TY - JOUR AB - Three strains (H4-D09T, S2-D11 and S9-F39) of a member of the genus Paracoccus attributed to a novel species were isolated from topsoil of temperate grasslands. The genome sequence of the type strain H4-D09T exhibited a complete set of genes required for denitrification as well as methylotrophy. The genome of H4-D09T included genes for two alternative pathways of formaldehyde oxidation. Besides the genes for the canonical glutathione (GSH)-dependent formaldehyde oxidation pathway, all genes for the tetrahydrofolate-formaldehyde oxidation pathway were identified. The strain has the potential to utilize methanol and/or methylamine as a single carbon source as evidenced by the presence of methanol dehydrogenase (mxaFI) and methylamine dehydrogenase (mau) genes. Apart from dissimilatory denitrification genes (narA, nirS, norBC and nosZ), genes for assimilatory nitrate (nasA) and nitrite reductases (nirBD) were also identified. The results of phylogenetic analysis based on 16S rRNA genes coupled with riboprinting revealed that all three strains represented the same species of genus Paracoccus. Core genome phylogeny of the type strain H4-D09T indicated that Paracoccus thiocyanatus and Paracoccus denitrificans are the closest phylogenetic neighbours. The average nucleotide index (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The major respiratory quinone is Q-10, and the predominant cellular fatty acids are C18 : 1ω7c, C19 : 0cyclo ω7c, and C16 : 0, which correspond to those detected in other members of the genus. The polar lipid profile consists of a diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), glycolipid (GL) and an unidentified lipid (L).On the basis of our results, we concluded that the investigated isolates represent a novel species of the genus Paracoccus, for which the name Paracoccus methylovorus sp. nov. (type strain H4-D09T=LMG 31941T= DSM 111585T) is proposed. AU - Timsy, T.* AU - Behrendt, U.* AU - Ulrich, A.* AU - Fösel, B. AU - Spanner, T.* AU - Neumann-Schaal, M.* AU - Wolf, J.* AU - Schloter, M. AU - Horn, M.A.* AU - Kolb, S.* C1 - 67565 C2 - 53552 CY - 14-16 Meredith St, London, England TI - Genomic evidence for two pathways of formaldehyde oxidation and denitrification capabilities of the species Paracoccus methylovorus sp. nov. JO - Int. J. Syst. Evol. Microbiol. VL - 72 IS - 10 PB - Microbiology Soc PY - 2022 SN - 1466-5026 ER - TY - JOUR AB - A novel strain was isolated from grassland soil that has the potential to assimilate ammonium by the reduction of nitrate in the presence of oxygen. Whole genome sequence analysis revealed the presence of an assimilatory cytoplasmic nitrate reductase gene nasA and the assimilatory nitrite reductase genes nirBD which are involved in the sequential reduction of nitrate to nitrite and further to ammonium, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represents a member of the genus Pseudomonas. The closest phylogenetic neighbours based on 16S rRNA gene sequence analysis are the type strains of Pseudomonas peli (98.17%) and Pseudomonas guineae (98.03%). In contrast, phylogenomic analysis revealed a close relationship to Pseudomonas alcaligenes. Computation of the average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) with the closest phylogenetic neighbours of S1-A32-2 revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. On the basis of these results, it was concluded that the soil isolate represents a novel species of the genus Pseudomonas, for which the name Pseu-domonas campi sp. nov. (type strain S1-A32-2 =LMG 31521 =DSM 110222 ) is proposed. T T T T AU - Timsy, T.* AU - Spanner, T.* AU - Ulrich, A.* AU - Kublik, S. AU - Fösel, B. AU - Kolb, S.* AU - Horn, M.A.* AU - Behrendt, U.