1.
Taxonomy (biology)
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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
2.
Bacterium
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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
3.
Proteobacteria
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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
4.
Gammaproteobacteria
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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
5.
Legionellales
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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
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Legionella
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Legionella may be readily visualized with a silver stain or cultured in cysteine-containing media such as BCYE. It is common in environments, including soil and aquatic systems. The bacterium, however, is not transmissible from person to person, furthermore, the side chains of the cell wall carry the bases responsible for the somatic antigen specificity of these organisms. Legionella acquired its name after an outbreak of a mystery disease sickened 221 persons. The outbreak was first noticed among people attending a convention of the American Legion—an association of U. S. military veterans, the convention occurred in Philadelphia during the U. S. Bicentennial year in July 21–24,1976, on January 18,1977, the causative agent was identified as a previously unknown bacterium subsequently named Legionella. See Legionnaires disease for full details, Legionella is traditionally detected by culture on buffered charcoal yeast extract agar. Legionella requires the presence of cysteine and iron to grow, so does not grow on blood agar media used for laboratory-based total viable counts or on-site dipslides. Heat or acid treatment are used to reduce interference from other microbes in the sample. After incubation for up to 10 days, suspect colonies are confirmed as Legionella if they grow on BCYE containing cysteine, immunological techniques are then commonly used to establish the species and/or serogroups of bacteria present in the sample. Consequently, the clinical and environmental prevalence of the bacteria is likely to be underestimated due to false negatives inherent in the current lab methodology. Many hospitals use the Legionella urinary antigen test for detection when Legionella pneumonia is suspected. New techniques for the detection of Legionella in water samples are emerging, including the use of polymerase chain reaction. These technologies can provide much faster results. Government public health surveillance has demonstrated increasing proportions of drinking water–associated outbreaks specifically in healthcare settings, in the natural environment, Legionella lives within amoebae such as Acanthamoeba spp. Upon inhalation, the bacteria can infect alveolar macrophages, subverting the normal host cell machinery to create a niche where the bacteria can replicate and this results in Legionnaires disease and the lesser form, Pontiac fever. Legionella transmission is via inhalation of water droplets from a source that has allowed the organism to grow. Less commonly, transmission can occur via aspiration of drinking water from an infected source, person-to-person transmission has not been demonstrated, though, it could be possible in rare cases
7.
Binomial nomenclature
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Such a name is called a binomial name, a binomen, binominal name or a scientific name, more informally it is also called a Latin name. The first part of the name identifies the genus to which the species belongs, for example, humans belong to the genus Homo and within this genus to the species Homo sapiens. The formal introduction of system of naming species is credited to Carl Linnaeus. But Gaspard Bauhin, in as early as 1623, had introduced in his book Pinax theatri botanici many names of genera that were adopted by Linnaeus. Although the general principles underlying binomial nomenclature are common to these two codes, there are differences, both in the terminology they use and in their precise rules. Similarly, both parts are italicized when a binomial name occurs in normal text, thus the binomial name of the annual phlox is now written as Phlox drummondii. In scientific works, the authority for a name is usually given, at least when it is first mentioned. In zoology Patella vulgata Linnaeus,1758, the original name given by Linnaeus was Fringilla domestica, the parentheses indicate that the species is now considered to belong in a different genus. The ICZN does not require that the name of the person who changed the genus be given, nor the date on which the change was made, in botany Amaranthus retroflexus L. – L. is the standard abbreviation used in botany for Linnaeus. – Linnaeus first named this bluebell species Scilla italica, Rothmaler transferred it to the genus Hyacinthoides, the ICN does not require that the dates of either publication be specified. Prior to the adoption of the binomial system of naming species. Together they formed a system of polynomial nomenclature and these names had two separate functions. First, to designate or label the species, and second, to be a diagnosis or description, such polynomial names may sometimes look like binomials, but are significantly different. For example, Gerards herbal describes various kinds of spiderwort, The first is called Phalangium ramosum, Branched Spiderwort, is aptly termed Phalangium Ephemerum Virginianum, Soon-Fading Spiderwort of Virginia. The Latin phrases are short descriptions, rather than identifying labels, the Bauhins, in particular Caspar Bauhin, took some important steps towards the binomial system, by pruning the Latin descriptions, in many cases to two words. The adoption by biologists of a system of binomial nomenclature is due to Swedish botanist and physician Carl von Linné. It was in his 1753 Species Plantarum that he first began using a one-word trivial name together with a generic name in a system of binomial nomenclature. This trivial name is what is now known as an epithet or specific name
8.
