Three-domain system

The three-domain system is a biological classification introduced by Carl Woese et al. in 1977[1][2] that divides cellular life forms into archaea, bacteria, and eukaryote domains. In particular, it emphasizes the separation of prokaryotes into two groups, originally called Eubacteria (now Bacteria) and Archaebacteria (now Archaea). Woese argued that, on the basis of differences in 16S rRNA genes, these two groups and the eukaryotes each arose separately from an ancestor with poorly developed genetic machinery, often called a progenote. To reflect these primary lines of descent, he treated each as a domain, divided into several different kingdoms. Woese initially used the term "kingdom" to refer to the three primary phylogenic groupings, and this nomenclature was widely used until the term "domain" was adopted in 1990.[2]

Parts of the three-domain theory have been challenged by scientists such as Radhey Gupta, who argues that the primary division within prokaryotes should be between those surrounded by a single membrane, and those with two membranes.

BacteriaArchaeaEucaryotaAquifexThermotogaCytophagaBacteroidesBacteroides-CytophagaPlanctomycesCyanobacteriaProteobacteriaSpirochetesGram-positive bacteriaGreen filantous bacteriaPyrodicticumThermoproteusThermococcus celerMethanococcusMethanobacteriumMethanosarcinaHalophilesEntamoebaeSlime moldAnimalFungusPlantCiliateFlagellateTrichomonadMicrosporidiaDiplomonad
A phylogenetic tree based on rRNA data, emphasizing the separation of bacteria, archaea, and eukaryotes, as proposed by Carl Woese et al. in 1990

Classification

The three-domain system includes the Archaea (represented by Sulfolobus, left), Bacteria (represented by S. aureus, middle) and Eukarya (represented by the Australian green tree frog, right)

RT8-4 scale
Staphylococcus aureus VISA 2
Australia green tree frog (Litoria caerulea) crop

The three-domain system adds a level of classification (the domains) "above" the kingdoms present in the previously used five- or six-kingdom systems. This classification system recognizes the fundamental divide between the two prokaryotic groups, insofar as Archaea appear to be more closely related to Eukaryotes than they are to other prokaryotes – bacteria-like organisms with no cell nucleus. The current system sorts the previously known kingdoms into these three domains: Archaea, Bacteria, and Eukarya.

Domain Archaea

The Archaea are prokaryotic, with no nuclear membrane, distinct biochemistry, and RNA markers from bacteria. The Archaeans possess unique, ancient evolutionary history for which they are considered some of the oldest species of organisms on Earth, most notably their diverse, exotic metabolisms, which allow them to feed on inorganic matter. Originally classified as exotic bacteria, and then reclassified as archaebacteria, the only easy way to distinguish them on sight from "true" bacteria is by the extreme, harsh environments in which they notoriously thrive.

Some examples of archaeal organisms are:

Domain Bacteria

The Bacteria are also prokaryotic; their domain consists of cells with bacterial rRNA, no nuclear membrane, and whose membranes possess primarily diacyl glycerol diester lipids. Traditionally classified as bacteria, many thrive in the same environments favored by humans, and were the first prokaryotes discovered; they were briefly called the Eubacteria or "true" bacteria when the Archaea were first recognized as a distinct clade.

Most known pathogenic prokaryotic organisms belong to bacteria (see [3] for exceptions). For that reason, and because the Archaea are typically difficult to grow in laboratories, Bacteria are currently studied more extensively than Archaea.

Some examples of bacteria include:

Domain Eukarya

Eukarya are uniquely organisms whose cells contain a membrane-bound nucleus (eukaryotes, eukaryotic). They include many large single-celled organisms and all known non-microscopic organisms. A partial list of eukaryotic organisms includes:

Kingdom Fungi or fungi
Kingdom Plantae or plants
Kingdom Animalia or animals

Niches

Each of the three cell types tends to fit into recurring specialties or roles. Bacteria tend to be the most prolific reproducers, at least in moderate environments. Archaeans tend to adapt quickly to extreme environments, such as high temperatures, high acids, high sulfur, etc. This includes adapting to use a wide variety of food sources. Eukaryotes are the most flexible with regard to forming cooperative colonies, such as in multi-cellular organisms, including humans. In fact, the structure of a Eukaryote is likely to have derived from a joining of different cell types, forming organelles.