* C1 - 62008 C2 - 50587 CY - 14-16 Meredith St, London, England TI - Pseudomonas campi sp. Nov., a nitrate-reducing bacterium isolated from grassland soil. JO - Int. J. Syst. Evol. Microbiol. VL - 71 IS - 5 PB - Microbiology Soc PY - 2021 SN - 1466-5026 ER - TY - JOUR AB - Azospirillum sp. strain Sp245(T), originally identified as belonging to Azospirillum brasilense, is recognized as a plant-growth-promoting rhizobacterium due to its ability to fix atmospheric nitrogen and to produce plant-beneficial compounds. Azospirillum sp. Sp245(T) and other related strains were isolated from the root surfaces of different plants in Brazil. Cells are Gram-negative, curved or slightly curved rods, and motile with polar and lateral flagella. Their growth temperature varies between 20 to 38 degrees C and their carbon source utilization is similar to other Azospirillum species. A preliminary 16S rRNA sequence analysis showed that the new species is closely related to A. brasilense Sp7(T) and A. formosense CC-Nfb-7(T). Housekeeping genes revealed that Azospirillum sp. Sp245T, BR 12001 and Vi22 form a separate cluster from strain A. formosense CC-Nfb-7(T), and a group of strains closely related to A. brasilense Sp7(T). Overall genome relatedness index (OGRI) analyses estimated based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between Azospirillum sp. Sp245(T) and its close relatives to other Azospirillum species type strains, such as A. brasilense Sp7(T) and A. formosense CC-Nfb-7(T) , revealed values lower than the limit of species circumscription. Moreover, core-proteome phylogeny including 1079 common shared proteins showed the independent clusterization of A. brasilense Sp7(T), A. formosense CC-Nfb-7(T) and Azospirillum sp. Sp245(T), a finding that was corroborated by the genome clustering of OGRI values and housekeeping phylogenies. The DNA G+C content of the cluster of Sp245(T) was 68.4-68.6 %. Based on the phylogenetic, genomic, phenotypical and physiological analysis, we propose that strain Sp245(T) together with the strains Vi22 and BR12001 represent a novel species of the genus Azospirillum, for which the name Azospirillum baldaniorum sp. nov. is proposed. The type strain is Sp245(T) (=BR 11005(T)=IBPPM 219(T)) (GCF_007827915.1, GCF_000237365.1, and GCF_003119195.2). AU - Ferreira, N.d.S.* AU - Sant' Anna, F.H.* AU - Reis, V.M.* AU - Ambrosini, A.* AU - Volpiano, C.G.* AU - Rothballer, M. AU - Schwab, S.* AU - Baura, V.A.* AU - Balsanelli, E.* AU - Pedrosa, F.d.O.* AU - Pereira Passaglia, L.M.* AU - de Souza, E.M.* AU - Hartmann, A.* AU - Cassan, F.D.* AU - Zilli, J.E.* C1 - 61127 C2 - 49769 CY - Charles Darwin House, 12 Roger St, London Wc1n 2ju, Erks, England SP - 6203-6212 TI - Genome-based reclassification of Azospirillum brasilense Sp245 as the type strain of Azospirillum baldaniorum sp. nov. JO - Int. J. Syst. Evol. Microbiol. VL - 70 IS - 12 PB - Microbiology Soc PY - 2020 SN - 1466-5026 ER - TY - JOUR AB - The anaerobic, non-motile strain HMT was isolated from the naphthalene-degrading, sulfate-reducing enrichment culture N47. For 20 years, strain HMT has been a stable member of culture N47 although it is neither able to degrade naphthalene nor able to reduce sulfate in pure culture. The highest similarity of the 16S rRNA gene sequence of strain HMT (89%) is with a cultivated member of the family Spirochaetaceae, Treponema caldarium strain H1T (=DSM 7334T), an obligately anaerobic, thermophilic spirochaete isolated from cyanobacterial mat samples collected at a freshwater hot spring in Oregon, USA. In contrast to this strain and the majority of spirochaete species described, strain HMT showed a rod-shaped morphology. Growth occurred at temperatures between 12 and 50 °C (optimum 37 °C) but the isolate was not able to grow at 60 °C. The strain fermented various sugars including D-glucose, D-fructose, lactose and sucrose. Addition of 0.1% (w/v) yeast extract or 0.1% (w/v) tryptone to the culture medium was essential for growth and could not be replaced by either the vitamin solutions tested or by 0.1% (w/v) peptone or 0.1% (w/v) casamino acids. The DNA G+C content of the isolate was 51.5 mol%. The major fatty acids were C14: 0, C18: 1ω13c, C16: 1ω9t, C16: 1ω11c and C16: 1ω9c. Based on the unique morphology and the phylogenetic distance from the closest cultivated relative, a novel genus and species, Rectinema cohabitans gen. nov., sp. nov., is proposed. The type strain is strain HMT (=DSM 100378T=JCM 30982T). AU - Kölschbach, J.S. AU - Mouttaki, H. AU - Pickl, C. AU - Heipieper, H.J.* AU - Rache, R.* AU - Lawson, P.A.* AU - Meckenstock, R.U.