Lydia Bourouiba

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.

The intermediate Rossby number range and two-dimensional-three-dimensional transfers in rotating decaying homogeneous turbulence

Rotating homogeneous turbulence in a finite domain is studied using numerical simulations, with a particular emphasis on the interactions between the wave and zero-frequency modes. Numerical simulations of decaying homogeneous turbulence subject to a wide range of background rotation rates are presented. The effect of rotation is examined in two finite periodic domains in order to test the effect of the size of the computational domain on the results obtained, thereby testing the accurate sampling of near-resonant interactions. We observe a non-monotonic tendency when Rossby number Ro is varied from large values to the small-Ro limit, which is robust to the change of domain size. Three rotation regimes are identified and discussed: the large-, the intermediate-, and the small-Ro regimes. The intermediate-Ro regime is characterized by a positive transfer of energy from wave modes to vortices. The three-dimensional to two-dimensional transfer reaches an initial maximum for Ro ≈ 0.2 and it is associated with a maximum skewness of vertical vorticity in favour of positive vortices. This maximum is also reached at Ro ≈ 0.2. In the intermediate range an overall reduction of vertical energy transfer is observed. Additional characteristic horizontal and vertical scales of this particular rotation regime are presented and discussed.

Spatial dynamics of bar-headed geese migration in the context of H5N1

Virulent outbreaks of highly pathogenic avian influenza (HPAI) since 2005 have raised the question about the roles of migratory and wild birds in the transmission of HPAI. Despite increased monitoring, the role of wild waterfowl as the primary source of the highly pathogenic H5N1 has not been clearly established. The impact of outbreaks of HPAI among species of wild birds which are already endangered can nevertheless have devastating consequences for the local and non-local ecology where migratory species are established. Understanding the entangled dynamics of migration and the disease dynamics will be key to prevention and control measures for humans, migratory birds and poultry. Here, we present a spatial dynamic model of seasonal migration derived from first principles and linking the local dynamics during migratory stopovers to the larger scale migratory routes. We discuss the effect of repeated epizootic at specific migratory stopovers for bar-headed geese (Anser indicus). We find that repeated deadly outbreaks of H5N1 on stopovers during the autumn migration of bar-headed geese could lead to a larger reduction in the size of the equilibrium bird population compared with that obtained after repeated outbreaks during the spring migration. However, the opposite is true during the first few years of transition to such an equilibrium. The age-maturation process of juvenile birds which are more susceptible to H5N1 reinforces this result.

Highly pathogenic avian influenza outbreak mitigated by seasonal low pathogenic strains: Insights from dynamic modeling

The spread of highly pathogenic avian influenza (HPAI) H5N1 remains a threat for both wild and domestic bird populations, while low pathogenic avian influenza (LPAI) strains have been reported to induce partial immunity to HPAI in poultry and some wild birds inoculated with both HPAI and LPAI strains. Here, based on the reported data and experiments, we develop a two-strain avian influenza model to examine the extent to which this partial immunity observed at the individual level can affect the outcome of the outbreaks among migratory birds in the wild at the population level during different seasons. We find a distinct mitigating effect of LPAI on the death toll induced by HPAI strain, and this effect is particularly important for populations previously exposed to and recovered from LPAI. We further investigate the effect of the dominant mode of transmission of an HPAI strain on the outcome of the epidemic. Four combinations of contact based direct transmission and indirect fecal-to-oral (or environmental) routes are examined. For a given infection peak of HPAI, indirect fecal-to-oral transmission of HPAI can lead to a higher death toll than that associated with direct transmission. The mitigating effect of LPAI can, in turn, be dependent on the route of infection of HPAI.

Rain-induced Ejection of Pathogens from Leaves: Revisiting the Hypothesis of Splash-on-Film using High-speed Visualization

Plant diseases are a major cause of losses of crops worldwide. Although rainfalls and foliar disease outbreaks are correlated, the detailed mechanism explaining their link remains poorly understood. The common assumption from phytopathology for such link is that a splash is generated upon impact of raindrops on contaminated liquid films coating sick leaves. We examine this assumption using direct high-speed visualizations of the interactions of raindrops and leaves over a range of plants. We show that films are seldom found on the surface of common leaves. We quantify the leaf-surfaces wetting properties, showing that sessile droplets instead of films are predominant on the surfaces of leaves. We find that the presence of sessile drops rather than that of films has important implications when coupled with the compliance of a leaf: it leads to a new physical picture consisting of two dominant rain-induced mechanisms of ejection of pathogens. The first involves a direct interaction between the fluids of the raindrop and the sessile drops via an off-centered splash. The second involves the indirect action of the raindrop that leads to the inertial detachment of the sessile drop via the leafs motion imparted by the impact of the raindrop. Both mechanisms are distinct from the commonly assumed scenario of splash-on-film in terms of outcome: they result in different fragmentation processes induced by surface tension, and, thus, different size-distributions of droplets ejected. This is the first time that modern direct high-speed visualizations of impacts on leaves are used to examine rain-induced ejection of pathogens at the level of a leaf and identify the inertial detachment and off-center splash ejections as alternatives to the classically assumed splash-on-film ejections of foliar pathogens.

