Scope of Microbiology

Microbiology is a specialized field of biology that investigates cellular organisms (bacteria, fungi, etc.) and acellular infectious agents (viruses, viroids, and prions) that are too small to see without magnification. A microorganism, also called a microbe, is an organism too small to be seen without magnification. Microbes are mostly unicellular, but simple multicellular microbes also exist.

Many microbes are pathogens. A pathogen is a disease-causing organism or virus that causes harm to a host organism. For example, Streptococcus pneumoniae is the bacterial pathogen that causes pneumonia, a disease affecting the lungs. Because pathogens have harmful effects on humans and other animals, a significant portion of microbiology is devoted to the identification of pathogens and the infections they cause. However, many microbes are beneficial to humans, other animals, and the environment, and branches of microbiology are dedicated to their study as well. The bacteria that live in the intestinal tracts of humans and other mammals aid in food digestion by producing enzymes that mammals do not possess. Soil bacteria are numerous and exhibit diverse functions, such as improving plant growth by synthesizing or liberating nutrients, or breaking down dead organic materials.

Microbes are ubiquitous in every ecosystem on Earth and their metabolic actions collectively alter geology and atmospheric chemistry. Bacteria are very small, exploit diverse resources, and reproduce rapidly to colonize new environments, including the human body where there are more bacterial cells than there are human cells.

Studying microbes is useful for understanding certain cellular processes because microbes have simple structures and quick reproduction time. The genomes of many microbes are also relatively simple, making them ideal model organisms for genomics. Microbes share much of the biochemistry of higher-level organisms and therefore can be used as models of more complex structures, such as organs and organ systems. The algae Chlamydomonas reinhardtii has mitochondria and chromosomes that pair like most eukaryotes, and chloroplasts like plants. C. reinhardtii is used extensively to understand photosynthesis, metabolism, and cell-to-cell recognition.

Additional benefits of model organisms like C. reinhardtii are their fast reproduction and growth under controlled laboratory conditions, and genomes amenable to modification. Microbes can be grown in large numbers for relatively low cost, and this growth can be precisely controlled. Moreover, most microbes have short generation times, so research that relies on the transfer of genetic information from one generation to the next can be completed in a reasonable time frame. Many species of yeast, such as brewer’s yeast, Saccharomyces cerevisiae, are capable of both asexual and sexual reproduction. The reproductive process used is experimentally inducible, and this ability has allowed researchers to study how genes pass from generation to generation. Large quantities of organisms are grown using asexual reproduction which are then used to perform specific mating experiments using sexual reproduction.

The major areas of study of microbiology include immunology, epidemiology, pathogenesis, virology, bioremediation, food microbiology, aquatic microbiology, microbial ecology, microbial physiology, and evolutionary microbiology.

Immunology is the study of immunity, which is the ability of an animal to resist infection by a particular pathogen via the action of its immune system. Most immunology focuses on humans, although veterinary immunology is a major discipline of veterinary medicine. One area of immunology focuses on vaccination, the technique of exposing an organism to a form of a pathogen to develop immunity against it. There are other areas of focus in immunology, including understanding the interaction between pathogens and their host, the study of natural and passive immunity, and the study of immunological disorders.

Epidemiology is a science that investigates the when, where, and how of disease transmission in a population. Because it identifies risk factors for disease, epidemiology is a critical component of public health initiatives and shapes policy decisions. This information can then be used to prevent further outbreaks.

Pathogenesis is the science of disease caused by pathogens, with a focus the mechanisms leading to the development and progression of disease. Both the pathogen and the host are relevant to the development of disease and both are studied in tandem to decipher mechanisms. Improved understanding of pathogenesis is useful for developing efficacious preventative and treatment options.

Virology is the study of viruses. The study of viruses can include their structure, genetics, evolution, classification, and ability to cause disease. The study of viruses provided many of the first breakthroughs in the field of molecular biology. Viruses are being modified in the development of therapies to treat cancer and many other diseases.

Bioremediation is the use of microbes to break down pollutants. Bioremediation involves the deliberate introduction of microbes to a polluted area, often the site of an industrial spill, such as an oil spill. Some microbes break down the pollutant into a compound that is easily removed. Other microbes digest it entirely, leaving only harmless compounds behind. A well-known example of bioremediation is the use of the oil-eating bacteria Alcanivorax borkumensis to clean up the ocean after the BP Gulf of Mexico oil spill in 2010. The microbes used in bioremediation are typically not pathogenic to humans.

Food microbiology is the study of microbes important to food production. Food spoilage is a major area of focus in food microbiology. Food microbiologists develop methods of eliminating microbes that cause food spoilage and methods of actively cultivating specific microbes to ferment foods. Many cultures have fermented food products, such as cheese, yogurt, and alcohol.. Yeasts have been used to in food production since at least 3100 BCE when common brewer’s yeast, Saccharomyces cerevisiae, was used to make a wine-like product in ancient Egypt. Leavening of bread is accomplished by carbon dioxide bubbles produced by yeast during cellular respiration. While all yeast can produce alcohol via fermentation, different strains of yeast can result in different flavors in the finished product.

Aquatic microbiology is the study of microbes living in water and is further classified as either freshwater microbiology or marine (saltwater) microbiology. Approximately half of the world's oxygen is generated by photosynthetic ocean microbes through photosynthesis, and these same microbes pull large quantities of carbon dioxide out of the atmosphere, collectively influencing global atmospheric chemistry and climate. Aquatic microbiology may also encompass the study of pathogens found in freshwater, for example, the amoeba Naegleria fowleri, which is found in warm freshwater. This amoeba is colloquially called the "brain-eating amoeba" because it moves from the nasal cavities to the frontal lobe of the brain, which serves as its food source. Another aspect of aquatic microbiology is the study of harmful algae overgrowth, a phenomenon called algal blooms. One type algal bloom is red tide. Red tides remove oxygen from the water and produce a toxin resulting in mass die-offs of marine organisms, such as the months long event off the coast of Florida in 2018 that killed dolphins, fish, manatees, and turtles.

Microbial ecology examines the role of microbes in the environment. Microbes are found—and play important roles—in every ecosystem on the planet. Because they are found in every ecosystem, microbes have a wide variety of metabolic and physiological differences. Microbial physiology is the branch of microbiology that examines physiological processes and differences. There have been microbes on this planet for billions of years; microbial evolution is the study of how they have changed and shaped the world.