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International audience; Inspired by agroecology, ecological aquaculture proposes an alternative model that uses ecology as a paradigm to develop innovative, more eco-friendly aquaculture with environmental, economic and social benefits. Integrated multi-trophic aquaculture (IMTA) is one application of this principle. Inspired by the natural trophic chain, it associates primary producers with primary or secondary consumers, providing a new source of biomass without requiring supplementary feed by recycling inorganic and organic wastes. Of these systems, land-based IMTAs demonstrate several advantages, especially easier control of nutrient flows, contaminants and/or predators. This study focused on a land-based marine IMTA, combining a recirculating aquaculture system for fish consecutively with a natural marine polyculture of microalgae and oyster cultivation. The objective was to assess the ability of the microalgal polyculture both to bioremediate fish nutrients and to sustain oyster growth. For the first time in a Mediterranean climate, we confirmed the feasibility of developing a microalgae community of interest for oysters maintained by fish effluent. Despite strong variability in microalgae production, this IMTA system resulted in significant oyster growth over the experimental period of one month, with growth results of the same order of magnitude as natural juvenile growth. In the conditions tested, this IMTA with reduced human intervention allowed a gain in recoverable biomass of 3.7 g of oyster produced per kg of fish feed distributed. By transforming waste into additional biomass, IMTAs offer a more promising, ecological avenue for aquaculture, based on a circular economy, which may in turn increase the social acceptability of fish farming.

International audience; Light is a key environmental factor for the growth of micro-algae, and optimizing the capture of light is critical for high efficiency production systems. As the density of the population of micro-algae increases, the availability of light decreases, leading to a reduction in the growth rate because of mutual shading, while other effects, such as photo-inhibition, might be especially frequent when the population density is low. Several models in the literature have been developed to take into account light phenomena and predict micro-algal growth, particularly in a mono-culture. With the help of a simple expression for the attenuation of the light, we propose and justify a new growth function that incorporates both photo-inhibition and photolimitation. In agreement with the experimental data, this new formulation describes the micro-algal response to a wide range of situations of excessive or insufficient light intensities through an explicit dependence on both the incident light and the biomass concentration. While simple, the proposed expression can be satisfactorily applied to practical cases under nutrient replete conditions in photo-bioreactors with different sizes and geometries. It extends naturally to the growth of different species, providing a dynamic model which can simulate experiments in a mono-culture as well as in polycultures. The investigation of the competition for light-limited growth shows that the model predicts competitive exclusion, which has also been experimentally demonstrated. This leads to new perspectives for the control and optimization of mixed micro-algal cultures.

International audience; The productivity of most marine ecosystems is limited by the availability of dissolved nitrogen (N) and phosphorus (P). Nutrient recycling is therefore a key process for ecosystem functioning. Fish recycle nutrients through the excretion of ammonia and phosphate and can influence the abundance and community structure of primary producers such as phytoplankton. However, the effect of fish on other plankton compartments, and whether all fish species have similar effects, is largely unknown. We used a tank experiment to test how 2 Mediterranean fish species, gilthead seabream Sparus aurata and golden mullet Chelon auratus, with distinctly different N and P excretion rates, can affect the abundance and community structure of 3 plankton compartments: phytoplankton, bacterioplankton, and microzooplankton. We found that the nutrients released by seabream (whose excreta had an N:P molar ratio greater than the Redfield ratio of 16:1) induced a substantial increase in the abundance of all plankton compartments. In addition, with seabream, the relative abundance of diatoms in the phytoplankton communities increased. However, no significant change was observed with mullet, which had a low excreta N:P molar ratio, suggesting that the growth of microbial plankton was limited by the availability of N. Our results demonstrate that nutrient excretion by fish affects the microbial food web through a species-specific bottom-up effect on the total abundance and community structure of the phytoplankton, bacterioplankton, and microzooplankton communities.

