Fortunately most microbes can not survive abrupt extreme changes in the environment. Several microbiologists have grouped the controls of microbes into three categories (1) physical (2) chemical (3) biological or therapeutic. Perhaps one of the original methods of destroying microbes was heat. In the mid-1700s John Needham used heat to destroy microbes and support the theory of biogenesis (disproved spontaneous generation). Heat is only one of numerous activities that microbiologists recognize to potentially reduce the spread and growth of microbes. Health care providers and others working with diseased organisms understand the importance of physical activities like gowning and wearing gloves, the friction of handwashing, and not smoking as possible methods of reducing the spread of microbes. Nurses and dieticians, as well as horticulture students, realize that organisms like E.coli from the human mouth and the tobacco mosaic virus may be transmitted by contact with cigarettes. Dairy scientists often brush cows and clip hooves to help reduce the growth and spread of microbes.

An important physical control of microbes is the use of filters to separate and eliminate microbes. Most microbes that are over 0.2 microns in size can be effectively filtered from liquids. The interest in viruses in the late 1800s made filter technology an important concept. Julius Petri, who invented the petri dish, developed a sand filter to separate bacteria from air. A filter can be used to purify media and beverages including beer. By using filters, it was possible to remove all yeasts from beer and making pasteurization unnecessary – quite a moment for draft beer drinkers. Filters can be made of ground glass, diatomaceous earth, charcoal, or cellulose (paper). The Berkefield filter is composed of the remains of unicellular algae from the ocean bottom (diatomaceous earth); and membrane filters made of cellulose can remove microbes from air and liquids. Some filters may be placed on a plate of culture media or have media added to the filter which permits the growth of microbes and counts of microbes possible. Other air filters are used to purify air entering burn units and to remove microbes from air leaving rooms of patients with respiratory diseases.

A second physical control if radiation. Ultraviolet light (UV) from the sun is an important factor in controlling microbes in the air and topsoil layers. One of the important benefits of tillage (turning up soil) is to expose sensitive possibly pathogenic soil microbes to the lethal effects of UV radiation. UV light does damage human skin cells and will not penetrate some liquids and solids. The microbes in the air and on surfaces in hospital rooms, toilet facilities, space crafts, and slaughtering houses can be reduced by UV light. The use of microwaves as a microbiological control is very limited and of little value. The high speed motion of water molecules from microwave exposure generates heat which if evenly dispersed throughout a food, may reduce some microbe growth. Sound waves (sonication) removes debris from surfaces so that microbes may be eliminated. There is evidence that gram-positive cocci have the ability to repair the DNA damage caused by ultra-violet radiation; and bacteria like Bacillus and Clostridium possess endospores that are not easily penetrated by UV light. The use of radiation to destroy microbes has not gained acceptance because of thye fear of possible radioactive contamination and production of possible toxic products or "off" tastes in foods. By carefully regulation of the radiation dose, the US Food and Drug Administration has approved the use of radiation in the sterilizing of surgical supplies, vaccines, drugs, and spices.

The most frequently used method of physically controlling microbes is heat. Increasing temperatures tends to become microbicidal (cidal = kills) and decreasing temperatures tends to become microbiostatic (static = inhibits). Two types of heat are "moist" and "dry" heat. The methods by which microbes are destroyed by heat are varied and complex. We do know that moist heat kills microbes more rapidly and at lower temperatures; and eventually moist and dry heat denature (change) the proteins and DNA in the cells thus killing the microbes. The shortest time at a certain temperature needed to kill all microbes is called the thermal death time (TDT). The TDT needed to destroy an average microbe (if there is such an organism) is about 176 degrees Fahrenheit (80 degrees Centigrade) for 10 minutes. Consequently, we set our college autoclave (pressure sterilizer) at 250 degrees Fahrenheit for 15 minutes to insure that all microbes in media and on equipment are killed and the products considered sterilized. Industrial canning operations heat low acid foods at 121 degrees Centigrade for 30 minutes to sterilize foods, yet maintaining palatable food texture (no mush). Microbes show surprising variations in tolerance to increased temperaturess. Bacteria like Staphylococcus survive for up to 60 minutes at a temperature of 60 degrees Centigrade, yet Neisseria (microbe causing gonorrhea) is killed in 3 minutes at 50 degrees Centigrade. Worm eggs like Neisseria are not very tolerant to heat. Viruses like the hepatitis virus survive 60 degrees Centigrade for up to 600 minutes. Other examples of increased temperatures that are used to control microbes include exposure to hot oil (160 degrees Centigrade), incineration (Bunsen burner flame may reach 1870 degrees Centigrade), pasteurization (71.6 degrees Centigrade for 15 seconds in flash method to prevent change taste in milk yet destroy potential pathogens like Mycobacterium and Coxiella), ultra-high temperatures (UTH to sterilize mild), and repeated or intermittent exposure to steam called tyndallization.

Reducing the temperature, including freezing, may kill some microbes; but it should be known that cold only retards the growth of most microbes. Several yeasts, viruses, and bacteria like Salmonella, Clostridium, Streptococcus, and Staphylococcus survive refrigerator temperatures for several months. Likewise, dessication or drying does not kill most microbes; in fact, a combination of freezing and drying (lyophilization) is a common method of preserving microbes.

In addition to filters, radiation, and heat some microbiologists would consider activities like crop rotation, tillage, simple handwashing (no soap), wind, insect killers, bioengineering of new resistant varieties, and cleaning vehicles (like boats that could spread purple loosestrife or zebra mussels) as applications of our knowledge of the physical control of microbes.