* C1 - 51382 C2 - 43046 SP - 1288-1295 TI - Rectinema cohabitans gen. nov., sp. nov., a rod-shaped spirochaete isolated from an anaerobic naphthalene-degrading enrichment culture. JO - Int. J. Syst. Evol. Microbiol. VL - 67 IS - 5 PY - 2017 SN - 1466-5026 ER - TY - JOUR AB - Two novel Gram- positive, rod shaped, halotolerent bacteria, strains JG 03T and JG 05 were isolated from the rhizosphere of Salicornia brachiata, an extreme halophyte. Comparative analyses of 16S rRNA gene sequence showed that they were closely related to members of the genus Zhihengliuella with sequence similarity of 96.9-99.1 %. Sequence similarity of strains JG 03T and JG 05 was 99.4 % with each other. DNA-DNA hybridization of JG 03T and JG 05 with other known species of Zhihengliuella showed reassociation value of 19.8% -53.4% and 91.4% in between themselves. The peptidoglycan type of both strains was A4α and MK-9 and MK-10 were predominant menaquinones. The predominant fatty acid in JG 03T was anteiso-C15:0 and anteiso-C17:0. However, iso-C15:0, anteiso-C15:0 and anteiso-C17:0 were the major fatty acid in strain JG 05. The DNA G+C content of strains JG 03T and JG 05 was 70.0 and 70.1 mol%, respectively. In nutrient broth medium both strains grew at NaCl concentrations up to 15% (w/v). On the basis of chemotaxonomic characteristics and phylogenetic analyses, strains JG 03T and JG 05 should be affiliated to the genus Zhihengliuella. Strains JG 03T and JG 05 represent a novel species of the genus Zhihengliuella, for which the names Zhihengliuella somnathii sp. nov. is proposed. The type strain is JG 03T ( =DSM 23187T =IMCC 253T ). AU - Jha, B.* AU - Singh, V.K.* AU - Weiss, A. AU - Hartmann, A. AU - Schmid, M. C1 - 46766 C2 - 37807 SP - 3137-3142 TI - Zhihengliuella somnathii sp. nov., a halotolerant actinobacterium from the rhizosphere of a halophyte Salicornia brachiata. JO - Int. J. Syst. Evol. Microbiol. VL - 65 IS - 9 PY - 2015 SN - 1466-5026 ER - TY - JOUR AB - A novel non-motile, Gram-staining-negative, yellow-pigmented bacterium, designated AG13T, isolated from a rain water pond in a plant nursery in Spain and characterised as a plant growth promoting bacterium, was investigated to determine its taxonomic status. The isolate grew best over a temperature range of 15-40°C and at pH 5.0-8.0 and with 0-4% (w/v) NaCl. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Chryseobacterium. The DNA G + C content of the novel strain was 37.2 mol%. The strain contained a polyamine pattern with sym-homospermidine as the major compound and produced flexirubin-type pigments. MK-6 was the dominant menaquinone and the major cellular fatty acids were iso-C15:0, C17:1ω9c and iso-C17:0 3-OH. The main polar lipids were phosphatidylethanolamine, aminolipids and several unidentified lipids. The 16S rRNA gene showed 92.0-97.2% sequence identity with the members of the genus Chyseobacterium. Based on chemotaxonomic, phenotypic traits and DNA-DNA hybridizations with the type strains of the most closely related species, the isolate is proposed to represent a novel species, Chyseobacterium hispalense, type strain AG13T (= DSM 25574T = CCUG 63019T). Emended descriptions of the species Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium are also provided. AU - Montero-Calasanz, M.* AU - Göker, M.* AU - Rohde, M.* AU - Spröer, C.* AU - Schumann, P.* AU - Busse, H.J.* AU - Schmid, M. AU - Tindall, B.J.* AU - Klenk, H.P.* AU - Camacho, M.* C1 - 28161 C2 - 32976 CY - Reading SP - 4386-4395 TI - Chryseobacterium hispalense sp. nov., a plant growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery and emendation of the species Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium. JO - Int. J. Syst. Evol. Microbiol. VL - 63 IS - 12 PB - Soc. General Microbiology PY - 2013 SN - 1466-5026 ER - TY - JOUR AB - A Gram-positive, aerobic, non-motile, coccoid shaped, halotolerant bacterium (JG 06 T) was isolated from roots of Salicornia brachiata, an extreme halophyte. Phylogenetic analysis based on 16S rRNA gene sequence showed sequence similarities of 99.2% to Brachybacterium paraconglomeratum, 99.0% to B. conglomeratum, and 98.2% to B. faecium. DNA-DNA hybridization with the close relatives Brachybacterium paraconglomeratum (DSM 46341T), B. conglomeratum (DSM 10241 T), B. faecium (DSM 4810T), B. tyrofermentans (DSM 10673 T), B. alimentarium (DSM 10672 T), B. fresconsis (DSM 14564 T), B. sacelli (DSM 14566 T) and