Name: preventing contamination in microbiology labs
Uploaded: 2023-04-30T06:35:10.000Z
Duration: 10 min 48 s
Channel: JoVE

K12 Standards

new-york-state-science-learning-standards

New York State Science Learning Standards

High School

Life Science

interdependent-relationships-in-ecosystems

Interdependent Relationships in Ecosystems

HS-LS2-2.

aseptic-technique-in-environmental-science

Aseptic Technique in Environmental Science

1. Preparation for Aseptic Work
<ol>
	<li>Obtain and apply the following PPE items: lab coat, latex or nitrile gloves (free from tears or holes), and safety goggles (Figure 1). For safety in the event of using an open flame, tie back long hair. 
	<img alt="Lab safety equipment including lab coat, goggles, and gloves on a bench for protection in experiments." src="/files/ftp_upload/10040/10040fig1.jpg" data-altupdatedat="1761830439000" data-alt="Figure 1"> 
	Figure 1: PPE: A lab coat, latex gloves, and safety goggles.</li>
	<li>A second important aspect of aseptic technique is the proper sterilization and storage of media/reagents to be used in the laboratory. Prepare liquid broth medium (e.g., tryptic soy broth) and agar-based media (e.g., R2A) by weighing the proper amount of dried base powder, which is added to the appropriate amount of de-ionized water. </li>
	<li>For the broth medium, dissolve the powder on a hot plate with low heat applied, and dispense the liquid either in 100-mL volumes into glass screw-top flasks, or in 10-mL volumes into glass screw-top test tubes. Using a magnetic stir bar, stir the agarose medium on the hot plate stirrer until the powder is fully dissolved. </li>
	<li>Apply autoclave tape to the containers, and autoclave the media according to the manufacturer’s instructions (e.g., 20 min at 121 °C) (Figures 2 and 3). Note that the color of stripes on the autoclave tape should change from white (pre-autoclave) to black (post-autoclave). Although the color change generally indicates that sterilization was successful, sterility checks using spore strip kits can be conducted to verify the autoclaving process. 
	<img alt="Erlenmeyer flask sealing process, experiment setup, laboratory research, orange glove, liquid sample." src="/files/ftp_upload/10040/10040fig2.jpg" data-altupdatedat="1761830439000" data-alt="Figure 2"> 
	Figure 2: Autoclave tape being applied to material. 
	<img alt="Erlenmeyer flask with brown chemical solution for lab synthesis experiment on dark surface." src="/files/ftp_upload/10040/10040fig3.jpg" data-altupdatedat="1761830439000" data-alt="Figure 3"> 
	Figure 3: Note the color change of stripes on autoclave tape from white (pre-autoclave) to black (post-autoclave).</li>
	<li>Cool the liquid broths to room temperature, and then store at room temperature or refrigerated at 4 °C. </li>
	<li>Cool the agarose medium by placing the container into a water bath set to ~50 °C. Once cooled, the media can be poured into sterile Petri dishes. Allow the medium to cool and solidify, then consolidate for storage under temperatures specified by the manufacturer.</li>
	<li>There are several varieties of culture media that cannot be autoclaved as the high temperatures degrade critical ingredients. Sterilizing these require filter-sterilization using a vacuum filtration system employing a 0.22-µm filter, followed by storage at the appropriate temperature.</li>
	<li>Prior to performing work on the benchtop, disinfect the surface using an appropriate solution (e.g., 500-ppm bleach). This lowers the risk of transferring contaminants from the working surface to cultures and sterile media. </li>
	<li>To establish a sterile field, turn on a Bunsen burner. The flame type best suited for sterilizing metal inoculating loops is an intense blue flame, with a definitive blue cone observed in the middle (Figure 4). 
	<img alt="Bunsen burner with blue flame, indicating combustion for heating in laboratory experiments." src="/files/ftp_upload/10040/10040fig4.jpg" data-altupdatedat="1761830439000" data-alt="Figure 4"> 
	Figure 4: A transfer of bacteria from one Petri plate displaying growth of a cultured isolate to another un-inoculated Petri plate containing an agar-based growth medium.</li>
	<li>Slowly pass the inoculating loop through the hottest part of the flame (tip of the blue cone). The loop should turn red hot for the purpose of sterilization.</li>
</ol>
2. Bacterial Transfers: From Petri Plate to Petri Plate
<ol>
	<li>One scenario of transferring bacteria is from one Petri plate displaying growth of a cultured isolate to another, sterile Petri plate containing an agar-based growth medium.</li>
	<li>To begin, slightly open the Petri plate containing the pure bacterial culture, and gently tap the hot, sterilized inoculating loop onto the agar surface. </li>
	<li>Retrieve one isolated colony from the surface of the plate using the cooled inoculating loop, and close the Petri plate.</li>
	<li>Perform a streak for isolation using a fresh Petri plate containing culture medium, with the lid slightly ajar. </li>
	<li>For each portion of the isolation streak (3 total per plate), flame-sterilize the inoculating loop just prior to use. Also, flame-sterilize the loop just after the final streak is performed in order to prevent contamination of the bench surface and as a consideration to others in the lab who may later use or come into contact with the inoculating loops.</li>