Parakaryon myojinensis (incertae sedis) is a single-celled organism known by a unique example. "This organism appears to be a life form distinct from prokaryotes and eukaryotes",[4] with features of both.

Alternatives

Parts of the three-domain theory have been challenged by scientists including Ernst Mayr, Thomas Cavalier-Smith, and Radhey S. Gupta.[5][6][7] In particular, Gupta argues that the primary division within prokaryotes should be among those surrounded by a single membrane (monoderm), including gram-positive bacteria and archaebacteria, and those with an inner and outer cell membrane (diderm), including gram-negative bacteria. He claims that sequences of features and phylogenies from some highly conserved proteins are inconsistent with the three-domain theory, and that it should be abandoned despite its widespread acceptance.

Recent work has proposed that Eukarya may have actually branched off from the domain Archaea. According to Spang et al. Lokiarchaeota forms a monophyletic group with eukaryotes in phylogenomic analyses. The associated genomes also encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities.[8] This work suggests a two-domain system as opposed to the near universally adopted three-domain system.

See also

References

  1. ^ Woese CR, Fox GE (November 1977). "Phylogenetic structure of the prokaryotic domain: the primary kingdoms". Proceedings of the National Academy of Sciences of the United States of America. 74 (11): 5088–90. Bibcode:1977PNAS...74.5088W. doi:10.1073/pnas.74.11.5088. PMC 432104. PMID 270744.
  2. ^ a b Woese CR, Kandler O, Wheelis ML (June 1990). "Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya". Proceedings of the National Academy of Sciences of the United States of America. 87 (12): 4576–9. Bibcode:1990PNAS...87.4576W. doi:10.1073/pnas.87.12.4576. PMC 54159. PMID 2112744.
  3. ^ Eckburg, Paul B.; Lepp, Paul W.; Relman, David A. (2003). "Archaea and their potential role in human disease". Infection and Immunity. 71 (2): 591–596. doi:10.1128/IAI.71.2.591-596.2003. PMC 145348. PMID 12540534.
  4. ^ Yamaguchi M, Mori Y, Kozuka Y, Okada H, Uematsu K, Tame A, Furukawa H, Maruyama T, Worman CO, Yokoyama K (2012). "Prokaryote or eukaryote? A unique microorganism from the deep sea". Journal of Electron Microscopy. 61 (6): 423–31. doi:10.1093/jmicro/dfs062. PMID 23024290.
  5. ^ Gupta, Radhey S. (1998). "Life's Third Domain (Archaea): An Established Fact or an Endangered Paradigm?: A New Proposal for Classification of Organisms Based on Protein Sequences and Cell Structure". Theoretical Population Biology. 54 (2): 91–104. doi:10.1006/tpbi.1998.1376. PMID 9733652.
  6. ^ Mayr, E. (1998). "Two empires or three?". Proc. Natl. Acad. Sci. USA. 95: 9720–9723. Bibcode:1998PNAS...95.9720M. doi:10.1073/pnas.95.17.9720. PMC 33883. PMID 9707542.
  7. ^ Cavalier-Smith, Thomas (2002). "The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification". Int J Syst Evol Microbiol. 52 (1): 7–76. doi:10.1099/00207713-52-1-7. PMID 11837318.
  8. ^ Spang, Anja (2015). "Complex archaea that bridge the gap between prokaryotes and eukaryotes". Nature. 521: 173–179. Bibcode:2015Natur.521..173S. doi:10.1038/nature14447. PMC 4444528. PMID 25945739.
Bacteria

Bacteria ( (listen); common noun bacteria, singular bacterium) are a type of biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. 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, and the deep portions of Earth's crust. Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only about 27 percent of the bacterial phyla have species that can be grown in the laboratory (specifically unculturable phyla, known as candidate phyla, make up 103 out of approximately 142 known phyla).