B. muris (DSM 15460 T) resulted in re-association values of 36.2%, 36.5%, 35.8%, 27.6%, 27.9%, 28.2%, 28.7% and 11.2%, respectively. The peptidoglycan type of strain JG 06 T was variant A4γ. The menaquinone content was MK7 (100%). The polar lipid profile consisted of diphosphatidyglycerol, phosphatidyglycerol, monogalactosyl diglyceride and three unidentified phospholipids and three glycolipids. The predominant fatty acid was anteiso-C15:0 (52.07%); significant amounts of iso-C16:0(12.38%), iso-C15:0(8.59%) and anteiso-C17:0(10.03%) were also present. The G+C content of DNA was 73.0 mol%. The strain formed a growth pellicle in nitrogen-free semisolid NFb medium containing NaCl up to 4% and reduced acetylene to ethylene, characteristic for N2 fixation. In nutrient broth medium it grew up to 15% NaCl. It also had the ability to produce IAA, siderophore, utilized ACC as sole source of nitrogen and possessed ACC deaminase enzyme. On the basis of physiological, biochemical data and phylogeny, strain JG 06 T should be placed in the genus Brachybacterium. This bacterium represents a novel species of genus Brachybacterium for which the name Brachybacterium saurashtrense sp. nov. is proposed, with type strain JG 06 T (= DSM 23186T = IMCC 252T). AU - Gontia, I.* AU - Kavita, K.* AU - Schmid, M. AU - Hartmann, A. AU - Jha, B.* C1 - 6733 C2 - 29172 CY - Reading, UK SP - 2799-2804 TI - Brachybacterium saurashtrense sp. nov., a halotolerant root-associated bacterium with plant growth promoting potential. JO - Int. J. Syst. Evol. Microbiol. VL - 61 IS - 12 PB - Society for General Microbiology PY - 2011 SN - 1466-5026 ER - TY - JOUR AB - Strain N35(T) was isolated from surface-sterilized wheat roots and is a Gram-negative, aerobic, motile straight rod. Strain N35(T) tested oxidase-positive and catalase-negative and grew optimally at pH 7.0, 30 °C and in the absence of NaCl. 16S rRNA gene sequence analysis showed over 97 % sequence similarity to strains of the environmental species Acidovorax delafieldii, A. facilis, A. defluvii, A. temperans, A. caeni and A. soli, as well as Acidovorax valerianellae, A. anthurii and Simplicispira metamorpha. DNA-DNA hybridization between strain N35(T) and phylogenetically closely related type strains was 25.3-55.7 %, which clearly separates the strain from these closely related species. Additionally, phenotypic properties, such as substrate metabolism profiles as determined by a Biolog GN2 assay and cell-wall fatty acid profiles, particularly contents of the fatty acids C(16 : 0), C(16 : 1)ω7c/t, C(17 : 0), C(17 : 0) cyclo, C(18 : 0) cyclo and C(19 : 0) cyclo, facilitated the differentiation of the newly isolated strain N35(T) from its closest relatives. The isolate underwent phenotypic variation at high frequency in laboratory media. The DNA G+C content was 64.9 mol%. We propose that strain N35(T) is classified as a representative of a novel species within the genus Acidovorax, and suggest the name Acidovorax radicis sp. nov. The type strain is strain N35(T) ( = DSM 23535(T)  = LMG 25767(T)). AU - Li, D. AU - Rothballer, M. AU - Schmid, M. AU - Esperschütz, J. AU - Hartmann, A. C1 - 6681 C2 - 29233 SP - 2589-2594 TI - Acidovorax radicis sp. nov., a wheat-root-colonizing bacterium. JO - Int. J. Syst. Evol. Microbiol. VL - 61 IS - 11 PB - International Union of Microbiological Societies PY - 2011 SN - 1466-5026 ER - TY - JOUR AB - Dissimilatory iron reduction plays a significant role in subsurface environments. Currently, it is assumed that members of the genus Geobacter constitute the majority of the iron-reducing micro-organisms that oxidize aromatic compounds in contaminated subsurface environments. Here, we report the isolation of two phylogenetically distinct pure cultures of iron-reducing degraders of monoaromatic hydrocarbons, strain TMJ1(T), which belongs to the genus Geobacter within the Deltaproteobacteria, and strain UKTL(T), belonging to the genus Desulfitobacterium within the Clostridia. Both strains utilize a wide range of substrates as carbon and energy sources, including the aromatic compounds toluene, phenol and p-cresol. Additionally, strain UKTL(T) utilizes o-xylene and TMJ1(T) utilizes m-cresol. Anaerobic degradation of toluene in both strains and o-xylene in strain