The genomic analysis of assemblages of organisms.
1Department of Biology, San Diego State University, 2Scripps Institution of Oceanography, University of California San Diego
Here, we present a comprehensive protocol to assess the organic and inorganic nutrient availability and the abundance and structure of microbial and viral communities in remote marine environments.
Published November 5, 2014. Keywords: Environmental Sciences, dissolved organic carbon, particulate organic matter, nutrients, DAPI, SYBR, microbial metagenomics, viral metagenomics, marine environment
JoVE Immunology and Infection
1Department of Microbial and Environmental Genomics, The J. Craig Venter Institute
Single Virus Genomics (SVG) is a method to isolate and amplify the genomes of single virons. Viral suspensions of a mixed assemblage are sorted using flow cytometry onto a microscope slide with discrete wells containing agarose, thereby capturing the virion and reducing genome shearing during downstream processing. Whole genome amplification is achieved using multiple displacement amplification (MDA) resulting in genomic material that is suitable for sequencing.
Published May 26, 2013. Keywords: Genetics, Microbiology, Immunology, Virology, Molecular Biology, Environmental Sciences, Genomics, environmental genomics, Single virus, single virus genomics, SVG, whole genome amplification, flow cytometry, viral ecology, virion, genome analysis, DNA, PCR, sequencing
1Department of Microbiology and Immunology, University of British Columbia - UBC
Construction of a fosmid library with environmental genomic DNA isolated from the vertical depth continuum of a seasonally hypoxic fjord is described. The resulting clone library is picked into 384-well plates and archived for downstream sequencing and functional screening by the application of an automated colony picking system.
Published September 23, 2009. Keywords: Basic Protocols, environmental genomic, metagenomic, genomic DNA, large insert library, fosmid, phage packaging, automated colony picking
1Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, 2Department of Microbial and Environmental Genomics, J. Craig Venter Institute, 3Donnelly Centre & Department of Molecular Genetics, University of Toronto, 4Lunenfeld Research Institute, Mt Sinai Hospital
The Green Monster method enables the rapid assembly of multiple deletions marked with a reporter gene encoding green fluorescent protein. This method is based on driving yeast strains through repeated cycles of sexual assortment of deletions and fluorescence-based enrichment of cells carrying more deletions.
Published December 15, 2012. Keywords: Microbiology, Genetics, Synthetic Biology, Environmental Genomics, Genomics, Bioengineering, Biomedical Engineering, Cellular Biology, Multi-site genomic engineering, genetic interaction, green fluorescent protein, GFP, flow cytometry, Saccharomyces cerevisiae, yeast, Green Monster
1Microbiology and Immunology, University of British Columbia - UBC
This protocol describes a high throughput screen for cellulolytic activity from a metagenomic library expressed in Escherichia coli. The screen is solution based and highly automated, and uses one-pot chemistry in 384 well microplates with the final readout as an absorbance measurement.
Published February 1, 2011. Keywords: Microbiology, Cellulase, cellulose, DNP-cellobioside, metagenomics, metagenome, environmental genomics, functional metagenomics
JoVE Immunology and Infection
1Department of Microbial and Environmental Genomics, The J. Craig Venter Institute, 2Department of Synthetic Biology and Bioenergy, The J. Craig Venter Institute
We describe an efficient method to separate single-stranded DNA, double-stranded DNA and RNA molecules from environmental viral communities. Nucleic acids are fractionated using hydroxyapatite chromatography with increasing concentrations of phosphate-containing buffers. This method permits the isolation of all viral nucleic acid types from environmental samples.
Published September 29, 2011. Keywords: Immunology, Hydroxyapatite, single-stranded DNA, double-stranded DNA, RNA, DNA, chromatography, viral ecology, virus, bacteriophage
1Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina
We provide an improved protocol for extracting high molecular weight DNA from hypersaline microbial mats. Microbial cells are separated from the mat matrix prior to DNA extraction and purification. This enhances the concentrations, quality, and size of the DNA. The protocol may be used for other refractory samples.
Published July 7, 2011. Keywords: Molecular Biology, Metagenomics, extracellular polymeric substances, DNA extraction, Microbial mats, hypersaline, extreme environment
Published June 2, 2007. Keywords: