Unveiling Microbial Diversity in Greek Urban Air and Recreational Seawater Using DNA Barcoding

Air and seawater samples were collected in 2022–2023 and analyzed through a common DNA extraction, purification, and Next-Generation Sequencing protocol. The study targeted bacteria, archaea, fungi, and plant-associated taxa to compare community structure across both milieus. Given the scarcity of data on environmental microbiomes in Greece, we aimed to investigate further the diversity and variability of these microbiomes for the first time, using barcoding to provide data on microbial signatures in the air and seawater. Sequencing data revealed significant spatial and seasonal variability and a high diversity and richness of microbiome communities in both habitats. After quality filtering, we detected 21 phyla and 345 genera of bacteria and archaea, 3 phyla and 149 genera of fungi, and 17 Viridiplantae orders in the urban air. At the same time, in the recreational waters, we isolated 20 phyla and 420 genera of bacteria and archaea, 2 phyla, and 53 genera of fungi and 19 orders of Viridiplantae. Many of the fungal and bacterial taxa detected in this study can be potentially pathogenic. These findings highlight the potential of DNA barcoding as a reliable tool for integrative environmental monitoring, offering insights into the composition of environmental microbiomes. Microbiome monitoring is valuable for the environment and health, and it will be more efficient by integrating DNA analysis with the development of open databases and artificial intelligence.