Cruoricaptor ignavus gen. nov., sp. nov., a novel bacterium of the family Flavobacteriaceae isolated from blood culture of a man with bacteraemia.

A Gram-reaction-negative bacterium, strain IMMIB L-12475(T), was isolated from blood cultures of a human with septicaemia. The yellowish orange pigmented strain contained flexirubin pigment. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain IMMIB L-12475(T) belonged to the family Flavobacteriaceae, forming a distinct phyletic line that is distantly related (79.1-89.4% sequence similarity) to described genera of this family. Membership to the family was confirmed by a fatty acid profile consisting of branched-chain and 3-hydroxy fatty acids with major amounts of iso-C(17:0) 3-OH and iso-C(15:0), by the presence of menaquinone MK-6 as the only respiratory quinone and a polyamine pattern that contained sym-homospermidine as major component. The phospholipids consisted of phosphatidylethanolamine and an unknown phospholipid. The genomic DNA mol% G+C content was 45.6%. The distant phylogenetic position as compared to other representative of the family and the significant phenotypic properties such as pigment composition, morphology, and physiology support the proposal of a novel genus and species Cruoricaptor ignavus gen. nov., sp. nov. The type strain is IMMIB L-12475(T) (=DSM 25479(T)=CCUG 62025(T)).

Auritidibacter ignavus gen. nov., sp. nov., of the family Micrococcaceae isolated from an ear swab of a man with otitis externa, transfer of the members of the family Yaniellaceae Li et al. 2008 to the family Micrococcaceae and emended description of the suborder Micrococcineae.

A Gram-reaction-positive, aerobic, catalase-positive, non-spore-forming, rod-shaped bacterium designated IMMIB L-1656(T) was isolated from an ear swab of a man and characterized using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain IMMIB L-1656(T) is related to members of the family Micrococcaceae (<95.1 % sequence similarity). Anaylsis using different phylogenetic algorithms consistently grouped strain IMMIB L-1656(T) with members of the genus Yaniella. The organism posessed a cell-wall murein based on L-lysine (variation A4α, type L-Lys-Gly-L-Glu), MK-10 as the predominant menaquinone and long-chain cellular fatty acids of straight-chain and branched-chain saturated types (with iso-C(15 : 0) and anteiso-C(17 : 0) predominating). The polar lipids included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol in addition to unknown glycolipids. The DNA G+C content was 59.7 mol%. Based on its distinctive genotypic and phenotypic characteristics, strain IMMIB L-1656(T) represents a novel species in a novel genus, for which the name Auritidibacter ignavus gen. nov., sp. nov. is proposed. We also propose that members of the family Yaniellaceae be transferred to the family Micrococcaceae with amendments to the description of the suborder Micrococcineae. The type strain of Auritidibacter ignavus is IMMIB L-1656(T) (=DSM 45359(T) =CCUG 57943(T)).

Arthrobacter equi sp. nov., isolated from veterinary clinical material.

A Gram-positive-staining, catalase-positive, non-spore-forming, rod-shaped bacterium, strain IMMIB L-1606(T), isolated from genital swabs of a horse, was characterized using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that the organism was related to members of the genus Arthrobacter, displaying sequence similarities of 93.5-99.1 % with the type strains of recognized species of the genus. Cell-wall analysis revealed peptidoglycan type A3α L-Lys-L-Ser-L-Thr-L-Ala. DNA-DNA hybridization data and biochemical characterization of strain IMMIB L-1606(T) enabled the isolate to be differentiated genotypically and phenotypically from phylogenetically closely related species of the genus Arthrobacter. Therefore, it is concluded that strain IMMIB L-1606(T) represents a novel species of the genus Arthrobacter, for which the name Arthrobacter equi sp. nov. is proposed. The type strain of Arthrobacter equi sp. nov. is IMMIB L-1606(T) ( = DSM 23395(T) = CCUG 59597(T)).

Comparative chemotaxonomic and phylogenetic studies on the genus Arcanobacterium Collins et al. 1982 emend. Lehnen et al. 2006: proposal for Trueperella gen. nov. and emended description of the genus Arcanobacterium.

