Viruses are integral components and critical regulators of microbial ecosystems. In terms of numbers alone, virus-like particles seemingly outnumber microbial cells in every ecosystem (Weinbauer and Rassoulzadegan, 2004), with a virus-to-microbe ratio typically ranging from 1 to 100 (Wigington et al., 2016). While challenging to assess, profound ecological and evolutionary impacts of virus-host interactions have nonetheless been uncovered across a broad range of ecosystems, from the bottom of the oceans to bubbling acidic hot springs, coral reefs and thawing permafrost (Suttle, 2007
Rohwer and Vega Thurber, 2009
Dell'Anno et al., 2015
Williamson et al., 2017
Emerson et al., 2018). Collectively, these studies highlighted multiple mechanisms by which viruses drive ecological and evolutionary processes in microbial ecosystems (Koskella and Brockhurst, 2014
Breitbart et al., 2018). While the ecological importance of viruses is now undeniable, a thorough assessment of their influence on any microbial system remains elusive. Two of the current challenges are (i) comprehensively exploring and classifying environmental viral diversity and (ii) establishing host linkages for uncultivated viruses. A number of recent methodological innovations suggest, however, that these hurdles may be overcome sooner rather than later (Mokili et al., 2012
Dang and Sullivan, 2014
Brum and Sullivan, 2015
Sepulveda et al., 2016
Sullivan et al., 2017). Here in this paper, based on these latest advances in the field of viral ecology and genomics, we try to imagine how a comprehensive host-resolved mapping of the viral sequence space will enable researchers to address long-standing viral ecology questions in an unprecedented way. We present these as three stories relating how we picture (and/or wish) viral ecology research could be conducted 10 years from now.