Methylophilus quaylei sp. nov., a new aerobic obligately methylotrophic bacterium

A new obligately methylotrophic bacterium (strain MTT) with the ribulose monophosphate pathway of carbon assimilation is described. The isolate, utilizing only methanol, is an aerobic, Gram-negative, asporogenous, non-motile short rod multiplying by binary fission. Its cellular fatty acids profile consists primarily of straight-chain saturated C16:0 and unsaturated C16:l acids. The major ubiquinone is Q-8. The dominant phospholipids are phosphatidylethanolamine and phosphatidylglycerol. Diphosphatidylglycerol (cardiolipin) is absent. Optimal growth conditions are 25-29 degree C, pH 6.5 - 7.5, 0.5% CH3OH and 0.05% NaCl. Strain MTT lacks alpha-ketoglutarate dehydrogenase, the glyoxylate shunt enzymes, and glutamate dehydrogenase. Ammonium is assimilated by the operation of the glutamate cycle enzymes: glutamine synthetase and glutamate synthase. An exopolysaccharide consisting of rhamnose, glucose and galactose is formed under nitrogen limitation. The G + C content of the DNA is 54.0 mol%. Based on 16S rDNA sequence analysis and DNA-DNA relatedness (29-34%) with type strains of the genus Methylophilus, the novel isolate was classified as a new species of this genus and named Methylophilus quaylei MTT (VKM B-2338T, DSMZ, etc.).     

Methylobacillus arboreus sp. nov., and Methylobacillus gramineus sp. nov., novel non-pigmented obligately methylotrophic bacteria associated with plants

Two newly isolated obligate methanol-utilizing bacteria (strains Iva^T and Lap^T) with the ribulose monophosphate pathway of C₁ assimilation are described. The isolates are strictly aerobic, Gram negative, asporogenous, motile rods multiplying by binary fission, mesophilic and neutrophilic, synthesize indole-3-acetate. The prevailing cellular fatty acids are straight-chain saturated C_16:0 and unsaturated C_16:1 acids. The major ubiquinone is Q-8. The predominant phospholipids are phosphatidylethanolamine, phosphatidylglycerol and cardiolipin. Ammonia is assimilated by glutamate dehydrogenase. The DNA G+C contents of strains Iva^T and Lap^T are 54.0 and 50.5 mol% (T_m), respectively.Based on 16S rRNA gene sequence analysis and DNA–DNA relatedness (38–45%) with type strains of the genus Methylobacillus, the novel isolates are classified as the new species of this genus and named Methylobacillus arboreus Iva^T (VKM B-2590^T, CCUG 59684^T, DSM 23628^T) and Methylobacillus gramineus Lap^T (VKM B-2591^T, CCUG 59687^T, DSM 23629^T).The GenBank accession numbers for the 16S rRNA gene and mxaF gene sequences of the strains Iva^T and Lap^T are GU937479, GU937478 and HM030736, HM030735, respectively.     

Methylophaga natronica sp. nov., a new alkaliphilic and moderately halophilic, restricted-facultatively methylotrophic bacterium from soda lake of the Southern Transbaikal region

A new, moderately haloalkaliphilic and restricted-facultatively methylotrophic bacterium (strain Bur2T) with the ribulose monophosphate pathway of carbon assimilation is described. The isolate, which utilizes methanol, methylamine and fructose, is an aerobic, Gram-negative, asporogenous, motile short rod multiplying by binary fission. It is auxotrophic for vitamin B12, and requires NaHCO3 or NaCl for growth in alkaline medium. Cellular fatty acids profile consists primarily of straight-chain saturated C16:0, unsaturated C16:1 and C18:1 acids. The major ubiquinone is Q-8. The dominant phospholipids are phosphatidylethanolamine and phosphatidylglycerol. Diphosphatidylglycerol is also present. Optimal growth conditions are 25-29 degrees C, pH 8.5-9.0 and 2-3% (w/v) NaCl. Cells accumulate ectoine and glutamate as the main osmoprotectants. The G + C content of the DNA is 45.0 mol%. Based on 16S rDNA sequence analysis and DNA-DNA relatedness (25-35%) with type strains of marine and soda lake methylobacteria belonging to the genus Methylophaga, the novel isolate was classified as a new species of this genus and named Methylophaga natronica (VKM B-2288T).     

