1.
Burkholderia pseudomallei
–
Burkholderia pseudomallei is a Gram-negative, bipolar, aerobic, motile rod-shaped bacterium. It is a soil-dwelling bacterium endemic in tropical and subtropical regions worldwide, particularly in Thailand and it infects humans and animals and causes the disease melioidosis. It is also capable of infecting plants, B. pseudomallei measures 2–5 μm in length and 0. 4–0.8 μm in diameter and is capable of self-propulsion using flagella. The bacteria can grow in a number of artificial nutrient environments, especially betaine-, in vitro, optimal proliferation temperature is reported around 40 °C in neutral or slightly acidic environments. The majority of strains are capable of fermentation of sugars without gas formation, bacteria produce both exo- and endotoxins. The role of the toxins identified in the process of melioidosis symptom development has not been fully elucidated, B. pseudomallei is not fastidious and grows on a large variety of culture media. Ashdowns medium may be used for selective isolation, cultures typically become positive in 24 to 48 hours. Colonies are wrinkled, have an appearance, and possess an earthy odour. On Gram staining, the organism is a Gram-negative rod with a safety pin appearance. On sensitivity testing, the organism appears highly resistant and that again differentiates it from B. mallei, for environmental specimens only, differentiation from the nonpathogenic B. thailandensis using an arabinose test is necessary. The laboratory identification of B. pseudomallei has been described in the literature, some suggest the Wayson stain is useful for this purpose, but this has been shown not to be the case. Laboratory identification of B. pseudomallei can be difficult, especially in Western countries where it is rarely seen, the large, wrinkled colonies look like environmental contaminants, so are often discarded as being of no clinical significance. Colony morphology is variable and a single strain may display multiple colony types. The organism grows more slowly than other bacteria that may be present in clinical specimens, nonsterile specimens should, therefore, be cultured in selective media. For heavily contaminated samples, such as faeces, a version of Ashdowns that includes norfloxacin, amoxicillin. In blood culture, the BacT/ALERT MB system by bioMérieux has been shown to have superior yields compared to conventional blood culture media. Again, because the disease is seen in Western countries. The pattern of resistance to antimicrobials is distinctive, and helps to differentiate the organism from P. aeruginosa, molecular methods of diagnosis are possible, but not routinely available for clinical diagnosis
Burkholderia pseudomallei
–
Burkholderia pseudomallei
2.
Taxonomy (biology)
–
Taxonomy is the science of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. The exact definition of taxonomy varies from source to source, but the core of the remains, the conception, naming. There is some disagreement as to whether biological nomenclature is considered a part of taxonomy, the broadest meaning of taxonomy is used here. The word taxonomy was introduced in 1813 by Candolle, in his Théorie élémentaire de la botanique, the term alpha taxonomy is primarily used today to refer to the discipline of finding, describing, and naming taxa, particularly species. In earlier literature, the term had a different meaning, referring to morphological taxonomy, ideals can, it may be said, never be completely realized. They have, however, a value of acting as permanent stimulants. Some of us please ourselves by thinking we are now groping in a beta taxonomy, turrill thus explicitly excludes from alpha taxonomy various areas of study that he includes within taxonomy as a whole, such as ecology, physiology, genetics, and cytology. He further excludes phylogenetic reconstruction from alpha taxonomy, thus, Ernst Mayr in 1968 defined beta taxonomy as the classification of ranks higher than species. This activity is what the term denotes, it is also referred to as beta taxonomy. How species should be defined in a group of organisms gives rise to practical and theoretical problems that are referred to as the species problem. The scientific work of deciding how to define species has been called microtaxonomy, by extension, macrotaxonomy is the study of groups at higher taxonomic ranks, from subgenus and above only, than species. While some descriptions of taxonomic history attempt to date taxonomy to ancient civilizations, earlier works were primarily descriptive, and focused on plants that were useful in agriculture or medicine. There are a number of stages in scientific thinking. Early taxonomy was based on criteria, the so-called artificial systems. Later came systems based on a complete consideration of the characteristics of taxa, referred to as natural systems, such as those of de Jussieu, de Candolle and Bentham. The publication of Charles Darwins Origin of Species led to new ways of thinking about classification based on evolutionary relationships and this was the concept of phyletic systems, from 1883 onwards. This approach was typified by those of Eichler and Engler, the advent of molecular genetics and statistical methodology allowed the creation of the modern era of phylogenetic systems based on cladistics, rather than morphology alone. Taxonomy has been called the worlds oldest profession, and naming and classifying our surroundings has likely been taking place as long as mankind has been able to communicate
Taxonomy (biology)
–
Title page of
Systema Naturae, Leiden, 1735
Taxonomy (biology)
–
Evolution of the
vertebrates at class level, width of spindles indicating number of families. Spindle diagrams are typical for
Evolutionary taxonomy
Taxonomy (biology)
–
The same relationship, expressed as a
cladogram typical for
cladistics
Taxonomy (biology)
–
Type specimen for
Nepenthes smilesii, a tropical
pitcher plant.
3.
Bacteria
–
Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods, Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only half of the bacterial phyla have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology, There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are approximately 5×1030 bacteria on Earth, forming a biomass which exceeds that of all plants, Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of bodies and bacteria are responsible for the putrefaction stage in this process. In March 2013, data reported by researchers in October 2012, was published and it was suggested that bacteria thrive in the Mariana Trench, which with a depth of up to 11 kilometres is the deepest known part of the oceans. Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States. According to one of the researchers, You can find microbes everywhere—theyre extremely adaptable to conditions, the vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial particularly in the gut flora. However several species of bacteria are pathogenic and cause diseases, including cholera, syphilis, anthrax, leprosy. The most common fatal diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year. In developed countries, antibiotics are used to treat infections and are also used in farming, making antibiotic resistance a growing problem. Once regarded as constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and these evolutionary domains are called Bacteria and Archaea. The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, for about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. In 2008, fossils of macroorganisms were discovered and named as the Francevillian biota, however, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. Bacteria were also involved in the second great evolutionary divergence, that of the archaea, here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea
Bacteria
–
Had'n
Bacteria
Bacteria
–
A
biofilm of thermophilic bacteria in the outflow of
Mickey Hot Springs,
Oregon, approximately 20 mm thick.
Bacteria
–
Helicobacter pylori electron micrograph, showing multiple flagella on the cell surface
4.
Proteobacteria
–
The Proteobacteria are a major phylum of Gram-negative bacteria. The name of the phylum has never been published as no type genus has been proposed. They include a variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, Yersinia. Others are free-living, and include many of the responsible for nitrogen fixation. Carl Woese established this grouping in 1987, calling it informally the purple bacteria, the Alphaproteobacteria grow at very low levels of nutrients and have unusual morphology such as stalks and buds. They include agriculturally important bacteria capable of inducing nitrogen fixation in symbiosis with plants, the type order is the Caulobacterales, comprising stalk-forming bacteria such as Caulobacter. The Betaproteobacteria are highly diverse and contain chemolithoautotrophs, photoautotrophs. The type order is the Burkholderiales, comprising a range of metabolic diversity. The Gammaproteobacteria are the largest class in terms of species with validly published names, the type order is the Pseudomonadales, which include the genera Pseudomonas and the nitrogen-fixing Azotobacter. The Deltaproteobacteria include bacteria that are predators on other bacteria and are important contributors to the side of the sulfur cycle. The type order is the Myxococcales, which includes organisms with self-organising abilities such as Myxococcus spp, the Epsilonproteobacteria are often slender, Gram-negative rods that are helical or curved. The type order is the Campylobacterales, which includes important food pathogens such as Campylobacter spp, the type order is the Oligoflexales, which contains the genus Oligoflexus. The Acidithiobacillia contain only sulfur-oxidising autotrophs, the type order is the Acidithiobacillales, which includes economically important organisms used in the mining industry such as Acidithiobacillus spp. All Proteobacteria are Gram-negative, though some may stain Gram-positive or Gram-variable in practice, many move about using flagella, but some are nonmotile or rely on bacterial gliding. The last include the Myxobacteriales, an order of bacteria that can aggregate to form fruiting bodies. Also, a variety in the types of metabolism exists. Most members are facultatively or obligately anaerobic, Chemolithoautotrophic, and heterotrophic, a variety of genera, which are not closely related to each other, convert energy from light through photosynthesis. Proteobacteria are associated with the imbalance of microbiota of the reproductive tract of women
Proteobacteria
–
Proteobacteria
5.
Order (biology)
–
In biological classification, the order is a taxonomic rank used in the classification of organisms and recognized by the nomenclature codes. Other well-known ranks are life, domain, kingdom, phylum, class, family, genus, an immediately higher rank, superorder, may be added directly above order, while suborder would be a lower rank. A taxonomic unit, a taxon, in that rank, in that case the plural is orders. Example, The Juglans and Hickory trees belong to the family Juglandaceae, what does and does not belong to each order is determined by a taxonomist, as is whether a particular order should be recognized at all. Often there is no agreement, with different taxonomists each taking a different position. There are no rules that a taxonomist needs to follow in describing or recognizing an order. Some taxa are accepted almost universally, while others are recognised only rarely, for some groups of organisms, consistent suffixes are used to denote that the rank is an order. The Latin suffix -formes meaning having the form of is used for the name of orders of birds and fishes. The suffix -ales is for the name of orders of plants, fungi, for some clades covered by the International Code of Zoological Nomenclature, a number of additional classifications are sometimes used, although not all of these are officially recognised. In their 1997 classification of mammals, McKenna and Bell used two levels between superorder and order, grandorder and mirorder. Michael Novacek inserted them at the same position, michael Benton inserted them between superorder and magnorder instead. This position was adopted by Systema Naturae 2000 and others, in botany, the ranks of subclass and suborder are secondary ranks pre-defined as respectively above and below the rank of order. Any number of further ranks can be used as long as they are clearly defined, the superorder rank is commonly used, with the ending -anae that was initiated by Armen Takhtajans publications from 1966 onwards. Carl Linnaeus was the first to apply it consistently to the division of all three kingdoms of nature in his Systema Naturae, for plants, Linnaeus orders in the Systema Naturae and the Species Plantarum were strictly artificial, introduced to subdivide the artificial classes into more comprehensible smaller groups. In French botanical publications, from Michel Adansons Familles naturelles des plantes and until the end of the 19th century, some of the plant families still retain the names of Linnaean natural orders or even the names of pre-Linnaean natural groups recognised by Linnaeus as orders in his natural classification. Such names are known as family names. In zoology, the Linnaean orders were used more consistently and that is, the orders in the zoology part of the Systema Naturae refer to natural groups. Some of his names are still in use
Order (biology)
–
Title page of the 1758 edition of Linnaeus's Systema Naturæ.
6.
Burkholderiales
–
The Burkholderiales are an order of Proteobacteria. Like all Proteobacteria, they are Gram-negative and they include several pathogenic bacteria, including species of Burkholderia, Bordetella, and Ralstonia. They also include Oxalobacter and related genera, which are unusual in using oxalic acid as their source of carbon, Burkholderiales J. P. Euzéby, List of Prokaryotic names with Standing in Nomenclature
Burkholderiales
–
Burkholderiales
7.
