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"Betaproteobacteria are a class of Gram-negative bacteria, and one of the eight classes of the phylum Proteobacteria. The Betaproteobacteria are a class comprising over 75 genera and 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, ammonium, 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. Phylogeny The Betaproteobacteria are one of the eight classes that make up the "Proteobacteria". The Betaproteobacteria are most closely related to the Gammaproteobacteria, Acidithiobacillia and Hydrogenophilalia, and together they make up a taxon which has previously been called "Chromatibacteria". Four orders of Betaproteobacteria are currently recognised — the Burkholderiales, the Neisseriales, the Nitrosomonadales and the Rhodocyclales. The name "Procabacteriales" was also 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 effectively published, and 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 (including 16S rRNA gene analyses and 53-protein ribosomal protein concatamer analyses using the rMLST Multilocus sequence typing system) 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 also merged the former order Methylophilales into the Nitrosomonadales. The four orders of the Betaproteobactera are sub-divided into families: Burkholderiales (type order) comprises the families Burkholderiacae (type family), Alcaliginaceae, Commamonadaceae, Oxalobacteraceae and Sutterellaceae. The order Burkholderiales comprises a range of morphologies, including rods, curved rods, cocci, spirillae and multicellular 'tablets'. Both heterotrophs and photoheterotrophs are found along with some facultative autotrophs. Neisseriales comprises the families Neisseriaceae (type family) and Chromobacteriaceae. The order Neisseriales comprises morphologies including cocci, curved rods, spirillae, rods, multicellular ribbons and filaments. Most organisms are heterotrophs with some facultative methylotrophs and chemolithoheterotrophs. Nitrosomonadales comprises the families Nitrosomonadaceae (type family), Methylophilacae, Thiobacillaceae, Sterolibacteriacae, Spirillaceae and Gallionellaceae. The order comprises morphologies including rods, spirillae and curved rods. Most organisms are chemolithoautotrophs with some methylotrophs and heterotrophs Rhodocyclales comprises the families Rhodocyclaceae (type family), Azonexaceae and Zoogloeaceae. Morphologies include rods, curved rods, rings, spirillae and cocci. Most species in this order are heterotrophs with some photoheterotrophs and chemolithoautotrophs. Role in disease 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 respectively, 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. Economic Importance 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 potentially 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 then nitrite and then reduction into molecular nitrogen gas, which leaves the ecosystem and is carried into the atmosphere. See also * Gammaproteobacteria * Hydrogenophilalia * Acidithiobacillia *Candidatus Glomeribacter gigasporarum References External links * Bacteria classes Proteobacteria "
"Alphaproteobacteria is a class of bacteria in the phylum Proteobacteria (See also bacterial taxonomy). Its members are highly 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. Characteristics The Alphaproteobacteria are a diverse taxon and comprises several phototrophic genera, several genera metabolising C1-compounds (e.g., Methylobacterium spp.), symbionts of plants (e.g., Rhizobium spp.), endosymbionts of arthropods (Wolbachia) and intracellular pathogens (e.g. Rickettsia). Moreover, the class includes (as an extinct member) the protomitochondrion, the bacterium that was engulfed by the eukaryotic ancestor and gave rise to the mitochondria, which are organelles in eukaryotic cells (See endosymbiotic theory). A species of technological interest is Rhizobium radiobacter (formerly Agrobacterium tumefaciens): scientists often use this species to transfer foreign DNA into plant genomes. Aerobic anoxygenic phototrophic bacteria, such as Pelagibacter ubique, are alphaproteobacteria that are a widely distributed and may constitute over 10% of the open ocean microbial community. Evolution and genomics There is some disagreement on the phylogeny of the orders, especially for the location of the Pelagibacterales, but overall there is some consensus. The discord stems from the large difference in gene content (e.g. genome streamlining in Pelagibacter ubique) and the large difference in GC-richness between members of several orders. Specifically, Pelagibacterales, Rickettsiales 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 (the traditional phylogenetic marker for prokaryotes) 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, even though they are more closely 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, Rickettsidae and Caulobacteridae. The basal group is Magnetococcidae, which is 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, Rhodospirillales, Sphingomonadales, Rhodobacterales, Caulobacterales, Kiloniellales, Kordiimonadales, Parvularculales and Sneathiellales. Comparative analyses of the sequenced genomes have also led to discovery of many conserved insertion-deletions (indels) in widely distributed proteins and whole proteins (i.e. signature proteins) that are distinctive characteristics of either all Alphaproteobacteria, or their different main orders (viz. Rhizobiales, Rhodobacterales, Rhodospirillales, Rickettsiales, Sphingomonadales and Caulobacterales) and families (viz. Rickettsiaceae, Anaplasmataceae, Rhodospirillaceae, Acetobacteraceae, Bradyrhiozobiaceae, Brucellaceae and Bartonellaceae). 