Second-generation biofuels could provide renewable energy while reducing the globaleconomy dependence on oil and mitigating climate change. However, their greenhouse gasemission balances, as well as their energy and environmental balances, are discussed,especially when they are produced from agricultural feedstock. The use of agriculturalfeedstock for energy purposes also raises the issue of competition with food production. Inthis context, this work contributes to the assessment of the sustainability of Miscanthus xgiganteus, a perennial C4 crop candidate to the production of second-generation ethanol. Theobjectives of this work are (i) to achieve a multicriteria evaluation of cropping systems basedon M. Giganteus using data collected in farmers’ fields and (ii) to compare these croppingsystems with cropping systems including other resources Agricultural candidates for biofuelproduction. The main contributions of this work are (i) the study of the variability of yieldsand winter nitrate losses in a network of commercial fields located in Burgundy (France), (ii)the characterization by modeling of M. giganteus long-term yield evolution and (iii) theintegration of these findings in a process of cropping systems design and assessment aimingat comparing M. giganteus with other feedstock candidate to the production of bioethanol.The study of M. giganteus in farmers’ fields shows that the high variability of yields andnitrate losses is linked to (i) crop age, (ii) soil type and (iii) the type of field (i.e. culturalhistory, size, shape, and environment). Contrasting yield scenarios, built by combining datacollected in commercial fields with a long-term yield evolution model, show that thesensitivity of assessment results regarding yields depends on the assessment field. Theinsertion of M. giganteus in a cropping system can significantly improve the greenhouse gasemission balance as well as the environmental balance, compared with a cropping systembased on a short cropping sequence. Economic results depend strongly on M. giganteus yield.Other agricultural feedstocks are also interesting, especially on soils where the yield potentialof M. giganteus is low: this is particularly the case of alfalfa stems, which can be used forsecond-generation ethanol production. / Second-generation biofuels could provide renewable energy while reducing the globaleconomy dependence on oil and mitigating climate change. However, their greenhouse gasemission balances, as well as their energy and environmental balances, are discussed,especially when they are produced from agricultural feedstock. The use of agriculturalfeedstock for energy purposes also raises the issue of competition with food production. Inthis context, this work contributes to the assessment of the sustainability of Miscanthus xgiganteus, a perennial C4 crop candidate to the production of second-generation ethanol. Theobjectives of this work are (i) to achieve a multicriteria evaluation of cropping systems basedon M. Giganteus using data collected in farmers’ fields and (ii) to compare these croppingsystems with cropping systems including other resources Agricultural candidates for biofuelproduction. The main contributions of this work are (i) the study of the variability of yieldsand winter nitrate losses in a network of commercial fields located in Burgundy (France), (ii)the characterization by modeling of M. giganteus long-term yield evolution and (iii) theintegration of these findings in a process of cropping systems design and assessment aimingat comparing M. giganteus with other feedstock candidate to the production of bioethanol.The study of M. giganteus in farmers’ fields shows that the high variability of yields andnitrate losses is linked to (i) crop age, (ii) soil type and (iii) the type of field (i.e. culturalhistory, size, shape, and environment). Contrasting yield scenarios, built by combining datacollected in commercial fields with a long-term yield evolution model, show that thesensitivity of assessment results regarding yields depends on the assessment field. Theinsertion of M. giganteus in a cropping system can significantly improve the greenhouse gasemission balance as well as the environmental balance, compared with a cropping systembased on a short cropping sequence. Economic results depend strongly on M. giganteus yield.Other agricultural feedstocks are also interesting, especially on soils where the yield potentialof M. giganteus is low: this is particularly the case of alfalfa stems, which can be used forsecond-generation ethanol production.