Neisseriales
–
The Neisseriaceae are a family of Proteobacteria, within the Neisseriales order. As a group, the Neisseriaceae are strictly aerobic and Gram-negative, occur mainly in pairs, bacteria of Medical Importance in Todars Online Textbook of Bacteriology. CS1 maint, Multiple names, authors list Ryan KJ, Ray CG
Neisseriales
–
Neisseriaceae
8.
Nitrosomonadales
–
The Nitrosomonadales are a small order of Proteobacteria. Like all Proteobacteria, they are Gram-negative and they include Nitrosomonas, Nitrosospira, Gallionella, and Spirillum. Members of the genus Nitrosomonas oxidize ammonia into nitrite, a process called nitrification and they are important in the nitrogen cycle. The species Spirillum minus causes rat-bite fever, Nitrosomonadales J. P. Euzéby, List of Prokaryotic names with Standing in Nomenclature Nitrosomonas MicrobeWki
Nitrosomonadales
–
Nitrosomonadales
9.
Gram-negative bacteria
–
Gram-negative bacteria are a group of 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 peptidoglycan cell wall sandwiched between an inner cytoplasmic cell membrane and a bacterial outer membrane. Gram-negative bacteria are spread worldwide, in all environments that support life. Several classes of antibiotics target gram-negative bacteria specifically, including aminoglycosides, historically, the kingdom Monera was divided into four divisions based on Gram staining, Firmacutes, Gracillicutes, Mollicutes and Mendocutes. Since 1987, the monophyly of the bacteria has been disproven with molecular studies. However some authors, such as Cavalier-Smith still treat them as a monophyletic taxon, bacteria are traditionally divided into the two groups, gram-positive and gram-negative, based on their Gram stain retention. These groups are thought of as lineages, with gram-negative bacteria more closely related to one another than to gram-positive bacteria. While this is true, the classification system breaks down in some cases. A given bacterias Gram stain result, bacterial membrane organization, as such, the Gram stain cannot be reliably used to assess familial relationships of bacteria. That said, Gram staining does often give information about the composition of the cell membrane. Of these two distinct groups of prokaryotic organisms, monoderm prokaryotes are indicated to be ancestral. In addition, a number of taxa that are either part of the phylum Firmicutes or branches in its proximity are also found to possess a diderm cell structure. Other notable groups of bacteria include the cyanobacteria, spirochaetes, green sulfur. Medically relevant gram-negative cocci include the four types that cause a sexually transmitted disease, a meningitis, medically relevant gram-negative bacilli include a multitude of species. Some of them cause primarily respiratory problems, primarily urinary problems, transformation is one of three processes for horizontal gene transfer, in which exogenous genetic material passes from bacterium to another, the other two being conjugation and transduction. In transformation, the material passes through the intervening medium. One of the unique characteristics of gram-negative bacteria is the structure of the bacterial outer membrane. The outer leaflet of this comprises a complex lipopolysaccharide whose lipid portion acts as an endotoxin
Gram-negative bacteria
–
Microscopic image of gram-negative
Pseudomonas aeruginosa bacteria (pink-red rods)
10.
Phylum
–
In biology, a phylum is a taxonomic rank below kingdom and above class. Traditionally, in botany the term division was used instead of phylum, although from 1993 the International Code of Nomenclature for algae, fungi, depending on definitions, the kingdom Animalia contains approximately 35 phyla, Plantae contains about 12, and Fungi contains around 7. Current research in phylogenetics is uncovering the relationships between phyla, which are contained in larger clades, like Ecdysozoa and Embryophyta, the definitions of zoological phyla have changed from their origins in the six Linnaean classes and the four embranchements of Georges Cuvier. Haeckel introduced the term phylum, based on the Greek word phylon, in plant taxonomy, Eichler classified plants into five groups, named divisions. Informally, phyla can be thought of as grouping organisms based on general specialization of body plan, the most important objective measure in the above definitions is the certain degree—how unrelated do organisms need to be to be members of different phyla. The minimal requirement is that all organisms in a phylum should be more closely related to one another than to any other group. So phyla can be merged or split if it becomes apparent that they are related to one another or not, a definition of a phylum based on body plan has been proposed by paleontologists Graham Budd and Sören Jensen. By Budd and Jensens definition, a phylum is defined by a set of shared by all its living representatives. This approach brings some small problems—for instance, ancestral characters common to most members of a phylum may have been lost by some members, also, this definition is based on an arbitrary point of time, the present. However, as it is based, it is easy to apply to the fossil record. A greater problem is that it relies on a decision about which groups of organisms should be considered as phyla. However, proving that a fossil belongs to the group of a phylum is difficult. Furthermore, organisms in the group of a phylum can possess the body plan of the phylum without all the characteristics necessary to fall within it. This weakens the idea that each of the phyla represents a body plan. A classification using this definition may be affected by the chance survival of rare groups. Representatives of many modern phyla did not appear until long after the Cambrian, the kingdom Plantae is defined in various ways by different biologists. All definitions include the living embryophytes, to which may be added the two green algae divisions, Chlorophyta and Charophyta, to form the clade Viridiplantae. The table below follows the influential Cavalier-Smith system in equating Plantae with Archaeplastida, a group containing Viridiplantae, the definition and classification of plants at the division level also varies from source to source, and has changed progressively in recent years
Phylum
–
The hierarchy of
biological classification 's eight major
taxonomic ranks. A
kingdom contains one or more phyla. Intermediate minor rankings are not shown.
11.
Genus
–
A genus is a taxonomic rank used in the biological classification of living and fossil organisms in biology. In the hierarchy of classification, genus comes above species. In binomial nomenclature, the name forms the first part of the binomial species name for each species within the genus. Felis catus and Felis silvestris are two species within the genus Felis, Felis is a genus within the family Felidae. The composition of a genus is determined by a taxonomist, the standards for genus classification are not strictly codified, so different authorities often produce different classifications for genera. Moreover, genera should be composed of units of the same kind as other genera. The term comes from the Latin genus, a noun form cognate with gignere, linnaeus popularized its use in his 1753 Species Plantarum, but the French botanist Joseph Pitton de Tournefort is considered the founder of the modern concept of genera. The scientific name of a genus may be called the name or generic epithet. It plays a role in binomial nomenclature, the system of naming organisms. The rules for the names of organisms are laid down in the Nomenclature Codes. The standard way of scientifically describing species and other lower-ranked taxa is by binomial nomenclature, the generic name forms its first half. For example, the gray wolfs binomial name is Canis lupus, with Canis being the name shared by the wolfs close relatives. The specific name is written in lower-case and may be followed by names in zoology or a variety of infraspecific names in botany. Especially with these names, when the generic name is known from context. Because animals are typically only grouped within subspecies, it is written as a trinomen with a third name. Dog breeds, meanwhile, are not scientifically distinguished, there are several divisions of plant species and therefore their infraspecific names generally include contractions explaining the relation. For example, the genus Hibiscus includes hundreds of other species apart from the Rose of Sharon or common garden hibiscus, Rose of Sharon doesnt have subspecies but has cultivars that carry desired traits, such as the bright white H. syriaca Diana. Hawaiian hibiscus, meanwhile, includes several separate species, since not all botanists agree on the divisions or names between species, it is common to specify the source of the name using author abbreviations
Genus
–
Number of reptile genera with a given number of species. Most genera have only one or a few species but a few may have hundreds. Based on data from the
Reptile Database (as of May 2015).
12.
Photoheterotroph
–
Photoheterotrophs are heterotrophic phototrophs—that is, they are organisms that use light for energy, but cannot use carbon dioxide as their sole carbon source. Consequently, they use organic compounds from the environment to satisfy their carbon requirements, these compounds include carbohydrates, fatty acids, examples of photoheterotrophic organisms include purple non-sulfur bacteria, green non-sulfur bacteria, and heliobacteria. Recent research has indicated that the hornet and some aphids may be able to use light to supplement their energy supply. Photoheterotrophs generate ATP using light, in one of two ways, they use a reaction center, or they use a bacteriorhodopsin. The chlorophyll-based mechanism is similar to that used in photosynthesis, where light excites the molecules in a reaction center and this flow of electrons through the proteins causes hydrogen ions to be pumped across a membrane. The energy stored in this gradient is used to drive ATP synthesis. Unlike in photoautotrophs, the electrons flow only in a pathway, electrons released from the reaction center flow through the ETS. They are not utilized to reduce any organic compounds, purple non-sulfur bacteria, green non-sulfur bacteria and heliobacteria are examples of bacteria that carry out this scheme of photoheterotrophy. Other organisms, including halobacteria and flavobacteria and vibrios have purple-rhodopsin-based proton pumps that supplement their energy supply, the archaeal version is called bacteriorhodopsin, while the eubacterial version is called proteorhodopsin. The pump consists of a single protein bound to a Vitamin A derivative, the pump may have accessory pigments associated with the protein. When light is absorbed by the molecule, the molecule isomerises. This drives the protein to change shape and pump a proton across the membrane, the hydrogen ion gradient can then be used to generate ATP, transport solutes across the membrane, or drive a flagellar motor. One particular flavobacterium cannot reduce carbon dioxide using light, but uses the energy from its system to fix carbon dioxide through anaplerotic fixation. The flavobacterium is still a heterotroph as it needs reduced carbon compounds to live and cannot subsist on only light and CO2. It cannot carry out reactions in the form of 2n CO2 + 2n DH2 + photons → 2n + 2n DO, autotroph Chemoautotroph Photoautotroph Heterotroph Chemoheterotroph Photoheterotroph Primary nutritional groups University of Wisconsin, Madison Microbiology Online Textbook
Photoheterotroph
–
General
Photoheterotroph
–
Population ecology
13.
Nitrification
–
Nitrification is the biological oxidation of ammonia or ammonium to nitrite followed by the oxidation of the nitrite to nitrate. The transformation of ammonia to nitrite is usually the limiting step of nitrification. Nitrification is an important step in the cycle in soil. Nitrification is a process performed by small groups of autotrophic bacteria. This process was discovered by the Russian microbiologist Sergei Winogradsky, the oxidation of ammonia into nitrite is performed by two groups of organisms, ammonia-oxidizing bacteria and ammonia-oxidizing archaea. AOB can be found among the β-proteobacteria and gammaproteobacteria, currently, two AOA, Nitrosopumilus maritimus and Nitrososphaera viennensis, have been isolated and described. In soils the most studied AOB belong to the genera Nitrosomonas, the second step is done by bacteria of the genus Nitrobacter and Nitrospira. Both steps are producing energy to be coupled to ATP synthesis, nitrifying organisms are chemoautotrophs, and use carbon dioxide as their carbon source for growth. Some AOB possess the enzyme, urease, which catalyzes the conversion of the molecule to two ammonia molecules and one carbon dioxide molecule. This feature may explain enhanced growth of AOB in the presence of urea in acidic environments, in most environments, organisms are present that will complete both steps of the process, yielding nitrate as the final product. However, it is possible to design systems in which nitrite is formed, nitrification is important in agricultural systems, where fertilizer is often applied as ammonia. Conversion of this ammonia to nitrate increases nitrogen leaching because nitrate is more water-soluble than ammonia, nitrification also plays an important role in the removal of nitrogen from municipal wastewater. The conventional removal is nitrification, followed by denitrification, the cost of this process resides mainly in aeration and the addition of an external carbon source for the denitrification. Nitrification can also occur in drinking water, in distribution systems where chloramines are used as the secondary disinfectant, the presence of free ammonia can act as a substrate for ammonia-oxidizing microorganisms. The associated reactions can lead to the depletion of the disinfectant residual in the system, the addition of chlorite ion to chloramine-treated water has been shown to control nitrification. Together with ammonification, nitrification forms a process that refers to the complete decomposition of organic material. The nitrification step of the cycle is of particular interest in the ocean because it creates nitrate, furthermore, as the ocean becomes enriched in anthropogenic CO2, the resulting decrease in pH could lead to decreasing rates of nitrification. Nitrification could potentially become a bottleneck in the nitrogen cycle, nitrification, as stated above, is formally a two-step process, in the first step ammonia is oxidized to nitrite, and in the second step nitrite is oxidized to nitrate
Nitrification
–
Nitrogen cycle
14.