The results of a study comparing the chemotaxonomic characteristics and phylogenetic positions of members of the genus Arcanobacterium indicated that the genus was not monophyletic and, therefore, was in need of taxonomic revision. Phylogenetically, the genus Arcanobacterium consisted of two distinct lines; a group comprising the species Arcanobacterium haemolyticum (the type species of the genus), A. hippocoleae, A. phocae and A. pluranimalium and a robust group consisting of the species A. abortisuis, A. bernardiae, A. bialowiezense, A. bonasi and A. pyogenes. On the basis of 16S rRNA signature nucleotide comparisons and menaquinone and phospholipid compositions, it is proposed that of these nine species only four, A. haemolyticum, A. hippocoleae, A. phocae and A. pluranimalium, should be affiliated with the genus Arcanobacterium and the species A. abortisuis, A. bernardiae, A. bialowiezense, A. bonasi and A. pyogenes should be reclassified as members of a new genus, Trueperella, as Trueperella abortisuis comb. nov., Trueperella bernardiae comb. nov., Trueperella bialowiezensis comb. nov., Trueperella bonasi comb. nov. and Trueperella pyogenes comb. nov. Positive results in Christie-Atkins-Munch-Petersen (CAMP) tests on A. haemolyticum, A. hippocoleae, A. phocae and A. pluranimalium also supported the rearrangement of the nine species in to separate genera. As such, an emended description of the genus Arcanobacterium is provided.

Chryseobacterium treverense sp. nov., isolated from a human clinical source.

A yellow-pigmented, Gram-reaction-negative bacterium isolated from a human clinical source was investigated using a polyphasic approach in order to clarify its taxonomic status. Comparative 16S rRNA gene sequence analysis showed that the new isolate constituted a distinct phyletic line within the genus Chryseobacterium, displaying >2.8 % sequence divergence with recognized species of this genus. The generic assignment was confirmed by chemotaxonomic data which revealed a fatty acid profile consisting of straight-chain saturated, monounsaturated and branched-chain fatty acids of iso-/anteiso-types as well as 3-hydroxylated fatty acids; a menaquinone with six isoprene units (MK-6) as the predominant respiratory quinone and sym-homospermidine as the predominant polyamine. The novel isolate could be distinguished from other members of the genus Chryseobacterium by a set of distinct biochemical properties. On the basis of phenotypic and phylogenetic evidence, it is proposed that the new isolate represents a novel species of the genus Chryseobacterium for which the name Chryseobacterium treverense sp. nov. is proposed. The type strain is IMMIB L-1519(T) (=DSM 22251(T)=CCUG 57657(T)).

Nocardiopsis potens sp. nov., isolated from household waste.

The taxonomic position of an actinomycete, designated strain IMMIB L-21(T), was determined using a polyphasic taxonomic approach. The organism, which had phenotypic properties consistent with its classification in the genus Nocardiopsis, formed a distinct clade in the 16S rRNA gene sequence tree together with the type strain of Nocardiopsis composta, but was readily distinguished from this species using DNA-DNA relatedness and phenotypic data. The genotypic and phenotypic data show that the organism represents a novel species of the genus Nocardiopsis, for which the name Nocardiopsis potens sp. nov. is proposed. The type strain is IMMIB L-21(T) (=DSM 45234(T)=CCUG 56587(T)).

Azospirillum picis sp. nov., isolated from discarded tar.

A polyphasic taxonomic study was performed on a pink-coloured unknown bacterium isolated from discarded road tar. Comparative analysis of the 16S rRNA gene sequence demonstrated that the isolate belongs phylogenetically to the genus Azospirillum with Azospirillum lipoferum, A. melinis and A. rugosum as its closest phylogenetic relatives (96.7, 96.6 and 96.6 % similarity to the respective type strains). The generic assignment was confirmed on the basis of chemotaxonomic data, which revealed a fatty acid profile characteristic for the genus Azospirillum, consisting of straight-chain saturated and unsaturated fatty acids, with C(18 : 1)omega7c as the major unsaturated non-hydroxylated fatty acid, and C(16 : 0) 3-OH as the major hydroxylated fatty acid, and a ubiquinone with ten isoprene units (Q-10) as the predominant respiratory quinone. On the basis of both the phenotypic and molecular genetic evidence, it is proposed that the unknown isolate should be classified within a novel species of the genus Azospirillum, for which the name Azospirillum picis sp. nov. is proposed. The type strain is IMMIB TAR-3(T) (=CCUG 55431(T) =DSM 19922(T)).

Desmospora activa gen. nov., sp. nov., a thermoactinomycete isolated from sputum of a patient with suspected pulmonary tuberculosis, and emended description of the family Thermoactinomycetaceae Matsuo et al. 2006.