Hansschlegelia plantiphila gen. nov. sp. nov., a new aerobic restricted facultative methylotrophic bacterium associated with plants

A new genus, Hansschlegelia, and a new species, Hansschlegelia plantiphila, are proposed for three strains of methanol-utilizing bacteria isolated from lilac buds (strain S(1)(T)), linden buds (strain S(2)) and blue spruce needles (strain S(4)), which were selected in winter at -17 degrees C. These bacteria are aerobic, Gram-negative, colorless, non-motile short rods that multiply by binary fission and employ the ribulose bisphosphate (RuBP) and the serine pathways for C(1) assimilation. The strains have a limited number of growth substrates and use methanol, methylamine, formate, CO(2)/H(2) and glycerol as carbon and energy sources. Only strain S(1)(T) grows with ethanol and inulin. The strains are neutrophilic and mesophilic, and synthesize phytohormones (auxins and cytokinins) and vitamin B(12). Their major cellular fatty acids are saturated C(16:0), straight-chain, unsaturated C(18:1)(omega)(7) and cyclopropane C(19 cyc) acids. The main ubiquinone is ubiquinone-10 (Q-10). The dominant phospholipids are phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol (cardiolipin). The DNA G+C content is 68.5+/-0.2 mol%. The strains share almost identical 16S rRNA gene sequences, a high DNA-DNA hybridization value (72-86%) and represent a novel lineage of autotrophic methanol-utilizing bacteria within the Alphaproteobacteria. Collectively, these strains comprise a new genus and species H. plantiphila gen. nov., sp. nov., with strain S(1)(T) (VKM B-2347(T), NCIMB 14035(T)) as the type strain.     

Methylovorus mays--novel species of aerobic, obligatory methylotrophic bacteria associated with plants

A bacterial strain utilizing methanol as the sole source of carbon and energy was isolated from the maize phyllosphere. Cells are nonpigmented gram-negative motile rods that do not form spores or prosthecae and reproduce by binary fission. The strain does not require vitamins or supplementary growth factors. It is obligately aerobic and urease-, oxidase-, and catalase-positive. The optimum growth temperature is 35-40 degrees C; the optimum pH is 7.0-7.5. The doubling time is 2 h. The bacterium implements the ribulose monophosphate pathway and possesses NAD(+)-dependent 6-phosphogluconate dehydrogenase and enzymes of the glutamate cycle. alpha-Ketoglutarate dehydrogenase and enzymes of the glyoxylate cycle (isocitrate lyase and malate synthase) are absent. Fatty acids are dominated by palmitic (C16:0) and palmitoleic (C16:1) acids. The major phospholipids are phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylcholine. Cardiolipin is present in minor amounts. The dominant ubiquinone is Q8. The bacterial genome contains genes controlling the synthesis and secretion of cytokinins. The G + C content of DNA is 57.2 mol %, as determined from the DNA thermal denaturation temperature (Tm). The bacterium shows low DNA homology (< 10%) with restricted facultative methylotrophic bacteria of the genus Methylophilus (M. methylotrophus NCIMB 10515T and M. leisingerii VKM B-2013T) and with the obligate methylotrophic bacterium (Methylobacillus glycogenes ATCC 29475T). DNA homology with the type representative of the genus Methylovorus, M. glucosetrophus VKM B-1745T, is high (58%). The new isolate was classified as a new species, Methylovorus mays sp. now.     

