PCAT Exam: Biological Processes - Microbial Ecology

Microbial ecology is the study of microorganisms and their relationship to each other and the environment. Microorganisms play a significant role in the cycling of environments and biological systems.


There are three major domains of life: Eukaryota, Archaea, and Bacteria.

Eukaryota includes all organisms made up of one or more cells that contain a cell nucleus and organelles enclosed by a membrane.

Archaea comprises single-celled organisms called prokaryotes, which means that they do not have a cell nucleus or organelles bound by membranes.

Bacteria is also made up of prokaryotic cells but unlike the species of Archaea, they do not have genes or metabolic pathways.

Viruses are microscopic parasites that can only live and reproduce within a host body. They are often even smaller than bacteria.

Eukaryotes, archaea, bacteria, and viruses have a symbiotic relationship. The endosymbiosis theory of evolution states that eukaryotes developed from larger prokaryotes engulfing smaller prokaryote cells without breaking them up. The small prokaryotes provided the larger prokaryotes with extra energy and eventually developed into mitochondria and chloroplasts.

Microorganisms help to provide each other and other organisms with energy sources to sustain the environment and biosphere. They play specific roles to keep nutrients cycling throughout the environment. In areas that lack light, chemosynthetic microorganisms can provide carbon and energy to organisms, as photosynthetic microorganisms are unable to do so. Microorganisms that are decomposers can use nutrients from other organisms’ waste as an energy source. Different organisms get their energy from different forms of the primary elements, mainly carbon, oxygen, and nitrogen. Microorganisms have a large diversity of metabolic pathways and can therefore provide other organisms with whichever form of the elements they need.

The Metabolic Processes and Impact of Microorganisms
Microorganisms perform many metabolic processes that provide energy to other organisms. They can take the elements of an environment and turn them into usable nutrients for other organisms. When microorganisms function as a carbon sink, they take carbon dioxide (CO2) from the atmosphere and store it for the long-term underground. Bacteria can take nitrogenous gas (N2) from the atmosphere and convert it to ammonia (NH3) in a process called nitrogen fixation. This allows plants and animals to access nitrogen from the atmosphere in a usable manner, as they cannot use nitrogen in the gaseous form. Nitrogen fixation also replenishes nitrogen found in soil. Methane metabolism by microorganisms is important for organisms that can only use methane as their source of carbon energy. Similarly, oxidation of sulfur is important for organisms that can produce ATP for energy from the oxidation process.

Microbial Resource Management 
Microbial resource management is a way to assess changes in the diversity of microbial communities over time. In the environment, there are thousands of different microorganisms working together to sustain the ecological system, with each playing a different role. Microbial resource management has three main parts. The first is genetic identification of different species in a mixed microbe environment. The second is to identify the metabolic roles of all species. The third is to distinguish the relationships between different microorganisms. This knowledge helps microbiologists to further understand the environmental cycling to which microorganisms contribute. In addition, as the environment changes, microbiologists can change the diversity of the microorganism population to keep the environment cycling in a beneficial manner. For example, with an increase in greenhouse gases in the atmosphere, it is important for there to be a larger presence of microorganisms that can convert the gases to usable resources for other organisms.

Microbes and Human Health
Microorganisms can be a major threat to human health. They can be especially dangerous for people who have compromised immune systems, infants, and elderly individuals. However, they are also harmful for healthy individuals. When humans come in contact with microorganisms, the microbes can enter the body and multiply. They may also release toxins and then damage cells, which leads to disease conditions. Transmission is the process by which a person gets infected by a microorganism. Direct transmission occurs when a person comes in direct contact with something infected with the microbe, such as soil or another person. Indirect transmission occurs when the microbe must travel to the person before they are infected.

These microorganisms can be airborne, vector-borne, or vehicle-borne.

Airborne microbes are suspended in the air between the source of the infection and potential recipients of the infection. Vector-borne microbes are carried in living organisms, such as mosquitos, fleas, and ticks. Vehicle-borne microbes are carried by inanimate objects, such as food, blood, or surgical instruments. The immune system tries to fight off the infection but isn’t always successful.

Food Microbiology 
Microorganisms are a large part of the food industry. Some are considered good, such as probiotics and the microorganisms that create cheese, yogurt, and fermented food and drinks. Others contaminate food and cause it to spoil. Food microbiology is an area of study about all of these helpful and harmful bacteria.

Spoilage, Food Preservation, and Fermented Foods 
Testing the safety of food products is very important. Microbiological tests are performed at every stage of the food production supply chain to ensure the product is free of contamination and will not spoil unexpectedly. These tests can detect spoilage organisms, determine germ content, and identify yeasts, molds, and salmonella. All of these precautions are imperative preventative measures for food poisoning outbreaks.
There are many techniques used in both home and industrial settings to prevent spoilage and preserve food products. Food preservation prevents or slows the growth of microorganisms that would cause the food to spoil. Some traditional techniques often used in home kitchens are curing, freezing, boiling, sugaring, and canning. Modern techniques used in the food industry are pasteurization, vacuum packing, artificial food additives, and irradiation.
Some foods actually use small amounts of specific microorganisms to prevent spoilage from occurring from other more harmful organisms. This process is called fermentation. These microorganisms convert starch and sugars into alcohol to create an environment that’s toxic for themselves and other microorganisms to live and multiply in.

Water Pollution 
Water pollution occurs when pollutants enter large bodies of water and adequate processes aren’t in place to remove the contaminants. Some microorganisms that contaminate water can carry diseases that spread through contact with water. These diseases include salmonella, norovirus, and giardia lamblia. Microorganisms can enter the water from sanitation systems, such as septic tanks, or inadequately-treated sewage discharge. Water pollution occurs more often in less-developed countries, where the infrastructure may be old and resources are limited to fix the problems.

Antimicrobial Agents
Antimicrobial agents include substances that act against microorganisms. They can be natural or synthetic, and can kill or inhibit growth of microbes without affecting the host organism. Antibacterial agents work against bacteria, antiviral agents work against viruses, antifungal agents work against fungi, and antiprotozoal agents work against protozoa. Antibacterial agents are the largest and most studied class of antimicrobial agents. Antibiotics are a specific type of antibacterial agent produced by one type of microorganism to act against another type. They can be used preventatively in populations with weakened immune systems, such as those with HIV, or to treat a current infection, such as an ear infection.