Details about Basic Microbiology 

Overview :

Microbiology is the study of microscopic organisms, either unicellular (single cell), multicellular (cell colony), or acellular (lacking cells). The term Microbiology derived from Greek μῑκρος, mīkros, "small"; βίος, bios, "life"; and -λογία, -logia. Microbiology encompasses numerous sub-disciplines including virology, mycology, parasitology, and bacteriology.

The term economics comes from the Ancient Greek (oikonomia, "management of a household, administration") from ”house") and (nomos, "custom" or "law"), hence "rules of the house(hold for good management)". 'Political economy' was the earlier name for the subject, but economists in the late 19th century suggested "economics" as a shorter term for "economic science" to establish itself as a separate discipline outside of political science and other social sciences.

Eukaryotic microorganisms possess membrane-bound cell organelles and include fungi and protists, whereas prokaryotic organisms which all are microorganisms are conventionally classified as lacking membrane-bound organelles and includeeubacteria and archaebacteria. Microbiologists traditionally relied on culture, staining, and microscopy. However, less than 1% of the microorganisms present in common environments can be cultured in isolation using current means. Microbiologists often rely on extraction or detection of nucleic acid, either DNA or RNA sequences.

Viruses have been variably classified as organisms, as they have been considered either as very simple microorganisms or very complex molecules. Prions, never considered microorganisms, have been investigated by virologists, however, as the clinical effects traced to them were originally presumed due to chronic viral infections, and virologists took search—discovering "infectious proteins".

As an application of microbiology, medical microbiology is often introduced with medical principles of immunology as microbiology and immunology. Otherwise, microbiology, virology, and immunology as basic sciences have greatly exceeded the medical variants, applied sciences

History of Microbiology :

Ancient History :

The existence of microorganisms was hypothesized for many centuries before their actual discovery. The existence of unseen microbiological life was postulated by Jainism which is based on Mahavira’s teachings as early as 6th century BCE. Paul Dundas notes that Mahavira asserted existence of unseen microbiological creatures living in earth, water, air and fire. Jain scriptures also describe nigodas which are sub-microscopic creatures living in large clusters and having a very short life and are said to pervade each and every part of the universe, even in tissues of plants and flesh of animals. The Roman Marcus Terentius Varro made references to microbes when he warned against locating a homestead in the vicinity of swamps "because there are bred certain minute creatures which cannot be seen by the eyes, which float in the air and enter the body through the mouth and nose and there by cause serious diseases."

In the medieval Islamic world,

At the golden age of Islamic civilization, some scientists had knowledge about microorganisms, such as Ibn Sina in his book The Canon of Medicine, Ibn Zuhr (also known as Avenzoar) who discovered scabies germs, and Al-Razi who spoke of parasites in his book The Virtuous Life (al-Hawi).

In 1546, Girolamo Fracastoro proposed that epidemic diseases were caused by transferable seedlike entities that could transmit infection by direct or indirect contact, or vehicle transmission.

However, early claims about the existence of microorganisms were speculative, and not based on microscopic observation. Actual observation and discovery of microbes had to await the invention of the microscope in the 17th century.

Modern History :

In 1676, Anton van Leeuwenhoek, who lived for most of his life in Delft, Holland, observed bacteria and other microorganisms using a single-lens microscope of his own design. While Van Leeuwenhoek is often cited as the first to observe microbes, Robert Hooke made the first recorded microscopic observation, of the fruiting bodies of molds, in 1665. It has, however, been suggested that a Jesuit priest called Athanasius Kircher was the first to observe micro-organisms. He was among the first to design magic lanterns for projection purposes, so he must have been well acquainted with the properties of lenses. One of his books contains a chapter in Latin, which reads in translation – ‘Concerning the wonderful structure of things in nature, investigated by Microscope.’ Here, he wrote ‘who would believe that vinegar and milk abound with an innumerable multitude of worms.’ He also noted that putrid material is full of innumerable creeping animalcule. These observations antedate Robert Hooke’s Micrographia by nearly 20 years and was published some 29 years before van Leeuwenhoek saw protozoa and 37 years before he described having seen bacteria.

The field of bacteriology (later a sub-discipline of microbiology) was founded in the 19th century by Ferdinand Cohn, a botanist whose studies on algae and photosynthetic bacteria led him to describe several bacteria including Bacillus and Beggiatoa. Cohn was also the first to formulate a scheme for the taxonomic classification of bacteria and discover spores. Louis Pasteur and Robert Koch were contemporaries of Cohn’s and are often considered to be the father of microbiology and medical microbiology, respectively. Pasteur is most famous for his series of experiments designed to disprove the then widely held theory of spontaneous generation, thereby solidifying microbiology’s identity as a biological science. Pasteur also designed methods for food preservation (pasteurization) and vaccines against several diseases such as anthrax, fowl cholera and rabies. Koch is best known for his contributions to the germ theory of disease, proving that specific diseases were caused by specific pathogenic micro-organisms. He developed a series of criteria that have become known as the Koch's postulates. Koch was one of the first scientists to focus on the isolation of bacteria in pure culture resulting in his description of several novel bacteria including Mycobacterium tuberculosis, the causative agent of tuberculosis.

While Pasteur and Koch are often considered the founders of microbiology, their work did not accurately reflect the true diversity of the microbial world because of their exclusive focus on micro-organisms having direct medical relevance. It was not until the late 19th century and the work of Martinus Beijerinck and Sergei Winogradsky, the founders of general microbiology (an older term encompassing aspects of microbial physiology, diversity and ecology), that the true breadth of microbiology was revealed. Beijerinck made two major contributions to microbiology: the discovery of viruses and the development of enrichment culture techniques. While his work on the Tobacco Mosaic Virus established the basic principles of virology, it was his development of enrichment culturing that had the most immediate impact on microbiology by allowing for the cultivation of a wide range of microbes with wildly different physiologies. Winogradsky was the first to develop the concept of chemolithotrophy and to thereby reveal the essential role played by micro-organisms in geochemical processes. He was responsible for the first isolation and description of both nitrifying and nitrogen-fixing bacteria. French-Canadian microbiologist Felix d'Herelle co-discovered bacteriophages and was one of the earliest applied microbiologists.