	<li>Place the streaked plates into an incubator for growth overnight.</li>
</ol>
3. Bacterial Transfers: From Broth Culture to Petri Plate
<ol>
	<li>A second scenario of transferring bacteria is from a broth culture exhibiting growth, as generally observed by turbidity, to a sterile Petri plate containing growth medium.</li>
	<li>Remove the cap from the test tube (or flask) containing the pure bacterial culture, and pass the opening of the container 2-3x through the hottest portion of the flame. To prevent contamination, do not set the cap down onto the benchtop.</li>
	<li>Carefully lower the sterilized inoculating loop into the tube/flask, and gently press against the side of the container to cool just prior to insertion into the broth culture.</li>
	<li>Remove one loopful of broth culture (Figure 5), and immediately replace the cap. 
	<img alt="Microscope image: hair structure, focus on shaft and cuticle." src="/files/ftp_upload/10040/10040fig5.jpg" data-altupdatedat="1761830439000" data-alt="Figure 5"> 
	Figure 5: One loopful of broth culture.</li>
	<li>Perform a streak for isolation using a fresh Petri plate containing culture medium, with the lid slightly ajar. </li>
	<li>For each portion of the streak (3 total per plate), flame-sterilize the inoculating loop just prior to use. Also, flame-sterilize the loop just after the final streak is performed in order to prevent contamination of the bench surface and as a consideration to others in the lab who may later use the inoculating loops.</li>
	<li>Place the streaked plates for isolation into an incubator for growth overnight.</li>
</ol>
4. Bacterial Transfers: From Petri Plate With Growth to Sterile Liquid Medium
<ol>
	<li>A third scenario of transferring bacteria is from a Petri plate containing an isolated culture streak to a tube/flask containing sterile liquid growth medium.</li>
	<li>Slightly open the Petri plate containing the pure bacterial culture, and cool the hot inoculating loop by tapping it gently onto the agar surface. </li>
	<li>Retrieve one isolated colony from the surface of the plate using the cooled inoculating loop, and close the Petri plate.</li>
	<li>Remove the cap from the test tube (or flask) containing the sterile liquid growth medium, and pass the opening of the container 2 to 3 times through the hottest portion of the flame. To prevent contamination, do not set the cap down onto the benchtop.</li>
	<li>Carefully lower the extracted colony into the liquid broth medium, and gently agitate the loop in order to release the bacteria. Immediately replace the cap.</li>
	<li>Flame-sterilize the inoculating loop in order to prevent contamination of the bench surface and as a consideration to others in the lab who may later use the inoculating loops.</li>
	<li>Place the flask into an incubator for growth overnight.</li>
	<li>Remove the flask from incubation the next day. Perform a dilution series in order to enumerate the culture.</li>
	<li>Plate the dilutions from the series onto agarose culture media, and incubate the plates overnight.</li>
	<li>Remove the plates the next day, and observe for any contamination.</li>
</ol>
5. Bacterial Transfers: From Broth Culture to Sterile Liquid Growth Medium
<ol>
	<li>A fourth scenario of transferring bacteria is from a broth culture exhibiting growth to a tube/flask containing sterile liquid growth medium.</li>
	<li>Remove the cap from the test tube (or flask) containing the pure bacterial culture, and pass the opening of the container twice through the hottest portion of the flame. To prevent contamination, do not set the cap down onto the benchtop.</li>
	<li>Carefully lower the inoculating loop into the tube/flask, and gently press against the side of the container to cool just prior to insertion into the broth culture.</li>
	<li>Remove one loopful of broth culture, and immediately replace the cap.</li>
	<li>Remove the cap from the test tube (or flask) containing the sterile liquid growth medium, and pass the opening of the container twice through the hottest portion of the flame. To prevent contamination, do not set the cap down onto the benchtop.</li>
	<li>Carefully lower the extracted loopful into the sterile liquid broth medium, and gently agitate the loop in order to release the bacteria. Immediately replace the cap.</li>
	<li>Flame-sterilize the inoculating loop (Figure 6) in order to prevent contamination of the bench surface and as a consideration to others in the lab who may later use the inoculating loops. 
	<img alt="Bunsen burner flame test, spectroscopy experiment for optical emission analysis in a lab setup." src="/files/ftp_upload/10040/10040fig6.jpg" data-altupdatedat="1761830439000" data-alt="Figure 6"> 
	Figure 6: Inoculating loop turning red hot while being sterilized with a Bunsen burner.</li>
	<li>Place the flask into an incubator for growth overnight.</li>
	<li>Remove the flask from incubation the next day. Perform a dilution series in order to enumerate the culture.</li>
	<li>Plate the dilutions from the series onto agarose culture media, and incubate the plates overnight.</li>
	<li>Remove the plates the next day, and observe for any contamination.</li>
</ol>

