bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rhizobium
Authors: Kuykendall L. David , Young John M. , Martínez‐Romero Esperanza , Kerr Allen , Sawada Hiroyuki 
Published: August 2015

Rhi.zo' bi.um. Gr. n.rhizaa root; Gr. n.bioslife; M.L. neut. n.Rhizobiumthat which lives in a root.Proteobacteria / Alphaproteobacteria / Rhizobiales / Rhizobiaceae / RhizobiumRods 0.5–1.0×1.2–3.0 µm. Nonsporeforming. Gram negative.Motile by 1–6 peritrichous flagella. Fimbriae have been described on some strains.Aerobic, possessing a respiratory type of metabolism with oxygen as the terminal electron acceptor. Optimal temperature for growth, 25–30°C; some species can grow at temperatures >40°C. Optimal pH for growth, 6–7; range pH 4–10. Generation times ofRhizobiumstrains are 1.5–5.0 h.Coloniesare usually white or beige, circular, convex, semi‐translucent or opaque, raised and mucilaginous,usually 2–4 mm in diameter within 3–5 days on yeast‐mannitol‐mineral salts agar(YMA).Growth on carbohydrate media is usually accompanied by copious amounts of extracellular polysaccharide. Pronounced turbidity develops after 2 or 3 days in aerated or agitated broth. Chemoorganotrophic, utilizing a wide range of carbohydrates and salts of organic acids as sole carbon sources, without gas formation. Cellulose and starch are not utilized.Produce an acidic reaction in mineral‐salts medium containing mannitol or other carbohydrates. Ammonium salts, nitrate, nitrite, and most amino acids can serve as nitrogen sources. Strains of some species will grow in a simple mineral salts medium with vitamin‐free casein hydrolysate as the sole source of both carbon and nitrogen, but strains of many species require one or more growth factors such as biotin, pantothenate, or nicotinic acid. Peptone is poorly utilized. Casein, starch, chitin, and agar are not hydrolyzed.All knownRhizobiumspecies include strains which induce hypertrophisms in plants as root nodules with or without symbiotic nitrogen fixation. Some cells of symbiotic bacterial species enter root hair cells of leguminous plants (Family Leguminosae) via invagination or by wounds (“crack entry”) and elicit the production of root nodules wherein the bacteria engage as intracellular symbionts, usually fixing nitrogen. Many well‐defined nodulation (nod) and nitrogen fixation (nif) genes are clustered on large plasmids or megaplasmids (pSyms). Plasmid transfer between species results in the expression and stable inheritance of the particular plant‐interactive properties of the plasmid‐donor species. Plant host specificity is usually for a few legume genera but may, in some strains, include a wide variety of legume genera and is to some extent determined by the chemical structure of the lipochito‐oligosaccharideNodfactors produced. These chitin‐like molecules induce nodule organogenesis in the absence of bacteria.In root nodules the bacteria occur as endophytes that exhibit pleomorphic forms,termed“bacteroids”,which reduce or fix gaseous atmospheric nitrogen into a combined form utilizable by the host plant.The mol%G+C of the DNA is: 57–66.Type species:Rhizobium leguminosarum(Frank 1879) Frank 1889, 338 (Schinzia leguminosarumFrank 1879, 397.)
Rhodospirillum
Authors: Imhoff Johannes F. 
Published: August 2015

Rho.do.spi.ril' lum. Gr. n.rhodonthe rose; M.L. neut. n.Spirilluma bacterial genus; M.L. neut. n.Rhodospirillumthe roseSpirillum.Proteobacteria / Alphaproteobacteria / Rhodospirillales / Rhodospirillaceae / RhodospirillumCells are vibrioid to spiral shaped, are motile by means of bipolar flagella, and multiply by binary fission.Gram negative,belonging to theAlphaproteobacteria. Internal photosynthetic membranes are present as vesicles or as lamellae forming a sharp angle to the cytoplasmic membrane. Photosynthetic pigments arebacteriochlorophylla(esterified with phytol or geranylgeraniol) andcarotenoids of the spirilloxanthin serieswith spirilloxanthin itself lacking in some species.Ubiquinones and rhodoquinones with 8 or 10 isoprene unitsare present.Major cellular fatty acids are C18:1,C16:1,and C16:0, with C18:1as dominant component (51–55% of total fatty acids).The mol%G+C of the DNA is: 62.1–63.5.Type species:Rhodospirillum rubrum(Esmarch 1887) Molisch 1907, 25 (Spirillum rubrumEsmarch 1887, 230.)
Holospora
Authors: Görtz Hans‐Dieter , Schmidt Helmut J. 
Published: August 2015

Ho.lo' spo.ra
. Gr. fem. adj.
holos
whole, complete; Gr. n.
sporus
seed; M.L. n.
spora
spore; M.L. fem. n.
Holospora
whole spore.

