Viral shunt

The microbial loop acts as a pathway and connection between different relationships in an ecosystem. The microbial loop connects the pool of DOM to the rest of the food web, specifically various microorganisms in the water column.[17] This allows for constant cycling of this dissolved organic matter. Stratification of the water column due to the pycnocline affects the amount of dissolved carbon in the upper mixing layer, and the mechanisms shows seasonal variation.

The microbial loop is based on micro-interactions between different trophic levels of microbes and organisms. When nutrients enter the microbial loop, they tend to remain in the photic zone longer, due to the location, and slow sinking rates of microbes. Eventually, through varying processes,[18] DOM, through use of available nutrients, is produced by phytoplankton, as well as consumed by bacteria.[17] Bacteria utilize this DOM, yet are then preyed on by larger microbes, such as microflagellates, which helps to regenerate nutrients.[17]

Viruses tend to outnumber bacterial abundance by about ten times and phytoplankton by about a hundred times in the upper mixing layer[19] and bacterial abundance tends to decrease with depth, while phytoplankton remain closer to shallow depths.[20] The effects of the viral shunt are more pronounced in the upper mixing layer. Viruses found can be non-specific (broad host range), abundant, and can infect all forms of microbes. Viruses are a magnitude higher in abundance in almost all aquatic locations compared to their microbial hosts, allowing high rates/levels of microbial infection.

The impact of the viral shunt varies seasonally as many microbes show seasonal abundance maximums in temperate and oligotrophic waters during different times of the year, meaning viral abundance also varies with season.[21]

The viral shunt may result in increased respiration from the system. It also helps export carbon through the biological pump. This is a very significant process as approximately 3 gigatonnes of carbon may be sequestered per year due to lysed and virus-infected cells having faster sinking rates.[22] The biological pump has an important role at sequestering carbon to the benthic zone, thereby impacting global carbon cycles, budget, and even affecting temperature. Crucial nutrients, such as nitrogen, phosphorus, cellular components, such as amino acids and nucleic acids, would be sequestered through the biological pump in the event of cells sinking.[23] Viral shunting helps increase the efficiency of the biological pump by mostly altering the proportion of carbon that is exported to deep water (such as the recalcitrant carbon-rich cell walls from virally lysed bacteria) in a process called the Shunt and Pump.[23] This allows the crucial nutrients to be retained in the surface waters. Concurrently, a more efficient biological pump also results in an increase in nutrient influx towards the surface, which is beneficial to primary production, especially in more oligotrophic region. Despite viruses being in the smallest scales of biology, the viral shunt pathway has a profound effect on food webs across marine environments as well as on a more macro scale on the global carbon budget.

Viral shunt influences carbon cycling in marine environments by infecting microbes and redirecting the type of organic matter that enters the carbon pool. Phototrophs constitute a large population of primary production in marine environments and are responsible for a large flux of carbon entering the carbon cycle in marine environments.[24] However, bacteria, zooplankton and phytoplankton, (and other free-floating organisms) also contribute to the global marine carbon cycle.[25] When these organisms eventually die and decompose, their organic matter either enters the pool of particulate organic matter (POM) or dissolved organic matter (DOM).[23] Much of the POM generated is composed of carbon-rich complex structures that is unable to be decomposed effectively by most prokaryotes and archaea in the oceans. Export of carbon-rich POM from the upper surface layer to deep oceans causes increased efficiency of the biological pump due to a higher carbon-to-nutrient ratio.[23]

DOM is smaller and tends to stay mixed within the euphotic zone of the water column. The labile DOM is easier for microbes to digest and recycle, allowing incorporation of carbon into biomass.  As microbial biomass increases due to the incorporation of DOM, most microbial populations such as heterotrophic bacteria will be preyed on by organisms at higher trophic levels such as grazers or zooplankton.[5] However, about 20 to 40 percent of the bacterial biomass (with similar and relative amounts of eukaryotes) will become infected by viruses.[26] The effect of this energy flow results is less carbon entering higher trophic levels and a significant portion being respired and cycled between the microbes in the water column.[27]

Based on this mechanism, as more carbon enters the DOM pool, most of the matter is used for increasing microbial biomass. When the viral shunt kills a portion of these microbes, it decreases the amount of carbon that gets transferred to higher trophic levels by converting it back to DOM and POM.[27] Most of the generated POM is recalcitrant and will eventually make it down to the deep oceans where it accumulates.[23] The resulting DOM that re-enters the DOM pool to be used by phototrophs and heterotrophs is less than the amount of DOM that originally entered the DOM pool. This phenomenon is due to the unlikeliness of organic matter being 100% DOM after a viral lytic infection.[5]

