Environmental Microbiology

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 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...

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,...

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.

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...

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...

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.

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 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...

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...

Bacteriophages are viruses that infect bacteria, and coliphages are the ones that infect coliform bacteria. These viruses can be found wherever coliform bacteria are present. The page focuses on how these phages relate to environmental samples, especially domestic wastewater.

Viruses are a special group of biological entities that can infect both eukaryotic and prokaryotic organisms. They are obligate parasites, which means they must use a host cell to make more virus particles. They have no...

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 in pure culture shows how one species increases under controlled laboratory conditions. Pure culture means that only one type of bacterium is being studied. Because bacteria grow quickly, their cell numbers can rise sharply in a short time.

Scientists measure how the bacterial population changes over time to create a growth curve. This curve helps show the rate of growth for the isolate being tested. It is a useful way to study bacteria in the lab instead of mixing many...

Algae can be counted in soil and water samples using a culture-based most probable number (MPN) method. These microorganisms share one key trait: they contain photosynthetic pigments. The method helps measure algae that may grow in swimming pools, surface waters, and soils.

Algae can create problems in lakes and reservoirs when blooms release toxins. They are also important in biofuel research because some species are being explored as energy sources. Blue-green algae are actually bacteria...