Wastewater treatment
–
The latter is called water reclamation and implies avoidance of disposal by use of treated wastewater effluent for various purposes. Treatment means removing impurities from water being treated, and some methods of treatment are applicable to water and wastewater. The physical infrastructure used for treatment is called a wastewater treatment plant. By-products from wastewater treatment plants, such as screenings, grit, if the wastewater is predominantly from municipal sources it is called sewage and its treatment is called sewage treatment. Although disposal or reuse occurs after treatment, it must be considered first, since disposal or reuse are the objectives of wastewater treatment, disposal or reuse options are the basis for treatment decisions. Acceptable impurity concentrations may vary with the type of use or location of disposal, ocean disposal is subject to international treaty requirements. International treaties may also regulate disposal into rivers crossing international borders, water bodies entirely within the jurisdiction of a single nation may be subject to regulations of multiple local governments. Acceptable impurity concentrations may vary widely among different jurisdictions for disposal of wastewater to evaporation ponds, infiltration basins, phase separation transfers impurities into a non-aqueous phase. Phase separation may occur at points in a treatment sequence to remove solids generated during oxidation or polishing. Grease and oil may be recovered for fuel or saponification, solids often require dewatering of sludge in a wastewater treatment plant. Disposal options for dried solids vary with the type and concentration of impurities removed from water, production of waste brine, however, may discourage wastewater treatment removing dissolved inorganic solids from water by methods like ion exchange, reverse osmosis, and distillation. Solids and non-polar liquids may be removed from wastewater by gravity when density differences are sufficient to overcome dispersion by turbulence, gravity separation of solids is the primary treatment of sewage, where the unit process is called primary settling tanks or primary sedimentation tanks. It is also used for the treatment of other wastewaters. Solids that are heavier than water will accumulate at the bottom of quiescent settling basins, more complex clarifiers also have skimmers to simultaneously remove floating grease like soap scum and solids like feathers or wood chips. Containers like the API oil-water separator are specifically designed to separate non-polar liquids, other types of water filters remove impurities by chemical or biological processes described below. Oxidation reduces the oxygen demand of wastewater, and may reduce the toxicity of some impurities. Secondary treatment converts some impurities to carbon dioxide, water, chemical oxidation is widely used for disinfection. Secondary treatment by biochemical oxidation of dissolved and colloidal organic compounds is used in sewage treatment and is applicable to some agricultural and industrial waste waters
Wastewater treatment
–
Clarifiers are widely used for wastewater treatment.
Wastewater treatment
–
Primary settling tank of wastewater treatment plant in Dresden-Kaditz, Germany
Wastewater treatment
–
Aeration tank of an
activated sludge process at the wastewater treatment plant in Dresden-Kaditz, Germany
Wastewater treatment
–
Overview of the wastewater treatment plant of Antwerpen-Zuid, located in the south of the agglomeration of Antwerp (Belgium)
15.
Gammaproteobacteria
–
Gammaproteobacteria are a class of several medically, ecologically, and scientifically important groups of bacteria. An exceeding number of important pathogens belong to this class, like all Proteobacteria, the Gammaproteobacteria are Gram-negative. The Gammaproteobacteria comprise several medically and scientifically important groups of bacteria, such as the Enterobacteriaceae, Vibrionaceae, a number of important pathogens belong to this class, e. g. Salmonella spp. Yersinia pestis, Vibrio cholerae, Pseudomonas aeruginosa, and Escherichia coli, important plant pathogens such as Xanthomonas axonopodis pv. citri and Pseudomonas syringae pv. actinidiae are also Gammaproteobacteria. Members of Chromatium are photosynthetic and oxidize hydrogen sulfide instead of water, some Gammaproteobacteria are methane oxidizers, and many are symbiotic with geothermic ocean vent-dwelling animals. Due to a genus, Acidithiobacillus, the Gammaproteobacteria class is paraphyletic to Betaproteobacteria. A number of bacteria have been described as members of Gammaproteobacteria, Betaproteobacteria Proteobacteria Gammaproteobacteria at the US National Library of Medicine Medical Subject Headings
Gammaproteobacteria
–
Gammaproteobacteria
16.
Taxon
–
In biology, a taxon is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. Although neither is required, a taxon is known by a particular name and given a particular ranking, especially if. It is not uncommon, however, for taxonomists to remain at odds over what belongs to a taxon, if a taxon is given a formal scientific name, its use is then governed by one of the nomenclature codes specifying which scientific name is correct for a particular grouping. Many modern systematists, such as advocates of phylogenetic nomenclature, use cladistic methods that require taxa to be monophyletic and their basic unit, therefore, is the clade rather than the taxon. Similarly, among those contemporary taxonomists working with the traditional Linnean nomenclature, an example of a well-established taxon that is not also a clade is the class Reptilia, the reptiles, birds are descendants of reptiles but are not included in the Reptilia. The term taxon was first used in 1926 by Adolf Meyer-Abich for animal groups, for plants, it was proposed by Herman Johannes Lam in 1948, and it was adopted at the VII International Botanical Congress, held in 1950. The Glossary of the International Code of Zoological Nomenclature defines a taxon, a taxon encompasses all included taxa of lower rank and individual organisms. A taxon can be assigned a rank, usually when it is given a formal name. Phylum applies formally to any domain, but traditionally it was always used for animals, whereas Division was traditionally often used for plants, fungi. A prefix is used to indicate a ranking of lesser importance, the prefix super- indicates a rank above, the prefix sub- indicates a rank below. In zoology the prefix infra- indicates a rank below sub-, for instance, among the additional ranks of class are superclass, subclass and infraclass. Rank is relative, and restricted to a particular systematic schema, for example, liverworts have been grouped, in various systems of classification, as a family, order, class, or division. Many cladists do not see any need to depart from traditional nomenclature as governed by the ICZN, ICN, etc
Taxon
–
African elephants form the
genus Loxodonta, a widely accepted taxon.
17.
Endosymbiont
–
An endosymbiont or endobiont is any organism that lives within the body or cells of another organism, i. e. forming an endosymbiosis. The most common examples of obligate endosymbioses are mitochondria and chloroplasts, some human parasites, e. g. Wuchereria bancrofti and Mansonella perstans, thrive in their intermediate insect hosts because of an obligate endosymbiosis with Wolbachia spp. They can both be eliminated from said hosts by treatments that target this bacterium, however, not all endosymbioses are obligate. Also, some endosymbioses can be harmful to either of the organisms involved, two major types of organelle in eukaryotic cells, mitochondria and plastids such as chloroplasts, originated as bacterial endosymbionts. Such symbiogenesis was first suggested in 1905, and articulated by the Russian botanist Konstantin Mereschkowski in 1910 and it was reintroduced by Lynn Margulis in the 1960s. Symbiogenesis explains the origins of such as mitochondria and chloroplasts in eukaryotic cells. The theory proposes that chloroplasts and mitochondria evolved from certain types of bacteria that eukaryotic cells engulfed through endophagocytosis and these cells and the bacteria trapped inside them entered a symbiotic relationship, a close association between different types of organisms over an extended time. However, to be specific, the relationship was endosymbiotic, meaning one of the organisms lived within the other. The theory suggests that an anaerobic cell probably ingested an aerobic bacterium, the aerobic bacterium flourished within the cell because the cells cytoplasm was abundant in half-digested food molecules. The bacterium digested these molecules with oxygen and gained great amounts of energy, because the bacterium had so much energy, it probably leaked some of it as adenosine triphosphate into the cells cytoplasm. This benefited the anaerobic cell because it was now able to breathe aerobically, eventually, the aerobic bacterium could no longer live independently from the cell, and it, therefore, became a mitochondrion. The origin of the chloroplast is very similar to that of the mitochondrion, a cell must have captured a photosynthetic cyanobacterium and failed to digest it. The cyanobacterium thrived in the cell and eventually evolved into the first chloroplast, there are several lines of evidence that support endosymbiosis theory. Mitochondria and chloroplasts contain their own supply of DNA, which may be remnants of the genome the organelles had when they were independent aerobic bacteria. The single most convincing evidence of the descent of organelles from bacteria is the position of mitochondria, mitochondria have sequences that clearly indicate origin from a group of bacteria called the alphaproteobacteria. Plastids have DNA sequences that indicate origin from the cyanobacteria, in addition, there are organisms alive today, called living intermediates, that are in a similar endosymbiotic condition to the prokaryotic cells and the aerobic bacteria. Living intermediates show that the proposed by the endosymbiont theory is possible. For example, the giant amoeba Pelomyxa lacks mitochondria but has aerobic bacteria that carry out a similar role, a variety of corals, clams, snails, and one species of Paramecium permanently host algae in their cells
Endosymbiont
–
A representation of the
endosymbiotic theory
18.
