Metagenomic surveys show a widespread diffusion of antibiotic resistance genes in a transect from urbanized to marine protected area

Ports are hot spots of pollution; they receive pollution from land-based sources, marine traffic and port infrastructures. Marine ecosystems of nearby areas can be strongly affected by pollution from port-related activities. Here, we investigated the microbiomes present in sea floor sediments along a transect from the harbour of Livorno (Central Italy) to a nearby marine protected area. Results of 16S rRNA amplicon sequencing and metagenome assembled genomes (MAGs) analyses indicated the presence of different trends of specific bacterial groups (e.g. phyla NB1-j, Acidobacteriota and Desulfobulbales) along the transect, correlating with the measured pollution levels. Human pathogenic bacteria and antibiotic resistance genes (ARGs) were also found. These results demonstrate a pervasive impact of human port activities and highlight the importance of microbiological surveillance of marine sediments, which may constitute a reservoir of ARGs and pathogenic bacteria. • Specific bacterial groups increased/decreased along a gradient of anthropic impact. • Chlamydiae were mostly present in the area with the highest anthropic impact. • A total of 111 antibiotic resistance genes were identified from metagenomes. • The genes for the potential resistance to vancomycin were among the most abundant.