<Emphasis Type="Italic">Methylophaga murata</Emphasis> sp. nov.: a Haloalkaliphilic Aerobic Methylotroph from Deteriorating Marble

The haloalkaliphilic methylotrophic bacterium (strain Kr3) isolated from material scraped off the deteriorating marble of the Moscow Kremlin masonry has been found to be able to utilize methanol, methylamine, trimethylamine, and fructose as carbon and energy sources. Its cells are gram-negative motile rods multiplying by binary fission. Spores are not produced. The isolate is strictly aerobic and requires vitamin B₁₂ and Na⁺ ions for growth. It is oxidase- and catalase-positive and reduces nitrates to nitrites. Growth occurs at temperatures between 0 and 40°C (with the optimum temperatures being 20–32°C), pH values between 6 and 11 (with the optimum at 8–9), and NaCl concentrations between 0.05 and 3 M (with the optimum at 0.5–1.5 M). The dominant cellular phospholipids are phosphatidylethanolamine, phosphatidylglycerol, and cardiolipin. The major cellular fatty acids are palmitic (C_16:0), palmitoleic (C_16:1), and octadecenoic (C_18:1) acids. The major ubiquinone is Q₈. It accumulates ectoine and glutamate, as well as a certain amount of sucrose, to function as osmoprotectants and synthesizes an exopolysaccharide composed of carbohydrate and protein components. It is resistant to heating at 70°C, freezing, and drying; utilizes methanol, with the resulting production of formic acid, which is responsible for the marble-degrading activity of the isolate; and implements the 2-keto-3-deoxy-6-phosphogluconate variant of the ribulose monophosphate pathway. The G+C content of its DNA is 44.6 mol %. Based on 16S rRNA gene sequencing and DNA-DNA homology levels (23–41%) with neutrophilic and alkaliphilic methylobacteria from the genus Methylophaga, the isolate has been identified as a new species, Methylophaga murata (VKM B-2303^T = NCIMB 13993^T).__________Translated from Mikrobiologiya, Vol. 74, No. 4, 2005, pp. 511–519.Original Russian Text Copyright © 2005 by Doronina, Lee, Ivanova, Trotsenko.     

Some characteristics of Methylococcus mobilis sp. nov.

A methane-assimilating coccus was isolated from a continuous culture. Under certain conditions, in pure culture the cells grew in sarcina-like, refractile clusters.That these clusters resembled multiple-bodied cysts was confirmed by electron microscopy. In addition, tube-like structures, not previously reported in methane-oxidizing bacteria, were found. Motile cells, with one or, rarely, two flagella were occasionally observed. Methane and methanol were exclusively assimilated as the sole source of carbon and energy. Formaldehyde, formate, lower alkanes, alcohols and aldehydes, with the exception of acetaldehyde, were oxidized by cell suspensions. The presence of a number of key enzymes in cell-free extracts suggested that the ribulose-monophosphate pathway of carbon assimilation is active. This agreed with the internal membrane structure found (type I organism).Nitrate, ammonia, peptone, yeast extract, asparagine, aspartic acid and glutamic acid were assimilated as sources of nitrogen. No nitrogen fixation could be demonstrated.The cells contained 9.1–9.7% nitrogen and 7–10% lipid, dependent on the growth conditions. Poly--hydroxybutyric acid could not be detected. The guanine+cytosine (G+C) content of the DNA was found to be 56.3%. As a name for the organism Methylococcus mobilis sp. nov. is proposed.Abbreviations used G+C Guanine+Cytosine     

Two new species of anaerobic oxalate-fermenting bacteria,Oxalobacter vibrioformis sp. nov. and Clostridium oxalicum sp. nov., from sediment samples

Two types of new anaerobic bacteria were isolated from anoxic freshwater sediments. They grew in mineral medium with oxalate as sole energy source and with acetate as main carbon source. Oxalate as well as oxamate (after deamination) were decarboxylated to formate with growth yields of 1.2–1.4 g dry cell matter per mol oxalate degraded. No other organic or inorganic substrates were used, and no electron acceptors were reduced. Strain WoOx3 was a Gramnegative, non-sporeforming, motile vibrioid rod with a guanine-plus-cytosine content of the DNA of 51.6 mol%. It resembled the previously described genus Oxalobacter, and is described as a new species, O. vibrioformis. Strain AltOx1 was a Gram-positive, spore-forming, motile rod with a DNA base ratio of 36.3 mol% guanine-plus-cytosine. This isolate is described as a new species of the genus Clostridium, C. oxalicum.     