Acanthamoeba
–
Acanthamoeba is a genus of amoebae, one of the most common single-celled eukaryote in soil, and frequently found in fresh water and other habitats. Acanthamoeba has two forms, the metabolically active trophozoite and a dormant, stress resistant cyst. Trophozoites are small, usually 15 to 35 μm in length, in nature, Acanthamoeba species are free-living bacterivores, but in certain situations they can cause infections in humans and other animals. Acanthamoeba spp. are among the most prevalent protozoa found in the environment, additionally, Acanthamoeba have been isolated from human skin, nasal cavities, throats, and intestines, as well as plants and other mammals. Diseases caused by Acanthamoeba include keratitis and granulomatous amoebic encephalitis, the latter is often but not always seen in immunosuppressed patients. GAE is caused by the entering the body through an open wound then spreading to the brain. The combination of host immune response and amoebal proteases causes massive brain swelling resulting in death in ~95% of those infected, granulomatous amoebic encephalitis is caused by amoeba infection of the central nervous system. It is characterized by symptoms including headache, seizures. These worsen progressively over weeks to months, leading to death in most patients, infection is generally associated with underlying conditions such as immunodeficiency, diabetes, malignancies, malnutrition, systemic lupus erythematosus, and alcoholism. The parasite enters the body through cuts in the skin or by being inhaled into the respiratory tract. The parasite then spreads through the blood into the nervous system. Acanthamoeba crosses the barrier by means that are not yet understood. Subsequent invasion of the tissue and induction of pro-inflammatory responses leads to neuronal damage that can be fatal within days. A perivascular cuffing with amoebae in necrotic tissue is usual finding in the AIDS, a post mortem biopsy reveals severe oedema and hemorrhagic necrosis. Due to the rarity of this parasite and a lack of knowledge, Acanthamoeba keratitis cases in the past, when were managed by atropine given as an adjuvant therapy without anti-parasitic drugs added to the regime, had been reported to halt the vision loss. Recent publications debate these successes related to an action of Atropine on muscarinic receptors on Acanthamoeba spp, infection usually mimics that of bacterial leptomeningitis, tuberculous meningitis, or viral encephalitis. The misdiagnosis often leads to erroneous, ineffective treatment, correct and timely diagnosis, as well as improved treatment methods and an understanding of the parasite are important factors in improving the outcome of infection by Acanthamoeba. A recent paper published in 2013 has shown effects of some FDA approved drugs with a kill rate above 90%
Acanthamoeba
–
Acanthamoeba
Acanthamoeba
Acanthamoeba
–
Acanthamoeba encephalitis. Scale bar: 10 μm
19.
Eukaryote
–
A eukaryote is any organism whose cells contain a nucleus and other organelles enclosed within membranes. Eukaryotes belong to the taxon Eukarya or Eukaryota, the presence of a nucleus gives eukaryotes their name, which comes from the Greek εὖ and κάρυον. Eukaryotic cells also contain other membrane-bound organelles such as mitochondria and the Golgi apparatus, in addition, plants and algae contain chloroplasts. Eukaryotic organisms may be unicellular or multicellular, only eukaryotes form multicellular organisms consisting of many kinds of tissue made up of different cell types. Eukaryotes can reproduce asexually through mitosis and sexually through meiosis and gamete fusion. In mitosis, one cell divides to produce two identical cells. In meiosis, DNA replication is followed by two rounds of division to produce four daughter cells each with half the number of chromosomes as the original parent cell. These act as sex cells resulting from genetic recombination during meiosis, the domain Eukaryota appears to be monophyletic, and so makes up one of the three domains of life. The two other domains, Bacteria and Archaea, are prokaryotes and have none of the above features, eukaryotes represent a tiny minority of all living things. However, due to their larger size, eukaryotes collective worldwide biomass is estimated at about equal to that of prokaryotes. Eukaryotes first developed approximately 1. 6–2.1 billion years ago, in 1905 and 1910, the Russian biologist Konstantin Mereschkowsky argued three things about the origin of nucleated cells. Firstly, plastids were reduced cyanobacteria in a symbiosis with a non-photosynthetic host, secondly, the host had earlier in evolution formed by symbiosis between an amoeba-like host and a bacteria-like cell that formed the nucleus. Thirdly, plants inherited photosynthesis from cyanobacteria, the split between the prokaryotes and eukaryotes was introduced in the 1960s. The concept of the eukaryote has been attributed to the French biologist Edouard Chatton, the terms prokaryote and eukaryote were more definitively reintroduced by the Canadian microbiologist Roger Stanier and the Dutch-American microbiologist C. B. van Niel in 1962. In his 1938 work Titres et Travaux Scientifiques, Chatton had proposed the two terms, calling the bacteria prokaryotes and organisms with nuclei in their cells eukaryotes. However he mentioned this in one paragraph, and the idea was effectively ignored until Chattons statement was rediscovered by Stanier. In 1967, Lynn Margulis provided microbiological evidence for endosymbiosis as the origin of chloroplasts and mitochondria in cells in her paper. In the 1970s, Carl Woese explored microbial phylogenetics, studying variations in 16S ribosomal RNA and this helped to uncover the origin of the eukaryotes and the symbiogenesis of two important eukaryote organelles, mitochondria and chloroplasts
Eukaryote
–
Had'n
Eukaryote
–
Longitudinal section through the flagellum of
Chlamydomonas reinhardtii
20.
Neisseria
–
Neisseria is a large genus of bacteria that colonize the mucosal surfaces of many animals. Of the 11 species that humans, only two are pathogens, N. meningitidis and N. gonorrhoeae. Most gonoccocal infections are asymptomatic and self-resolving, and epidemic strains of the meningococcus may be carried in >95% of a population where systemic disease occurs at <1% prevalence, Neisseria species are Gram-negative bacteria included among the proteobacteria, a large group of Gram-negative forms. Neisseria diplococci resemble coffee beans when viewed microscopically and this genus of parasitic bacteria grow in pairs and occasionally tetrads, and thrive best at 98.6 °F in the animal body or serum media. The genus includes, N. gonorrhoeae, which causes gonorrhea, N. meningitidis, one of the most common causes of bacterial meningitis and the causative agent of meningococcal septicaemia. These two species have the ability of breaching the barrier, local cytokines of the area become secreted to initiate an immune response. Neisseria species are able to alter their antigens to avoid being engulfed by a process called antigenic variation. The pathogenic species along with some species, have type IV pili which serve multiple functions for this organism. Neisseria bacteria have also shown to be an important factor in the early stages of canine plaque development. Fa that is exhibited in N. meningitidis and some species is the main inhibitor of the alternative complement pathway. FHbp protects meningococci from complement-mediated death in human experiments, but has also been shown to protect meningococci from antimicrobial peptides in vitro. Factor H binding protein is key to the pathogenesis of N. meningitidis, porins are also an important factor for complement inhibition for both pathogenic and commensal species. Porins are important for nutrient acquisition, porins are also recognized by TLR2, they bind complement factors. Cooperation with pili for CR3-mediated internalization is another function of porins, ability to translocate into host cells and modulate reactive oxygen species production and apoptosis is made possible by porins, as well. Strains of the species can express different porins. The genus Neisseria is named after the German bacteriologist Albert Neisser, who in 1879 discovered its first example, Neisseria gonorrheae, Neisser also codiscovered the pathogen that causes leprosy, Mycobacterium leprae. These discoveries were made possible by the development of new staining techniques which he helped to develop, all the medically significant species of Neisseria are positive for both catalase and oxidase. Different Neisseria species can be identified by the sets of sugars from which they will produce acid, for example, N. gonorrheae makes acid from only glucose, but N. meningitidis produces acid from both glucose and maltose
Neisseria
–
Neisseria
21.
Neisseria gonorrhoeae
–
Neisseria gonorrhoeae, also known as gonococci, or gonococcus, is a species of Gram-negative coffee bean-shaped diplococci bacteria responsible for the sexually transmitted infection gonorrhea. N. gonorrhoeae was first described by Albert Neisser in 1879, Neisseria species are fastidious Gram-negative cocci that require nutrient supplementation to grow in laboratory cultures. To be specific, they grow on agar with carbon dioxide. These cocci are facultatively intracellular and typically appear in pairs, in the shape of coffee beans, of the 11 species of Neisseria that colonize humans, only two are pathogens. N. gonorrhoeae is the agent of gonorrhea and is transmitted via sexual contact. Further testing to differentiate the species includes testing for oxidase and the carbohydrates maltose, sucrose, N. gonorrhoeae possess many dynamic polymeric protein filaments called type IV pili, which allow the bacteria to adhere and move along surfaces. The bacterial movement is mediated by twitching motility powered by the extension and retraction of the type IV pilus, pili extend and attach to a substrate that signals the pilus to retract, dragging the cell forward. N. gonorrhoeae is able to pull 100,000 times its own weight, the pulling of type IV pilus is powered by a set of ATPases proteins, Pil F and Pil T. The type IV pilus in N. gonorrhoeae adhesive properties also play a role in microcolony aggregation, N. gonorrhoeae is naturally competent for DNA exchange, which is also dependent on type IV pilus dynamics, specifically proteins Pil Q and Pil T. These processes allow for the DNA of N. gonorrhoeae to acquire or spread new genes, especially dangerous from the aspect of healthcare is the ability to conjugate, since this can lead to antibiotic resistance. N. gonorrhoeae has surface proteins called Opa proteins, which bind to receptors on immune cells, in so doing, N. gonorrhoeae is able to prevent an immune response. The host is unable to develop an immunological memory against N. gonorrhoeae – which means that future reinfection is possible. The many permutations of proteins make it more difficult for immune cells to recognize N. gonorrhoeae. The genomes of several strains of N. gonorrhoeae have been sequenced, most of them are about 2.1 Mb in size and encode 2,100 to 2,600 proteins. For instance, strain NCCP11945 consists of one circular chromosome encoding 2,662 predicted ORFs, the estimated coding density over the entire genome is 87%, and the average G+C content is 52. 4%, values that are similar to those of strain FA1090. The NCCP11945 genome encodes 54 tRNAs and four copies of 16S-23S-5S rRNA operons, N. gonorrhoeae is transmitted from person to person during sexual relations. Traditionally, the bacteria was thought to move attached to spermatozoon, a recent study suggests that rather than “surf” on wiggling sperm, N. gonorrhoeae bacteria uses hairlike structures called pili to anchor onto proteins in the sperm and move through coital liquid. It can also be transmitted to the fetus in utero and afterward become apparent as a neonatal infection, symptoms of infection with N. gonorrhoeae differ, depending on the site of infection
Neisseria gonorrhoeae
–
The growth of Neisseria gonorrhoeae colonies on New York City medium agar, a specialised and selective media for Gonococci
Neisseria gonorrhoeae
–
Neisseria gonorrhoeae
22.
Neisseria meningitides
–
The bacterium is referred to as a coccus because it is round, and more specifically, diplococcus because of its tendency to form pairs. About 10% of adults are carriers of the bacteria in their nasopharynx, as an exclusively human pathogen it is the main cause of bacterial meningitis in children and young adults, causing developmental impairment and death in about 10% of cases. It causes the form of bacterial meningitis known to occur epidemically, mainly Africa. It occurs worldwide in both epidemic and endemic form, N. meningitidis is spread through saliva and respiratory secretions during coughing, sneezing, kissing, chewing on toys and even freshwater. It infects the cell by sticking to it with long thin extensions called pili, meningococcus can cause meningitis and other forms of meningococcal disease. It initially produces general symptoms like fatigue, fever, and headache and can progress to neck stiffness, coma. Symptoms of meningococcal meningitis are easily confused with those caused by bacteria, such as Hemophilus influenzae. Suspicion of meningitis is an emergency and immediate medical assessment is recommended. Current guidance in the United Kingdom is that if a case of meningitis or septicaemia is suspected intravenous antibiotics should be given. This means that laboratory tests may be likely to confirm the presence of Neisseria meningitidis as the antibiotics will dramatically lower the number of bacteria in the body. The UK guidance is based on the idea that the ability to identify the bacteria is outweighed by reduced chance of death. Septicaemia caused by Neisseria meningitidis has received less public attention than meningococcal meningitis even though septicaemia has been linked to infant deaths. Meningococcal septicaemia typically causes a rash, that does not lose its color when pressed with a glass. This means the condition may be ignored by those not aware of the significance of the rash, septicaemia carries an approximate 50% mortality rate over a few hours from initial onset. N. meningitidis is a Gram-negative bacterium since it has an outer and inner membranes with a layer of peptidoglycan in between. It tests positive for the cytochrome c oxidase. N. meningitidis is a part of the normal flora in the nasopharynx of up to 5–15% of adults. It colonizes and infects only humans, and has never been isolated from other animals and this is thought to stem from the bacteriums inability to get iron sources other than human transferrin and lactoferrin
Neisseria meningitides
–
The growth of Neisseria meningitidis colonies on New York City Medium Agar
Neisseria meningitides
–
Neisseria meningitidis
23.
