Section: New Results

Fields of application

Bioenergy

Modelling microalgae production

Participants : Olivier Bernard, Antoine Sciandra, Walid Djema, Ignacio Lopez, David Demory, Ouassim Bara, Jean-Philippe Steyer.

Experimental developments

Running experiments in controlled dynamical environments. The experimental platform made of continuous photobioreactors driven by a set of automaton controlled by the ODIN software is a powerful and unique tool which gave rise to a quantity of very original experiments. Such platform improved knowledge of several biological processes such as lipid accumulation or cell cycle under light fluctuation, etc [69].

This experimental platform was used to control the long term stress applied to a population of microalgae [72]. This Darwinian selection procedure generated several new strains more resistant to oxidative stresses after several months in the so called selectiostats [58].

Experiments were run to understand the interactions in a simplified ecosystem between microalgae and cyanobacteria. The initial idea was to use a nitrogen fixing cyanobacteria providing nitrogen to the microalgae. It turns out that negative interactions appear in this ecosystem, first because of the mutual shadowing of these organisms, and second because of the production of allelopathic substances inhibiting the competitive organisms [79].

On top of this, we carried out outdoor pilot experiments with solar light. We tested the impact of various temperatures, resulting from different shadowing configurations on microalgal growth rate.

Experimental work was also carried out in collaboration with the Inalve startup with microalgal biofilm to determine the impact of light and dark sequences on cell growth and photoacclimation [26], [63]. The architecture of the biofilms was also observed for different species with confocal microscopic techniques [23].

These works have been carried out in collaboration with A. Talec and E. Pruvost (CNRS/Sorbonne Université -Oceanographic Laboratory of Villefranche-sur-Mer LOV).

Metabolism of carbon storage and lipid production. A metabolic model has been set up and validated for the microalgae Isochrysis luthea, on the basis of the DRUM framework , in order to simulate autotophic, heterotropic and mixotrophic growth, and to determine how to reduce substrate inhibition. The model was extended for other substrates such as glucose or glycerol. A simplified model was developed by I. Lopez to represent the dynamics of polar lipids, especially when faced to higher oxygen concentration. In particular, this model represents the microalgae growth under different conditions of temperature, light and oxygen.

Modeling photosynthetic biofilms. Several models have been developed to represent the growth of microalgae within a biofilm. A first structured physiological model, extending the one proposed in [95] uses mixture theory to represent the microalgae growth, based on the consideration of intracellular reserves triggering the processes of growth, respiration and excretion. We consider separately the intracellular storage carbon (lipids and carbohydrates) and the functional part of microalgae . Another approach accounts for the dynamics of the light harvesting systems when cells are submitted to rapid successions of light and dark phases [28], [71]. A simpler model was developed and used to identify the optimal working mode of a process based on photosynthetic biofilm growing on a conveyor belt [45]. The model was used to identify the worldwide potential of microalgal biofilms under different climates [26].

Modeling microalgae production processes.

A synthesis has been written on the different aspects for developing models of microalgae in the field of wastewater treatment [38]. The paper is completed by a position paper proposing guidelines for the development of models in biotechnology [31]. A model representing the dynamics of microalgae when growing in suboptimal conditions of light, nitrogen and phosphorus was developed. It consists in an extension of the Droop model accounting for the two quota of nitrogen and phosphorus [65]. This was the topic of the internship of Luis Plaza Alvarez. The model also represents the pigment acclimation to various light intensities. We have studied in [75] the response of a Droop model forced by periodic light or temperature signals. We transformed the model into a planar periodic system generating a monotone dynamical system. Combined with results on periodic Kolmogorov equations, the global dynamics of the system can be described.

Modeling thermal adaptation in microalgae.

Experiments have been carried out in collaboration with A.-C. Baudoux (Biological Station of Roscoff) in order to study growth of various species of the microalgae genus Micromonas at different temperatures. After calibration of our models, we have shown that the pattern of temperature response is strongly related to the site where cells were isolated. We derived a relationship to extrapolate the growth response from isolation location. With this approach, we proved that the oceanwide diversity of Micromonas species is very similar to the oceanwide diversity of the phytoplankton [22]. We have used Adaptive Dynamics theory to understand how temperature drives evolution in microalgae. We could then predict the evolution of this biodiversity in a warming ocean and show that phytoplankton must be able to adapt within 1000 generation to avoid a drastic reduction in biodiversity [22].

Modeling viral infection in microalgae. In collaboration with A.-C. Baudoux (Biological Station of Roscoff) a model was developed to account for the infection of a Micromonas population, with population of susceptible, infected and also free viruses. The model turned out to accurately reproduce the infection experiments at various temperatures, and the reduction of virus production above a certain temperature [22]. The model was then extrapolated to the whole ocean to better understand how the warming will impact the mortality due to viruses.

