Alphaproteobacteria is a class of bacteria in the phylum Proteobacteria. Its members are diverse and possess few commonalities, but share a common ancestor. Like all Proteobacteria, its members are gram-negative and some of its intracellular parasitic members lack peptidoglycan and are gram variable; the Alphaproteobacteria is a diverse taxon and comprises several phototrophic genera, several genera metabolising C1-compounds, symbionts of plants, endosymbionts of arthropods and intracellular pathogens. Moreover, the class includes the protomitochondrion, the bacterium, engulfed by the eukaryotic ancestor and gave rise to the mitochondria, which are organelles in eukaryotic cells. A species of technological interest is Rhizobium radiobacter: scientists use this species to transfer foreign DNA into plant genomes. Aerobic anoxygenic phototrophic bacteria, such as Pelagibacter ubique, are alphaproteobacteria that are a distributed and may constitute over 10% of the open ocean microbial community.
There is some disagreement on the phylogeny of the orders for the location of the Pelagibacterales, but overall there is some consensus. The discord stems from the large difference in gene content and the large difference in GC-richness between members of several orders. Pelagibacterales and Holosporales contain species with AT-rich genomes, it has been argued that it could be a case of convergent evolution that would result in an artefactual clustering. However, several studies disagree. Furthermore, it has been found that the GC-content of ribosomal RNA little reflects the GC-content of the genome. One example of this atypical decorrelation of ribosomal GC-content with phylogeny is that members of the Holosporales have a much higher ribosomal GC-content than members of the Pelagibacterales and Rickettsiales though they are more related to species with high genomic GC-contents than to members of the latter two orders; the Class Alphaproteobacteria is divided into three subclasses Magnetococcidae and Caulobacteridae.
The basal group is Magnetococcidae, composed by a large diversity of magnetotactic bacteria, but only one is described, Magnetococcus marinus. The Rickettsidae is composed of the intracellular Rickettsiales and the free-living Pelagibacterales; the Caulobacteridae is composed of the Holosporales, Sphingomonadales, Caulobacterales, Kordiimonadales and Sneathiellales. Comparative analyses of the sequenced genomes have led to discovery of many conserved insertion-deletions in distributed proteins and whole proteins that are distinctive characteristics of either all Alphaproteobacteria, or their different main orders and families; these molecular signatures provide novel means for the circumscription of these taxonomic groups and for identification/assignment of new species into these groups. Phylogenetic analyses and conserved indels in large numbers of other proteins provide evidence that Alphaproteobacteria have branched off than most other phyla and Classes of Bacteria except Betaproteobacteria and Gammaproteobacteria.
The accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature and National Center for Biotechnology Information and the phylogeny is based on 16S rRNA-based LTP release 106 by'The All-Species Living Tree' Project Notes:♠ Strains found at the National Center for Biotechnology Information but not listed in the List of Prokaryotic names with Standing in Nomenclature Although only a few studies have been reported on natural genetic transformation in the Alphaproteobacteria, this process has been described in Agrobacterium tumefaciens, Methylobacterium organophilum, Bradyrhizobium japonicum. Natural genetic transformation is a sexual process involving DNA transfer from one bacterial cell to another through the intervening medium, the integration of the donor sequence into the recipient genome by homologous recombination. Alphaproteobacteria at the US National Library of Medicine Medical Subject Headings Bacterial Phylogeny Webpage: Alpha Proteobacteria
Fusarium /fjuˈzɛəriəm/ is a large genus of filamentous fungi, part of a group referred to as hyphomycetes distributed in soil and associated with plants. Most species are harmless saprobes, are abundant members of the soil microbial community; some species produce mycotoxins in cereal crops that can affect human and animal health if they enter the food chain. The main toxins produced by these Fusarium species are trichothecenes. Despite most species being harmless, some Fusarium species and subspecific groups are among the most important fungal pathogens of plants and animals; the name of Fusarium comes from Latin fusus. The taxonomy of the genus is complex. A number of different schemes have been used, up to 1,000 species have been identified at times, with approaches varying between wide and narrow concepts of speciation. Phylogenetic studies indicate seven major clades within the genus. Various schemes have subdivided the genus into subgenera and sections. There is a poor correlation between phylogenetic clades.
