Temperate infection in a virus-host system previously known for virulent dynamics.

The blooming cosmopolitan coccolithophore Emiliania huxleyi and its viruses (EhVs) are a model for density-dependent virulent dynamics. EhVs commonly exhibit rapid viral reproduction and drive host death in high-density laboratory cultures and mesocosms that simulate blooms. Here we show that this system exhibits physiology-dependent temperate dynamics at environmentally relevant E. huxleyi host densities rather than virulent dynamics, with viruses switching from a long-term non-lethal temperate phase in healthy hosts to a lethal lytic stage as host cells become physiologically stressed. Using this system as a model for temperate infection dynamics, we present a template to diagnose temperate infection in other virus-host systems by integrating experimental, theoretical, and environmental approaches. Finding temperate dynamics in such an established virulent host-virus model system indicates that temperateness may be more pervasive than previously considered, and that the role of viruses in bloom formation and decline may be governed by host physiology rather than by host-virus densities.

Bacterial community composition responds to changes in copepod abundance and alters ecosystem function in an Arctic mesocosm study.

Combining a minimum food web model with Arctic microbial community dynamics, we have suggested that top-down control by copepods can affect the food web down to bacterial consumption of organic carbon. Pursuing this hypothesis further, we used the minimum model to design and analyse a mesocosm experiment, studying the effect of high (+Z) and low (-Z) copepod density on resource allocation, along an organic-C addition gradient. In the Arctic, both effects are plausible due to changes in advection patterns (affecting copepods) and meltwater inputs (affecting carbon). The model predicts a trophic cascade from copepods via ciliates to flagellates, which was confirmed experimentally. Auto- and heterotrophic flagellates affect bacterial growth rate and abundance via competition for mineral nutrients and predation, respectively. In +Z, the model predicts low bacterial abundance and activity, and little response to glucose; as opposed to clear glucose consumption effects in -Z. We observed a more resilient bacterial response to high copepods and demonstrate this was due to changes in bacterial community equitability. Species able to use glucose to improve their competitive and/or defensive properties, became predominant. The observed shift from a SAR11-to a Psychromonodaceae - dominated community suggests the latter was pivotal in this modification of ecosystem function. We argue that this group used glucose to improve its defensive or its competitive abilities (or both). Adding such flexibility in bacterial traits to the model, we show how it creates the observed resilience to top-down manipulations observed in our experiment.

Simple models combining competition, defence and resource availability have broad implications in pelagic microbial food webs.

In food webs, interactions between competition and defence control the partitioning of limiting resources. As a result, simple models of these interactions contain links between biogeochemistry, diversity, food web structure and ecosystem function. Working at hierarchical levels, these mechanisms also produce self-similarity and therefore suggest how complexity can be generated from repeated application of simple underlying principles. Reviewing theoretical and experimental literature relevant to the marine photic zone, we argue that there is a wide spectrum of phenomena, including single cell activity of prokaryotes, microbial biodiversity at different levels of resolution, ecosystem functioning, regional biogeochemical features and evolution at different timescales; that all can be understood as variations over a common principle, summarised in what has been termed the 'Killing-the-Winner' (KtW) motif. Considering food webs as assemblages of such motifs may thus allow for a more integrated approach to aquatic microbial ecology.

Linking bacterial community structure to advection and environmental impact along a coast-fjord gradient of the Sognefjord, western Norway.

Here we present novel data on bacterial assemblages along a coast-fjord gradient in the Sognefjord, the deepest (1308 m) and longest (205 km) ice-free fjord in the world. Data were collected on two cruises, one in November 2012, and one in May 2013. Special focus was on the impact of advective processes and how these are reflected in the autochthonous and allochthonous fractions of the bacterial communities. Both in November and May bacterial community composition, determined by Automated Ribosomal Intergenic Spacer Analyses (ARISA), in the surface and intermediate water appeared to be highly related to bacterial communities originating from freshwater runoff and coastal water, whereas the sources in the basin water were mostly unknown. Additionally, the inner part of the Sognefjord was more influenced by side-fjords than the outer part, and changes in bacterial community structure along the coast-fjord gradient generally showed higher correlation with environmental variables than with geographic distances. High resolution model simulations indicated a surprisingly high degree of temporal and spatial variation in both current speed and direction. This led to a more episodic/discontinuous horizontal current pattern, with several vortices (10-20 km wide) being formed from time to time along the fjord. We conclude that during periods of strong wind forcing, advection led to allochthonous species being introduced to the surface and intermediate layers of the fjord, and also appeared to homogenize community composition in the basin water. We also expect vortices to be active mixing zones where inflowing bacterial populations on the southern side of the fjord are mixed with the outflowing populations on the northern side. On average, retention time of the fjord water was sufficient for bacterial communities to be established.