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 later than most other phyla and Classes of Bacteria except Betaproteobacteria and Gammaproteobacteria. Phylogeny The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI) and the phylogeny is based on 16S rRNA-based LTP release 106 by 'The All-Species Living Tree' Project 'The All-Species Living Tree' Project. Notes: ♠ Strains found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LSPN). Aquaspirillum is now regarded to belong to Betaproteobacteria. A newer tree based on 16S and 23S rRNA (and other data) is given by Ferla et al. (2013) as follows: Natural genetic transformation 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, and Bradyrhizobium japonicum. Natural genetic transformation is a sexual process involving DNA transfer from one bacterial cell to another through the intervening medium, and the integration of the donor sequence into the recipient genome by homologous recombination. References External links Bacterial (Prokaryotic) Phylogeny Webpage: Alpha Proteobacteria. Bacteria classes "
"Starcross engine house The South Devon Railway engine houses were built in Devon, England, to power the atmospheric trains on the South Devon Railway between Exeter St Davids and Plymouth Millbay railway stations. They contained boilers that provided the power to pumps that created the partial vacuum to move the trains. Three of them still stand largely intact alongside the line. History The South Devon Railway was built by Isambard Kingdom Brunel who proposed moving the trains by atmospheric power. Brunel and other engineers travelled to Dalkey in Ireland in 1843 to view such a system undergoing tests on the Dublin and Kingstown Railway. There, Brunel's engineer of locomotives for the GWR, Daniel Gooch, calculated that conventional locomotives could work the proposed line at lower cost, but Brunel's concerns about the heavy grades led him to try the system regardless. The South Devon Railway directors agreed on 28 August 1844 to Brunel's proposal to use atmospheric power on their line. Brunel estimated that by reducing the double-track locomotive worked line to a single track atmospheric line a saving of £8,000 per year could be made. Double track lines were favoured at that time even for lightly worked lines as this reduced the chances of a collision between trains, but the atmospheric system precludes the possibility of two trains travelling in opposite directions on the same section of track. The pipes were ordered from George Hennet, an engineering contractor who worked on many of Brunel's lines. He established a factory at Bridgwater, Somerset, to make them. The line opened with conventional steam locomotives to Teignmouth on 30 May 1846 and was extended to Newton on 30 December 1846. The first piston carriage (which connected the train to the pipe) was delivered on 25 February 1847 and experimental running with atmospheric power started immediately. Public services were run to Teignmouth from 13 September 1847 and extended to Newton from 10 January 1848. At this time some trains were still worked by locomotives, but from 23 February 1848 all scheduled trains were powered by the atmospheric system. The leather valve along the top of the pipe tended to dry out and air could then leak in, but this was mitigated slightly by the passing trains spraying water on the leather. The harsh environment of the line, which runs adjacent to the sea for much of its length and is often soaked with salt spray, presented difficulties in maintaining the leather flaps provided to seal the vacuum pipes, which had to be kept supple by being greased with tallow; even so, air leaked in, reducing the pressure difference. Many trains arrived at Exeter from the Bristol and Exeter Railway very late. Because the South Devon line was only equipped with a telegraph that linked the stations, the engines had to start pumping for when the timetable said that the trains were due to enter their section and then keep pumping until the train eventually passed. This meant that the engines pumped for twice as long as was necessary and meant that much more coke was consumed than would have been the case if pumping had only been undertaken when the train was actually ready to be run. The engine houses were connected to the telegraph system on 2 August 1848 but a lack of trained staff meant that it was not fully used. The railway company had set up a committee to investigate the efficiency of atmospheric working on 23 May 1848. In August Brunel gave a lengthy report on the system, and discussions with Joseph Samuda were held with a view to making repairs to the valve and guaranteeing its operation. On 29 August 1848 the directors, following Brunel's advice, recommended to the shareholders the suspension of atmospheric working. Atmospheric-powered service thus lasted less than a year, to 9 September 1848; the last engine pumping was at Exeter, where an up goods train arrived in the early hours of 10 September. The engines and buildings were sold to other users, and most of the pipes were sold back to George Hennet for scrap. The atmospheric had cost the railway over £433,000 and about £81,000 was raised from the sales of redundant materials. (Reprinted by Alan Sutton Publishing, 1985 () Despite the building of engine houses on towards Plymouth and on the Torquay branch the system never expanded beyond Newton. Similarly, the proposal to use the same system on Brunel's Cornwall Railway between Plymouth, Falmouth and Padstow was not pursued. Three of the engine houses (Starcross, Torquay