Microbial-based evaluation of anaerobic membrane bioreactors

201 Pages·2017·3.3 MB·English

Microbial-based evaluation of anaerobic membrane bioreactors
(AnMBRs) for the sustainable and efficient treatment of municipal
wastewater

Dissertation by

Moustapha Harb

In partial fulfillment of the requirements
for the degree of Doctor of Philosophy

King Abdullah University of Science and Technology
Thuwal, Kingdom of Saudi Arabia

March, 2017
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EXAMINATION COMMITTEE PAGE

The dissertation of Moustapha Harb is approved by the examination committee.

Committee Chairperson: Dr. Peiying Hong
Committee Members: Dr. Pascal Saikaly, Dr. Mani Sarathy, Dr. Jeremy Guest
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© March, 2017
Moustapha Harb
All Rights Reserved
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ABSTRACT
Microbial-based evaluation of anaerobic membrane bioreactors (AnMBRs) for the
sustainable and efficient treatment of municipal wastewater
Moustapha Harb

Conventional activated sludge-based wastewater treatment is an energy and resource-
intensive process. Historically it has been successful at producing safely treated
wastewater effluents in the developed world, specifically in places that have the
infrastructure and space to support its operation. However, with a growing need for safe
and efficient wastewater treatment across the world in both urban and rural settings, a
paradigm shift in waste treatment is proving to be necessary. The sustainability of the
future of wastewater treatment, in a significant way, hinges on moving towards energy
neutrality and wastewater effluent reuse. This potential for reuse is threatened by the
recent emergence and study of contaminants that have not been previously taken into
consideration, such as antibiotics and other organic micropollutants (OMPs), antibiotic
resistance genes, and persistent pathogenic bacteria.

This dissertation focuses on investigating the use of anaerobic membrane bioreactor
(AnMBR) technology for the sustainable treatment of municipal-type wastewaters.
Specifically, a microbial approach to understanding biofouling and methane recovery
potential in anaerobic MBR systems has been employed to assess different reactor
systems’ efficiency. This dissertation further compares AnMBRs to their more widely
used aerobic counterparts. This comparison specifically focuses on the removal and
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biodegradation of OMPs and antibiotics in both anaerobic and aerobic MBRs, while also
investigating their effect on the proliferation of antibiotic resistance genes. Due to rising
interest in wastewater effluent reuse and the lack of a comprehensive understanding of
MBR systems’ effects on pathogen proliferation, this dissertation also investigates the
presence of pathogens in both aerobic and anaerobic MBR effluents by using molecular-
based detection methods.