Branches of Microbiology:

The branches of microbiology can be classified into pure and applied sciences. Microbiology can be also classified based on taxonomy, in the cases of bacteriology, mycology, protozoology, and phycology. There is considerable overlap between the specific branches of microbiology with each other and with other disciplines, and certain aspects of these branches can extend beyond the traditional scope of microbiology.

 

Pure Microbiology

Taxonomic Arrangement

1. Bacteriology: The study of Bacteria.
2. Mycology: The study of Fungi.
3. Protozoology: The study of Protozoa.
4. Phycology (or algology): The study of Algae.
5. Parasitology: The study of Parasites.
6. Immunology: The study of the Immune System.
7. Virology: The study of Viruses.
8. Nematology:The study of the Nematodes
9. Microbiology:The study of Microbes.

Integrative Arrangement

1. Microbial Cytology: The study of microscopic and submicroscopic details of microorganisms.
2. Microbial physiology: The study of how the microbial cell functions biochemically. Includes the study of microbial growth, microbial metabolism and microbial cell structure.
3. Microbial Ecology: The relationship between microorganisms and their environment.
4. Microbial Genetics: The study of how genes are organized and regulated in microbes in relation to their cellular functions. Closely related to the field of molecular biology.
5. Cellular Microbiology: A discipline bridging microbiology and cell biology.
6. Evolutionary Microbiology: The study of the evolution of microbes. This field can be subdivided into:
7. Generation Microbiology: The study of those microorganisms that have the same characters as their parents.
8. Systems Microbiology: A discipline bridging systems biology and microbiology.
9. Molecular Microbiology: The study of the molecular principles of the physiological processes in microorganisms.

Other

1. Nano microbiology: The study of those organisms on nano level.
2. Exo microbiology (or Astro microbiology): The study of microorganisms in outer space (see: List of microorganisms tested in outer space)
3. Biological Agent: The study of those microorganisms which are being used in weapon industries.

Nanotechnology and microbiology

Microbiology relates to nanoscience at a number of levels. Many bacterial entities are nano-machines in nature, including molecular motors like flagella and pili. Bacteria also form biofilms by the process of self-assembly (for example the formation of Curli-film by E. coli). The formation of aerial hyphae by bacteria and fungi is also directed by the controlled and ordered assembly of building blocks. Also, the formation of virus capsids is a classical process of molecular recognition and self-assembly at the nano-scale.

Nanotechnology involves creating and manipulating organic and inorganic matter at the nanoscale. It promises to provide the means for designing nanomaterials; materials with tailor-made physical, chemical and biological properties controlled by defined molecular structures and dynamics. The present molecular biology techniques of genetic modification of crops are already forms of what has been termed nanotechnology.

Nanotechnology can provide for the future development of far more precise and effective methods of, and other forms of, manipulation of food polymers and polymeric assemblages to provide tailor-made improvements to food quality and food safety. Nanotechnology promises not only the creation of novel and precisely defined material properties, it also promises that these materials will have self-assembling, self-healing and maintaining properties.

Typical size of nano- and microsized biological objects (horizontal axis: log-scale) from left- to right: (a) Hydrogen atom (∼0.1nm) , (b) water molecule (diameter: ∼0.4nm), (c) peptide aptamer (size ∼3nm), (d) lipid bilayer (thickness ∼5nm), (e) protein (size ∼10nm), (f) antibody (size ∼10nm), (g) ribosome (diameter ∼30nm), (h) human papilloma virus (diameter ∼60nm), (i) mitochondrium (length ∼1 µm), (j) Helicobacter pylori (length ∼3µm), (k) nucleus (diameter ∼3µm), (l) erythrocyte (diameter ∼8µm), mammalian cell (diameter ∼20µm).

Nanoscience does have an impact on several areas of microbiology. It allows for the study and visualization at the molecular-assembly levels of a process. It facilitates identification of molecular recognition and self-assembly motifs as well as the assessment of these processes. Specifically, there are three areas where microbiologists use nanotechnologists' techniques:

Imaging single molecules

Poking and pulling nanoscale objects (laser traps, optical tweezer)

Determining spatial organization in living microbes (AFM, near/far field microscope)

Nanotechnology in food microbiology

Detection of very small amounts of a chemical contaminant, virus or bacteria in food systems is another potential application of nanotechnology. The exciting possibility of combining biology and nanoscale technology into sensors holds the potential of increased sensitivity and therefore a significantly reduced response-time to sense potential problems.

Nanosensors that are being developed by researchers at both Purdue and Clemson universities use nanoparticles, which can either be tailor-made to fluoresce different colors or, alternatively, be manufactured out of magnetic materials. These nanoparticles can then selectively attach themselves to any number of food pathogens. Employees, using handheld sensors employing either infrared light or magnetic materials, could then note the presence of even minuscule traces of harmful pathogens. The advantage of such a system is that literally hundreds and potentially thousands of nanoparticles can be placed on a single nanosensor to rapidly, accurately and affordably detect the presence of any number of different bacteria and pathogens. A second advantage of nanosensors is that, given their small size, they can gain access into the tiny crevices where the pathogens often hide.