International audience; Recently, CO2 recycling for the production of valuable microalgae has acquired substantial interest. Most studies investigating CO2 conversion efficiency in algal cultures were based on single species, although a stabilising effect of algal diversity on biomass production was recently highlighted. However, addition of CO2 into polyalgal cultures requires a careful control of pH; performance of CO2 conversion, growth and carbon biomass production are affected by pH differently, depending on the species of microalgae. This study investigates the efficiency of CO2 conversion by natural marine algal assemblage cultivated in open, land-based raceways (4.5 m3, 10 m2), working as high rate algal ponds (HRAP). Ponds were enriched with nitrogen and phosphate, pure CO2 was added and algal cultures were grown under three different fixed pH levels: pH 6, 7 and 8. The highest conversion of photosynthetically fixed CO2 into carbon biomass (40%) was reached at pH 7, an intermediate level, due to the partial CO2 asphyxiation of algal predators (copepods, ciliates), while being under the suboptimal conditions for the development of marine amoebae. Under this pH, the theoretical maximal biological conversion of available CO2 into carbon biomass was estimated to be 60% in naturally inoculated open ponds.

International audience; We address the problem of determining functional framing from experimental data points in view of robust time-varying predictions, which is of crucial importance in bioprocess monitoring. We propose a method that provides guaranteed functional bounds, instead of sets of parameters values for growth functions such as the classical Monod or Haldane functions commonly used in bioprocess modeling. We illustrate the applicability of the method with bioreactor simulations in batch and continuous mode, as well as on real data. We also present two extensions of the method adding flexibility in its application, and discuss its efficiency in providing guaranteed state estimations.

International audience; Dziani Dzaha is a maar the age of which is close to 4000 years. While its water is thought to have originated from seawater it is now considered as an extreme environment due to its hypersaline and alkaline characteristics. Those extreme features have led to the simplification of the trophic network. Cyanobacteria account for up to 95% of the photosynthetic biomass. The main biogeochemical processes, i.e. photosynthesis, bacterial sulfate reduction and methanogenesis could explain the current water composition. As far as we know, this ecosystem could be unique on Earth, extending the nature and chemical limits of aquatic inland ecosystems.

The Proterozoic Era records two periods of abundant positive carbon isotope excursions (CIEs), conventionally interpreted as resulting from increased organic carbon burial and leading to Earth’s surface oxygenation. As strong spatial variations in the amplitude and duration of these excursions are uncovered, this interpretation is challenged. Here, by studying the carbon cycle in the Dziani Dzaha Lake, we propose that they could be due to regionally variable methane emissions to the atmosphere. This lake presents carbon isotope signatures deviated by ~ + 12‰ compared to the modern ocean and shares a unique combination of analogies with putative Proterozoic lakes, interior seas or restricted epireic seas. A simple box model of its Carbon cycle demonstrates that its current isotopic signatures are due to high primary productivity, efficiently mineralized by methanogenesis, and to subsequent methane emissions to the atmosphere. By analogy, these results might allow the reinterpretation of some positive CIEs as at least partly due to regionally large methane emissions. This supports the view that methane may have been a major greenhouse gas during the Proterozoic Era, keeping the Earth from major glaciations, especially during periods of positive CIEs, when increased organic carbon burial would have drowned down atmospheric CO2.

Most older methods of fish farming, or aquaculture, have focused on growing only a single species of sea life, for example, salmon. Modern aquaculture systems involve the cultivation of two or more species together, based on what happens normally in the food chain, so that one species can provide a source of food for another species in the farm. This article describes the results of an experiment combining fish culture with algae culture and oyster culture. We show that algae can grow using fish waste, and oysters can eat algae to produce good-quality, healthy food, which reduces the pollution generated by aquaculture.

