Rhizobium ruizarguesonis sp. nov., isolated from nodules of Pisum sativum L

Four strains, coded as UPM1132, UPM1133^T, UPM1134 and UPM1135, and isolated from nodules of Pisum sativum plants grown on Ni-rich soils were characterised through a polyphasic taxonomy approach. Their 16S rRNA gene sequences were identical and showed 100% similarity with their closest phylogenetic neighbors, the species included in the ‘R. leguminosarum group’: R. laguerreae FB206^T, R. leguminosarum USDA 2370^T, R. anhuiense CCBAU 23252^T, R. sophoreae CCBAU 03386^T, R. acidisoli FH13^T and R. hidalgonense FH14^T, and 99.6% sequence similarity with R. esperanzae CNPSo 668^T. The analysis of combined housekeeping genes recA, atpD and glnII sequences showed similarities of 92-95% with the closest relatives. Whole genome average nucleotide identity (ANI) values were 97.5-99.7% ANIb similarity among the four strains, and less than 92.4% with closely related species, while digital DNA-DNA hybridization average values (dDDH) were 82-85% within our strains and 34-52% with closely related species. Major fatty acids in strain UPM1133^T were C18:1 ω7c / C18:1 ω6c in summed feature 8, C14:0 3OH/ C16:1 iso I in summed feature 2 and C18:0. Colonies were small to medium, pearl-white coloured in YMA at 28 °C and growth was observed in the ranges 8-34 °C, pH 5.5-7.5 and 0-0.7% (w/v) NaCl. The DNA G + C content was 60.8 mol %. The combined genotypic, phenotypic and chemotaxonomic data support the classification of strains UPM1132, UPM1133^T, UPM1134 and UPM1135 into a novel species of Rhizobium, for which the name Rhizobium ruizarguesonis sp. nov. is proposed. The type strain is UPM1133^T (=CECT 9542^T = LMG 30526^T).     

Rhizobium cauense sp. nov., isolated from root nodules of the herbaceous legume Kummerowia stipulacea grown in campus lawn soil

Three bacterial isolates (CCBAU 101002^T, CCBAU 101000 and CCBAU 101001) originating from root nodules of the herbaceous legume Kummerowia stipulacea grown in the campus lawn of China Agricultural University were characterized with a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that the isolates shared 99.85–99.92% sequence similarities and had the highest similarities to the type strains of Rhizobium mesoamericanum (99.31%), R. endophyticum (98.54%), R. tibeticum (98.38%) and R. grahamii (98.23%). Sequence similarity of four concatenated housekeeping genes (atpD, glnII, recA and rpoB) between CCBAU 101002^T and its closest neighbor (R. grahamii) was 92.05%. DNA–DNA hybridization values between strain CCBAU 101002^T and the four type strains of the most closely related Rhizobium species were less than 28.4 ± 0.8%. The G + C mol% of the genomic DNA for strain CCBAU 101002^T was 58.5% (Tm). The major respiratory quinone was ubiquinone (Q-10). Summed feature 8 (18:1ω7cis/18:1ω6cis) and 16:0 were the predominant fatty acids. Strain CCBAU 101002^T contained phosphatidylcholine and phosphatidylethanolamine as major polar lipids, and phosphatidylglycerol and cardiolipin as minor ones. No glycolipid was detected. Unlike other strains, this novel species could utilize dulcite or sodium pyruvate as sole carbon sources and it was resistant to 2% (w/v) NaCl. On the basis of the polyphasic study, a new species Rhizobium cauense sp. nov. is proposed, with CCBAU 101002^T (=LMG 26832^T = HAMBI 3288^T) as the type strain.     

Rahnella victoriana sp. nov., Rahnella bruchi sp. nov., Rahnella woolbedingensis sp. nov., classification of Rahnella genomospecies 2 and 3 as Rahnella variigena sp. nov. and Rahnella inusitata sp. nov., respectively and emended description of the genus Rahnella

Isolations from oak symptomatic of Acute Oak Decline, alder and walnut log tissue, and buprestid beetles in 2009–2012 yielded 32 Gram-negative bacterial strains showing highest gyrB sequence similarity to Rahnella aquatilis and Ewingella americana. Multilocus sequence analysis (using partial gyrB, rpoB, infB and atpD gene sequences) delineated the strains into six MLSA groups. Two MLSA groups contained reference strains of Rahnella genomospecies 2 and 3, three groups clustered within the Rahnella clade with no known type or reference strains and the last group contained the type strain of E. americana. DNA–DNA relatedness assays using both the microplate and fluorometric methods, confirmed that each of the five Rahnella MLSA groups formed separate taxa. Rahnella genomospecies 2 and 3 were previously not formally described due to a lack of distinguishing phenotypic characteristics. In the present study, all five Rahnella MLSA groups were phenotypically differentiated from each other and from R. aquatilis. Therefore we propose to classify the strains from symptomatic oak, alder and walnut and buprestid beetles as: Rahnella victoriana sp. nov. (type strain FRB 225^T = LMG 27717^T = DSM 27397^T), Rahnella variigena sp. nov. (previously Rahnella genomosp. 2, type strain CIP 105588^T = LMG 27711^T), Rahnella inusitata sp. nov. (previously Rahnella genomosp. 3, type strain DSM 30078^T = LMG 2640^T), Rahnella bruchi sp. nov. (type strain FRB 226^T = LMG 27718^T = DSM 27398^T) and Rahnella woolbedingensis sp. nov. (type strain FRB 227^T = LMG 27719^T = DSM 27399^T).     

Flavobacterium circumlabens sp. nov. and Flavobacterium cupreum sp. nov., two psychrotrophic species isolated from Antarctic environmental samples

A taxonomic study of 24 Gram-stain-negative rod-shaped bacteria originating from the Antarctic environment is described. Phylogenetic analysis using 16S rRNA gene sequencing differentiated isolated strains into two groups belonging to the genus Flavobacterium. Group I (n = 20) was closest to Flavobacterium aquidurense WB 1.1-56^T (98.3% 16S rRNA gene sequence similarity) while group II (n = 4) showed Flavobacterium hydatis DSM 2063^T as its nearest neighbour (98.5–98.9% 16S rRNA gene sequence similarity). Despite high 16S rRNA gene sequence similarity, these two groups represented two distinct novel species as shown by phenotypic traits and low genomic relatedness assessed by rep-PCR fingerprinting, DNA-DNA hybridization and whole-genome sequencing. Common to representative strains of both groups were the presence of major menaquinone MK-6 and sym-homospermidine as the major polyamine. Common major fatty acids were C_15:0 iso, C_15:1 iso G, C_15:0 iso 3-OH, C_17:0 iso 3OH and Summed Feature 3 (C_16:1 ω7c/C_16:1 ω6c). Strain CCM 8828^T (group I) contained phosphatidylethanolamine, three unidentified lipids lacking a functional group, three unidentified aminolipids and single unidentified glycolipid in the polar lipid profile. Strain CCM 8825^T (group II) contained phosphatidylethanolamine, eight unidentified lipids lacking a functional group, three unidentified aminolipids and two unidentified glycolipids in the polar lipid profile. These characteristics corresponded to characteristics of the genus Flavobacterium. The obtained results showed that the analysed strains represent novel species of the genus Flavobacterium, for which the names Flavobacterium circumlabens sp. nov. (type strain CCM 8828^T = P5626^T = LMG 30617^T) and Flavobacterium cupreum sp. nov. (type strain CCM 8825^T = P2683^T = LMG 30614^T) are proposed.     