The findings of this dissertation demonstrate that membrane-associated anaerobic
digestion processes have significant potential to improve the sustainability of wastewater
treatment. This is exemplified by attributes of AnMBR systems associated with both
increased system efficiency and wastewater reuse potential through methane recovery
and lower abundance of effluent microbial contaminants, respectively. Overall, the
studies collated in this dissertation have shown that understanding the microbial
communities of AnMBRs can play a central role in further improving these attributes and
in reducing the risks posed by emerging contaminants and pathogens in wastewater
treatment systems.
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ACKNOWLEDGEMENTS
I would like to thank my committee chair, Dr. Peiying Hong for her strong support and
guidance throughout the course of my Ph.D. work. I would also like to thank my
committee members, Dr. Saikaly, Dr. Sarathy, and Dr. Guest, for generously providing
their expertise and insight in support of this research.
My sincerest appreciation goes to my friends at KAUST, the members of the Peiying
Hong research group, and the members of the Water Desalination and Reuse Center for
making my time here a great experience.
Finally, my heartfelt gratitude is extended to my parents Constance and Jalal and my
brothers Ahmed and Mahmoud for their unwavering encouragement, patience, and
support.
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TABLE OF CONTENTS
EXAMINATION COMMITTEE PAGE ........................................................................ 2
ABSTRACT ....................................................................................................................... 4
ACKNOWLEDGEMENTS ............................................................................................. 6
TABLE OF CONTENTS ................................................................................................. 7
LIST OF ABBREVIATIONS ........................................................................................ 10
LIST OF FIGURES ........................................................................................................ 12
LIST OF TABLES .......................................................................................................... 14
Chapter 1 ......................................................................................................................... 15
1. Introduction .............................................................................................................. 16
1.1. Conventional wastewater treatment and MBRs ............................................ 16
1.2. Background: Sustainability and safety issues of AnMBR systems .............. 22
1.2.1. AnMBRs and operational sustainability ...................................................... 24
1.2.2. Emerging contaminants in MBR Systems ................................................... 27
1.2.3. Microbial safety of MBR effluents for reuse ............................................... 29
1.3. Objectives........................................................................................................... 31
1.4. References .......................................................................................................... 34
Chapter 2 ......................................................................................................................... 43
2. Differences in microbial communities and performance between suspended and
attached growth anaerobic membrane bioreactors treating synthetic municipal
wastewater ....................................................................................................................... 44
2.1. Introduction ....................................................................................................... 46
2.2. Materials & methods ........................................................................................ 49
2.2.1. Reactor operating conditions ........................................................................ 49
2.2.2. Chemical and physical water quality measurements ................................. 51
2.2.3. Biogas measurement ...................................................................................... 52
2.2.4. Sludge and membrane biomass sampling for microbial analysis .............. 53
2.2.5. DNA extraction and barcoded amplification of 16S rRNA genes ............. 54
2.2.6. Ion Torrent sequencing of 16S rRNA genes and data analysis ................. 55
2.2.7. Reactor SMP and membrane biofilm EPS extraction and analysis .......... 56
2.2.8. Membrane surface categorization ................................................................ 58
2.3. Results ................................................................................................................ 59
2.3.1. Reactor performance ..................................................................................... 59
2.3.2. Membrane operation ..................................................................................... 61
2.3.3. Microbial similarity analysis in AnMBR sludge and membrane biofilms 62
2.3.4. Reactor-based microbial comparison .......................................................... 63
2.3.5. Microbial differences between attached and suspended biomass ............. 66
2.3.6. Membrane biofilm EPS content ................................................................... 68
2.3.7. AnMBR retentate SMP profile dynamics .................................................... 69
2.3.8. SMP and EPS fractions – potential relation to PES membrane fouling ... 70
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2.3.9. Membrane characterization .......................................................................... 73
2.4. Discussion........................................................................................................... 73
2.5. Conclusion ......................................................................................................... 80
2.6. Acknowledgements ........................................................................................... 81
2.7. References .......................................................................................................... 82
Chapter 3 ......................................................................................................................... 87
3. Organic micropollutants in aerobic and anaerobic membrane bioreactors:
Changes in microbial communities and gene expression ............................................ 88
3.1. Introduction ....................................................................................................... 89
3.2. Material and methods ....................................................................................... 91
3.2.1. Description of treatment systems and operational conditions ................... 91
3.2.2. Liquid chromatography – mass spectrometry ............................................ 92
3.2.3. Amplicon-based next-generation sequencing .............................................. 93
3.2.4. Quantitative PCR (qPCR) ............................................................................. 94
3.2.5. Metatranscriptomics ...................................................................................... 94
3.3. Results & Discussion ......................................................................................... 95
3.3.1. Overall Reactor Performances and OMP removal efficiency ................... 95
3.3.2. Effect of OMPs on reactor microbial communities .................................... 97
3.3.2.1. Aerobic System ......................................................................................... 98
3.3.2.2. Anaerobic system .................................................................................... 101
3.3.3. Changes in biodegradation gene expression .............................................. 104
3.3.3.1. Gene group-based analysis ..................................................................... 104
3.3.3.2. Gene function-based analysis ................................................................. 107
3.3.4. Implications of OMPs for antibiotic resistance gene fate in MBRs ........ 111
3.4. Conclusions ...................................................................................................... 115
3.5. Supplementary Data ....................................................................................... 115
3.6. Acknowledgements ......................................................................................... 116
3.7. References ........................................................................................................ 117
Chapter 4 ....................................................................................................................... 122
4. Molecular-based detection of potentially pathogenic bacteria in membrane
bioreactor (MBR) systems treating municipal wastewater: a case study ................ 123
4.1. Introduction ..................................................................................................... 124
4.2. Materials & methods ...................................................................................... 126
4.2.1. Full-scale aerobic MBR system description and sampling protocol ....... 126
4.2.2. Lab-scale anaerobic MBR system description and sampling protocol ... 127
4.2.3. Water quality and biogas measurements ................................................... 128
4.2.4. DNA extraction and 16S rRNA gene-based next generation sequencing 128
4.2.5. Species-targeted digital PCR (dPCR) ........................................................ 130
4.2.6. Quantitative microbial risk assessment (QMRA) ..................................... 130
4.3. Results .............................................................................................................. 132
4.3.1. AeMBR and AnMBR water quality measurements and performance ... 132
4.3.2. Estimation of total bacteria by rpoB gene quantification ........................ 132
4.3.3. Microbial communities of municipal wastewater influent ....................... 133
4.3.4. Microbial communities of effluents of AeMBR and AnMBR systems .... 134
4.3.5. Detection of pathogenic species in MBR systems using dPCR ................ 136
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4.3.6. Quantitative microbial risk assessment (QMRA) ..................................... 138
4.4. Discussion......................................................................................................... 140
4.5. Conclusions ...................................................................................................... 146
4.6. Acknowledgements ......................................................................................... 147
4.7. References ........................................................................................................ 148
Chapter 5 ....................................................................................................................... 154
5. Conclusions ............................................................................................................. 155
5.1. General Conclusions ....................................................................................... 155
5.2. Future Work .................................................................................................... 158
5.3. References ........................................................................................................ 163
Appendices ..................................................................................................................... 166
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LIST OF ABBREVIATIONS
AOB ammonia-oxidizing bacteria
AFM atomic force microscopy
AeMBR aerobic membrane bioreactor
AnMBR anaerobic membrane bioreactor
ARG antibiotic resistance gene
BDG biodegradation gene
BSA bovine serum albumin
CA cellulose acetate
CAS conventional activated sludge
COD chemical oxygen demand
CSTR continuously stirred tank reactor
DBP disinfection byproduct
DEET diethyltoluamide
dPCR digital polymerase chain reaction
ENA European Nucleotide Archive
EPS extracellular polymeric substances
HRT hydraulic retention time
LC-MS/MS liquid chromatography tandem mass spectrometry
LCFA long chain fatty acid
LMH liters per square meter per hour
LRV log reduction value
MBR membrane Bioreactor
MF microfiltration
MG-RAST metagenomic rapid annotation using subsystems technology
MLSS mixed liquor suspended solids
mMDS metric multidimensional scaling
MWCO molecular weight cutoff
NCBI National Center for Biotechnology Information
NF nanofiltration
NOB nitrite-oxidizing bacteria
OMP organic micropollutants
OTU operational taxonomic unit
PAC power activated carbon
PBS phosphate buffered saline
pKa acid dissociation constant
PCA principal component analysis
PES polyethersulfone