Other than using Bunsen burners, aseptic working environments can also be maintained in specialized workstations known as laminar flow hoods, which use directed airflow and filters to maintain sterility.
Proper use of aseptic technique is vital for environmental microbiologists when sampling in the field and in the laboratory when working with media, reagents, and cultured isolates.&#160; Poor aseptic technique in the field can result in the transfer of microorganisms from the technician to cr...

aseptic technique in environmental science

Source: Laboratories of Dr. Ian Pepper and Dr. Charles Gerba - The University of Arizona 
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.

The outcome of the procedure demonstrates proper aseptic technique and poor aseptic technique. Figure 7 illustrates the contamination that can arise from poor aseptic technique when pouring agarose plates (top plate: sterile medium; bottom plates: contaminated media).
<img alt="Petri dish cultures; fungal growth experiment setup showing colony formation on agar plates." src="/files/ftp_upload/10040/10040fig7.jpg" data-altupdatedat="1761830...

Source: Laboratories of Dr. Ian Pepper and Dr. Charles Gerba - The University of Arizona
Demonstrating Author: Luisa Ikner
Aseptic technique is a ...

Aseptic technique is a fundamental skill in microbiology, and has crucial applications in environmental research.If microbiological cultures are contaminated, the time, labor, and financial costs that would be required of a lab to "clean up" or replace the cultures, particularly rare isolates from unique environments, could be very high and prohibitive, and some samples may be irreplaceable.Proper use of aseptic techniques reduces the likelihood of bacterial and fungal contamination of reagents, culture media, and environmental samples, and also avoids cross-contamination between samples. It is also a safety measure that diminishes the potential transmission of microbes to the experimenter, which is especially important when working with pathogens.This video will introduce the principles of asepsis; several important techniques to maintain sterile reagents and cultures; and finally, some of their uses in environmental science.The goal of using aseptic techniques is to create and maintain a sterile working environment, equipment, and reagents, so as to minimize contamination of biological samples. Common sources of contamination include airborne microorganisms, microbes present on the laboratory bench or equipment, and those from the hair, body, and clothing of the researcher.Two types of agents are central to removing or preventing contamination in the laboratory: disinfectant chemicals and heat. Solutions such as 70% ethanol and dilute bleach are often used to disinfect equipment, working surfaces, and experimenters' gloves before engaging in aseptic work.At the same time, microbes on or in tools, glassware, and liquid media can be heat-killed in an autoclave, which is a chamber that sterilizes contents via exposure to high-temperature pressurized steam. In addition, tools such as glass rods used for spread plating and metal inoculation loops can be heat-sterilized using a flame source, such as a Bunsen burner.The use of a flame source is also one of the most common ways to establish an aseptic working environment. The heat from the flame causes air convection, generating an updraft that lifts any airborne contaminants away from the vicinity of the burner, and creating a "sterile field" in which to conduct aseptic experimental work.Now that you understand the principles behind aseptic techniques and why they are important, let's go through a protocol for creating an aseptic working environment, making up sterile growth media, and aseptically transferring bacteria between different culturing conditions.Before beginning aseptic work, it is important for the experimenter to don proper personal protective equipment, or PPE. The purpose of this is both to prevent the experimenter from contaminating the samples and lab cultures, and also to prevent the transfer of potentially pathogenic microbes to the researcher. PPE items include a lab coat, gloves, and safety goggles.The next step is to properly sterilize and store the growth media to be used for culturing the microbial samples. First, weigh out the proper amount of solid medium components, and add them to the proper volume of liquid solvent specified by the manufacturer, such as deionized water, in an autoclavable container Add a magnetic stir bar, place the container on a hot plate stirrer, and dissolve the solid medium components with low heat and stirring.Close the medium containers. If using a glass vessel with screw-on cap, be sure to not tighten the cap completely, as the air inside the vessels will expand due to heating during autoclaving and needs to escape. Without escape, the gas could cause the vessel to rupture. Put a piece of autoclave tape on the vessels, and autoclave the media according to the manufacturer's instructions, such as 20 min at 121 ?C. After autoclaving, verify that the stripes on the autoclave tapes turned black, indicating the proper temperature was reached.For liquid growth media, let