SCIENCE EDUCATION > Environmental Sciences

Environmental Microbiology

This collection provides an introduction to microbial communities in the environment and their roles in ecosystems; and also explores common methods used to study environmental microbiology.

  • Environmental Microbiology

    06:15
    Determination of Moisture Content in Soil

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

    Soils normally contain a finite amount of water, which can be expressed as the “soil moisture content.” This moisture exists within the pore spaces in between soil aggregates (inter-aggregate pore space) and within soil aggregates (intra-aggregate pore space) (Figure 1). Normally this pore space is occupied by air and/or water. If all the pores are occupied by air, the soil is completely dry. If all the pores are filled with water, the soil is said to be saturated. Figure 1. Pore space in soil.

  • Environmental Microbiology

    10:47
    Aseptic Technique in Environmental Science

    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 likelihood of bacterial or fungal contamination of reagents, culture media, and environmental samples. Aseptic technique is also vital to ensure data integrity and maintain the purity of culture libraries that may be comprised of very rare and difficult to culture isolates. Sources of contamination in the laboratory environment include airborne microorganisms (including those adhering to dust and lint particles), microbes present on the laboratory bench workspace or on unsterilized glassware or equipment, and microbes transferred from the body and hair of the researcher. The use of aseptic technique is also a safety measure that lowers the potential for the transmission of microorganisms to researchers, which is particularly important when working with pathogens.

  • Environmental Microbiology

    09:30
    Gram Staining of Bacteria from Environmental Sources

    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 containing unknown bacterial isolates, the ability to quickly and visually discern culturable populations of interest remains of great import to environmental microbiologists even today with the abundance of molecular techniques available for use. This video will demonstrate one such technique, known as Gram staining.

  • Environmental Microbiology

    10:03
    Visualizing Soil Microorganisms via the Contact Slide Assay and Microscopy

    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 the soil’s texture. The biotic portion incorporates plant residues, roots, organic matter, and microorganisms. Soil microbe abundance and diversity is expansive, as one gram of soil contains 107-8 bacteria, 106-8 actinomycetes, 105-6 fungi, 103 yeast, 104-6 protozoa, 103-4 algae, and 53 nematodes. Together, the biotic and abiotic factors form architectures around plant roots, known as the rhizosphere, that provide favorable conditions for soil microorganisms. Biotic and abiotic factors promote life in soils. However, they also contribute stressful dynamics that limit microbes. Biotic stress involves competition amongst life to adapt and survive in environmental conditions. For example, microbes can secrete inhibitory or toxic substances to harm neighboring microorganisms. Penicillium notatum is a notorious fungus, as it reduces competition for nutrients by producing an antimicrobial, which humans harvest to create the pharmaceutical penicillin. Abiotic stresses arise from physical or chemical properties limiting microbial survival, such as light, moisture, temperature, p

  • Environmental Microbiology

    08:57
    Filamentous Fungi

    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 matter and organic contaminants. White rot fungi (phanerochaete chryosporium) for example, (Figure 1) are known to degrade aromatics. Figure 1. White rot on birch.

  • Environmental Microbiology

    09:58
    Community DNA Extraction from Bacterial Colonies

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

    Traditional methods of analysis for microbial communities within soils have usually involved either cultural assays utilizing dilution and plating methodology on selective and differential media or direct count assays. Direct counts offer information about the total number of bacteria present, but give no information about the number or diversity of populations present within the community. Plate counts allow enumeration of total cultural or selected cultural populations, and hence provide information on the different populations present. However, since less than 1% of soil bacteria are readily culturable, cultural information offers only a piece of the picture. The actual fraction of the community that can be cultured depends on the medium chosen for cultural counts. Any single medium will select for the populations that are best suited to that particular medium. In recent years, the advantages of studying community DNA extracted from soil samples have become apparent. This nonculture-based approach is thought to be more representative of the actual community present than culture-based approaches. In addition to providing information about the types of populations present, this approach can also provide information about their genetic potential. As with any technique, there are limitations

  • Environmental Microbiology

    13:33
    Detecting Environmental Microorganisms with the Polymerase Chain Reaction and Gel Electrophoresis

