The microbiome of perennial ryegrass Lolium perenne L.

Abstract

Perennial ryegrass (Lolium perenne L.) is the most critical agricultural plant supporting New Zealand’s intensive pasture-based dairy industry. A substantial body of research exists on the physiology, genetics, and management of perennial ryegrass; however, the perennial ryegrass microbiome has not yet been investigated in detail. Poor persisting perennial ryegrass pastures are ongoing in some areas of the country. Microbiome research has already targeted one pasture persistence problem by applying Epichloë endophytes to combat invertebrate pest herbivory. The success of Epichloë encourages future research to explore additional microorganism applications to mitigate other significant contributors to poor pasture persistence, such as drought and water stress. This study explores the bacterial and fungal communities associated with the perennial ryegrass cultivar/Epichloë combination, One50 AR37. In total, 80 samples were collected from plots across four different New Zealand farming regions during April/May 2021 and examined alongside spatial, environmental, and host-plant-related metadata. Cultivation-independent methods, including DNA extraction, 16S and ITS rRNA gene PCR amplicon sequencing analysis (via amplicon sequence variants - ASVs), were used to characterise the perennial ryegrass bacterial and fungal communities. The below-ground (bulk soil, rhizosphere, and root endosphere) compared to the aboveground (shoot endosphere and phyllosphere) perennial ryegrass microbiome habitats represented significantly different ecological niches, correlating to differences in ASV richness, alpha and beta diversity, and the relative abundance of dominant genera. This study demonstrated evidence that the perennial ryegrass microbiome is strongly influenced by farming location and management practices. The large proportion of unique, site-specific taxa found at each farming location holds the potential to explain differences in pasture productivity and persistence. Location differences indicate that future microbiome research should compare ryegrass pastures on a regional basis rather than extrapolating the results to all New Zealand farming locations. A core microbiome was not identified in the current study; however, there is evidence for a wider functional selection of taxa across the individual microbiome habitats. Future studies should incorporate metagenomic sequencing to better understand the functional microbiome trends rather than solely focusing on taxa composition. This study provides the foundation for future perennial ryegrass research as it confirms the general trends and common taxa associated with the five microbiome habitats of this important pasture plant. Future pasture persistence research should compare the microbiome of high producing / persistent ryegrass pastures with low-producing ryegrass pastures whilst controlling as many variables as possible. Bacteria of interest, such as Bacillus and Pseudomonas, should be explored in greater detail at the species level and isolated and applied in manipulative trials to assess the effects on ryegrass production and persistence.