Proteobacteria / Alphaproteobacteria / Rickettsiales / Holosporaceae / Holospora
The description of the genus is that of the family. Diagnostic characteristics are given in Table 1.

Type species
:
Holospora undulata
(ex Hafkine 1890) Gromov and Ossipov 1981, 351.
Orientia
Authors: Yu Xue‐jie , Walker David H. 
Published: August 2015

O' ri.en' ti.a. M.L. fem. n.Orientiapertaining to the Orient, the area where the organisms are widely distributed.Proteobacteria / Alphaproteobacteria / Rickettsiales / Rickettsiaceae / OrientiaShort rods 0.5–0.8 × 1.2–3.0 µm.Obligately intracellular.Grow free in the cytosol of the host cell; rarely invade the nucleus. Bacterial cells are released surrounded by host cell membrane.Cell walls lack lipopolysaccharide and peptidoglycan. The outer leaflet of the cell wall is considerably thicker than the inner leaflet, unlike the wall of rickettsiae. The genome ofOrientiais 1.1–1.5 × 109Da, larger than that ofRickettsia. Maintained by transovarian transmission in its varioustrombiculid mite hosts.Etiological agents of scrub typhus in humans. Transmitted to humans by mite larvae. Found in Asia and Australia.The mol%G+C of the DNA is: 28.1–30.5 (HPLC).Type species:Orientia tsutsugamushi(Hayashi 1920) Tamura, Ohashi, Urakami and Miyamura 1995, 590 (Rickettsia tsutsugamushi(Hayashi 1920) Ogata 1931, 252; “Theileria tsutsugamushi” Hayashi 1920, 63.)
Alcaligenes
Authors: Busse Hans‐Jürgen , Auling Georg 
Published: August 2015

Al.ca.li' ge.nes. Arabicalthe; Arabic n.galiythe ash of saltwort; French n.alcalialkali; Gr. v.gennaioto produce; M.L. masc. n.Alcaligenesalkali‐producing (bacteria).Proteobacteria / Betaproteobacteria / Burkholderiales / Alcaligenaceae / AlcaligenesRods or coccobacilli, 0.5–1.2 × 1.0–3.0 µm, usually occurring singly. Resting stages not known.Gram negative.Motilewith one to nineperitrichousflagella.Obligately aerobic, possessing a strictly respiratory type of metabolism with oxygen as the terminal electron acceptor. Some strains are capable of anaerobic respiration in the presence of nitrate or nitrite. Optimal growth temperature: 20–37°C. Colonies on nutrient agar arenonpigmented.Oxidase positive.Catalase positive. Indole not produced. Cellulose, esculin, gelatin, and DNA usually not hydrolyzed.Chemoorganotrophic,using a variety of organic acids and amino acids as carbon sources.Alkali producedfrom several organic salts and amides. Carbohydrates usually not utilized.Characteristic fatty acids are C17:0 cyclo,C16:0,C14:0 3OH,C16:1,and C12:0 2OH.Ubiquinone Q‐8.Polyamine patterns with the predominant compound putrescine and the unusual diamine 2‐hydroxyputrescine. Isolated from water, soil, and clinical specimens such as blood, spinal fluid, pleural fluid, peritoneal fluid, pus, urine, stools, and swabs of eyes, ears, and pharynxes. Frequently found in unsterilized distilled water and in chlorhexidine solutions in hospitals. Occasionally causing opportunistic infections in humans.The mol%G+C of the DNA is: 56–60.Type species:Alcaligenes faecalisCastellani and Chalmers 1919, 936AL(Achromobacter arsenoxydans‐tresTurner 1954, 475; “Pseudomonas odorans” (Málek and Kazdová‐Košiskova 1946; Málek, Radochová and Lysenko 1963, 353; “Alcaligenes odoransvar. viridans” Mitchell and Clarke 1965, 347.
Bordetella
Authors: Sanden Gary N. , Weyant Robbin S. 
Published: August 2015