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

    Polymerase chain reaction (PCR) is a technique used to detect microorganisms that are present in soil, water, and atmospheric environments. By amplifying specific sections of DNA, PCR can facilitate the detection and identification of target microorganisms down to the species, strain, and serovar/pathovar level. The technique can also be utilized to characterize entire communities of microorganisms in samples. The culturing of microorganisms in the laboratory using specialized growth media is a long-established technique and remains in use for the detection of microorganisms in environmental samples. Many microbes in the natural environment, while alive, maintain low levels of metabolic activity and/or doubling times and are thus referred to as viable but non-culturable (VBNC) organisms. The use of culture-based techniques alone cannot detect these microbes and, therefore, does not provide a thorough assessment of microbial populations in samples. The use of PCR allows for the detection of culturable microbes, VBNC organisms, and those that are no longer alive or active, as the amplification of genetic sequences does not generally require the pre-enrichment of microorganisms present in environmental samples. However, PCR cannot differentiate the aforementioned states of viability and activ

  • Environmental Microbiology

    12:03
    RNA Analysis of Environmental Samples Using RT-PCR

    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 deoxyribonucleic acids (DNA), RT-PCR enables the amplification of ribonucleic acids (RNA) through the formation of complementary DNA (cDNA). This enables RNA-based organisms found within the environment to be analyzed utilizing methods and technologies that are designed for DNA. Many viruses found in the environment use RNA as their genetic material. Several RNA-based viral pathogens, such as Norovirus, and indicator organisms, such as pepper mild mottle virus (PMMoV), do not have culture-based detection methods for quantification. In order to detect for the presence of these RNA viruses in environmental samples from soil, water, agriculture, etc., molecular assays rely on RT-PCR to convert RNA into DNA. Without RT-PCR, microbiologists would not be able to assay and research numerous RNA-based viruses that pose risks to human and environmental health. RT-PCR can also be employed as a tool to measure microbial activity in the environment. Messenger RNA (mRNA) is the single-stranded template for protein translation, and measuring the levels of different mRNAs indicates which genes from

  • Environmental Microbiology

    09:56
    Quantifying Environmental Microorganisms and Viruses Using qPCR

    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

    08:16
    Water Quality Analysis via Indicator Organisms

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

    Water quality analysis monitors anthropogenic influences such as pollutants, nutrients, pathogens, and any other constituent that can impact the water’s integrity as a resource. Fecal contamination contributes microbial pathogens that threaten plant, animal, and human health with disease or illness. Increasing water demands and strict quality standards require that water being supplied for human or environmental resources be monitored for low pathogen levels. However, monitoring each pathogen associated with fecal pollution is not feasible, as laboratory techniques involve extensive labor, time, and costs. Therefore, detection for indicator organisms provides a simple, rapid, and cost effective technique to monitor pathogens associated with unsanitary conditions.

  • Environmental Microbiology

    10:57
    Isolation of Fecal Bacteria from Water Samples by Filtration

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

    The quality of water destined for use in agricultural, recreational, and domestic settings is of great importance due to the potential for outbreaks of waterborne disease. Microbial agents implicated in such events include parasites, bacteria, and viruses that are shed in high numbers in the feces of infected people and animals. Transmission to new and susceptible hosts may then occur via the fecal-oral route upon ingestion of contaminated water. Therefore, the ability to monitor water sources for the presence of pathogenic microorganisms is significant in order to ensure public health. Due to the sheer number and variety of potential fecal-oral pathogens that may be present in water and their variable concentrations, it is impractical and expensive to assay directly for each one of them on a regular basis. Therefore, the microbiological assays for water quality monitoring employ coliform indicator bacteria. Coliforms comprise, in part, the normal intestinal microflora of warm-blooded mammals, are non-pathogenic, and are consistently excreted in the feces. Therefore, the detection of coliform bacteria in water means that a fecal release occurred, and that harmful pathogenic microorganisms may also be present.

  • Environmental Microbiology

    09:16
    Detection of Bacteriophages in Environmental Samples

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

    Viruses are a unique group of biological entities that infect both eukaryotic and prokaryotic organisms. They are obligate parasites that have no metabolic capacity, and in order to replicate, rely on host metabolism to produce viral parts that self-assemble inside host cells.

