Urbanisation Shapes the Diversity, Composition, and Functional Profile of Endophytic Bacteriome in Common Urban Tree Species

Urbanisation is a major driver of ecological change, altering the composition and functioning of ecosystems through land use conversion, pollution, and environmental fragmentation. Although some authors reported that air pollutants could be absorbed and detoxified by the endophytic microbiome of urban trees, the specific mechanisms by which urban air pollution shapes the endophytic microbiome and, consequently, the trees’ capacity for pollutant degradation, remain largely unexplored. The aim of the present study was to: (1) analyse the structure of endophytic bacteriome of the phyllosphere of three widely planted ornamental tree species—Tilia tomentosa, Fraxinus excelsior, and Pinus nigra, growing at four locations within the city of Plovdiv, Bulgaria, with different anthropogenic load; and (2) assess the effects of host species and urban environmental exposure on bacteriome diversity, taxonomic composition, and functional capacity. Functional profiling based on 16S rRNA gene sequencing revealed enrichment of the metabolic pathways associated with nitrogen cycling, carbon metabolism, and hydrocarbon degradation, particularly in samples originating from more urbanised or polluted locations. These predicted functional traits suggest that endophytic bacteria may actively contribute to detoxification processes within plant tissues. Tilia tomentosa and Fraxinus excelsior were enriched in nitrogen and carbon cycling pathways, including denitrification, methanol oxidation, and methanotrophy—functions associated with oxidative stress mitigation and nutrient regulation. In contrast, Pinus nigra showed higher relative abundance of chemoheterotrophy, ureolysis, and sulphur respiration, indicating a more conservative and stress-tolerant microbiome. Although the study involved only one settlement, these results suggest that endophytic communities may contribute to urban tree sustainability by supporting ecosystem functions under stress conditions. By integrating microbial ecology with urban environmental assessment, this research provides new insights into the adaptive potential of endophytic microbiota in urban forests and highlights their importance in the sustainable management of green infrastructure through microbiome-informed strategies.