Field Plant Biodiversity and Carbon Farming Shape Leaf Microbiomes

Abstract

Carbon farming practices are increasingly adopted as part of regenerative agriculture to enhance soil carbon sequestration and improve agricultural sustainability. However, their effects on the phyllosphere microbiome, and how these interact with field biodiversity, remain poorly understood. We investigated how field biodiversity and carbon farming practices (cover crops, all- in mixes, adaptive grazing and ley mixture) influence leaf microbial communities across 19 Finnish farms using ITS and 16S amplicon sequencing. Foliar fungal—but not bacterial— diversity increased with plant species richness. Carbon farming altered both fungal and bacterial community composition, but only fungal community was positively associated with disease load. Network analysis identified three candidate keystone taxa: Alternaria sp. (FASV 34) and Sporobolomyces roseus (FASV 2070), which were mutually exclusive, and Methylobacterium sp. (BASV 75), which co-occurred with FASV 2070. Together, these findings demonstrate that different carbon farming practices shape distinct leaf microbiomes cover crop systems tending to favor potential fungal pathogens, whereas ley mixture and adaptive grazing strategies promote microbial taxa associated with healthier phyllosphere communities. Our study underscores the importance of understanding the complex microbial interactions within leaf ecosystems to inform sustainable agricultural practices.