Micromonas versus virus: New experimental insights challenge viral impact.

Viruses have recurrently been hypothesized as instrumental in driving microbial population diversity. Nonetheless, viral mediated co-existence of r/k-strategists, predicted in the Killing-the-Winner (KtW) hypothesis, remains controversial and demands empirical evidence. Therefore, we measured the life strategy parameters that characterize the relevant system Micromonas-Micromonas Virus (MicV). A large number of host and viral strains (37 and 17, respectively) were used in a total of 629 cross-infectivity tests. Algal and viral abundances were monitored by flow cytometry and used to calculate values of growth rate, resistance capacity, and viral production. Two main assumptions of the KtW model, namely (1) a resistance-associated cost on growth and (2) a negative correlation between resistance and viral production capacity, were mildly observed and lacked statistical significance. Micromonas strains infected by more MicV strains presented higher lysis and viral production rates as the number of infectious virus strains increased, suggesting a 'one-gate' regulation of infection in this system. MicV strains demonstrated a vast range of virion production capacity, which unexpectedly grew with increasing host-range. Overall, the significant trends observed in here demonstrate strong co-interactions at different levels between Micromonas and MicV populations, however, the role of viruses as major driving force in phytoplankton fitness wasn't explicitly observed.

Linking internal and external bacterial community control gives mechanistic framework for pelagic virus-to-bacteria ratios.

For more than 25 years, virus-to-bacteria ratios (VBR) have been measured and interpreted as indicators of the importance of viruses in aquatic ecosystems, yet a generally accepted theory for understanding mechanisms controlling VBR is still lacking. Assuming that the denominator (total bacterial abundance) is primarily predator controlled, while viral lysis compensates for host growth rates exceeding this grazing loss, the numerator (viral abundance) reflects activity differences between prokaryotic hosts. VBR is then a ratio between mechanisms generating structure within the bacterial community and interactions between different plankton functional types controlling bacterial community size. We here show how these arguments can be formalized by combining a recently published model for co-evolutionary host-virus interactions, with a previously published "minimum" model for the microbial food web. The result is a framework where viral lysis links bacterial diversity to microbial food web structure and function, creating relationships between different levels of organization that are strongly modified by organism-level properties such as cost of resistance.

Fractal Hypothesis of the Pelagic Microbial Ecosystem-Can Simple Ecological Principles Lead to Self-Similar Complexity in the Pelagic Microbial Food Web?

Trophic interactions are highly complex and modern sequencing techniques reveal enormous biodiversity across multiple scales in marine microbial communities. Within the chemically and physically relatively homogeneous pelagic environment, this calls for an explanation beyond spatial and temporal heterogeneity. Based on observations of simple parasite-host and predator-prey interactions occurring at different trophic levels and levels of phylogenetic resolution, we present a theoretical perspective on this enormous biodiversity, discussing in particular self-similar aspects of pelagic microbial food web organization. Fractal methods have been used to describe a variety of natural phenomena, with studies of habitat structures being an application in ecology. In contrast to mathematical fractals where pattern generating rules are readily known, however, identifying mechanisms that lead to natural fractals is not straight-forward. Here we put forward the hypothesis that trophic interactions between pelagic microbes may be organized in a fractal-like manner, with the emergent network resembling the structure of the Sierpinski triangle. We discuss a mechanism that could be underlying the formation of repeated patterns at different trophic levels and discuss how this may help understand characteristic biomass size-spectra that hint at scale-invariant properties of the pelagic environment. If the idea of simple underlying principles leading to a fractal-like organization of the pelagic food web could be formalized, this would extend an ecologists mindset on how biological complexity could be accounted for. It may furthermore benefit ecosystem modeling by facilitating adequate model resolution across multiple scales.