A novel Gram-positive, aerobic, catalase-positive, filamentous micro-organism, designated strain IMMIB L-1269(T), originating from sputum was characterized using phenotypic and molecular taxonomic methods. It showed cell-wall chemotype III, phospholipid type PII (with phosphatidylethanolamine as the diagnostic phospholipid) and contained an unsaturated menaquinone with seven isoprene units (MK-7) as the predominant isoprenoid quinone. It synthesized long-chain cellular fatty acids of the straight-chain saturated, monounsaturated and iso- and anteiso-branched types (with iso-C(15 : 0), C(16 : 0) and iso-C(17 : 0) predominating) and possessed a DNA G+C content of 49.3 mol%. On the basis of its morphological, biochemical and chemical characteristics, strain IMMIB L-1269(T) did not conform to any presently recognized taxon. Comparative analyses based on 16S rRNA gene sequences confirmed the distinctiveness of the isolate, as it displayed sequence-divergence values greater than 7.7 % with respect to recognized Gram-positive taxa. Phylogenetic treeing analysis served to reinforce the view that strain IMMIB L-1269(T) was distinct from recognized taxa, as it formed a relatively long subline branching within a 16S rRNA gene sequence cluster that encompassed the genera Thermoactinomyces, Laceyella, Mechercharimyces, Thermoflavimicrobium, Planifilum, Seinonella and Shimazuella of the family Thermoactinomycetaceae. On the basis of phenotypic and molecular phylogenetic evidence, strain IMMIB L-1269(T) represents a novel genus and species, for which the name Desmospora activa gen. nov., sp. nov. is proposed. The type strain of Desmospora activa is strain IMMIB L-1269(T) (=DSM 45169(T) =CCUG 55916(T)). An emended description of the family Thermoactinomycetaceae is also given.

Azospirillum rugosum sp. nov., isolated from oil-contaminated soil.

The taxonomic status of a light-orange-coloured bacterial isolate from an oil-contaminated soil sample was characterized by using a polyphasic taxonomic approach. Comparative analysis of 16S rRNA gene sequences demonstrated that the isolate belonged phylogenetically to the genus Azospirillum, with Azospirillum canadense, Azospirillum brasilense and Azospirillum doebereinerae as its closest phylogenetic relatives (97.3, 97.0 and 97.0 % similarity, respectively). DNA-DNA pairing studies showed that the unidentified organism displayed 25.0, 17.0 and 19.0 % relatedness to the type strains of A. brasilense, A. canadense and A. doebereinerae, respectively. The generic assignment was confirmed by chemotaxonomic data, which revealed a fatty acid profile that was characteristic of the genus Azospirillum, consisting of straight-chain saturated and unsaturated fatty acids with C18 : 1 omega 7c as the major fatty acid, and ubiquinone with ten isoprene units (Q-10) as the predominant respiratory quinone. On the basis of both the phenotypic and molecular genetic evidence, it is proposed that the unknown isolate be classified as a representative of a novel species of the genus Azospirillum, for which the name Azospirillum rugosum sp. nov. is proposed. The type strain is IMMIB AFH-6T (=CCUG 53966T=DSM 19657T).

Gordonia malaquae sp. nov., isolated from sludge of a wastewater treatment plant.

The taxonomic status of a bacterial isolate from the sludge of a wastewater treatment plant was characterized by using a polyphasic taxonomic approach. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV, short-chain mycolic acids that co-migrated with those extracted from members of the genus Gordonia, fatty acids C(16 : 0) and C(18 : 0) (found by pyrolysis gas chromatography) and a dihydrogenated menaquinone with nine isoprene units [MK-9(H2)] as the predominant menaquinone. The genus assignment was confirmed by 16S rRNA gene sequencing. Comparative analysis of the 16S rRNA gene sequence showed that the novel isolate constitutes a hitherto unknown subline within the genus Gordonia, displaying 95.9 to 97.6 % gene sequence similarity to the recognized species of the genus. The novel isolate was distinguished from the type strains of phylogenetically related species by using a set of phenotypic features. The genotypic and phenotypic data show that the new strain merits classification as a novel species of the genus Gordonia, for which the name Gordonia malaquae sp. nov. is proposed. The type strain is IMMIB WWCC-22(T) (=DSM 45064(T)=CCUG 53555(T)).

Lysobacter defluvii sp. nov., isolated from municipal solid waste.