Control and Optimization of microalgae production

Optimization of the bioenergy production systems

A model predictive control algorithm was run based on simple microalgae models coupled with physical models where culture depth influences thermal inertia. Optimal operation in continuous mode for outdoor cultivation was determined when allowing variable culture depth. Assuming known weather forecasts considerably improved the control efficiency [21].

Control of microalgal biofilms.

Determining the optimal operating conditions for a rotating algal biofilm process [63] is a difficult question. A 1D model was developed, and the gradient associated to the productivity at the process scale was computed. Then the conditions maximizing productivity were derived, playing on the conveyer belt velocity and geometry [71].

Interactions between species. We have proposed an optimal control strategy to select in minimal time the microalgal strain with the lowest pigment content [51]. The control takes benefit from photoinhibition to compute light stresses penalizing the strains with a higher pigment content and finally selecting microalgae with lower chlorophyll content. Another optimal control problem was considered for selecting a strain of interest within two species competing for the same substrate, when dynamics is represented by a Droop model [52], [73], [74]. In both cases, the optimal control derived from the Pontryagin maximum principle also exhibit a turnpike behaviour. This is a collaboration with team MCTAO.

Strategies to improve the temperature response have also been studied. We modelled the adaptive dynamics for a population submitted to a variable temperature [58]. This was used at the LOV to design experiments with periodic temperature stresses aiming at enhancing polyunsaturated long chain fatty acids content of Tisochrysis lutea [72].

Modelling mitochondrial inheritance patterns

Most eukaryotes inherit their mitochondria from only one of their parents. When there are different sexes, it is almost always the maternal mitochondria that are transmitted. Indeed, maternal uniparental inheritance has been reported for the brown alga Ectocarpus but we show in this study [33] that different strains of Ectocarpus can exhibit different patterns of inheritance: Ectocarpus siliculosus strains showed maternal uniparental inheritance, as expected, but crosses using different Ectocarpus species 7 strains exhibited either paternal uniparental inheritance or an unusual pattern of transmission where progeny inherited either maternal or paternal mitochondria, but not both. A possible correlation between the pattern of mitochondrial inheritance and male gamete parthenogenesis was investigated. Moreover, in contrast to observations in the green lineage, we did not detect any change in the pattern of mitochondrial inheritance in mutant strains affected in life cycle progression. Finally, an analysis of field-isolated strains provided evidence of mitochondrial genome recombination in both Ectocarpus species.

Biological depollution

Control and optimization of bioprocesses for depollution

Participants : Olivier Bernard, Carlos Martinez Von Dossow, Jean-Luc Gouzé.

We consider artificial ecosystems including microalgae, cyanobacteria and bacteria in interaction. The objective is to more efficiently remove inorganic nitrogen and phosphorus from wastewater, while producing a microalgal biomass which can be used for biofuel or bioplastic production. Models have been developed including predators grazing the microalgae. Experiments with nitrogen fixing cyanobacteria were carried out, and simple models of the ecosystem where developed to assess the potential of such organisms to support the nitrogen need of microalgae [79].

Coupling microalgae to anaerobic digestion

Participants : Olivier Bernard, Antoine Sciandra, Jean-Philippe Steyer, Frédéric Grognard, Carlos Martinez Von Dossow.

The coupling between a microalgal pond and an anaerobic digester is a promising alternative for sustainable energy production and wastewater treatment by transforming carbon dioxide into methane using light energy. The ANR Phycover project is aiming at evaluating the potential of this process [96].

We have proposed several models to account for the biodiversity in the microalgal pond and for the interaction between the various species. These models were validated with data from the Saur company. More specifically, we have included in the miroalgae model the impact of the strong turbidity, and derived a theory to better understand the photolimitation dynamics especially when accounting for the photo-inhibition in the illuminated periphery of the reactor [91]. Control strategies playing with the dilution rate, shadowing or modifying depth were then proposed [90].

Finally, a study of the possible sensors which would enhance the monitoring of these process was proposed [30], [29]

Life Cycle Assessment

Participants : Olivier Bernard, Jean-Philippe Steyer, Marjorie Alejandra Morales Arancibia.

Environmental impact assessment. To follow up the pioneering life cycle assessment (LCA) work of [87], we identified the obstacles and limitations which should receive specific research efforts to make microalgae production environmentally sustainable [93].