Pantoea endophytica sp. nov., novel endophytic bacteria isolated from maize planting in different geographic regions of northern China

Four endophytic bacterial strains were isolated from root, stem and leaf of maize planted in different regions of northern China. The four strains possessed almost identical 16S rRNA gene sequences. However, REP-PCR fingerprint patterns discriminated that they were not from one clonal origin. Furthermore, the average nucleotide identity (ANI) values among them were higher than 95%, suggesting they all belong to one species. Based on 16S rRNA gene phylogeny, the four strains were clustered together with Pantoea rodasii LMG 26273^T and Pantoea rwandensis LMG 26275^T, but on a separate branch. Multilocus sequence analysis (MLSA) indicated that the four strains form a novel Pantoea species. Authenticity of the novel species was confirmed by ANI comparisons between strain 596^T and its closest relatives, since obtained values were considerably below the proposed thresholds for the species delineation. The genome size of 596^T was 5.1Mbp, comprising 4896 predicted genes with DNA G + C content of 57.8 mol%. The respiratory quinone was ubiquinone-8 (Q-8) and the polar lipid profile consisted of phosphatidylethanolamin, diphosphatidylglycerol, phosphatidylglycerol, unidentified aminophospholipid and unidentified phospholipid. The major fatty acids of strain 596^T were C_16:0, summed feature 2 (C_12:0 aldehyde), summed feature 3 (C_16:1ω7c and/or C_16:1ω6c) and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, the four isolates are considered to represent a novel species of the genus Pantoea, for which the name Pantoea endophytica sp. nov., is proposed, with 596^T (= DSM 100,785^T = CGMCC 1.15280^T) as type strain.     

Agrobacterium bohemicum sp. nov. isolated from poppy seed wastes in central Bohemia

Two non-pathogenic strains R89-1 and R90^T isolated from poppy seed (Papaver somniferum L.) wastes were phenotypically and genotypically characterized. Multilocus sequence analysis (MLSA) was conducted with six genes (atpD, glnA, gyrB, recA, rpoB, 16S rRNA). The strains represented a new species which clustered with Agrobacterium rubi NBRC 13261^T and Agrobacterium skierniewicense Ch11^T type strains. MLSA was further accompanied by whole-genome phylogeny, in silico DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) analyses for both strains. ANI and dDDH values were deep below the species delineation threshold. Phenotypic features of the novel strains unequivocally allowed their differentiation from all other Agrobacterium species. Unlike other agrobacteria, the strains were salt sensitive and were able to biotransform morphine alkaloids. The dominant cellular fatty acids are 18:1 w7c, 16:0 and 12:0 aldehyde/16:1 iso I/14:0 3OH summed in feature 2 and the major respiratory quinine is Q-10 (87%). The DNA G + C content is 56 mol%. Microbial community analysis indicated probable association with P. somniferum plant material. Altogether, these characteristics showed that strains R90^T and R89-1 represent a new species of the genus Agrobacterium which we propose to name Agrobacterium bohemicum. The type strain of A. bohemicum is R90^T (=CCM 8736^T = DSM 104667^T).     

Methylnickel compounds containing 2-phosphinylethanolato ligands – Syntheses,properties, and ethene coupling reactions

Combining dimethylphosphinylethanols HO(R¹R²)CCH₂PMe₂ (1: R¹ = R² = C₆H₅; 2: R¹ = R² = 4-OMe–C₆H₄; 5: R¹ = R² = 4-NMe₂–C₆H₄) with methyl(methoxo)(trimethylphosphine)nickel gave mononuclear methyl(trimethylphosphine)nickel(chelate) compounds 7–9. Ligand 6 (R¹ = Me, R² = 4-OMe–C₆H₅) afforded a dinuclear methylnickel compound 14. By reacting (TMEDA)lithium-dimethylphosphinylmethanide with ketones OC(R¹R²), the dimethylphosphinylethanols HO(R¹R²)CCH₂PMe₂ (3: R¹R² = 9-fluorenyl; 4: R¹ = H, R² = C₆H₅) were synthesized as prechelate ligands. Under otherwise similar conditions, the fluorenyl substituted anion in 3 gave rise to a mononuclear complex 10 which was found to act as a source of trimethylphosphine forming dinuclear 11 and at the same time to act as an acceptor of trimethylphosphine forming pentacoordinate 10 · PMe₃. Ni(COD)(PMe₃)₂ was used as a scavenger of PMe₃ in converting 8 or 9 to the dinuclear methylnickel compounds 12 and 13, respectively. Modifying the P,O chelating unit of a methyl nickel compound by introducing 2-phosphinylethanolato ligands leads to novel single-component catalysts for ethene oligomerization showing moderate reactivity and thermal stability.     

