Microbiology is the study of microorganisms, those being unicellular, multicellular, or acellular. Microbiology encompasses numerous sub-disciplines including virology, parasitology and bacteriology. Eukaryotic microorganisms possess membrane-bound cell organelles and include fungi and protists, whereas prokaryotic organisms—all of which are microorganisms—are conventionally classified as lacking membrane-bound organelles and include Bacteria and Archaea. Microbiologists traditionally relied on culture and microscopy. However, less than 1% of the microorganisms present in common environments can be cultured in isolation using current means. Microbiologists rely on molecular biology tools such as DNA sequence based identification, for example 16s rRNA gene sequence used for bacteria identification. Viruses have been variably classified as organisms, as they have been considered either as simple microorganisms or complex molecules. Prions, never considered as microorganisms, have been investigated by virologists, however, as the clinical effects traced to them were presumed due to chronic viral infections, virologists took search—discovering "infectious proteins".
The existence of microorganisms was predicted many centuries before they were first observed, for example by the Jains in India and by Marcus Terentius Varro in ancient Rome. The first recorded microscope observation was of the fruiting bodies of moulds, by Robert Hooke in 1666, but the Jesuit priest Athanasius Kircher was the first to see microbes, which he mentioned observing in milk and putrid material in 1658. Antonie van Leeuwenhoek is considered a father of microbiology as he observed and experimented with microscopic organisms in 1676, using simple microscopes of his own design. Scientific microbiology developed in the 19th century through the work of Louis Pasteur and in medical microbiology Robert Koch; the existence of microorganisms was hypothesized for many centuries before their actual discovery. The existence of unseen microbiological life was postulated by Jainism, based on Mahavira’s teachings as early as 6th century BCE. Paul Dundas notes that Mahavira asserted the existence of unseen microbiological creatures living in earth, water and fire.
Jain scriptures describe nigodas which are sub-microscopic creatures living in large clusters and having a short life, said to pervade every part of the universe 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 thereby cause serious diseases."In the golden age of Islamic civilization, Iranian scientists hypothesized the existence of microorganisms, such as Avicenna in his book The Canon of Medicine, Ibn Zuhr who discovered scabies mites, Al-Razi who gave the earliest known description of smallpox in his book The Virtuous Life. 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.
In 1676, Antonie van Leeuwenhoek, who lived most of his life in Delft, observed bacteria and other microorganisms using a single-lens microscope of his own design. He is considered a father of microbiology as he pioneered the use of simple single-lensed microscopes of his own design. While Van Leeuwenhoek is cited as the first to observe microbes, Robert Hooke made his first recorded microscopic observation, of the fruiting bodies of moulds, in 1665, it has, been suggested that a Jesuit priest called Athanasius Kircher was the first to observe microorganisms. Kircher was among the first to design magic lanterns for projection purposes, so he must have been well acquainted with the properties of lenses, he wrote "Concerning the wonderful structure of things in nature, investigated by Microscope" in 1646, stating "who would believe that vinegar and milk abound with an innumerable multitude of worms." He noted that putrid material is full of innumerable creeping animalcules. He published his Scrutinium Pestis in 1658, stating that the disease was caused by microbes, though what he saw was most red or white blood cells rather than the plague agent itself.
The field of bacteriology 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 the first to formulate a scheme for the taxonomic classification of bacteria, to discover endospores. Louis Pasteur and Robert Koch were contemporaries of Cohn, are considered to be the father of microbiology and medical microbiology, respectively. Pasteur is most famous for his series of experiments designed to disprove the widely held theory of spontaneous generation, thereby solidifying microbiology's identity as a biological science. One of his students, Adrien Certes, is considered the founder of marine microbiology. Pasteur designed methods for food preservation 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 microorganisms.