Bor.de.tel' la. M.L. dim ending ‐ella;M.L. fem. n.Bordetellanamed after Jules Bordet, who with O. Gengou first isolated the organism causing pertussis.Proteobacteria / Betaproteobacteria / Burkholderiales / Alcaligenaceae / BordetellaMinute coccobacillus, 0.2–0.5 µm in diameter and 0.5–2.0 µm in length, often bipolar stained, and arranged singly or in pairs, more rarely in chains. Gram negative.Nonmotileormotileby peritrichous flagella.Strictly aerobic.Optimal temperature,35–37°C. Colonies on Bordet–Gengou medium are smooth, convex, pearly, glistening, nearly transparent, and surrounded by a zone of hemolysis without definite periphery.Respiratory metabolism. Chemoorganotrophic.Require nicotinamide,organic sulfur(e.g., cysteine), andorganic nitrogen(amino acids).Utilize oxidativelyglutamic acid, proline, alanine, aspartic acid, and serine, with production of ammonia and CO2. Litmus milk is made alkaline. Mammalian and avian parasite and pathogen. Most species localize and multiply among the epithelial cilia of the respiratory tract.The mol%G+C of the DNA is: 66–70.Type species:Bordetella pertussis(Bergey, Harrison, Breed, Hammer and Huntoon 1923a) Moreno‐López 1952, 178 (Microbe de coqueluche Bordet and Gengou 1906, 731;Haemophilus pertussisBergey, Harrison, Breed, Hammer and Huntoon 1923a, 269.)
Comamonas
Authors: Willems Anne , Gillis Monique 
Published: August 2015

Co.ma.mo' nas. L. n.comalock of hair; Gr. n.monasa unit, monad; M.L. fem. n.Comamonascell with a polar tuft of flagella.Proteobacteria / Betaproteobacteria / Burkholderiales / Comamonadaceae / ComamonasStraight or slightly curved rods or spirilla, 0.3–0.8 × 1.1–4.4 µm; occasionally longer (5–7 µm), irregularly curved cells or spirilla may occur. Cells occur separately or in pairs andare motile by means of polar or bipolar tufts of 1–5 flagellaexcept forC.koreensis, which is nonmotile.Gram negative. No diffusible pigments are produced on nutrient agar.Oxidase and catalase positive.Aerobic.Chemoorganotrophic, oxidative carbohydrate metabolism with oxygen as the terminal electron acceptor.C.nitrativoransis also capable of denitrification. Good growth on media containing organic acids, amino acids, or peptone; few carbohydrates are used. Major fatty acids are hexadecanoic acid (C16:0), hexadecenoic acid (C16:1) and octadecenoic acid (C18:1); 3‐hydroxydecanoic acid (C10:0 3OH) is always present.The major quinone is ubiquinone Q‐8.The mol%G+C of the DNA is: 60–69.Type species:Comamonas terrigena(ex Hugh 1962) De Vos, Kersters, Falsen, Pot, Gillis, Segers and De Ley 1985b, 450, emend. Willems, Pot, Falsen, Vandamme, Gillis, Kersters and De Ley 1991c, 439.
Macromonas
Authors: Dubinina Galina A. , Rainey Fred A. , Gijs Kuenen J. 
Published: August 2015

Ma' cro.mo' nas
. Gr. adj.
macrus
large; Gr. n.
monas
a unit, monad; M.L. fem. n.
Macromonas
a large monad.

Proteobacteria / Betaproteobacteria / Burkholderiales / Comamonadaceae / Macromonas
Large cells are colorless, cylindrical, bean‐shaped, or slightly bent. Gram negative. Sluggish or rapidly motile by means of a polar tuft of flagella. Strictly aerobic or microaerophilic. A typical characteristic is the presence of several large inclusions of calcium oxalate, previously believed to be calcium carbonate. Sulfur globules may also be present. Multiplication by constriction followed by fission. No resting stages are known. The genus is composed of two species; the type species has not been grown in pure culture. Several strains of the second species have been studied in pure culture.