Author Correction: Demonstration of facilitation between microalgae to face environmental stress. In Scientific Reports, vol; 10, n°1, Article : 3557 ; DOI: 10.1038/s41598-020-59860-0 ; WOS:000563252500001 Author Correction: Demonstration of facilitation between microalgae to face environmental stress. In Scientific Reports, vol; 10, n°1, Article : 3557 ; DOI: 10.1038/s41598-020-59860-0 ; WOS:000563252500001The original version of this Article omitted an affiliation for Emna Krichen and the Acknowledgements section contained typographical errors and was incomplete. This erratum is available as an annex file.; International audience; Positive interactions such as facilitation play an important role during the biological colonization and species succession in harsh or changing environments. However, the direct evidence of such ecological interaction in microbial communities remains rare. Using common freshwater microalgae isolated from a High Rate Algal Pond HRAP treating wastewaters, we investigated with both experimental and modeling approaches the direct facilitation between two algal strains during the colonization phase. Our results demonstrate that the first colonization by microalgae under a severe chemical condition arose from the rapid growth of pioneer species such as Chlorella sorokiniana, which facilitated the subsequent colonization of low growth specialists such as Scenedesmus pectinatus. The pioneer species rapidly depleted the total available ammonia nitrogen favoring the specialist species initially inhibited by free ammonia toxicity. This latter species ultimately dominated the algal community through competitive exclusion under low nutrient conditions. We show that microbial successions are not only regulated by climatic conditions but also by interactions between species based on the ability to modify their growth conditions. We suggest that facilitation within the aquatic microbial communities is a widespread ecological interaction under a vast range of environmental stress.

Phytoplankton and bacterioplankton are the key components of the organic matter cycle in aquatic ecosystems, and their interactions can impact the transfer of carbon and ecosystem functioning. The aim of this work was to assess the consequences of chemical contamination on the coupling between phytoplankton and bacterioplankton in two contrasting marine coastal ecosystems: lagoon waters and offshore waters. Bacterial carbon demand was sustained by primary carbon production in the offshore situation, suggesting a tight coupling between both compartments. In contrast, in lagoon waters, due to a higher nutrient and organic matter availability, bacteria could rely on allochthonous carbon sources to sustain their carbon requirements, decreasing so the coupling between both compartments. Exposure to chemical contaminants, pesticides and metal trace elements, resulted in a significant inhibition of the metabolic activities (primary production and bacterial carbon demand) involved in the carbon cycle, especially in offshore waters during spring and fall, inducing a significant decrease of the coupling between primary producers and heterotrophs. This coupling loss was even more evident upon sediment resuspension for both ecosystems due to the important release of nutrients and organic matter. Resulting enrichment alleviated the toxic effects of contaminants as indicated by the stimulation of phytoplankton biomass and carbon production, and modified the composition of the phytoplankton community, impacting so the interactions between phytoplankton and bacterioplankton.

International audience; Several studies focused on wastewater treatment in High Rate Algal Ponds (HRAP) suggest that highly variable climatic conditions cause large variations of microalgal biomass productivity. In the present study, we show that similar carbon, nitrogen and phosphorus removal efficiencies were reached in different HRAPs treating urban wastewaters located in two different temperate (Mediterranean and oceanic) climates. Furthermore, similar ecological successions were observed in these HRAPs. During the start-up phase, the consumption of organic matter by detritivores, already present in the wastewater, appears to be necessary for the microalgae to grow within two weeks in spring. The growth of the rapid-growing species, Chlorella sp., followed by the grazing-resilient species, Scenedesmus sp., combined with nitrifying and denitrifying bacterial activity, removed most the ammonia. The resulting exhaustion of ammonia would limit the complete removal of dissolved COD by bacteria and phosphate by microalgae in the HRAPs. This study shows that similar biological and environmental constraints were applied on the HRAPs, making the process efficiency highly reproducible under different temperate latitudes.

