Virus-Host Interactions Drive Contrasting Bacterial Diel Dynamics in the Ocean.

Marine organisms perform a sea of diel rhythmicity. Planktonic diel dynamics have been shown to be driven by light, energy resources, circadian rhythms, and the coordinated coupling of photoautotrophs and heterotrophic bacterioplankton. Here, we explore the diel fluctuation of viral production and decay and their impact on the total and active bacterial community in the coastal and open seawaters of the South China Sea.

The smallest in the deepest: the enigmatic role of viruses in the deep biosphere.

It is commonly recognized that viruses control the composition, metabolism, and evolutionary trajectories of prokaryotic communities, with resulting vital feedback on ecosystem functioning and nutrient cycling in a wide range of ecosystems. Although the deep biosphere has been estimated to be the largest reservoir for viruses and their prokaryotic hosts, the biology and ecology of viruses therein remain poorly understood. The deep virosphere is an enigmatic field of study in which many critical questions are still to be answered.

Reduced bacterial mortality and enhanced viral productivity during sinking in the ocean.

Particle sinking is an important process in the ocean, influencing the biogeochemical cycle and driving the long-term preservation of carbon into the deep sea via the biological pump. However, as an important component of marine ecosystems, the role of viruses during sinking is still poorly understood. Therefore, we performed a series of transplantation experiments in the South China Sea to simulate environmental changes during sinking and investigate their effects on viral eco-dynamics and life strategy.

Viral Lysis Alters the Optical Properties and Biological Availability of Dissolved Organic Matter Derived from Picocyanobacteria.

Phytoplankton contribute almost half of the world's total primary production. The exudates and viral lysates of phytoplankton are two important forms of dissolved organic matter (DOM) in aquatic environments and fuel heterotrophic prokaryotic metabolism. However, the effect of viral infection on the composition and biological availability of phytoplankton-released DOM is poorly understood.

Aquatic Viruses and Climate Change.

The viral component in aquatic systems clearly needs to be incorporated into future ocean and inland water climate models. Viruses have the potential to influence carbon and nutrient cycling in aquatic ecosystems significantly. Changing climate likely has both direct and indirect influence on virus-mediated processes, among them an impact on food webs, biogeochemical cycles and on the overall metabolic performance of whole ecosystems.

Viral control of biomass and diversity of bacterioplankton in the deep sea.

Viral abundance in deep-sea environments is high. However, the biological, ecological and biogeochemical roles of viruses in the deep sea are under debate. In the present study, microcosm incubations of deep-sea bacterioplankton (2,000 m deep) with normal and reduced pressure of viral lysis were conducted in the western Pacific Ocean.

Effects of elevated pCO2 and feeding on net calcification and energy budget of the Mediterranean cold-water coral Madrepora oculata.

Ocean acidification is a major threat to calcifying marine organisms such as deep-sea cold-water corals (CWCs), but related knowledge is scarce. The aragonite saturation threshold (Ω) for calcification, respiration and organic matter fluxes were investigated experimentally in the Mediterranean Madrepora oculata Over 10 weeks, colonies were maintained under two feeding regimes (uptake of 36.75 and 7.

Colonization and release processes of viruses and prokaryotes on artificial marine macroaggregates.

Marine organic aggregates are sites of high of viral accumulation; however, still little is known about their colonization processes and interactions with their local bacterial hosts. By taking advantage of a novel approach (paramagnetic functionalized microsphere method) to create and incubate artificial macroaggregates, we examined the small-scale movements of viruses and bacteria between such marine snow particles and the surrounding water. The examination of the codynamics of both free-living and attached viral and bacterial abundance, over 12 hours of incubation in virus-free water, suggests that aggregates are rather comparable to viral factories than to viral traps where a significant part of the virions production might be locally diverted to the water column.

Comparison of deep-water viromes from the atlantic ocean and the mediterranean sea.

The aim of this study was to compare the composition of two deep-sea viral communities obtained from the Romanche Fracture Zone in the Atlantic Ocean (collected at 5200 m depth) and the southwest Mediterranean Sea (from 2400 m depth) using a pyro-sequencing approach. The results are based on 18.7% and 6.

Interactive effects of viral and bacterial production on marine bacterial diversity.

A general model of species diversity predicts that the latter is maximized when productivity and disturbance are balanced. Based on this model, we hypothesized that the response of bacterial diversity to the ratio of viral to bacterial production (VP/BP) would be dome-shaped. In order to test this hypothesis, we obtained data on changes in bacterial communities (determined by terminal restriction fragment length polymorphism of 16S rRNA gene) along a wide VP/BP gradient (more than two orders of magnitude), using seawater incubations from NW Mediterranean surface waters, i.

End of the century pCO₂ levels do not impact calcification in Mediterranean cold-water corals.

Ocean acidification caused by anthropogenic uptake of CO₂ is perceived to be a major threat to calcifying organisms. Cold-water corals were thought to be strongly affected by a decrease in ocean pH due to their abundance in deep and cold waters which, in contrast to tropical coral reef waters, will soon become corrosive to calcium carbonate. Calcification rates of two Mediterranean cold-water coral species, Lophelia pertusa and Madrepora oculata, were measured under variable partial pressure of CO₂ (pCO₂) that ranged between 380 µatm for present-day conditions and 930 µatm for the end of the century.

Response of bacterioplankton to a glucose gradient in the absence of lysis and grazing.

Bacterial utilization of dissolved organic matter plays an important role in marine carbon cycling. In this study, the response of bacterioplankton to a gradient of carbon (glucose) addition was investigated experimentally in a subtropical coastal environment in the absence of top-down control by viruses and flagellates. Bacterial abundance and production were stimulated by glucose addition corresponding to a gradient of glucose.