Bordetella pertussis
–
Bordetella pertussis is a Gram-negative, aerobic, pathogenic, encapsulated coccobacillus of the genus Bordetella, and the causative agent of pertussis or whooping cough. Unlike B. bronchiseptica, B. pertussis is not motile and its virulence factors include pertussis toxin, filamentous hæmagglutinin, pertactin, fimbria, and tracheal cytotoxin. The bacterium is spread by airborne droplets, its period is to human whooping cough in average 9–10 days. Humans are the only known reservoir for B. pertussis, the complete B. pertussis genome of 4,086,186 base pairs was published in 2003. Pertussis is an infection of the respiratory system characterized by a sound when the person breathes in. In the US, it killed between 10,000 and 20,000 people per year before a vaccine was available, vaccination has transformed this, between 1985 and 1988, fewer than 100 children died from pertussis. Worldwide in 2000, according to the WHO, around 39 million people were infected annually, a graph is available showing the dramatic effect of introducing vaccination in England. B. pertussis infects its host by colonizing lung epithelial cells, the bacterium contains a surface protein, filamentous haemagglutinin adhesin, which binds to the sulfatides found on cilia of epithelial cells. Once anchored, the bacterium produces tracheal cytotoxin, which stops the cilia from beating and this prevents the cilia from clearing debris from the lungs, so the body responds by sending the host into a coughing fit. These coughs expel some bacteria into the air, which are free to infect other hosts, B. pertussis has the ability to inhibit the function of the hosts immune system. The toxin, known as pertussis toxin, inhibits G protein coupling that regulates an adenylate cyclase-mediated conversion of ATP to cyclic AMP. The end result is phagocytes convert too much ATP to cyclic AMP, which can cause disturbances in cellular signaling mechanisms and this is unique in that many bacterial infections illustrate neutrophil-predominance instead. The infection occurs mostly in children under the age of one when they are unimmunized, or children with faded immunity, the signs and symptoms are similar to a common cold, runny nose, sneezing, mild cough, and low-grade fever. The patient becomes most contagious during the stage of infection. It may become airborne when the person coughs, sneezes, or laughs, pertussis vaccine is part of the diphtheria, tetanus, and acellular pertussis immunization. The paroxysmal cough precedes a crowing inspiratory sound characteristic of pertussis, after a spell, the patient might make a “whooping” sound when breathing in, or may vomit. Adults have milder symptoms, such as prolonged coughing without the “whoop”, infants less than six months also may not have the typical whoop. A coughing spell may last a minute or more, producing cyanosis, apnoea, however, when not in a coughing fit, the patient does not experience trouble breathing
Bordetella pertussis
–
Bordetella pertussis
24.
Burkholderia cepacia
–
B. cepacia is an opportunistic human pathogen that most often causes pneumonia in immunocompromised individuals with underlying lung disease. Patients with sickle-cell haemoglobinopathies are also at risk, the species also attacks young onion and tobacco plants, as well as displaying a remarkable ability to digest oil. BCC organisms are found in water and soil and can survive for prolonged periods in moist environments. They show a relatively poor virulence, virulence factors include adherence to plastic surfaces and production of several enzymes such as elastase and gelatinase. Also relevant might be the ability to survive to nonoxidative killing by neutrophils, person-to-person spread has been documented, as a result, many hospitals, clinics, and camps have enacted strict isolation precautions for those infected with BCC. Infected individuals are treated in a separate area from uninfected patients to limit spread, since BCC infection can lead to a rapid decline in lung function. Diagnosis of BCC involves culturing the bacteria from clinical specimens, such as sputum or blood, BCC organisms are naturally resistant to many common antibiotics, including aminoglycosides and polymyxin B. and this fact is exploited in the identification of the organism. It also contains phenol red pH indicator which turns pink when it reacts with alkaline byproducts generated by the bacteria when it grows, alternatively, oxidation-fermentation polymyxin-bacitracin-lactose agar can be used. Treatment typically includes multiple antibiotics and may include ceftazidime, doxycycline, piperacillin, meropenem, chloramphenicol, B. cepacia has a large genome, containing twice the amount of genetic material as E. coli. Contamination control Barlasov J, Sutton S, Jakober R. Recovery of Stressed Burkholderia cepacia Complex Organisms, UMR, Burkholderia cepacia CFF, Research Pathema-Burkholderia Resource Loutet SA, Valvano MA. A decade of Burkholderia cenocepacia virulence determinant research, type strain of Burkholderia cepacia complex at BacDive - the Bacterial Diversity Metadatabase
Burkholderia cepacia
–
Burkholderia cepacia complex
25.
Necrosis
–
Necrosis is a form of cell injury which results in the premature death of cells in living tissue by autolysis. Necrosis is caused by external to the cell or tissue, such as infection, toxins. In contrast, apoptosis is a naturally occurring programmed and targeted cause of cellular death, while apoptosis often provides beneficial effects to the organism, necrosis is almost always detrimental and can be fatal. This initiates in the tissue a inflammatory response which attracts leukocytes. However, microbial damaging substances released by leukocytes would create collateral damage to surrounding tissues, too much collateral damage would inhibit the healing process. Thus, untreated necrosis results in a build-up of decomposing dead tissue, for this reason, it is often necessary to remove necrotic tissue surgically, a procedure known as debridement. Coagulation occurs as a result of protein denaturation, causing albumin to transform into a firm and this pattern of necrosis is typically seen in hypoxic environments, such as infarction. Coagulative necrosis occurs primarily in tissues such as the kidney, heart, severe ischemia most commonly causes necrosis of this form. Liquefactive necrosis, in contrast to necrosis, is characterized by the digestion of dead cells to form a viscous liquid mass. This is typical of bacterial, or sometimes fungal, infections because of their ability to stimulate an inflammatory response, the necrotic liquid mass is frequently creamy yellow due to the presence of dead leukocytes and is commonly known as pus. Gangrenous necrosis can be considered a type of coagulative necrosis that resembles mummified tissue and it is characteristic of ischemia of lower limb and the gastrointestinal tracts. The necrotic tissue appears as white and friable, like clumped cheese, dead cells disintegrate but are not completely digested, leaving granular particles. Microscopic examination shows amorphous granular debris enclosed within a distinctive inflammatory border, fat necrosis is specialized necrosis of fat tissue, resulting from the action of activated lipases on fatty tissues such as the pancreas. Calcium, magnesium or sodium may bind to these lesions to produce a chalky-white substance, the calcium deposits are microscopically distinctive and may be large enough to be visible on radiographic examinations. To the naked eye, calcium deposits appear as gritty white flecks, fibrinoid necrosis is a special form of necrosis usually caused by immune-mediated vascular damage. It is marked by complexes of antigen and antibodies, sometimes referred to as “immune complexes” deposited within arterial walls together with fibrin, there are also very specific forms of necrosis such as gangrene, gummatous necrosis and hemorrhagic necrosis. Some spider bites may lead to necrosis, in the United States, only spider bites from the brown recluse spider reliably progress to necrosis. In other countries, spiders of the genus, such as the Chilean recluse in South America, are also known to cause necrosis
Necrosis
–
Severe tissue necrosis following
B. asper envenomation - the victim was an 11-year-old boy, bitten two weeks earlier in
Ecuador, but treated only with
antibiotics.
Necrosis
–
Structural changes of cells undergoing necrosis and
apoptosis
26.
International Standard Book Number
–
The International Standard Book Number is a unique numeric commercial book identifier. An ISBN is assigned to each edition and variation of a book, for example, an e-book, a paperback and a hardcover edition of the same book would each have a different ISBN. The ISBN is 13 digits long if assigned on or after 1 January 2007, the method of assigning an ISBN is nation-based and varies from country to country, often depending on how large the publishing industry is within a country. The initial ISBN configuration of recognition was generated in 1967 based upon the 9-digit Standard Book Numbering created in 1966, the 10-digit ISBN format was developed by the International Organization for Standardization and was published in 1970 as international standard ISO2108. Occasionally, a book may appear without a printed ISBN if it is printed privately or the author does not follow the usual ISBN procedure, however, this can be rectified later. Another identifier, the International Standard Serial Number, identifies periodical publications such as magazines, the ISBN configuration of recognition was generated in 1967 in the United Kingdom by David Whitaker and in 1968 in the US by Emery Koltay. The 10-digit ISBN format was developed by the International Organization for Standardization and was published in 1970 as international standard ISO2108, the United Kingdom continued to use the 9-digit SBN code until 1974. The ISO on-line facility only refers back to 1978, an SBN may be converted to an ISBN by prefixing the digit 0. For example, the edition of Mr. J. G. Reeder Returns, published by Hodder in 1965, has SBN340013818 -340 indicating the publisher,01381 their serial number. This can be converted to ISBN 0-340-01381-8, the check digit does not need to be re-calculated, since 1 January 2007, ISBNs have contained 13 digits, a format that is compatible with Bookland European Article Number EAN-13s. An ISBN is assigned to each edition and variation of a book, for example, an ebook, a paperback, and a hardcover edition of the same book would each have a different ISBN. The ISBN is 13 digits long if assigned on or after 1 January 2007, a 13-digit ISBN can be separated into its parts, and when this is done it is customary to separate the parts with hyphens or spaces. Separating the parts of a 10-digit ISBN is also done with either hyphens or spaces, figuring out how to correctly separate a given ISBN number is complicated, because most of the parts do not use a fixed number of digits. ISBN issuance is country-specific, in that ISBNs are issued by the ISBN registration agency that is responsible for country or territory regardless of the publication language. Some ISBN registration agencies are based in national libraries or within ministries of culture, in other cases, the ISBN registration service is provided by organisations such as bibliographic data providers that are not government funded. In Canada, ISBNs are issued at no cost with the purpose of encouraging Canadian culture. In the United Kingdom, United States, and some countries, where the service is provided by non-government-funded organisations. Australia, ISBNs are issued by the library services agency Thorpe-Bowker
International Standard Book Number
–
A 13-digit ISBN, 978-3-16-148410-0, as represented by an
EAN-13 bar code
27.
