Effect of Epichloë on ryegrass plant and soil microbiome

Perennial ryegrass (Lolium perenne) is the most common livestock forage species for pastures in New Zealand and other temperate countries. It can form mutualistic symbiosis with a shoot endophytic Epichloë fungus which produces a diverse range of alkaloid metabolites protecting plants from invertebrate pest damage. There is limited understanding of the effect of Epichloë on plant-associated and soil microbiomes. We aimed to address this knowledge gap and examine whether such effects are Epichloë strain dependent.

A field trial was established with six ryegrass cultivar/ Epichloë strain combinations, enabling comparison of Epichloë strain specific effects as well as cultivar/strain interactions on plant and soil microbiomes. Samples were collected multiple times across 1.5 year, both before and after grazing. Microbiomes associated with bulk soil, rhizosphere soil, endophytic roots and shoots were analysed using MiSeq 16S and ITS sequencing. Additionally, the microbiomes associated with seeds used for the trial were examined.

Strong Epichloë effects were detected for seed microbiome. However, in samples obtained from the field trial, sampling niches and time played more substantial roles in shaping the microbiome compared to cultivar and Epichloë. Different strains of Epichloë showed various impacts on specific microbial phylum and classes in individual niches, including shoots, root, rhizosphere and soil microbiomes. Our study demonstrated that the aboveground shoot endophyte Epichloë only had minor impact on shoot microbiome as well as belowground microbiomes (root, rhizosphere and soil). Some of the impacts were strain specific. Further studies or metagenomic analyses are required to examine biological impact of Epichloë on plant and soil microbiome.