## 3 Results
### Functional Profile and Main AMGs in the Different Regions  
The differences evident in the geographical distribution of bacteriophage sequences were also reflected in the profiles of genes associated with functional roles (assessed by the relative abundance of genes matching Pfams in the different samples). The functional profiles were distinctly different between the surface and deep samples, i.e., photic vs. the aphotic zone, across all sampled sites (Figure 6b).  
Structural genes and genes involved in DNA replication and repair were amongst the most abundant in samples collected between 500-4000 m. ABC transporters were the main auxiliary metabolic genes (AMGs) present in deep samples (Figure 6c). Deep samples also displayed a relative increase in genes related to phage lysogenic strategies, especially integrases (Figure 6d), although the observed increased was not statistically significant (ANOVA followed by [PERSON]'s test in R). However, an analysis of the depth distribution of integrases in the complete gene catalogue from both the microbial and viral fraction did show a significant difference in phage life strategies between the surface and deep samples (\(p<0.001\)) (Supplementary Figure S3).  
Figure 5: Community composition for the different clusters of the 50 most abundant prokaryotic taxa in the metagenomes represented at the family level. Taxonomy was estimated from SSU rRNA genes (bacteria and archaea), reconstructed from shotgun metagenomes using phyloFlash.  
Figure 6: (**a**) Differential distribution of the 80 most abundant Pfam in the different clusters of the euphotic zone. Function was assigned with Interproscan (v.5). Pfam descriptions are colour coded based on corresponding functional categories [38]. Samples are grouped based on hierarchal clusters, calculated using the SIMPROF test (Clustsig). Size of the bubble is relative to Pfam abundance. (**b**) Venn diagram illustrating the differential distribution of shared and unique annotated viral genes between the aphotic and the euphotic zone. (**c**) Differential distribution of the 17 most abundant Pfam in the aphotic zone. (**d**) Log scaled depth distribution of integrase genes from the viral database.  
In the photic zone, the most abundant genes encoded deoxyribonucleotide biosynthesis enzymes. EAC samples were characterised by a high prevalence of AMGs usually encoded by phages that infect cyanobacteria. Genes that encode for proteins involved in photosynthetic activity (_psbA_, _psbD_, T-type Phycobiliprotein Lyase) and in nitrogen-related stress (2 OG-Fe-oxygenase) were amongst the most common, followed by transaldolase (PPP), MazG which is involved in cell survival under nutritional stress conditions, and multiple peptidase families. The functional profile for the samples collected in the Tasman Sea was characterised by a prevalence of genes that encode for an enzyme related to the radical SAM superfamily (\(p<0.01\)), a 4 Fe-4S single cluster domain, and also RmID, an enzyme involved in the biosynthesis of the precursor of L-Rhamnose. Furthermore, Tasman Sea samples were enriched with different methyltransferases, glycosyltransferases and pyrophosphohydrolases, some of which were almost absent in the EAC (Figure 6a).