Sections described include. The genus includes a number of economically important plant pathogenic species. Fusarium graminearum infects barley if there is rain late in the season, it is of economic impact to the brewing industries, as well as feed barley. Fusarium contamination in barley can result in head blight, in extreme contaminations, the barley can appear pink; the genome of this wheat and maize pathogen has been sequenced. F. graminearum can cause root rot and seedling blight. The total losses in the US of barley and wheat crops between 1991 and 1996 have been estimated at $3 billion. Fusarium oxysporum f.sp. cubense is a fungal plant pathogen that causes Panama disease of banana known as fusarium wilt of banana. Panama disease affects a wide range of banana cultivars, which are propagated asexually from offshoots and therefore have little genetic diversity. Panama disease is one of the most destructive plant diseases of modern times, caused the commercial disappearance of the once dominant Gros Michel cultivar.
A more recent strain affects the Cavendish cultivars used as a substitute for Gros Michel. It is considered inevitable that this susceptibility will spread globally and commercially wipe out the Cavendish cultivar, for which there are no acceptable replacements. Fusarium oxysporum f. sp. narcissi causes rotting of the bulbs and yellowing of the leaves of daffodils. Some species may cause a range of opportunistic infections in humans. In humans with normal immune systems, fusarial infections may occur in the cornea. In humans whose immune systems are weakened in a particular way, aggressive fusarial infections penetrating the entire body and bloodstream may be caused by members of the Fusarium solani complex, Fusarium oxysporum, Fusarium verticillioides, Fusarium proliferatum and other fusarial species. Fusarium venenatum is produced industrially for use as a human food by Marlow Foods, Ltd. and is marketed under the name Quorn in Europe and North America. Some consumers of fusarium products have shown food allergies similar in nature to peanut and other food allergies.
People with known sensitivities to molds should exercise caution. Mass casualties occurred in the Soviet Union in the 1930s and 1940s when Fusarium-contaminated wheat flour was baked into bread, causing alimentary toxic aleukia with a 60% mortality rate. Symptoms began with abdominal pain, diarrhea and prostration, within days, chills and bone marrow depression with granulocytopenia and secondary sepsis occurred. Further symptoms included pharyngeal or laryngeal ulceration and diffuse bleeding into the skin, bloody diarrhea, hematemesis, vaginal bleeding and gastrointestinal ulceration. Fusarium sporotrichoides contamination was found in affected grain in 1932, spurring research for medical purposes and for use in biological warfare; the active ingredient was found to be trichothecene T-2 mycotoxin, it was produced in quantity and weaponized prior to the passage of the Biological Weapons Convention in 1972. The Soviets were accused of using the agent, dubbed "yellow rain", to cause 6,300 deaths in Laos and Afghanistan between 1975 and 1981.
The "biological warfare agent" was purported to be bee feces, but the issue remains disputed. Following an outbreak of Fusarium oxysporum that affected coca plantations in Peru, other crops planted in the area, the United States has proposed the use of the agent as a mycoherbicide in drug eradication. In 2000, a proposal was passed to use the agent as part of Plan Colombia. In response to concerns use of the fungus could be perceived as biological warfare, the Clinton Administration "waived" this use of Fusarium. A subsequent law passed in 2006 has mandated the testing of mycoherbicide agents - either Fusarium oxysporum or Crivellia papaveracea - in field trials in U. S. territory. Use of
The Pseudomonadaceae are family of bacteria which includes the genera Azomonas, Azorhizophilus, Cellvibrio, Pseudomonas, Rhizobacter and Serpens. The family Azotobacteriaceae was reclassified into this family. Pseudomonad means false unit, being derived from the Greek pseudo and monas; the term "monad" was used in the early history of microbiology to denote single-celled organisms. Because of their widespread occurrence in nature, the pseudomonads were observed early in the history of microbiology; the generic name Pseudomonas created for these organisms was defined in rather vague terms in 1894 as a genus of Gram-negative, rod-shaped, polar-flagellated bacteria. Soon afterwards, a large number of species was assigned to the genus. Pseudomonads were isolated from many natural niches. New methodology and the inclusion of approaches based on the studies of conservative macromolecules have reclassified many species. Pseudomonas aeruginosa is recognized as an emerging opportunistic pathogen of clinical relevance.