International audience; Integrated multi-trophic aquaculture (IMTA) systems are a promising solution for sustainable aquaculture combining nutrient recycling with increased biomass production. An innovative land-based recirculating aquaculture system (RAS) was studied in France for a 60-day experiment. It combined a European sea bass (Dicentrarchus labrax) RAS with two other production systems: high rate algal ponds (HRAP) with natural marine polyspecific algal assemblages, and oysters in separate open tanks. The objective was the assessment of: 1) the efficiency and the stability of the microalgae bioremediation of the effluent from a fish RAS in spring and summer, 2) the abundance and the diversity patterns of the microalgae biomass for consumption in the oyster compartment of the IMTA. Silicate was added every week after the beginning of the experiment for maintaining a Si:N:P molar ratio of 10:5:1 in the HRAP to encourage the growth of diatoms. The HRAP have an overall removal efficiency of 98.6 ± 0.2% for NO3-N, 98.0 ± 0.4% for NO2-N, 97.3 ± 0.7% for NH4-N and 96.1 ± 0.6% for PO4-P, with removal rates of 335.8 ± 0.8, 23.6 ± 0.2, 30.9 ± 0.2, and 22.3 ± 0.2 mgm−2 d−1, respectively. The concentration of total suspended solid (TSS) and chlorophyll a (chl a) increased during the experiment and reached maximum values on day 46 (135.3 ± 34.7 mg TSS l−1 and 0.42 ± 0.03 mg chl a l−1) after which the microalgae collapsed due to a CO2 limitation (pH ca. 10). Sequencing analysis revealed that the microalgae community was dominated by Tetraselmis sp. from day 1 to day 16 (45.7% to 73.8% relative abundance). From day 30 to day 43 the culture was dominated by diatoms, Phaeodactylum sp. (83.4% to 98.1% relative abundance). Although the stable carbon isotope signatures confirmed that the microalgae were consumed, oysters' growth was limited in the RAS-IMTA, suggesting that oysters were under stress or not fed enough

When microalgae are exposed to contaminants, the role of associated bacteria within the phycosphere, the microenvironment surrounding algal cells, remains largely unknown. The present study investigated the importance of algae-associated bacteria on the responses of microalgae growth to metallic and organic toxicant exposure. The effects of a polluted sediment elutriate, and of metal or pesticide mixtures at environmentally relevant concentrations (

Recent observations in polar marine waters have shown that a large fraction of primary production may be lost to respiration by planktonic bacteria due to very low bacterial growth efficiencies in cold waters. Here we report that sea temperature may be a key factor (but not the only one) influencing the interaction between bacteria and primary production in North Atlantic and Arctic waters, suggesting that low primary production rates could not sustain bacterial carbon demand in the coldest Arctic waters. The use of freshly produced phytoplankton exudate by bacteria in early- and mid-summer was assessed, together with the bacterial uptake of dissolved inorganic nitrogen (DIN = nitrate and ammonium), in surface waters along a latitudinal gradient from the North Sea to the Arctic sea ice. Bacterial production was independent of the low primary production measured in the coldest waters. Under these conditions, heterotrophic bacteria can consume a large fraction of DIN and N-rich organic matter, making them strong contributors to N fluxes in these waters.

International audience; This study investigated the influence of light and temperature on Chlorella sorokiniana grown on a mixture of acetate and butyrate, two of the volatile fatty acids produced by dark fermentation. Exposure to light caused autotrophic biomass production (56% of the final biomass) and reduced the time to reach butyrate exhaustion to 7 days at 25°C from 10 days in the dark. For growth on acetate at the optimum temperature (35°C), the presence of butyrate reduced the growth rate (by 46%) and the carbon yield (by 36%). For successful microalgae growth on dark fermentation effluent, butyrate inhibition may be reduced by setting the temperature to 30°C and providing light.

International audience; Coupling dark fermentation (DF), which produces hydrogen from diverse effluents or solid waste, and heterotrophic cultivation of microalgae, which produces lipids, carbohydrates and proteins, is a promising and innovative solution for developing sustainable biorefineries. The use of a raw DF effluent, containing acetate and butyrate, to support the heterotrophic growth of Chlorella sorokiniana was investigated. All the acetate in sterilized and unsterilized DF effluent was exhausted in less than three days of heterotrophic cultivation, whereas butyrate was not used by the microalgae. The microalgae biomass reached 0.33 g L− 1 with a carbon yield on acetate of 55%. The algal yield was higher than previously reported for synthetic DF effluent. It was concluded that compounds other than volatile fatty acids were present in the DF effluent and these could be consumed by the microalgae. After the acetate had been exhausted, butyrate was consumed by facultative and strict aerobic bacteria originating from the DF effluent. The concentration of the bacterial community increased during the experiment but did not have any significant impact on heterotrophic microalgae growth. A high microalgal biomass yield was achieved without requiring the DF effluent to be sterilized.

