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Manipulation of the Hydrogen Pool Available in the Rumen to Reduce Methane Emissions from Ruminants Jessie Guyader

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Manipulation of the Hydrogen Pool Available in the Rumen to Reduce Methane Emissions from Ruminants Jessie Guyader Manipulation of the hydrogen pool available in the rumen to reduce methane emissions from ruminants Jessie Guyader To cite this version: Jessie Guyader. Manipulation of the hydrogen pool available in the rumen to reduce methane emissions from ruminants. Agricultural sciences. Université Blaise Pascal - Clermont-Ferrand II, 2015. English. NNT : 2015CLF22543. tel-01325219 HAL Id: tel-01325219 https://tel.archives-ouvertes.fr/tel-01325219 Submitted on 2 Jun 2016 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. UNIVERSITE BLAISE PASCAL UNIVERSITE D’AUVERGNE N° D.U. : 2543 ANNEE : 2015 ECOLE DOCTORALE SCIENCES DE LA VIE, SANTE, AGRONOMIE, ENVIRONNEMENT N° d’ordre : 659 Thèse Présentée à l’Université Blaise Pascal Pour l’obtention du grade de DOCTEUR D’UNIVERSITE Spécialité : Ecologie microbienne Soutenue le 19 janvier 2015 Jessie GUYADER Manipulation du pool d’hydrogène disponible dans le rumen pour limiter les émissions de méthane par les ruminants Manipulation of the hydrogen pool available in the rumen to reduce methane emissions from ruminants Directrice de thèse: Dr. Cécile MARTIN (Directrice de recherche ; INRA) Membres du jury: Dr. Diego MORGAVI (Directeur de Recherche ; INRA): Président Dr. Veerle FIEVEZ (Research Scientist, Professor ; Ghent University): Rapporteur Dr. Jamie NEWBOLD (Director of Research, Professor ; Aberystwyth University): Rapporteur Dr. Christine GERARD (Ingénieur R&D ; InVivo NSA): Examinateur Dr. Stefan MUETZEL (Senior research scientist ; AgResearch): Examinateur Dr. Corinne PETIT-BIDERRE (Chargée de Recherche ; CNRS-UBP): Examinateur Préparée dans l’Equipe Digestion Microbienne et Absorption (DIMA) Unité Mixte de Recherches sur les Herbivores / INRA centre Clermont-Ferrand / Theix Acknowledgements First, I would like to thank Prof. Veerle Fievez (Ghent University) and Prof. Jamie Newbold (Aberystwyth University) for accepting to review this manuscript. I am also very grateful to Dr Christine Gerard (InVivo NSA), Dr Cécile Martin (INRA Theix), Dr Diego Morgavi (INRA Theix), Dr Stefan Muetzel (AgResearch, NZ) and Dr Corinne Petit-Biderre (Université Blaise Pascal, Clermont Ferrand) for accepting to be examiners of this PhD thesis. Je suis particulièrement reconnaissante envers l’INRA et la Région Auvergne pour la bourse de recherche qui m’a été attribué, et envers InVivo NSA qui a financé les frais expérimentaux de cette thèse. Je remercie aussi Dr Christine Gerard (InVivo NSA), Dr Christelle Loncke (INZO), Dr Stefan Muetzel (AgResearch), Dr Pierre Peyret (Université d’Auvergne) et Dr Daniel Sauvant (AgroParis Tech), membres de mon comité de thèse, pour votre disponibilité, votre expertise et pour l’ensemble de vos conseils. Cette thèse n’est pas seulement le fruit d’un travail personnel, mais d’un travail d’équipe, que je me dois de remercier chaleureusement. La première personne que je souhaite remercier est Cécile. Je suis très admirative devant tes compétences et connaissances scientifiques, que tu m’as fait partager. Merci de m’avoir fait confiance en me laissant de l’autonomie dans les différents projets, tout en me donnant des conseils précieux durant ce parcours. Mais je n’ai pas seulement été impressionnée par ta rigueur scientifique : tes qualités humaines m’ont également beaucoup touchée. Merci de ta patience, ton temps, ta disponibilité : tout simplement merci de m’avoir soutenue pendant ces trois années. Je remercie également l’ensemble de l’équipe DIMA pour votre soutien scientifique et technique, pour votre bonne humeur et vos encouragements ! Plus particulièrement, je remercie Pierre pour m’avoir formée à la méta-analyse et pour tes conseils scientifiques tout au long de la thèse. Merci à Diego et Milka de m’avoir fait partager leurs connaissances en microbiologie et surtout, merci pour votre patience et d’avoir répondu à toutes mes questions… Maguy, je te remercie pour tes conseils en méta-analyse, pour m’avoir formée à l’utilisation des enceintes, et pour toutes nos discussions ! Merci Mathieu pour ton aide au cours des expériences et pour le temps passé à la relecture de cette thèse, mais aussi merci d’être devenu un confident et un vrai soutien en cette fin de thèse. Et puisque l’un ne va plus sans l’autre, Michel, merci pour tous tes conseils et pour m’avoir transmis ta passion et tes connaissances: merci mes deux super héros d’avoir été deux adorables compagnons de voyage et d’avoir confiance en moi… ☺ J’ai également beaucoup apprécié de discuter avec Benoît, à qui je souhaite plein de bonheur à venir ! Enfin, le travail réalisé au cours de cette thèse n’aurait pas été possible sans Yvanne, Lulu