UKTL(T) is initiated by activation with fumarate addition to the methyl group. The genomic DNA G+C contents of strains TMJ1(T) and UKTL(T) are 54.4 and 47.7 mol%, respectively. Based on a detailed physiological characterization and phylogenetic analysis of the 16S rRNA genes of both strains, we propose the names Desulfitobacterium aromaticivorans sp. nov. (type strain UKTL(T) =DSM 19510(T) =JCM 15765(T)) and Geobacter toluenoxydans sp. nov. (type strain TMJ1(T) =DSM 19350(T) =JCM 15764(T)) to accommodate these strains. To the best of our knowledge, strain UKTL(T) is the first described spore-forming, iron-reducing bacterium that can degrade aromatic hydrocarbons. AU - Kunapuli, U. AU - Jahn, M.K. AU - Lüders, T. AU - Geyer, R.* AU - Heipieper, H.J.* AU - Meckenstock, R.U. C1 - 66 C2 - 27210 SP - 686-695 TI - Desulfitobacterium aromaticivorans sp. nov. and Geobacter toluenoxydans sp. nov., iron-reducing bacteria capable of anaerobic degradation of monoaromatic hydrocarbons. JO - Int. J. Syst. Evol. Microbiol. VL - 60 IS - 3 PB - Society for General Microbiology PY - 2010 SN - 1466-5026 ER - TY - JOUR AB - Strain D24TN(T) was enriched and isolated from sediment collected from a tar oil-contaminated aquifer at a former gasworks site located in Duesseldorf-Flingern, Germany. Cells of strain D24TN(T) were rod-shaped, non-spore-forming and stained Gram-negative. Thiosulfate was used as an electron donor. The organism was obligately chemolithoautotrophic and facultatively anaerobic, and grew with either oxygen or nitrate as electron acceptor. Growth was observed at pH values between 6.3 and 8.7 and at temperatures of -2 to 30 degrees C; optimum growth occurred at pH 7.5-8.3 and 25-30 degrees C. The DNA G + C content was 61.5 mol%. On the basis of the 16S rRNA gene sequence analysis, strain D24TN(T) clustered in the Betaproteobacteria and was most closely related to Thiobacillus denitrificans (97.6%) and Thiobacillus thioparus (97.5%). Based on the phenotypic, chemotaxonomic and phylogenetic data, strain D24TN(T) represents a novel species of the genus Thiobacillus, for which the name Thiobacillus thiophilus sp. nov. is proposed. The type strain is D24TN(T) (=DSM 19892(T)=JCM 15047(T)). AU - Kellermann, C. AU - Griebler, C. C1 - 931 C2 - 26064 SP - 583-588 TI - Thiobacillus thiophilus sp. nov., a chemolithoautotrophic, thiosulfate-oxidizing bacterium isolated from contaminated aquifer sediments. JO - Int. J. Syst. Evol. Microbiol. VL - 59 IS - 3 PB - Soc General Microbiology PY - 2009 SN - 1466-5026 ER - TY - JOUR AB - Two Gram-negative, rod-shaped, non-spore-forming bacteria, PR17(T) and DSM 7216(T), isolated from the potato rhizosphere and an industrial environment, respectively, were studied for their taxonomic allocation. By rrs (16S rRNA) gene sequencing, these strains were shown to belong to the Alphaproteobacteria, most closely related to Ochrobactrum pseudogrignonense (98.4 and 99.3 % similarity to the type strain, respectively). Chemotaxonomic data (major ubiquinone Q-10; major polyamines spermidine, sym-homospermidine and putrescine; major polar lipids phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol and phosphatidylcholine and the Ochrobactrum-specific unidentified aminolipid AL2; major fatty acids C(18 : 1)omega7c and C(19 : 0) cyclo omega8c) supported the genus affiliation. The results of DNA-DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of the isolates from all hitherto-described Ochrobactrum species. Hence, both isolates represent novel species of the genus Ochrobactrum, for which the names Ochrobactrum rhizosphaerae sp. nov. (type strain PR17(T) =CCUG 55411(T) =CCM 7493(T) =DSM 19824(T)) and Ochrobactrum thiophenivorans sp. nov. (type strain DSM 7216(T) =CCUG 55412(T) =CCM 7492(T)) are proposed. AU - Kämpfer, P.* AU - Sessitsch, A.* AU - Schloter, M. AU - Huber, B.* AU - Busse, H.J.* AU - Scholz, H.C.* C1 - 134 C2 - 25354 SP - 1426-1431 TI - Ochrobactrum rhizosphaerae sp. nov. and Ochrobactrum thiophenivorans sp. nov., isolated from the environment. JO - Int. J. Syst. Evol. Microbiol. VL - 58 IS - 6 PB - SGM PY - 2008 SN - 1466-5026 ER - TY - JOUR AU - Rothballer, M. AU - Schmid, M. AU - Klein, I. AU - Gattinger, A. AU - Grundmann, S. AU - Hartmann, A. C1 - 4460 C2 - 23993 SP - 1341-1348 TI - Herbaspirillum hiltneri sp. nov., isolated from surface-sterilized wheat roots. JO - Int. J. Syst. Evol. Microbiol. VL - 56 PY - 2006 SN - 1466-5026 ER - TY - JOUR AU - Tripathi, A.K.