that defy much of the conventional wisdom about viral life history (e.g. the discovery of “giant” algal-infecting viruses [18,19] and even viruses that exploit other viruses ). Altogether, it is well established that a diverse reservoir of viruses infect and lyse bacteria, archaea and microeukaryotes at the base of the ocean's food web [2,21]. Despite the growing literature on viruses of microbes, we remain relatively poorly informed concerning the dynamic, ecological effects of virus infection of marine microbes. In this report, we focus on the functional role of viruses within oceanic waters. In doing so, we highlight knowns, unknowns and challenges in three areas: (i) the role of ocean viruses in shaping microbial community composition; (ii) the role of ocean viruses in determining carbon and nutrient availability; (iii) modelling efforts to link viral infection of microbes with ecosystem-scale consequences.
Viral infection and microbial community composition
Viruses, in general, and viruses of microbes, in particular, infect a subset of available hosts in any environment. The subset of hosts that a virus typically infects is narrower than the range of microbes that are typically consumed by a grazer species (e.g. a protist or zooplankton). However, there is evidence that viruses of microbes can infect hosts from different species or even different genera. For example, some cyanophages can infect different strains within the same cyanobacteria species, either Synechococcus or Prochlorococcus, as well as strains of different cyanobacterial genera . The quantitative study of the host-range of viruses of microbes is in its infancy [22-26], an issue we return to later. Successful viral infections can lead to lysis of hosts as well as the conversion of hosts into lysogens where the viral genome is integrated into that of the host, subsequently altering host physiology [2,21,27]. Lytic viral infection of microbes and its effects are our primary concerns here.
Viral lysis of microbes is thought to have direct effects on microbial community composition. Ostensibly, viral lysis should decrease the abundance of specific microbial lineages that are targeted by viral infection . Estimates of bacterial-induced mortality suggest that viruses are, in some cases, as important as grazers in selectively killing microbes [29,30], whereas, in other cases, they may be the dominant source of microbial mortality [31,32]. The depletion of susceptible bacteria leads to the possibility of dynamic fluctuations in viral and microbial populations, a result predicted by simple population models . Nonetheless, direct evidence for coupled oscillations between virus-microbe systems in the oceans is limited. The reasons are complex, but likely due to the fact that the emergence of new (or previously rare) viral subtypes occurs frequently and rapidly [34-37]. The changing identities of strains and their populations can make it difficult to infer the consequences of virus-microbe interactions. Hence, paradoxically, the seemingly most apparent consequences of viral-induced lysis of microbes may be hard to observe in practice. We anticipate that observations of virus and microbial abundances in situ via genomic and metagenomic methods, with improved time-scale resolution, will provide direct evidence for specific functional relationships between viruses and microbial hosts.
Viral infection and the availability of carbon and nutrients
Virus-induced mortality of microbes has direct effects on ecosystem function. Lysis of microbes involves the release of organic carbon and other nutrients back into the environment. This redirection is known as the viral shunt . The viral shunt denotes the fact that cellular materials released as particular or dissolved organic material are not directly available for utilization by organisms from higher trophic levels (e.g. plankton and fish) (see Figure 1) but are primarily utilized by predominantly heterotrophic bacteria, although some efforts have shown nutrients released in this manner to be rapidly assimilated by eukaryo