A bacterial isolate obtained from soil from a municipal landfill site in India was characterized using a polyphasic taxonomic approach. The colonies of the isolate were found to be yellow and highly mucoid. Comparative analysis of the 16S rRNA gene sequence showed that this isolate constitutes a distinct phyletic line within the genus Lysobacter, displaying >3 % sequence divergence with respect to recognized Lysobacter species. The generic assignment was confirmed by chemotaxonomic data, which revealed the presence of a fatty acid profile characteristic of members of the genus Lysobacter and consisting of saturated, unsaturated, straight-chain and branched-chain fatty acids as well as iso-C(11 : 0) 3-OH as hydroxylated fatty acid, and the presence of an ubiquinone with eight isoprene units (Q-8) as the predominant respiratory quinone. The genotypic and phenotypic data show that strain IMMIB APB-9(T) merits classification as representing a novel species of the genus Lysobacter, for which the name Lysobacter defluvii sp. nov. is proposed. The type strain is IMMIB APB-9(T) (=CCUG 53152(T)=DSM 18482(T)).

Williamsia serinedens sp. nov., isolated from an oil-contaminated soil.

The taxonomic status of a bacterium designated strain IMMIB SR-4(T) isolated from an oil-contaminated soil sample was characterized by using a polyphasic approach. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV, short-chain mycolic acids that co-migrated with those extracted from members of the genus Williamsia and that on pyrolysis GC produce C(16 : 0) and C(18 : 0) fatty acids, and dihydrogenated menaquinone with nine isoprene units as the predominant menaquinone. The generic assignment was confirmed by 16S rRNA gene sequence analysis. Comparative analysis of the 16S rRNA gene sequence showed that strain IMMIB SR-4(T) formed a distinct phyletic line within the genus Williamsia, displaying sequence similarities of 95.5-98.1 % with the type strains of recognized Williamsia species. Strain IMMIB SR-4(T) was distinguished from the type strains of recognized species of the genus Williamsia based on a set of phenotypic features. The genotypic and phenotypic data indicated that strain IMMIB SR-4(T) represents a novel species of the genus Williamsia, for which the name Williamsia serinedens sp. nov. is proposed. The type strain is IMMIB SR-4(T) (=DSM 45037(T)=CCUG 53151(T)).

Dietzia cinnamea sp. nov., a novel species isolated from a perianal swab of a patient with a bone marrow transplant.

The taxonomic status of a bacterium isolated from a perianal swab of a patient with a bone marrow transplant was characterized using a polyphasic taxonomic approach. Chemotaxonomic investigations revealed the presence of cell wall chemotype IV, short chain mycolic acids that co-migrated with those extracted from members of the genus Dietzia, and a dihydrogenated menaquinone with eight isoprene units as the predominant menaquinone. Generic assignment was confirmed by 16S rRNA gene sequencing. Comparative analysis of the 16S rRNA gene sequence showed that this isolate constitutes a distinct phyletic line within the genus Dietzia, displaying 97.5-98.7% sequence similarity with Dietzia species with validly published names. The isolate could be distinguished from the type strain of Dietzia maris (1.6% sequence divergence) and other species of the genus Dietzia by DNA-DNA hybridization, as well as by using a set of biochemical tests. Genotypic and phenotypic data show that the strain merits classification as a novel species of the genus Dietzia for which the name Dietzia cinnamea sp. nov. is proposed; the type strain is IMMIB RIV-399T (= DSM 44904T = CCUG 50875T).

Williamsia deligens sp. nov., isolated from human blood.

The taxonomic status of two bacterial strains isolated from human blood was characterized using a polyphasic approach. Chemotaxonomic investigations revealed the presence of cell-wall chemotype IV, short-chain mycolic acids that co-migrated with those extracted from members of the genus Williamsia and that produce C(16 : 0) and C(18 : 0) fatty acids on pyrolysis GC, and dihydrogenated menaquinone with nine isoprene units as the predominant isoprenologue. The generic assignment was confirmed by 16S rRNA gene sequencing. Comparative analysis of the 16S rRNA gene sequence showed that these isolates constitute a distinct phyletic line within the genus Williamsia, displaying 96.2 and 97.2 % sequence similarities to Williamsia muralis and Williamsia maris, respectively. The two isolates could be distinguished from the type strains of the latter species on the basis of several phenotypic traits. The genotypic and phenotypic data show that the strains merit classification as a novel species of Williamsia, for which the name Williamsia deligens sp. nov. is proposed, with type strain IMMIB RIV-956T (= DSM 44902T = CCUG 50873T).

C-to-U conversion in the intercistronic ndhI/ ndhG RNA of plastids from monocot plants: conventional editing in an unconventional small reading frame?

