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Environmental Microbiology: The study of microorganisms living in a variety of environments (air, soil, water, etc.) and their pathogenic relationship to other organisms including man.

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…

 Environmental Microbiology

Gram Staining of Bacteria from Environmental Sources

JoVE 10092

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


The spectrum of research in environmental microbiology is broad in scope and application potential. Whether the work is bench-scale with known bacterial isolates, or in the field collecting soil or water samples…

 Environmental Microbiology

Aseptic Technique in Environmental Science

JoVE 10040

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


Aseptic technique is a fundamental skill widely practiced in the field of environmental microbiology that requires a balance of mindfulness and practice in the laboratory. Proper use of this technique reduces the…

 Environmental Microbiology

RNA Analysis of Environmental Samples Using RT-PCR

JoVE 10104

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


Reverse transcription-polymerase chain reaction (RT-PCR) involves the same process as conventional PCR — cycling temperature to amplify nucleic acids. However, while conventional PCR only amplifies…

 Environmental Microbiology

Visualizing Soil Microorganisms via the Contact Slide Assay and Microscopy

JoVE 10053

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


Soil comprises the thin layer at the earth’s surface, containing biotic and abiotic factors that contribute to life. The abiotic portion includes inorganic particles ranging in size and shape that determine…

 Environmental Microbiology

Bacterial Signaling

JoVE 10713

At times, a group of bacteria behaves like a community. To achieve this, they engage in quorum sensing, the perception of higher cell density that results in a shift in gene expression. Quorum sensing involves both extracellular and intracellular signaling. The signaling cascade starts with a molecule called an autoinducer (AI). Individual bacteria produce AIs that move out of the bacterial cell membrane into the extracellular space. AIs can move passively along a concentration gradient out of the cell, or be actively transported across the bacterial membrane. When cell density in the bacterial populations is low, the AIs diffuse away from the bacteria, keeping the environmental concentration of AIs low. As bacteria reproduce and continue to excrete AIs, the concentration of AIs increases, eventually reaching a threshold concentration. This threshold permits AIs to bind membrane receptors on the bacteria, triggering changes in gene expression across the whole bacterial community. Many bacteria are broadly classified as gram positive or gram negative. These terms refer to the color that the bacteria take on when treated with a series of staining solutions which were developed by Hans Christian Joachim Gram over a century ago. If bacteria pick up a purple color, they are gram-positive; if they look red, they are gram-negative. These stain colors are pic

 Core: Biology

Filamentous Fungi

JoVE 10030

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


Fungi are heterotrophic eukaryotic organisms, and with the exception of yeasts, are aerobic. They are abundant in surface soils and are important for their role in nutrient cycling and the decomposition of organic…

 Environmental Microbiology

Serial Dilutions and Plating: Microbial Enumeration

JoVE 10507

Source: Jonathan F. Blaize1, Elizabeth Suter1, and Christopher P. Corbo1
1 Department of Biological Sciences, Wagner College, 1 Campus Road, Staten Island NY, 10301


Quantitative assessment of prokaryotes can be onerous given their abundance, propensity for exponential proliferation, species diversity within a population, and specific …

 Microbiology

The Sulfur Cycle

JoVE 10936

Sulfur, an important element in the chemical makeup of proteins, is recycled through the atmosphere and aquatic and terrestrial environments. Found in the atmosphere as sulfur dioxide (SO2), sulfur is released by decaying organisms, weathered rocks, geothermal vents, volcanos, and burning fossil fuels. It is deposited into the ecosystem, cycled through the biotic community, and either released back into the atmosphere as gas or deposited in marine sediment for long-term storage and eventual release back into the soil and atmosphere. Sulfur is essential to biological systems and is a component of certain amino acids, such as cysteine, which plays an important role in the structure of proteins. Sulfur is distributed to terrestrial (i.e., land) ecosystems by the precipitation of weak sulfuric acid, direct fallout from the atmosphere, weathering of sulfur-containing rocks, and geothermal vents. From the soil, it is taken up by microorganisms and plants and converted into organic forms that can be used by consumers in the ecosystem. When organisms die, decomposers break the organic sulfur compounds down into gases, such as hydrogen sulfide, which is oxidized in the atmosphere to form sulfur dioxide. Additionally, some chemoautotrophs use sulfur as a biological energy source and recycle sulfur molecules directly through ecosystems. Sulfur