Top-down and bottom-up control on bacterial diversity in a western Norwegian deep-silled fjord.

We investigated the relationship between viruses and co-occurring bacterial communities in the Sognefjord, a deep-silled fjord in Western Norway. A combination of flow cytometry and automated ribosomal intergenic spacer analysis (ARISA) was used to assess prokaryote and viral abundances, and bacterial diversity and community composition, respectively, in depth profiles and at two different sampling seasons (November and May). With one exception, bacterial diversity did not vary between samples regardless of depth or season. The virus and prokaryote abundances as well as bacterial community composition, however, varied significantly with season and depth, suggesting a link between the Sognefjord viral community and potential bacterial host community diversity. To our knowledge, these findings provide the first description of microbial communities in the unique Sognefjord ecosystem, and in addition are in agreement with the simple model version of the 'Killing the Winner' theory (KtW), which postulates that microbial community diversity is a feature that is essentially top-down controlled by viruses, while community composition is bottom-up controlled by competition for limiting growth substrates.

Contrasting response to nutrient manipulation in Arctic mesocosms are reproduced by a minimum microbial food web model.

A minimum mathematical model of the marine pelagic microbial food web has previously shown to be able to reproduce central aspects of observed system response to different bottom-up manipulations in a mesocosm experiment Microbial Ecosystem Dynamics (MEDEA) in Danish waters. In this study, we apply this model to two mesocosm experiments (Polar Aquatic Microbial Ecology (PAME)-I and PAME-II) conducted at the Arctic location Kongsfjorden, Svalbard. The different responses of the microbial community to similar nutrient manipulation in the three mesocosm experiments may be described as diatom-dominated (MEDEA), bacteria-dominated (PAME-I), and flagellated-dominated (PAME-II). When allowing ciliates to be able to feed on small diatoms, the model describing the diatom-dominated MEDEA experiment give a bacteria-dominated response as observed in PAME I in which the diatom community comprised almost exclusively small-sized cells. Introducing a high initial mesozooplankton stock as observed in PAME-II, the model gives a flagellate-dominated response in accordance with the observed response also of this experiment. The ability of the model originally developed for temperate waters to reproduce population dynamics in a 10°C colder Arctic fjord, does not support the existence of important shifts in population balances over this temperature range. Rather, it suggests a quite resilient microbial food web when adapted to in situ temperature. The sensitivity of the model response to its mesozooplankton component suggests, however, that the seasonal vertical migration of Arctic copepods may be a strong forcing factor on Arctic microbial food webs.

What difference does it make if viruses are strain-, rather than species-specific?

Theoretical work has suggested an important role of lytic viruses in controlling the diversity of their prokaryotic hosts. Yet, providing strong experimental or observational support (or refutation) for this has proven evasive. Such models have usually assumed "host groups" to correspond to the "species" level, typically delimited by 16S rRNA gene sequence data. Recent model developments take into account the resolution of species into strains with differences in their susceptibility to viral attack. With strains as the host groups, the models will have explicit viral control of abundance at strain level, combined with explicit predator or resource control at community level, but the direct viral control at species level then disappears. Abundance of a species therefore emerges as the combination of how many strains, and at what abundance, this species can establish in competition with other species from a seeding community. We here discuss how species diversification and strain diversification may introduce competitors and defenders, respectively, and that the balance between the two may be a factor in the control of species diversity in mature natural communities. These models can also give a dominance of individuals from strains with high cost of resistance; suggesting that the high proportion of "dormant" cells among pelagic heterotrophic prokaryotes may reflect their need for expensive defense rather than the lack of suitable growth substrates in their environment.

A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes.