The application of nanotechnologies on the detection of pathogenic organisms in food and the development of nanosensors for food safety is also studied at the Bioanalytical Microsystems and Biosensors Laboratory at Cornell University. The focus of the research performed at Cornell University is on the development of rapid and portable biosensors for the detection of pathogens in the environment, food and for clinical diagnostics. The bioanalytical microsystems use the same biological principles as were used in the simple biosensors, i.e. RNA recognition via DNA/RNA hybridization and liposome amplification. The bioanalytical microsystems that are studied focus on the very rapid detection of pathogens in routine drinking water testing, food analysis, environmental water testing and in clinical diagnostics (see "Nanotechnology and its applications in the food sector").

Nanotechnology in medical biology – application of nanodiagnostics in infectious diseases

The rapid and sensitive detection of pathogenic bacteria at the point of care is extremely important. Limitations of most of the conventional diagnostic methods are the lack of ultrasensitivity and delay in getting results. A bioconjugated nanoparticle-based bioassay for in situ pathogen quantification can detect a single bacterium within 20 minutes.

Detection of single-molecule hybridization has been achieved by a hybridization-detection method using multicolor oligonucleotide-functionalized QDs as nanoprobes. In the presence of various target sequences, combinatorial self-assembly of the nanoprobes via independent hybridization reactions leads to the generation of discernible sequence specific detection of multiple relevant sequences ("Multiplexed Hybridization detection with multicolor colocalization of quantum dot nanoprobes").

A spectroscopic assay based on SERS using silver nanorods, which significantly amplify the signal, has been developed for rapid detection of trace levels of viruses with a high degree of sensitivity and specificity. The technique measures the change in frequency of a near- infrared laser as it scatters viral DNA or RNA. That change in frequency is as distinct as a fingerprint. This novel SERS assay can detect spectral differences between viruses, viral strains, and viruses with gene deletions in biological media. The method provides rapid diagnostics (60 s) for detection and characterization of viruses generating reproducible spectra without viral manipulation. This method is also inexpensive and easily reproducible (see for instance: "Nanotechnology: A new frontier in virus detection in clinical practice").

The use of nanoparticles as tags or labels allows for the detection of infectious agents in small sample volumes directly in a very sensitive, specific and rapid format at lower costs than current in-use technologies. This advance in early detection enables accurate and prompt treatment.

Quantum dot technology is currently the most widely employed nanotechnology in this area. The recently emerging cantilever technology is the most promising. The technology strengthens and expands the DNA and protein microarray methods and has applications in genomic analysis, proteomics, and molecular diagnostics.

Waveguide technology is an emergent area with many diagnostic applications. Nanosensors are the new contrivance for detection of bioterrorism agents. All these new technologies would have to be evaluated in clinical settings before their full import is appreciated and accepted ("New frontiers in nanotechnology for cancer treatment" and "Cancer nanotechnology: opportunities and challenges").

Nanotechnology in water microbiology – water treatment by detection of microbial pathogens An adequate supply of safe drinking water is one of the major prerequisites for a healthy life, but waterborne diseases is still a major cause of death in many parts of the world, particularly in young children, the elderly, or those with compromised immune systems. As the epidemiology of waterborne diseases is changing, there is a growing global public health concern about new and reemerging infectious diseases that are occurring through a complex interaction of social, economic, evolutionary, and ecological factors.

An important challenge is therefore the rapid, specific and sensitive detection of waterborne pathogens. Presently, microbial tests are based essentially on time-consuming culture methods. However, newer enzymatic, immunological and genetic methods are being developed to replace and/or support classical approaches to microbial detection. Moreover, innovations in nanotechnologies and nanosciences are having a significant impact in biodiagnostics, where a number of nanoparticle-based assays and nanodevices have been introduced for biomolecular detection (see for instance: Nanotechnology in Water Treatment Applications and Environmental Microbiology: Current Technology and Water Applications).

Astro Microbiology

Astro microbiology, or exo microbiology, is the study of microorganisms in outer space. It stems from an interdisciplinary approach, which incorporates both microbiology and astrobiology. Astrobiology's efforts are aimed at understanding the origins of life and the search for life other than on Earth. Because microorganisms are the most widespread form of life on Earth, and are capable of colonising almost any environment, scientists usually focus on microbial life in the field of astrobiology. Moreover, small and simple cells usually evolve first on a planet rather than larger, multicellular organisms, and have an increased likelihood of being transported from one planet to another via the panspermia theory.

Planetary Exploration

The search for extraterrestrial microbial life have focused mostly on Mars due to its promising environment and close proximity; however, other astrobiological sites include the moons Europa, Titan and Enceladus. All of these sites currently have or have had a recent history of possessing liquid water, which scientists hypothesize as the most consequential precursor for biological life. Europa and Enceladus appear to have large amounts of liquid water hidden beneath the layers of ice that covers their surfaces. Titan, on the other hand, is only planetary body besides Earth with liquid hydrocarbons on its surface. Mars is the main area of interest for the search for life primarily because of convincing evidence that suggests surface liquid water activity in recent history. Furthermore, Mars has an atmosphere containing abundant amounts of carbon and nitrogen, both essential elements needed for life.

Discoveries

So far, the search for microbial life in extraterrestrial locations have been less than successful. The first of such attempts, occurred through NASA's Viking program in the 1970s, in which two Mars landers were used to conduct experiments that searched for biosignatures of life on Mars. The landers utilized robotic arms to collect soil samples into sealed containers that were brought back to Earth. The results were largely inconclusive, although some scientists still dispute them.

In 2008, Russian cosmonauts reported findings of sea plankton living on the outside surfaces of the International Space stations windows. They have yet to find explanations for the discovery, but it seems to have been a result of human contamination, though this may never be proven.

