Quantification and modelling of carbon and nitrogen fate in alternative cropping systems experiments on the long term Benedicte Autret To cite this version: Benedicte Autret. Quantification and modelling of carbon and nitrogen fate in alternative cropping systems experiments on the long term. Agricultural sciences. Institut agronomique, vétérinaire et forestier de France, 2017. English. NNT : 2017IAVF0023. tel-02119362 HAL Id: tel-02119362 https://tel.archives-ouvertes.fr/tel-02119362 Submitted on 3 May 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. NNT°: 2017IAVF0023 THESE DE DOCTORAT préparée à l’Institut des sciences et industries du vivant et de l’environnement (AgroParisTech) pour obtenir le grade de Docteur de l’Institut agronomique vétérinaire et forestier de France Spécialité : Sciences agronomiques École doctorale n°581 Agriculture, alimentation, biologie, environnement et santé (ABIES) par Bénédicte AUTRET Quantification and modelling of carbon and nitrogen fate in alternative cropping systems experiments on the long term Directeur de thèse : Bruno MARY Co-encadrement de la thèse : Nicolas BEAUDOIN Thèse présentée et soutenue à Paris, le 10 novembre 2017 : Composition du jury : Mme Sylvie RECOUS, Directeur de recherche, INRA UMR FARE Présidente M. Carlo GRIGNANI, Professor, Universita degli Studi di Torino Rapporteur M. Jens LEIFELD, Senior Scientist, Agroscope Zürich Rapporteur Mme Joëlle FUSTEC, Enseignant chercheur, ESA Angers UR LEVA Examinatrice M. Jørgen Eivind OLESEN, Professor, Aarhus University Examinateur M. Bruno MARY, Directeur de recherche, INRA UR AgroImpact Directeur de thèse Nom de l’Unité d’accueil : INRA AgroImpact Adresse de l’Unité de recherche : 180 rue Pierre Gilles de Gennes, Pôle du Griffon, 02000 BARENTON BUGNY Abstract Agricultural activities can lead to imbalanced carbon (C) and nitrogen (N) dynamics compared to natural terrestrial eco-systems, causing potential damages for soil, water and air quality. Among these prejudices, decreased soil C and N stocks, increased nitrate leaching in waters and gaseous N emissions towards the atmosphere are of a major concern. To reduce these environmental impacts, innovative and sustainable farming systems are promoted, such as low inputs cropping systems, “conservation” agriculture or organic farming. At a larger scale, the diffusion of such systems could play an important role in mitigating and adapting agriculture to climate change, assuming their assessment in the long term. The objectives of this work were i) to quantify the long term impact of different alternative cropping systems on the fate of C and N in the soil-plant-atmosphere system and ii) to simulate C and N dynamics with the agro- environmental model STICS. For this purpose, we studied three long-term field trials, namely the experiment of La Cage (France) established in 1998, the DOK (Switzerland) started in 1978 and the Foulum Organic (Denmark) established in 1998. The methodological approach combined experimentation and modelling. While La Cage trial enabled an in situ quantification of soil organic C and N storage, N leaching, nitrous oxide (N2O) emissions and greenhouse gas (GHG) balance in alternative cropping systems compared to conventional, the Swiss and Danish experiments were used for in silico estimation of the C and N fates in organic cropping systems, after adaptation of the STICS model to simulate new cropping practices, followed by calibration and evaluation of the model. After 16 years, significant annual SOC and SON accumulation was found under conservation agriculture (630 kg C and 54 kg N ha-1 yr-1) and organic farming (280 kg C and 31 kg N ha-1 yr-1) on 0-30 cm at La Cage, whereas no significant change was observed in the low input and the conventional systems. We measured the specific SOC and SON mineralization rates (per unit of SOC and SON) of the four systems through a four-month soil incubation and did not detect any difference between systems. Using these results and the AMG model, we conclude that the higher C and N storage in soil observed in the conservation and organic systems was mainly driven by increased C and N inputs deriving from cover crop and catch crop residues, rather than by the effect of no tillage practiced in conservation agriculture. The N surplus, i.e. the difference between N inputs and N exports at the field scale, varied widely between treatments, from +47 to +181 kg N ha-1 yr-1 in low input and conservation systems, respectively. i The fate of this N surplus also varied between systems with wide variations in SON storage and gaseous losses but no differences in N leaching. The cumulative N2O emissions measured continuously during 3.3 years were highly correlated with the calculated gaseous N losses (volatilization and denitrification), with higher losses in the conservation system. Our