A5042621165- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Methane Hydrates and Related Phenomena
- Marine and coastal ecosystems
- Photosynthetic Processes and Mechanisms
- Microbial Fuel Cells and Bioremediation
- Photoreceptor and optogenetics research
- Algal biology and biofuel production
- Marine Biology and Ecology Research
- Protist diversity and phylogeny
- Microbial Metabolic Engineering and Bioproduction
- Biofuel production and bioconversion
- Microbial bioremediation and biosurfactants
- Environmental DNA in Biodiversity Studies
- Medical Imaging and Pathology Studies
- CO2 Sequestration and Geologic Interactions
- Genetics, Bioinformatics, and Biomedical Research
- Biocrusts and Microbial Ecology
- TiO2 Photocatalysis and Solar Cells
- Wastewater Treatment and Nitrogen Removal
- Micro and Nano Robotics
- Enzyme Production and Characterization
- Geochemistry and Elemental Analysis
- Atmospheric and Environmental Gas Dynamics
- Radioactive element chemistry and processing
Agriculture and Agri-Food Canada
2025
Lethbridge Research and Development Centre
2025
University of Calgary
2018-2023
Innovative Genomics Institute
2023
University of California, Berkeley
2023
Planetary Science Institute
2023
Dalhousie University
2018-2019
Mount Allison University
2014-2015
In alkaline soda lakes, concentrated dissolved carbonates establish productive phototrophic microbial mats. Here we show how phototrophs and autotrophs contribute to this exceptional productivity. Amplicon shotgun DNA sequencing data of mats from four Canadian lakes indicate the presence > 2,000 species Bacteria Eukaryotes. We recover metagenome-assembled-genomes for a core microbiome < 100 abundant bacteria, present in all lakes. Most these are related microbes previously detected sediments...
Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the potential of microbial genomes metagenomes. Here we present Calgary approach ANnoTating HYDrocarbon genes (CANT-HYD), a database 37 HMMs marker involved in anaerobic aerobic aliphatic aromatic hydrocarbons. Using this database, understudied or overlooked many phyla. We also demonstrate its application analyzing high-throughput sequence data by predicting utilization...
The fundamental role of bacteria in global biogeochemical cycles warrants a thorough understanding the factors controlling bacterial community structure. In this study, integrated effect seasonal differences and spatial distribution on structure diversity were investigated at regional scale. We conducted comprehensive survey, with 451 samples Scotian Shelf sector Northwest Atlantic Ocean during spring fall 2014 2016, to analyze effects physicochemical gradients Throughout region,...
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...
Ammonia-oxidizing bacteria (AOB) are important members of terrestrial, marine, and industrial microbial communities play a fundamental role in the Nitrogen cycle within these systems. They responsible for first step nitrification, ammonia oxidation to nitrite. Although ammonia-oxidizing widespread essential environmental systems, where they regularly experience fluctuations availability, no comparative studies physiological response diverse AOB species at protein level exist. In present...
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...
ABSTRACT The gut microbiome of the European honey bee ( Apis mellifera ) is vital to its health, yet large-scale studies are scarce. We present metagenomic sequencing data from 180 samples collected near and far eight crops across Canada over 2 years. These sets will help address various biological environmental questions.
Marine Synechococcus and Prochlorococcus are picocyanobacteria predominating in subtropical, oligotrophic marine environments, a niche predicted to expand with climate change. When grown under common low light conditions WH 8102 MED 4 show similar Cytochrome b6f Photosystem I contents normalized II content, while MIT 9313 has twice the content four times of other strains. Interestingly, strains contain only one third half RUBISCO catalytic subunits compared strain. The maximum electron...
Fermentation and dissimilatory manganese (Mn) reduction are inter-related metabolic processes that microbes can perform in anoxic environments. is less energetically favorable often not considered to compete for organic carbon with metal reduction. Therefore, the aim of our study was investigate outcome competition lactate between fermentation Mn oxide (birnessite) a mixed microbial community. A birnessite reducing enrichment culture obtained from activated sludge as substrates. This further...
Summary Extraction of natural gas from unconventional hydrocarbon reservoirs by hydraulic fracturing raises concerns about methane migration into groundwater. Microbial oxidation can be a significant sink. Here, we inoculated replicated, sand‐packed, continuous mesocosms with groundwater field release experiment. The experienced thirty‐five weeks dynamic methane, oxygen and nitrate concentrations. We determined concentrations stable isotope signatures carbon dioxide monitored microbial...
A new haloalkaliphilic species of Wenzhouxiangella, strain AB-CW3, was isolated from a system hypersaline alkaline soda lakes in the Kulunda Steppe using cells Staphylococcus aureus as growth substrate. AB-CW3's complete, circular genome assembled combined nanopore and Illumina sequencing its proteome determined for three different experimental conditions. AB-CW3 is an aerobic gammaproteobacterium feeding mainly on proteins peptides. Unique among it uses flagellum motility, fimbria cell...
