Biology subjects

Gourbiere, S.

Publications and source records attributed to Gourbiere, S..

9 recordsLinked to original sources

bioRxiv2026

Epidemiological model selection unravels the molecular processes of antiviral resistance from experimental phytoplankton-virus dynamics

Phytoplankton-virus interactions are pivotal in understanding the intertwined dynamics of these key players of the global carbon cycle. Although antiviral resistance is the main hypothesis to solve the apparent paradox of their coexistence, identifying its molecular determinisms and mechanisms, as well as their dynamical consequences, remains challenging. By combining hypotheses about such determinisms and mechanisms, we designed 36 dynamical models and fitted them to experimental infection kinetics in a pioneering selection model approach. Through such a multiple hypotheses testing, we identified that resistance in the model species Ostreococcus tauri is most likely to be predominantly intracellular, to control lysis through budding, and to be acquired by phenotypic plasticity. We further showed that viral kinetics are strongly impacted by both the antiviral resistance's molecular determinants and virions' inactivation through attachment to lysis detritus, as the latter generates a key negative feedback loop during the 'bust' stage of the interaction dynamics.

ecology↗

bioRxiv2026

How do the molecular determinants of antiviral resistance shape the dynamic of phytoplankton-virus interaction?

Phytoplankton sustain all marine ecosystems and are key components of the carbon cycle being responsible for ~50% of the global primary production. A major hypothesis to explain their coexistence with highly efficient lytic viruses is antiviral resistance. Although intracellular and extracellular mechanisms have been shown to underly such resistance and while its determinism is commonly associated to a genomic polymorphism or a (random or virus induced) phenotypic plasticity, comparisons of the impact of those molecular determinants on phytoplankton-virus population dynamic are genuinely lacking. We combined 12 epidemiological models with an unprecedented set of parameter estimates derived from experimental studies of the ubiquitous species Ostreococcus tauri and its prasinoviruses to provide such comprehensive predictions. We show that 'bet-hedging' strategies corresponding to random phenotypic switches between susceptible and resistant cells provide the strongest barrier to virus emergence. When such resistance is associated to intracellular mechanisms the virus' R0 is at least halved because of the strong 'dilution effect' produced by the 'dead-end' hosts. In addition, once the virus has spread, both random and virus-induced phenotypic plasticity strongly stabilize the otherwise 'boom and bust' phytoplankton-virus dynamics, which is highly consistent with the experimental dynamics observed for such interactions.

ecology↗

bioRxiv2025

Modelling the dynamics of transposable elements in genomes under asexual reproduction using agent-based model

Transposable elements (TEs) are abundantly present in eukaryotic genomes and can be likened to parasites colonizing a genome due to their properties. From this perspective, a population-based approach has been developed to model interactions between TEs and a genome population. The distribution of TEs within a population of genomes is studied over the long term to understand the mechanisms allowing TEs to persist despite their deleterious effects on genomes. Under this single restrictive assumption, the results show that the population of TEs can persist for a very long time within the genome population, when the genome population is highly diverse in terms of the distribution of TEs quantities. When there is no mechanism for silencing TEs, the proposed model of asexual reproduction either purges TEs or leads to co-extinction of genomes and TEs. On the other hand, with a high proportion of silenced TEs, the population of TEs can be maintained for a long time in the population of genomes.

genetics↗

bioRxiv2025

An integrative field and modelling study of the bottom-up, top-down and indirect effects of native species on invasive insects and their biological control : the case of the worldwide chestnut tree pest, Dryocosmus kuriphilus, in the French Eastern Pyrenees

