Introduction

Microbes have many beneficial effects in our environment. In fact, microorganism are necessary and essential for life as we know it to exist. Many common biological interactions would be impossible without microbes.

Diversity and Habitats

Prokaryotic microbes (comprising the Bacteria and Archaea domains) live in every possible habitat on earth, including many that are inhabitable by humans. Bacterial species have been isolated from geothermal springs and deep ocean vents (both of which can reach temperatures of 90 °C (194 °F) as well as from snow and ice sample cores and super cooled salt water (at a temperature of -10 °C or 14 °F) from Antarctica. We would not survive very long at those temperatures! In addition to being able to survive in extreme temperatures, microorganisms have developed ways to grow without oxygen, light, or nutrients that we require to survive. Furthermore, they can live and thrive in regions of very high or very low pH (highly alkaline or highly acidic conditions) and in regions of high salt concentrations (some microbes isolated from Antarctic live in water that has four times as much salt as normal seawater). Microorganism that inhabit these extreme environments are called extremophiles. Specific enzymes isolated from many of these organisms have been utilized by various industries since the enzymes can survive industrial conditions that would inactivate enzymes from normal microbes.

Figure 1: Norris Geyser Basin in Yellowstone National Park. The green and orange colors seen here are derived from different microorganisms that grow in the high acidity (pH of 2 - 3), high temperature (80 - 90 °C). Additionally, these areas are typically high in sulfur and many microbes living here metabolize sulfur, rather than oxygen, for survival.

Microbiology of Soils

Soils host a wide variety of organisms, both microscopic and macroscopic, that exist as a active, interrelated community. Soils contain both beneficial and harmful bacteria. Beneficial bacteria in soils include those genera that produce common antibiotics, such as Bacillus (bacitracin), Streptomyces (a number of different antibiotics), Penicillium (penicillin), and Cephalosporium (cephalosporin). These antibiotics are used in medicine as well as in the microbiology lab to control the growth of specific types of microbes. Pathogenic bacteria in soil may include those from the genus Clostridium, which can cause tetanus and botulism.

In addition to bacteria, fungal species are important components of soil. Mycorrhizae are fungi that grow on roots of plants (in a symbiotic relationship) and aid in nutrient absorption by increasing the surface area of the root system. Additionally, the mycorrhizae can contribute to the breakdown of organic matter which further helps the plant absorb the nutrients.

Mycorrhizae exist in two forms: endomycorrhizae and ectomycorrhizae. Endomycorrhizae grow on approximately 70% of plants in nature, including the majority of grasses, herbaceous plants, and some tree species. Ectomycorrhizae primarily grow on the roots of various tree species, including oaks, beech, birch, and evergreens. They are an important component of the soil at commercial tree farms.

Counts of bacteria in soils are performed using a variety of nutrients on agar plates, but the actual number of bacteria are usually underestimated since different bacteria have widely different metabolic requirements. The great diversity of microbes contributes to the decomposition and recycling of organic material (from plant and animal sources) in the soil. This process supplies essential elements back to the environment so that they can be used again in living systems. The cycling of essential elements is collectively called biogeochemical cycles.

Biogeochemical Cycles

Many professions classify natural processes into cycles. For example, the water cycle describes how the amount of water in the environment remains constant by cycling through various phases (gas, liquid, solid). There are a number of other natural cycles, which are essential for life on earth, that rely on microorganisms. These biogeochemical cycles consist of the carbon cycle, the nitrogen cycle, the sulfur cycle, and the phosphorus cycle. Microorganisms play a critical role in each of these cycles.

Figure 2: Black (pictured here) and white truffles are highly prized delicacies and can cost up to $250 per ounce. Truffles are ectomycorrhizae, commonly associated with oak trees. Pigs have been used for centuries to root through the ground and find these high priced treats by smell.

All living things are composed of large amounts of carbon; it is estimated that half of the dry weight of living organisms is carbon. Bacteria, such as cyanobacteria, transfer the carbon from carbon dioxide to carbohydrates (sugars) using water as an electron (hydrogen) donor and sunlight as an energy source, liberating oxygen in the process. Other bacteria (green and purple sulfur bacteria) perform the same operation but use hydrogen sulfide as the electron donor and generate elemental sulfur. The bacteria are eaten by other organisms up through the food chain and therefore the incorporated carbon atoms are transferred from microorganisms to macroorganisms. Some of this carbon is exhaled from animals as carbon dioxide, thus beginning the process again. Some of this carbon is retained until the organism dies; it then is liberated as the organism is decomposed by bacteria and fungi in the soil.

