Phyllosphere microbiomes uncovered: Research trends, geographic disparities, and key microbial players

In recent years, significant efforts have been made to understand the phyllosphere microbiome. To clarify current research trends and identify knowledge gaps, we conducted a systematic review of the literature and investigated the methodologies used to analyze microbiome communities associated with plants, along with the objectives of these studies. Applying systematic review principles, we assessed 333 reports from the Web of Science database for eligibility. Articles were included if they presented original research on microbiomes associated with phyllosphere tissues identified by next-generation sequencing. Of these, 268 reports, published from 2009 to March 2025, were retrieved. These reports were used to extract data in a controlled and methodical manner. The analyses identified the most frequently studied plant species and primary tissues, the geographical locations sampled, the variables investigated in the phyllosphere microbiome, and the methodologies and tools employed. A comparison of the number of studies on below-ground (n=1562) versus above-ground tissue (n=375) underscores the relatively unexplored nature of above-ground research. We notice a surprisingly low number of studies from the Southern Hemisphere. Additionally, through data mining, we identify the most dominant bacteria and fungi reported in phyllosphere studies. Based on these findings, we offer recommendations for future research on the phyllosphere.