* AU - Verma, S.C.* AU - Chowdhury, S.P.* AU - Lebuhn, M.* AU - Gattinger, A. AU - Schloter, M. C1 - 5226 C2 - 23621 SP - 1677-1680 TI - Ochrobactrum oryzae sp. nov., an endophytic bacterial species isolated from deep-water rice in India. JO - Int. J. Syst. Evol. Microbiol. VL - 56 PY - 2006 SN - 1466-5026 ER - TY - JOUR AB - In an ecological survey of nitrogen-fixing bacteria isolated from the rhizosphere and as endophytes of sugarcane, maize and teosinte plants in Brazil, Mexico and South Africa, a new phylogenetically homogeneous group of N2-fixing bacteria was identified within the genus Burkholderia. This polyphasic taxonomic study included microscopic and colony morphology, API 2ONE tests and growth on different culture media at different pH and temperatures, as well as carbon source assimilation tests and whole-cell protein pattern analysis. Analysis of 16S rRNA gene sequences showed 99.2-99.9 % similarity within the novel species and 97.2 % similarity to the closest related species, Burkholderia sacchari. The novel species was composed of four distinct amplified 16S rDNA restriction analysis groups. The DNA-DNA reassociation values within the novel species were greater than 70% and less than 42% for the closest related species, B. sacchari. Based on these results and on many phenotypic characteristics, a novel N2-fixing species is proposed for the genus Burkholderia, Burkholderia tropica sp. nov., with the type strain Ppe8T (=ATCC BAA-831T=LMG 22274T=DSM 15359T), B. tropica was isolated from plants grown in geographical regions with climates ranging from temperate subhumid to hot humid. © 2004 IUMS. AU - Reis, V.M.* AU - Estrada-de los Santos, P.* AU - Tenorio-Salgado, S.* AU - Vogel, J.* AU - Stoffels, M. AU - Guyon, S.* AU - Mavingui, P.* AU - Baldani, V.L.D.* AU - Schmid, M. AU - Baldani, J.I.* AU - Balandreau, J.* AU - Hartmann, A. AU - Caballero-Mellado, J.* C1 - 3436 C2 - 22313 SP - 2155-2162 TI - Burkholderia tropica sp. nov., a novel nitrogen-fixing, plant-associated bacterium. JO - Int. J. Syst. Evol. Microbiol. VL - 54 IS - 6 PY - 2004 SN - 1466-5026 ER - TY - JOUR AB - A new group of nitrogen-fixing Azospirillum sp. bacteria was isolated from the roots of the C4-gramineous plant Miscanthus. Polyphasic taxonomy was performed, including auxanography using API galleries, physiological tests and 16S rRNA sequence comparison. The ability of the isolates to fix dinitrogen was evaluated by amplification of the nifD gene, immunodetection of the dinitrogenase reductase and acetylene-reduction assay. On the basis of these results, the nitrogen-fixing isolates represent a new species within the genus Azospirillum. Its closest phylogenetic neighbours, as deduced by 16S rDNA-based analysis, are Azospirillum lipoferum, Azospirillum largimobile and Azospirillum brasilense with 96.6, 96.6 and 95.9% sequence similarity, respectively. Two 16S rRNA-targeting oligonucleotide probes were developed which differentiate the new species from the other Azospirillum species by whole-cell fluorescence hybridization. Strains of the new species are curved rods or S-shaped, 1.0-1.5 microm in width and 2,0-3.0 microm in length, Gram-negative and motile with a single polar flagellum. Optimum growth occurs at 30 degrees C and at pH values between 6.0 and 7.0. No growth takes place at 37 degrees C. They have a respiratory type of metabolism, grow well on arabinose, D-fructose, gluconate, glucose, glycerol, malate, mannitol and sorbitol. They differ from A. largimobile and A. lipoferum by their inability to use N-acetylglucosamine and D-ribose, from A. lipoferum by their ability to grow without biotin supplementation and from A. brasilense by their growth with D-mannitol and D-sorbitol as sole carbon sources. Nitrogen fixation occurs in microaerobic nitrogen-limited conditions. For this species, the name Azospirillum doebereinerae sp. nov. is suggested, with strain GSF71T as the type strain (= DSM 13131T; reference strain Ma4 = DSM 13400). Its G+C content is 70.7 mol%. AU - Eckert, B. AU - Weber, O.B.