Shotgun metagenomics uncovers novel features of the cyanobacterial community in a large, shallow lake in Central Italy

This study aimed to unravel the taxonomic structure and functional potential of the cyanobacterial community in a large, shallow meso-eutrophic lake in Central Italy (Lake Trasimeno) through shotgun metagenomic analysis. The metagenomic profiling of samples allowed to characterize the structure of the bacterial community, also including the identification of rare species, not detected with the determination of metagenome-assembled genomes (MAGs), in the successive assembling and binning steps. The taxonomic identification of MAGs was based on the computation of genome similarity metrics (average nucleotide and amino acid identity values; ANI, AAI) and phylogenomic analyses, which confirmed the presence of several cyanobacteria previously identified during the monitoring campaigns, and the identification of taxa new for the Mediterranean region, such as Prochlorothrix hollandica and an uncharacterized Prochlorothrix. The genome annotation of the Prochlorothrix MAGs was consistent with that of oxygenic, non-diazotrophic, chlorophyll-b-producing, photosynthetic cyanobacteria. The annotation of cyanobacterial MAGs did not reveal the presence of operons encoding cyanotoxins. Based on a conservative analysis, the presence of antimicrobial resistance genes (ARGs) was exclusively identified in Vibrio cholerae (Enterobacterales) and in a few unbinned contigs, confirming the global relevance of the ARGs spread in freshwater environments