 Core: Biology

Single-throughput Complementary High-resolution Analytical Techniques for Characterizing Complex Natural Organic Matter Mixtures

1Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, 2Department of Soil, Water and Environmental Science, University of Arizona, 3Department of Earth Ocean and Atmospheric Sciences, Florida State University, 4Bruker Daltonics Inc., 5Biological Sciences Division, Pacific Northwest National Laboratory

JoVE 59035

 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

VirWaTest, A Point-of-Use Method for the Detection of Viruses in Water Samples

1Laboratory of Viruses Contaminants of Water and Food (VIRCONT), Department of Genetics, Microbiology and Statistics, Section of Microbiology, Virology and Biotechnology, University of Barcelona, 2Grupo de Investigación Biodiversidad, Medio Ambiente y Salud (BIOMAS), Facultad de Ingenierías y Ciencias Agropecuarias (FICA), Ingeniería en Biotecnología, Universidad de las Américas, 3Municipal Laboratory - Waters of Mataró, 4GenIUL

JoVE 59463

 Immunology and Infection

Live Cell Analysis of Shear Stress on Pseudomonas aeruginosa Using an Automated Higher-Throughput Microfluidic System

1Department of Chemistry, Doane University, 2Department of Biology, Doane University, 3Department of Pathology and Microbiology, University of Nebraska Medical Center, 4Department of Physics and Engineering, Doane University

JoVE 58926

 Bioengineering

Luminescence Lifetime Imaging of O2 with a Frequency-Domain-Based Camera System

1Marine Biological Section, Department of Biology, University of Copenhagen, 2Center for Electromicrobiology, Aarhus University, 3PCO AG, 4Climate Change Cluster, University of Technology Sydney, 5Aarhus University Centre for Water Technology, Section for Microbiology, Department of Bioscience, Aarhus University

JoVE 60191

 Chemistry

Using Tg(Vtg1:mcherry) Zebrafish Embryos to Test the Estrogenic Effects of Endocrine Disrupting Compounds

1Department of Aquaculture, Institute of Aquaculture and Environmental Safety, Faculty of Agricultural and Environmental Sciences, Szent István University, 2Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham

Video Coming Soon

JoVE 60462

 JoVE In-Press

Fluorescence-Activated Cell Sorting for the Isolation of Scleractinian Cell Populations

1Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 2Department of Biology, University of Miami, 3The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, and Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev

Video Coming Soon

JoVE 60446

 JoVE In-Press

Development of a Larval Zebrafish Infection Model for Clostridioides difficile

1Division of Cellular and Molecular Neurobiology, Zoological Institute, Technische Universität Braunschweig, 2Department of Molecular Biotechnology, Turkish-German University, 3Institut für Mikrobiologie, Technische Universität Braunschweig, 4Braunschweig Integrated Centre of Systems Biology, 5Helmholtz Centre for Infection Research

JoVE 60793

 Developmental Biology

Laser-Induced Fluorescence Emission (L.I.F.E.) as Novel Non-Invasive Tool for In-Situ Measurements of Biomarkers in Cryospheric Habitats

1Institute of Ecology, University of Innsbruck, 2Austrian Polar Research Institute, University of Vienna, 3BrainLinks-BrainTools, Bernstein Center Freiburg, 4Atom Science, Kasevich Lab, Stanford University, 5Institute of Experimental Physics, University of Innsbruck, 6Department of Physics, Extraterrestrial Vehicle Instruments Laboratory, Harvey Mudd College

JoVE 60447

 Environment

A Tuberculosis Molecular Bacterial Load Assay (TB-MBLA)

1Division of Infection and Global Health, School of Medicine, University of St Andrews, 2National Institute for Medical Research (NIMR)-Mbeya Medical Research Centre, 3Instituto Nacional de Saúde (INS), Ministério da Saúde, 4Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow

Video Coming Soon

JoVE 60460

 JoVE In-Press

Prospecting Microbial Strains for Bioremediation and Probiotics Development for Metaorganism Research and Preservation

1LEMM, Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro (UFRJ), 2Genome Center, University of California, Davis, 3IMAM-AquaRio - Rio de Janeiro Aquarium Research Center

JoVE 60238

 Bioengineering
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