In the Purple Sun ANR-project, we studied a new paradigm to improve the energy balance by combining biofuel production with photovoltaic electricity. The LCA of a greenhouse with, at the same time, photovoltaic panels and low emissivity glasses was carried out. Depending on the period of the year, changing the species can both improve productivity and reduce environmental footprint [34].

We have also studied the environmental impact of protein production from microalgae in an algal biofilm process and compared it to other sources (fisheries, soy,...). This study confirms the interest of microalgae for reducing the environmental impact.

This work is the result of a collaboration with Arnaud Helias of INRA-LBE (Laboratory of Environmental Biotechnology, Narbonne).

Design of ecologically friendly plant production systems

Controlling plant arthropod pests

Participants : Frédéric Grognard, Ludovic Mailleret, Suzanne Touzeau, Yves Fotso Fotso.

Optimization of introduction processes. The question of how many and how frequently natural enemies should be introduced into crops to most efficiently fight a pest species is an important issue of integrated pest management. The topic of optimization of natural enemies introductions has been investigated for several years [89], and extends more generally to pulse perturbations in population dynamics.

A central theoretical result concerns the unveiling of the crucial influence of within-predator density dependent processes. To evaluate this theoretical prediction in a more realistic, stochastic and spatially explicit setting, a stochastic individual based model has been built in Python MESA, on the basis of a previous work in NetLogo. Extensive simulatory experiments were performed to assess the effects of density dependent processes as well as spatial structure and stochasticity on augmentative biological control performance and variability [88]. The modelling platform is interactive and can be accessed online at http://popintro.sophia.inra.fr/.

In a more general setting, we studied the impact on the introduction success of a population of the interplay of Allee effects, stochasticity in introduction sizes, and occurrence of catastrophes that temporarily wipe out the population. The mean first passage time (MFPT) for a population to reach a viable size was used as a measure of establishment success for the introduction processes [14].

Characteristics of space and the behavior and population dynamics of biological control agents. We studied the influence of the spatial structure and characteristics of the environment on the establishment and spread of biological control agents through computer simulations and laboratory experiments on parasitoids of the genus Trichogramma. This was the topic of Thibaut Morel Journel [94] and Marjorie Haond’s PhD theses [85]. The last article associated with Thibaut Morel Journel's Thesis appeared this year [35]. We explored the influence of different characteristics of the structural connectivity of an invaded habitat on the invading population. We demonstrated how spread was hindered by habitat clusters and accelerated by the presence of hubs. These results highlight the importance of considering the structure of the invaded area to predict the outcome of invasions.

In a different study stemming from Marjorie Haond Thesis, we showed how habitat richness [86] as represented by its local carrying capacity can positively influence the spreading speeed of an expanding population. This work has been published as a preprint recommended by Peer Community in Ecology and is on the verge to be submitted to a regular scientific journal. This work has been performed in collaboration with Elodie Vercken (ISA) and Lionel Roques (BioSP, Avignon).

In a different context, we studied how predatory mite population development can be enhanced by the provision of artificial habitats. One paper focused on the influence of different artificial materials on the oviposition and survival of predatory mites appeared this year [16]. This topic was also at the core of the Master 2 intership of Lucas Etienne [81] during which he studied the combined influences of artificial habitats and additional food on the development of a predatory mite and on the control of a phytophagous mite. An article reporting on this study is currently under preparation.

Modelling and control of coffee berry borers. We developed a model describing the coffee berry borer dynamics based on the insect life-cycle and the berry availability during a single cropping season. A control was introduced, based on a biopesticide (entomopathogenic fungus such as Beauveria bassiana) that is sprayed and persist on the berries. An optimal control problem was solved (see Section 7.1.1.2). The aim was to maximise the yield at the end of the cropping season, while minimising the borer population for the next cropping season and the control costs. Depending on the initial pest infestation, the optimal solution structure varied [60], [62]. This research pertains to Yves Fotso Fotso's PhD thesis, who visited BIOCORE during 5 months in 2019 through the EPITAG associate team.

Controlling plant pathogens

Participants : Frédéric Grognard, Ludovic Mailleret, Suzanne Touzeau, Clotilde Djuikem.

Sustainable management of plant resistance. We studied other plant protection methods dedicated to fight plant pathogens. One such method is the introduction of plant strains that are resistant to one pathogen. This often leads to the appearance of virulent pathogenic strains that are capable of infecting the resistant plants.

We have developed a (spatio-)temporal epidemiological model of the phoma stem canker of oilseed rape, to test and assess the durability of deployment strategies of various cultivars. Based on this model, we aim at developing a user-friendly, upgradeable and efficient simulation tool designed for researchers as well as non academic partners from technical institutes and agriculture cooperatives. We hence applied and obtained the SiDRes AMDT, which will start in 2020.