Insect pests invading an ecosystem typically face various forces regulating their population growth and spread. While the resources they feed on and their natural enemies have bottom-up and top-down effects on insect invasion success, other native species, more distant in the local trophic network, can have indirect effects on the ecosystems susceptibility to invasion. Resolving the mechanisms underlying these naturally occurring indirect interactions and their impact on invasion dynamics is a key challenge toward risk assessment and environmental management. In this contribution, we investigated how indirect interactions with several native species contribute to variations in Dryocosmus kuriphilus infestation level in 24 natural chestnut tree populations of the French Eastern Pyrenees. This invasive gall-forming hymenopteran parasites cultivated and wild Castanea sativa stands, and its hymenopteran parasitoid, Torymus sinensis, is world widely used as a control agent. We combined ecological, molecular and statistical approaches to quantify the effects of Quercus pubescens, Fagus sylvatica and the parasitic fungus Cryphonectria parasitica on the pest oviposition rate (effect i), its host detection capacity (effect ii), the production of native parasitoids (effect iii) and in providing alternative hosts for the control agent (effect iv). The integration of these effects into a specifically designed D. kuriphilus - T. sinensis dynamical model, provided clear evidence of the quantitative impacts of Q. pubescens and C. parasitica on the invasion potential of the pest and its biological control.

ecology↗

bioRxiv2025

Anticipating invasion of parasite with graph theory: Dryocosmus kuriphilus, a threat for Castanea sativa

The increase in world trade contributed to a rise in the number of insect biological invasions. The colonisation success of herbivorous pests depends mostly on the abundance of vegetal resource across the newly invaded territory. The explicit spatial representation of plant distribution offers a cost-effective approach to anticipate the spread of herbivorous insects over areas with fragmented and heterogeneous vegetal populations. In this article, we focus on the case of the recent invasion of chestnut trees (Castanea sativa) of the French Eastern Pyrenees by its most virulent pest, the gall-forming parasite Dryocosmus kuriphilus. Using tools from graph theory and available public data on the mesh size and distribution of chestnut trees, we model the spatial distribution of the pest resource across natural forests. In this framework, a graph provides a mapping of 1 km2 quadrats that constitute the territory. Quadrats are grouped to form communities, which are areas with homogeneous chestnut tree distribution, and in which the risk of parasite infestation and propagation is similar. Graph traversal algorithms then measure the vulnerability and the dangerousness of each patch, defined as their susceptibility to become infected and to contribute to the pest propagation. Such a spatial assessment of the invasion risk provides unique insights into potential propagation scenarios, improving the early detection and spread monitoring of these insect invaders. Author summary

ecology↗

bioRxiv2025

Effect of cellular nutrient economy on the evolution of genome size in phytoplankton

The origin of genome size variation remains a central question in evolutionary biology. Previous analyses suggest that the energetic costs of small insertions and deletions (indels) influence genome size by altering the cellular energy budget. Here, we present a theoretical framework for genome evolution in phytoplankton--the main producers of the sunlit ocean--whose growth depends on nutrient availability. We derive an expression for the selection coefficient on indels as a function of the minimum amount of nutrient inside the cell. Parameter estimates indicate that 1-bp indels can be counterselected in phytoplankton with minimal nutrient requirements. We then test three predictions of nutrient-driven selection on genome evolution. Altogether, this model provides a quantitative and mathematical basis for the genome streamlining hypothesis.

ecology↗

bioRxiv2025

Source-sink dynamics explains the co-existence of the invasive pest Dryocosmus kuriphilus and its biological control agent Torymus sinensis across French Eastern Pyrenees.