The study of bacteria is known as bacteriology, a branch of microbiology.

Virtually all animal life on earth is dependent on bacteria for their survival as only bacteria and some archea possess the genes and enzymes necessary to synthesize vitamin B12, also known as cobalamin, and provide it through the food chain. Vitamin B12 is a water-soluble vitamin that is involved in the metabolism of every cell of the human body. It is a cofactor in DNA synthesis, and in both fatty acid and amino acid metabolism, It is particularly important in the normal functioning of the nervous system via its role in the synthesis of myelin.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 and animals. 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 dead bodies; bacteria are responsible for the putrefaction stage in this process. In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. Data reported by researchers in October 2012 and published in March 2013 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—they're extremely adaptable to conditions, and survive wherever they are."The famous notion that bacterial cells in the human body outnumber human cells by a factor of 10:1 has been debunked. There are approximately 39 trillion bacterial cells in the human microbiota as personified by a "reference" 70 kg male 170 cm tall, whereas there are 30 trillion human cells in the body. This means that although they do have the upper hand in actual numbers, it is only by 30%, and not 900%.The largest number exist in the gut flora, and a large number on the skin. 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 infectious diseases, including cholera, syphilis, anthrax, leprosy, and bubonic plague. The most common fatal bacterial diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year, mostly in sub-Saharan Africa. In developed countries, antibiotics are used to treat bacterial infections and are also used in farming, making antibiotic resistance a growing problem. In industry, bacteria are important in sewage treatment and the breakdown of oil spills, the production of cheese and yogurt through fermentation, the recovery of gold, palladium, copper and other metals in the mining sector, as well as in biotechnology, and the manufacture of antibiotics and other chemicals.Once regarded as plants 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 rarely harbour membrane-bound organelles. Although the term bacteria traditionally included all prokaryotes, the scientific classification changed after the discovery in the 1990s that prokaryotes consist of two very different groups of organisms that evolved from an ancient common ancestor. These evolutionary domains are called Bacteria and Archaea.

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 (binary nomenclature), which is a lower level of a hierarchy of ranks. 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, since the rank "kingdom" is disused at present in bacterial taxonomy. When bacterial nomenclature was controlled under the Botanical Code, the term division was used, but now that bacterial nomenclature (with the exception of cyanobacteria) is controlled under the Bacteriological Code, the term phylum is preferred.

In this classification scheme, Bacteria is (unofficially) 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, the analysis of bulk samples from the environment. 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, or over 50 including candidate phyla. The total number has been estimated to exceed 1,000 bacterial phyla.At the base of the clade Bacteria, close to the last universal common ancestor of all living things, some scientists believe there may be a definite branching order, whereas other scientists, such as Norman Pace, believe there was a large hard polytomy, a simultaneous multiple speciation event.

Biology

Biology is the natural science that studies life and living organisms, including their physical structure, chemical processes, molecular interactions, physiological mechanisms, development and evolution. Despite the complexity of the science, there are certain unifying concepts that consolidate it into a single, coherent field. Biology recognizes the cell as the basic unit of life, genes as the basic unit of heredity, and evolution as the engine that propels the creation and extinction of species. Living organisms are open systems that survive by transforming energy and decreasing their local entropy to maintain a stable and vital condition defined as homeostasis.Sub-disciplines of biology are defined by the research methods employed and the kind of system studied: theoretical biology uses mathematical methods to formulate quantitative models while experimental biology performs empirical experiments to test the validity of proposed theories and understand the mechanisms underlying life and how it appeared and evolved from non-living matter about 4 billion years ago through a gradual increase in the complexity of the system. See branches of biology.