and Totnes) are still standing and the location of two others (Turf and Dawlish) are clearly visible. A section of the pipe, without the leather covers, is preserved at Didcot Railway Centre mounted on a short section of track which is inclined to show the gradient of the line from Newton to Dainton. Technical details A reconstructed section of atmospheric track at Didcot Railway Centre The system was designed and patented by the Samuda Brothers. The pipe was laid in sections between the broad gauge rails with a continuous slot along the top that was sealed by a leather valve. The buildings that housed the boilers and engines were built in a decorative Italianate style with square chimneys and spaced at around intervals. The 1845 contract for 24 engines comprised sixteen of 33 inch cylinder diameter (approx 45HP), and eight of 12HP, and was split between Boulton and Watt and 'Messrs Rennie',Atmospheric Railway Engines, The Practical Mechanic and Engineer's magazine, February 1845, p139 probably J. and G. Rennie. The engine that pumped each section was the one towards which the train was travelling, for example a train leaving Exeter was powered by the Countess Wear engine creating a partial vacuum in the pipe in front of the train which was then propelled forward by the normal atmospheric pressure in the pipe behind the train's piston. Pumping started up to eight minutes before the scheduled departure of the train so as to build up a sufficient vacuum. At stations a smaller pipe was laid alongside the track and a piston in this was connected to the train by a rope to start it moving. On arrival at the next station it was up to the driver to bring the train to a stop using its brakes. Engine houses were situated at every station except Exeter St Thomas where the driver had to hold the train against the atmospheric pressure with the brakes. The level portions used pipes but the steeper gradients west of Newton were to have used pipes. It is not clear how the change between the two pipe sizes would have been achieved unless the piston carriages were changed at Newton. It is also unclear how the level crossing at Turf was operated as the pipe projected some way above the rails. Speeds of up to 70 mph (112 km/h) were achieved, but service speeds were usually around 40 mph (64 km/h). The timetable allowed 55 minutes for the journey, but records show that 36% of trains arrived more than five minutes early, some by more than ten minutes. Engine house remains =Turf= The remains of Turf engine house can be seen on the river side of the line just where the railway comes alongside the River Exe near Turf Lock, the entrance to the Exeter Canal. The square pond surrounded by trees on the river side of the line was the main water reservoir. Just to the south of this, the foundations of some buildings can be seen. This was where the engine house itself was built, although some of the foundations are from later alterations. The building was demolished about 1860 and the stone used in a nearby farm. =Starcross= Starcross The most familiar engine house, and the most intact one which actually saw service, is situated on the landward side of the line at the south end of Starcross railway station. The chimney, reduced in height for safety many years ago, had for a while a new pitched roof, but it has since been removed. Unlike the other engine houses this one is built of Heavitree stone from Exeter, a coarse red sandstone that has not weathered well. The accompanying photograph from 2007 shows the original wall along the narrow street called The Strand, but within the next decade it had to be rebuilt with a concrete surface painted to resemble stones. After the engines ceased work, the boiler house was used by coal merchants until 1981. The engine area was used as a Wesleyan Church from 1867 to 1958, after which it was used as a youth club for a few years. The whole building was sold and reopened as a museum for the atmospheric railway in 1982. This has since closed and the building was developed internally for use by the local Starcross Fishing and Cruising Club. =Dawlish= Although largely demolished in 1873, part of the engine house wall can be seen at the back of Dawlish railway station car park. =Torquay= Torquay By the time the railway opened to Torquay the decision had already been made to abandon atmospheric working, so this engine house was never used. However it was completed and is the surviving example with the least amount of exterior modification. It is also the one least easy to see from trains; it is about on the side of (on the right hand side of the line approaching from Newton Abbot) but is on a higher level above the line. It can be more easily viewed from a supermarket car park in Newton Road. The location so far from the terminal but uphill from it shows that southbound trains were intended to run the last mile by gravity. =Totnes= Totnes The engine house adjacent to Totnes railway station was never brought into use. It was converted for use as a milk processing plant for Dairy Crest but this has since closed. The original chimney, still present in a photograph of 1925, was removed many years ago. References Further reading * Records of the South Devon Railway can be consulted at The National Archives * A series of detailed watercolors by W Dawson showing the line with atmospheric pipes installed are in the collection of the Institution of Civil Engineers * External links * Totnes On Line – Brunel engine house photographs Engine houses Rail transport in Devon Buildings and structures in Devon Works of Isambard Kingdom Brunel Industrial archaeological sites in Devon "