048 | Metagenome-assembled genomes reveal spatial and seasonal variability of coastal microbial communities along the Calabrian coast

Carmen Rizzo^1|2, Rosario Calogero^1|3, Erika Arcadi¹, Francesco Fabiano^1|4|6, Vittoria Dias^1|5, Angelina Lo Giudice², Teresa Romeo^6|7|8, Silvestro Greco^3|9 | ¹Stazione Zoologica Anton Dohrn, Sicily Marine Centre, Messina, Italy; ²National Research Council, Institute of Polar Sciences, Messina, Italy; ³Calabrian Research Centre and Advanced Marine Infrastructures, CRIMAC; ⁴University of Palermo, Palermo, Italy; ⁵University of Milano Bicocca, Milano, Italy; ⁶National Biodiversity Future Centre NBFC, Italy; ⁷Zoologica Anton Dohrn, Sicily Marine Centre, Milazzo, Italy; ⁸National Institute for Environmental Protection and Research, Milazzo, Italy; ⁹Università delle Scienze Gastronomiche di Pollenzo UNISG, Cuneo, Italy.

Coastal marine environments host highly dynamic microbial communities that play a key role in ecosystem functioning and biogeochemical cycles. In this study, we investigated the taxonomic and functional structure of microbial communities along the Calabrian coasts (Southern Italy) using whole metagenome sequencing of seawater samples collected at three sites: Reggio Calabria, Vibo Valentia, and Gioia Tauro, across two different seasons. Metagenomic reads were assembled and binned to reconstruct metagenome-assembled genomes (MAGs), enabling high-resolution analysis of community composition. High quality reads were mapped using the KMA algorithm to known antimicrobial resistance gene sequences from the manually curated CARD v4.0.5 database and the wildcard v4.0.2 extension. Resistance gene identification was performed using the Resistance Gene Identifier tool, and the output was subsequently standardized using the PHA4GE hARMonization tool. MAG-based analysis revealed marked differences in microbial community structure both among the studied coastal areas and between seasons, highlighting the strong influence of spatial and temporal variability on microbial assemblages. Among the 162 bacterial MAGs recovered, 75.9% were classified to the genus level, distributed across 17 phyla. Pseudomonadota, Bacteroidota, and Patescibacteria represented the dominant phyla. The most abundant MAGs across samples were identified as MAG_013 (Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae), MAG_038 (Bacteroidota; Bacteroidia; Flavobacteriales; Flavobacteriaceae; UBA3478), MAG_044 (Pseudomonadota; Gammaproteobacteria; Pseudomonadales; Nitrincolaceae), MAG_068 (Bacteroidota; Bacteroidia; Flavobacteriales; Flavobacteriaceae; GCA001735715), MAG_076 (Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; LGRT01; LGRT01 sp016778765), and MAG_161 (Patescibacteria; Saccharimonadia; Saccharimonadales; UBA4665; BOG-1338). Functional screening of the reconstructed MAGs allowed the identification of antibiotic resistance genes. The genes msrE (msr-type ABC-F protein), mphE (macrolide phosphotransferase (MPH)), and tet (tetracycline-resistant ribosomal protection protein) showed the highest coverage percentages across the analyzed samples, indicating their widespread presence within the studied microbial communities. The results provide an integrated overview of the taxonomic and functional diversity of microbial communities, with additional assessment of the spread of microbial antibiotic resistance in coastal areas. The high-resolution MAG approach enhances our understanding of microbial ecology and potential public health–relevant traits in coastal waters. Future analyses will integrate metagenomic data with chemical parameters to further elucidate the relationships between microbial communities and environmental conditions.