Biology subjects

Guichard, F.

Publications and source records attributed to Guichard, F..

6 recordsLinked to original sources

bioRxiv2026

A winding road to coexistence: Interdependence of niche and fitness differences in E. coli with targeted resource uptake gene deletions

Resource competition theory typically assumes static traits and continuous supply of resources. Yet microbial communities often experience feast-famine cycles and rapid trait change. To investigate coexistence under these nonequilibrium conditions, we integrate modern coexistence theory (MCT) with a genome-scale metabolic model that explicitly links resource use (traits) to metabolic fluxes and growth. MCT partitions competitive interactions into niche and fitness differences, to predict when trait-driven departures from neutrality result in coexistence or exclusion. Using dynamic flux balance analysis, we define a function that maps trait-resource matching to niche and fitness differences between species in a two-species two-resource system. This mapping shows that niche and fitness differences are not independently tunable under resource competition: changes in transporter-mediated resource uptake and changes in resource concentration ratios generate constrained trajectories through coexistence space. Specifically, we show that the minimum niche difference required for coexistence increases linearly with the absolute difference in maximal growth rates on limiting resources, showing how limiting similarity between species can emerge from intracellular metabolic constraints. Furthermore, we find that in batch culture simulations, initial conditions (inoculum size, total resource concentration) determine the timescale of the transient growth phase, with niche differences saturating and fitness differences increasing as the timescale grows, thereby governing competition outcomes. Finally, we test these predictions experimentally using E. coli strains with targeted resource transporter knockouts under both equal and skewed resource concentrations. Our results confirm that transporter-mediated trait changes and resource concentration ratio modulation can be harnessed to engineer coexistence. Together, our work demonstrates that trait-resource matching imposes structured constraints on the joint evolution of niche and fitness differences, thereby shaping biodiversity maintenance in microbial communities under nonequilibrium conditions.

ecology↗

bioRxiv2025

Doallochthonous flows explain deviations from the Redfield ratio in lakes?

Lakes or streams show strong deviations of their stoichiometry compared to the Redfield ratio measured in oceans. Allochthonous inflows of resources might contribute to those deviations directly, by changing composition of detritus in ecosystems, but also indirectly, by shaping local community dynamics and stoichiometric constrains within aquatic ecosystems. Here, we developed a stoichiometric model to understand those direct and indirect mechanisms through which allochthonous inflows affect seston stoichiometry. Our results emphasize that increasing allochthonous inflows promotes heterotrophic functioning, and relax decomposer carbon limitation. This release of stoichiometric constrain of decomposers (i) destabilizes the aquatic ecosystem by promoting competition between phytoplankton and decomposers, (ii) decreases the ability of the lake to regulate allochthonous flows, and (iii) push seston stoichiometry away from the Redfield ratio. Our study emphasize how the quantity and the stoichiometry of inflows shape community dynamics and the elemental constraints within the ecosystem, and open perspectives for stoichiometry at the landscape extent.

ecology↗

bioRxiv2024

Resource-use plasticity governs the causal relationship between traits and community structure in model microbial communities

Resolving the relationship between species traits and their relative abundance is a central challenge in ecology. Current hypotheses assume relative abundances either result from or are independent of traits. However, despite some success, these hypotheses do not integrate the reciprocal and feedback interactions between traits and abundances to predictions of community structure such as relative abundance distributions. Here we study how plasticity in resource-use traits govern the causal relationship between traits and relative abundances. We adopt a consumer-resource model that incorporates resource-use plasticity that operates to optimize organism growth, underpinned by investment constraints in physiological machinery for acquisition of resources. We demonstrate that the rate of plasticity controls the coupling strength between trait and abundance dynamics, predicting species relative abundance variation. We first show how plasticity in a single species in a community allows all other non-plastic species to coexist, a case of facilitation emerging from competitive interactions where a plastic species minimizes its similarity with competitors and maximizes resource-use efficiency in its environment. We apply this environment-competition trade-off to predict trait-abundance relationships and reveal that initial traits are better predictors of equilibrium abundances than final trait values. This result highlights the importance of transient dynamics that drive species sorting. The temporal scale of transients determines the strength of species sorting due to the emergence of ecological equivalence at equilibrium. We propose trait-abundance feedback as an eco-evolutionary mechanism linking community structure and assembly, highlighting trait plasticitys role in community dynamics.