Viral lysis of microbial hosts releases organic matter that can then be assimilated by nontargeted microorganisms. Quantitative estimates of virus-mediated recycling of carbon in marine waters, first established in the late 1990s, were originally extrapolated from marine host and virus densities, host carbon content and inferred viral lysis rates. Yet, these estimates did not explicitly incorporate the cascade of complex feedbacks associated with virus-mediated lysis. To evaluate the role of viruses in shaping community structure and ecosystem functioning, we extend dynamic multitrophic ecosystem models to include a virus component, specifically parameterized for processes taking place in the ocean euphotic zone. Crucially, we are able to solve this model analytically, facilitating evaluation of model behavior under many alternative parameterizations. Analyses reveal that the addition of a virus component promotes the emergence of complex communities. In addition, biomass partitioning of the emergent multitrophic community is consistent with well-established empirical norms in the surface oceans. At steady state, ecosystem fluxes can be probed to characterize the effects that viruses have when compared with putative marine surface ecosystems without viruses. The model suggests that ecosystems with viruses will have (1) increased organic matter recycling, (2) reduced transfer to higher trophic levels and (3) increased net primary productivity. These model findings support hypotheses that viruses can have significant stimulatory effects across whole-ecosystem scales. We suggest that existing efforts to predict carbon and nutrient cycling without considering virus effects are likely to miss essential features of marine food webs that regulate global biogeochemical cycles.

Optimal defense strategies in an idealized microbial food web under trade-off between competition and defense.

Trophic mechanisms that can generate biodiversity in food webs include bottom-up (growth rate regulating) and top-down (biomass regulating) factors. The top-down control has traditionally been analyzed using the concepts of "Keystone Predation" (KP) and "Killing-the-Winner" (KtW), predominately occuring in discussions of macro- and micro-biological ecology, respectively. Here we combine the classical diamond-shaped food web structure frequently discussed in KP analyses and the KtW concept by introducing a defense strategist capable of partial defense. A formalized description of a trade-off between the defense-strategist's competitive and defensive ability is included. The analysis reveals a complex topology of the steady state solution with strong relationships between food web structure and the combination of trade-off, defense strategy and the system's nutrient content. Among the results is a difference in defense strategies corresponding to maximum biomass, production, or net growth rate of invading individuals. The analysis thus summons awareness that biomass or production, parameters typically measured in field studies to infer success of particular biota, are not directly acted upon by natural selection. Under coexistence with a competition specialist, a balance of competitive and defensive ability of the defense strategist was found to be evolutionarily stable, whereas stronger defense was optimal under increased nutrient levels in the absence of the pure competition specialist. The findings of success of different defense strategies are discussed with respect to SAR11, a highly successful bacterial clade in the pelagic ocean.

A theoretical analysis of how strain-specific viruses can control microbial species diversity.

Pelagic prokaryote communities are often dominated by the SAR11 clade. The recent discovery of viruses infecting this clade led to the suggestion that such dominance could not be explained by assuming SAR11 to be a defense specialist and that the explanation therefore should be sought in its competitive abilities. The issue is complicated by the fact that prokaryotes may develop strains differing in their balance between competition and viral defense, a situation not really captured by present idealized models that operate only with virus-controlled "host groups." We here develop a theoretical framework where abundance within species emerges as the sum over virus-controlled strains and show that high abundance then is likely to occur for species able to use defense mechanisms with a low trade-off between competition and defense, rather than by extreme investment in one strategy or the other. The J-shaped activity-abundance community distribution derived from this analysis explains the high proportion low-active prokaryotes as a consequence of extreme defense as an alternative to explanations based on dormancy or death due to nutrient starvation.

Strong seasonality and interannual recurrence in marine myovirus communities.

The temporal community dynamics and persistence of different viral types in the marine environment are still mostly obscure. Polymorphism of the major capsid protein gene, g23, was used to investigate the community composition dynamics of T4-like myoviruses in a North Atlantic fjord for a period of 2 years. A total of 160 unique operational taxonomic units (OTUs) were identified by terminal restriction fragment length polymorphism (TRFLP) of the gene g23. Three major community profiles were identified (winter-spring, summer, and autumn), which resulted in a clear seasonal succession pattern. These seasonal transitions were recurrent over the 2 years and significantly correlated with progression of seawater temperature, Synechococcus abundance, and turbidity. The appearance of the autumn viral communities was concomitant with the occurrence of prominent Synechococcus blooms. As a whole, we found a highly dynamic T4-like viral community with strong seasonality and recurrence patterns. These communities were unexpectedly dominated by a group of persistently abundant viruses.

SAR11 viruses and defensive host strains.