Domain (biology)

In biological taxonomy, a domain ( or ) (Latin: regio), also superkingdom or empire, is the highest taxonomic rank of organisms in the three-domain system of taxonomy designed by Carl Woese et.al. in 1990.

According to this system, 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.

Eocyte hypothesis

The Eocyte hypothesis is a biological classification that indicates eukaryotes emerged within the prokaryotic Crenarchaeota (formerly known as eocytes), a phylum within the archaea. This hypothesis was originally proposed by James A. Lake and colleagues in 1984 based on the discovery that the shapes of ribosomes in the Crenarchaeota and eukaryotes are more similar to each other than to either bacteria or the second major kingdom of archaea, the Euryarchaeota.

Eukaryote

Eukaryotes () are organisms whose cells have a nucleus enclosed within membranes, unlike prokaryotes (Bacteria and Archaea), which have no membrane-bound organelles. Eukaryotes belong to the domain Eukaryota or Eukarya. Their name comes from the Greek εὖ (eu, "well" or "true") and κάρυον (karyon, "nut" or "kernel"). Eukaryotic cells also contain other membrane-bound organelles such as mitochondria and the Golgi apparatus, and in addition, some cells of plants and algae contain chloroplasts. Unlike unicellular archaea and bacteria, eukaryotes may also be multicellular and include organisms consisting of many cell types forming different kinds of tissue. Animals and plants are the most familiar eukaryotes.

Eukaryotes can reproduce both asexually through mitosis and sexually through meiosis and gamete fusion. In mitosis, one cell divides to produce two genetically identical cells. In meiosis, DNA replication is followed by two rounds of cell division to produce four haploid daughter cells. These act as sex cells (gametes). Each gamete has just one set of chromosomes, each a unique mix of the corresponding pair of parental chromosomes resulting from genetic recombination during meiosis.

The domain Eukaryota appears to be monophyletic, and makes up one of the domains of life in the three-domain system. 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 generally much larger size, their collective worldwide biomass is estimated to be about equal to that of prokaryotes. Eukaryotes evolved approximately 1.6–2.1 billion years ago, during the Proterozoic eon.

George E. Fox

George Edward Fox (born December 17, 1945) is a researcher at the University of Houston. In the 1970s, Fox and Carl Woese classified Archaea as a separate domain of life within the three-domain system. Fox and Woese also introduced the idea of a progenote as a primordial entity in the evolution of life. While with Woese, he pioneered use of comparative analysis in prediction of RNA secondary structure. Using comparative analysis, he also recognized the limitations that RNA sequences could provide when identifying closely related species. His research centers around understanding the early evolution of life. Fox contends that one of the earliest components of the genetic machinery to appear in a form bearing resemblance to its modern equivalent was the ribosome. His research is actively involved in the search for biosignatures on Mars.

Fox received his B.A. degree in 1967, and completed his Ph.D. degree in 1974; both in chemical engineering at Syracuse University. From 1973 till 1977, he was a research associate with Carl Woese at the University of Illinois. He became an assistant professor of Biochemical & Biophysical Sciences at the University of Houston in 1977; he became a full professor there in 1986.

Gracilicutes

Gracilicutes (Latin: gracilis, slender, and cutis, skin, referring to the cell wall) is a controversial taxon in bacterial taxonomy.

Traditionally gram staining results were most commonly used as a classification tool, consequently until the advent of molecular phylogeny, the Kingdom Monera (as the domains Bacteria and Archaea were known then) was divided into four phyla,

Gracilicutes (gram-negative, it is split in many groups, but some authors still use it in a narrower sense)

Firmacutes [sic] (gram-positive, subsequently corrected to Firmicutes, today it includes the Mollicutes but excludes the Actinobacteria)

Mollicutes (gram variable, posteriorly renamed as Tenericutes, e.g. Mycoplasma)

