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Title:Investigating the roles of microbial immigration in wastewater treatment processes
Author(s):Mei, Ran
Director of Research:Liu, Wen-Tso
Doctoral Committee Chair(s):Liu, Wen-Tso
Doctoral Committee Member(s):Maslov, Sergei; Nguyen, Thanh H; Cusick, Roland; Narihiro, Takashi
Department / Program:Civil & Environmental Eng
Discipline:Environ Engr in Civil Engr
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):microbial immigration
wastewater treatment
Abstract:Microbial communities are groups of microorganisms co-occurring and interacting in an ecosystem. The assembly of a community could be determined by multiple mechanisms, such as competition, niche differentiation, death, birth, and immigration. Among them, microbial immigration describes the process of microorganisms travelling from an upstream to a downstream community. It has been widely observed in natural and engineered ecosystems, such as lakes, rivers, drinking water treatment distribution systems, and wastewater treatment processes. Immigration can play important roles in biological wastewater treatment because different bioreactors are physically connected, and the flux of biomass can be higher than those in natural systems. However, currently available methods do not differentiate active and inactive immigrants, which poses a challenge to accurately quantifying immigration’s contribution to the assembly and function of the downstream community. In this dissertation, an ecogenomics-based mass balance (EGMB) approach is developed and applied to evaluate microbial activity and quantify the contribution of immigration in wastewater treatment processes. Chapter 1 reviewed the concept of microbial community assembly and the phenomenon of immigration in various ecosystems, including natural environments, engineered environments, and human microbiome. Methods that were commonly used to quantify the roles of immigration were introduced and their limitations were identified. The EGMB approach was briefly introduced and applied to anaerobic digestion (AD) as the model system to study the roles of microbial immigration. Chapter 2 describes the investigation microbial immigration from one wastewater treatment plant (WWTP), i.e., Stickney Water Reclamation Plant that was one of the largest WWTPs in the world. The results revealed that around 25% of the microbial populations in the Stickney’s AD were inactive immigrants introduced by the feed sludge. They were primarily aerobic microorganisms had negative growth rates, in contrast to native AD populations that were obligate anaerobes and had positive growth rates. The presence of these immigration-resulted residue populations led to the fact that digestion efficiency can never reach 100%. Chapter 3 expands the investigation of immigration to the global AD microbiome. Fifty- one full-scale municipal WWTPs were sampled and analyzed using 16S rRNA gene sequencing. It was found that feed sludge introduced immigrants were ubiquitously present in AD microbiome, which has been overlooked by previous studies. On the other hand, the abundances of immigrants varied significantly from less than 1% of the total AD populations to over 30%, which was affected by operation conditions such as pretreatment and operation temperature. In Chapter 4, genomics-guided batch experiments were conducted to shed lights on the activities of immigrants in AD. Metagenomics and metatranscriptomics analyses were used to demonstrate that feed sludge-associated immigrants were capable of anaerobic respiration using nitrate, nitrite, sulfate, and sulfur. When these electron acceptors were added to fresh AD sludge, populations with stimulated growth based on the measurement of rRNA and mRNA abundance were observed to match those identified by metagenomics. Anaerobic respiration was further detected to be prevalent in full-scale ADs but represented a very minor process compared methanogenesis. These microbial populations using electron acceptors were observed with negative growth rates in Chapter 2. With the successful identification of inactive immigrants, it also allows to efficiently pinpoint native AD populations that actively contribute to the digestion process, such as those capable of anaerobic amino acids degradation. Chapter 5 and Chapter 6 examines the key amino-acid degraders in using continuous enrichment with single amino acids as the substrates and AD sludge as the inoculum. In Chapter 5, a clear community shift between short-term and long-term enrichment was observed along a time course of 18 months. Uncultured populations related to the order Bacteroidales were observed to be predominant (>20% 16S rRNA abundance) in the short-term enrichment, but were competed out (<1% 16S rRNA abundance) by isolated amino acids degraders after long-term enrichment. In Chapter 6, metagenomic and metatranscriptomic analyses were further applied to recover the genomes of the uncultured Bacteroidales populations and explored their metabolic potentials. The populations observed in the short-term enrichment represented a family-level lineage that has not been cultured or characterized. The genomes possessed complete metabolic pathways of degrading 16 to 17 types of amino acids based on metagenomics, and highly expressed these pathways in cultures fed with respective substrates based on metatranscriptomics. A large number of genes (>50) that encode peptidase were also highly expressed, suggesting a proteolytic lifestyle compared to cultured amino acids degraders that might rely on monomer substrates. Finally, these proteolytic amino acids degraders were found to be prevalent and active in full-scale anaerobic digesters, indicating their important ecological roles in protein degradation in the native habitats. Chapter 7 investigates microbial immigration in an industrial wastewater treatment process configured with an upper-flow anaerobic sludge blanket reactor followed by an activated sludge process. Microbial immigrants were shown to have low abundance in the downstream activated sludge, in contrast to most ADs studied in Chapter 2 and Chapter 3. Moreover, a machine learning tool revealed that the change of environmental parameters had weaker impacts on inactive immigrants than on active community members. The observation was consistent with the results that immigrants had negative growth rate and were less active in the downstream environment. Chapter 8 summarizes the key findings of this dissertation and discusses the implication to ecological theories, environmental researches, and engineering applications. Multiple limitations of the methods are identified and further research directions are discussed. Overall, the findings described in this dissertation demonstrate that the EGMB approach is effective in quantifying microbial activity in a complex ecosystem, and elucidate the roles of immigration in community assembly. In the case of full-scale ADs, the findings in this dissertation, for the first time, reveal that microbial immigrants associated with feed sludge represents a significant portion of the AD microbiome. Majority of them are not actively participating in the digestion process but a small fraction can serve as seed populations and possibly maintain the stability of the AD process. In addition to drawing the attention to the overlooked roles of microbial immigration in wastewater treatment processes, the EGMB approach and the findings can be applied to a variety of environments, where the roles of microbial immigration remain to be further characterized.
Issue Date:2020-06-11
Type:Thesis
URI:http://hdl.handle.net/2142/108658
Rights Information:Copyright 2020 Ran Mei
Date Available in IDEALS:2020-10-07
Date Deposited:2020-08


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