* AU - Kirchhof, G. AU - Halbritter, A.* AU - Stoffels, M. AU - Hartmann, A. C1 - 23010 C2 - 31112 SP - 17-26 TI - Azospirillum doebereinerae sp. nov., a nitrogen-fixing bacterium associated with the C4-grass Miscanthus. JO - Int. J. Syst. Evol. Microbiol. VL - 51 PB - Society of General Microbiology PY - 2001 SN - 1466-5026 ER - TY - JOUR AB - The enrichment of nitrogen-fixing bacteria from the C4-fibre plants, Spartina pectinata, Miscanthus sinensis, Miscanthus sacchariflorus and Pennisetum purpureum, with nitrogen-free semi-solid media led to the isolation of Herbaspirillum-like strains among other diazotrophic bacteria. On the basis of physiological properties, phylogenetic analysis comparing 16S rDNA sequences and DNA-DNA hybridization experiments of chromosomal DNA the new isolates could be grouped together in a new species with the proposed name Herbaspirillum frisingense sp. nov. Morphological characteristics, such as cell size and shape, colony appearance, motility and flagellation are largely identical to the known species Herbaspirillum rubrisubalbicans and Herbaspirillum seropedicae. On the basis of utilization of adipate (-), N-acetyl-D-glucosamine (+), meso-erythritol (-), L-rhamnose (-) and meso-inositol (-) Herbaspirillum frisingense sp. nov. can be distinguished from other known Herbaspirillum spp. Nitrogen-fixing capability was examined by PCR amplification of the nifD gene and an acetylene reduction assay, and was found with all isolates tested. 16S rDNA sequence similarity to the other Herbaspirillum spp. is 98.5-99.1%. In genomic DNA-DNA hybridization experiments Herbaspirillum frisingense sp. nov. forms a homogeneous group with 70-100+/-10% similarity, clearly distinct from Herbaspirillum seropedicae and Herbaspirillum rubrisubalbicans with 1-34% similarity. 16S rRNA-targeted oligonucleotide probes, specific for the whole genus Herbaspirillum and for three Herbaspirillum species were designed and are suitable for fluorescence in situ hybridization. The DNA G+C content of Herbaspirillum frisingense sp. nov. is 63+/-2 mol%, in agreement with the values of 61-65% for the genus. PCR fingerprinting exhibits a consistent pattern for groups of strains isolated from the same plant, suggesting a low genomic diversity among bacteria inhabiting C4-gramineous plant tissues. Low genetic DNA diversity seems to be common between probable endophytic bacterial isolates of the same taxon. The type strain of Herbaspirillum frisingense sp. nov. is GSF30T (= DSM 13128T). AU - Kirchhof, G. AU - Eckert, B. AU - Stoffels, M. AU - Baldani, J.I.* AU - Reis, V.M.* AU - Hartmann, A. C1 - 23012 C2 - 31113 SP - 157-168 TI - Herbaspirillum frisingense sp. nov., a new nitrogen-fixing bacterial species that occurs in C4-fibre plants. JO - Int. J. Syst. Evol. Microbiol. VL - 51 PB - Society of General Microbiology PY - 2001 SN - 1466-5026 ER - TY - JOUR AB - A large collection of bacterial strains, immunotrapped from soil and from the wheat rhizoplane, was subjected to polyphasic taxonomy by examining various pheno- and genotypic parameters. Strains were grouped on (inter) repetitive extragenic palindromic DNA (REP) PCR profiles at the intraspecies level. Pheno- and genotypic characters were assessed for representatives from 13 different REP groups. Strains of nine REP groups constituting two physiological BIOLOG clusters fell in the coherent DNA-DNA reassociation group of Ochrobactrum anthropi. Strains of two REP groups constituting a separate BIOLOG cluster fell in the coherent DNA-DNA reassociation group of Ochrobactrum intermedium. Additional phenotypic characters differentiating O. anthropi and O. intermedium were found. REP group K strains constituted a different BIOLOG cluster, a separate DNA-DNA reassociation group and a distinct phylogenetic lineage in 165 rDNA homology analysis, indicating that REP group K strains represent a new species. Diagnostic phenotypic characters were found. Closest relatives were Ochrobactrum species. The name Ochrobactrum grignonense sp. nov. is proposed (type strain OgA9aT = LMG 18954T = DSM 13338T). REP group J strains again constituted a different BIOLOG cluster, a separate DNA-DNA reassociation group and showed, as a biological particularity, a strict preference for the rhizoplane as habitat. Diagnostic phenotypic characters were found. This indicated that REP group J strains represent a further new species, although phylogenetic analyses using 16S rDNA homology were not able to separate the cluster of REP group J sequences significantly from 16S rDNA sequences of Ochrobactrum anthropi. The name Ochrobactrum tritici sp. nov. is proposed (type strain SCII24T = LMG 18957T = DSM 13340T). AU - Lebuhn, M. AU - Achouak, W.