A5102881242- Microbial Community Ecology and Physiology
- Methane Hydrates and Related Phenomena
- Gut microbiota and health
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Genomics and Phylogenetic Studies
- Atmospheric and Environmental Gas Dynamics
- Biocrusts and Microbial Ecology
- Hydrocarbon exploration and reservoir analysis
- Biofuel production and bioconversion
- Microbial bioremediation and biosurfactants
- Aeolian processes and effects
- Enzyme Production and Characterization
- Bacterial biofilms and quorum sensing
- Probiotics and Fermented Foods
- Aquatic Ecosystems and Phytoplankton Dynamics
- Marine Biology and Ecology Research
- Migration, Health and Trauma
- Genetic Mapping and Diversity in Plants and Animals
- Oral microbiology and periodontitis research
- Protist diversity and phylogeny
- Paleontology and Stratigraphy of Fossils
- Marine and coastal ecosystems
Pacific Northwest National Laboratory
2024
The University of Queensland
2023
University of British Columbia
2006-2013
St. Paul's Hospital
2006
Oxygen minimum zones, also known as oceanic "dead zones," are widespread oceanographic features currently expanding because of global warming. Although inhospitable to metazoan life, they support a cryptic microbiota whose metabolic activities affect nutrient and trace gas cycling within the ocean. Here, we report metagenomic analyses ubiquitous abundant but uncultivated oxygen zone microbe (SUP05) related chemoautotrophic gill symbionts deep-sea clams mussels. The SUP05 metagenome harbors...
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...
An active microbiota, reaching up to 10 E+7 cells/g, was found inhabit a naturally occurring asphalt lake characterized by low water activity and elevated temperature. Geochemical molecular taxonomic approaches revealed novel deeply branching microbial assemblages mediating anaerobic hydrocarbon degradation, metal respiration C1 utilization pathways. These results open window into the origin adaptive evolution of life within recalcitrant matrices, establish site as useful analog for liquid...
Functional metagenomics has emerged as a powerful method for gene model validation and enzyme discovery from natural human engineered ecosystems. Here we report development of high-throughput functional metagenomic screen incorporating bioinformatic biochemical analyses features. A fosmid library containing 6144 clones sourced mining bioremediation system was screened cellulase activity using 2,4-dinitrophenyl β-cellobioside, previously proven cellulose substrate. Fifteen active were...
Biocrusts play important roles in rangeland ecosystems by protecting soil surfaces and fixing carbon nitrogen. Their responses to management practices, however, are poorly understood. Here, we characterised the impacts of cattle grazing fire (controlled 2- or 4-yearly burning versus no fire) on diversity composition biocrust associated bacterial communities (0–1 cm depth) a long-term (30–60 years) field experiment Northern Territory, Australia. Both experiments were replicated two types...
is recognized for its ability to anaerobically ferment dichloromethane (DCM), and a catabolic model has recently been proposed.
Abstract Summary: DataBiNS is a custom-designed BioMoby Web Service workflow that integrates non-synonymous coding single nucleotide polymorphisms (nsSNPs) data with structure/function and pathway for the relevant protein. A KEGG Pathway Identifier representing specific human biological initializes workflow. The retrieves list of publications, gene ontology annotations nsSNP information each involved in pathway. Manual inspection output from several trial runs confirms all expected...
Abstract Summary: Multi-dimensional Automated Clustering Genotyping Tool (MACGT) is a Java application that clusters complex multi-dimensional vector data derived from single nucleotide polymorphism (SNP) genotyping experiments using mini-sequencing based microarray chemistries such as arrayed primer extension (APEX). Spot intensity output files across multiple samples are imported into MACGT. The datasets can include four channels of for each spot, replica spots SNP probe and types (APEX...
Urbanization is a leading cause of global biodiversity loss, but its impact on soil microorganisms and biogeochemistry remains uncertain. To address this gap, we investigate urban microbiome composition using metagenomic sequences from the Global Urban Soil Environment Ecology Network (GLUSEEN). We seek to reveal (1) changes in taxonomic functional potential (2) ubiquitous (core) taxa metabolisms across microbiome. hypothesize that diversity are correlated due unique selective pressures...