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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: Cell Signaling

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

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

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: Ecosystems

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

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

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

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

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

1Department of Biology, San Diego State University, 2Computational Science Research Center, San Diego State University, 3Bioinformatics and Medical Informatics Research Center, San Diego State University, 4Department of Mathematics and Statistics, San Diego State University, 5Department of Computer Science, San Diego State University, 6Mathematics and Computer Science Division, Argonne National Laboratory, 7SPARC Committee, Broad Institute

JoVE 52854

 Immunology and Infection

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

Video Coming Soon

JoVE 60447

 JoVE In-Press

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

Video Coming Soon

JoVE 60238

 JoVE In-Press

Single Cell Micro-aspiration as an Alternative Strategy to Fluorescence-activated Cell Sorting for Giant Virus Mixture Separation

1Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, 2Microbes, Evolution, Phylogeny and Infection (MEΦI), Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique - Hôpitaux de Marseille (AP-HM)

Video Coming Soon

JoVE 60148

 JoVE In-Press

Isolation of Lamina Propria Mononuclear Cells from Murine Colon Using Collagenase E

1Department of Pediatrics, Division of Hematology / Oncology and Bone Marrow Transplantation, University of Miami Miller School of Medicine, 2Batchelor Children's Research Institute, University of Miami Miller School of Medicine, 3Department of Microbiology & Immunology, University of Miami Miller School of Medicine, 4Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 5Holtz Children's Hospital, University of Miami Miller School of Medicine

JoVE 59821

 Immunology and Infection

Analysis of Interactions between Endobiotics and Human Gut Microbiota Using In Vitro Bath Fermentation Systems

1Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 2College of Food and Biological Engineering, Zhejiang Gongshang University

JoVE 59725

 Immunology and Infection
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