A5017561108- Methane Hydrates and Related Phenomena
- Earthquake Detection and Analysis
- Seismic Waves and Analysis
- Microbial Community Ecology and Physiology
- Anaerobic Digestion and Biogas Production
- Biofuel production and bioconversion
- Genomics and Phylogenetic Studies
- Wastewater Treatment and Nitrogen Removal
- Microbial Fuel Cells and Bioremediation
- SARS-CoV-2 detection and testing
- Advanced biosensing and bioanalysis techniques
- Microbial Metabolic Engineering and Bioproduction
- Biosensors and Analytical Detection
- Gut microbiota and health
- Pharmaceutical and Antibiotic Environmental Impacts
- SARS-CoV-2 and COVID-19 Research
- Environmental DNA in Biodiversity Studies
- Water Treatment and Disinfection
- Analytical chemistry methods development
- Molecular Biology Techniques and Applications
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Bacteriophages and microbial interactions
- Effects and risks of endocrine disrupting chemicals
- Constructed Wetlands for Wastewater Treatment
University of British Columbia
2017-2024
Genome British Columbia
2023
BC Centre for Disease Control
2021-2023
Simon Fraser University
2021
University of Washington
2014-2019
Microorganisms in biogas reactors are essential for degradation of organic matter and methane production. However, a comprehensive genome-centric comparison, including relevant metadata each sample, is still needed to identify the globally distributed community members serve as reliable repository.Here, 134 publicly available metagenomes derived from different were used recover 1635 metagenome-assembled genomes (MAGs) representing bacterial archaeal species. All estimated be > 50% complete...
On the 26th of November 2021, World Health Organization (WHO) designated newly detected B.1.1.529 lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron Variant Concern (VOC). The genome VOC contains more than 50 mutations, many which have been associated with increased transmissibility, differing disease severity, and potential to evade immune responses developed for previous VOCs such as Alpha Delta. In days since designation a VOC, infections reported in countries...
Abstract Fats, oils and greases (FOG) are energy-dense wastes that can be added to anaerobic digesters substantially increase biomethane recovery via their conversion through long-chain fatty acids (LCFAs). However, a better understanding of the ecophysiology syntrophic LCFA-degrading microbial communities in is needed develop operating strategies mitigate inhibitory LCFA accumulation from FOG. In this research, DNA stable isotope probing (SIP) was coupled with metagenomic sequencing for...
Small genes (<150 nucleotides) have been systematically overlooked in phage genomes. We employ a large-scale comparative genomics approach to predict >40,000 small-gene families ∼2.3 million genome contigs. find that small genomes are approximately 3-fold more prevalent than host prokaryotic Our enriches for translated microbiomes, suggesting the identified coding. More 9,000 encode potentially secreted or transmembrane proteins, 5,000 predicted anti-CRISPR and 500 antimicrobial proteins. By...
Wastewater-based testing (WBT) for SARS-CoV-2 has rapidly expanded over the past three years due to its ability provide a comprehensive measurement of disease prevalence independent clinical testing. The development and simultaneous application WBT measured biomarkers research activities pursuit public health goals, both areas with well-established ethical frameworks. Currently, practitioners do not employ standardized review process, introducing potential adverse outcomes professionals...
In water resource recovery facilities, sidestream biological nitrogen removal via anaerobic ammonium oxidation (anammox) is more energy and cost efficient than conventional nitrification-denitrification. However, under mainstream conditions, nitrite oxidizing bacteria (NOB) out-select anammox for produced by (AOB). Therefore, production the bottleneck in removal. Nitrate-dependent denitrifying methane archaea (n-damo) oxidize reduce nitrate to nitrite. The supply challenge implementation...
Abstract High-throughput amplicon sequencing of large genomic regions remains challenging for short-read technologies. Here, we report a high-throughput approach combining unique molecular identifiers (UMIs) with Oxford Nanopore Technologies or Pacific Biosciences CCS sequencing, yielding high accuracy single-molecule consensus sequences regions. Our generates and >10,000 bp in length mean error-rate 0.0049-0.0006% chimera rate <0.022%.
