Evolution of the microbial communities involved in the H2- and CO2-assisted fermentation of a complex organic substrate to medium chain carboxylates

Details

Supervisors

Gerin, Patrick A. ; Stenuit, Benoît

Faculty

Faculté des bioingénieurs

Degree label

Master [120] : bioingénieur en sciences agronomiques, à finalité spécialisée

Abstract

With the depletion of non-renewable resources and the increase in waste production, there is a need to find sustainable bio-sourcing methods. Medium chain carboxylates (MCCs; C6-C10) are platform molecules with multiples usages currently mostly petrosourced. However, in recent years, the microbial chain elongation has been identified as a key opportunity for the MCCs bioproduction: bacteria ferment organic feedstock into short chain carboxylates that are then elongated to MCCs. However, the microbial processes used to produce MCCs are not yet fully understood. The aim of this master's thesis was to gain insights into microbial population dynamics and the possible links between the microbial community, the physicochemical conditions of the fermentation, and the product spectrum during the H2&CO2-assisted brewer’s spent grain fermentation in order to generate medium-chain carboxylates. Microbial DNA was extracted from H2&CO2-assisted BSG fermentation samples and amplified by one-step PCR using different tailed primer pairs, prepared for targeted sequencing, that target the region V4 of the phylogenetic marker gene 16S rRNA. PCR amplicon libraries were for sequencing on MiSeq illumina platform to determine the composition and the dynamics of the microbial populations under specific conditions. In a first screening experiment, samples from four different bioreactors were analyzed to investigate the impact of different operating conditions on the general dynamics of microbial community composition and structure. It was found that the use of an adapted inoculum could improve the production of caproate by bringing in more chain elongating bacteria. It was also found that the absence of organic substrate has no significative impact on the abundance of chain-elongating bacteria. However, caproate production by these elongators appears to be less efficient when only H2&CO2 is available as a substrate. In a second experiment, two bioreactors were analyzed in greater depth to better assess the link between community status and metabolite production. Megasphaera was found to be the dominant taxa during the chain elongation phases. It is the first time that Megasphaera was significant during H2&CO2-based chain elongation. Prevotella was the dominant taxa during acidogenesis phases. The genus Prevotella has been reported to have important polysaccharide degradation capabilities and the ability to ferment carbohydrates and proteins into various SCCs. Prevotella was also surprisingly abundant during homoacetogenesis, despite, to the best of the author's knowledge, Prevotella is lacking the Wood-Ljungdahl pathway involved in the homoacetogenesis.