Currently, the Mars Science Laboratory mission has a rover on Mars that continues to be operational. Launched on 26 November 2011, and landing at Gale Crater on 6 August 2012, its goals are to assess the habitability of Mars' environment – amongst its collection of data for Martian geology, climate and availability of water, are instruments that search for biosignatures daily. Thus far, its results have not been fruitful.

Future Missions

Mission Title	Launch Date	Agency	Objectives
ExoMars	2018	European Space Agency & Russian Federal Space Agency	Search for past and present Martian life
Mars 2020 Rover	2020	NASA	Mobile rover unit that will scavenge Mars' surfaces and collect soil samples
Red Dragon	2018	NASA	Launch of satellite that will orbit Mars and provide highly sophisticated imaging
Icebreaker Life	2018	NASA	Robotic Mars lander equipped with a 1-meter drill to search for organic molecules trapped under ice-rich surfaces
Europa Clipper	TBD	NASA	Satellite launch that will orbit Jupiter's moon Europa and perform detailed reconnaissance of environmental conditions as well as search for potential landing sites

Experimentation

Earth

Many studies on Earth have been conducted to collect data on the response of terrestrial microbes to various simulated environmental conditions of outer space. The responses of microbes, such as viruses, bacterial cells, bacterial and fungal spores, and lichens, to isolated factors of outer space (microgravity, galactic cosmic radiation, solar UV radiation, and space vacuum) were determined in space and laboratory simulation experiments. In general, microorganisms tended to thrive in the simulated space flight environment – subjects showed symptoms of enhanced growth and an uncharacteristic ability to proliferate despite the presence of normally suppressive levels of antibiotics. The mechanisms responsible for explaining these enhanced responses have yet to be discovered.

Space

The ability of microorganisms to survive in an outer space environment was investigated to approximate upper boundaries of the biosphere and to determine the accuracy of the interplanetary transport theory for microorganisms. Among the investigated variables, solar UV radiation had the most harmful effect on microbial samples. Among all the samples, only lichens (Rhizocarpon geographicum and Xanthoria elegans) fully survived the 2 weeks of exposure to outer space. Earth's ozone layer greatly protects against the deleterious effects of solar UV, which is why organisms typically are unable to survive without ozone protection. When shielded against solar UV, various samples were able to survive for long periods of times; spores of B. subtilis, for example, were able to proliferate in space for up to 6 years. The data support the likelihood of interplanetary transfer of microorganisms within meteorites, called lithopanspermia hypothesis.

Mars

Anabaena flosaquae, a cyanobacterium that would thrive on Mars Modern technology has already allowed us to use microbes to assist us in extracting materials on Earth, including over 25% of the our current copper supply. Similarly, microbes could help serve a similar purpose on other planets to mine resources, extract useful materials, or create self-sustaining reactors. The most promising of these candidates known to date is cyanobacteria. Billions of years ago, cyanobacteria originally helped us create a habitable Earth by pumping oxygen into the atmosphere, and manage to exist in the darkest corners of the Earth. Cyanobacteria, along with some other rock-eating microbes, seem to be able to withstand the harsh conditions of the vacuum of space without much effort. On Mars, however, cyanobacteria will not even have to endure such harsh conditions.

Scientists are currently working on the possibility of installing bioreactors or similar facilities on Mars, which would run entirely on cyanobacteria and provide material for the creation of fuel cells, soil crust formation, regolith amelioration, extraction of useful metals/elements, nutrient release into the soil, and dust removal; a variety of other potentially useful functions are also in the works.

Biological Agent

A Biological Agent; also called Bio-Agent, Biological Threat Agent, Biological Warfare Agent, Biological Weapon, or Bioweapon

Biological Agent is a bacterium, virus, protozoan, parasite, or fungus that can be used purposefully as a weapon in bioterrorism or biological warfare (BW). In addition to these living and/or replicating pathogens, biological toxins are also included among the bio-agents. More than 1,200 different kinds of potentially weaponizable bio-agents have been described and studied to date.

Biological agents have the ability to adversely affect human health in a variety of ways, ranging from relatively mild allergic reactions to serious medical conditions, including death. Many of these organisms are ubiquitous in the natural environment where they are found in water, soil, plants, or animals. Bio-agents may be amenable to "weaponization" to render them easier to deploy or disseminate. Genetic modification may enhance their incapacitating or lethal properties, or render them impervious to conventional treatments or preventives. Since many bio-agents reproduce rapidly and require minimal resources for propagation, they are also a potential danger in a wide variety of occupational settings.

The Biological Weapons Convention (1972) is an international treaty banning the use or stockpiling of bio-agents; it currently has 165 state signatories. Bio-agents are, however, widely studied for defensive purposes under various biosafety levels and within biocontainment facilities throughout the world. In 2008, according to a U.S. Congressional Research Service report, China, Cuba, Egypt, Iran, Israel, North Korea, Russia, Syria and Taiwan were considered, with varying degrees of certainty, to be maintaining bio-agents in an offensive BW program capacity.

Applied Microbiology :

Medical Microbiology

Medical microbiology is a branch of medicine concerned with the prevention, diagnosis and treatment of infectious diseases. In addition, this field of science studies various clinical applications of microbes for the improvement of health. There are four kinds of microorganisms that cause infectious disease: bacteria, fungi, parasites and viruses.

A Medical Microbiologist studies the characteristics of Pathogens , their modes of transmission, mechanisms of infection and growth. Using this information a treatment can be devised. Medical microbiologists often serve as consultants for physicians, providing identification of pathogens and suggesting treatment options. Other tasks may include the identification of potential health risks to the community or monitoring the evolution of potentially virulent or resistant strains of microbes, educating the community and assisting in the design of health practices. They may also assist in preventing or controlling epidemics and outbreaks of disease. Not all medical microbiologists study microbial pathology; some study common, non-pathogenic species to determine whether their properties can be used to develop antibiotics or other treatment methods.