He developed a series of criteria. Koch was one of the first scientists to focus on the i
Catalase is a common enzyme found in nearly all living organisms exposed to oxygen. It catalyzes the decomposition of hydrogen peroxide to oxygen, it is a important enzyme in protecting the cell from oxidative damage by reactive oxygen species. Catalase has one of the highest turnover numbers of all enzymes. Catalase is a tetramer of each over 500 amino acids long, it contains four iron-containing heme groups that allow the enzyme to react with the hydrogen peroxide. The optimum pH for human catalase is 7, has a broad maximum: the rate of reaction does not change appreciably between pH 6.8 and 7.5. The pH optimum for other catalases varies between 11 depending on the species; the optimum temperature varies by species. Human catalase forms a tetramer composed of four subunits, each of which can be conceptually divided into four domains; the extensive core of each subunit is generated by an eight-stranded antiparallel b-barrel, with nearest neighbor connectivity capped by b-barrel loops on one side and a9 loops on the other.
A helical domain at one face of the b-barrel is composed of four C-terminal helices and four helices derived from residues between b4 and b5. Alternative splicing may result in different protein variants. Catalase was not noticed until 1818 when Louis Jacques Thénard, who discovered H2O2, suggested its breakdown is caused by an unknown substance. In 1900, Oscar Loew was the first to give it the name catalase, found it in many plants and animals. In 1937 catalase from beef liver was crystallised by James B. Sumner and Alexander Dounce and the molecular weight was found in 1938; the amino acid sequence of bovine catalase was determined in 1969, the three-dimensional structure in 1981. 2 H2O2 → 2 H2O + O2The presence of catalase in a microbial or tissue sample can be demonstrated by adding hydrogen peroxide and observing the reaction. The production of oxygen can be seen by the formation of bubbles; this easy test, which can be seen with the naked eye, without the aid of instruments, is possible because catalase has a high specific activity, which produces a detectable response, as well as the fact that one of the products is a gas.
While the complete mechanism of catalase is not known, the reaction is believed to occur in two stages: H2O2 + Fe-E → H2O + O=Fe-EH2O2 + O=Fe-E → H2O + Fe-E + O2Here Fe-E represents the iron center of the heme group attached to the enzyme. Fe-E is a mesomeric form of Fe-E, meaning the iron is not oxidized to +V, but receives some stabilising electron density from the heme ligand, shown as a radical cation; as hydrogen peroxide enters the active site, it interacts with the amino acids Asn148 and His75, causing a proton to transfer between the oxygen atoms. The free oxygen atom coordinates, freeing the newly formed water molecule and Fe=O. Fe =O reacts with a second hydrogen peroxide molecule to produce water and oxygen; the reactivity of the iron center may be improved by the presence of the phenolate ligand of Tyr358 in the fifth coordination position, which can assist in the oxidation of the Fe to Fe. The efficiency of the reaction may be improved by the interactions of His75 and Asn148 with reaction intermediates.
In general, the rate of the reaction can be determined by the Michaelis-Menten equation. Catalase can catalyze the oxidation, by hydrogen peroxide, of various metabolites and toxins, including formaldehyde, formic acid, phenols and alcohols, it does so according to the following reaction: H2O2 + H2R → 2H2O + RThe exact mechanism of this reaction is not known. Any heavy metal ion can act as a noncompetitive inhibitor of catalase. Furthermore, the poison cyanide is a noncompetitive inhibitor of catalase at high concentrations of hydrogen peroxide. Arsenate acts as an activator. Three-dimensional protein structures of the peroxidated catalase intermediates are available at the Protein Data Bank. Hydrogen peroxide is a harmful byproduct of many normal metabolic processes. To this end, catalase is used by cells to catalyze the decomposition of hydrogen peroxide into less-reactive gaseous oxygen and water molecules. Mice genetically engineered to lack catalase are phenotypically normal. However, catalase deficiency in mice may increase the likelihood of developing obesity, fatty liver, type 2 diabetes.
