Master's supplementary data (all additional results for the project entitled Metagenomic and morphological characterization of marine phages from the Agulhas Current system)

Marine environments provide important ecosystem services. Previous studies have shown the importance of microbial communities as mediators of these ecosystem services via the biological pump. Although there is some understanding regarding the contributions of phytoplankton, bacteria, and archaea, we lack comparative insights regarding viral contributions especially in understudied regions of the ocean. The Agulhas current facilitates the exchange of microbes between geographically distinct regions such as the Indian Ocean, Atlantic Ocean, and Southern Ocean. Such interactions involve horizontal gene transfer (HGT) between bacteriophages and their hosts, which might increase bacterial survival under various stress conditions and influence the emergence of pathogens within the marine environment. Despite this, research on the phage taxonomy and their antimicrobial and virulence gene profiles within the Agulhas Current (AC) is limited. The current study aims to address this research gap by exploring the potential of AC phages to act as reservoirs for bacterial antimicrobial resistance genes (ARGs) and virulence genes (VGs). To achieve this aim, the following objectives are addressed: (1) viral-enriched metagenomic sample were obtained from surface water of the AC, (2) the phage population from this sample was characterised in terms of morphology, viral taxonomy, and host taxonomy, (3) ARGs and VGs were identified within phage genomes, and (4) the ecological role of these specific genes were assessed using available literature. Transmission electron microscopy indicated that the Agulhas Current was dominated by morphologies similar to Plectroviridae, Microviridae, and Podoviridae and archaea-targeting viruses like Clavaviridae, Globuloviridae, Zobellviridae, and Authographiviridae. Bioinformatic analysis identified a total of 1,205 viral operational taxonomic units, of which the majority represented Synechococcus-phages and Pelagibacter-phages, targeting Cyanobacterial hosts. Taxonomic analysis also revealed the presence of 43 high-quality, unclassified viral genomes, suggesting that the AC serves as a source for novel phages. β-lactam resistance genes, sulfonamide resistance gens and a single triclosan resistance gene were detected within phage genomes. Structural modelling of the predicted ARGs revealed that 17 out of 20 detected lacked conserved functional domains, while three (dfrF, clpL, rpoD) exhibited significant structural conservation. A total of 110 potential VGs associated with effector delivery, virulence-associated proteins, and bacterial adherence were detected within phage genomes. However, only five virulence gene had conserved structures, including four copies of the CsgG gene and a single copy of the clpA gene. These genes could potentially influence the evolution of the bacterial host by increased pathogenicity or by allowing adaptation to harsh environmental conditions. These findings reveal a diverse array of phages in the Agulhas Current with significant potential for encoding ARGs and VGs, confirming that phages from the Agulhas Current act as reservoirs for bacterially-derived ARGs and VGs. These results lay the foundation for future in vitro studies on the potential impact of phage-induced horizontal gene transfer (HGT) within the marine environment.