Studies suggest the emergence of antibiotic resistance in P. aeruginosa. In 2000, the complete genome of a Pseudomonas species was sequenced. Several pathovars of Pseudomonas syringae have been sequenced, including pathovar tomato DC3000, pathovar syringae B728a, pathovar phaseolica 1448A. Oxidase positive - due to the presence of cytochrome c oxidase enzyme Nonfermentative Many metabolise glucose by the Entner Doudoroff pathway mediated by 6-phosphoglyceraldehyde dehydrogenase and aldolase Polar flagella, enabling motility Many members produce derivatives of the fluorescent pigment pyoverdinThe presence of oxidase and polar flagella and inability to carry out fermentation differentiate pseudomonads from the Enterobacteriaceae
The Nectriaceae comprise a family of fungi in the order Hypocreales. It was circumscribed by brothers Charles and Louis René Tulasne in 1865; this is an incomplete list of genera in the Nectriaceae family
Betaproteobacteria are a class of gram-negative bacteria, one of the eight classes of the phylum Proteobacteria. The Betaproteobacteria are a class comprising over 400 species of bacteria. Together, the Betaproteobacteria represent a broad variety of metabolic strategies and occupy diverse environments from obligate pathogens living within host organisms to oligotrophic groundwater ecosystems. Whilst most members of the Betaproteobacteria are heterotrophic, deriving both their carbon and electrons from organocarbon sources, some are photoheterotrophic, deriving energy from light and carbon from organocarbon sources. Other genera are autotrophic, deriving their carbon from bicarbonate or carbon dioxide and their electrons from reduced inorganic ions such as nitrite, thiosulfate or sulfide - many of these chemolithoautotrophic Betaproteobacteria are economically important, with roles in maintaining soil pH and in elementary cycling. Other economically important members of the Betaproteobacteria are able to use nitrate as their terminal electron acceptor and can be used industrially to remove nitrate from wastewater by denitrification.
A number of Betaproteobacteria are diazotrophs, meaning that they can fix molecular nitrogen from the air as their nitrogen source for growth - this is important to the farming industry as it is a primary means of ammonium levels in soils rising without the presence of leguminous plants. The Betaproteobacteria are one of the eight classes that make up the "Proteobacteria"; the Betaproteobacteria are most related to the Gammaproteobacteria, Acidithiobacillia and Hydrogenophilalia, together they make up a taxon, called "Chromatibacteria". Four orders of Betaproteobacteria are recognised - the Burkholderiales, the Neisseriales, the Nitrosomonadales and the Rhodocyclales; the name "Procabacteriales" was proposed for an order of endosymbionts of Acanthamoeba, but since they cannot be grown in culture and studies have been limited, the name has never been validly or published, thus is no more than a nickname without any standing in nomenclature. An extensive reclassification of families and orders of the class based on a polyphasic analysis was published in 2017, that removed the order Hydrogenophilales from the class and into a novel class of the "Proteobacteria", the Hydrogenophilalia.
The same study merged the former order Methylophilales into the Nitrosomonadales. The four orders of the Betaproteobactera are sub-divided into families:Burkholderiales comprises the families Burkholderiacae, Commamonadaceae and Sutterellaceae; the order Burkholderiales comprises a range of morphologies, including rods, curved rods, cocci and multicellular'tablets'. Both heterotrophs and photoheterotrophs are found along with some facultative autotrophs. Neisseriales comprises the families Chromobacteriaceae; the order Neisseriales comprises morphologies including cocci, curved rods, rods, multicellular ribbons and filaments. Most organisms are heterotrophs with some facultative chemolithoheterotrophs. Nitrosomonadales comprises the families Nitrosomonadaceae, Thiobacillaceae, Sterolibacteriacae and Gallionellaceae; the order comprises morphologies including rods and curved rods. Most organisms are chemolithoautotrophs with some methylotrophs and heterotrophs Rhodocyclales comprises the families Rhodocyclaceae and Zoogloeaceae.