results allowed to establish a full GHG balance, which was high and positive in conventional and low input systems, smaller in conservation system, and lowest and negative in the organic system. These trends were maintained when the GHG balance was expressed per unit of N input or N exported. Therefore the four agricultural systems dissimilarly impacted the N fate. N fate could not be predicted by the N surplus. The GHG balance is a much better indicator of the environmental impact of cropping systems relative to C and N fluxes. In the Danish and Swiss experiments, the soil-crop model STICS was used to mimic crop production, N uptake and N surplus. The model was first adapted and evaluated to simulate organic farming systems involving a wider diversity of crops and practices than in conventional systems. The model could satisfactorily simulate crop production, N uptake, N surplus and SON storage in the organic and conventional systems of these two long-term experiments. Model outputs suggested that the N fate could be contrasted according to fertilization and crop management, and that N losses were not systematically reduced in organic compared to conventional cropping systems. This study challenges the frequent belief that alternative cropping systems necessarily improve the global C and N environmental impacts of agriculture. It points out the complex interactions occurring between alternative practices, and the compensations which can occur between C and N processes. Some of them leading to increased soil C and N stocks, decreased N leaching and gaseous N emissions. Further work should focus on assessing the on-farm performances of these practices on C and N fates and evaluating STICS model in other alternative cropping conditions. Keyword: carbon storage, nitrogen storage, organic matter turnover, nitrogeN surplus, nitrate leaching, N2O emissions, GHG balance, organic farming, conservation agriculture, low-input, no-till, modelling ii Funding This thesis project was funded by a research grant from the French Ministry of Agriculture, within the frame of a FCPR (“Formation complémentaire par la recherche”) for IAE officials (“Ingénieur de l’agriculture et de l’environnment”). The thesis benefited of the funding of the ENBIO project by the Seine Normandie Water Agency and the PIREN Seine for the experimental part of the work based at “La Cage” (Versailles, France) and the collaboration with the University of Aarhus in Denmark. The collaboration with partners from FiBL and Agroscope (Switzerland) was funded by the European project Climate-CAFE (http://www6.inra.fr/climate-cafe). The project was carried out in the AgroImpact Research Unit of INRA, based in Laon and Mons (France). iii iv Acknowledgements Ce document de thèse ne serait rien sans toutes les personnes qui, à leur manière, y ont apporté leur contribution : un grand merci à tous ! En premier lieu, je souhaite remercier très chaleureusement mon directeur et encadrant de thèse Bruno Mary, ainsi que mon co-encadrant de thèse Nicolas Beaudoin. Je leur suis très reconnaissante de m’avoir fait confiance dès nos premiers échanges, de m’avoir prodigué leur grande expérience et leurs méthodes de travail. Je les remercie pour toutes les discussions scientifiques et non scientifiques partagées, pour leur grande disponibilité ainsi que pour leur gentillesse et leur générosité. Un grand merci à vous deux ! I greatly acknowledge the members of my thesis jury, particularly Carlo Grignani (University of Turin, Italy) and Jens Leifeld (Agroscope, Sitzerland) for accepting to repport this work, as well as Sylvie Recous (UMR FARE INRA, France), Joëlle Fustec (USC LEVA INRA, France) and Jørgen E. Olesen (Aarhus University, Denmark) for examinating the thesis. I would like to acknowledge the different foreign collaborators from FiBL and Agroscope (Switzerland), especially Paul Mäder, Colin Skinner, Frédéric Perrochet, Jochen Mayer and Lucie Gunst, as well as Jørgen E. Olesen from Aarhus University in Denmark. Thank you for accepting the data exchange, for receiving me in your premises, for your expertise of the long term experiments and for your advices in modelling. I would also like to thank all people who have been involved in the monitoring of the DOK and the Foulum experiments since their starts. Je remercie l’ensemble des membres du CGAEER du Ministère français de l’agriculture, de l’alimentation et de la forêt de m’avoir accordée l’opportunité de réaliser cette formation complémentaire par la recherche (FCPR). Je souhaite de plus remercier Alexandre Péry, directeur de l’Ecole doctorale ABIES et directeur de la promotion des FCPR 2014-2017, pour sa très grande disponibilité et pour son suivi régulier de l’avancement de la thèse. Je remercie Joël Léonard pour m’avoir accueillie au sein de l’unite de recherche AgroImpact qu’il dirigie.