them cool to room temperature, and store them at room temperature or with refrigeration as appropriate. For agar-based solid growth media, let them cool to approximately 50 ?C, then pour into sterile Petri dishes. Allow the agar to cool and solidify before storing at the appropriate temperature.For media that cannot be autoclaved due to the presence of heat-sensitive components, filter sterilize using a 0.22-?m filter.A core technique in microbiological work is to aseptically transfer bacterial cultures between different growth media, both solid and liquid. Prior to beginning, clean the lab bench surface with a disinfectant. This lowers the risk of contaminating cultures or sterile media.Transferring bacterial cultures commonly makes use of a tool called an inoculating loop, which needs to be sterilized prior to use by heating in a flame.Turn on a flame source. Slowly pass the inoculating loop through the tip of the flame. The loop will turn red hot. To transfer a bacterial colony from a solid agar plate, open the Petri plate slightly, and gently tap the hot inoculating loop onto an empty part of the agar surface to avoid heat-killing the bacteria. Scrape a single colony with the inoculating loop, and close the plate.To transfer bacteria from a liquid growth medium, remove the cap from the culture container. To help prevent contamination, avoiding setting the cap down onto the bench. Pass the mouth of the container 2-3 times through the hottest portion of the flame. Then, carefully touch the hot, sterilized inoculation loop onto the inside of the container and let it cool before inserting it into the broth culture. Remove one loopful of the culture, and immediately close the cap.For transferring the obtained bacteria to a sterile growth medium, remove the cap from a container with the sterile broth and pass the container's opening through the flame 2-3 times. Then, carefully lower the inoculation loop into the medium, and agitate gently to release the bacteria. Immediately close the cap. Sterilize the inoculation loop after use.If transferring bacteria onto a sterile agar plate, open the lid of a fresh Petri plate with uninoculated agar. Streak the inoculation loop with the bacterial culture back-and-forth across one sector of the agar. Sterilize the loop and cool it by touching an empty part of the agar, then make another streak on the agar at an obtuse angle to the first streak, making sure to cross the first streak on the first 1-2 strokes but avoid touching the first streak on subsequent strokes. Repeat the sterilization and streaking 2 more times. Close the Petri plate, and sterilize the inoculation loop.Once inoculated, the broth or agar plate should then be incubated at the ideal growth temperature for the given microorganism to obtain viable culture. On solid medium, a lawn or continuous strand of bacteria would be visible on agar covered by the first two streaks, but individual colonies should be obtained on the final streak. Poor aseptic techniques would result in the growth of mold and other contaminants on the plate.Aseptic techniques are important in many experiments involving microbial samples from the environment. In this study, researchers isolated bacteriophages, which are bacteria-infecting viruses, from the common soil bacterium Arthrobacter. Arthrobacter cultures were first grown under aseptic conditions. Soil samples were then washed and filtered in phage buffer, and the phage solution was mixed with the bacterial culture and plated onto agar plates. A bacterial lawn would form on the plate, but there would be clearings, or "plaques", at spots where the virus had infected and killed the bacteria. Phage could then be purified from these plaques for further study.Other than using Bunsen burners, aseptic working environments can also be maintained in specialized workstations known as laminar flow hoods, which use directed airflow and filters to maintain sterility. Here, scientists worked in a flow hood to isolate potential pathogenic bacteria and viruses from water samples. These isolates were then cultured together with amoebae. Because amoebae normally eat or "phagocytose" bacteria, any bacteria that were able to resist amoebal digestion and remain in these organisms can also potentially remain viable in human cells and cause diseases.Finally, sterile conditions permit detailed study of ecological mechanisms such as the formation of root nodules in legume plants - bacteria-filled organs that "fix" atmospheric nitrogen into ammonia, which is used by the plant for growth. Researchers here created "microcosms" for studying the nodulation process using notched Petri plates with plant growth medium, placed seedlings into them and inoculated the seedlings with nodule-forming rhizobial bacteria. The aseptic environment of the flow hood prevents contamination of the cultures with other bacteria or fungi.You've just watched JoVE's video on aseptic techniques in environmental science. You should now understand why aseptic working conditions are important; how to aseptically perform microbiological experiments; and some applications of aseptic techniques to environmental research. As always, thanks for watching!

