Integrated Omics Analysis of the Microbial Ecology in the Anaerobic Digestion of Lignocellulosic Biomass

Abstract

Anaerobic digestion (AD) of lignocellulosic biomass for biogas production represents one of the most promising and widely operated processes for renewable energy production, not only because of its high energy recovery rate, but also its inherent carbon neutral attribute. As the conversion process of lignocellulose to biogas is completed driven by microorganisms, a better understanding of the AD microbiome is the prerequisite to more efficient and reliable biogas production. The overall goal of this research is to investigate the microbial ecology of AD from a number of different perspectives, regarding the microbial community evolution and composition, activity of both the abundant and rare taxa in the AD microbiome, and the ecological roles of microbial populations and their interactions at the population genomic level.

In the first section of this thesis, the evolution of AD microbial community during enrichment was investigated. Five stable methanogenic cellulose- or xylan-digesting enrichment cultures were successfully established after two years enrichment with inocula from two different wastewater anaerobic digesters not primarily treating cellulose or xylan. Physiological properties of the enrichment cultures were studied and the long-term dynamics of microbial communities along the two years enrichment process were monitored via 16S rRNA gene amplicon sequencing. The study found that certain taxonomic and functional microbes were selected and enriched under specific conditions, leading to the convergence of microbial community functions and compositions under the same enrichment condition regardless of the origin of the inocula.

Based on the microbial community composition, the dynamics and activity of both the abundant and rare taxa were queried in the five enriched communities during batch culture. Significant and positive correlations were observed between 16S rRNA and 16S rDNA for all five enrichment cultures and at any time point. These results indicated that the microbial activity of taxa in general was congruent with their abundance in the enrichments, although very high potential growth rates were observed for some of the rare taxa. Further examination of the abundant populations revealed different growth rates and dynamics during the batch culture fermentation for even phylogenetically closely related taxa, which implied differences in their potential functions and ecological roles in AD.

In order to further study the functional properties, ecological roles and interactions between different players in the five established enrichment cultures, metagenomic and metatranscriptomic sequencing approaches were applied in tandem. A total of 107 population genomes were binned from the metagenomes, and phylogenetic analysis of the recovered population genomes further confirmed the convergence of microbial populations under the same culture conditions. Large shifts of the major active microbial populations were observed for the two mesophilic cellulose cultures over the duration of the experiment. Clostridium cellulolyticum-related populations performed substrate hydrolysis and primary fermentation during the early phase, and populations related to Clostridium leptum dominated the communities as secondary fermenters and lipid and long-chain fatty acid scavengers during the late phase. In all the cellulose and xylan mesophilic cultures, primary and secondary fermenters produced hydrogen and interacted closely with the hydrogenotrophic Methanobacteria populations, which in turn kept the hydrogen partial pressure low so that hydrogen production was feasible for the fermenters. A conceptual model was constructed for each of the enrichment cultures illustrating the meta-metabolic carbon flows and the synergistic interactions among the core active microbial populations.

Overall, the work conducted in this thesis provided insights into the biological mechanisms of AD. The results of this research can be used to guide the rational design of AD microbiome and optimization of the AD process to enhance energy production and waste treatment.

Date of Award	27 Oct 2017
Original language	English
Awarding Institution	City University of Hong Kong
Supervisor	Patrick Kwan Hon LEE (Supervisor)