Effects of sodium azide on the abundance of prokaryotes and viruses in marine samples.

Flow cytometry is set to become the standard method for enumerating prokaryotes and viruses in marine samples. However, the samples need to be flash-frozen in liquid nitrogen directly after aldehyde fixation. Because liquid nitrogen may not always be available, we tested the potential of sodium azide as a preservative for prokaryotes and viruses in marine samples as a possible alternative.

Development of phoH as a novel signature gene for assessing marine phage diversity.

Phages play a key role in the marine environment by regulating the transfer of energy between trophic levels and influencing global carbon and nutrient cycles. The diversity of marine phage communities remains difficult to characterize because of the lack of a signature gene common to all phages. Recent studies have demonstrated the presence of host-derived auxiliary metabolic genes in phage genomes, such as those belonging to the Pho regulon, which regulates phosphate uptake and metabolism under low-phosphate conditions.

Association of marine viral and bacterial communities with reference black carbon particles under experimental conditions: an analysis with scanning electron, epifluorescence and confocal laser scanning microscopy.

Black carbon (BC), the product of incomplete combustion of fossil fuels and biomass, constitutes a significant fraction of the marine organic carbon pool. However, little is known about the possible interactions of BC and marine microorganisms. Here, we report the results of experiments using a standard reference BC material in high concentrations to investigate basic principles of the dynamics of natural bacterial and viral communities with BC particles.

Randomly amplified polymorphic DNA reveals tight links between viruses and microbes in the bathypelagic zone of the Northwestern Mediterranean Sea.

The study site located in the Mediterranean Sea was visited eight times in 2005 and 2006 to collect samples from the epipelagic (5 m), mesopelagic (200 m, 600 m), and bathypelagic (1,000 m, 2,000 m) zones. Randomly amplified polymorphic DNA PCR (RAPD-PCR) analysis was used to obtain fingerprints from microbial and viral size fractions using two different primers each. Depending on the primer used, the number of bands in the water column varied between 12 to 24 and 6 to 19 for the microbial size fraction and between 16 to 26 and 8 to 22 for the viral size fraction.

Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean.

The biological pump is a process whereby CO(2) in the upper ocean is fixed by primary producers and transported to the deep ocean as sinking biogenic particles or as dissolved organic matter. The fate of most of this exported material is remineralization to CO(2), which accumulates in deep waters until it is eventually ventilated again at the sea surface. However, a proportion of the fixed carbon is not mineralized but is instead stored for millennia as recalcitrant dissolved organic matter.

Trade-offs between competition and defense specialists among unicellular planktonic organisms: the "killing the winner" hypothesis revisited.

A trade-off between strategies maximizing growth and minimizing losses appears to be a fundamental property of evolving biological entities existing in environments with limited resources. In the special case of unicellular planktonic organisms, the theoretical framework describing the trade-offs between competition and defense specialists is known as the "killing the winner" hypothesis (KtW). KtW describes how the availability of resources and the actions of predators (e.

Assessing niche separation among coexisting Limnohabitans strains through interactions with a competitor, viruses, and a bacterivore.

We investigated potential niche separation in two closely related (99.1% 16S rRNA gene sequence similarity) syntopic bacterial strains affiliated with the R-BT065 cluster, which represents a subgroup of the genus Limnohabitans. The two strains, designated B4 and D5, were isolated concurrently from a freshwater reservoir.

Viral control of bacterial biodiversity--evidence from a nutrient-enriched marine mesocosm experiment.

We demonstrate here results showing that bottom-up and top-down control mechanisms can operate simultaneously and in concert in marine microbial food webs, controlling prokaryote diversity by a combination of viral lysis and substrate limitation. Models in microbial ecology predict that a shift in the type of bacterial growth rate limitation is expected to have a major effect on species composition within the community of bacterial hosts, with a subsequent shift in the composition of the viral community. Only moderate effects would, however, be expected in the absolute number of coexisting virus-host pairs.

Viral and flagellate control of prokaryotic production and community structure in offshore Mediterranean waters.

A dilution and size fractionation approach was used to study the separate and combined effects of viruses and flagellates on prokaryotic production ([(3)H]leucine incorporation) and community composition (16S rRNA gene PCR and denaturing gradient gel electrophoresis [DGGE]) in the upper mixed layer and the deep chlorophyll maximum in the offshore Mediterranean Sea. Four experiments were established using differential filtration: a resource control without predators (C treatment), treatment in the presence of viruses (V treatment), treatment in the presence of flagellates (F treatment), and treatment in the presence of both predators (VF treatment). The V and VF treatments increased prokaryotic abundance (1.

Annual changes of bacterial mortality due to viruses and protists in an oligotrophic coastal environment (NW Mediterranean).

The impact of viruses and protists on bacterioplankton mortality was examined monthly during 2 years (May 2005-April 2007) in an oligotrophic coastal environment (NW Mediterranean Sea). We expected that in such type of system, (i) bacterial losses would be caused mainly by protists, and (ii) lysogeny would be an important type of virus-host interaction. During the study period, viruses and grazers together were responsible for 50.

Dynamics and diversity of newly produced virioplankton in the North Sea.

Viral diversity has been studied in a variety of marine habitats and spatial and seasonal changes have been documented. Most of the bacteriophages are considered host specific and are thought to affect fast growing prokaryotic phylotypes more than slow growing ones. We hypothesized that viral infection and consequently, lysis occurs in pulses with only a few prokaryotic phylotypes lysed at any given time.