et Pierre : merci pour votre aide dans l’analyse des échantillons. I would like to warmly thank Stefan Muetzel for supervising me during my 3-month internship in AgResearch. Vielen Dank für Ihre Zeit, Ihre Geduld, Ihre Beratung und für die große Diskussion, die wir hatten. Ich werde auch nicht vergessen, wie Sie mich in schwierigen Momenten unterstützt haben... I also would like to send a very big thank you to Gemma Henderson, and to all the members of the Ruminant Nutrition group, and especially to Mike Tavendale for the interesting discussions we had, and to Sarah Lewis for your kindness, your warm welcome and your help. Thanks to the French Academy of Agriculture (« bourse de recherche Jean et Marie Louise Dufrenoy ») for the help in travelling expenses to New Zealand. Je tiens également à remercier l’ensemble de l’équipe de l’installation expérimentale des « Cèdres » : merci beaucoup à Sylvie, Dominique et Christophe pour vos conseils et votre disponibilité. Et « si ça ne te dérange pas », merci Lionel d’avoir toujours été prêt à m’aider… Je suis aussi très reconnaissante envers les différents laboratoires auvergnats qui m’ont été d’une grande aide à différents moments de la thèse : l’Observatoire de Physique du Globe (Aubière), le Laboratoire Vétérinaire et Biologique (Lempdes, Mr. Gilles Gaume), le CHU Gabriel Montpied (Clermont-Ferrand, Mr. Damien Richard) et l’Institut Pascal (Aubière, Mme Christine Gardarin). Un grand salut aux différents stagiaires et thésards qui ont croisé mon chemin : Inès, Lahlou, Julie, Claire, Benoît-Pierre, Giuseppe, Claudio, Clothilde, Laura…, with a special mention to Reza : thanks for your help, your happiness and your honesty. Un énorme bisou à Elena : merci pour ta bonne humeur et ton optimisme à toute épreuve ! Je termine ces remerciements par les personnes qui me sont le plus chères : merci à ma famille et surtout merci Papou, Maman, Julie, Yohann, pour votre réconfort et votre soutien quotidien. Je ne le dis pas assez, mais je suis très fière de vous. Et je garde le meilleur pour la fin : merci Arnaud de m’aimer, de me soutenir, et d’être toujours là pour moi malgré cette distance. Résumé La réduction des émissions de méthane (CH 4) des ruminants permet de limiter les impacts environnementaux négatifs de leur élevage et d’améliorer leur efficacité digestive. Dans le rumen, le CH 4 est majoritairement produit par les méthanogènes à partir de l’hydrogène (H 2). La disponibilité de l’H 2 pour ces micro-organismes est réduite en limitant sa production par les protozoaires ( via un apport de lipides ou extraits de plantes dans la ration) ou en stimulant des voies utilisatrices d’H2 compétitives à la méthanogenèse (via un apport alimentaire de nitrate). Aucune étude n’a porté sur l’association de stratégies alimentaires jouant à la fois sur la production et l’utilisation d’H 2 pour diminuer les émissions de CH 4. Notre objectif était de comprendre l’importance des différentes voies métaboliques de l’H 2 dans le rumen. Nous avons émis l’hypothèse que manipuler simultanément la production et l’utilisation de l’H 2 permet une diminution plus importante des émissions de CH 4 plutôt que d’agir sur un seul niveau. Nos résultats expérimentaux ont montré l’additivité de l’association lipides du lin-nitrate sur la méthanogenèse des bovins. Cet effet était persistant mais non bénéfique pour les performances digestives et laitières des animaux. L’association saponine de thé-nitrate n’a pas été efficace pour réduire les émissions de CH 4 car l’effet dépressif de la saponine sur les protozoaires n’a pas été observé. Cette thèse ouvre la possibilité d’étudier le potentiel anti-méthanogène de nouvelles associations de stratégies alimentaires ayant des mécanismes d’action différents dans le rumen. Les conditions d’utilisation de ces stratégies en élevage devront être délimitées, et leur rentabilité prouvée, pour être acceptées par l’éleveur. Mots clés: Fermentation; Hydrogène; Méthane; Microbiote; Ruminants; Stratégies de réduction. Abstract Reduction of methane (CH 4) emissions from ruminants may limit the negative environmental impacts of their breeding and may improve their digestive efficiency. In the rumen, CH 4 is mainly produced by methanogens from hydrogen (H2). Hydrogen availability for these micro-organisms is reduced by limiting its production by protozoa ( via lipids or plants extracts supplementation in diets) or by stimulating pathways competing with methanogenesis for H 2 consumption ( via nitrate supplementation in diets). No study tested association of dietary strategies acting on both H 2 production and consumption to reduce CH 4 emissions. Our objective was to understand the importance of the different H 2 metabolic pathways in the rumen. We assumed that simultaneous manipulation of H2 production and consumption reduces CH 4 emissions to a higher extent than acting on a single pathway.
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