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Environmental Sciences

Environmental Microbiology

preventing contamination in microbiology labs

Aseptic technique helps prevent contamination in environmental microbiology labs. It is a careful lab skill that takes practice and attention. When used correctly, it lowers the chance that bacteria or fungi will contaminate reagents, culture media, or environmental samples.

This technique also protects data quality. Keeping samples and cultures clean helps preserve the purity of culture libraries, including rare isolates that are difficult to grow. In this way, aseptic technique supports reliable results in environmental science labs.

Contamination can come from several places in the lab. Airborne microorganisms can ride on dust and lint particles. Microbes can also be present on the lab bench, on unsterilized glassware or equipment, and on the body or hair of the researcher.

Aseptic technique is also a safety measure. It reduces the chance that microorganisms will be passed to researchers, which matters even more when working with pathogens.

Preventing Contamination in Microbiology Labs

preventing-contamination-in-microbiology-labs

determination of moisture content in soil

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Soil Pore Space and Water Content

Soil pore space holds water and air. Soil moisture content is the amount of water present in soil. This water sits in the spaces between soil aggregates and inside the aggregates themselves. These spaces are called inter-aggregate pore space and intra-aggregate pore space. In normal soil, pore space is usually filled by air, water, or both. If the pores contain only air, the soil is completely dry. If the pores are filled with water, the soil is saturated.

Aseptic technique helps prevent contamination in environmental microbiology labs. It is a careful lab skill that takes practice and attention. When used correctly, it lowers the chance that bacteria or fungi will contaminate reagents, culture media, or environmental samples. This technique also protects data quality. Keeping samples and cultures clean helps preserve the purity of culture libraries, including rare isolates that are difficult to grow. In this way, aseptic technique supports...

gram staining of bacteria from environmental sources

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Visualizing Environmental Bacteria with Gram Stain

Gram staining helps scientists visualize bacteria collected from environmental sources. It is a fast, practical method for sorting culturable bacterial populations of interest. For environmental microbiologists, this can be useful whether the sample comes from a known isolate in the lab or from soil or water collected in the field. Environmental microbiology includes many kinds of research, from bench-scale work to field sampling. Soil and water samples often contain unknown bacterial...

visualizing soil microorganisms via the contact slide assay and microscopy

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Soil Life, Microbes, and the Rhizosphere

Soil is the thin layer at Earth’s surface that supports life. It contains both abiotic factors, which are nonliving parts, and biotic factors, which are living or once-living parts. The abiotic portion includes inorganic particles of different sizes and shapes that help determine soil texture. The biotic portion of soil includes plant residues, roots, organic matter, and microorganisms. Soil is especially rich in microbes. One gram of soil can contain large numbers of bacteria, actinomycetes,...

