Microbial community analysis using next-generation sequencing and bioinformatics tools to better understand biological waste and wastewater treatment

Nguyen, Quynh Anh

Microbial community analysis using next-generation sequencing and bioinformatics tools to better understand biological waste and wastewater treatment

Nguyen, Quynh Anh

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Publication Type:: Thesis
Issue Date:: 2022

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Field	Value	Language
dc.contributor.author	Nguyen, Quynh Anh
dc.date.accessioned	2022-12-14T00:59:13Z
dc.date.available	2022-12-14T00:59:13Z
dc.date.issued	2022
dc.identifier.uri	http://hdl.handle.net/10453/164384
dc.description	University of Technology Sydney. Faculty of Engineering and Information Technology.	en_US.UTF-8
dc.description.abstract	Waste/wastewater treatment often rely on microbes and biotransformation for removing contaminants and environmental restoration. Insights into the microbial communities associated with these processes can help develop better operational strategies. Three common environmental engineering processes were investigated in this thesis to demonstrate the application of next-generation sequencing and bioinformatics tools to elucidate the link between microbial community and process performance. The first process was membrane fouling in membrane bioreactors (MBRs). Nutritional deficiency led to endogenous decay and sludge bulking, which in turn triggered membrane fouling under sub-critical flux. The mixed liquor and fouling layer possessed similar microbial composition. The most dominant filamentous order Thiotrichales (>60%) positively correlated with fouling severity. Under high-flux conditions, MBR biofilm and mixed liquor possessed different microbial structures. Low-abundance taxa (<1%) such as Victivallales and Blastocatellia 11-24 drove the divergence between the two communities. These taxa also played key roles in fouling development and positively correlated with fouling indicators. Knowledge of MBR fouling-associated microbial taxa can help improve fouling control strategies, reduce the cost of membrane cleaning and energy consumption, enhance MBR application and increase the treated water quality. The second process was lignocellulosic biomass (LCBM) valorisation using rumen microbes. Biomethane potential analysis showed that rumen microbes can produce four times more volatile fatty acids (VFA) than anaerobic sludge. However, VFA accumulation led to pH drop which in turn resulted in process inhibition, suggesting the need for continuous extraction of VFA from the system. A novel rumen-MBR was evaluated, showing continuous VFA production at 438 mg VFA/g substrate. Acetic and propionic acids accounted for >80% of the total VFA produced. Most of the produced VFA (73 ± 15%) was continuously extracted by an ultrafiltration membrane. Shifts in dominant rumen microbes during operation did not impact VFA yield. This work provides an important foundation for the development of a sustainable pathway for producing renewable chemicals in a circular economy. The third process was chiral inversion of 2-arylpropionic acids (2-APAs) in biological waste and wastewater treatment. Despite possessing highly similar chemical structures, eleven 2-APAs exhibited diverse and distinctive chiral inversion behaviours. Both unidirectional and bidirectional chiral inversions of 2-APAs were observed under aerobic and anaerobic conditions. Potential microbes involved in chiral inversion, including Candidatus_Microthrix, Rhodococcus, Mycobacterium, Gordonia, and Sphingobium, are aerobic or facultative anaerobic bacteria. This is the first study to report chiral inversion behaviours of a comprehensive suite of 2-APAs during biological treatment.	en_US.UTF-8
dc.format	Thesis (PhD)
dc.language.iso	en_US	en_US.UTF-8
dc.relation	https://opus.lib.uts.edu.au/bitstream/10453/164384/2/02whole.pdf
dc.rights	The author owns the copyright in this thesis including all reproduction and reuse rights for the work. The work may not be altered without the permission of the copyright owner. Attribution is essential when quoting or paraphrasing from this thesis.
dc.rights	au.edu.uts.lib/ppc
dc.rights	info:eu-repo/semantics/openAccess
dc.title	Microbial community analysis using next-generation sequencing and bioinformatics tools to better understand biological waste and wastewater treatment	en_US.UTF-8
dc.type	Thesis
utslib.copyright.status	open_access	*

Abstract:

Waste/wastewater treatment often rely on microbes and biotransformation for removing contaminants and environmental restoration. Insights into the microbial communities associated with these processes can help develop better operational strategies. Three common environmental engineering processes were investigated in this thesis to demonstrate the application of next-generation sequencing and bioinformatics tools to elucidate the link between microbial community and process performance. The first process was membrane fouling in membrane bioreactors (MBRs). Nutritional deficiency led to endogenous decay and sludge bulking, which in turn triggered membrane fouling under sub-critical flux. The mixed liquor and fouling layer possessed similar microbial composition. The most dominant filamentous order Thiotrichales (>60%) positively correlated with fouling severity. Under high-flux conditions, MBR biofilm and mixed liquor possessed different microbial structures. Low-abundance taxa (<1%) such as Victivallales and Blastocatellia 11-24 drove the divergence between the two communities. These taxa also played key roles in fouling development and positively correlated with fouling indicators. Knowledge of MBR fouling-associated microbial taxa can help improve fouling control strategies, reduce the cost of membrane cleaning and energy consumption, enhance MBR application and increase the treated water quality. The second process was lignocellulosic biomass (LCBM) valorisation using rumen microbes. Biomethane potential analysis showed that rumen microbes can produce four times more volatile fatty acids (VFA) than anaerobic sludge. However, VFA accumulation led to pH drop which in turn resulted in process inhibition, suggesting the need for continuous extraction of VFA from the system. A novel rumen-MBR was evaluated, showing continuous VFA production at 438 mg VFA/g substrate. Acetic and propionic acids accounted for >80% of the total VFA produced. Most of the produced VFA (73 ± 15%) was continuously extracted by an ultrafiltration membrane. Shifts in dominant rumen microbes during operation did not impact VFA yield. This work provides an important foundation for the development of a sustainable pathway for producing renewable chemicals in a circular economy. The third process was chiral inversion of 2-arylpropionic acids (2-APAs) in biological waste and wastewater treatment. Despite possessing highly similar chemical structures, eleven 2-APAs exhibited diverse and distinctive chiral inversion behaviours. Both unidirectional and bidirectional chiral inversions of 2-APAs were observed under aerobic and anaerobic conditions. Potential microbes involved in chiral inversion, including Candidatus_Microthrix, Rhodococcus, Mycobacterium, Gordonia, and Sphingobium, are aerobic or facultative anaerobic bacteria. This is the first study to report chiral inversion behaviours of a comprehensive suite of 2-APAs during biological treatment.

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