Polyphasic characterization of two novel Lactobacillus spp. isolated from blown salami packages: Description of Lactobacillus halodurans sp. nov. and Lactobacillus salsicarnum sp. nov.

Microbiota analysis of blown pack spoiled salami revealed five distinguishable Lactobacillus isolates we could not assign to a known species. Two of the isolates (TMW 1.2172^T and TMW 1.1920) are rod-shaped, whilst three isolates (TMW 1.2098^T, TMW 1.2118 and TMW 1.2188) appear coccus shaped or as short rods. All isolates are Gram-stain positive, facultative anaerobic, catalase and oxidase negative, non-motile and non-sporulating. Phylogenetic analysis of the 16S rRNA, dnaK, pheS and rpoA gene sequences revealed two distinct lineages within the genus Lactobacillus (L.). The isolates are members of the Lactobacillus alimentarius group with Lactobacillus ginsenosidimutans DSM 24154^T (99.4% 16S similarity), Lactobacillus versmoldensis DSM 14857^T (97.9%) and Lactobacillus furfuricola DSM 27174^T (97.7%) as phylogenetic closest related species and L. alimentarius DSM 20249^T (97.7%) and Lactobacillus paralimentarius DSM 13961^T (97.5%) as closest relatives, respectively. Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the isolates and their close related type strains are lower than 80% and 25%, respectively. For both designated type strains, the peptidoglycan type is A4α l-Lys-d-Asp and the major fatty acids are C_16:0, C_18:1ω9c and summed feature 7. Based on phylogenetic, phenotypic and chemotaxonomic analysis we demonstrated that the investigated isolates belong to two novel Lactobacillus species for which we propose the names Lactobacillus salsicarnum with the type strain TMW 1.2098^T = DSM 109451^T = LMG 31401^T and Lactobacillus halodurans with the type strain TMW 1.2172^T = DSM 109452^T = LMG 31402^T.     

Uptake and allocation of 13C by Enhalus acoroides at sites differing in light availability

Carbon fixation and allocation were studied using ¹³C incubation and leaf marking techniques in mature monospecific stands of Enhalus acoroides L.f. Royle in August 1998 and January 1999 in Banten Bay, Indonesia. The highest rate of ¹³C uptake (>0.008 g ¹³C g C⁻¹ d⁻¹) was found in the middle to distal parts of leaves of E. acoroides. Young and senescing leaves numbers had lower ¹³C incorporation compared to mature leaves. The incorporation of ¹³C by epiphytes on the leaves was higher than that of the leaves themselves (>0.01 g ¹³C g C⁻¹ d⁻¹). The results showed that turbidity of the water influenced the leaf growth, productivity and Relative Growth Rate of E. acoroides, which were lower at Kepuh Island, the more turbid site. However, at Kepuh Island, where the water column was turbid, the plant could still harvest sufficient light for an uptake rate of ¹³C, higher than the uptake rates at Kubur and Panjang Islands, stations with a much more transparent water column (on average 0.0047 g ¹³C g C⁻¹ d⁻¹ at Kepuh Island, versus 0.0045 g ¹³C g C⁻¹ d⁻¹ at Panjang Island and 0.0034 g ¹³C g C⁻¹ d⁻¹ at Kubur Island). There was evidence that ¹³C was exported from the incubated shoots to the roots and rhizomes and to neighboring shoots of E. acoroides in clear water, but not in turbid water. We suggest that single shoots of E. acoroides are able to grow in turbid water under low light conditions. They assimilate sufficient carbon for their own maintenance but are not able to export to neighboring plant parts.     