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Fungi in Soil and Nutrient Cycling

Fungi are heterotrophic eukaryotic organisms that play an important role in soil. With the exception of yeasts, they are aerobic, which means they use oxygen. They are abundant in surface soils and help break down organic matter and some organic contaminants. These organisms also support nutrient cycling in the environment. White rot fungi, such as Phanerochaete chrysosporium, are a well-known example. They can degrade aromatics, which are ring-shaped organic compounds found in many materials.

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Soil Microbe Study Using Community DNA

Community DNA from soil helps scientists study microbial communities without relying only on culture tests. Traditional methods use dilution and plating on selective or differential media, or they use direct count assays. Direct counts show the total number of bacteria present, but they do not show how many populations are in the community or how diverse those populations are. Plate counts can measure total culturable bacteria or selected culturable groups. That makes them useful for comparing...

detecting environmental microorganisms with the polymerase chain reaction and gel electrophoresis

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PCR for Tracking Microbes in Soil and Water

PCR is used to track microorganisms in soil, water, and air samples by detecting their DNA. The technique copies a specific DNA segment, which helps identify target microbes at the species, strain, and serovar or pathovar level. It can also help describe whole microbial communities in a sample. Culture-based methods are still used to detect microorganisms in environmental samples. These methods grow microbes on special media in the lab. They are useful, but they can miss microbes that are...

rna analysis of environmental samples using rt-pcr

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RT-PCR for Detecting RNA in Samples

RT-PCR is used to detect RNA in environmental samples by first converting RNA into DNA. It follows the same temperature-cycling steps as conventional PCR, but it begins with ribonucleic acid (RNA) instead of deoxyribonucleic acid (DNA). The RNA is turned into complementary DNA, or cDNA, so DNA-based tools can be used to study it. This method is important for finding RNA-based organisms in soil, water, and agricultural samples. Many viruses in the environment use RNA as their genetic material.

quantifying environmental microorganisms and viruses using qpcr

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qPCR for Detecting Waterborne Viruses

Quantitative polymerase chain reaction (qPCR), also called real-time PCR, is a molecular method used to measure microorganisms in environmental samples. It helps researchers estimate how much microbial material is present, including disease-causing pathogens. This makes qPCR useful in environmental microbiology when samples need accurate counts. Before qPCR, scientists mainly relied on culture-based methods to quantify microbes. Those methods can be difficult to use with environmental samples.

water quality analysis via indicator organisms

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Indicator Organisms for Safe Water Testing

Water quality analysis can use indicator organisms to check for contamination in a fast and practical way. It helps monitor pollutants, nutrients, pathogens, and other substances that can affect water as a resource. When water is affected by human activity, its integrity can change. Fecal contamination is especially important because it can introduce microbial pathogens. These pathogens can threaten plant, animal, and human health and lead to disease or illness. As water demand increases and...

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Coliform Testing in Water Safety Monitoring

Coliform testing helps monitor water safety in agricultural, recreational, and domestic settings. It is used because contaminated water can spread waterborne disease to people and animals. The microorganisms linked to these outbreaks include parasites, bacteria, and viruses. They are shed in high numbers in the feces of infected hosts. Infection can then spread by the fecal-oral route when a person ingests contaminated water. Testing every possible pathogen in water is not practical or...

detection of bacteriophages in environmental samples

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Bacteriophages and Coliphages in Wastewater

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culturing and enumerating bacteria from soil samples

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Soil Bacteria and Actinomycete Plating

Soil bacteria can be counted and grown using dilution and plating methods. Surface soils contain inorganic and organic particles that form secondary aggregates. The spaces between these aggregates hold air and water. That mix creates a good habitat for bacteria, and soil often contains more than 1 million bacteria per gram. Bacteria are the simplest microorganisms and are known as prokaryotes. A special group within this group is the actinomycetes. Actinomycetes are bacteria with a filamentous...

bacterial growth curve analysis and its environmental applications

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Tracking Bacterial Growth in Pure Culture

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algae enumeration via culturable methodology

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Counting Algae in Soil and Water Samples

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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. 

Learn how aseptic technique helps prevent contamination in environmental microbiology labs, protect culture purity, and improve safety when working with microbes.