International audience; The impact of fish and oysters on components of the pelagic microbial food web (MFW) was studied in a 10 d mesocosm experiment using Mediterranean coastal waters. Two mesocosms contained natural water only (‘Controls’), 2 contained natural water with Crassostrea gigas (‘Oyster’), and 2 contained natural water with Atherina spp. (‘Fish’). Abundances and biomasses of microorganisms (viruses, bacteria, phytoplankton, heterotrophic flagellates, and ciliates) were measured to estimate their contribution to the total microbial carbon biomass. Two MFW indices, the microbial autotroph:heterotroph C biomass ratio (A:H) structural index and the gross primary production:respiration ratio (GPP:R) functional index, were defined. In the Fish mesocosms, selective predation on zooplankton led to a trophic cascade with 51% higher phyto- plankton C biomass and consequently higher A:H and GPP:R than in the Controls. By the end of the experiment, the Oyster mesocosms had a bacterial C biomass 87% higher and phytoplankton C biomass 93% lower than the Controls, giving significantly lower A:H and GPP:R (1), whereas oyster activities made the MFW more hetero- trophic (both indices

International audience; Rivers are known to be major contributors to eutrophication in marine coastal waters, but little is known on the short-term impact of freshwater surges on the structure and functioning of the marine plankton community. The effect of adding river water, reducing the salinity by 15 and 30%, on an autumn plankton community in a Mediterranean coastal lagoon (Thau Lagoon, France) was determined during a 6-day mesocosm experiment. Adding river water brought not only nutrients but also chlorophyceans that did not survive in the brackish mesocosm waters. The addition of water led to initial increases (days 1-2) in bacterial production as well as increases in the abundances of bacterioplankton and picoeukaryotes. After day 3, the increases were more significant for diatoms and dinoflagellates that were already present in the Thau Lagoon water (mainly Pseudo-nitzschia spp. group delicatissima and Prorocentrum triestinum) and other larger organisms (tintinnids, rotifers). At the same time, the abundances of bacterioplankton, cyanobacteria, and picoeukaryote fell, some nutrients (NH4 (+), SiO4 (3-)) returned to pre-input levels, and the plankton structure moved from a trophic food web based on secondary production to the accumulation of primary producers in the mesocosms with added river water. Our results also show that, after freshwater inputs, there is rapid emergence of plankton species that are potentially harmful to living organisms. This suggests that flash flood events may lead to sanitary issues, other than pathogens, in exploited marine areas.

International audience; This work describes a method to model the optical properties over the (400-750 nm) spectral range of a dense microalgal culture using the chemical and physical properties of the algal cells. The method was based on a specific program called AlgaSim coupled with the adding-doubling method: at the individual cell scale, AlgaSim simulates the spectral properties of one model, three-layer spherical algal cell from its size and chemical composition. As a second step, the adding-doubling method makes it possible to retrieve the total transmittance of the algal medium from the optical properties of the individual algal cells. The method was tested by comparing the simulated total transmittance spectra for dense marine microalgal cultures of Isochrysis galbana (small flagellates) and Phaeodactylum tricornutum (diatoms) to spectra measured using an experimental spectrophotometric setup. Our study revealed that the total transmittance spectra simulated for the quasi-spherical cells of Isochrysis galbana were in good agreement with the measured spectra over the whole spectral range. For Phaeodactylum tricornutum, large differences between simulated and measured spectra were observed over the blue part of the transmittance spectra, probably due to non-spherical shape of the algal cells. Prediction of the algal cell density, mean size and pigment composition from the total transmittance spectra measured on algal samples was also investigated using the reversal of the method. Mean cell size was successfully predicted for both species. The cell density was also successfully predicted for spherical Isochrysis galbana, with a relative error below 7%, but not for elongated Phaeodactylum tricornutum with a relative error up to 26%. The pigments total quantity and composition, the carotenoids:chlorophyll ratio in particular, were also successfully predicted for Isochrysis galbana with a relative error below 8%. However, the pigment predictions and measurements for Phaeodactylum tricornutum showed large discrepancies, with a relative error up to 88%. These results give strong support for the development of a promising tool providing rapid and accurate estimations of biomass and physiological status of a dense microalgal culture based on only light transmittance properties.