    Viruses are ultramicroscopic—too small to be viewed with the light microscope, visible only with the greater resolution of the electron microscope. A viral particle consists of a nucleic acid genome, either DNA or RNA, surrounded by a protein coat, known as a capsid, composed of protein subunits or capsomers. In some more complex viruses, the capsid is surrounded by an additional lipid envelope, and some have spike-like surface appendages or tails. Viruses that infect the intestinal tract of humans and animals are known as enteric viruses. They are excreted in feces and can be isolated from domestic wastewater. Viruses which infect bacteria are known as bacteriophages, and those which infect coliform bacteria are called coliphages (Figure 1). The phages of coliform bacteria are found anywhere coliform bacteria are found. Figure 1. Coliphage T2.

  • Environmental Microbiology

    10:56
    Culturing and Enumerating Bacteria from Soil Samples

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

    Surface soils are a heterogeneous mixture of inorganic and organic particles that combine together to form secondary aggregates. Within and between the aggregates are voids or pores that visually contain both air and water. These conditions create an ideal ecosystem for bacteria, so all soils contain vast populations of bacteria, usually over 1 million per gram of soil. Bacteria are the simplest of microorganisms, known as prokaryotes. Within this prokaryotic group, there are the filamentous microbes known as actinomycetes. Actinomycetes are actually bacteria, but they are frequently considered to be a unique group within the classification of bacteria because of their filamentous structure, which consists of multiple cells strung together to form hyphae. This experiment uses glycerol case media that select for actinomycete colonies, during dilution and plating. Typically, actinomycetes are approximately 10% of the total bacterial population. Bacteria and actinomycetes are found in every environment on Earth, but the abundance and diversity of these microbes in soil is unparalleled. These microbes are also essential for human life and affect what people eat, drink, breathe, or touch. In addition, there are bacterial species that can infect people and cause disease, and ther

  • Environmental Microbiology

    12:22
    Bacterial Growth Curve Analysis and its Environmental Applications

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

    Bacteria are among the most abundant life forms on Earth. They are found in every ecosystem and are vital for everyday life. For example, bacteria affect what people eat, drink, and breathe, and there are actually more bacterial cells within a person’s body than mammalian cells. Because of the importance of bacteria, it is preferable to study particular species of bacteria in the laboratory. To do this, bacteria are grown under controlled conditions in pure culture, meaning that only one type of bacterium is under consideration. Bacteria grow quickly in pure culture, and cell numbers increase dramatically in a short period of time. By measuring the rate of cell population increase over time, a “growth curve” to be developed. This is important when aiming to utilize or inoculate known numbers of the bacterial isolate, for example to enhance plant growth, increase biodegradation of toxic organics, or produce antibiotics or other natural products at an industrial scale.

  • Environmental Microbiology

    09:28
    Algae Enumeration via Culturable Methodology

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

    Algae are a highly heterogeneous group of microorganisms that have one common trait, namely the possession of photosynthetic pigments. In the environment, algae can cause problems for swimming pool owners by growing in the water. Algae can also cause problems in surface waters, such as lakes and reservoirs, due to algal blooms that release toxins. More recently, algae are being evaluated as novel sources of energy via algal biofuels. Blue-green algae are actually bacteria classified as cyanobacteria. Cyanobacteria not only photosynthesize, but also have the ability to fix nitrogen gas from the atmosphere. Other algae are eukaryotic, ranging from single-celled organisms to complex multicellular organisms, like seaweeds. These include the green algae, the euglenoids, the dinoflagellates, the golden brown algae, diatoms, the brown algae, and the red algae. In soils, algal populations are frequently 106 per gram. These numbers are lower than corresponding numbers for bacteria, actinomycetes, and fungi, mostly because the sunlight required for photosynthesis cannot penetrate far beneath the soil surface. Because algae are phototrophic, obtaining energy from photosynthesis and carbon for biomass from carbon dioxide, they can be grown in growth media consisting entirely of inorganic nutrients a

JoVE IN THE CLASSROOM

PROVIDE STUDENTS WITH THE TOOLS TO HELP THEM LEARN.

JoVE IN THE CLASSROOM