Whilst Epidemiology is the study of the patterns, causes, and effects of health and disease conditions in populations, medical microbiology primarily focuses on the presence and growth of microbial infections in individuals, their effects on the human body and the methods of treating those infections.

Pharmaceutical Microbiology

Pharmaceutical Microbiology is an applied branch of Microbiology. It involves the study of microorganisms associated with the manufacture of pharmaceuticals e.g. minimizing the number of microorganisms in a process environment, excluding microorganisms and microbial by-products like exotoxin and endotoxin from water and other starting materials, and ensuring the finished pharmaceutical product is sterile. Other aspects of pharmaceutical microbiology include the research and development of anti-infective agents, the use of microorganisms to detect mutagenic and carcinogenic activity in prospective drugs, and the use of microorganisms in the manufacture of pharmaceutical products like insulin and human growth hormone.

Industrial Microbiology

Industrial microbiology is an area of applied microbiology which deals with screening, improvement , management,and exploitation of microorganisms for the production of various useful end products on a large scale.

Microorganisms are used in industrial processes; for example, in the production of high-value products such as drugs, chemicals, fuels and electricity.

Industrial microbiology includes the use of microorganisms to manufacture food or industrial products in large quantities. Numerous microorganisms are used within industrial microbiology; these include naturally occurring organisms, laboratory selected mutants, or even genetically modified organisms (GMOs). Currently, the debate in the use of genetically modified organisms (GMOs) in food sources is gaining both momentum, with more and more supporters on both sides. However, the use of microorganisms at an industrial level is deeply rooted into today's society. The following is a brief overview of the various microorganisms that have industrial uses, and of the roles they play.

Archaea are specific types of prokaryotic microbes that exhibit the ability to sustain populations in unusual and typically harsh environments. Those suriving in the most hostile and extreme settings are known as extremophile archaea. The isolation and identification of various types of Archaea, particularly the extremophile archaea, have allowed for analysis of their metabolic processes, which have then been manipulated and utilized for industrial purposes.

Extremophile archaea species are of particular interest due to the enzymes and molecules they produce that allow them to sustain life in extreme climates, including very high or low temperatures, extremely acid or base solutions, or when exposed to other harmful factors, including radiation. Specific enzymes which have been isolated and used for industrial purposes include thermostable DNA polymerases from the Pyrococcus furiosus. This type of polymerase isa common tool in molecular biology; it is capable of withstanding the high temperatures that are necessary to complete polymerase chain reactions. Additional enzymes isolated from Pyrococcus speciesinclude specific types of amylases and galactosidases which allow food processing to occur at high temperatrues as well.

Corynebacteria are characterized by their diverse origins. They are found in numerous ecological niches and are most often used in industry for the mass production of amino acids and nutritional factors. In particular, the amino acids produced by Corynebacterium glutamicum include the amino acid glutamic acid. Glutamic acid is used as a common additive in food production, where it is known as monosodium glutamate (MSG). Corynebacterium can also be used in steroid conversion and in the degradation of hydrocarbons. Steroid conversion is an important process in the development of pharmaceuticals. Degradation of hydrocarbons is key in the breakdown and elimination of environmental toxins. Items such as plastics and oils are hydrocarbons; the use of microorganisms which exhibit the ability to breakdown these compounds is critical for environmental protection .

Xanthomonas, a type of Proteobacteria, is known for its ability to cause disease in plants. The bacterial species which are classified under Xanthomonas exhibit the ability to produce the acidic exopolysaccharide commonly marketed as xanthan gum, used as a thickening and stabilizing agent in foods and in cosmetic ingredients to prevent separation.

Another type of microorganism utilized by industry includes various species of Aspergillus. Thisgenusincludes several hundred types of mold. Aspergillus has become a key component in industrial microbiology, where it is used in the production of alcoholic beverages and pharmaceutical development. Aspergillus niger is most commonly used to produce citric acid, which is used in numerous products ranging from household cleaners, pharmaceuticals, foods, cosmetics, photography and construction. Aspergillus is also commonly used in large-scale fermentation in the production of alcoholic beverages such as Japanese sake.

Food Microbiology

Food microbiology is the study of the microorganisms that inhabit, create, or contaminate food, including the study of microorganisms causing food spoilage. "Good" bacteria, however, such as probiotics, are becoming increasingly important in food science. In addition, microorganisms are essential for the production of foods such as cheese, yogurt, bread, beer, wine and, other fermented foods.

Food Safety

Food safety is a major focus of food microbiology. Pathogenic bacteria, viruses and toxins produced by microorganisms are all possible contaminants of food. However, microorganisms and their products can also be used to combat these pathogenic microbes. Probiotic bacteria, including those that produce bacteriocins, can kill and inhibit pathogens. Alternatively, purified bacteriocins such as nisin can be added directly to food products. Finally, bacteriophages, viruses that only infect bacteria, can be used to kill bacterial pathogens. Thorough preparation of food, including proper cooking, eliminates most bacteria and viruses. However, toxins produced by contaminants may not be liable to change to non-toxic forms by heating or cooking the contaminated food due to other safety conditions.

Fermentation

Fermentation is one of the methods to preserve food and alter its quality. Yeast, especially Saccharomyces cerevisiae, is used to leaven bread, brew beer and make wine. Certain bacteria, including lactic acid bacteria, are used to make yogurt, cheese, hot sauce, pickles, fermented sausages and dishes such as kimchi. A common effect of these fermentations is that the food product is less hospitable to other microorganisms, including pathogens and spoilage-causing microorganisms, thus extending the food's shelf-life. Some cheese varieties also require molds to ripen and develop their characteristic flavors.

