Exploration of biogas systems to unveil the acetogen community: who are they and can we find them?

Biogas production through the anaerobic digestion of organic waste streams has great potential for reducing and replacing our dependency on fossil fuels, while also valorising organic wastes. Anaerobic digestion is a stepwise degradation process of organic material by a series of microorganisms. Among the groups of microorganisms involved, acetogens play a critical role. Their main product, acetate, is a crucial precursor for the methane producing microorganisms in the final degradation step. Acetogens are a ubiquitous group of microbes that can be found across many anoxic environments, from gastrointestinal systems to soil/sediments and biogas reactors. They have been well studied in other environments, but acetogens remain enigmatic in terms of identity and function in the biogas system. Unveiling novel acetogens and their functional pathways in such systems can provide tools for the optimisation of biogas systems. Moreover, acetogens are interesting due to their potential for use in carbon capture and biochemical production.The aim of this thesis was to reveal knowledge on the acetogenic players responsible for the penultimate step of anaerobic digestion. Biogas environments were explored utilizing both molecular and cultivation-based methods. The investigation included 16S rRNA gene sequencing analysis, further supplemented with metagenome data analysis. The results showed the presence of several unknown/uncultured potential acetogens, supported by the possession of gene encoding for the enzymes of the reductive acetyl-CoA pathway (Wood-Ljungdahl pathway, WLP). However, while investigating several unknown candidates, the pathway analysis revealed a lack of key WLP enzymes, such as carbon monoxide dehydrogenase and acetyl-CoA synthase, calling into question the definition of acetogens and requiring an exploration of alternative pathways.