were the primary factors influencing microbiome variation. The correlation between the Epichloë strain and variations in the bacterial and fungal communities within perennial ryegrass were inconsistent, except for the shoot endosphere communities at one site (Burnham). However, differences in the relative abundance of individual fungal amplicon sequence variants were observed across sites between Epichloë treatments. The absence of significant correlations between Epichloë and the microbiome, coupled with the identification of core microbiota across all samples, contributes evidence that the Epichloë incorporation may not induce substantial variations in the microbiome of 3-year-old established perennial ryegrass pastures.