Fluid fragmentation shapes rain-induced foliar disease transmission

Plant diseases represent a growing threat to the global food supply. The factors contributing to pathogen transmission from plant to plant remain poorly understood. Statistical correlations between rainfalls and plant disease outbreaks were reported; however, the detailed mechanisms linking the two were relegated to a black box. In this combined experimental and theoretical study, we focus on the impact dynamics of raindrops on infected leaves, one drop at a time. We find that the deposition range of most of the pathogen-bearing droplets is constrained by a hydrodynamical condition and we quantify the effect of leaf size and compliance on such constraint. Moreover, we identify and characterize two dominant fluid fragmentation scenarios as responsible for the dispersal of most pathogen-bearing droplets emitted from infected leaves: (i) the crescent-moon ejection is driven by the direct interaction between the impacting raindrop and the contaminated sessile drop and (ii) the inertial detachment is driven by the motion imparted to the leaf by the raindrop, leading to catapult-like droplet ejections. We find that at first, decreasing leaf size or increasing compliance reduces the range of pathogen-bearing droplets and the subsequent epidemic onset efficiency. However, this conclusion only applies for the crescent moon ejection. Above a certain compliance threshold a more effective mechanism of contaminated fluid ejection, the inertial detachment, emerges. This compliance threshold is determined by the ratio between the leaf velocity and the characteristic velocity of fluid fragmentation. The inertial detachment mechanism enhances the range of deposition of the larger contaminated droplets and suggests a change in epidemic onset pattern and a more efficient potential of infection of neighbouring plants. Dimensionless parameters and scaling laws are provided to rationalize our observations. Our results link for the first time the mechanical properties of foliage with the onset dynamics of foliar epidemics through the lens of fluid fragmentation. We discuss how the reported findings can inform the design of mitigation strategies acting at the early stage of a foliar disease outbreak.

THE INTERACTION OF MIGRATORY BIRDS AND DOMESTIC POULTRY AND ITS ROLE IN SUSTAINING AVIAN INFLUENZA

We investigate the role of migratory birds in the spread of H5N1 avian influenza, focusing on the interaction of a migratory bird species with nonmigratory poultry. The model is of patch type and is derived with the aid of reaction-advection equations for the migratory birds in the air along the flyways. Poultry may reside at some or all of the four patches of the model, which consist of the breeding patch for the migratory birds, their winter feeding patch, and two stopover patches where birds rest and refuel on their migration. Outward and return migratory routes can be different. The equations for the migratory birds contain time delays which represent the flight times for migratory birds along particular sectors. Delays also appear in the model coefficients via quantities which represent flight survival probabilities for the various sectors. We establish results on positivity, boundedness, global asymptotic stability of the disease-free equilibrium, and the persistence of infection. We also discuss extensions of the model to include the seasonality of the migration phenomenon. Numerical simulations support the analytical findings; here we used data on H5N1 infected ducks in the Poyang Lake region of China.

Moving with Bubbles: A Review of the Interactions between Bubbles and the Microorganisms that Surround them

Bubbles are ubiquitous in biological environments, emerging during the complex dynamics of waves breaking in the open oceans or being intentionally formed in bioreactors. From formation, through motion, until death, bubbles play a critical role in the oxygenation and mixing of natural and artificial ecosystems. However, their life is also greatly influenced by the environments in which they emerge. This interaction between bubbles and microorganisms is a subtle affair in which surface tension plays a critical role. Indeed, it shapes the role of bubbles in mixing or oxygenating microorganisms, but also determines how microorganisms affect every stage of the bubbles life. In this review, we guide the reader through the life of a bubble from birth to death, with particular attention to the microorganism-bubble interaction as viewed through the lens of fluid dynamics.

From regional pulse vaccination to global disease eradication: insights from a mathematical model of poliomyelitis

Mass-vaccination campaigns are an important strategy in the global fight against poliomyelitis and measles. The large-scale logistics required for these mass immunisation campaigns magnifies the need for research into the effectiveness and optimal deployment of pulse vaccination. In order to better understand this control strategy, we propose a mathematical model accounting for the disease dynamics in connected regions, incorporating seasonality, environmental reservoirs and independent periodic pulse vaccination schedules in each region. The effective reproduction number,