Some humans have low levels of catalase, yet show few ill effects. The increased oxidative stress that occurs with aging in mice is alleviated by over-expression of catalase. Over-expressing mice do not exhibit the age-associated loss of spermatozoa, testicular germ and Sertoli cells seen in wild-type mice. Oxidative stress in wild-type mice ordinarily induces oxidative DNA damage in sperm with aging, but these damages are reduced in aged catalase over-expressing mice. Furthermore, these over-expressing mice show no decrease in age-dependent number of pups per litter. Overexpression of catalase targeted to mitochondria extends the lifespan of mice. Catalase is located in a cellular organelle called the peroxisome. Peroxisomes in plant cells are involved in photorespiration and symbiotic nitrogen fixation (the breaking apart of diatomic nitrog
Redox is a chemical reaction in which the oxidation states of atoms are changed. Any such reaction involves both a reduction process and a complementary oxidation process, two key concepts involved with electron transfer processes. Redox reactions include all chemical reactions; the chemical species from which the electron is stripped is said to have been oxidized, while the chemical species to which the electron is added is said to have been reduced. It can be explained in simple terms: Oxidation is the loss of electrons or an increase in oxidation state by a molecule, atom, or ion. Reduction is a decrease in oxidation state by a molecule, atom, or ion; as an example, during the combustion of wood, oxygen from the air is reduced, gaining electrons from carbon, oxidized. Although oxidation reactions are associated with the formation of oxides from oxygen molecules, oxygen is not included in such reactions, as other chemical species can serve the same function; the reaction can occur slowly, as with the formation of rust, or more in the case of fire.
There are simple redox processes, such as the oxidation of carbon to yield carbon dioxide or the reduction of carbon by hydrogen to yield methane, more complex processes such as the oxidation of glucose in the human body. "Redox" is a portmanteau of the words "reduction" and "oxidation". The word oxidation implied reaction with oxygen to form an oxide, since dioxygen was the first recognized oxidizing agent; the term was expanded to encompass oxygen-like substances that accomplished parallel chemical reactions. The meaning was generalized to include all processes involving loss of electrons; the word reduction referred to the loss in weight upon heating a metallic ore such as a metal oxide to extract the metal. In other words, ore was "reduced" to metal. Antoine Lavoisier showed. Scientists realized that the metal atom gains electrons in this process; the meaning of reduction became generalized to include all processes involving a gain of electrons. Though "reduction" seems counter-intuitive when speaking of the gain of electrons, it might help to think of reduction as the loss of oxygen, its historical meaning.
Since electrons are negatively charged, it is helpful to think of this as reduction in electrical charge. The electrochemist John Bockris has used the words electronation and deelectronation to describe reduction and oxidation processes when they occur at electrodes; these words are analogous to protonation and deprotonation, but they have not been adopted by chemists worldwide. The term "hydrogenation" could be used instead of reduction, since hydrogen is the reducing agent in a large number of reactions in organic chemistry and biochemistry. But, unlike oxidation, generalized beyond its root element, hydrogenation has maintained its specific connection to reactions that add hydrogen to another substance; the word "redox" was first used in 1928. The processes of oxidation and reduction occur and cannot happen independently of one another, similar to the acid–base reaction; the oxidation alone and the reduction alone are each called a half-reaction, because two half-reactions always occur together to form a whole reaction.
When writing half-reactions, the gained or lost electrons are included explicitly in order that the half-reaction be balanced with respect to electric charge. Though sufficient for many purposes, these general descriptions are not correct. Although oxidation and reduction properly refer to a change in oxidation state — the actual transfer of electrons may never occur; the oxidation state of an atom is the fictitious charge that an atom would have if all bonds between atoms of different elements were 100% ionic. Thus, oxidation is best defined as an increase in oxidation state, reduction as a decrease in oxidation state. In practice, the transfer of electrons will always cause a change in oxidation state, but there are many reactions that are classed as "redox" though no electron transfer occurs. In redox processes, the reductant transfers electrons to the oxidant. Thus, in the reaction, the reductant or reducing agent loses electrons and is oxidized, the oxidant or oxidizing agent gains electrons and is reduced.
