A5101613208- Microbial Community Ecology and Physiology
- Methane Hydrates and Related Phenomena
- Hydrocarbon exploration and reservoir analysis
- Genomics and Phylogenetic Studies
- Atmospheric and Environmental Gas Dynamics
- Enhanced Oil Recovery Techniques
- Gut microbiota and health
- Microbial bioremediation and biosurfactants
- SARS-CoV-2 detection and testing
- COVID-19 Clinical Research Studies
- SARS-CoV-2 and COVID-19 Research
- Hydraulic Fracturing and Reservoir Analysis
- Environmental DNA in Biodiversity Studies
- Mine drainage and remediation techniques
- Smart Grid Energy Management
- Drilling and Well Engineering
- Metal Extraction and Bioleaching
- Geology and Paleoclimatology Research
- Biosensors and Analytical Detection
- Advanced Control Systems Optimization
- Wastewater Treatment and Nitrogen Removal
- Marine Biology and Ecology Research
- Advanced biosensing and bioanalysis techniques
- Arsenic contamination and mitigation
- Petroleum Processing and Analysis
University of Calgary
2017-2024
University of Alberta
2013-2020
Microbial community structure can be analyzed by quantifying cell numbers or biomass for individual populations. Methods are already available (e.g., fluorescence in situ hybridization, 16-S rRNA gene amplicon sequencing), yet high-throughput methods assessing terms of lacking. Here we present metaproteomics-based microbial using protein abundance as a measure contributions We optimize the accuracy and sensitivity method artificially assembled communities show that it is less prone to some...
Abstract The lack of microbial genomes and isolates from the deep seabed means that very little is known about ecology this vast habitat. Here, we investigate energy carbon acquisition strategies communities three petroleum seeps (3 km water depth) in Eastern Gulf Mexico. Shotgun metagenomic analysis reveals each sediment harbors diverse chemoheterotrophs chemolithotrophs. We recovered 82 metagenome-assembled affiliated with 21 different archaeal bacterial phyla. Multiple encode enzymes for...
Oil in subsurface reservoirs is biodegraded by resident microbial communities. Water-mediated, anaerobic conversion of hydrocarbons to methane and CO2, catalyzed syntrophic bacteria methanogenic archaea, thought be one the dominant processes. We compared 160 community compositions ten hydrocarbon resource environments (HREs) sequenced twelve metagenomes characterize their metabolic potential. Although communities were common, cores from oil sands coal beds had unexpectedly high proportions...
At marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Cold seep sediments are known host taxonomically diverse microorganisms, but little is about their metabolic potential depth distribution in relation hydrocarbon electron acceptor availability. Here we combined geophysical, geochemical, metagenomic metabolomic measurements profile microbial activities at a newly discovered sea. Metagenomic profiling revealed...
SARS-CoV-2 has been detected in wastewater and its abundance correlated with community COVID-19 cases, hospitalizations deaths. We sought to use wastewater-based detection of assess the epidemiology hospitals. Between August December 2020, twice-weekly samples from three tertiary-care hospitals (totaling > 2100 dedicated inpatient beds) were collected. Hospital-1 Hospital-2 could be captured a single sampling point whereas Hospital-3 required separate monitoring sites. Wastewater...
Wastewater-based epidemiology (WBE) is an emerging surveillance tool that has been used to monitor the ongoing COVID-19 pandemic by tracking SARS-CoV-2 RNA shed into wastewater. WBE was performed occurrence and spread of from three wastewater treatment plants (WWTP) six neighborhoods in city Calgary, Canada (population 1.44 million). A total 222 WWTP 192 neighborhood samples were collected June 2020 May 2021, encompassing end first-wave (June 2020), second-wave (November December 2020)...
Microbial community profiling by barcoded 16S rRNA gene amplicon sequencing currently has many applications in microbial ecology. The low costs of the parallel multiplexed samples, combined with relative ease data processing and interpretation (compared to shotgun metagenomes) have made this an entry-level approach. Here we present MetaAmp pipeline for SSU other non-coding or protein-coding investigators that are inexperienced bioinformatics procedures. It accepts single-end paired-end...
Marine cold seeps transmit fluids between the subseafloor and seafloor biospheres through upward migration of hydrocarbons that originate in deep sediment layers. It remains unclear how geofluids influence composition seabed microbiome if they transport subsurface life up to surface. Here we analyzed 172 marine surficial sediments from deep-water Eastern Gulf Mexico assess whether hydrocarbon fluid is a mechanism for microbial dispersal. While 132 these contained migrated liquid...
Microbiome analysis through 16S rRNA gene sequencing is a crucial tool for understanding the microbial ecology of any habitat or ecosystem. However, workflows require large equipment, stable internet, and extensive computing power such that most work performed far away from sample collection in both space time. Performing amplicon at would have positive implications many instances including remote fieldwork point-of-care medical diagnoses. Here we present SituSeq, an offline portable...