Morphologies include rods, curved rods, rings and cocci. Most species in this order are heterotrophs with some chemolithoautotrophs; some members of the Betaproteobacteria can cause disease in various eukaryotic organisms, including in humans, such as members of the genus Neisseria: N. gonorrhoeae and N. meninngitides being primary examples, which cause gonorrhea and meningitis as well as Bordetella pertussis which causes whooping cough. Other members of the class can infect plants, such as Burkholderia cepacia which causes bulb rot in onions as well as Xylophilus ampelinus which causes necrosis of grapevines. Various human activities, such as fertilizer production and chemical plant usage, release significant amounts of ammonium ions into rivers and oceans. Ammonium buildup in aquatic environments is dangerous because high ammonium content can lead to eutrophication. Biological wastewater treatment systems, as well as other biological ammonium-removing methods, depend on the metabolism of various Bacteria including members of the Nitrosomonadales of the Betaproteobacteria that undergo nitrification and a wide range of organisms capable of denitrification to remove excessive ammonia from wastewater by first oxidation into nitrate and nitrite and reduction into molecular nitrogen gas, which leaves the ecosystem and is carried into the atmosphere.
Gammaproteobacteria Hydrogenophilalia Acidithiobacillia Betaproteobacteria at the US National Library of Medicine Medical Subject Headings
The Hypocreales are an order of fungi within the class Sordariomycetes. In 2008, it was estimated that it contained some 237 genera, 2647 species in seven families. Since a considerable number of further taxa have been identified, including an additional family, the Stachybotryaceae. Species of Hypocreales are recognized by their brightly colored, perithecial ascomata, or spore-producing structures; these are yellow, orange or red. According to the 2007 Outline of Ascomycota, the following genera within the Hypocreales have an uncertain taxonomic placement, have not been assigned to any family. Bulbithecium Emericellopsis †Entropezites Escovopsis Geosmithia Hapsidospora Leucosphaerina Metadothella †Mycetophagites Nigrosabulum Payosphaeria Peloronectria Pseudomeliola Scopinella Ticonectria Tilakidium Trichothecium Ustilaginoidea Media related to Hypocreales at Wikimedia Commons
Rhizobium is a genus of Gram-negative soil bacteria that fix nitrogen. Rhizobium species form an endosymbiotic nitrogen-fixing association with roots of legumes and Parasponia; the bacteria colonize plant cells within root nodules, where they convert atmospheric nitrogen into ammonia using the enzyme nitrogenase and provide organic nitrogenous compounds such as glutamine or ureides to the plant. The plant, in turn, provides the bacteria with organic compounds made by photosynthesis; this mutually beneficial relationship is true of all of the rhizobia, of which the genus Rhizobium is a typical example. Martinus Beijerinck was the first to isolate and cultivate a microorganism from the nodules of legumes in 1888, he named it Bacillus radicicola, now placed in Bergey's Manual of Determinative Bacteriology under the genus Rhizobium. Rhizobium forms a symbiotic relationship with certain plants such as legumes, fixing nitrogen from the air into ammonia, which acts as a natural fertilizer for the plants.
Current research is being conducted by Agricultural Research Service microbiologists to discover a way to use Rhizobium’s biological nitrogen fixation. This research involves the genetic mapping of various rhizobial species with their respective symbiotic plant species, like alfalfa or soybean; the goal of this research is to increase the plants’ productivity without using fertilizers. In molecular biology, Rhizobium has been identified as a contaminant of DNA extraction kit reagents and ultrapure water systems, which may lead to its erroneous appearance in microbiota or metagenomic datasets; the presence of nitrogen fixing bacteria as contaminants may be due to the use of nitrogen gas in ultra-pure water production to inhibit microbial growth in storage tanks. The accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature and National Center for Biotechnology Information and the phylogeny is based on 16S rRNA-based LTP release 106 by The All-Species Living Tree Project.
Current research on Rhizobium leguminosarum at the Norwich Research Park Video and commentary on root nodules and Rhizobium in White Clover