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This dissertation, Linking Microbial Communities, Environmental Factors and Performance of Biological Treatment Reactors Using Metagenomics by Feng, Ju, 鞠峰, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: The thesis was conducted to reveal the associations among microbial communities, environmental factors (i.e., operational and physicochemical conditions) and performance of biological treatment reactors of activated sludge (AS) and anaerobic digestion (AD) using metagenomics. Moreover, environmental and biological factors that govern microbiome assembly and population dynamics were examined with emphasis on core, functional and uncultured microorganisms. Additionally, occurrence of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs) in digested sludge and their removal and dissemination during AD were evaluated. Full-scale AS reactors in wastewater treatment plants (WWTPs) were extensively investigated both spatially (50 grab samples, 27 reactors, 17 cities) and temporally (58 monthly samples, 1 reactor, Hong Kong). Metagenomics and network analysis of spatio-temporal data show that AS bacterial communities are nonrandomly assembled by taxonomic relatedness, which is induced by multiple deterministic processes, including habitat filtering and competition. Moreover, bacterial communities in full-scale municipal AS reactor follow no apparent seasonal succession over five years and biological interactions dominate over environmental conditions (mainly sludge retention time (SRT) and inorganic nitrogen) in determining bacterial assembly and population dynamics. Additionally, a core set of cosmopolitan functional microorganisms (e.g., nitrogen-cycling-related bacteria) widely occur in globally distributed AS reactors. Besides AS systems in WWTPs, performance of downstream AD reactors that receive primary and/or secondary sludge is also related with biological and environmental factors. First, multivariate, correlation and network analyses of three-year data of two full-scale municipal AD reactors show that methane production and percentage are significantly correlated (P-values Last, comparative genomics of 23 prokaryotic genomes reconstructed from phenol-degrading methanogenic reactors reveals that temperature difference induced colonization of sulfate/sulfite/sulfur (20oC) or nitrate/nitrite-respiring (37℃) sub-communities as competitors of methanogens, which differentiates methanogenesis from phenol. The discovery of interspecific competition justifies attempts towards biological manipulation for maximizing methanogenesis in anaerobic reactors. Combined, this thesis presents a large-scale meta

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