Dispersed clay particles in mine tailings and soft sediments remain suspended for decades, hindering consolidation challenging effective management of these aqueous slurries. Current geotechnical engineering models self-weight do not consider microbial contribution to sediment behavior, however, here we show that microorganisms indigenous oil sands change the porewater chemistry accelerate tailings. A companion paper describes role microbes alteration Microbial metabolism mature fine (MFT)...
Consolidation of clay particles in aqueous tailings suspensions is a major obstacle to effective management oil sands ponds northern Alberta, Canada. We have observed that microorganisms indigenous the accelerate consolidation mature fine (MFT) during active metabolism by using two biogeochemical pathways. In Pathway I, microbes alter porewater chemistry indirectly increase MFT. Here, we describe II comprising significant, direct and complementary reactions with MFT mineral surfaces. An...
The deep biosphere is the largest microbial habitat on Earth and features abundant bacterial endospores. Whereas dormancy survival at theoretical energy minima are hallmarks of physiology in subsurface, ecological processes such as dispersal selection remain poorly understood. We investigated biogeography dispersing bacteria sea where upward hydrocarbon seepage was confirmed by acoustic imagery geochemistry. Thermophilic endospores permanently cold seabed correlated with underlying seep...
iso-Alkanes are major components of petroleum and have been considered recalcitrant to biodegradation under methanogenic conditions. However, indigenous microbes in oil sands tailings ponds exposed solvents rich 2-methylbutane, 2-methylpentane, 3-methylpentane, n-pentane, n-hexane produce methane situ. We incubated defined mixtures iso- or n-alkanes with mature fine from two different ages historically solvents: one, ∼10 years old, receiving C5–C6 paraffins the other, ∼35 naphtha. A lengthy...
Abstract Dormant endospores of thermophilic bacteria (thermospores) can be detected in cold marine sediments following high-temperature incubation. Thermospores the seabed may explained by a dispersal history originating deep biosphere oil reservoir habitats where upward migration petroleum fluids at hydrocarbon seeps transports viable cells into overlying ocean. We assessed this deep-to-shallow hypothesis through geochemical and microbiological analyses 111 from water Eastern Gulf Mexico....
Deep sea hydrocarbon seep detection relies predominantly on geochemical analyses of seabed marine sediment cores to identify the presence gas or oil. The seeping hydrocarbons in these locations alters local redox stratification and microbial community structure. Cultivation-independent biodiversity surveys communities can offer a proxy for hydrocarbons, but this strategy has not been extensively investigated deep water settings. In study, 16S rRNA gene sequencing bacterial was performed...
Microorganisms are the ocean's first responders to marine pollution events, yet baseline studies rarely focus on microbial communities. Temporal and spatial biodiversity baselines were established using bacterial 16S rRNA gene amplicon sequencing of seafloor sediments in a deep-water oil prospective area along Scotian Slope off Canada's east coast sampled during 2015-2018. Bacterial diversity was generally similar space time, with members family Woeseiaceae detected consistently >1 %...
Endospore-forming bacteria make up an important and numerically significant component of microbial communities in a range settings including soils, industry, hospitals marine sediments extending into the deep subsurface. Bacterial endospores are non-reproductive structures that protect DNA improve cell survival during periods unfavourable for bacterial growth. An determinant withstanding extreme environmental conditions is 2,6-pyridine dicarboxylic acid (i.e. dipicolinic acid, or DPA), which...
Dormant endospores of anaerobic, thermophilic bacteria found in cold marine sediments offer a useful model for studying microbial biogeography, dispersal, and survival. The dormant endospore phenotype confers resistance to unfavorable environmental conditions, allowing dispersal be isolated studied independently other factors such as selection. To study the resilience thermospores conditions relevant survival extreme their viability following different freezing treatments was tested. Marine...
Abstract Microbial community profiling by barcoded 16S rRNA gene amplicon sequencing currently has many applications in microbial ecology. The low costs of the parallel multiplexed samples, combined with relative ease data processing and interpretation (compared to shotgun metagenomes) have made this an entry-level approach. Here we present MetaAmp pipeline for SSU other non-coding or protein-coding investigators that are inexperienced bioinformatics procedures. It accepts single-end...
Abstract Assessment of microbial community composition is the cornerstone ecology. Microbial can be analyzed by quantifying cell numbers or biomass for individual populations. However, as volumes differ orders magnitude, these two approaches yield vastly different results. Methods are already available (e.g. fluorescence in situ hybridization, 16S rRNA gene amplicon sequencing), yet methods assessing terms lacking. We developed metaproteomics based using protein abundance a measure...
Abstract At marine cold seeps, gaseous and liquid hydrocarbons migrate from deep subsurface origins to the sediment-water interface. Cold seep sediments are known host taxonomically diverse microorganisms, but little is about their metabolic potential depth distribution in relation hydrocarbon electron acceptor availability. In this work, we combined geochemical, metagenomic metabolomic measurements distinct sediment redox regimes profile microbial activities within uppermost 350 cm of a...