Type species
:
Macromonas mobilis
(Lauterborn 1915) Utermöhl and Koppe
in
Koppe 1924, 632 (“
Achromatium mobile
” Lauterborn 1915)
Oxalobacter
Authors: Allison Milton J. , MacGregor Barbara J. , Sharp Richard , Stahl David A. 
Published: August 2015

Ox.al.o.bac' ter. Gr. n.oxalpertaining to oxalate; M.L. n.bacterthe masculine form of the Gr. neut. n.bactruma rod; M.L. masc. n.Oxalobacteran oxalate rod.Proteobacteria / Betaproteobacteria / Burkholderiales / Oxalobacteraceae / OxalobacterStraight or curved to vibrioid,Gram‐negative,nonsporeforming rods 0.4–0.6×1.0–2.5μm in length. Flagella may be present or absent.Strictly anaerobic. Chemoorganotroph.Oxalate is used as the major carbon and energy source.Oxamate may also be used,but neither carbohydrates nor any of a wide variety of other compounds will replace oxalate as the growth substrate. Acetate is assimilated for cell synthesis and is required by some, and perhaps by all, strains. Oxalate utilization is accompanied by alkalization of the medium, and formate is produced in approximately equimolar proportions to the amount of oxalate metabolized. Strains have been isolated from the rumens of cattle and sheep, from cecal and fecal samples from humans, guinea pigs, swine, domestic and wild rats, and from freshwater lake and marine sediments. It is probable that these bacteria colonize many other anaerobic habitats.Oxalobacteris currently classified in the classBetaproteobacteria, the orderBurkholderiales, and the familyOxalobacteraceae.The mol%G+C of the DNA is: 48–52.Type species:Oxalobacter formigenesAllison, Dawson, Mayberry and Foss 1985b, 375 (Effective publication: Allison, Dawson, Mayberry and Foss 1985a, 6.)
Thiobacillus
Authors: Kelly Donovan P. , Wood Ann P. , Stackebrandt Erko 
Published: August 2015

Thi.o.ba.cil' lus. Gr. n.thiossulfur; L nbacillusa small rod; M. L. masc n.Thiobacillussulfur rodlet.Proteobacteria / Betaproteobacteria / Hydrogenophilales / Hydrogenophilaceae / ThiobacillusSmall, Gram‐negative, rod‐shaped cells (0.3–0.5 × 0.9–4.0 µm). Some species are motile by means of polar flagella. No resting stages known. Energy is derived by the oxidation of one or more reduced sulfur compounds, including sulfides, sulfur, thiosulfate, polythionates, and thiocyanate. Sulfate is the end product of sulfur‐compound oxidation, but sulfur, sulfite, and polythionates may be accumulated by most species, sometimes transiently. All species can fix carbon dioxide by means of the Benson–Calvin cycle and are capable of autotrophic growth; some species are obligately chemolithotrophic, while others are chemoorganotrophic. The genus currently includes obligate aerobes and facultative denitrifiers. Optimal pH of 2–8 with optimal temperature of 28–43°C. Distribution is seemingly ubiquitous in marine, freshwater, and soil environments, especially where oxidizable sulfur is abundant (e.g., sulfur springs, sulfide minerals, sulfur deposits, sewage treatment areas, and sources of sulfur gases, such as sediments or anaerobic soils releasing H2S).The mol%G+C of the DNA is: 62–67.Type species:Thiobacillus thioparusBeijerinck 1904b, 597.
Chromobacterium
Authors: Gillis Monique , Logan Niall A. 
Published: August 2015

