Optimisation of Slurry-based Anaerobic Digestion for Enhanced Biogas Production and Sanitisation Leads to Microbial Community Tailoring

Background: The urgent need to adopt sustainable agricultural practices has positioned anaerobic digestion (AD) as a pivotal technology. Indeed, slurry-based AD can mitigate agricultural pollution by capturing greenhouse gas from stored slurry and converting it into biomethane, a valuable source of renewable energy, while generating digestate that can be used as fertiliser. For such a strategy to be effectively and widely deployed however, AD must be optimised. To this end, efforts have typically focused solely on biogas yields, yet improvements in pathogen load reduction may potentially negate the need for a costly pasteurisation step. Hence, optimisation of AD for sanitisation as well as improved biogas output is desirable. To address this, we set up triplicate 10-L CSTR bioreactors, which were fed with a combination of slurry and fats, oils and grease for 240 days. The bioreactors were initially operated on a 5-day feeding regime, before switching to a 3-day feeding regime. Results: After an initial period of adaptation to the new operating conditions, methane production increased significantly in all bioreactors with an average of 58% higher methane yield per gram VS fed. Additionally, the change in feeding regime also resulted in the required reduction in E. coli numbers to satisfy EU sanitisation standards. Interestingly, process optimisation led to a more tailored microbial community as revealed by metagenomics. Specifically, we observed selection for improved carbon oxidation, syntrophic acetate oxidation and methanogenesis, as well as overall reduced microbial richness and decreased functional diversity. This could potentially lead to a reduced ecosystem stability however the emergence of Methanosarcina prevalence, known for its robustness, together with the detection of the two main methanogenic pathways - acetoclastic and hydrogenotrophic - after process optimisation might confer some resistance against future perturbations. However, the impact of reduced diversity on ecosystem stability needs to be further assessed experimentally. Conclusions: Taken together, we demonstrate the manipulation of AD for concomitant improved sanitisation and biogas production and highlight the need to better understand the impact of microbial dynamics in response to process optimisation.