PubMed Identifier
–
PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval, from 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home-, the PubMed system was offered free to the public in June 1997, when MEDLINE searches via the Web were demonstrated, in a ceremony, by Vice President Al Gore. Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog. As of 5 January 2017, PubMed has more than 26.8 million records going back to 1966, selectively to the year 1865, and very selectively to 1809, about 500,000 new records are added each year. As of the date,13.1 million of PubMeds records are listed with their abstracts. In 2016, NLM changed the system so that publishers will be able to directly correct typos. Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMeds search window, when a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are, Article Type, Secondary identifiers, Language, publication type parameter enables many special features. As these clinical girish can generate small sets of robust studies with considerable precision, since July 2005, the MEDLINE article indexing process extracts important identifiers from the article abstract and puts those in a field called Secondary Identifier. The secondary identifier field is to store numbers to various databases of molecular sequence data, gene expression or chemical compounds. For clinical trials, PubMed extracts trial IDs for the two largest trial registries, ClinicalTrials. gov and the International Standard Randomized Controlled Trial Number Register, a reference which is judged particularly relevant can be marked and related articles can be identified. If relevant, several studies can be selected and related articles to all of them can be generated using the Find related data option, the related articles are then listed in order of relatedness. To create these lists of related articles, PubMed compares words from the title and abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm. The related articles function has been judged to be so precise that some researchers suggest it can be used instead of a full search, a strong feature of PubMed is its ability to automatically link to MeSH terms and subheadings. Examples would be, bad breath links to halitosis, heart attack to myocardial infarction, where appropriate, these MeSH terms are automatically expanded, that is, include more specific terms. Terms like nursing are automatically linked to Nursing or Nursing and this important feature makes PubMed searches automatically more sensitive and avoids false-negative hits by compensating for the diversity of medical terminology. The My NCBI area can be accessed from any computer with web-access, an earlier version of My NCBI was called PubMed Cubby
PubMed Identifier
–
PubMed
28.
Medical Subject Headings
–
Medical Subject Headings is a comprehensive controlled vocabulary for the purpose of indexing journal articles and books in the life sciences, it serves as a thesaurus that facilitates searching. Created and updated by the United States National Library of Medicine, it is used by the MEDLINE/PubMed article database, MeSH is also used by ClinicalTrials. gov registry to classify which diseases are studied by trials registered in ClinicalTrials. gov. MeSH was introduced in 1960, with the NLMs own index catalogue, the yearly printed version of MeSH was discontinued in 2007 and MeSH is now available online only. It can be browsed and downloaded free of charge through PubMed, originally in English, MeSH has been translated into numerous other languages and allows retrieval of documents from different languages. The 2009 version of MeSH contains a total of 25,186 subject headings, most of these are accompanied by a short description or definition, links to related descriptors, and a list of synonyms or very similar terms. This additional information and the structure make the MeSH essentially a thesaurus. The descriptors or subject headings are arranged in a hierarchy, a given descriptor may appear at several locations in the hierarchical tree. The tree locations carry systematic labels known as numbers. The tree numbers of a given descriptor are subject to change as MeSH is updated, every descriptor also carries a unique alphanumerical ID that will not change. Most subject headings come with a description or definition. See the MeSH description for diabetes type 2 as an example, the explanatory text is written by the MeSH team based on their standard sources if not otherwise stated. References are mostly encyclopaedias and standard textbooks of the subject areas, references for specific statements in the descriptions are not given, instead readers are referred to the bibliography. In addition to the hierarchy, MeSH contains a small number of standard qualifiers. For example, Measles is a descriptor and epidemiology is a qualifier, the epidemiology qualifier can be added to all other disease descriptors. Not all descriptor/qualifier combinations are allowed some of them may be meaningless. In all there are 83 different qualifiers, in addition to the descriptors, MeSH also contains some 139,000 supplementary concept records. These do not belong to the vocabulary as such, instead they enlarge the thesaurus. Many of these records describe chemical substances, by default, a search for a descriptor will include all the descriptors in the hierarchy below the given one
Medical Subject Headings
–
Medical Subject Headings
29.
Prokaryote
–
A prokaryote is a unicellular organism that lacks a membrane-bound nucleus, mitochondria, or any other membrane-bound organelle. The word prokaryote comes from the Greek πρό before and καρυόν nut or kernel, prokaryotes can be divided into two domains, Archaea and bacteria. In contrast, species with nuclei and organelles are placed in the domain Eukaryota, in the prokaryotes, all the intracellular water-soluble components are located together in the cytoplasm enclosed by the cell membrane, rather than in separate cellular compartments. Bacteria, however, do possess protein-based bacterial microcompartments, which are thought to act as primitive organelles enclosed in protein shells, some prokaryotes, such as cyanobacteria may form large colonies. Others, such as myxobacteria, have multicellular stages in their life cycles, molecular studies have provided insight into the evolution and interrelationships of the three domains of biological species. Eukaryotes are organisms, including humans, whose cells have a well defined membrane-bound nucleus, the division between prokaryotes and eukaryotes reflects the existence of two very different levels of cellular organization. Distinctive types of prokaryotes include extremophiles and methanogens, these are common in extreme environments. Prokaryotes have a cytoskeleton, albeit more primitive than that of the eukaryotes. At least some also contain intracellular structures that can be seen as primitive organelles. Membranous organelles are known in some groups of prokaryotes, such as vacuoles or membrane systems devoted to special metabolic properties, in addition, some species also contain carbohydrate-enclosed microcompartments, which have distinct physiological roles. Most prokaryotes are between 1 µm and 10 µm, but they can vary in size from 0.2 µm to 750 µm, Bacteria and archaea reproduce through asexual reproduction, usually by binary fission. DNA transfer between prokaryotic cells occurs in bacteria and archaea, although it has mainly studied in bacteria. In bacteria, gene transfer occurs by three processes and these are bacterial virus -mediated transduction, plasmid-mediated conjugation, and natural transformation. Transduction of bacterial genes by bacteriophage appears to reflect an occasional error during intracellular assembly of virus particles, the transfer of bacterial DNA is under the control of the bacteriophage’s genes rather than bacterial genes. Conjugation in the well-studied E. coli system is controlled by plasmid genes, infrequently during this process, a plasmid may integrate into the host bacterial chromosome, and subsequently transfer part of the host bacterial DNA to another bacterium. Plasmid mediated transfer of host bacterial DNA also appears to be a process rather than a bacterial adaptation. Natural bacterial transformation involves the transfer of DNA from one bacterium to another through the intervening medium, for a bacterium to bind, take up and recombine donor DNA into its own chromosome, it must first enter a special physiological state called competence. About 40 genes are required in Bacillus subtilis for the development of competence, the length of DNA transferred during B. subtilis transformation can be as much as a third to the whole chromosome
Prokaryote
–
Cell structure of a
bacterium, a member of one of the two domains of prokaryotic life
30.
Bacterial phyla
–
The bacterial phyla are the major lineages, known as phyla or divisions, of the domain Bacteria. In the scientific classification established by Carl von Linné, each bacterial strain has to be assigned to a species, currently, the most accepted mega-classification system is under the three-domain system, which is based on molecular phylogeny. In that system, bacteria are members of the domain Bacteria and phylum is the rank below domain, in this classification scheme, Bacteria is subdivided into 30 phyla with representatives cultured in a lab. Many major clades of bacteria that cannot currently be cultured are known solely and somewhat indirectly through metagenomics, if these possible clades, candidate phyla, are included, the number of phyla is 52 or higher. Therefore, the number of major phyla has increased from 12 identifiable lineages in 1987, to 30 in 2014, the total number has been estimated to exceed 1,000 bacterial phyla. Traditionally, phylogeny was inferred and taxonomy established based on studies of morphology, recently molecular phylogenetics has been used to allow better elucidation of the evolutionary relationship of species by analysing their DNA and protein sequences, for example their ribosomal DNA. Another candidate phylum, called Tectomicrobia, was found living in symbiosis with sponges. And Nitrospina gracilis, which had long eluded phylogenetic placement, was proposed to belong to a new phylum, other candidate phyla that have been the center of some studies are TM7, the genomes of organisms of which have even been sequenced, WS6 and Marine Group A. One species, Caldisericum exile, of the candidate phylum OP5 was cultured, the candidate phylum VadinBE97 is now known as Lentisphaerae after Lentisphaera araneosa and Victivallis vadensis were cultured. Despite the unclear branching order for most bacterial phyla, several groups of phyla have clear clustering and are referred to as superphyla, the PVC group includes Chlamydiae, Lentisphaerae, candidate phylum Omnitrophica, Planctomycetes, candidate phylum Poribacteria, and Verrucomicrobia. The proposed superphylum, Patescibacteria, includes candidate phyla Gracilibacteria, Microgenomates, Parcubacteria and these same candidate phyla, along with candidate phyla Berkelbacteria, CPR2, CPR3, Kazan, Perigrinibacteria, SM2F11, WS6, and WWE3 were more recently proposed to belong to the larger CPR Group. To complicate matters, it has suggested that several of these phyla are themselves actually superphyla. The proposed superphylum, Terrabacteria, includes Actinobacteria, Cyanobacteria, Deinococcus–Thermus, Chloroflexi, Firmicutes and it has been proposed that several of the classes of the phylum Proteobacteria are phyla in their own right, which would make Proteobacteria a superphylum. Several candidate phyla and several accepted phyla have been suggested to actually be superphyla that were described as phyla because rules for defining a bacterial phylum are lacking. As of January 2016, there are 30 phyla in the domain Bacteria accepted by LPSN, there are no fixed rules to the nomenclature of bacterial phyla. The Acidobacteria is most abundant bacterial phylum in many soils, additionally, they phenotypically diverse and include not only acidophiles, but also many non-acidophiles. Generally its members divide slowly, exhibit slow metabolic rates under low-nutrient conditions, the Actinobacteria is a phylum of monoderm Gram positive bacteria, many of which are notable secondary metabolite producers. Notable genera/species include Streptomyces, Propionibacterium acnes and Propionibacterium freudenreichii The Aquificae contains only 14 genera, the species are hyperthermophiles and chemolithotrophs
Bacterial phyla
31.