Arising from Y. Zhao et al. Nature 494, 357­360 (2013). The recent findings of abundant SAR11 viruses by Zhao et al. are intriguing, and add new insight into the on-going discussion of why SAR11 bacteria are highly successful in the pelagic ocean. On the basis of high SAR11 virus abundance, Zhao et al. claim that SAR11 bacteria are competition specialists. Alternatively, we show here how their findings could be consistent with a dominance of defensive SAR11 strains. Considering their high abundance, understanding why SAR11 bacteria are so successful has important implications for the study of the pelagic ecosystem. There is a Reply to this Brief Communication Arising by Giovannoni, S., Temperton, B. & Zhao, Y. Nature 499, http://dx.doi.org/10.1038/nature12388 (2013).

Adding a cost of resistance description extends the ability of virus-host model to explain observed patterns in structure and function of pelagic microbial communities.

By adding a generic description of cost of resistance (COR) to the existing 'killing-the-winner' model, we show how this expands the model's explanatory power to include rank-abundance relationships in the host population. The model can predict a counter-intuitive relationship previously suggested in the literature, where abundant viruses are associated with rare hosts and vice versa. The model explains the observed dominance of slow-growing prokaryotes as the result of successful defence strategies, rather than as dormancy of hosts lacking essential substrates. In addition to these important conceptual aspects, the model is able to reproduce realistic values for virus : host ratios and partitioning of bacterial production between predatory loss and viral lysis. A high COR is also shown to increase the community's richness and Shannon diversity index. This model thus not only couples life strategies at the cellular level with system properties, but it also links the two system level properties of biogeochemical flows and diversity to each other. The model operates with host groups, and consequences for biodiversity when interpreting these groups in terms of species and strains are discussed.

An unaccounted fraction of marine biogenic CaCO3 particles.

Biogenic production and sedimentation of calcium carbonate in the ocean, referred to as the carbonate pump, has profound implications for the ocean carbon cycle, and relate both to global climate, ocean acidification and the geological past. In marine pelagic environments coccolithophores, foraminifera and pteropods have been considered the main calcifying organisms. Here, we document the presence of an abundant, previously unaccounted fraction of marine calcium carbonate particles in seawater, presumably formed by bacteria or in relation to extracellular polymeric substances. The particles occur in a variety of different morphologies, in a size range from <1 to >100 µm, and in a typical concentration of 10(4)-10(5) particles L(-1) (size range counted 1-100 µm). Quantitative estimates of annual averages suggests that the pure calcium particles we counted in the 1-100 µm size range account for 2-4 times more CaCO(3) than the dominating coccolithophoride Emiliania huxleyi and for 21% of the total concentration of particulate calcium. Due to their high density, we hypothesize that the particles sediment rapidly, and therefore contribute significantly to the export of carbon and alkalinity from surface waters. The biological and environmental factors affecting the formation of these particles and possible impact of this process on global atmospheric CO(2) remains to be investigated.

Effect of increased pCO(2) on bacterial assemblage shifts in response to glucose addition in Fram Strait seawater mesocosms.

Ocean acidification may stimulate primary production through increased availability of inorganic carbon in the photic zone, which may in turn change the biogenic flux of dissolved organic carbon (DOC) and the growth potential of heterotrophic bacteria. To investigate the effects of ocean acidification on marine bacterial assemblages, a two-by-three factorial mescosom experiment was conducted using surface sea water from the East Greenland Current in Fram Strait. Pyrosequencing of the V1-V2 region of bacterial 16S ribosomal RNA genes was used to investigate differences in the endpoint (Day 9) composition of bacterial assemblages in mineral nutrient-replete mesocosms amended with glucose (0 µM, 5.3 µM and 15.9 µM) under ambient (250 µatm) or acidified (400 µatm) partial pressures of CO(2) (pCO(2)). All mesocosms showed low richness and diversity by Chao1 estimator and Shannon index, respectively, with general dominance by Gammaproteobacteria and Flavobacteria. Nonmetric multidimensional scaling analysis and two-way analysis of variance of the Jaccard dissimilarity matrix (97% similarity cut-off) demonstrated that the significant community shift between 0 µM and 15.9 µM glucose addition at 250 µatm pCO(2) was eliminated at 400 µatm pCO(2). These results suggest that the response potential of marine bacteria to DOC input may be altered under acidified conditions.