Diverse but temporally stable virome in a 1.2 km deep karst aquifer accessed via Moab Khotsong mine, South Africa

Abstract Despite their ubiquity, viruses remain understudied in many of Earth’s environments. The deep subsurface contains a large portion of Earth’s biomass and can be expected to hold a rich store of viruses as well. We investigated the viral community in a 1.2-kilometer-deep dolomitic aquifer accessed in the Moab Khotsong gold mine in South Africa by microscopically quantifying virus-like particles (VLP) and cells and conducting a metagenomic survey of viruses and their associations with the microbial community. VLP:cell ratios were low (~1:1). Viral sequences were recovered from filtered (0.2 μm) water, presumably representing free virions, and from the >0.2-μm fraction that also included microbial cells. Viruses were diverse and 78% novel, and the viral communities were relatively unchanged at four sampling dates spanning five years. Host prediction indicated viral infection of the dominant bacterial taxon, Rhodocyclaceae, with temperate phages. Other sulfur-oxidizing bacteria, e.g. Thiomicrospiraceae, were also associated with temperate phages. Viral genomes include auxiliary metabolic genes (AMGs), with most of them being class II, which favor host persistence. Taken together, the low VLP:cell ratio, class II AMGs, and temporally stable viromes point to dominance of lysogeny and piggyback-the-persistent viral-host interactions in this deep aquifer. The many novel viruses observed here suggest that the terrestrial subsurface is an untapped reservoir of viral diversity.