Microbial ecology

[[File:Great-plate-count-anomaly.svg|thumb|upright=1.3|The great plate count anomaly. Counts of cells obtained via cultivation are orders of magnitude lower than those directly observed under the microscope. This is because microbiologists are able to cultivate only a minority of naturally occurring microbes using current laboratory techniques, depending on the environment. Microorganisms are known to have beneficial, neutral and harmful ecological relationships within their species and other species. to understand the specific roles that these microorganisms have in biological and chemical pathways and the evolution of these microorganisms. Currently, there are several types of biotechnologies that have allowed scientists to analyze the biological and chemical properties of these microorganisms.

Many of these microorganisms have been known to form different symbiotic relationships with other organisms in their environment. Some symbiotic relationships include mutualism, commensalism, amensalism, and parasitism.

In addition, certain antimicrobial substances in the environment can kill microorganisms, thus preventing them from interacting with their environment. These can be antibiotic, antifungal, or antiviral. These principles have served as a foundation for scientists in viewing the relationship between microbes and their environment. Pasteur stated that life can only come from life and not nonliving materials.

Robert Koch was a physician-scientist who implemented the use of an oil-immersion lens and a condenser while using microscopes, to increase the imagery of viewing bacteria. This led Koch to be the first publisher of bacteria photographs. As a result, Koch was able to study wound infections in animals at the microscopic level. In these extreme conditions, the chemosynthetic microbes provide energy and carbon to other organisms. Chemosynthetic microorganisms gain energy by oxidizing inorganic compounds such as hydrogen, nitrite, ammonia, sulfur and iron (II). These organisms can be found in both aerobic and anaerobic environment.

The nitrogen cycle, phosphorus cycle, sulphur cycle, and carbon cycle depend on microorganisms also. Each cycle involves microorganisms in certain processes. For example, nitrogen gas makes up 78% of the Earth's atmosphere, but it is almost chemically inert; as a result, it is unavailable to most organisms. It has to be converted biologically to an available form by microorganism, through nitrogen fixation. Through these biogeochemical cycles, microorganisms are able to make nutrients such as nitrogen, phosphorus and potassium available in the soil. Microorganisms play a role in solubilizing phosphate, improving soil health, and plant growth.

Microbial applications in biotechnology

Microbial interactions are found in bioremediation. Bioremediation is a technology that removes contaminants from soil and wastewater using microorganisms. Examples of some microorganisms that play a role in bioremediation are the following: Pseudomonas, Bacillus, Arthrobacter, Corynebacterium, Methosinus, Rhodococcus, Stereum hirsutum, methanogens, Aspergilus niger, Pleurotus ostreatus, Rhizopus arrhizus, Azotobacter, Alcaligenes, Phormidium valderium, and Ganoderma applantus.

Microbial evolution

Due to high levels of horizontal gene transfer among microbial communities, Mutualism in microbial ecology is a relationship between microbial species and other species (example humans) that allows for both sides to benefit. Microorganisms form mutualistic relationships with other microorganism, plants or animals. One example of microbe-microbe interaction would be syntrophy, also known as cross-feeding, of which Methanobacterium omelianskii is a classic example. Syntrophy has been hypothesized to play a significant role in energy and nutrient-limited environments, such as deep subsurface, where it can help the microbial community with diverse functional properties to survive, grow and produce maximum amount of energy. Anaerobic oxidation of methane (AOM) is carried out by mutualistic consortium of a sulfate-reducing bacterium and an anaerobic methane-oxidizing archaeon. The reaction used by the bacterial partner for the production of H<sub>2</sub> is endergonic (and so thermodynamically unfavored) however, when coupled to the reaction used by archaeal partner, the overall reaction becomes exergonic. This relationship begins when chemical signals are exchanged between the plant and the fungi leading to the metabolic stimulation of the fungus. The fungus then attacks the epidermis of the plant's root and penetrates its highly branched hyphae into the cortical cells of the plant. Also, microorganisms are involved in mutualistic relationship with mammals such as humans. As the host provides shelter and nutrient to the microorganisms, the microorganisms also provide benefits such as helping in the growth of the gastrointestinal tract of the host and protecting host from other detrimental microorganisms.

Commensalism

Commensalism is very common in microbial world, literally meaning "eating from the same table". It is a relationship between two species where one species benefits with no harm or benefit for the other species.

Amensalism

Amensalism (also commonly known as antagonism) is a type of symbiotic relationship where one species/organism is harmed while the other remains unaffected. When co-existing in an environment, Pseudomonas taetrolens shows inhibited growth and decreased production of lactobionic acid (its main product) most likely due to the byproducts created by Lactobacillus casei during its production of lactic acid.

Parasitism

Certain microorganisms are known to have a host-parasite interaction with other organisms. For example, phytopathogenic fungi are known to infect and damage plants. The phytopathogenic fungi is a major issue in agriculture, because it has the capacity to infect its host by their root system. These organisms are known to cause river blindness and lymphatic filariasis in humans. Natural products are therefore vital in the discovery of pharmaceutical agents. Most of the naturally obtained antibiotics are produced by organism under the phylum Actinobacteria. The genus Streptomyces are responsible for most of the antibiotic substances produced by Actinobacteria. These natural products with antimicrobial properties belong to the terpenoids, spirotetronate, tetracenedione, lactam, and other groups of compounds. Examples include napyradiomycin, nomimicin, formicamycin, and isoikarugamycin. Some metals, particularly copper, silver, and gold also have antimicrobial properties. Using antimicrobial copper-alloy touch surfaces is a technique that has begun to be used in the 21st century to prevent the transmission of bacteria. Due to the antimicrobial properties certain metals possess, products such as medical devices are made using those metals.