Pure culture, co-culture and whole ecosystem investigations of single anaerobes, partnerships and microbial communities in anaerobic digestion

Abstract

Anaerobic digestion (AD) is a multi-stage process whereby biodegradable material is broken down by complex microbial consortia into renewable CH4 in the absence of oxygen during waste and wastewater treatment. Anaerobic granules are spherical microbial biofilms which form in digesters such as upflow anaerobic sludge blanket (UASB) and expanded granular sludge blanket (EGSB) systems. There is a fundamental knowledge gap in the microbial dynamics and metabolic interactions among microorganisms within AD bioreactors. This thesis addressed some growth and chemical aspects resulting from microbial interplay between three model pure cultures found in AD digesters under various temperature and substrate conditions. The methanogen Methanosarcina barkeri is a metabolically diverse organism, independent of temperature, which was demonstrated to grow synergistically with the homoacetogen Acetobacterium woodii. The competitive interaction between Methanosarcina barkeri and the hydrogenotrophic methanogen Methanococcus maripaludis is novel within the literature. Methanococcus maripaludis out-competed Methanosarcina barkeri for H2-CO2 but both pure cultures were able to grow together. Physical, physiological and phylogenetic properties of anaerobic granules were significantly different at three designated size distributions. Physiological and phylogenetic characteristics of anaerobic granules from three sources were significantly different. Individual anaerobic granules had significantly similar physical characteristics and active community structures based on 16S rRNA Illumina sequencing. Single anaerobic granules were described as “whole ecosystems” because they had a statistically similar active microbial profile. Micro Sequencing Batch Reactors were employed to analyse how individual anaerobic granules/“whole ecosystems” respond to various environmental stresses. Results from VFA profiling and sequencing indicated that single granules demonstrated replicated shifts in metabolic and community structure patterns. In conclusion, a combination of both pure cultures and high-throughput sequencing studies of mixed microbial communities show potential as one tool to underpin the understanding of complex systems such as anaerobic digestion.