Abstract
This PhD thesis is focused on studying the dynamics of inhibition and recovery in the anaerobic digestion process of animal slurry to find indicators to predict process failures, minimize methane (CH4) losses, and evaluate best management practices at biogas plant level. 
To fulfill this objective, five trials were designed and conducted. Firstly, an experiment was designed to monitor physicochemical changes and gas emission of two types of aged pig slurry during 15 consecutive weeks of storage in summer conditions. Secondly, different sulphate (SO42-) concentration in pig and cattle slurry were monitored in terms of CH4 yield and physicochemical changes in a batch assay. Thermophilic anaerobic degradation of organic matter (OM) and the inhibitory SO42- dose were investigated. Thirdly, the effects of including SO42- acidified pig slurry in an anaerobic co-digestion process with conventional slurry on process performance in two scale studies (laboratory and full scale) were determined. Key process indicators were identified. Fourthly, a combination of two methods, quantitative real-time polymerase chain reaction (qPCR) and qualitative scanning electron microscopy (SEM) was used to evaluate changes in the microbial population of anaerobic sludge digesters during the addition of pig slurry. Finally, the CH4 yield, physicochemical composition and microbiological community structure and dynamics were evaluated during the start-up of anaerobic digestion of pig slurry in a laboratory scale. The tested strategies were feedless and non-feedless, followed by a gradual or an abrupt addition of pig slurry
The results presented in this PhD thesis allowed concluding that in the anaerobic degradation of OM from aged pig slurry, there is a relevant transformation of the more degradable into soluble OM during the first three weeks of storage. However, production of CH4 did not occur until five weeks of storage. Regarding the use of acidified slurry in anaerobic digestion, added SO42- concentrations in pig and cattle slurries for anaerobic digestion higher than 2000 mg SO42- L-1 and 1500 mg SO42- L-1 respectively, decreased CH4 yield. However, SO42- concentration of 500 mg SO42- L-1 in pig slurry resulted in an increase in CH4 yield. Additionally, the most important traits to be taken into account to detect process failure in anaerobic digestion using acidified pig slurry were: SO42- content of the slurry, alkalinity parameters, total volatile fatty acids (VFA), especially acetic and butyric acids. Pig slurry addition to unadapted anaerobic digesters caused a deterioration of the anaerobic digestion process and the sludge characteristics lowering the pH, increasing VFA concentration, decreasing volatile solids degradation and reducing CH4 yield in all digesters. During the adaptation period to pig slurry in anaerobic thermophilic conditions, an increase in total bacteria and archaea was observed through qPCR, as well as a change in microbial morphotypes through SEM. The change in microbial morphotypes was attributable to the addition of pig slurry. Regarding the start-up strategies, the strategy which best minimized CH4 yields losses was non-feedless subjected to an abrupt change in substrate, although differences in microbial population among treatments were low. Moreover, hydrogenotrophic methanogenesis was the main metabolic route in CH4 formation during the recovery period after star-up. Methanomicrobiales first and Methanobacteriales second, were the dominant archaeal orders throughout the recovery period, being useful process indicators
This PhD thesis provides useful practical information for monitoring anaerobic digestion of animal slurry during inhibition and recovery phases.