Domain (biology)
–
In biological taxonomy, a domain is the highest taxonomic rank of organisms in the three-domain system of taxonomy designed by Carl Woese, an American microbiologist and biophysicist. According to the Woese system, introduced in 1990, the tree of life consists of three domains, Archaea, Bacteria, and Eukarya, the first two are all prokaryotic microorganisms, or single-celled organisms whose cells have no nucleus. All life that has a nucleus and membrane-bound organelles, and multicellular organisms, is included in the Eukarya, stefan Luketa in 2012 proposed the five-domain system of life with both cellular and non-cellular organisms. The term domain is proposed by Woese et al. in his three-domain system and this term represents a synonym for the category of dominion, introduced by Moore in 1974. However, only S. Luketa uses the term dominion, each of these three domains of life recognized by biologists today contain unique rRNA. This fact in itself forms the basis of the three-domain system, Archaea are prokaryotic cells, typically characterized by membrane lipids that are branched hydrocarbon chains attached to glycerol by ether linkages. The presence of ether linkages in Archaea adds to their ability to withstand extreme temperatures and highly acidic conditions. Halophiles, organisms that thrive in salty environments, and hyperthermophiles. Archaea evolved many cell sizes, but all are relatively small and their size ranges from 0.1 to 15 μ diameter and up to 200 μ long. They are about the size of bacteria or similar to the size of a mitochondrion in a eukaryotic cell, members of the genus Thermoplasma are the smallest of the archaea. Even though bacteria are prokaryotic cells just like Archaea, their membranes are made of unbranched fatty acid chains attached to glycerol by ester linkages, cyanobacteria and mycoplasmas are two examples of bacteria. They characteristically do not have ether linkages like Archaea, and they are grouped into a different category—and hence a different domain. There is a deal of diversity in this domain. Members of the domain Eukarya have membrane-bound organelles and are represented by four kingdoms, Plantae, Protista, Animalia, none of the three systems currently include non-cellular life. As of 2011 there is talk about Nucleocytoplasmic large DNA viruses possibly being a branch domain of life. Stefan Luketa in 2012 proposed a system, adding Prionobiota and Virusobiota to the traditional three domains. Alternative classifications of life so far proposed include, The two-empire system or superdomain system, the eocyte hypothesis, first proposed by James A. Lake et al. in 1984, which posits two domains
Domain (biology)
–
The three-domain system comprises,
Eukaryota (represented by the
Australian green tree frog, left),
Bacteria (represented by
Staphylococcus aureus, middle) and
Archaea (represented by
Sulfolobus, right).
Domain (biology)
Domain (biology)
32.
Kingdom (biology)
–
In biology, kingdom is the second highest taxonomic rank below domain. Kingdoms are divided into groups called phyla. Traditionally, textbooks from the United States used a system of six kingdoms while textbooks in Great Britain, India, Australia, Latin America and other countries used five kingdoms. Later two further main ranks were introduced, making the kingdom, phylum or division, class, order, family, genus. In the 1960s a rank was introduced above kingdom, namely domain, prefixes can be added so subkingdom and infrakingdom are the two ranks immediately below kingdom. Superkingdom may be considered as an equivalent of domain or empire or as an independent rank between kingdom and domain or subdomain, in some classification systems the additional rank branch can be inserted between subkingdom and infrakingdom. Taxonomic ranks, including kingdoms, were to be groups of organisms with a common ancestor, based on such RNA studies, Carl Woese thought life could be divided into three large divisions and referred to them as the three primary kingdom model or urkingdom model. In 1990, the domain was proposed for the highest rank. This term represents a synonym for the category of dominion, introduced by Moore in 1974, unlike Moore, Whoese et al. did not suggest a Latin term for this category, which represents a further argument supporting the accurately introduced term dominion. It was also found that the eukaryotes are more related to the Archaea than they are to the Eubacteria. Although the primacy of the Eubacteria-Archaea divide has been questioned, it has been upheld by subsequent research, there is no consensus on how many kingdoms exist in the classification scheme proposed by Woese. In 2004, a article by Simpson and Roger noted that the Protista were a grab-bag for all eukaryotes that are not animals. On this basis, the diagram opposite showed the real kingdoms of the eukaryotes, a classification which followed this approach was produced in 2005 for the International Society of Protistologists, by a committee which worked in collaboration with specialists from many societies. It divided the eukaryotes into the same six supergroups, the published classification deliberately did not use formal taxonomic ranks, including that of kingdom. In this system the multicellular animals are descended from the same ancestor as both the unicellular choanoflagellates and the fungi which form the Opisthokonta, Plants are thought to be more distantly related to animals and fungi. Beyond this, there does not appear to be a consensus, rogozin et al. in 2009 noted that The deep phylogeny of eukaryotes is an extremely difficult and controversial problem. The classification of living things into animals and plants is an ancient one, aristotle classified animal species in his History of Animals, while his pupil Theophrastus wrote a parallel work, the Historia Plantarum, on plants. Carl Linnaeus laid the foundations for biological nomenclature, now regulated by the Nomenclature Codes
Kingdom (biology)
33.
Bacterial outer membrane
–
The bacterial outer membrane is found in gram-negative bacteria. Coli it is linked to the cells peptidoglycan by Brauns lipoprotein, porins can be found in this layer. If lipid A, part of the LPS, enters the system it causes a toxic reaction by activating TLR4. Lipid A is very pathogenic and not immunogenic, however, the polysaccharide component is very immunogenic, but not pathogenic, causing an aggressive response by the immune system. The sufferer will have a temperature and respiration rate and a low blood pressure. This may lead to shock, which may be fatal. The machinery and the source that drive this process are not yet fully understood. O-antigen repeat units are then polymerised in the periplasm by the Wzy polymerase, the LPS transport machinery is composed of LptA, LptB, LptC, LptD, LptE. This supported by the fact that depletion of any one of these blocks the LPS assembly pathway. Moreover, the location of at least one of five proteins in every cellular compartment suggests a model for how the LPS assembly pathway is organised and ordered in space. LptC is required for the translocation of lipopolysaccharide from the membrane to the outer membrane. LptE forms a complex with LptD, which is involved in the assembly of LPS in the leaflet of the outer membrane and is essential for envelope biogenesis
Bacterial outer membrane
–
Structure of gram-negative cell envelope
34.
Terrabacteria
–
Terrabacteria is a taxon containing approximately two-thirds of prokaryote species, including those in the gram positive phyla as well as the phyla Cyanobacteria, Chloroflexi, and Deinococcus-Thermus. It derives its name from the pressures of life on land. Terrabacteria possess important adaptations such as resistance to hazards and oxygenic photosynthesis. Also, the properties of the cell wall in gram-positive taxa. These results now leave open the possibility that terrestrial adaptations may have played a role in prokaryote evolution than currently understood. Terrabacteria was proposed in 2004 for Actinobacteria, Cyanobacteria, and Deinococccus-Thermus and was expanded later to include Firmicutes, other phylogenetic analyses have supported the close relationships of these phyla. Most species of prokaryotes not placed in Terrabacteria were assigned to the taxon Hydrobacteria, Terrabacteria and Hydrobacteria were inferred to have diverged approximately 3 billion years ago, suggesting that land had been colonized by prokaryotes at that time. Together, Terrabacteria and Hydrobacteria form a group containing 99% of all Eubacteria
Terrabacteria
–
Terrabacteria
35.
Thermophile
–
A thermophile is an organism—a type of extremophile—that thrives at relatively high temperatures, between 41 and 122 °C. Thermophilic eubacteria are suggested to have been among the earliest bacteria, unlike other types of bacteria, thermophiles can survive at much hotter temperatures, whereas other bacteria would be damaged and sometimes killed if exposed to the same temperatures. As a prerequisite for their survival, thermophiles contain enzymes that can function at high temperatures, some of these enzymes are used in molecular biology, and in washing agents. Thermophile is derived from the Greek, θερμότητα, meaning heat, thermophiles are classified into 1. obligate and 2. Facultative 3. hyper thermophiles, Obligate thermophiles require such high temperatures for growth, whereas Facultative thermophiles can thrive at high temperatures, hyperthermophiles are particularly extreme thermophiles for which the optimal temperatures are above 80 °C. Bacteria within the Alicyclobacillus genus are acidophilic thermophiles, which can cause contamination in fruit juice drinks. Thermophiles, meaning heat-loving, are organisms with a growth temperature of 50 °C or more, a maximum of up to 70 °C or more, and a minimum of about 40 °C. Some extreme thermophiles require a high temperature for growth. Their membranes and proteins are stable at these extremely high temperatures. Thus, many important biotechnological processes use thermophilic enzymes because of their ability to withstand intense heat, many of the hyperthermophiles Archea require elemental sulfur for growth. Some are anaerobes that use the sulfur instead of oxygen as an electron acceptor during cellular respiration, some are lithotrophs that oxidize sulfur to sulfuric acid as an energy source, thus requiring the microorganism to be adapted to very low pH. These organisms are inhabitants of hot, sulfur-rich environments usually associated with volcanism, such as hot springs, geysers, in these places, especially in Yellowstone National Park, zonation of microorganisms according to their temperature optima occurs. Often, these organisms are colored, due to the presence of photosynthetic pigments, thermophiles can be discriminated from mesophiles from genomic features. Sulfolobus solfataricus and Sulfolobus acidocaldarius are hyperthermophilic archaea, when these organisms are exposed to the DNA damaging agents UV irradiation, bleomycin or mitomycin C, species-specific cellular aggregation is induced. In S. acidocaldarius, UV-induced cellular aggregation mediates chromosomal marker exchange with high frequency, recombination rates exceed those of uninduced cultures by up to three orders of magnitude. Van Wolferen et al. in discussing DNA exchange in the hyperthermophiles under extreme conditions and they suggested that this process is crucial under DNA damaging conditions such as high temperature. Hyperthermophile Mesophile Psychrophile Anaerobic digestion Archaea Sulfolobus Thermoprotei, Extreme Thermophile
Thermophile
–
Thermophiles produce some of the bright colors of
rainbow, Graystone National Park
Thermophile
–
A colony of thermophiles in the outflow of
Mickey Hot Springs,
Oregon, the water temperature is approximately 60°C.
36.
Cyanobacteria
–
The name cyanobacteria comes from the color of the bacteria. Sometimes, they are called blue-green algae, and incorrectly so, because cyanobacteria are prokaryotes, like other prokaryotes, cyanobacteria have no membrane-sheathed organelles. Photosynthesis is performed in distinctive folds in the membrane of the cell. Biologists commonly agree that chloroplasts found in eukaryotes have their ancestry in cyanobacteria, via a process called endosymbiosis, Cyanobacteria are a group of photosynthetic, nitrogen fixing bacteria that live in a wide variety of habitats such as moist soils and in water. They may be free-living or form relationships with plants or with lichen-forming fungi as in the lichen genus Peltigera. They range from unicellular to filamentous and include colonial species, colonies may form filaments, sheets, or even hollow balls. Cyanobacteria can fix nitrogen in anaerobic conditions by means of specialized cells called heterocysts. Heterocysts may also form under the environmental conditions when fixed nitrogen is scarce. Free-living cyanobacteria are present in the column in rice paddies, and cyanobacteria can be found growing as epiphytes on the surfaces of the green alga, Chara. Cyanobacteria such as, can provide rice plantations with biofertilizer, many cyanobacteria form motile filaments of cells, called hormogonia, that travel away from the main biomass to bud and form new colonies elsewhere. The cells in a hormogonium are often thinner than in the state. To break away from the parent colony, a hormogonium often must tear apart a weaker cell in a filament, each individual cell of a cyanobacterium typically has a thick, gelatinous cell wall. They lack flagella, but hormogonia of some species can move about by gliding along surfaces, many of the multicellular filamentous forms of Oscillatoria are capable of a waving motion, the filament oscillates back and forth. In water columns, some cyanobacteria float by forming gas vesicles and these vesicles are not organelles as such. They are not bounded by membranes, but by a protein sheath. Cyanobacteria can be found in almost every terrestrial and aquatic habitat—oceans, fresh water, damp soil, temporarily moistened rocks in deserts, bare rock and soil and they can occur as planktonic cells or form phototrophic biofilms. They are found in almost every endolithic ecosystem, a few are endosymbionts in lichens, plants, various protists, or sponges and provide energy for the host. Some live in the fur of sloths, providing a form of camouflage, aquatic cyanobacteria are known for their extensive and highly visible blooms that can form in both freshwater and marine environments
Cyanobacteria
–
Had'n
Cyanobacteria
–
A cyanobacterial bloom near
Fiji
Cyanobacteria
–
Colonies of
Nostoc pruniforme
Cyanobacteria
–
Cylindrospermum sp.