ecology↗

bioRxiv2022

Supply-driven evolution: mutation bias and trait-fitness distributions can drive macro-evolutionary dynamics

Many well-documented macro-evolutionary phenomena, such as increases in organization hierarchy, or sudden and episodic creation of new taxa, still challenge current evolutionary theories. Here we show a new mechanism that can explain them. We begin by showing how the order of mutations can alter evolutionary trajectories. We present a framework integrating both mutation and environmental biases and show that mutation bias can strongly outweigh any environmental bias, a regime we call "supply-driven" evolution. We then show how a common type of mutation bias, where detrimental mutations are more common than beneficial mutations, can drive the locking-in of structural hierarchies such as eukaryotism or multicellularity, independently from the environment. Finally, we generalize this result to show how any mutation (or sets of mutations) that creates the possibility of new phenotypes can persist for a very long period of time. That is, innovations that make possible a large range of new phenotypes can become frozen in time. By becoming frozen, these novel structures can no longer change, which means a range of phenotypes also become impossible. This opening and closing of phenotypic space is a new mechanism of macro-evolution.

evolutionary biology↗

bioRxiv2020

Dynamic larval dispersal can mediate the response of marine metapopulations to multiple climate change impacts

Climate change is having multiple impacts on marine species characterized by sedentary adult and pelagic larval phases, from increasing adult mortality to changes in larval duration and ocean currents. Recent studies have shown impacts of climate change on species persistence through direct effects on individual survival and development, but few have considered the indirect effects mediated by ocean currents and species traits such as pelagic larval duration. We used a density-dependent and stochastic metapopulation model to predict how changes in adult mortality and dynamic connectivity can affect marine metapopulation stability. We analyzed our model with connectivity data simulated from a biophysical ocean model of the northeast Pacific coast forced under current (1998-2007) and future (2068-2077) climate scenarios in combination with scenarios of increasing adult mortality and decreasing larval duration. Our results predict that changes of ocean currents and larval duration mediated by climate change interact in complex and opposing directions to shape local mortality and metapopulation connectivity with synergistic effects on regional metapopulation stability: while species with short larval duration are most sensitive to temperature-driven reduction in larval duration, the response of species with longer larval duration are mostly mediated by changes in both the mean and variance of larval connectivity driven by ocean currents. Our results emphasize the importance of considering the spatiotemporal structure of connectivity in order to predict how the multiple effects of climate change will impact marine populations.

ecology↗

bioRxiv2020

Networks of marine protected areas under fluctuating connectivity: the importance of within-MPA dynamics

The design of marine protected areas (MPAs) has been optimized under assumptions of spatially and temporally homogeneous larval dispersal, despite complex spatiotemporal patterns displayed by ocean currents. Here we studied the effect of dispersal variability on the effectiveness of MPA networks across scales. We adopted a nested approach integrating the dynamics of both within and among MPA connectivity into a stochastic metapopulation model and first derived metapopulation persistence (required reproductive effort) and stability over MPA networks by partitioning within and among MPA contributions in relation to the spatial resolution of within-MPA connectivity. We applied this framework over a range of dispersal traits (spawning time and pelagic larval duration) and MPA network configurations, based on simulated biophysical connectivity along the northeast Pacific coast. Our results show how within-MPA dynamics affect predictions based on parameters of MPA networks such as MPA size, spacing, and pelagic larval duration. Increasing within-MPA spatial resolution predicted increasing population persistence and stability independently of other network properties. High-resolution within-MPA dynamics also predicted a negative relationship between species persistence and MPA spacing while that relationship was non-monotonic under low-resolution within-MPA dynamics. Our analysis also resolved the role of pelagic larval duration for scaling up within-MPA dynamics to MPA networks: species with short larval duration led to increasing network stability with MPA spacing while the opposite was observed for species with long larval duration. Our study stresses the importance of integrating fluctuating larval connectivity, both within and among MPAs, and more specifically suggest the benefit of small and nearby MPAs under increasing ocean variability.

ecology↗