abstract: Nitrous oxide (N2O) is an important greenhouse gas and an oxidant respired by a diverse range of anaerobic microbes, but its sources and sinks are poorly understood. The overarching goal of my dissertation is to explore abiotic N2O formation and microbial N2O consumption across reducing environments of the early and modern Earth. By combining experiments as well as diffusion and atmospheric modeling, I present evidence that N2O production can be catalyzed on iron mineral surfaces that may have been present in shallow waters of the Archean ocean. Using photochemical models, I showed that tropospheric N2O concentrations close to modern ones (ppb range) were possible before O2 accumulated. In peatlands of the Amazon basin (modern Earth), unexpected abiotic activity became apparent under anoxic conditions. However, care has to be taken to adequately disentangle abiotic from biotic reactions. I identified significant sterilant-induced changes in Fe2+ and dissolved organic matter pools (determined by fluorescence spectroscopy). Among all chemical and physical sterilants tested, γ - irradiation showed the least effect on reactant pools. Targeting geochemically diverse peatlands across Central and South America, I present evidence that coupled abiotic and biotic cycling of N2O could be a widespread phenomenon. Using isotopic tracers in the field, I showed that abiotic N2O fluxes rival biotic ones under in-situ conditions. Moreover, once N2O is produced, it is rapidly consumed by N2O-reducing microbes. Using amplicon sequencing and metagenomics, I demonstrated that this surprising N2O sink potential is associated with diverse bacteria, including the recently discovered clade II that is present in high proportions at Amazonian sites based on nosZ quantities. Finally, to evaluate the impact of nitrogen oxides on methane production in peatlands, I characterized soil nitrite (NO2–) and N2O abundances along soil profiles. I complemented field analyses with molecular work by deploying amplicon-based 16S rRNA and mcrA sequencing. The diversity and activity of soil methanogens was affected by the presence of NO2– and N2O, suggesting that methane emissions could be influenced by N2O cycling dynamics. Overall, my work proposes a key role for N2O in Earth systems across time and a central position in tropical microbial ecosystems. / Dissertation/Thesis / Doctoral Dissertation Microbiology 2020

Cette thèse porte sur les réactions abiotiques catalysées par un acide dans les systèmes biologiques. Elles sont définis comme des systèmes réactionnels composés d'un substrat xénobiotique - un acétal cyclique dans ce travail - stable dans des conditions biologiques et clivable à un pH bas et d'un catalyseur acide hétérogène correspondant biocompatible. Le défi de cette approche est de maintenir le catalyseur actif dans un milieu biologique tamponné et toujours capable d'hydrolyser le substrat xénobiotique d'acétal et de maintenir le pH tamponné du système vivant dans son état d'origine. Dans la première partie de ce travail, nous nous concentrons sur le réglage précis des acétals cycliques. Nous identifions 4 structures acétales et montrons que les changements structurels conduisent à une réactivité différente dans différentes gammes de pH, chacune correspondant à des applications possibles in vivo, notamment des lieurs stables pour les conjugués anticorps-médicaments et des lieurs clivables dans des conditions physiologiques pour la bioconjugaison.La deuxième partie est axée sur le catalyseur biocompatible. Ici, nous identifions deux catalyseurs biocompatibles solides, ayant différents degrés d'hydrophobie et de propriétés d’adsorption : le copolymère Nafion NR-50 et le copolymère PEG-AASA. Nous démontrons qu’avec un traitement approprié, ils peuvent maintenir un pH interne inférieur à 4, hydrolyser le substrat et ne pas affecter le biofluide hautement tamponné utilisé comme solvant. / This thesis object is acid-catalysed abiotic reactions in biological systems. They are defined as reaction systems composed by a xenobiotic substrate – a cyclic acetal in this work - stable in biological conditions and cleavable at low pH and a corresponding biocompatible heterogeneous acid catalyst. The challenge of this approach is to keep the catalyst active in a buffered biological media and still capable of hydrolysing the xenobiotic acetal substrate and to maintain the buffered pH of the living system in its original state. In the first part of this work we focus on the fine-tuning of cyclic acetals. We identify 4 acetal structures and we show that structural changes lead to a different reactivity in different pH ranges, each corresponding to possible applications in vivo, including stable linkers for antibody drug conjugates and linkers cleavable in physiological conditions for bioconjugation.The second part is focused on the biocompatible catalyst. Herein we identify two solid biocompatible catalysts, with different degree of hydrophobicity and adsorbance properties: Nafion NR-50 and PEG-AASA co-polymer. We demonstrate that, upon proper treatment, they can maintain an inner pH < 4, hydrolyse the substrate and do not affect the highly buffered biofluid used as solvent.