The pair of an oxidizing and reducing agent that are involved in a particular reaction is called a redox pair. A redox couple is a reducing species and its corresponding oxidizing form, e.g. Fe2+/Fe3+ Substances that have the ability to oxidize other substances are said to be oxidative or oxidizing and are known as oxidizing agents, oxidants, or oxidizers; that is, the oxidant removes electrons from another substance, is thus itself reduced. And, because it "accepts" electrons, the oxidizing agent is called an electron acceptor. Oxygen is the quintessential oxidizer. Oxidants are chemical substances with elements in high oxidation states, or else electronegative elements that can gain extra electrons by oxidizing another substance. Substances that have the ability to reduce other substances are said to be reductive or reducing and are known as
The Enterobacteriaceae are a large family of Gram-negative bacteria. This family is the only representative in the order Enterobacteriales of the class Gammaproteobacteria in the phylum Proteobacteria. Enterobacteriaceae includes, along with many harmless symbionts, many of the more familiar pathogens, such as Salmonella, Escherichia coli, Yersinia pestis and Shigella. Other disease-causing bacteria in this family include Proteus, Enterobacter and Citrobacter. Phylogenetically, in the Enterobacteriales, several peptidoglycan-less insect endosymbionts form a sister clade to the Enterobacteriaceae, but as they are not validly described, this group is not a taxon. Members of the Enterobacteriaceae can be trivially referred to as enterobacteria or "enteric bacteria", as several members live in the intestines of animals. In fact, the etymology of the family is enterobacterium with the suffix to designate a family —not after the genus Enterobacter —and the type genus is Escherichia. Members of the Enterobacteriaceae are bacilli, are 1–5 μm in length.
They appear as medium to large-sized grey colonies on blood agar, although some can express pigments. Most have many flagella used to move about. Most members of Enterobacteriaceae have peritrichous, type I fimbriae involved in the adhesion of the bacterial cells to their hosts, they are not spore-forming. Like other proteobacteria, enterobactericeae have Gram-negative stains, they are facultative anaerobes, fermenting sugars to produce lactic acid and various other end products. Most reduce nitrate to nitrite, although exceptions exist. Unlike most similar bacteria, enterobacteriaceae lack cytochrome C oxidase, although there are exceptions. Catalase reactions vary among Enterobacteriaceae. Many members of this family are normal members of the gut microbiota in humans and other animals, while others are found in water or soil, or are parasites on a variety of different animals and plants. Escherichia coli is one of the most important model organisms, its genetics and biochemistry have been studied.
Some enterobacteria are important pathogens, e.g. Salmonella, Shigella, or Yersinia, e.g. because they produce endotoxins. Endotoxins reside in the cell wall and are released when the cell dies and the cell wall disintegrates; some members of the Enterobacteriaceae produce endotoxins that, when released into the bloodstream following cell lysis, cause a systemic inflammatory and vasodilatory response. The most severe form of this is known as endotoxic shock, which can be fatal. To identify different genera of Enterobacteriaceae, a microbiologist may run a series of tests in the lab; these include: Phenol red Tryptone broth Phenylalanine agar for detection of production of deaminase, which converts phenylalanine to phenylpyruvic acid Methyl red or Voges-Proskauer tests depend on the digestion of glucose. The methyl red tests for acid endproducts; the Voges Proskauer tests for the production of acetylmethylcarbinol. Catalase test on nutrient agar tests for the production of enzyme catalase, which splits hydrogen peroxide and releases oxygen gas.
Oxidase test on nutrient agar tests for the production of the enzyme oxidase, which reacts with an aromatic amine to produce a purple color. Nutrient gelatin tests to detect activity of the enzyme gelatinase. In a clinical setting, three species make up 80 to 95% of all isolates identified; these are Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis. Several Enterobacteriaceae strains have been isolated which are resistant to antibiotics including carbapenems, which are claimed as "the last line of antibiotic defense" against resistant organisms. For instance, some Klebsiella pneumoniae strains are carbapenem resistant. Enterobacteriaceae genomes and related information at PATRIC, a Bioinformatics Resource Center funded by NIAID Evaluation of new computer-enhanced identification program for microorganisms: adaptation of BioBASE for identification of members of the family Enterobacteriaceae Brown, A. E.. Benson's microbiological applications: laboratory manual in general microbiology. New York: McGraw- Hill
Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the gram-staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall sandwiched between an inner cytoplasmic cell membrane and a bacterial outer membrane. Gram-negative bacteria are found everywhere, in all environments on Earth that support life; the gram-negative bacteria include the model organism Escherichia coli, as well as many pathogenic bacteria, such as Pseudomonas aeruginosa, Neisseria gonorrhoeae, Chlamydia trachomatis, Yersinia pestis. They are an important medical challenge, as their outer membrane protects them from many antibiotics. Additionally, the outer leaflet of this membrane comprises a complex lipopolysaccharide whose lipid A component can cause a toxic reaction when these bacteria are lysed by immune cells; this toxic reaction can include fever, an increased respiratory rate, low blood pressure — a life-threatening condition known as septic shock.
