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A Lipid Extraction and Analysis Method for Characterizing Soil Microbes in Experiments with Many Samples

1Department of Agronomy and Great Lakes Bioenergy Research Center, University of Wisconsin - Madison, 2Department of Soil Science, University of Wisconsin - Madison, 3Department of Soil, Water, and Climate, University of Minnesota, 4Faculty of Science and Engineering, Curtin University

JoVE 55310


 Environment

Extraction and Analysis of Microbial Phospholipid Fatty Acids in Soils

1Department of Renewable Resources, University of Alberta, 2Department of Science, Augustana Faculty, University of Alberta, 3Laboratoire Génie Civil et géo-Environnement, Université de Lille, 4Department of Earth and Environmental Sciences, Mount Royal University, 5Forest Ecology & Production, Great Lakes Forestry Centre, Natural Resources Canada

JoVE 54360


 Environment

Development of Sulfidogenic Sludge from Marine Sediments and Trichloroethylene Reduction in an Upflow Anaerobic Sludge Blanket Reactor

1Bioprocesses Department, Laboratory of Environmental Biotechnology, Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, 2Laboratory of Molecular Biology, Escuela Superior de Medicina, Instituto Politécnico Nacional

JoVE 52956


 Environment

Removal of Exogenous Materials from the Outer Portion of Frozen Cores to Investigate the Ancient Biological Communities Harbored Inside

1Biogeochemical Sciences Branch, Cold Regions Research and Engineering Laboratory, US Army Engineer Research & Development Center, Hanover, NH, 2Environmental Processes Branch, Environmental Laboratory, US Army Engineer Research & Development Center, Vicksburg, MS, 3Terrestrial and Cryospheric Scienes Branch, Cold Regions Research and Engineering Laboratory, US Army Engineer Research & Development Center, Hanover, NH, 4Biogeochemical Sciences Branch, Cold Regions Research and Engineering Laboratory, US Army Engineer Research & Development Center, Fairbanks, AK

JoVE 54091


 Biology

Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health

1Vegetable Crop Research Unit, USDA-ARS, 2Department of Entomology, University of Wisconsin-Madison, 3Department of Horticulture, University of Wisconsin-Madison, 4Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, 5Department of Bacteriology, University of Wisconsin-Madison, 6Laboratory of Genetics, Genome Center of Wisconsin, 7DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, 8J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison

JoVE 54631


 Environment

A Hybrid DNA Extraction Method for the Qualitative and Quantitative Assessment of Bacterial Communities from Poultry Production Samples

1Egg Safety and Quality Research Unit, USDA-Agricultural Research Service, 2Poultry Microbiological Safety and Processing Research Unit, USDA-Agricultural Research Service, 3Department of Biochemistry and Biophysics, Oregon State University, 4College of Public Health, University of Georgia, 5Department of Biological Sciences, Center for Microbial Genetics and Genomics, Northern Arizona University

JoVE 52161


 Biology

Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions

1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 2Department of Energy, Joint Genome Institute, 3Joint BioEnergy Institute, 4Department of Environmental Science Policy and Management, University of California

Video Coming Soon

JoVE 57170


 JoVE In-Press

Rearing the Fruit Fly Drosophila melanogaster Under Axenic and Gnotobiotic Conditions

1Department of Plant and Wildlife Sciences, Brigham Young University, 2Department of Entomology, Cornell University, 3Department of Molecular Biology and Genetics, Cornell University, 4Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, 5Biological Sciences, SUNY Oswego

JoVE 54219


 Developmental Biology

Concentration of Metabolites from Low-density Planktonic Communities for Environmental Metabolomics using Nuclear Magnetic Resonance Spectroscopy

1Biosphere Oriented Biology Research Unit, RIKEN Advanced Science Institute, 2Graduate School of Nanobioscience, Yokohama City University, 3Advanced NMR Metabomics Research Team, RIKEN Plant Science Center, 4Graduate School of Bioagricultural Science, Nagoya University

JoVE 3163


 Biology

Quantifying Environmental Microorganisms and Viruses Using qPCR

JoVE 10186

Source: Laboratories of Dr. Ian Pepper and Dr. Charles Gerba - Arizona University
Demonstrating Author: Bradley Schmitz

Quantitative polymerase chain reaction (qPCR), also known as real-time PCR, is a widely-used molecular technique for enumerating microorganisms in the environment. Prior to this approach, quantifying microorganisms was limited largely to classical culture-based techniques. However, the culturing of microbes from environmental samples can be particularly challenging, and it is generally held that as few as 1 to 10% of the microorganisms present within environmental samples are detectable using these techniques. The advent of qPCR in environmental microbiology research has therefore advanced the field greatly by allowing for more accurate determination of concentrations of microorganisms such as disease-causing pathogens in environmental samples. However, an important limitation of qPCR as an applied microbiological technique is that living, viable populations cannot be differentiated from inactive or non-living populations. This video demonstrates the use of qPCR to detect pepper mild mottle virus from an environmental water sample.


 Environmental Microbiology

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