Reductive acetogenesis via the acetyl-CoA pathway is a hydrogenotrophic pathway that has the potential to reduce methanogenesis from ruminant livestock. However our understanding of the organisms capable of this transformation (acetogens) is hindered by a lack of specific molecular tools for this group. In the present thesis, a PCR primer set specific for a wide range of acetogens was developed, targeting the acetyl-CoA synthase (ACS) gene which is unique to the acetyl-CoA pathway. ACS was found to be useful marker for potential acetogens and ACS sequences could be used to infer family-level phylogeny for many acetogens. ACS gene specific primers were used in combination with existing molecular tools targeting the gene encoding formyltetrahydrofolate synthetase (FTHFS, present in the acetyl-CoA pathway but not unique to it) and 16S rRNA genes, as well as cultivation techniques, to investigate acetogen diversity in the rumen and two analogous gut systems where microbial hydrogenotrophy differs: the forestomach of a native Australian marsupial, the tammar wallaby Macropus eugenii; and the developing rumen of young lambs. Novel potential acetogens present naturally in the rumen of pasture fed and grain fed cattle affiliated with the Ruminococcaceae/Blautia group and distantly with the Lachnospiraceae. A large diversity of potential acetogens with functional genes affiliating broadly between the Lachnospiraceae and Clostridiaceae though without a close sequence from a cultured relative were also detected. Rumen acetogen enrichment cultures revealed the presence of a known acetogen, Eubacterium limosum, in grain fed cattle, as well as novel acetogens affiliating with the Lachnospiraceae and Ruminococcaceae/Blautia group. The novel potential acetogen population detected in this study may represent an important hydrogenotrophic group in the rumen that we understand very little about and that requires further investigation. The tammar wallaby, which exhibits foregut fermentation analogous to that of the rumen but resulting in lower methane emissions, housed a different acetogen population to that of the bovine rumen (LIBSHUFF, p <0.0001) though novel potential acetogens in the tammar wallaby forestomach affiliated broadly in the same family groups (Blautia group, Lachnospiraceae and between Lachnospiraceae and Clostridiaceae without a close cultured isolate). Acetogen enrichment cultures from the tammar wallaby forestomach facilitated isolation of a novel acetogen, which was closely related to potent reductive acetogens from kangaroos. The differences between the acetogen population of the tammar wallaby forestomach and the bovine rumen may be a factor in explaining lower methane emissions and methanogen numbers in tammar wallabies relative to ruminants. Using a gnotobiotically reared lamb model, the unique acetogen population present in the developing rumen was identified and it’s response to methanogen colonisation examined. The acetogen E. limosum and potential acetogen Ruminococcus obeum were identified as well as a small diversity of novel potential acetogens affiliating with the Blautia group and the Lachnospiraceae. A small but diverse population of naturally resident methanogens were also identified in gnotobiotically reared lambs that had been isolated at 17 hours of age. After inoculation with Methanobrevibacter sp. 87.7, methanogen numbers in gnotobiotically reared lambs significantly increased but acetogen diversity was not altered, indicating that this population is resilient to methanogen colonisation to some degree. The potential acetogen population in gnotobiotically reared lambs was significantly different (LIBSHUFF, p < 0.0001) to that in conventionally reared sheep, which indicates that factors other than methanogen establishment alone, probably relating to other microbes and associated hydrogen concentrations in the rumen, affect acetogens during rumen development.

Toutes les formes de vie assemblent et désassemblent continuellement des composés chimiques via un processus de consommation d'énergie appelé métabolisme. Le métabolisme est généralement modélisé en chimie et biologie par un cycle. Ce modèle dynamique traduit la transformation de composés de base en une cascade de produits appelés métabolites. Celui-ci est comparable à un ouragan à l’échelle moléculaire. De manière analogique et imagée un cyclone est constitué de deux éléments, l'air et l'eau, et transforme l’environnement qui l’entoure par un processus endothermique (consommateur d’énergie). Traditionnellement, la recherche chimique sur les origines de la vie est concentrée principalement sur la synthèse de composés chimiques sans suffisamment apprécier leur place dans la plus grande organisation biochimique de la vie. La vie construit toutes ses molécules à partir du dioxyde de carbone, pourtant elle manque étonnamment d'innovation à cet égard. Malgré presque 4 milliards d'années d'évolution, les organismes autotrophes utilisent seulement six voies différentes pour construire leurs molécules à partir du CO2. Parmi elles, deux voies – la voie de l’acétyle CoA (aussi appelée voie Wood-Ljungdahl) et le cycle du rTCA (également appelé le cycle de Krebs inverse) - sont considérées comme primitives, et contiennent les cinq molécules servant de précurseurs chimiques universels pour toute la biochimie. Comment et pourquoi les voies de l’acétyle CoA et du rTCA sont-elles apparues? Pour répondre à cette question, une recherche systématique a été effectuée afin de trouver des catalyseurs chimiques non-enzymatiques ou des minéraux simples, ainsi que des réactifs pouvant promouvoir les réactions d'anabolisme principal, particulièrement la voie de l’Acétyle CoA et le cycle de rTCA. A l’origine, pour créer les molécules organiques complexes comme les enzymes il a fallu que des molécules plus simples avec un moins grand nombre de carbone se forme sur terre et cela à partir du CO2. On peut donc supposer que les premiers produits à plusieurs carbones sont issus de synthèse totalement inorganique comme celles développer dans notre laboratoire, plutôt que d’une évolution chimique et organométallique simultanée, c’est-à-dire une interaction efficace entre une molécule carbonée et un ou plusieurs métaux à l’instar de certains enzymes. Après avoir trouvé autant de façons possible de promouvoir individuellement chaque étapes des cycles catalytiques étudiés, seules les conditions réactionnelles mutuellement compatibles (à savoir des conditions permettant de produire l’ensemble des métabolites dans le bon ordre) ont été retenu. / All life forms continuously build up and break down its constituent chemical building blocks, through an energy consuming process called metabolism. Just like a hurricane’s dynamic patterns and its building blocks (air and water) as being equally fundamental to its nature, so too should metabolism’s dynamic chemical patterns and chemical building blocks be viewed as equally characteristic. Traditionally, much chemical research on the origins of life is overly focused on the synthesis of chemical building blocks without sufficiently appreciating their place in life’s larger biochemical self-organization. Life ultimately builds all of its molecules from carbon dioxide, yet it is surprisingly lacking in innovation in this respect. Despite nearly 4 billion years of evolution, autotrophic organisms use only six pathways to build their molecules from CO2. Two of these pathways – the acetyl CoA pathway (also known as the Wood-Ljungdahl pathway) and rTCA cycle (also known as the reverse Krebs cycle) - are thought to be ancestral, with just five molecules within them serving as the universal chemical precursors for all of biochemistry. How and why did these pathways get their start? To answer this question, a systematic search was designed to find simple, non-enzymatic chemical or mineral catalysts and reagents, that can promote the reactions of core anabolism, particularly the acetyl CoA pathway and the rTCA cycle. After finding as many ways as possible to promote each reaction, they could be narrowed down to mutually compatible conditions where many reactions can occur in sequence. The more of core anabolism that can be achieved under a single set of purely chemical conditions, the more likely it is to have constituted early prebiotic chemistry rather than a later product of chemical and biological evolution.