## 5 Conclusions  
In conclusion, using both a genome and gene-centric approach, we provide the first insights into the distribution and functional diversity of the main bacteriophage inhabiting the EAC and the Tasman Sea. Meso- and bathypelagic bacteriophages are still mostly unknown, but they possibly represent one of the major players in deep nutrient recycling. Moreover, phage communities from the aphotic zone were similar across a wide latitudinal gradient, but different from the phage found in the euphotic zone. The euphotic zone instead presented different bacteriophage communities associated with either the EAC or Tasman Sea. The difference in bacteriophage communities could possibly be explained by the regional distribution of their specific host, such as cyanophage in the EAC. The genomic content associated with the different environments provide an indication as to how phage adapt their specific repertoire of auxiliary metabolic genes (AMGs) to better exploit their host, based on a change in nutrient bioavailability and temperature.  
**Supplementary Materials:** The following are available online at [[http://www.mdpi.com/1999-4915/12/3/317/s1](http://www.mdpi.com/1999-4915/12/3/317/s1)]([http://www.mdpi.com/1999-4915/12/3/317/s1](http://www.mdpi.com/1999-4915/12/3/317/s1)), Supplementary Figure S1: Distribution of the main bacteriophage family. Supplementary Figure S2: Distribution of the main bacteriophage species. Supplementary Figure S3: Distribution of integrase genes. Supplementary Table S1: Environmental parameters of the location where the samples were collected. Supplementary Table S2: Reads mapping statistics. Supplementary Table S3: Functional categories in the virome selected contigs and in the total virome database.  
**Author Contributions:** Conceptualization A.F., M.O. and I.P.; Formal analysis, A.F. and M.O.; Funding acquisition, M.O., M.V.B. and I.P.; Investigation, A.F., M.O., K.G. and M.V.B.; Methodology, A.F.; Resources, M.O. and I.P.; Visualization, A.F.; Writing--original draft, A.F.; Writing--review and editing, A.F., M.O., M.V.B., and I.P. All authors have read and agree to the published version of the manuscript.  
**Funding:** This work was supported by Australian Research Council awards FL140100021 to.P. and DP150102326 & DP170101925 to M.V.B., M.O.  
**Acknowledgments:** The authors would like to thank the Chief Scientist [PERSON] and officers and crew of the _R/V Investigator_ during cruise IN16_v04. We would like to acknowledge the contribution of the Marine Microbes Project consortium ([[https://data.biopilatforms.com/organization/pages/bpa-marine-microbes/consortium](https://data.biopilatforms.com/organization/pages/bpa-marine-microbes/consortium)]([https://data.biopilatforms.com/organization/pages/bpa-marine-microbes/consortium](https://data.biopilatforms.com/organization/pages/bpa-marine-microbes/consortium))) in the generation of part of the data used in this publication. Sections of these data were sourced as part of the Integrated Marine Observing System (IMOS)--IMOS is also supported by the Australian Government through NCRIS. We would like to thank the numerous crew members and scientists involved in the generation, curation, and deposition of IMOS oceanographic data.  
**Conflicts of Interest:** The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.