37.
Alphaproteobacteria
–
Alphaproteobacteria is a class of bacteria in the phylum Proteobacteria. Its members are diverse and possess few commonalities, but nevertheless share a common ancestor. Like all Proteobacteria, its members are Gram-negative and some of its intracellular parasitic members lack peptidoglycan and are consequently gram variable. Moreover, the class includes the protomitochondrion, the bacterium that was engulfed by the ancestor and gave rise to the mitochondria. A species of technological interest is Rhizobium radiobacter, scientists use this species to transfer foreign DNA into plant genomes. There is some disagreement on the phylogeny of the orders, especially for the location of the Pelagibacterales and this issue stems form the large difference in gene content and the large difference in GC-richness between members of several order. Specifically, Pelagibacterales, Rickettsiales and Holosporales contains species with AT-rich genomes and it has been argued that it could be a case of convergent evolution that would result in an artefactual clustering. The basal group is Magnetococcidae, which is composed by a diversity of magnetotactic bacteria. The Rickettsidae is composed of the intracellular Rickettsiales and the free-living Pelagibacterales, the Caulobacteridae is composed of the Holosporales, Rhodospirillales, Sphingomonadales, Rhodobacterales, Caulobacterales, Kiloniellales, Kordiimonadales, Parvularculales and Sneathiellales. These molecular signatures provide novel means for the circumscription of these taxonomic groups, alphaproteobacteria at the US National Library of Medicine Medical Subject Headings Bacterial Phylogeny Webpage, Alpha Proteobacteria
Alphaproteobacteria
–
Alphaproteobacteria
38.
Rhizobiales
–
The Rhizobiales are an order of Gram-negative Alphaproteobacteria. The rhizobia, which fix nitrogen and are symbiotic with plant roots, the four families Bradyrhizobiaceae, Hyphomicrobiaceae, Phyllobacteriaceae, and Rhizobiaceae contain at least six genera of nitrogen-fixing, legume-nodulating, microsymbiotic bacteria. Examples are the genera Bradyrhizobium and Rhizobium, species of the Methylocystaceae are methanotrophs, they use methanol or methane as their sole energy and carbon sources. Other important genera are Bartonella and Agrobacterium, natural genetic transformation has been reported in at least three Rhizobiales species, Agrobacterium tumefaciens, Methylobacterium organophilum, and Bradyrhizobium japonicum. Kuykendall, L. D. and Dazzo, F. B, in Brenner, Krieg, Staley and Garrity, The Alpha-, Beta-, Delta- and Epsilonproteobacteria, The Proteobacteria, Part C, Bergey’s Manual of Systematic Bacteriology, 2nd. Vol.2, Springer, New York, NY, pp. 345–346, kuykendall, L. D.2005 Genus Azorhizobium. In Brenner, Krieg, Staley and Garrity, The Alpha-, Beta-, Delta- and Epsilonproteobacteria, The Proteobacteria, Part C, Bergey’s Manual of Systematic Bacteriology,2, Springer, New York, NY, pp. 505–506. In, Bergeys Manual of Systematic Bacteriology, 2nd Edition, 2nd Volume, george Garrity, Springer–Verlag, New York, NY, pp. 438–443. Chen, W. X. E. T. Wang, in, Bergeys Manual of Systematic Bacteriology, 2nd Edition, 2nd Volume. George Garrity, Springer–Verlag, New York, NY, pp. 403–408, J. M. Young, E. Martínez-Romero, A. Kerr, and H. Sawada. Genus Rhizobium, a highly divergent genus in a revised family, in, Bergeys Manual of Systematic Bacteriology, 2nd Edition, 2nd Volume. George Garrity, Springer–Verlag, New York, NY, pp. 324–340
Rhizobiales
–
Rhizobiales
39.
Rickettsiales
–
The Rickettsiales, also called rickettsias, are an order of small proteobacteria. Most of those described survive only as endosymbionts of other cells, some are notable pathogens, including Rickettsia, which causes a variety of diseases in humans. On the other end of the scale, genetic studies support the theory according to which mitochondria. Some have also speculated that viruses might have developed from them, the Rickettsiales are among the most mysterious groups of Proteobacteria, owing largely to difficulties in cultivating them. The group includes all obligate endosymbiont bacteria, however, a number of species have been removed, such as Coxiella burnetii, the cause of Q fever. The Rickettsiales has an order the Pelagibacterales, which is composed of free living bacteria with extremely streamlined genomes. The relation between the two order is retained in the subclass, the Rickettsidae, which include the Rickettsiales, the Pelagibacteriales and the extinct protomitochondrion
Rickettsiales
–
Rickettsias
40.
Alteromonadales
–
The Alteromonadales are an order of Proteobacteria. Although they have been treated as a family, the Alteromonadaceae. The cells are straight or curved rods and they are motile by the use of a single flagellum. Most of the species are marine, george M. Garrity, Bergeys Manual of Systematic Bacteriology. Springer, New York,2005, Volume 2, The Proteobacteria, Part B, The Gammaproteobacteria Elena P. Ivanova, Sebastien Flavier, phylogenetic relationships among marine Alteromonas-like proteobacteria, emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov. Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov, international Journal of Systematic and Evolutionary Microbiology 54, 1773-1788
Alteromonadales
–
Alteromonadales
41.
Legionellales
–
The Legionellales are an order of Proteobacteria. Like all Proteobacteria, they are Gram-negative and they comprise two families, typified by Legionella and Coxiella, both of which include notable pathogens. For example, Q fever is caused by Coxiella burnetii and Legionella pneumophila causes Legionnaires disease, Legionellales LPSN List of Prokaryotic names with Standing in Nomenclature
Legionellales
–
Legionellales
42.
Methylococcales
–
The Methylococcaceae are a family of bacteria that obtain their carbon and energy from methane, called methanotrophs. They comprise the type I methanotrophs, in contrast to the Methylocystaceae or type II methanotrophs and they belong among the gamma subdivision of the Proteobacteria, and are typically given their own order. The Methylococcaceae have internal membranes in the form of flattened discs, methane is oxidized to give formaldehyde, which is fixed by a process called the RuMP cycle. Here formaldehyde is combined with sugar ribulose, producing hexulose and this, in turn, is broken down to produce glyceraldehyde, which is used to produce new ribulose and other organic compounds. Catabolism does not involve a complete citric acid cycle, some species of the Methylococcaceae have formed with certain marine mussels endosymbiotic relationships. Methylococcaceae J. P. Euzéby, List of Prokaryotic names with Standing in Nomenclature
Methylococcales
–
Methylococcaceae
43.
Oceanospirillales
–
The Oceanospirillales are an order of Proteobacteria, with seven families. Most species of order are halotolerant or halophilic. One strain of Oceanospirillales is an endosymbiont of the Osedax worms and they are not present in Osedax oocytes so they are later acquired. J. P. Euzéby, List of Prokaryotic names with Standing in Nomenclature
Oceanospirillales
–
Oceanospirillales
44.
Pasteurellales
–
The Pasteurellaceae comprise a large family of Gram-negative bacteria. Most members live as commensals on mucosal surfaces of birds and mammals, Pasteurellaceae are typically rod-shaped, and are a notable group of facultative anaerobes. Their biochemical characteristics can be distinguished from the related Enterobacteriaceae by the presence of oxidase, Haemophilus influenzae was the first organism to have its genome sequenced and has been studied intensively by genetic and molecular methodologies. The Haemophilus genus is a human pathogen associated with bacteremia, pneumonia, meningitis. Other pathogenic members belonging to the Pasteurellaceae family include Aggregatibacter, Mannheimia, Pasteurella, based upon many other CSIs that are specific for subgroups of Pasteurellaceae species, it has been proposed to divide the family into at least two clades. These genera demonstrate extensive polyphyly across the family, however, CSIs have been found to be shared by certain species that form a monophyletic group within each respective genus. The distribution of CSIs corresponds to sensu stricto clades of true Actinobacillus, Haemophilus, CSIs have also been found that are specific for Aggregatibacter and Mannheimia, two clinically relevant genera. The Pasteurellales, along with Enterobacteriales, are of the most recently divergent orders within the Gammaproteobacteria and their distinction from all other orders are supported by the presence of several conserved signature proteins that are shared by these two orders, and absent from all other bacteria
Pasteurellales
–
Pasteurellaceae
45.
Pseudomonadales
–
The Pseudomonadales are an order of Proteobacteria. A few members are opportunistic pathogens, such as species of Pseudomonas, Moraxella, and Acinetobacter, P. aeruginosa can cause chronic opportunistic infections that have become increasingly apparent in immunocompromised patients and the ageing population of industrialised societies. The genome sequences of several pseudomonads have become available in recent years and researchers are beginning to use the data to new discoveries about this bacterium. The genus Acinetobacter is a group of Gram-negative, nonmotile and nonfermentative bacteria belonging to the family Moraxellaceae and they are important soil organisms where they contribute to the mineralisation of, for example, aromatic compounds. Acinetobacter species are able to survive on surfaces in the hospital environment. These bacteria are resistant to many classes of antibiotics. In addition, Acinetobacter is uniquely suited to exploitation for biotechnological purposes
Pseudomonadales
–
Pseudomonadales
46.
Vibrionales
–
The Vibrionaceae are a family of Proteobacteria given their own order. Inhabitants of fresh or salt water, several species are pathogenic, including the type species Vibrio cholerae, most bioluminescent bacteria belong to this family, and are typically found as symbionts of deep-sea animals. Vibrionaceae are Gram-negative organisms and facultative anaerobes, capable of fermentation and they contain oxidase and have one or more flagella, which are generally polar. Originally, these characteristics defined the family, which was divided into four genera, two of these, Vibrio and Photobacterium, correspond to the modern group, although several new genera have been defined. Genetic studies have shown the two original members—Aeromonas and Plesiomonas—belong to separate families. As mentioned above, Vibrionaceae bacteria are in symbiosis with marine organisms. A characteristic of the family is the broad host range susceptible to infection by vibrios, pathogens of man, other than V. cholerae, include V. parahemolyticus, a cause of gastroenteritis and V. vulnificus that can lead to acute and fatal septicaemia. Species such as V. tubiashii cause disease in larval stages of Pacific oyster while V. harveyi causes luminous vibriosis in penaeid shrimps. The extent of the host range is seen with such as V. mediterranei and V. coralliilyticus, which can infect zooxanthellae. These species of Vibrio are thought to be a cause of coral bleaching
Vibrionales
–
Vibrionaceae