Photosynthetic microorganisms, such as algae, are sources of bioproducts. Because they require only sunlight, water, and carbon dioxide to grow, have potential for future mitigation CO2 emissions. However, inefficient growth these organisms remains an issue realizing emission reductions, primarily in terms photosynthetic efficiency, photoinhibition, photolimitation. Here, we show how use light filtration through semi-transparent films comprised organic π-conjugated molecules photovoltaic...
Abstract In alkaline soda lakes, high concentrations of dissolved carbonates establish an environment favouring productive phototrophic microbial mat communities. Here we show how different species phototrophs and autotrophs contribute to this exceptional productivity. Four years amplicon shotgun DNA sequencing data from mats four lakes indicated the presence over 2,000 Bacteria Eukaryotes. Metagenome-assembled-genomes were obtained for a core microbiome <100 abundant bacteria, which was...
Abstract Dissolved hydrogen measurements were made at high resolution in surface waters along a tropical north Atlantic transect between Guadeloupe and Cape Verde 2015 (Meteor 116). Parallel water samples acquired to assess the relative abundance of nifH gene from several types diazotrophs, indicated that Trichodesmium UCYN‐A dominant this region. We show degree correlation exists saturations UCYN‐ A abundance, weak with . The findings suggest nitrogen fixation by is major contributor...
Abstract Cyanobacteria are central to biogeochemical cycling, climate change, and eutrophication. While they readily develop associations with environmental microorganisms, the question of whether consistently recruit specific microbiomes remains unresolved. Here, we established in vitro cyanobacterial consortia by inoculating five different strains from three freshwater environments determine if similar non-cyanobacterial organisms were recruited into stable cyanobacteria-based communities....
Abstract Quantifying the temporal change of bacterial communities is essential to understanding how both natural and anthropogenic pressures impact functions coastal marine ecosystems. Here we use weekly microbial DNA sampling across four years show that phyla have distinct seasonal niches, with a richness peak in winter (i.e., an inverse relationship daylength). Our results suggest fluctuations, rather than kinetic energy or resource hypotheses, dominated pattern diversity. These findings...
A large fraction of any bacterial genome consists hypothetical protein-coding open reading frames (ORFs). While most these ORFs are present only in one or a few sequenced genomes, conserved, often across phylogenetic distances. Such conservation provides clues to likely uncharacterized cellular functions that need be elucidated. Marine cyanobacteria from the Prochlorococcus/marine Synechococcus clade dominant bacteria oceanic waters and significant contributors global primary production....
Cyanobacteria form dense multicellular communities that experience transient conditions in terms of access to light and oxygen. These systems are productive but also undergo substantial biomass turnover through cell death, supplementing heightened heterotrophic respiration. Here we use metagenomics metaproteomics survey the molecular response a mat-forming cyanobacterium undergoing mass lysis after exposure dark anoxic conditions. A lack evidence for viral, bacterial, or eukaryotic...
Abstract Quantifying the temporal change of bacterial communities is essential to understanding how both natural and anthropogenic pressures impact functions coastal ecosystems. Here we use weekly microbial DNA sampling across four years, show that phyla have distinct seasonal niches, with a richness peak in winter (i.e., an inverse relationship daylength). Our results suggest fluctuations rather than kinetic energy or resource hypotheses, dominate pattern diversity. These findings...
Abstract Photosynthetic microorganisms, such as algae, are sources of bioproducts and pharmaceuticals. As they require only sunlight carbon dioxide to grow, have potential for future mitigation CO2 emissions. However, inefficiencies in the growth these organisms remains an issue realizing emission reductions, primarily terms photosynthetic efficiency, photoinhibition, photolimitation. Here, we show how use light filtration through semi-transparent films comprised organic π-conjugated...
Abstract Cyanobacteria form dense multicellular communities that experience transient conditions in terms of access to light and oxygen. These systems are productive but also undergo substantial biomass turnover, supplementing heightened heterotrophic respiration oxygen drawdown. Here we use metagenomics metaproteomics survey the cellular response a mat-forming cyanobacterium undergoing mass cell lysis after exposure dark anoxic conditions. A lack evidence for visral, bacterial, or...
Abstract 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...
ABSTRACT Discovery of microbial hydrocarbon degradation pathways has traditionally relied on laboratory isolation and characterization microorganisms. Although many metabolic for have been discovered, the absence tools dedicated to their annotation makes it difficult identify relevant genes predict potential genomes metagenomes. Furthermore, sequence homology between with other functions often results in misannotation. A tool that systematically identifies is therefore needed. We present...
Summary paragraph The deep biosphere is the largest microbial habitat on Earth and features abundant bacterial endospores 1,2 . Whereas dormancy survival at theoretical energy minima are hallmarks of subsurface populations 3 , roles fundamental ecological processes like dispersal selection in these environments poorly understood 4 Here we combine geophysics, geochemistry, microbiology genomics to investigate biogeography subsurface, focusing a deep-sea setting characterized by thermogenic...