Nitrogen is also essential for life on earth. Nitrogen is incorporated into all amino acids, DNA and RNA, and other nitrogen containing compounds. Nitrogen is abundant in our atmosphere (comprising approximately 79% of atmospheric gases) but this form of nitrogen (gaseous N₂) is not usable by most organisms. Nitrogen must be “fixed” or converted from this unusable form to the usable organic form, ammonium ion. The nitrogen cycle has four processes: ammonification, nitrification, denitrification, and nitrogen fixation. Bacteria play critical roles in each of these processes.

Ammonification is the release of nitrogen in the form of amino groups from amino acids (deamination); these amino groups result from the breakdown of proteins by microbial decomposition of dead organisms. A large number of different bacteria and fungi contribute to ammonification and the resulting amino groups are converted to ammonia (NH₃). Ammonia is a gas that is rapidly converted to ammonium ions (NH₄⁺) in moist soil. Ammonium ions can then be incorporated into bacterial amino acids and proteins.

Nitrification depends on nitrifying soil bacteria from the genera Nitrosomonas and Nitrobacter. Nitrification is the conversion of ammonium ions (NH₄ ⁺) to nitrate ions (NO₃ ^-), which is readily used by plants for protein synthesis. Nitrosomonas first catalyzes the oxidation of ammonium to nitrite (NO₂ ^-); Nitrobacter then oxidizes nitrite to nitrate.

anaerobic conditions, denitrifying bacteria (predominantly Pseudomonas and Bacillus species) use anaerobic respiration to produce energy (in the form of ATP) and use nitrate as the final substrate in the process. Through the process of denitrification, nitrate is converted back to gaseous nitrogen and is released back to the atmosphere. Denitrification can also generate nitrous oxide (N₂O), a potent green house gas.

As mentioned above, gaseous nitrogen is predominant in our atmosphere and the only organisms that can use it directly nitrogen fixing bacteria, such as cyanobacteria, Azotobacter, some species of Clostridium, Beijerinckia, Rhizobium, and Bradyrhizobium. The latter two are symbiotic with the roots of agriculturally important plants, such as legumes; the former are free-living in the soil. All nitrogen fixing bacteria use the enzyme nitrogenase to convert nitrogen to ammonium that is usable by plants and other bacteria. Nitrogen fixation is very energy demanding so it is not performed if other forms of organic nitrogen (ammonium, nitrite, nitrate) are available.

Microorganisms use sulfur for energy or incorporate it into organic molecules (such as sulfur-containing amino acids in proteins). The sulfur cycle describes the transformation of sulfur from reduced (hydrogen sulfide) to elemental (sulfur) to oxidized (sulfate) forms. Green and purple sulfur bacteria use hydrogen sulfide (H₂S) as an electron donor to produce carbohydrates according to the following reaction:

6 CO₂ + 12 H₂S + light → C₆H₁₂O₆ (glucose) + 6 H₂O + 12 S

Sulfur utilizing bacteria are commonly found in deep ocean vents and near thermal springs due to the low oxygen concentrations and high levels of hydrogen sulfide.

Microorganisms and Water Quality

Contamination of water sources by human and animal feces is a world-wide health hazard. Approximately 2 million global deaths annually are reportedly due to fecal contamination of open water sources. In the U.S. alone, it is estimated that 900,000 people fall ill from contaminated water. There are many different diseases that are transmitted by a fecal to oral route; typhoid fever and cholera are just two examples. Municipalities routinely test for the presence of fecal water contamination by looking for the presence of indicator organisms, called fecal coliforms, of which E. coli is the most prominent organism. E. coli is commonly found in the human intestine, where it is non-pathogenic; importantly, the coliform organisms are not normally pathogenic but indicate whether fecal contamination is present, which could mean pathogenic bacteria are present. Coliforms are typically gram-negative and anaerobic and have a distinct appearance on selective media. Counts are obtained from the sampled water source and if they are above a threshold limit, disinfection methods can be employed to limit the spread of disease.