Species
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In biology, a species is the basic unit of biological classification and a taxonomic rank. A species is defined as the largest group of organisms in which two individuals can produce fertile offspring, typically by sexual reproduction. While this definition is often adequate, looked at more closely it is problematic, for example, with hybridisation, in a species complex of hundreds of similar microspecies, or in a ring species, the boundaries between closely related species become unclear. Other ways of defining species include similarity of DNA, morphology, all species are given a two-part name, a binomial. The first part of a binomial is the genus to which the species belongs, the second part is called the specific name or the specific epithet. For example, Boa constrictor is one of four species of the Boa genus, Species were seen from the time of Aristotle until the 18th century as fixed kinds that could be arranged in a hierarchy, the great chain of being. In the 19th century, biologists grasped that species could evolve given sufficient time, Charles Darwins 1859 book The Origin of Species explained how species could arise by natural selection. Genes can sometimes be exchanged between species by horizontal transfer, and species may become extinct for a variety of reasons. In his biology, Aristotle used the term γένος to mean a kind, such as a bird or fish, a kind was distinguished by its attributes, for instance, a bird has feathers, a beak, wings, a hard-shelled egg, and warm blood. A form was distinguished by being shared by all its members, Aristotle believed all kinds and forms to be distinct and unchanging. His approach remained influential until the Renaissance, when observers in the Early Modern period began to develop systems of organization for living things, they placed each kind of animal or plant into a context. Many of these early delineation schemes would now be considered whimsical, animals likewise that differ specifically preserve their distinct species permanently, one species never springs from the seed of another nor vice versa. In the 18th century, the Swedish scientist Carl Linnaeus classified organisms according to shared physical characteristics and he established the idea of a taxonomic hierarchy of classification based upon observable characteristics and intended to reflect natural relationships. At the time, however, it was widely believed that there was no organic connection between species, no matter how similar they appeared. However, whether or not it was supposed to be fixed, by the 19th century, naturalists understood that species could change form over time, and that the history of the planet provided enough time for major changes. Jean-Baptiste Lamarck, in his 1809 Zoological Philosophy, described the transmutation of species, proposing that a species could change over time, in 1859, Charles Darwin and Alfred Russel Wallace provided a compelling account of evolution and the formation of new species. Darwin argued that it was populations that evolved, not individuals and this required a new definition of species. Darwin concluded that species are what appear to be, ideas
9.
Compost
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Compost is organic matter that has been decomposed and recycled as a fertilizer and soil amendment. Compost is a key ingredient in organic farming, modern, methodical composting is a multi-step, closely monitored process with measured inputs of water, air, and carbon- and nitrogen-rich materials. The decomposition process is aided by shredding the plant matter, adding water, worms and fungi further break up the material. Bacteria requiring oxygen to function and fungi manage the process by converting the inputs into heat, carbon dioxide. The ammonium is the form of nitrogen used by plants, when available ammonium is not used by plants it is further converted by bacteria into nitrates through the process of nitrification. It is used in gardens, landscaping, horticulture, and agriculture, the compost itself is beneficial for the land in many ways, including as a soil conditioner, a fertilizer, addition of vital humus or humic acids, and as a natural pesticide for soil. In ecosystems, compost is useful for control, land and stream reclamation, wetland construction. Organic ingredients intended for composting can alternatively be used to generate biogas through anaerobic digestion, Composting of waste is an aerobic method of decomposing solid wastes. The process involves decomposition of waste into humus known as compost which is a good fertilizer for plants. However, the term composting is used worldwide with differing meanings, some composting textbooks narrowly define composting as being an aerobic form of decomposition, primarily by aerobic or facultative microbes. An alternative form of decomposition to composting is anaerobic digestion. For many people, composting is used to refer to different types of biological processes. In North America, anaerobic composting is still a term for what much of the rest of the world. The microbes used and the involved are quite different between composting and anaerobic digestion. Nitrogen — to grow and reproduce more organisms to oxidize the carbon, high nitrogen materials tend to be green and wet. Oxygen — for oxidizing the carbon, the decomposition process, water — in the right amounts to maintain activity without causing anaerobic conditions. Certain ratios of these materials will provide beneficial bacteria with the nutrients to work at a rate that heat up the pile. In that process much water will be released as vapor, the hotter the pile gets, the more often added air and water is necessary, the air/water balance is critical to maintaining high temperatures until the materials are broken down
. PMID 1968736.