Biological invasions have become a major cause of ecological and economic costs in many (agro-)ecosystems. Understanding the regulation of their local dynamics by resources limitation and natural enemies, i.e. bottom-up and top-down determinants, through inherently heterogenous environments stands as a critical challenge to provide efficient risk assessments and management measures. Here, we propose an unprecedented integrative modelling approach based on a spatial extension of the seminal Nicholson-Bailey model parameterized by a comprehensive field assessment of all the bottom-up and top-down determinants affecting the spread of a worldwide invasive pest, Dryocosmus kuriphilus, in 23 natural chestnut tree populations of the French Eastern Pyrenees. The analysis of the within-site dynamics allowed to quantify the spatial heterogeneity in the two types of regulatory forces across the study area, and to identify 16/23 sites where the control agent, Torymus sinensis, is expected to persist and control the invasive pest. The comparison of these predictions with the levels of D. kuriphilus hyperparasitism by T. sinensis, observed in all 23 forest sites, suggested hidden source-sink dynamics within the study area. The investigation of such dynamics by the coupling of any two local dynamics predicted in each of the 23 sites showed that i) low rates of D. kuriphilus and T. sinensis dispersal lead to a synchronization to the dynamic expected in the site with the highest chestnut tree frequency, while ii) higher rates typically allow for a stable equilibrium. Those predictions provide quantitative evidences for the persistence of T. sinensis in the 7 predicted sink sites sustained by its local 16 source populations. Dispersal then tends to homogenize the local efficiencies of the control agent while decreasing its global impact on the pest invasion. Overall, this pioneer spatial modelling of D. kuriphilus - T. sinensis interaction suggests that both introduced species are likely to persist in the European forest environments in a co-invasion scenario.

ecology↗

bioRxiv2024

Unravelling the bottom-up and top-down control of a worldwide chestnut tree pest invader through integrative ecological genomics

Biological invasions have become a major threat to all agro-ecosystems. Estimating the bottom-up and top-down forces controlling the spread of invasive insects is a key challenge to lessen their burden on crops, forestry, and biodiversity. We combined ecological, metabarcoding and population genomics analyses with an integrative modelling of the invasion of a global insect pest to identify the impacts of its chestnut tree resource, natural enemies and biological control agent in Eastern Pyrenees. The host tree frequency and genomic variation associated with common resistance pathways had effects 4-10 times greater than the native hyperparasite community on the pests invasion potential (R0). The >90% field rates of hyperparasitism by the control agent and the associated 80% reduction in pest infestation are likely to be deceptive as our modelling consistently predicts their long-term coexistence with periodic re-emergences. Such a persistent co-invasion scenario calls for a thorough assessment of the impact of these global pest and control agent on natural forest ecosystems.

systems biology↗

bioRxiv2019

Virus-host coexistence in phytoplankton through the genomic lens

Phytoplankton-virus interactions are major determinants of geochemical cycles in the oceans. Viruses are responsible for the redirection of carbon and nutrients away from larger organisms back towards microorganisms via the lysis of microalgae in a process coined the viral shunt. Virus-host interactions are generally expected to follow boom and bust dynamics, whereby a numerically dominant strain is lysed and replaced by a virus resistant strain. Here, we isolated a microalga and its infective nucleo-cytoplasmic large DNA virus (NCLDV) concomitantly from the environment in the surface NW Mediterranean Sea, Ostreococcus mediterraneus, and show continuous growth in culture of both the microalga and the virus. Evolution experiments through single cell bottlenecks demonstrate that, in the absence of the virus, susceptible cells evolve from one ancestral resistant single cell, and vice-versa; that is that resistant cells evolve from one ancestral susceptible cell. This provides evidence that the observed sustained viral production is the consequence of a minority of virus-susceptible cells. The emergence of these cells is explained by low-level phase switching between virus-resistant and virus-susceptible phenotypes, akin to a bet hedging strategy. Whole genome sequencing and analysis of the ~14 Mb microalga and the ~200 kb virus points towards ancient speciation of the microalga within the Ostreococcus species complex and frequent gene exchanges between prasinoviruses infecting Ostreococcus species. Re-sequencing of one susceptible strain demonstrated that the phase switch involved a large 60 Kb deletion of one chromosome. This chromosome is an outlier chromosome compared to the streamlined, gene dense, GC-rich standard chromosomes, as it contains many repeats and few orthologous genes. While this chromosome has been described in three different genera, its size increments have been previously associated to antiviral immunity and resistance in another species from the same genus. Mathematical modelling of this mechanism predicts microalga-virus population dynamics consistent with the observation of continuous growth of both virus and microalga. Altogether, our results suggest a previously overlooked strategy in phytoplankton-virus interactions.

evolutionary biology↗