Preventing Contamination in Microbiology Labs | JoVE K12

Natural Selection and Evolution

HS-LS4-5.

Overview

Principles of Aseptic Technique

Preparation for Aseptic Work

Aseptic Transfer of Bacteria Between Liquid Media and Petri Plates

Applications

Summary

What is Central Tendency?

Descriptive statistics describe or summarize relevant characteristics of a sample and aid in the analysis of data of interest. When analyzing large ...

Arithmetic Mean

The arithmetic mean is the most commonly used measure of the central tendency of a data set. It is defined as the sum of all the elements constituting the ...

Geometric Mean

The mean is a measure of the central tendency of a data set. In some data sets, the data is inherently multiplicative, and the arithmetic mean is not ...

Harmonic Mean

The arithmetic mean is usually skewed towards the larger values in the data set. Therefore, to avoid this inherent bias towards smaller values, the ...

Trimmed Mean

While measuring the mean of a data set, care needs to be taken when associating the mean to its central tendency. The same goes for the arithmetic mean, ...

Weighted Mean

While taking the arithmetic, geometric, or harmonic mean of a sample data set, equal importance is assigned to all the data points. However, all the ...

Root Mean Square

If in an experiment, data values have a probability of being both positive and negative, neither the arithmetic mean, the geometric mean, nor the harmonic ...

What is a Mode?

The mode is one of the commonly used measures of a central tendency. It is defined as the most frequent value in a data set.
There can be more than one ...

Median

Besides mean, the median is a widely used measure of central tendency. Typically, median is defined as the central or middle value of a data set, measured ...

Multiple Bar Graph

As the name suggests, a multiple bar graph is the same as a bar graph but has multiple bars to depict relationships between different data values. One can ...

Pareto Chart

A Pareto chart is a bar graph or a combination of both line and bar graphs. The bar lengths represent the individual values or the frequency, while the ...

Pie Chart

A pie chart (or a pie graph) is a circular graphical chart or a pictorial representation of categorical data. It is divided into slices of pie each ...

Community Diversity

Populations do not live in isolation; thus, every population interacts with others in certain ways. These interactions give rise to a network of ...

What is Biodiversity?

Biodiversity describes the variety of living things at multiple organizational levels: genetic, species and ecosystem diversity. Species diversity ...

Measuring Biodiversity

Diverse ecosystems are important for the health of the planet and our survival as humans; it is therefore incredibly important for us to understand and ...

Quadrats and Transects Preparation
ExpandStart by tying a knot at the beginning, end and every 5 feet of six 20-foot pieces of rope.
Then, identify three ...

Quadrats and Transects
ExpandIn this activity, you will be using quadrats along transect lines to take biodiversity measurements of the plant species in ...

What are Populations and Communities?

Populations are groups of individuals of the same species that inhabit a shared environment. Communities include multiple co-existing, interacting ...

What is an Ecosystem?

Overview

An ecosystem is the interaction between all abiotic and biotic factors in an environment and can be classified as terrestrial or aquatic. ...

Population Growth

Population Models
An ecological population is a group of individuals of a single species living in an area at the same time. To persist, a population must ...

Species Distribution and Biogeography

Species Distribution

Biogeography is the study of species distribution across geographic space and the processes that shape these distributions. This ...

Threats to Biodiversity

There have been five major extinction events throughout geological history, resulting in the elimination of biodiversity, followed by a rebound of species ...

What is Conservation Biology?

Conservation biology is a scientific field that focuses on the preservation of biodiversity in order to protect ecosystems while meeting the needs of the ...

Algae Enumeration via Culturable Methodology

Source: Laboratories of Dr. Ian Pepper and Dr. Charles Gerba - The University of Arizona
Demonstrating Author: Bradley Schmitz
Algae are a highly ...

an-introduction-to-the-chick-gallus-gallus-domesticus

An Introduction to the Chick: Gallus gallus domesticus

The chicken embryo (Gallus gallus domesticus) is an extremely valuable model organism for research in developmental biology, in part because most of their ...

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An Introduction to the Laboratory Mouse: Mus musculus

Mice (Mus musculus) are an important research tool for modeling human disease progression and development in the lab. Despite differences in their size ...