Viral shunt is a big component to the cycling of nitrogen in marine environments. Nitrogen gas from the atmosphere gets dissolved into surface of the water. Nitrogen fixing cyanobacteria, such as Trichodesmium and Anabaena, convert the nitrogen gas (N₂) into ammonium (NH₄⁺) for microbes to use. The process of converting nitrogen gas to ammonia (and related nitrogen compounds) is called nitrogen fixation. The process of uptake of ammonium by microbes to be used in protein synthesis is called nitrogen assimilation. The viral shunt causes mass death of heterotrophic bacteria. The decomposition of these microbes releases particulate organic nitrogen (PON) and dissolved organic nitrogen (DON), which either stay in the upper mixing layer or sink to the deeper parts of the ocean.[28] In the deep ocean, PON and DON are converted back into ammonium by remineralisation. This ammonium can be used by deep ocean microbes, or undergo nitrification and be oxidized into nitrites and nitrates.[28] The sequence of nitrification is:

NH₄⁺ → NO₂⁻ → NO₃⁻

Dissolved nitrates can be consumed by microbes to become re-assimilated, or revert in nitrogen gas by denitrification. The resultant nitrogen gas can then be fixed back into ammonium for assimilation or exit the ocean reservoir and back into atmosphere.[28]

Viral shunt is also able to increase ammonium production.[29] The basis for this claim is based on fluctuating carbon-to-nitrogen (C:N in atoms) ratios caused by the viral shunt. Susceptible microorganisms such as bacteria in the water column are more likely to be infected and killed off by viruses, releasing DOM and nutrients containing carbon and nitrogen (about 4C:1N). The remaining microbes that are still alive are assumed to be resistant to that viral infection episode. The DOM and nutrients generated from the death and lysis of susceptible microorganisms are available for uptake by virus-resistant eukaryotes and prokaryotes. The resistant-bacteria uptakes and utilizes the DOC, regenerate ammonium, thereby lowering the C:N ratio. When C:N ratios decrease, ammonium (NH₄⁺) regeneration increases.[30] The bacteria begin converting the dissolved nitrogen into ammonium, which can be used by phytoplankton for growth and biological production. As phytoplankton use up the ammonium (and subsequently limited by nitrogen-species), the C:N ratio begins increasing again and NH₄⁺ regeneration slows down.[29] The phytoplankton also shows enhanced growth rates due to uptake of ammonium.[29][31] The viral shunt is continuously causing changes to the C:N ratio, affecting the composition and presence of nutrients at any given time.

A significant fraction of the world's oceans are iron limited,[32] thus the regeneration of iron-nutrients is an important process that is needed for sustaining an ecosystem in this environment. Viral infection of microorganisms (mostly heterotrophs and cyanobacteria) is hypothesized to be an important process in the maintenance of high-nutrient low chlorophyll (HNLC) marine environments.[33] The viral shunt plays a key role in releasing assimilated iron back into the microbial loop which helps sustain primary productivity in these ecosystems.[34][35] Dissolved iron usually binds with organic matter to form an organic-iron complex that enhances bioavailability of this nutrient to plankton.[36] Some species of bacteria and diatoms are capable of high uptake rates of these organic-iron complexes.[33] Continued viral activity by the viral shunt helps sustain growing ecosystems in iron-limited HNLC regions.[33]

There are many different microbes present in aquatic communities. Phytoplankton, specifically Picoplankton, are the most important organism in this microbial loop. They provide a foundation as primary producers; they are responsible for the majority of primary production in the ocean and around 50% of primary production of the entire planet.[43]

Generally, marine microbes are useful in the microbial loop due to their physical characteristics. They are small, and have high surface area to biomass ratios, allowing for high rates of uptake, even in low concentrations of nutrients. The microbial loop is considered a sink for nutrients such as carbon. Their small size allows for more efficient cycling of nutrients and organic matter compared to larger organisms.[44] Additionally, microbes tend to be pelagic, floating freely in photic surface waters, before sinking down to deeper layers of the ocean. The microbial food web is important because it is the direct target of the viral shunt pathway and all subsequent effects are based on how the viruses affect their microbial hosts. Infection of these microbes through lysis or latent infection have a direct impact of the nutrients recycled, availability, and export within the microbial loop, which can have resonating effects throughout the trophic levels.

Shallow water hydrothermal vents found in the Mediterranean Sea contain a diverse and abundant microbial community known as “hotspots”.[45] These communities also contain temperate viruses. An increase in these viruses can cause large mortality of vent microbes, thereby reducing chemoautotrophic carbon production, while at the same time enhancing the metabolism of heterotrophs through recycling of DOC.[46] These results indicate a tight coupling of viruses and primary/secondary production found in these hydrothermal vent communities, as well as having a major effect on the food web energy transfer efficiency to higher trophic levels.