Food Testing

To ensure safety of food products, microbiological tests such as testing for pathogens and spoilage organisms are required. This way the risk of contamination under normal use conditions can be examined and food poisoning outbreaks can be prevented. Testing of food products and ingredients is important along the whole supply chain as possible flaws of products can occur at every stage of production. Apart from detecting spoilage, microbiological tests can also determine germ content, identify yeasts and molds, and salmonella. For salmonella, scientists are also developing rapid and portable technologies capable of identifying unique variants of Salmonella

Polymerase Chain Reaction (PCR) is a quick and inexpensive method to generate numbers of copies of a DNA fragment at a specific band ("PCR (Polymerase Chain Reaction)," 2008). For that reason, scientists are using PCR to detect different kinds of viruses or bacteria, such as HIV and anthrax based on their unique DNA patterns. Various kits are commercially available to help in food pathogen nucleic acids extraction, PCR detection, and differentiation. The detection of bacterial strands in food products is very important to everyone in the world, for it helps prevent the occurrence of food borne illness. Therefore, PCR is recognized as a DNA detector in order to amplify and trace the presence of pathogenic strands in different processed food.

Agricultural Microbiology

Agricultural Microbiology is a branch of microbiology dealing with plant-associated microbes and plant and animal diseases. It also deals with the microbiology of soil fertility, such as microbial degradation of organic matter and soil nutrient transformations.

The study of agriculturally relevant microorganisms. This field can be further classified into the following:

1. Plant microbiology and Plant pathology
2. Soil Microbiology

Plant Microbiology

The green algae are a large group of photosynthetic eukaryotes that include many microscopic organisms. Although some green algae are classified as protists, others such as charophyta are classified with embryophyte plants, which are the most familiar group of land plants. Algae can grow as single cells, or in long chains of cells. The green algae include unicellular and colonial flagellates, usually but not always with two flagella per cell, as well as various colonial, coccoid, and filamentous forms. In the Charales, which are the algae most closely related to higher plants, cells differentiate into several distinct tissues within the organism. There are about 6000 species of green algae.

Plant Pathology

Plant Pathology (also Phytopathology) is the scientific study of plant diseases caused by pathogens (infectious organisms) and environmental conditions (physiological factors). Organisms that cause infectious disease include fungi, oomycetes, bacteria, viruses, viroids, virus-like organisms, phytoplasmas, protozoa, nematodes and parasitic plants. Not included are ectoparasites like insects, mites, vertebrate, or other pests that affect plant health by consumption of plant tissues. Plant pathology also involves the study of pathogen identification, disease etiology, disease cycles, economic impact, plant disease epidemiology, plant disease resistance, how plant diseases affect humans and animals, pathosystem genetics, and management of plant diseases.

Soil Microbiology

Soil Microbiology is the study of organisms in soil, their functions, and how they affect soil properties. It is believed that between two and four billion years ago, the first ancient bacteria and microorganisms came about in Earth's primitive seas. These bacteria could fix nitrogen, in time multiplied and as a result released oxygen into the atmosphere. This release of oxygen led to more advanced microorganisms. Microorganisms in soil are important because they affect the structure and fertility of different soils. Soil microorganisms can be classified as bacteria, actinomycetes, fungi, algae, and protozoa. Each of these groups has different characteristics that define the organisms and different functions in the soil it lives in.

Veterinary Microbiology

Veterinary Microbiology is concerned with microbial (bacterial, fungal, viral) diseases of domesticated vertebrate animals (livestock, companion animals, fur-bearing animals, game, poultry, fish) that supply food, other useful products or companionship. In addition, Microbial diseases of wild animals living in captivity, or as members of the feral fauna will also be considered if the infections are of interest because of their interrelation with humans (zoonoses) and/or domestic animals.

Veterinary microbiology and immunology entail the study of bacteria, fungi and viruses that infest animals. Those who become veterinarians may work directly with animals kept as pets, used for food production or housed in zoos. Read on to learn more.

Inside Veterinary Microbiology and Immunology

Veterinary microbiology and immunology are concerned with the range of beneficial and harmful microbial life harbored by animals and how animal immune systems cope with them. The fields synthesize concepts from bacteriology, biochemistry, cell biology, molecular genetics, mycology and virology. A variety of commercial interests depend upon their findings.

Veterinary microbiologists learn to recognize external signs of infection or animal behaviors that point to an infection. They also learn the internal and population-wide progression patterns of infectious agents, as well as measures of control and prevention. In addition, these professionals are skilled in data analysis and the use of examination equipment, such as mass spectrometry.

Environmental Microbiology

Microbial ecology (or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life Eukaryota, Archaea, and Bacteria as well as viruses.

Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine. As a consequence of the quantitative magnitude of microbial life (Whitman and coworkers calculated 5.0×1030 cells, eight orders of magnitude greater than the number of stars in the observable universe) microbes, by virtue of their biomass alone, constitute a significant carbon sink. Aside from carbon fixation, microorganisms’ key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling. The immensity of microorganisms’ production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.

1. Microbial Ecology
2. Microbially mediated nutrient cycling
3. Geomicrobiology
4. Microbial diversity
5. Bioremediation

Aquatic Microbiology

Aquatic microbiology is the science that deals with microscopic living organisms in fresh or salt water systems. While aquatic microbiology can encompass all microorganisms , including microscopic plants and animals, it more commonly refers to the study of bacteria, viruses, and fungi and their relation to other organisms in the aquatic environment .

Veterinary microbiology and immunology entail the study of bacteria, fungi and viruses that infest animals. Those who become veterinarians may work directly with animals kept as pets, used for food production or housed in zoos. Read on to learn more.