Thermococcus litoralis sp. nov.: A new species of extremely thermophilic marine archaebacteria

We describe a new species, Thermococcus litoralis, which is different from the type species Thermococcus celer in molecular, morphological and physiological characteristics.Abbreviations 3 x SSC (standard saline citrate) - 0.45 M NaCl 0.045 M Na₃-citrate     

New species of psychrophilic acetogens: Acetobacterium bakii sp. nov., A. paludosum sp. nov., A. fimetarium sp. nov.

Three strains of new acetogenic bacteria were isolated from several low temperature environments. Cells were gram-positive, oval-shaped flagellated rods. The organisms fermented H₂/CO₂, CO, formate, lactate, and several sugars to acetate. Strains Z-4391 and Z-4092 grew in the temperature range from 1 to 30°C with an optimum at 20°C; strain Z-4290 grew in the range from 1 to 35°C with an optimum at 30°C. The DNA G+C content of strains Z-4391, Z-4092, and Z-4290 was 42.1, 41.7, and 45.8 mol% respectively.     

Candida alocasiicola sp. nov., Candida hainanensis sp. nov., Candida heveicola sp. nov. and Candida musiphila sp. nov., novel anamorphic, ascomycetous yeast species isolated from plants

In a taxonomic study on the ascomycetous yeasts isolated from plant materials collected in tropical forests in Yunnan and Hainan Provinces, southern China, four strains isolated from tree sap (YJ2E(T)) and flowers (YF9E(T), YWZH3C(T) and YYF2A(T)) were revealed to represent four undescribed yeast species. Molecular phylogenetic analysis based on the large subunit (26S) rRNA gene D1/D2 domain sequences showed that strain YJ2E(T) was located in a clade together with Candida haemulonii and C. pseudohaemulonii. Strain YF9E(T) was most closely related to C. azyma and strain YWZH3C(T) to C. sorbophila and C. spandovensis. Strain YYF2A(T) was clustered in a clade containing small-spored Metschnikowia species and related anamorphic Candida species. The new strains differed from their closely related described species by more than 10% mismatches in the D1/D2 domain. No sexual states were observed for the four strains on various sporulation media. The new species are therefore assigned to the genus Candida and described as Candida alocasiicola sp. nov. (type strain, YF9E(T) = AS 2.3484(T) = CBS 10702(T)), Candida hainanensis sp. nov. (type strain, YYF2A(T) = AS 2.3478(T) = CBS 10696(T)), Candida heveicola sp. nov. (type strain, YJ2E(T) = AS 2.3483(T) = CBS 10701(T)) and Candida musiphila sp. nov. (type strain, YWZH3C(T) = AS 2.3479(T) = CBS 10697(T)).     

Bullera anomala sp. nov. and Bullera pseudovariabilis sp. nov., two new ballistoconidium-forming yeast species from Yunnan,China

Two ballistoconidium-forming yeast strains, CH 2.504 and CH 2.509, were isolated from the wilting leaves of Parthenocissus sp. collected in Yunnan, China in 1996. These two strains were assigned to the genus Bullera Derx by the characteristics of forming rotationally symmetric ballistoconidia, containing xylose in the cell hydrolysates and having Q-10 as the major ubiquinone. Molecular phylogenetic analysis based on small subunit ribosomal RNA gene (18S rDNA) and internal transcribed spacer (ITS) region sequences revealed that CH 2.504 is closely related to B. variabilis Nakase & Suzuki, while CH 2.509 is located in a clearly separate clade among the described Bullera species and related taxa. The results indicated that CH 2.509 represents a new species, for which Bullera anomala sp. nov. is the proposed name (type strain AS 2.2094^T). Further DNA-DNA reassociation data showed that CH 2.504 also represents a distinct species, for which the name Bullera pseudovariabilis sp. nov. is given (type strain AS 2.2092^T). This revised version was published online in June 2006 with corrections to the Cover Date.     

Methanogenium,a new genus of marine methanogenic bacteria,and characterization ofMethanogenium cariaci sp. nov. andMethanogenium marisnigri sp. nov.