Mendosicutes (uneven gram stain, "methanogenic bacteria" now known as methanogens and classed as Archaea)This classification system was abandoned in favour of the three-domain system based on molecular phylogeny started by C. Woese.This taxon was revived in 2006 by Cavalier-Smith as an infrakindgom containing the phyla Spirochaetae, Sphingobacteria (FCB), Planctobacteria (PVC), and Proteobacteria. It is a gram-negative clade that branched off from other bacteria just before the evolutionary loss of the outer membrane or capsule, and just after the evolution of flagella. This taxon is not generally accepted and the three-domain system is followed.An almost identical taxon called Hydrobacteria was defined in 2009 using bioinfomatic methods. It is in contrast to the other major group of eubacteria called Terrabacteria. The analysis also altered the internal phylogeny of this group, with PVC-FCB-Spirochaetae placed forming a clade next to Proteobacteria. What was PVC is described as polyphyletic.

History of evolutionary thought

Evolutionary thought, the conception that species change over time, has roots in antiquity – in the ideas of the ancient Greeks, Romans, and Chinese as well as in medieval Islamic science. With the beginnings of modern biological taxonomy in the late 17th century, two opposed ideas influenced Western biological thinking: essentialism, the belief that every species has essential characteristics that are unalterable, a concept which had developed from medieval Aristotelian metaphysics, and that fit well with natural theology; and the development of the new anti-Aristotelian approach to modern science: as the Enlightenment progressed, evolutionary cosmology and the mechanical philosophy spread from the physical sciences to natural history. Naturalists began to focus on the variability of species; the emergence of paleontology with the concept of extinction further undermined static views of nature. In the early 19th century Jean-Baptiste Lamarck (1744 – 1829) proposed his theory of the transmutation of species, the first fully formed theory of evolution.

In 1858 Charles Darwin and Alfred Russel Wallace published a new evolutionary theory, explained in detail in Darwin's On the Origin of Species (1859). Unlike Lamarck, Darwin proposed common descent and a branching tree of life, meaning that two very different species could share a common ancestor. Darwin based his theory on the idea of natural selection: it synthesized a broad range of evidence from animal husbandry, biogeography, geology, morphology, and embryology. Debate over Darwin's work led to the rapid acceptance of the general concept of evolution, but the specific mechanism he proposed, natural selection, was not widely accepted until it was revived by developments in biology that occurred during the 1920s through the 1940s. Before that time most biologists regarded other factors as responsible for evolution. Alternatives to natural selection suggested during "the eclipse of Darwinism" (c. 1880 to 1920) included inheritance of acquired characteristics (neo-Lamarckism), an innate drive for change (orthogenesis), and sudden large mutations (saltationism). Mendelian genetics, a series of 19th-century experiments with pea plant variations rediscovered in 1900, was integrated with natural selection by Ronald Fisher, J. B. S. Haldane, and Sewall Wright during the 1910s to 1930s, and resulted in the founding of the new discipline of population genetics. During the 1930s and 1940s population genetics became integrated with other biological fields, resulting in a widely applicable theory of evolution that encompassed much of biology—the modern synthesis.

Following the establishment of evolutionary biology, studies of mutation and genetic diversity in natural populations, combined with biogeography and systematics, led to sophisticated mathematical and causal models of evolution. Paleontology and comparative anatomy allowed more detailed reconstructions of the evolutionary history of life. After the rise of molecular genetics in the 1950s, the field of molecular evolution developed, based on protein sequences and immunological tests, and later incorporating RNA and DNA studies. The gene-centered view of evolution rose to prominence in the 1960s, followed by the neutral theory of molecular evolution, sparking debates over adaptationism, the unit of selection, and the relative importance of genetic drift versus natural selection as causes of evolution. In the late 20th-century, DNA sequencing led to molecular phylogenetics and the reorganization of the tree of life into the three-domain system by Carl Woese. In addition, the newly recognized factors of symbiogenesis and horizontal gene transfer introduced yet more complexity into evolutionary theory. Discoveries in evolutionary biology have made a significant impact not just within the traditional branches of biology, but also in other academic disciplines (for example: anthropology and psychology) and on society at large.