Chro.mo.bac.te' ri.um.Gr. n.chromacolor; Gr. n.bakteriona small rod; M.L. neut. n.Chromobacteriuma small, colored rod.Proteobacteria / Betaproteobacteria / Neisseriales / Neisseriaceae / ChromobacteriumCells straight,round‐ended,often coccoid,but usually occuring as rods, 0.6–0.9×1.5–3.0μm, occurring singly, sometimes in pairs or short chains. No definite capsules are evident. No resting stages known. Gram negative. Usually contain poly‐β‐hydroxy‐butyrate crystals (80% of strains positive), but rarely contain metachromatic granules.Motile by means of both a single polar flagellum and, usually, one or more subpolar or lateral flagella.Facultative anaerobes.Minimum temperature for growth 10–15°C; maximum about 40°C; optimal growth at 30–35°C. Optimal pH 7–8; no growth occurs below pH 5. Grow on ordinary peptone media; no distinctive organic growth factor requirements. Colonies are smooth, but rough variants may occur; colonies are of butyrous consistency and are easily emulsified in water.Most strains produce the violet pigment violacein, but strains producing nonpigmented colonies are sometimes encountered, and subcultures of pigmented strains often contain partially or completely unpigmented colonies. Growth in nutrient broth produces a violet ring at the surface with a fragile pellicle. Chemoorganotrophs;most strains(80%)attack carbohydrates fermentatively, some(20%)oxidatively, producing small amounts of acidbut usually no gas. Lactate is oxidized to CO2. Usually oxidase positive by the method of Sivendra and Lo (1975). No growth in media containing 6% or more NaCl. Catalase positive, but very sensitive to hydrogen peroxide. Indole negative, Voges–Proskauer negative. Nitrate and nitrite reduced. Ammonia produced from peptone. Arginine hydrolyzed.Hydrogen cyanide produced.Resistant to benzylpenicillin, 10 mg/ml.Sensitive to tetracycline, 30 mg/ml.Resistant to O/129(2,4‐diamino‐6,7‐diisopropyl pteridine) by disc diffusion method, 50 mg/disc. Soil and water organisms, occasionally causing infections of humans and other mammals. 16S rRNA gene sequence data placeChromobacteriumin the classBetaproteobacteria.The mol%G+C of the DNA is: 65–68 (Tm).Type species:Chromobacterium violaceumBergonzini 1881, 153.
Eikenella
Authors: Bottone Edward J. , Jackson Francis L. , Goodman Yvonne E. 
Published: August 2015

Ei.ke.nel' la. M.L. dim. ending ‐ella; M.L. fem. n.Eikenellanamed after M. Eiken, who first named the type species of the genus.Proteobacteria / Betaproteobacteria / Neisseriales / Neisseriaceae / EikenellaStraight rods, 0.3–0.4 × 1.5–04.0 µm, unbranched, with rounded ends and a regular morphology. Short filaments are occasionally formed. Nonsporeforming. Gram negative.Nonmotile, possessing no flagella; however, a “twitching motility” may occur on agar surfaces.Facultatively anaerobic. Optimal growth temperature, 35–37°C.Colonies may appear to corrode the surface of the agar; noncorroding strains may also occur. Nonhemolytic; a slight greening of blood media around colonies may occur.Oxidase positive(Kovacs method).Negative for catalase,urease,arginine dihydrolase,and indole.Lysine‐decarboxylase positive. Nitrates are reduced to nitrites.No acid is formed from glucose or other carbohydrates.Hemin is usually required for growth under aerobic conditions. Occur in the human mouth and intestine; can be opportunistic pathogens.The mol%G+C of the DNA is: 56–58.Type species:Eikenella corrodens(Eiken 1958) Jackson and Goodman 1972, 75 (Bacteroides corrodensEiken 1958, 415.)
Neisseria
Authors: Tønjum Tone 
Published: August 2015

Neis.se' ri.a. M.L. fem. n.Neisserianamed after Albert Neisser, who discovered the etiological agent of gonorrhea in the pus of patients in 1889.Proteobacteria / Betaproteobacteria / Neisseriales / Neisseriaceae / NeisseriaCocci 0.6–1.9 µm in diameter, occurring singly but often in pairs with adjacent sides flattened; two species (Neisseria elongataandN.weaveri) are exceptions and consist of short rods 0.5 µm wide, often arranged as diplobacilli or in chains. Division of the coccal species is in two planes at right angles to each other, sometimes resulting in tetrads. Capsules and fimbriae (pili) may be present. Endospores are not present. Gram negative, but there is a tendency to resist decolorization. Swimming motility does not occur and flagella are absent. Aerobic. Some species produce a yellow carotenoid pigment. Some species are nutritionally fastidious and hemolytic. Optimal temperature, 35–37°C. Oxidase positive. Catalase positive except most strains ofN.elongata. Carbonic anhydrase is produced by all species. All species reduce nitrite exceptN.gonorrhoeaeandN.canis.Neisseriaspp. produce acid from carbohydrates by oxidation, not fermentation. Chemoorganotrophic. Exotoxins are not produced. Some species are saccharolytic. Inhabitants of the mucous membranes of mammals. Some species are primary pathogens of humans. The genusNeisseriabelongs to the familyNeisseriaceaeof theBetaproteobacteria.The mol%G+C of the DNA is: 48–56.Type species:Neisseria gonorrhoeae(Zopf 1885) Trevisan 1885, 106 (Merismopedia gonorrhoeaeZopf 1885, 54.)
Gallionella
Authors: Hallbeck Lotta E‐L. , Pedersen Karsten 
Published: August 2015