Several classes of antibiotics have been designed to target gram-negative bacteria, including aminopenicillins, ureidopenicillins, beta-lactam-betalactamase combinations, Folate antagonists and carbapenems. Many of these antibiotics cover gram positive organisms; the drugs that target gram negative organisms include aminoglycosides and Ciprofloxacin. Gram-negative bacteria display these characteristics: An inner cell membrane is present A thin peptidoglycan layer is present Has outer membrane containing lipopolysaccharides in its outer leaflet and phospholipids in the inner leaflet Porins exist in the outer membrane, which act like pores for particular molecules Between the outer membrane and the cytoplasmic membrane there is a space filled with a concentrated gel-like substance called periplasm The S-layer is directly attached to the outer membrane rather than to the peptidoglycan If present, flagella have four supporting rings instead of two Teichoic acids or lipoteichoic acids are absent Lipoproteins are attached to the polysaccharide backbone Some contain Braun's lipoprotein, which serves as a link between the outer membrane and the peptidoglycan chain by a covalent bond Most, with few exceptions, do not form spores Along with cell shape, gram-staining is a rapid diagnostic tool and once was used to group species at the subdivision of Bacteria.
The kingdom Monera was divided into four divisions based on gram-staining: Firmacutes, Gracillicutes and Mendocutes. Since 1987, the monophyly of the gram-negative bacteria has been disproven with molecular studies; however some authors, such as Cavalier-Smith still treat them as a monophyletic taxon and refer to the group as a subkingdom "Negibacteria". Bacteria are traditionally classified based on their gram-staining response into the gram-positive and gram-negative groups, it was traditionally thought that the groups represent lineages, i.e. the extra membrane only evoved once, such that gram-negative bacteria are more related to one another than to any gram-positive bacteria. While this is true, the classification system breaks down in some cases, with lineage groupings not matching the staining result. Thus, gram-staining cannot be reliably used to assess familial relationships of bacteria. Staining gives reliable information about the composition of the cell membrane, distinguishing between the presence or absence of an outer lipid membrane.
Of these two structurally distinct groups of prokaryotic organisms, monoderm prokaryotes are thought to be ancestral. Based upon a number of different observations including that the gram-positive bacteria are the major reactors to antibiotics and that gram-negative bacteria are, in general, resistant to them, it has been proposed that the outer cell membrane in gram-negative bacteria evolved as a protective mechanism against antibiotic selection pressure; some bacteria such as Deinococcus, which stain gram-positive due to the presence of a thick peptidoglycan layer, but possess an outer cell membrane are suggested as intermediates in the transition between monoderm and diderm bacteria. The diderm bacteria can be further differentiated between simple diderms lacking lipopolysaccharide; the conventional LPS-diderm group of gram-negative bacteria are uniquely identified by a few conserved signature indel in the HSP60 protein. In addition, a number of bacterial taxa that are either part of the phylum Firmicutes or branches in its proximity are found to possess a diderm cell structure.