Kingdom (biology)

In biology, kingdom (Latin: regnum, plural regna) is the second highest taxonomic rank, just below domain. Kingdoms are divided into smaller groups called phyla.

Traditionally, some textbooks from the United States used a system of six kingdoms (Animalia, Plantae, Fungi, Protista, Archaea/Archaebacteria, and Bacteria/Eubacteria) while textbooks in countries like Great Britain, India, Greece, Australia, Latin America and other countries used five kingdoms (Animalia, Plantae, Fungi, Protista and Monera).

Some recent classifications based on modern cladistics have explicitly abandoned the term "kingdom", noting that the traditional kingdoms are not monophyletic, i.e., do not consist of all the descendants of a common ancestor.

Mark Wheelis

Mark L. Wheelis is an American microbiologist. Wheelis is currently a professor in the College of Biological Sciences, University of California, Davis. Carl Woese and Otto Kandler with Wheelis wrote the important paper Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya that proposed a change from the Two-empire system of Prokaryotes and Eukaryotes to the Three-domain system of the domains Eukaryota, Bacteria and Archaea.Wheelis's research interests include the history of biological warfare. He co-authored (with Larry Gonick) The Cartoon Guide to Genetics (1983). Wheelis provided the scientific knowledge and text, while Gonick contributed the illustrations and humor.

Microorganism

A microorganism, or microbe, is a microscopic organism, which may exist in its single-celled form or in a colony of cells.

The possible existence of unseen microbial life was suspected from ancient times, such as in Jain scriptures from 6th century BC India and the 1st century BC book On Agriculture by Marcus Terentius Varro. Microbiology, the scientific study of microorganisms, began with their observation under the microscope in the 1670s by Antonie van Leeuwenhoek. In the 1850s, Louis Pasteur found that microorganisms caused food spoilage, debunking the theory of spontaneous generation. In the 1880s, Robert Koch discovered that microorganisms caused the diseases tuberculosis, cholera and anthrax.

Microorganisms include all unicellular organisms and so are extremely diverse. Of the three domains of life identified by Carl Woese, all of the Archaea and Bacteria are microorganisms. These were previously grouped together in the two domain system as Prokaryotes, the other being the eukaryotes. The third domain Eukaryota includes all multicellular organisms and many unicellular protists and protozoans. Some protists are related to animals and some to green plants. Many of the multicellular organisms are microscopic, namely micro-animals, some fungi and some algae, but these are not discussed here.

They live in almost every habitat from the poles to the equator, deserts, geysers, rocks and the deep sea. Some are adapted to extremes such as very hot or very cold conditions, others to high pressure and a few such as Deinococcus radiodurans to high radiation environments. Microorganisms also make up the microbiota found in and on all multicellular organisms. A December 2017 report stated that 3.45-billion-year-old Australian rocks once contained microorganisms, the earliest direct evidence of life on Earth.Microbes are important in human culture and health in many ways, serving to ferment foods, treat sewage, produce fuel, enzymes and other bioactive compounds. They are essential tools in biology as model organisms and have been put to use in biological warfare and bioterrorism. They are a vital component of fertile soils. In the human body microorganisms make up the human microbiota including the essential gut flora. They are the pathogens responsible for many infectious diseases and as such are the target of hygiene measures.

Monera

Monera () (Greek - μονήρης (monḗrēs), "single", "solitary") is a kingdom that contains unicellular organisms with a prokaryotic cell organization (having no nuclear membrane), such as bacteria. They are single-celled organisms with no true nuclear membrane (prokaryotic organisms).

The taxon Monera was first proposed as a phylum by Ernst Haeckel in 1866. Subsequently, the phylum was elevated to the rank of kingdom in 1925 by Édouard Chatton. The last commonly accepted mega-classification with the taxon Monera was the five-kingdom classification system established by Robert Whittaker in 1969.

