Losses of corals worldwide emphasize the need to understand what drives reef decline. Stressors such as overfishing and nutrient pollution may reduce resilience of coral reefs by increasing coral–algal competition and reducing coral recruitment, growth and survivorship. Such effects may themselves develop via several mechanisms, including disruption of coral microbiomes. Here we report the results of a 3-year field experiment simulating overfishing and nutrient pollution. These stressors increase turf and macroalgal cover, destabilizing microbiomes, elevating putative pathogen loads, increasing disease more than twofold and increasing mortality up to eightfold. Above-average temperatures exacerbate these effects, further disrupting microbiomes of unhealthy corals and concentrating 80% of mortality in the warmest seasons. Surprisingly, nutrients also increase bacterial opportunism and mortality in corals bitten by parrotfish, turning normal trophic interactions deadly for corals. Thus, overfishing and nutrient pollution impact reefs down to microbial scales, killing corals by sensitizing them to predation, above-average temperatures and bacterial opportunism.

Coral reefs occur in nutrient-poor shallow waters, constitute biodiversity and productivity hotspots, and are threatened by anthropogenic disturbance. This Review provides an introduction to coral reef virology and emphasizes the links between viruses, coral mortality and reef ecosystem decline. We describe the distinctive benthic-associated and water-column- associated viromes that are unique to coral reefs, which have received less attention than viruses in open-ocean systems. We hypothesize that viruses of bacteria and eukaryotes dynamically interact with their hosts in the water column and with scleractinian (stony) corals to influence microbial community dynamics, coral bleaching and disease, and reef biogeochemical cycling. Last, we outline how marine viruses are an integral part of the reef system and suggest that the influence of viruses on reef function is an essential component of these globally important environments.

Experiments were conducted to investigate spatiotemporal patterns in lytic and lysogenic viral infection using water samples collected on the Canadian Arctic Shelf, southern Beaufort Sea. Viral production (VP) and viralinduced mortality of bacteria (VMB) were determined using a viral reduction approach during a full seasonal cycle, while the percentage of lysogenic bacteria (PLB) in spring and summer was determined in virus-reduced samples by induction with mitomycin C. Overall, VP (range: 0.3 3 10 8 -77 3 10 8 viruses L 21 d 21 ), VMB (range: 0.2 3 10 7 -43 3 10 7 bacteria L 21 d 21 ), and PLB (range: 4-38%) displayed marked spatiotemporal variations concomitant with changes in chlorophyll a, bacterial abundance, and production. Highest VP and VMB occurred in summer when the water was warmest, stratified, and most productive, and when viruses removed up to 29% of bacterial standing stock d 21 and released up to 4.3 mg of organic carbon L 21 d 21 . In contrast, the highest PLB occurred in spring when the water was colder, well mixed, and oligotrophic. Correlative and regression analyses indicated viral lytic and lysogenic variables were significantly coupled with chlorophyll a and the abundance, production, and growth rate of bacteria, implying that viral lytic and lysogenic lifestyles were dependent on system productivity. Furthermore, lytic VP and the proportion of lysogenized bacteria were inversely related, suggesting a dynamic interplay between viral infection pathways. Lytic infection was more pronounced when system productivity was high, while lysogeny prevailed when system productivity was low. These data demonstrate the important role of viruses in bacterial mortality and carbon cycling in the Arctic Ocean, and show how their effect is influenced by trophic status.

1. Samples from 16 lakes in central (n = 145) and western (n = 12) North America, the coastal northeast Pacific (n = 302) and the western Canadian Arctic Oceans (n = 142) were collected and analysed for viral, bacterial and cyanobacterial abundances and chlorophyll-a concentration.2. Viral abundance was significantly different among the environments. It was highest in the coastal Pacific Ocean and lowest in the coastal Arctic Ocean. The abundances of bacteria and cyanobacteria as well as chlorophyll-a concentrations also differed significantly among the environments, with both bacterial abundance and chlorophyll-a concentration highest in lakes. As a consequence, the association of these variables with viral abundance varied among the environments. 3. Discriminant analyses with the abundance data indicated that the marine and freshwater environments were predictably different from each other. Multiple-regression analysis included bacterial and cyanobacterial abundances, and chlorophyll-a concentration as significant variables in explaining viral abundance in lakes. In regression models for the coastal Pacific Ocean, bacterial and cyanobacterial abundances were significant variables, and for the coastal Arctic Ocean viral abundance was predicted by bacterial abundance and chlorophyll-a concentration. 4. The relationship of viral and bacterial abundance differed between the investigated freshwater and marine environments, probably because of differences in viral production and loss rates. However, freshwaters had fewer viruses compared to bacteria, despite previously documented higher burst sizes and frequencies of infected cells, suggesting that loss rates may be more important in lakes. 5. Together, these findings suggest that there are different drivers of viral abundance in different aquatic environments, including lakes and oceans.

For many laboratories, flow cytometry is becoming the routine method for quantifying viruses in aquatic systems because of its high reproducibility, high sample throughput, and ability to distinguish several subpopulations of viruses. Comparison of viral counts between flow cytometry and epifluorescence microscopy typically shows slopes that are statistically not distinguishable from 1, thus confirming the usefulness of flow cytometry. Here we describe in detail all steps in the procedure, discuss potential problems, and offer solutions.