A new genus of marine methanogenic bacteria and two species within this genus are described.Methanogenium is the proposed genus andMethanogenium cariaci the type species. Cells of the type species are Gram-negative, peritrichously flagellated, irregular cocci with a periodic wall surface pattern. Colonies formed by these bacteria are yellow, circular and umbonate with entire edges. The DNA base composition is 52 mol% guanine plus cytosine. Formate or hydrogen and carbon dioxide serve as substrates for growth. Cells ofMethanogenium marisnigri are of similar shape but smaller diameter thanM. cariaci. The colonies ofM. marisnigri are convex, and the DNA base composition is 61 mol % G+C. Formate or hydrogen and carbon dioxide are growth substrates. Sodium chloride is required for growth of both methanogens.Abbreviations SDS sodium dodecylsulfate - PIPES piperazine-N,N-bis (2 ethanesulfonic acid) - HS-CoM coenzyme M, 2-mercaptoethanesulfonic acid     

A novel plant-associated thermotolerant alkaliphilic methylotroph of the genusParacoccus

Strain GB isolated from the maize rhizosphere is a gram-negative, aerobic, non-spore-forming, nonpigmented, nonmotile, chemolithotrophic, facultatively methylotrophic bacterium. Cells are cocci or short rods. The strain does not require vitamins. Optimum growth in a medium with methanol occurs at 38–42°C at pH 8.0–9.2. The doubling time is 12 h. In addition to methanol, the bacterium can grow on methylamine, dimethylformamide, acetone, thiosulfate + NaHCO₃, and in an atmosphere of H₂ + CO₂ + O₂. Methanol and methylamine are oxidized by the respective dehydrogenases to CO₂ via formaldehyde and formate, respectively. The CO₂ produced is assimilated via the ribulose bisphosphate pathway. Fatty acids are dominated by cyclopropanoic (58–61%), palmitic (24–26%), and octadecanoic (8–9%) acids. The main phospholipids are phosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. The major ubiquinone is Q₁₀. The bacterial genome contains genes controlling the synthesis and secretion of cytokinins. The culture liquid exhibits cytokinin activity. The G+C content of DNA is 62.5 mol %, as determined from the DNA thermal denaturation temperature T_m). Strain GB shows a moderate degree of DNA-DNA homology (<40%) with the type representatives of the genusParacoccus. Based on the data obtained, the bacterium was classified as a new species of this genus, namedP. kondratievae.     

Description of four novel species of Xenorhabdus, family Enterobacteriaceae: Xenorhabdus budapestensis sp. nov., Xenorhabdus ehlersii sp. nov., Xenorhabdus innexi sp. nov., and Xenorhabdus szentirmaii sp. nov

The taxonomic affiliation was determined for four Xenorhabdus strains isolated from four Steinernema hosts from different countries. As compared to the five validly described Xenorhabdus species, i.e., X. nematophila, X. japonica, X. beddingii, X. bovienii and X. poinarii, these isolates represented novel species on the basis of 16S rRNA gene sequences and riboprint patterns, as well as by physiological and metabolic properties. They were named Xenorhabdus budapestensis sp. nov., type strain DSM 16342^T, isolated from Steinernema bicornutum; Xenorhabdus ehlersii sp. nov., type strain DSM 16337^T, isolated from Steinernema serratum; Xenorhabdus innexi sp. nov., type strain DSM 16336^T isolated from Steinernema scapterisci; and Xenorhabdus szentirmaii sp. nov., type strain DSM 16338^T, isolated from Steinernema rarum.     

Zygozyma suomiensis,sp. nov. (Lipomycetaceae), a new species from Finland

A new species of the genus Zygozyma, Z. suomiensis, is described, based on the study of a single strain, derived from a bovine skin lesion.     