Editing of plastid RNAs proceeds by C-to-U, in hornwort species also by extensive U-to-C, transitions, which predominantly lead to the restoration of codons for structurally and/or functionally important, conserved amino acid residues. So far, only one instance of editing outside coding regions has been reported - in the psbL/ psbF intergenic region of Ginkgo biloba. This site was proposed to have no functional importance. Here we present an evaluation of an editing site in the ndhI/ ndhG intergenic region in a related group of monocot plants. Efficient editing of this site, as well as the phylogenetic conservation of the resulting uridine residue, point at an important role for the sequence restored by editing. Two potential functions can be envisaged. (1) RNA secondary structure predictions suggest that the C-to-U conversion at this site can lead to a modified stem/loop structure of the ndhG 5' UTR, which could influence ndhG expression. (2) Alternatively, editing of the ndhI/ ndhG intergenic region may tag a so far unidentified small (12-codon) ORF, and lead to the restoration of a conserved phenylalanine codon. A screen with specific antibodies elicited against the putative peptide failed to detect such a peptide in chloroplast fractions. However, this failure may be attributable to its low and/or development-specific expression.

Stability and electrophilicity of phosphorus analogues of arduengo carbenes--an experimental and computational study

A variety of differently substituted 1,3,2-diazaphospholenium salts and P-halogeno-1,3,2-diazaphospholenes (X = F, Cl, Br) were synthesized, and their molecular structures, bonding situation, and Lewis acid properties were characterized by experimental (single-crystal X-ray diffraction, NMR and IR/Raman spectroscopy, MS, conductometry, titrations with Lewis bases) and computational methods. Both experimental and computational investigations confirmed that the structure and bonding in the diazaphospholenium cations of OTf and BF4 salts resembles that of neutral Arduengo carbenes and that the cations should not be described as genuinely aromatic. P-Halogenodiazaphospholenes are, in contrast to earlier assumptions, molecular species with covalent P-X bonds whose bonding situation can be expressed in terms of hyperconjugation between the six pi electrons in the C2N2 unit and the sigma*(P-X) orbital. This interaction induces a weakening of the P-X bonds, whose extent depends subtly on substituent influences and contributes fundamentally to the amazing structural similarity of ionic and covalent diazaphospholene compounds. A further consequence of this effect is the unique polarizability of the P-Cl bonds in P-chlorodiazaphospholenes, which is documented in a considerable spread of P-X distances and bond orders. Measurement of the stability constants for complexes of diazaphospholene compounds with Lewis bases confirmed the lower Lewis acidities and higher stabilities of diazaphospholenium ions as compared with nonconjugated phosphenium ions; this had been inferred from computed energies of isodesmotic halide-transfer reactions, and permitted also to determine equilibrium constants for P-Cl bond dissociation reactions. The results suggest, in accord with conductance measurements, that P-chlorodiazaphospholenes dissociate in solution only to a small extent. On the basis of these findings, the unique solvatochromatic behavior of NMR chemical shifts of these compounds was attributed to solvent-dependent P-Cl bond polarization rather than to shifts in dissociation equilibria.

Complete nucleotide sequence of the Oenothera elata plastid chromosome, representing plastome I of the five distinguishable euoenothera plastomes.

We describe the 159,443-bp [corrected] sequence of the plastid chromosome of Oenothera elata (evening primrose). The Oe. elata plastid chromosome represents type I of the five genetically distinguishable basic plastomes found in the subsection Euoenothera. The genus Oenothera provides an ideal system in which to address fundamental questions regarding the functional integration of the compartmentalised genetic system characteristic of the eukaryotic cell. Its highly developed taxonomy and genetics, together with a favourable combination of features in its genetic structure (interspecific fertility, stable heterozygous progeny, biparental transmission of organelles, and the phenomenon of complex heterozygosity), allow facile exchanges of nuclei, plastids and mitochondria, as well as individual chromosome pairs, between species. The resulting hybrids or cybrids are usually viable and fertile, but can display various forms of developmental disturbance.

Regioselective template synthesis, X-ray structure, and chiroptical properties of a topologically chiral sulfonamide catenane.

The synthesis of a topologically chiral in,out-bis-sulfonamide catenane and its "dimer" are reported. The structures of the amide wheel and of the catenane were resolved by X-ray analysis. NMR-titration of the monosulfonamide-wheel yielded conclusive association constants supporting the proposed regioselective mechanism of the catenane formation. The enantioseparation of the catenane via chiral HPLC was successful. The enantiomers show pronounced Cotton effects in the aromatic region of the CD-spectrum. Since the template synthesis was carried out leading to the in-oriented sulfonamide-wheel blocked with an N-methyl group at its reactive sulfonamide functionality, the catenane represents the first monofunctional topologically chiral amide-based catenane. Reaction with 1,2-bis(2-iodoethoxy)ethane led to a bis-catenane containing two topological units. The meso- and the RR/SS-isomers represent a new type of topological diastereomers.