Gal.li.o.nel' la. M.L. dim. ending ‐ella; M.L. fem. n.Gallionellanamed for B. Gaillon, a customs agent and zoologist (1782–1839) in Dieppe, France.Proteobacteria / Betaproteobacteria / Nitrosomonadales / Gallionellaceae / GallionellaGram‐negative,bean‐shaped cells, usually 0.5–0.8 × 1.6–2.5 µm, that secrete an extracellulartwisted stalkfrom the concave side, 0.3–0.5 µm in width and up to 400 µm or more in length. The stalk is composed of numerous 2 nm‐wide fibers and is produced under microaerophilic conditions when cells are in late exponential or stationary growth phase. Motile by means of a polar flagellum.Microaerophilic; chemolithotrophic growthcan be obtainedin vitrousing oxygen and ferrous iron concentration gradients in a salt medium withCO2as sole carbon source(Table BXII.β.108).Mixotrophic metabolismhas been demonstrated with glucose, fructose, and sucrose. Can be found where anaerobicgroundwater with ferrous ironreaches an oxygen‐containing environment. Belongs to theBetaproteobacteria, familyGallionellaceae, with one known species,G. ferruginea. Most closely related species according to 16S rDNA sequence analysis is the chemolithotrophNitrosospira multiformis, distantly related with a 16S rDNA sequence similarity of 90%.The mol%G+C of the DNA is: 51–54.6 (Hanert, 1989).Type species:Gallionella ferrugineaEhrenberg 1838, 166.
Adaptive set‐point regulation of discrete‐time nonlinear systems
Authors: Hanba Shigeru 
Published: August 2015

SummaryIn this paper, adaptive set‐point regulation controllers for discrete‐time nonlinear systems are constructed. The system to be controlled is assumed to have a parametric uncertainty, and an excitation signal is used in order to obtain the parameter estimate. The proposed controller belongs to the category of indirect adaptive controllers, and its construction is based on the policy of calculating the control input rather than that of obtaining a control law. The proposed method solves the adaptive set‐point regulation problem under the assumption that the target state is reachable for each fixed parameter value. Additional feature of the proposed method is that Lyapunov‐like functions have not been used in the construction of the controllers. Copyright © 2015 John Wiley & Sons, Ltd.
Cationic Rhodium(III)‐Catalyzed Direct C‐2 Carboxamidation of Indoles with Isocyanates via CH Bond Functionalization
Authors: Xu Jun , Sharma Nandini , Sharma Upendra K. , Li Zhenghua , Song Gonghua , Van der Eycken Erik V. 
Published: August 2015

AbstractA pentamethylcyclopentadienylrhodium(III)‐catalyzed regioselective synthesis of indole‐2‐carboxamides is described employing N‐pyrimidylindoles and isocyanates as coupling partners via CH functionalization. A wide variety of indole‐2‐carboxamides can be synthesized via this method under relatively mild conditions with broad functional group tolerance. The effect of various directing group on this transformation was also studied, unveiling the pyrimidyl group as an easily installable and removable directing group.magnified image
Aluminium‐Catalysed Oxazolidinone Synthesis and their Conversion into Functional Non‐Symmetrical Ureas
Authors: Laserna Victor , Guo Wusheng , Kleij Arjan W. 
Published: August 2015

AbstractAn efficient and practical aluminium‐catalysed approach towards a range of functional oxazolidinones is reported. The method is based on cheap and readily available starting materials including terminal and internal (bicyclic) epoxides and phenyl carbamate. The oxazolidinones serve as highly useful synthons for the high yield preparation of non‐symmetrical ureas by nucleophilic ring‐opening affording the targeted urea compounds with excellent functional group diversity, high regioselectivity and isolated yields up to >99%.magnified image