New anamorphic yeast species: Candida infanticola sp. nov., Candida polysorbophila sp. nov., Candida transvaalensis sp. nov. and Trigonopsis californica sp. nov

Three new species of Candida and a new species of Trigonopsis are described based on their recognition from phylogenetic analysis of gene sequences from large subunit ribosomal RNA, ITS1/ITS2 rRNA, mitochondrial small subunit rRNA and cytochrome oxidase II. Candida infanticola sp. nov. (type strain NRRL Y-17858, CBS 7922) was isolated from the ear of an infant in Germany and is closely related to Candida sorbophila. Candida polysorbophila sp. nov. (type strain NRRL Y-27161, CBS 7317) is a member of the Zygoascus clade and was isolated in South Africa as a contaminant from an emulsion of white oil and polysorbate. Candida transvaalensis sp. nov. (type strain NRRL Y-27140, CBS 6663) was obtained from forest litter, the Transvaal, South Africa, and forms an isolated clade with Candida santjacobensis. Trigonopsis californica sp. nov. (type strain NRRL Y-27307, CBS 10351) represents a contaminant from wine in California, and forms a well-supported clade with Trigonopsis cantarellii, Trigonopsis variabilis and Trigonopsis vinaria.     

Clostridium grantii sp. nov., a new obligately anaerobic,alginolytic bacterium isolated from mullet gut

A gram-positive, motile, rod-shaped, strictly anaerobic, sporulating bacterium was isolated from an enrichment initiated with mullet gut contents. The organism grew optimally at 30°C and pH6.5, and at a salinity of 1–10³. Out of a variety of polysaccharides tested as growth substrates, only alginate supported growth in either semidefined or complex culture medium. The organism also grew on a variety of mono- and disaccharides. Moles product per 100mol of alginate monomer degraded were: acetate, 186; ethanol, 19; formate, 54; and CO₂, 0.19. Moles product per 100mol of hexose in cellobiose or glucose degraded were: acetate, 135; ethanol,61; formate, 63: and CO₂, 61. Hydrogen was not detectable during the incubations (detection limit, <10^-5atm) and propionate, butyrate, lactate, or succinate were not produced as fermentation end products (<2 mol per 100 mol of monomer). The G+C content of DNA from the bacterium was 30.2±0.3 mol%, and the cell walls contained the peptidoglycan component meso-diaminopimelic acid. A phylogenetic analysis of the 16S rDNA sequence indicated that the organism grouped closely with members of the RNA-DNA homology group 1 of the genus Clostridium. However, it differed from other species of the genus with regard to morphology, growth temperature optimum, substrate range, and fermentation pattern and is therefore designated as a new species of Clostridium; the type strain is A-1 (DSM 8605).     

Methyloligella halotolerans gen. nov., sp. nov. and Methyloligella solikamskensis sp. nov., two non-pigmented halotolerant obligately methylotrophic bacteria isolated from the Ural saline environments

Two newly isolated halotolerant obligately methylotrophic bacteria (strains C2^T and SK12^T) with the serine pathway of C₁ assimilation are described. The isolates are strictly aerobic, Gram negative, asporogenous, non-motile rods, forming rosettes, multiplying by binary fission. Mesophilic and neutrophilic, accumulate intracellularly compatible solute ectoine and poly-β-hydroxybutyrate. The novel strains are able to grow at 0 up to 16% NaCl (w/v), optimally at 3–5% NaCl. The major cellular fatty acids are C_18:1ω7c and C_19:0cyc and the prevailing quinone is Q-10. The predominant phospholipids are phosphatidylcholine, phosphatidylglycerol, phosphatidyldimethylethanolamine and phosphatidylethanolamine. Assimilate NH₄⁺ by glutamate dehydrogenase and via the glutamate cycle (glutamine synthetase and glutamate synthase). The DNA G + C contents of strains C2^T and SK12^T are 60.9 and 60.5 mol% (Tm), respectively. 16S rRNA gene sequence similarity between the two new isolates are 99% but below 94% with other members of the Alphaproteobacteria thus indicating that they can be assigned to a novel genus Methyloligella. Rather low level of DNA–DNA relatedness (53%) between the strains C2^T and SK12^T indicates that they represent two separate species of the new genus, for which the names Methyloligella halotolerans gen. nov., sp. nov. and Methyloligella solikamskensis sp. nov. are proposed. The type strain of Methyloligella halotolerans is C2^T (=VKM B-2706^T = CCUG 61687^T = DSM 25045^T) and the type strain of Methyloligella solikamskensis is SK12^T (=VKM B-2707^T = CCUG 61697^T = DSM 25212^T).