The community assemblages from two distant hypersaline systems (Solar Salterns of Es Trenc in Spain and the thalasohaline lake of Aran-Bidgol lake in Iran) were challenged by permutating their cellular fractions with the sterile-filtered supporting brines with and without the free-suspended virus fraction. Comparative metagenomics were used to assess whether the change of environment and the presence/absence of autochthonous/allochthonous viruses generated an ecological response in the transplanted communities.