Vibrio taketomensis sp. nov. by genome taxonomy

Two novel strains C4III282^T and C4III291 were isolated from seawater collected a site off the Taketomi coral reef. Phylogenetic analysis based on the 16S rRNA sequences revealed that the two strains belong to the genus Vibrio. MLSA using eight protein-coding genes (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA, and topA) showed that C4III282^T and C4III291 are closely related to the members of the Ponticus clade, namely Vibrio panuliri JCM 19500^T, Vibrio ponticus DSM 16217^T, and “Vibrio rhodolitus” G98. ANI and in silico DDH values with members of the Ponticus clade were 77.6-78.7% and 22.2-23.1, respectively. The name Vibrio taketomensis sp. nov. is proposed with C4III282^T (CAIM 1928^T = DSM 106943^T = JCM 33434^T) as the type strain.     

Ensifer shofinae sp. nov., a novel rhizobial species isolated from root nodules of soybean (Glycine max)

Two bacterial strains isolated from root nodules of soybean were characterized phylogenetically as members of a distinct group in the genus Ensifer based on 16S rRNA gene comparisons. They were also verified as a separated group by the concatenated sequence analyses of recA, atpD and glnII (with similarities ≤93.9% to the type strains for defined species), and by the average nucleotide identities (ANI) between the whole genome sequence of the representative strain CCBAU 251167^T and those of the closely related strains in Ensifer glycinis and Ensifer fredii (90.5% and 90.3%, respectively). Phylogeny of symbiotic genes (nodC and nifH) grouped these two strains together with some soybean-nodulating strains of E. fredii, E. glycinis and Ensifer sojae. Nodulation tests indicated that the representative strain CCBAU 251167^T could form root nodules with capability of nitrogen fixing on its host plant and Glycine soja, Cajanus cajan, Vigna unguiculata, Phaseolus vulgaris and Astragalus membranaceus, and it formed ineffective nodules on Leucaena leucocephala. Strain CCBAU 251167^T contained fatty acids 18:1 ω9c, 18:0 iso and 20:0, differing from other related strains. Utilization of l-threonine and d-serine as carbon source, growth at pH 6.0 and intolerance of 1% (w/v) NaCl distinguished strain CCBAU 251167^T from other type strains of the related species. The genome size of CCBAU 251167^T was 6.2 Mbp, comprising 7,581 predicted genes with DNA G+C content of 59.9 mol% and 970 unique genes. Therefore, a novel species, Ensifer shofinae sp. nov., is proposed, with CCBAU 251167^T (=ACCC 19939^T = LMG 29645^T) as type strain.     

Description of Maribellus sediminis sp. nov., a marine nitrogen-fixing bacterium isolated from sediment of cordgrass and mangrove

Two marine bacterial strains designated Y2-1-60^T and GM1-28 were isolated from sediments of cordgrass and mangrove along the Luoyang estuary in Quanzhou Bay, China, respectively. Both strains were Gram-staining-negative, straight rod-shaped, non-flagellum, facultatively anaerobic, nitrogen-fixing, and did not contain carotenoid pigment. Catalase activities were found to be weak positive and oxidase activities negative. The 16S rRNA gene sequences of the two strains were identical and had maximum similarity of 98.0% with Maribellus luteus XSD2^T, and of <94.5% with other species. ANI value (96.9%) and DDH estimate (71.5%) between the two strains supported that they belonged to the same species. ANI value and DDH estimate between the two strains and M. luteus XSD2^T was 74.3% and 19.4%, respectively, indicating that they represent a novel species. Phylogenetic analysis based on 16S rRNA gene and phylogenomic analysis indicated that strains Y2-1-60^T and GM1-28 formed a monophyletic branch within the genus Maribellus. The respiratory quinone was menaquinone MK-7. The major fatty acid (>10%) consisted of iso-C_15:0, and iso-C_17:0 3-OH. The polar lipids consisted of phosphatidylethanolamine and several unidentified lipids. The genomic G + C contents were 41.9–42.0 mol%. Gene annotation revealed that strains Y2-1-60^T and GM1-28 contained a set of nif gene cluster (nifHDKENB) responsible for nitrogen fixation. Based on the above characteristics, strains Y2-1-60^T and GM1-28 represent a novel species within the genus Maribellus. Thus, Maribellus sediminis sp. nov. is proposed with type strain Y2-1-60^T (=MCCC 1K04285^T = KCTC 72884^T), isolated from cordgrass sediment and strain GM1-28 (=MCCC 1K04384 = KCTC 72880), isolated from mangrove sediment.     

