Metagenomic approach for characterization of phyllosphere microbiome in fresh tea leaves

Identification of the phyllosphere microbiome in fresh tea leaves is important for assessing the potential of resident microorganisms to enhance tea quality. The phyllosphere microbiome comprises a diverse array of microorganisms, many of which are undetectable by traditional culture-dependent methods. Metagenomic studies offer a comprehensive view of these microbial communities, revealing their diversity and functional potential in plant associations. This study aimed to investigate the phyllosphere microbial community of fresh tea leaves collected from three elevations in Sri Lanka through next-generation sequencing-based metagenomic analysis. The microbial communities of bacteria, yeasts and molds from samples collected across ten different tea estates exhibited a comparable diversity of phyla. The most abundant bacterial phyla were Bacteroidetes (48.1%), followed by Proteobacteria (46.3%), Firmicutes (2.9%) and Actinobacteria (2.0%) and all these consistently present across the samples. As fungal phyla, Ascomycota (17.0%), Basidiomycota (7.1%) and Mucoromycota (0.7%) were the most prevalent groups, with fungi belong to Ascomycota identified in every sample. Seventy-four bacterial genera were identified, with Pedobacter (34.6%) being the most abundant, followed by Pseudomonas , Sphingomonas , Luteibacter , Epilithonimonas , Enterobacter , Chryseobacterium and Bacillus . Among yeasts and molds, the genera Aspergillus , Papiliotrema , Fusarium and Candida were dominant. The taxonomic composition of phyllosphere microbiomes was highest in samples from low-elevation regions compared with those from up country and mid country elevations. This may be influenced by environmental factors and tea cultivars specific to each elevation. This study provides new insights into the complex microbiomes present in the phyllosphere of tea leaves. Understanding these microbial communities may offer opportunities to enhance tea quality through targeted management of beneficial microorganisms. • Phyllosphere microbiome of tea leaves consist of bacteria, yeasts and molds. • Bacteroidetes as dominant bacterial phylum, Pedobacter being the most abundant bacteria. • Ascomycota as predominant fungal phylum, Aspergillus and Candida were the most prevalent . • Microbial diversity was highest in tea leaves grown at low elevations in Sri Lanka.