Under the three-domain system of taxonomy, introduced by Carl Woese in 1977, which reflects the evolutionary history of life, the organisms found in kingdom Monera have been divided into two domains, Archaea and Bacteria (with Eukarya as the third domain). Furthermore, the taxon Monera is paraphyletic (does not include all descendants of their most-recent common ancestor), as Archaea and Eukarya are currently believed to be more closely related than either is to Bacteria. The term "moneran" is the informal name of members of this group and is still sometimes used (as is the term "prokaryote") to denote a member of either domain.Most bacteria were classified under Monera; however, Cyanobacteria (often called the blue-green algae) were initially classified under Plantae due to their ability to photosynthesize.

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 (pro) "before" and κάρυον (karyon) "nut or kernel". Prokaryotes are divided into two domains, Archaea and Bacteria. Species with nuclei and organelles are placed in the third domain, Eukaryota. Prokaryotes reproduce without fusion of gametes. The first living organisms are thought to have been prokaryotes.

In the prokaryotes, all the intracellular water-soluble components (proteins, DNA and metabolites) 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 (containing chromosomal DNA) and organelles. 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 some extreme environments.

Taxonomy (biology)

In biology, taxonomy (from Ancient Greek τάξις (taxis), meaning 'arrangement', and -νομία (-nomia), meaning 'method') is the science of naming, defining (circumscribing) and classifying groups of biological organisms on the basis of shared characteristics. Organisms are grouped together into taxa (singular: taxon) and these groups are given a taxonomic rank; groups of a given rank can be aggregated to form a super-group of higher rank, thus creating a taxonomic hierarchy. The principal ranks in modern use are domain, kingdom, phylum (division is sometimes used in botany in place of phylum), class, order, family, genus, and species. The Swedish botanist Carl Linnaeus is regarded as the founder of the current system of taxonomy, as he developed a system known as Linnaean taxonomy for categorizing organisms and binomial nomenclature for naming organisms.

With the advent of such fields of study as phylogenetics, cladistics, and systematics, the Linnaean system has progressed to a system of modern biological classification based on the evolutionary relationships between organisms, both living and extinct.

Two-empire system

The two-empire system (two-superkingdom system) was the top-level biological classification system in general use before the establishment of the three-domain system. It classified life into Prokaryota and Eukaryota. When the three-domain system was introduced, some biologists preferred the two-superkingdom system, claiming that the three-domain system overemphasized the division between Archaea and Bacteria. However, given the current state of knowledge and the rapid progress in biological scientific advancement, especially due to genetic analyses, that view has all but vanished.

Some prominent scientists, such as Thomas Cavalier-Smith, still hold to the two-empire system. The late Ernst Mayr, one of the 20th century's leading evolutionary biologists, wrote dismissively of the three-domain system, "I cannot see any merit at all in a three empire cladification." Additionally, the scientist Radhey Gupta argues for a return to the two-empire system, claiming that the primary division within prokaryotes should be among those surrounded by a single membrane (monoderm), including gram-positive bacteria and archaebacteria, and those with an inner and outer cell membrane (diderm), including gram-negative bacteria.

This system was preceded by Haeckel's three-kingdom system: Animalia, Plantae and Protista.

Woeseian revolution

The Woeseian revolution was the progression of the phylogenetic tree of life from two main divisions, known as the Prokarya and Eukarya, into three domains now classified as Bacteria, Archaea, and Eukaryotes. The discovery of the new domain stemmed from the work of biophysicist Carl Woese in 1997 from a principle of evolutionary biology designated as Woese's dogma. It states that the evolution of ribosomal RNA (rRNA) was a necessary precursor to the evolution of modern life forms. Although the three-domain system has been widely accepted, the initial introduction of Woese’s discovery received criticism from the scientific community.

Zoology

Zoology () is the branch of biology that studies the animal kingdom, including the structure, embryology, evolution, classification, habits, and distribution of all animals, both living and extinct, and how they interact with their ecosystems. The term is derived from Ancient Greek ζῷον, zōion, i.e. "animal" and λόγος, logos, i.e. "knowledge, study".

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