Bacteria are quite diverse in nature . The scientific classification of bacteria divides them into 19 major groups based on their shape, cell structure, staining properties (used in the laboratory for identification), and metabolic functions. Bacteria occur in many sizes as well ranging from 0.1 micrometer to greater than 500 micrometers. Some are motile and have flagella, which are tail-like structures used for movement.

Although soil is the most common habitat of fungi, they are also found in aquatic environments. Aquatic fungi are collectively called water molds or aquatic Phycomycetes. They are found on the surface of decaying plant and animal matter in ponds and streams. Some fungi are parasitic and prey on algae and protozoa.

Viruses are the smallest group of microorganisms and usually are viewed only with the aid of an electron microscope. They are disease-causing organisms that are very different than bacteria, fungi, and other cellular life-forms. Viruses are infectious nucleic acid enclosed within a coat of protein. They penetrate host cells and use the nucleic acid of other cells to replicate.

Bacteria, viruses, and fungi are widely distributed throughout aquatic environments. They can be found in fresh water rivers, lakes, and streams, in the surface waters and sediments of the world's oceans, and even in hot springs. They have even been found supporting diverse communities at hydrothermal vents in the depths of the oceans.

Microorganisms living in these diverse environments must deal with a wide range of physical conditions, and each has specific adaptations to live in the particular place it calls home. For example, some have adapted to live in fresh waters with very low salinity , while others live in the saltiest parts of the ocean. Some must deal with the harsh cold of arctic waters, while those in hot springs are subjected to intense heat. In addition, aquatic microorganisms can be found living in environments where there are extremes in other physical parameters such as pressure, sunlight, organic substances, dissolved gases, and water clarity.

Aquatic microorganisms obtain nutrition in a variety of ways. For example, some bacteria living near the surface of either fresh or marine waters, where there is often abundant sunlight, are able to produce their own food through the process of photosynthesis . Bacteria living at hydrothermal vents on the ocean floor where there is no sunlight can produce their own food through a process known as chemosynthesis , which depends on preformed organic carbon as an energy source. Many other microorganisms are not able to produce their own food. Rather, they obtain necessary nutrition from the breakdown of organic matter such as dead organisms.

Aquatic microorganisms play a vital role in the cycling of nutrients within their environment, and thus are a crucial part of the food chain/web . Many microorganisms obtain their nutrition by breaking down organic matter in dead plants and animals. As a result of this process of decay, nutrients are released in a form usable by plants. These aquatic microorganisms are especially important in the cycling of the nutrients nitrogen , phosphorus , and carbon. Without this recycling , plants would have few, if any, organic nutrients to use for growth.

In addition to breaking down organic matter and recycling it into a form of nutrients that plants can use, many of the microorganisms become food themselves. There are many types of animals that graze on bacteria and fungi. For example, some deposit-feeding marine worms ingest sediments and digest numerous bacteria and fungi found there, later expelling the indigestible sediments. Therefore, these microorganisms are intimate members of the food web in at least two ways.

Humans have taken advantage of the role these microorganisms play in nutrient cycles. At sewage treatment plants, microscopic bacteria are cultured and then used to break down human wastes. However, in addition to the beneficial uses of some aquatic microorganisms, others may cause problems for people because they are pathogens, which can cause serious diseases. For example, viruses such as Salmonella typhi, S. paratyphi, and the Norwalk virus are found in water contaminated by sewage can cause illness. Fecal coliform (E. coli ) bacteria and Enterococcus bacteria are two types of microorganisms that are used to indicate the presence of disease causing microorganisms in aquatic environments.

Aeromicrobiology

Aeromicrobiology is the study of living microbes which are suspended in the air. These microbes are referred to as bioaerosols (Brandl et. al, 2008). Though there are significantly less atmospheric microorganisms than there are in oceans and in soil, there is still a large enough number that they can affect the atmosphere (Amato, 2012). Once suspended in the air column, these microbes have the opportunity to travel long distances with the help of wind and precipitation, increasing the occurrence of widespread disease by these microorganisms. These aerosols are ecologically significant because they can be associated with disease in humans, animals and plants. Typically microbes will be suspended in clouds, where they are able to perform processes that alter the chemical composition of the cloud, and may even induce precipitation.

Physical Environment

There are many factors within the physical environment that affect the launching, transport and deposition of bioaerosols. Particles which become suspended in the air column arise mainly from terrestrial and aquatic environments and are typically launched by air turbulence (Pepper 2011). Winds are the primary means of transport for bioaerosols. Bioaerosols can be deposited by a number of mechanisms, including gravity pulling them down, making contact with surfaces, or combining with rain which pulls the particles back down to earth's surface.

Atmosphere

Along with water droplets, dust particles and other matter, air contains microbes (Al-Dagal 1990). Microbes follow a particular pathway in which they are suspended into the atmosphere. First they are launched into the air. The source of the launching of airborne microbes stems from humans, animals and vegetation. (Al-Dagal 1990). then they are transported (by various methods including winds, machinery and people) and finally are deposited somewhere new. The atmosphere can have a variety of physical characteristics, and can be very extreme in terms of the relative humidity, temperature and radiation. These factors play a huge role in what kinds of microbes will survive in the atmosphere and how long they will stay alive.

Clouds

One area that bioaerosols can be found in is within clouds. Cloud water is a mixture of organic and inorganic compounds suspended within moisture (contribution of microbial activity yo clouds). The conditions in clouds are not conducive to much life, as microbes present there must withstand freezing temperatures, the threat of desiccation, and extreme UV rays. Clouds are also an acidic environment, with a pH ranging from 3 to 7. Nevertheless, there are extremophile microbes which can withstand all of these environmental pressures. Clouds serve as a transport for these microbes, dispersing them over long distances .

