Deciphering Trifolium pratense L. holobiont reveals a microbiome resilient to future climate changes. Rhizosphere and endosphere of red clover (Trifolium pratense)

The plant microbiome supports plant growth, fitness, and resistance against climate change. Trifolium pratense (red clover), an important forage legume crop, positively contributes to ecosystem sustainability. However, T. pratense is known to have limited adaptive ability toward climate change. Here, the T. pratense microbiomes (including both bacteria and fungi) of the rhizosphere and the root, shoot, and flower endospheres were comparatively examined using metabarcoding in a field located in Central Germany that mimics the climate conditions projected for the next 50-70 years in comparison to the current climate conditions. Additionally, the ecological functions and metabolic genes of the microbial communities colonising each plant compartment were predicted using FUNGuild, FAPROTAX and Tax4Fun annotation tools. Our results showed that the individual plant compartments were colonised by specific microbes. The bacterial and fungal community compositions of the belowground plant compartments did not vary under future climate conditions. However, future climate conditions slightly altered the relative abundances of specific fungal classes of the aboveground compartments. We predicted several microbial functional genes of the T. pratense microbiome involved in plant growth processes, such as biofertilisation (nitrogen fixation, phosphorus solubilisation, and siderophore biosynthesis) and biostimulation (phytohormone and auxin production). Our findings indicated that T. pratense microbiomes show a degree of resilience to future climate changes. Additionally, microbes inhabiting T. pratense may not only contribute to plant growth promotion, but also to ecosystem sustainability.