A stochastic model was developed to help determine the efficiency of pyramiding qualitative resistance and quantitative resistance narrowing population bottlenecks exerted on plant viruses, the latter aiming at slowing down virus adaptation to the qualitative resistance. It showed the efficiency of pyramiding when the fitness cost of RB virus variants in susceptible plants is intermediate [36]. This studiy provide a framework to select plants with appropriate virus-evolution-related traits to avoid or delay resistance breakdown. This was done in collaboration with Frédéric Fabre (INRA Bordeaux) and Benoît Moury (INRA Avignon).

Taking advantage of plant diversity and immunity to minimize disease prevalence. An epidemiological model of gene-for-gene interaction considering a mechanism related to the specific defense response of plants, the systemic acquired resistance (SAR) was developed. SAR provides a sort of immunity to virulent pathogens for resistant plants having undergone an infection attempt by an avirulent pathogen. This model showed that there exists an optimal host mixture that ensures the lowest plant disease prevalence, so as to optimize the crop yield. It is especially efficient for pathogens with a low or intermediate basic reproduction rate and hosts with a high SAR efficiency [61]. This was done in collaboration with Pauline Clin and Frédéric Hamelin (Agrocampus Ouest).

Plant-nematode interactions

Participants : Valentina Baldazzi, Frédéric Grognard, Ludovic Mailleret, Suzanne Touzeau, Israël Tankam Chedjou, Samuel Nilusmas.

Plant-parasitic nematodes are small little-mobile worms that feed and reproduce on plant roots, generating considerable losses in numerous crops all over the world. Most eco-friendly plant protection strategies are based on the use of resistant crops, but agricultural practices also contribute to nematode control.

Based on an interaction model between plantain roots and Radopholus similis, we solved an optimisation problem (see Section 7.1.1.2). It aimed at determining the duration between cropping seasons (fallow period) that maximises the farmer's cumulated yield, which is affected by the nematode population, while minimising the costs of nematode control and nursery-bought pest-free suckers, on a fixed time horizon that lasts several cropping seasons. Fallow periods reduce the nematode population in the soil, as these pests need roots to feed on and reproduce. For a relatively long time horizon, deploying one season less than the maximum possible number of cropping seasons resulted in a better multi-seasonal profit. The optimal solution consisted in applying long fallows at the beginning, to drastically reduce the nematode population. The profit was lower for more regular fallows, but the final soil infestation was also lower [67]. This research pertains to Israël Tankam Chedjou's PhD thesis, who visited BIOCORE during 5 months in 2019 through the EPITAG associate team.

We also studied resistance-based root-knot nematode control. As virulent nematodes exhibit a reduced fitness on susceptible crops, alternating resistant and susceptible plants could help increase the efficiency and durability of such control methods. Optimal crop rotations (see Section 7.1.1.2 were characterised by low ratios of resistant plants and were robust to parameter uncertainty. Rotations provided significant gains over resistant-only strategies, especially for intermediate fitness costs and severe epidemic contexts. Switching from the current general deployment of resistant crops to custom rotation strategies could not only maintain or increase crop yield, but also preserve the few and valuable R-genes available. This research pertains to Samuel Nilusmas' PhD thesis. This work has been publisehd as a pre-print [76] and is currently under review. It has also been presented at several national and international conferences this year [66], [42].

Optimality/games in population dynamics

Participants : Frédéric Grognard, Ludovic Mailleret, Pierre Bernhard.

Optimal resource allocation. Mycelium growth and sporulation are considered for phytopathogenic fungi. For biotrophic fungi, a flow of resource is uptaken by the fungus without killing its host; in that case, life history traits (latency-sporulation strategy) have been computed based on a simple model considering a single spore initiating the mycelium, several spores in competition and applying optimal resource allocation, and several spores in competition through a dynamic game through the analytico-numerical solution of the Hamilton-Jacobi-Bellman-Isaacs equation [39]. This work is done with Fabien Halkett of INRA Nancy.

Optimal foraging and residence times variations. In this work, we built on our re-analysis of the Marginal Value Theorem (MVT) [4] to study the effect on the optimal foraging strategy of habitat conversion, whereby patches are converted from one existing type to another, hence changing the frequency of each type in the environment. We studied how realized fitness and the average rate of movement should respond to changes in the frequency distribution of patch-types, and how they should covary. We found that the initial pattern of patch-exploitation in a habitat can help predict the qualitative responses of fitness and movement rate following habitat conversion. We conclude that taking into account behavioral responses may help better understand the ecological consequences of habitat conversion [17].