Physical Environment Stresses

The atmosphere is a difficult place for a microbe to survive. Dessication is the primary stress that aeromicrobes face, and it limits the amount of time that they can survive while suspended in the air (Pepper 2011). Humidity within the air is a second factor which can affect the survival of organisms. Certain bacteria, including Gram + bacteria, are more tolerant of high humidity in the air, while others are more tolerant of dessication and dry conditions, such as Gram + cells (Pepper 2011). Temperature must be in an intermediate range, as too hot of temperatures can denature proteins, and too cold of temperatures can cause ice crystal formation (Pepper 2011). Finally, radiation poses a potential hazard for aeromicrobes, as it can damage DNA within the cells.

Microbial Communities

Many different microorganisms can be in aerosol form in the atmosphere, including viruses, bacteria, fungi, yeasts and protozoans. In order to survive in the atmosphere, it is important that these microbes adapt to some of the harsh climatic characteristics of the exterior world, including temperature, gasses and humidity. Many of the microbes that are capable of surviving harsh conditions can readily form endospores, which can withstand extreme conditions (Al-Dagal 336).

Many of these microorganisms can be associated with specific and commonly known diseases. Below are two tables. Table 1 below shows examples of Airborne Plant pathogens, and Table 2 shows examples of airborne human pathogens.

Bacterial

One such bacterial microorganism that can resist environmental stresses is Bacillus anthracis. It is a gram positive rod shaped bacteria that utilizes spore formation to resist environmental stresses. The spore is a dehydrated cell with extremely thick cell walls which can remain inactive for many years. This spore makes Bacillus anthracis a highly resilient bacteria, allowing it can survive extreme temperatures, chemical contamination, and low nutrient environments (Gatchalian 2010). This bacteria is associated with Anthrax, which is a severe respiratory disease that infects humans.

Fungal

Another such microorganism that can resist environmental stresses is Aspergillus fumigatus, which is a major airborne fungal pathogen (McCormick 2010). This pathogen is capable of causing many human diseases when conidia are inhaled into the lungs. While A. fumigatus lacks virulence traits, it is very adaptable to changing environmental conditions and therefore is still capable of mass infection.

(McCormick 2010).

Viral

An example of a viral airborne pathogen is the Avian Influenza Virus, which is a single stranded RNA visur that can infect a broad range of animal species as well as humans and cause the Avian Influenza.

Microbial Processes

The figure on the bottom right depicts the processes that a microbe undergoes during its life cycle. The microbes undergo the emission process, in which they are emitted from surfaces such as water, soil or vegetation and become airborne and transported into the airstream.

Table 1: Examples of Airborne Plant Pathogens. Table from Maier, chapter 5

The red boxes indicate some of the harsh environmental conditions that the microbes must withstand while airborne. The microbes that are able to withstand and survive these environmental pressures are the more resistant varieties. The microbes make it into clouds, where they can begin the breakdown of organic compounds. Finally, the microbes are "rained" out of the clouds through wet deposition, and they begin colonization of their new location (Amato 2012).

Droplet Formation

The emission process mentioned above, in which microbes are lifted in the air often involves microbes being suspended in droplets, which are large enough to keep the microbes hydrated and large enough to maintain a virulent amount of pathogen, but are still small enough to stay suspended in the air (Robinson 2012).

Advantage of Microbiology :

While some fear microbes due to the association of some microbes with various human illnesses, many microbes are also responsible for numerous beneficial processes such as industrial fermentation (e.g. the production of alcohol, vinegar and dairy products), antibiotic production and as vehicles for cloning in more complex organisms such as plants. Scientists have also exploited their knowledge of microbes to produce biotechnologically important enzymes such as Taq polymerase, reporter genes for use in other genetic systems and novel molecular biology techniques such as the yeast two-hybrid system.

Bacteria can be used for the industrial production of amino acids. Corynebacterium glutamicum is one of the most important bacterial species with an annual production of more than two million tons of amino acids, mainly L-glutamate and L-lysine.

A variety of biopolymers, such as polysaccharides, polyesters, and polyamides, are produced by microorganisms. Microorganisms are used for the biotechnological production of biopolymers with tailored properties suitable for high-value medical application such as tissue engineering and drug delivery. Microorganisms are used for the biosynthesis of xanthan, alginate, cellulose, cyanophycin, poly(gamma-glutamic acid), levan, hyaluronic acid, organic acids, oligosaccharides and polysaccharide, and polyhydroxyalkanoates.

Microorganisms are beneficial for microbial biodegradation or bioremediation of domestic, agricultural and industrial wastes and subsurface pollution in soils, sediments and marine environments. The ability of each microorganism to degrade toxic waste depends on the nature of each contaminant. Since sites typically have multiple pollutant types, the most effective approach to microbial biodegradation is to use a mixture of bacterial and fungal species and strains, each specific to the biodegradation of one or more types of contaminants.

Symbiotic microbial communities are known to confer various benefits to their human and animal hosts’ health including aiding digestion, production of beneficial vitamins and amino acids, and suppression of pathogenic microbes. Some benefit may be conferred by consuming fermented foods, probiotics (bacteria potentially beneficial to the digestive system) and/or prebiotics (substances consumed to promote the growth of probiotic microorganisms). The ways the microbiome influences human and animal health, as well as methods to influence the microbiome are active areas of research.

Research has suggested that microorganisms could be useful in the treatment of cancer. Various strains of non-pathogenic clostridia can infiltrate and replicate within solid tumors. Clostridial vectors can be safely administered and their potential to deliver therapeutic proteins has been demonstrated in a variety of preclinical models.

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