* AU - Schloter, M. AU - Berge, O.* AU - Meier, H.* AU - Barakat, M.* AU - Hartmann, A. AU - Heulin, T.* C1 - 23016 C2 - 31140 SP - 2207-2223 TI - Taxonomic characterization of Ochrobactrum sp. isolates from soil samples and wheat roots, and description of Ochrobactrum tritici sp. nov. and Ochrobactrum grignonense sp. nov. JO - Int. J. Syst. Evol. Microbiol. VL - 50 PB - Society of General Microbiology PY - 2000 SN - 1466-5026 ER - TY - JOUR AB - [Pseudomonas] rubrisubalbicans, a mild plant pathogen. Herbaspirillum seropedicae, and EF group 1 strains (clustered by an immunological method) were investigated by a polyphasic approach with DNA-rRNA and DNA-DNA hybridizations and auxanography on 147 substrates. Our results show that they all belong to the genus Herbaspirillum. In addition to H. seropedicae, two other species are described: Herbaspirillum rubrisubalbicans and a new unnamed species, Herbaspirillum species 3, containing mainly strains of clinical origin. The three species can be differentiated on the basis of their auxanographic features and DNA-DNA similarities. The type strain of H. rubrisubalbicans is NCPPB 1027 (=LMG 2286); representative strains of the third Herbaspirillum species are strains CCUG 189 (=LMG 5523), CCUG 10263 (=LMG 5934), and CCUG 11060 (=LMG 5321). It has been confirmed that H. rubrisubalbicans is an endophytic diazotroph. It colonizes the roots, the stems, and predominantly the leaves of sugarcane (Saccharum spp.), while Herbaspirillum seropedicae colonizes in large numbers many different species of the Gramineae. Both diazotrophic Herbaspirillum species could be differentiated with meso-erythritol and N-acetylglucosamine. Oligonucleotide probes based on partial sequences of the 23S rRNA of H. seropedicae and H. rubrisubalbicans (HS and HR probes, respectively), were constructed and used as diagnostic probes. AU - Baldani, J.I.* AU - Pot, B.* AU - Kirchhof, G. AU - Falsen, E.* AU - Baldani, V.L.* AU - Olivares, F.L.* AU - Hoste, B.* AU - Kersters, K.* AU - Hartmann, A. AU - Gillis, M.* AU - Döbereiner, J.* C1 - 23178 C2 - 31197 SP - 802-810 TI - Emended description of Herbaspirillum; Inclusion of [Pseudomonas] rubrisubalbicans, a milk plant pathogen, as Herbaspirillum rubrisubalbicans comb. nov.; and classification of a group of clinical isolates (EF group 1) as Herbaspirillum species 3. JO - Int. J. Syst. Evol. Microbiol. VL - 46 IS - 3 PB - American Society of Microbiology PY - 1996 SN - 1466-5026 ER - TY - JOUR AB - Thirty-five nitrogen-fixing, hydrogen-oxidizing bacteria, all members of Cory-nebacterium autotrophicum Baumgarten, Reh, and Schlegel 1974, and including the type strain of this species, were compared with 28 strains of coryneform bacteria by numerical taxonomy methods. The nitrogen-fixing hydrogen bacteria formed a well defined cluster; their similarity to the other strains tested was low, however. Furthermore, the chemotaxonomic characters of these strains excluded them from the coryneform bacteria. Therefore C. autotrophicum was reclassified, following the keys of Bergey's Manual of Determinative Bacteriology (8th ed.) as a species of the family Azotobacteraceae. Although taxonomically close to Beijerinckia and Derxia, the nitrogen-fixing, hydrogen-oxidizing bacteria are regarded as representing a new genus, for which we propose the name Xanthobacter. C. autotrophicum Baumgarten, Reh, and Schlegel is transferred to the new genus as Xanthobacter autotrophicus (Baumgarten et al.) comb. nov. AU - Wiegel, J.W. AU - Wilke, D.* AU - Baumgarten, J.* AU - Opitz, R. AU - Schlegel, H.G. C1 - 33179 C2 - 35590 SP - 573-581 TI - Transfer of the nitrogen fixing hydrogen bacterium Corynebacterium autotrophicum Baumgarten et al. to Xanthobacter gen. nov. JO - Int. J. Syst. Evol. Microbiol. VL - 28 IS - 4 PY - 1978 SN - 1466-5026 ER -