In recent years, coupling bacterial dark fermentation (DF) and heterotrophic cultivation of microalgae (HCM) has been pointed out as a promising sustainable approach for producing both gaseous and liquid biofuels. Complex organic waste and effluents that are not susceptible to be directly degraded by microalgae are first converted into volatile fatty acids (VFAs) and hydrogen by DF. In this work, the feasibility of using DF effluents to sustain has been thoroughly reviewed and evaluated. Promising perspectives in terms of microalgae biomass and lipids production are proposed and can be extended as guidelines to promote HCM whatever the organic waste used. Abiotic and biotic factors from DF effluents that promote or inhibit microalgae growth are discussed as well as the use of unsterile DF effluents. Overall, the microalgae growth is favored on effluents containing high acetate concentration (> 3 g L−1), with a high acetate:butyrate ratio (> 2.5), and when pH is strictly controlled. At a low acetate:butyrate ratio (10 g L−1), a low substrate:microalgae ratio and the presence of light appear to enhance microalgae growth. Butyrate content appears to be a key factor when coupling DF/HCM since high butyrate concentration inhibits the microalgae growth.

The importance of heterotrophic bacteria relative to phytoplankton in the uptake of ammonium and nitrate was studied in Mediterranean coastal waters (Thau Lagoon) during autumn, when the Mediterranean Sea received the greatest allochthonous nutrient loads. Specific inhibitors and size-fractionation methods were used in combination with isotopic 15N tracers. NO3 − and NH4 + uptake was dominated by phytoplankton (60 % on average) during the study period, which included a flood event. Despite lower biomass specific NH4 + and NO3 uptake rates, free-living heterotrophic bacteria contributed significantly (>30 %) to total microbial NH4 + and NO3 − uptake rates in low chlorophyll waters. Under these conditions, heterotrophic bacteria may be responsible for more than 50 % of primary production, using very little freshly produced phytoplankton exudates. In low chlorophyll coastal waters as reported during the present 3-month study, the heterotrophic bacteria seemed to depend to a greater extent on allochthonous N and C substrates than on autochthonous substrates derived from phytoplankton.

International audience; The growth of two lipid-producing Chlorella species on fermentative end-products acetate, butyrate and lactate, was investigated using a kinetic modeling approach. Chlorella sorokiniana and Auxenochlorella protothecoides were grown on synthetic media with various (acetate:butyrate:lactate) ratios. Both species assimilated efficiently acetate and butyrate with yields between 0.4 and 0.5 g carbon of biomass/g carbon of substrate, but did not use lactate. The highest growth rate on acetate, 2.23 d−1, was observed for C. sorokiniana, and on butyrate, 0.22 d−1, for A. protothecoides. Butyrate removal started after complete acetate exhaustion (diauxic effect). However, butyrate consumption may be favored by the increase of biomass concentration induced by the initial use of acetate. A model combining Monod and Haldane functions was then built and fitted the experimental data well for both species. Butyrate concentration and (acetate:butyrate) ratios were identified as key parameters for heterotrophic growth of microalgae on fermentative metabolites.