Face à la pollution généralisée des masses d’eau souterraines par les nitrates et les pesticides, l’agriculture biologique (AB) est présentée comme un outil pertinent pour la reconquête de la qualité des eaux sur les aires d’alimentation de captage (AAC). Ce travail vise à mieux définir l’opportunité d’un développement de l’AB sur des zones à enjeu eau. L’objectif de la thèse est d’évaluer conjointement la faisabilité des conversions sur les exploitations de l’AAC et l’efficacité de ces conversions par rapport aux enjeux de reconquête de la qualité de l’eau.Etudier l’opportunité d’un développement de l’AB à l’échelle territoriale suppose d’instruire la diversité des exploitations et des profils d’agriculteurs sur la zone à enjeu eau. Pour être en mesure de tester l’opportunité des conversions, une méthode typologique permettant d’analyser conjointement la variabilité actuelle des pressions sur les zones à enjeu eau et la propension des agriculteurs conventionnels à la conversion est nécessaire.Pour produire cette typologie, nous avons développé une méthode innovante d’analyse compréhensive des pratiques, centrée sur les principes d’action à l’origine des systèmes de culture. Les principes d’action correspondent à des méta-raisonnements à l’origine de l’organisation concrète des pratiques agricoles sur le territoire d’exploitation. Par l’analyse conjointe du discours des agriculteurs et de la variabilité des règles de décision, nous avons élaboré des typologies basées sur les postures techniques des agriculteurs pour i) identifier des principes d’action associés aux pratiques à risque et ii) dégager des proximités éventuelles entre agriculteurs biologiques et agriculteurs conventionnels. La méthode a été testée sur deux territoires à enjeu eau en Rhône-Alpes, sur lesquels des entretiens semi-directifs ont été réalisés auprès d’exploitants conventionnels et biologiques.Cinq principes d’action génériques à l’origine de l’organisation de l’assolement et cinq principes d’action génériques à l’origine des pratiques culturales ont été dégagés. A partir des différents principes d’action, des typologies des postures techniques ont été produites sur les deux terrains. Les pressions à l’origine de la lixiviation des nitrates et des pesticides ont été évaluées et spatialisées via le recours à des indicateurs agro-environnementaux. Nous avons démontré que la variabilité forte des indicateurs et leur distribution spatiale sur les AAC étaient liées à la diversité des postures techniques entre agriculteurs.Nous avons comparé les principes d’action mobilisés par les agriculteurs conventionnels et les agriculteurs biologiques « références » présents sur les zones à enjeu eau. Par l’étude des spécificités des postures techniques en AB, trois critères de propension à la conversion ont été identifiés. Plusieurs degrés de propension à la conversion ont été dégagés parmi les agriculteurs conventionnels des deux territoires.L’analyse croisée des degrés de propension à la conversion et des différentiels de pressions entre systèmes conventionnels et biologiques nous a permis d’évaluer l’opportunité d’un développement de l’AB sur les deux territoires. Nos résultats ont mis en évidence des niveaux de pression limités quant à la lixiviation des nitrates sur les systèmes biologiques : un développement exhaustif de l’AB à l’échelle des deux AAC entrainerait potentiellement une réduction forte de la lixiviation des nitrates. Néanmoins, l’opportunité d’un tel développement doit être relativisée. Les agriculteurs présentant une propension réelle ou forte à la conversion sont minoritaires sur les AAC. Ensuite, le différentiel des pressions entre systèmes conventionnels et systèmes biologiques diminue à mesure que la propension à la conversion augmente. Pour envisager une diminution forte des pressions sur les zones à enjeu eau, la conversion devrait concerner des exploitants pour lesquels cette conversion est difficilement envisageable à moyen terme. / Many problems with nitrate and pesticide contamination from agriculture exist in European drinking water catchments. In France, a new mitigation approach aims at preventing water quality degradation in explicitly targeting agricultural non-point source pollutions associated with leaching of nitrates and pesticides. This work aims at assessing the opportunity to develop organic farming in water catchment areas in order to reduce nitrate and pesticide leaching from root zone. The objective was to analyze both i) feasibility of conversions to organic farming on farms concerned by water preservation and ii) the potential impacts of these conversions in terms of nitrate and pesticide leaching reduction.To explore the potential contribution of organic farming in water catchment areas, we develop an innovative typology approach to characterize farmers’ conceptions and strategies related to cropping systems’ organization on the farm territory. Our method was tested in two French water catchment areas characterized by diversified production systems, where semi-structured interviews were carried out with conventional and organic farmers. Resulting typologies of farmers were used to assess leaching risks variability related with current cropping systems and to identify potential similarities between conventional and organic farmers’ conceptions. Nitrate and pesticide leaching risks for cropping systems were assessed and spatialized by using four agro-environmental indicators. Our results show major variations for all indicators at both study sites, for example N-surpluses which range from -105 to 192 kg N ha-1 year-1. These variations are deeply related with diversity of farmers’ conceptions summarized in typologies. To assess proximity of conventional farmers to organic farming, we used typologies to compare conceptions related to organization of cropping systems between conventional and organic farmers. By analyzing specificities of organic farmers’ conceptions, we determined three main criteria of proximity to organic farming; these criteria were then used to identify various degrees of proximity to organic farming among conventional farmers in the catchment areas.To assess potential contribution of organic farming to water preservation in catchment areas, we firstly compared nitrate leaching risks between conventional and organic cropping systems. Our results reveal low leaching risks from organic systems, characterized by reduced N-surpluses and lower bare soils frequencies in autumn. According to these results, massive development of organic farming should decrease nitrate leaching in our two water catchment areas. However, analysis of similarities between conventional and organic farmers’ conceptions shows that a majority of farmers are characterized by a low level of proximity to organic farming. Moreover, the farmers who show strongest similarities with organic farmers’ conceptions are already those with low leaching risks cropping systems. To significantly lower nitrate leaching risks, conversions should concern conventional farmers with low degree of proximity to organic farming.