They lack the GroEL signature. The presence of this CSI in all se
Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group on the periodic table, a reactive nonmetal, an oxidizing agent that forms oxides with most elements as well as with other compounds. By mass, oxygen is the third-most abundant element in the universe, after helium. At standard temperature and pressure, two atoms of the element bind to form dioxygen, a colorless and odorless diatomic gas with the formula O2. Diatomic oxygen gas constitutes 20.8% of the Earth's atmosphere. As compounds including oxides, the element makes up half of the Earth's crust. Dioxygen is used in cellular respiration and many major classes of organic molecules in living organisms contain oxygen, such as proteins, nucleic acids and fats, as do the major constituent inorganic compounds of animal shells and bone. Most of the mass of living organisms is oxygen as a component of water, the major constituent of lifeforms. Oxygen is continuously replenished in Earth's atmosphere by photosynthesis, which uses the energy of sunlight to produce oxygen from water and carbon dioxide.
Oxygen is too chemically reactive to remain a free element in air without being continuously replenished by the photosynthetic action of living organisms. Another form of oxygen, ozone absorbs ultraviolet UVB radiation and the high-altitude ozone layer helps protect the biosphere from ultraviolet radiation. However, ozone present at the surface is a byproduct of thus a pollutant. Oxygen was isolated by Michael Sendivogius before 1604, but it is believed that the element was discovered independently by Carl Wilhelm Scheele, in Uppsala, in 1773 or earlier, Joseph Priestley in Wiltshire, in 1774. Priority is given for Priestley because his work was published first. Priestley, called oxygen "dephlogisticated air", did not recognize it as a chemical element; the name oxygen was coined in 1777 by Antoine Lavoisier, who first recognized oxygen as a chemical element and characterized the role it plays in combustion. Common uses of oxygen include production of steel and textiles, brazing and cutting of steels and other metals, rocket propellant, oxygen therapy, life support systems in aircraft, submarines and diving.
One of the first known experiments on the relationship between combustion and air was conducted by the 2nd century BCE Greek writer on mechanics, Philo of Byzantium. In his work Pneumatica, Philo observed that inverting a vessel over a burning candle and surrounding the vessel's neck with water resulted in some water rising into the neck. Philo incorrectly surmised that parts of the air in the vessel were converted into the classical element fire and thus were able to escape through pores in the glass. Many centuries Leonardo da Vinci built on Philo's work by observing that a portion of air is consumed during combustion and respiration. In the late 17th century, Robert Boyle proved. English chemist John Mayow refined this work by showing that fire requires only a part of air that he called spiritus nitroaereus. In one experiment, he found that placing either a mouse or a lit candle in a closed container over water caused the water to rise and replace one-fourteenth of the air's volume before extinguishing the subjects.
From this he surmised that nitroaereus is consumed in both combustion. Mayow observed that antimony increased in weight when heated, inferred that the nitroaereus must have combined with it, he thought that the lungs separate nitroaereus from air and pass it into the blood and that animal heat and muscle movement result from the reaction of nitroaereus with certain substances in the body. Accounts of these and other experiments and ideas were published in 1668 in his work Tractatus duo in the tract "De respiratione". Robert Hooke, Ole Borch, Mikhail Lomonosov, Pierre Bayen all produced oxygen in experiments in the 17th and the 18th century but none of them recognized it as a chemical element; this may have been in part due to the prevalence of the philosophy of combustion and corrosion called the phlogiston theory, the favored explanation of those processes. Established in 1667 by the German alchemist J. J. Becher, modified by the chemist Georg Ernst Stahl by 1731, phlogiston theory stated that all combustible materials were made of two parts.
One part, called phlogiston, was given off when the substance containing it was burned, while the dephlogisticated part was thought to be its true form, or calx. Combustible materials that leave little residue, such as wood or coal, were thought to be made of phlogiston. Air did not play a role in phlogiston theory, nor were any initial quantitative experiments conducted to test the idea. Polish alchemist and physician Michael Sendivogius in his work De Lapide Philosophorum Tractatus duodecim e naturae fonte et manuali experientia depromti described a substance contained in air, referring to it as'cibus vitae', this substance is identical with oxygen. Sendivogius, during his experiments performed between 1598 and 1604, properly recognized that the substance is equivalent to the gaseous byproduct released by the thermal decomposition of potassium nitrate. In Bugaj’s view, the isolation of oxygen and the proper association of the substance to that part of air, required for life, lends sufficient weight to the discovery of oxygen by Sendivogius.