The stability and the performances of microalgae production systems are challenging issues, particularly in the context of the use of microalgae for the bioremediation of effluents and the production of biomass ofindustrial interest. One of the challenging axes of research is to take advantage of the diversity of microalgae through the use of assemblages (polycultures) for improving the overall production performances. However, theexploitation of these complex assemblages in an open system is subject to various stresses : biotic (undesirable microalgae or competing bacteria) and abiotic (limitation of resources, especially nitrogen and light). Thesestressing factors could influence interactions within assemblages, making thereby difficult the prediction and the optimization of the overall production. The objective of this thesis is to propose methods and tools forunderstanding, predicting, and optimizing the biomass production of an algal assemblage (natural or artificially designed microbial consortium) under the fluctuation of resources and culture conditions. More specifically,we have developed mathematical models based on dynamical systems that can be compared to laboratory and pilot-scale experiments. Firstly, an experimental method was defined for characterizing the specific growth rate of photosynthetic microorganisms, according to the limiting resource. Furthermore, a new functional estimation method is proposed. This method provides two growth curves that envelop scattering growth rate data and thus allow dynamic estimates of the state variables with guaranteed intervals. Secondly, the type of the interactions between two microalgae Chlorella sorokiniana and Scenedesmus pectinatus, which typically have successional trends in the outdoor ponds used for the treatment of urban wastewater, has been characterized ; first according to the fluctuation of the different forms of nitrogen (NH+4/NH3), and secondly to the light availability. The mathematical models associated with the experiments carried out during this thesis demonstrate that the initial development of an opportunistic microalgal species, which is more resistant to high levels of NH+4/NH3 was required for the subsequent development of a more efficient microalgal species under low light availability in these turbid processes. Third, we explored the paradoxical interactions occurring between microalgae and heterotrophic bacteria. Through the exudation of carbon, microalgae stimulate its competitors for common resources : nitrogen or phosphorus. We have thus studied the influence of this phenomenon by proposing a four-dimensional model. The mathematical analysis revealed that the equilibrium of coexistence is unique, and the installation of bacteria is robust, as it has been shown that the equilibrium without bacteria is unstable. We show that when the concentration of the mineral resource that continuously feeds the bioreactor is large enough, there are renewal rate values for which there is coexistence, while bacteria could not grow in the absence of microalgae under these same operating conditions. Finally, it has been shown, using simulations, that during coexistence their biomasses can oscillate. These results demonstrate the complexity of biotic interactions, provide methods applicable to other model organisms, and raise promising application possibilities for the optimization and the control of bioprocess dynamical systems for future work., Dans le contexte de l’utilisation des microalgues pour la bioremédiation d’effluents et la production de biomasse d’intérêt industriel, la stabilité et les performances des systèmes de production sont des enjeux majeurs. Unedes voies de recherche privilégiées est la mise à profit de la diversité des microalgues en assemblages (polycultures) pour l’amélioration des performances de la production. Néanmoins, l’exploitation de ces assemblages complexes en système ouvert extérieur est sujette à divers stress biotiques (microalgues indésirables ou bactéries compétitrices) et abiotiques (limitation des ressources, notamment l’azote et la lumière) qui influencent les interactions au sein des assemblages, rendant difficiles la prédiction et l’optimisation de la production. L’objectif de la présente thèse est de proposer des méthodes et des outils permettant de comprendre, prédire et optimiser la production de biomasse d’un assemblage algal (consortium microbien naturel ou artificiellement composé) sous la fluctuation des ressources et des conditions de culture. Plus particulièrement, nous avons développé des modèles mathématiques basés sur des systèmes dynamiques, qui peuvent être confrontés à des expériences en laboratoire et à l’échelle-pilote. Les premiers travaux de cette thèse ont consisté à choisir une méthode expérimentale pour la caractérisation de la vitesse de croissance spécifique des microorganismes photosynthétiques en fonction de la ressource limitante. Par ailleurs, une nouvelle méthode d’estimation fonctionnelle est proposée produisant deux courbes de croissance qui encadrent les données de vitesse de croissance et permettant ainsi des estimations dynamiques des variables d’état par intervalles garantis. Dans un deuxième temps, la nature des interactions entre deux microalgues Chlorella sorokiniana et Scenedesmus pectinatus, qui se succèdent classiquement dans les bassins extérieurs utilisés pour le traitement des eaux usées urbaines, a été caractérisée en fonction de la fluctuation des différentes formes de l’azote (NH+4/NH3) et ensuite de la lumière disponible. Les modèles mathématiques associés aux expérimentations menées au cours de cette thèse ont permis de démontrer que le développement initial d’une espèce microalgale de type opportuniste, plus résistante aux fortes teneurs en NH+4/NH3 était nécessaire pour que puisse s’établir ensuite une espèce microalgale plus efficace vis-à-vis de la faible lumière disponible dans ces procédés très turbides. Dans un troisième temps, nous avons exploré les interactions paradoxales qui existent entre les microalgues et les bactéries hétérotrophes. En effet, les microalgues stimulent, à travers l’exsudation du carbone, leurs compétiteurs pour une ressource commune : l’azote ou le phosphore. Nous avons étudié l’influence de ce phénomène en proposant un modèle dynamique en dimension quatre. L’analyse mathématique a révélé l’unicité de l’équilibre de coexistence et la robustesse de l’installation des bactéries, car il a été démontré que l’équilibre en absence de bactéries est répulsif. Nous montrons que lorsque la concentration de la ressource minérale alimentant en continu le bioréacteur est suffisamment grande, il existe des valeurs du taux de renouvellement du réacteur pour lesquelles il y a coexistence, alors que les bactéries ne pourraient pas se développer en l’absence de microalgues dans ces mêmes conditions opératoires. Enfin, il a été montré à l’aide de simulations que lors de la coexistence, leur biomasse respectives peut osciller. Ces résultats témoignent de la complexité des interactions biotiques, fournissent des méthodes applicables à d’autres organismes modèles permettant de les étudier, et soulèvent des possibilités d’application prometteuses pour l’optimisation et le contrôle des systèmes dynamiques de procédés pour les travaux futurs.