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An Introduction to the Zebrafish: Danio rerio

Zebrafish (Danio rerio) are small freshwater fish that are used as model organisms for biomedical research. The many strengths of these fish include their ...

determination-of-nox-in-automobile-exhaust-using-uv-vis-spectroscopy

Determination Of NOx in Automobile Exhaust Using UV-VIS Spectroscopy

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
In the troposphere, ozone is naturally formed when sunlight splits nitrogen ...

analysis-of-earthworm-populations-in-soil

Analysis of Earthworm Populations in Soil

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Using mustard, Lumbricus terrestris earthworm populations can be sampled ...

Dissolved Oxygen in Surface Water

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Dissolved oxygen (DO) measurements calculate the amount of gaseous oxygen ...

Drosophila Maintenance

Drosophila melanogaster, commonly known as fruit flies, are a frequently used model organism for life science research. Although starting a collection of ...

Bacterial Growth Curve Analysis and its Environmental Applications

Source: Laboratories of Dr. Ian Pepper and Dr. Charles Gerba - The University of Arizona
Demonstrating Author: Luisa Ikner
Bacteria are among the most ...

drosophila-melanogaster-embryo-and-larva-harvesting-and-preparation

Drosophila melanogaster Embryo and Larva Harvesting and Preparation

Drosophila melanogaster embryos and larvae are easy to manipulate and develop rapidly by mechanisms that are analogous to other organisms, including ...

Bacterial Transformation: Electroporation

The term &#x201C;transformation&#x201D; refers cellular ingestion of foreign DNA.  In nature, transformation can occur in certain types of bacteria.  In ...

Filamentous Fungi

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

bacterial-transformation-the-heat-shock-method

Bacterial Transformation: The Heat Shock Method

Transformation is the process that occurs when a cell ingests foreign DNA from its surroundings. Transformation can occur in nature in certain types of ...

Introduction to the Spectrophotometer

The spectrophotometer is a routinely used instrument in scientific research.  Spectrophotometry is the quantitative measurement of how much a chemical ...

Basic Mouse Care and Maintenance

Mice (Mus musculus) are small rodents that breed and sexually mature quickly, making them perfectly suited to generating large animal colonies for ...

Isolation of Fecal Bacteria from Water Samples by Filtration

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

C. elegans Maintenance

Ceanorhabditis elegans has been, and is still, used to great success as a model organism for studying a variety of developmental, genetic, molecular and ...

lead-analysis-of-soil-using-atomic-absorption-spectroscopy

Lead Analysis of Soil Using Atomic Absorption Spectroscopy

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Lead occurs naturally in soil, in levels ranging from 10-50 ppm. However, ...

Culturing and Enumerating Bacteria from Soil Samples

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

Measuring Tropospheric Ozone

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Ozone is a form of elemental oxygen (O3), a molecule of three oxygen atoms ...

Detection of Bacteriophages in Environmental Samples

Source: Laboratories of Dr. Ian Pepper and Dr. Charles Gerba - The University of Arizona
Demonstrating Author: Alex Wassimi
Viruses are a unique group of ...

Nutrients in Aquatic Ecosystems

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
Nitrogen and phosphorus are essential plant nutrients found in aquatic ...

Passaging Cells

Cell lines are frequently used in biomedical experiments, as they allow rapid culture and expansion of cell types for experimental analysis. Cell lines ...

Plasmid Purification

Plasmid purification is a technique used to isolate and purify plasmid DNA from genomic DNA, proteins, ribosomes, and the bacterial cell wall. A plasmid ...

Quantifying Environmental Microorganisms and Viruses Using qPCR

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

tree-identification-how-to-use-a-dichotomous-key

Tree Identification: How To Use a Dichotomous Key

Source: Laboratories of Margaret Workman and Kimberly Frye - Depaul University
A dichotomous key is a tool that identifies items in nature, such as ...

tree-survey-point-centered-quarter-sampling-method

Tree Survey: Point-Centered Quarter Sampling Method

A number of methods are available for sampling forest communities. Point-centered quarter is one such method. It is used to gather information on the ...

Use mathematical representations to support and revise explanations based on evidence about factors affecting biodiversity and populations in ecosystems of different scales.

Preventing Contamination in Microbiology Labs

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