 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 eukaryotic plankton .
Direct efforts to estimate the viral shunt are rare, with most indirectly determining virus turnover rates and from this inferring virus-mediated elemental release. While several approaches exist to estimate virus production , currently favoured approaches all depend on the same steps: dilution of samples and estimates of virus reoccurrence . Application of these approaches in recent years has begun to provide a broad overview of the variability of virus effects across different oceanic realms [40-43], with all observations pointing to differing constraints on virus activities in different systems.
In addition, recent evidence suggests that viral lysis of microbes changes the relative distribution of dissolved organic matter with many indirect effects in ocean ecosystems. For example, viral lysis of microbes shifts organic matter from cells into dissolved and particular organic pools. The type of organic material released in viral lysis includes a spectrum of molecules ranging from bio-available (i.e. “labile”) to recalcitrant (see Figure 2) and may be dependent as much on the location of the lytic event as the players involved . In the deep ocean, the fate of virus-released organic matter remains a mystery, but this process may drive the generation of the ancient organic carbon measured by marine chemists . Moreover, it is known that virus activity may drive the formation of marine snow by releasing “sticky” components from within cells , while at the same time disaggregating particles through cell lysis . Overall, we still know little about how virus activity changes the character of dissolved organic matter, the effect of viruses on carbon distribution (i.e. fixation, respiration, mineralization and export) in marine systems, despite the potential impacts on global budgets on both short-term and geological time scales.
In addition to direct effects, the differential conversion of cellular material by viruses into a spectrum of dissolved organic material may indirectly affect the growth of microb