Growing microalgae in heterotrophic mode present several advantages over autotrophic mode such as a higher productivity in terms of biomass and lipids for biofuels production. Nevertheless, this process is limited by the production cost associated with the organic substrate (i.e. glucose) and fermenters sterilization costs. Dark fermentation effluents, mainly composed of acetate and butyrate, could be used as a low-cost medium to grow microalgae heterotrophically or mixotrophically. The aims of this PhD were i) to optimize microalgae growth on various mixtures of fermentations metabolites using the presence or absence of light and different cultivation temperatures and ii) to assess the feasibility of using unsterilized fermentation effluents. First, a model based on mass balance was built to characterize heterotrophic growth rates and yields when Chlorella sorokiniana and Auxenochlorella protothecoides were supplemented with different mixtures of acetate and butyrate. Results showed that the acetate:butyrate ratio and the butyrate concentration per se were two key parameters for promoting heterotrophic growth. Then, further studies showed that the presence of light and the use of suboptimal temperature (30 °C) could reduce the butyrate inhibition on growth by either triggering autotrophic production of biomass or enhancing growth on acetate. Finally, it was shown that microalgae could outcompete fermentation bacteria for acetate when growing on raw dark fermentation effluents, thanks to a fast algal growth on acetate (1.75 d-1) and a drastic change of culture conditions to the detriment of bacterial growth.; La production de microalgues en hétérotrophie présente plusieurs avantages pour la production de biocarburants par rapport à la production autotrophe, comme une productivité plus importante en termes de biomasse et de lipides. Cependant, le développement industriel de ce procédé est limité par les coûts de productions associés au substrat organique (i.e. glucose) et à ceux liés à la stérilisation des fermenteurs. Les effluents de fermentation sombre, composés principalement d’acétate et de butyrate, pourraient être utilisés comme milieux de culture peu onéreux pour la culture hétérotrophe ou mixotrophe de microalgues. Les objectifs de cette thèse étaient i) de mieux appréhender la croissance algale sur des mélanges variés d’acétate et de butyrate en fonction de la présence ou l’absence de lumière et de la température de croissance et ii) d’évaluer la faisabilité d’utiliser des effluents de fermentation non stérilisés pour soutenir la croissance de microalgues oléagineuses. Tout d’abord, un modèle basé sur des bilans de masse a été construit afin de caractériser (taux de croissance et rendements) la croissance hétérotrophe de Chlorella sorokiniana et Auxenochlorella protothecoides sur des mélanges d’acétate et de butyrate. Les résultats ont montré que le rapport acétate:butyrate et la concentration en butyrate étaient deux paramètres clés pour soutenir la croissance hétérotrophe. Puis, il a été démontré que la présence de lumière et l’utilisation d’une température suboptimale (30 °C) pour la croissance algale permettaient de réduire l’inhibition du butyrate en permettant une production de biomasse autotrophe ou en améliorant la croissance sur acétate. Enfin, il a été montré que les microalgues peuvent être compétitives sur l’acétate lors de la croissance sur des effluents bruts de fermentation sombre en présence de bactéries fermentaires, grâce à la croissance rapide des microalgues sur acétate (1.75 j-1) et à un changement drastique des conditions de culture peu favorables à la croissance des bactéries d’origine fermentaire.