Wastewater-based genomic surveillance of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus shows promise to complement epidemiology efforts. Multiplex tiling PCR is a desirable approach for targeted genome sequencing SARS-CoV-2 in wastewater due its low cost and rapid turnaround time. However, it not clear how different multiplex primer schemes or sample matrices impact resulting coverage. The objective this work was assess performance three schemes, consisting 150-bp,...
During the coronavirus disease 2019 (COVID-19) pandemic, wastewater surveillance has become an important tool for monitoring spread of severe acute respiratory syndrome 2 (SARS-CoV-2) within communities. In particular, reverse transcription-quantitative PCR (RT-qPCR) been used to detect and quantify SARS-CoV-2 RNA in wastewater, while viral genome mutations requires separate approaches such as deep sequencing. A high throughput sequencing platform (ATOPlex) that uses a multiplex tiled...
In many anoxic environments, syntrophic acetate oxidation (SAO) is a key pathway mediating the conversion of into methane through obligate cross-feeding interactions between SAO bacteria (SAOB) and methanogenic archaea. The particularly important in engineered environments such as anaerobic digestion (AD) systems operating at thermophilic temperatures and/or with high ammonia. Despite widespread importance SAOB to stability AD process, little known about their situ physiologies due typically...
The ecophysiology of long-chain fatty acid-degrading syntrophic β-oxidizing bacteria has been poorly understood due to a lack quantitative abundance data. Here, TaqMan PCR (qPCR) assays targeting the 16S rRNA gene known mesophilic bacterial genera Syntrophomonas and Syntrophus were developed validated. Microbial community dynamics followed using qPCR Illumina-based high-throughput amplicon sequencing in triplicate methanogenic bioreactors subjected five consecutive batch feedings oleic acid....
Summary This study examined whether the abundance and expression of microbial 16S rRNA genes were associated with elemental concentrations substrate conversion biokinetics in 20 full‐scale anaerobic digesters, including seven municipal sewage sludge ( SS ) digesters 13 industrial codigesters. digester contents had higher methane production rates from acetate, propionate phenyl acetate compared to codigesters distinctly clustered based on their concentrations, NH 3 ‐N, Cl, K Na observed...
Abstract Background Microorganisms in biogas reactors are essential for degradation of organic matter and methane production through anaerobic digestion process. However, a comprehensive genome-centric comparison, including relevant metadata each sample, is still needed to identify the globally distributed community members serve as reliable repository. Results Here, 134 publicly available datasets derived from different were used recover 1,635 metagenome-assembled genomes (MAGs)...
Linking the genomic content of uncultivated microbes to their metabolic functions remains a critical challenge in microbial ecology. Resolving this has implications for improving our management key interactions biotechnologies such as anaerobic digestion, which relies on slow-growing syntrophic and methanogenic communities produce renewable methane from organic waste. In study, we combined DNA stable-isotope probing (SIP) with genome-centric metagenomics recover genomes populations enriched...
Using genome-centric metagenomics, we discovered a new Methanothrix harundinacea subspecies that appears to be halotolerant acetoclastic methanogen with the flexibility for adaptation in anaerobic digestion process both at low (5 g/L Na + ) and high salinity conditions (20 ). Annotation of recovered M. genome revealed stress-related functions, including modification EPS glycoconjugates production compatible solutes.
Abstract Amplicon sequencing of small subunit (SSU) rRNA genes is a foundational method for studying microbial communities within various environmental, human, and engineered ecosystems. Currently, short-read platforms are commonly employed high-throughput applications SSU amplicon sequencing, but at the cost poor taxonomic classification. The low-cost Oxford Nanopore Technologies (ONT) platform capable full-length genes, lower raw-read accuracies previous ONT chemistries have limited...
The removal of the potent endocrine-disrupting estrogen hormone, 17α-ethinylestradiol (EE2), in municipal wastewater treatment plant (WWTP) activated sludge (AS) processes can occur through biodegradation by heterotrophic bacteria growing on other organic substrates. Different kinetic and metabolic substrate utilization conditions created with AS bioselector affect population composition AS. primary goal this research was to determine if these changes also specific EE2 kinetics. A series...