Climatic dependency of soil organic carbon isotopic composition along the S–N Transect from 34°N to 52°N in central-east Asia

We explored the relationships between surface-soil (1–20 cm) organic carbon isotopic signatures and associated climatic factors in central-east Asia in an attempt to develop transfer functions that can be used to retrieve the paleoclimatic information stored in the thick eolian–paleosol sequences within the area. Our analysis shows that the negative correlation between the surface-soil organic δ¹³C values and the mean annual precipitation is robust (R² = 0.453; n = 196; p < 0.05) and the negative correlation with the growing-season (April–September) precipitation is more significant (R² = 0.4966; n = 196; p < 0.05). Our study further shows that the positive correlation between the surface-soil organic δ¹³C values and mean growing-season aridity is most significant (R² = 0.5805; n = 196; p < 0.05). We have smoothed both the organic δ¹³C values and the mean growing-season aridity values using a 3-point moving-window average-filter method in an attempt to remove some of random errors and found that the positive correlation between the two is further increased (R² =  0.7784; n =  192; p < 0.05). These robust linear relationships demonstrate their value in reconstructing paleoclimate changes in the study area. The documented climatic dependency of the surface-soil carbon isotopic composition in the study area might have resulted both from the humidity-related isotopic enrichment processes of the dominant C₃ plants (stomatal conductance and photosynthetic discrimination) and from the aridity-related abundance of C₄ plants (mainly Chenopodiaceae species) along the S–N bioclimatic gradient.     

Caulobacter zeae sp. nov. and Caulobacter radicis sp. nov., novel endophytic bacteria isolated from maize root (Zea mays L.)

Four bacterial strains designated 410^T, 441, 695^T and 736 were isolated from maize root in Beijing, P. R. China. Based on 16S rRNA gene phylogeny, the four strains formed two clusters in the genus Caulobacter. Since strain 441 was a clonal variety of strain 410^T, only three strains were selected for further taxonomic studies. The whole genome average nucleotide identity (ANI) value between strains 410^T and 695^T was 94.65%, and both strains shared less than 92.10% ANI values with their close phylogenetic neighbors Caulobacter vibrioides DSM 9893^T, Caulobacter segnis ATCC 21756^T and Caulobacter flavus CGMCC 1.15093^T. Strains 410^T and 695^T contained Q-10 as the sole ubiquinone and their major fatty acids were C_{16:0, 11-methyl C18:1ω 0}, 11-methyl C_{18: 1}ω7c, summed feature 3 (C_{16:1ω7c and/or C16:1ω 1}ω7c and/or C_{16: 1}ω6c) and summed feature 8 (C_{18:1ω7c and/or C18:1ω 1}ω7c and/or C_{18: 1}ω6c). Their major polar lipids consisted of glycolipids and phosphatidylglycerol, and phenotypic tests differentiated them from their closest phylogenetic neighbors. Based on the results obtained, it is proposed that the three strains represent two novel species, for which the names Caulobacter zeae sp. nov. (type strain 410^T = CGMCC 1.15991 = DSM 104304) and Caulobacter radicis sp. nov. (type strain 695^T = CGMCC 1.16556 = DSM 106792) are proposed.     

Novel insights into cyclooxygenases,linoleate diol synthases,and lipoxygenases from deuterium kinetic isotope effects and oxidation of substrate analogs

Cyclooxygenases (COX) and 8R-dioxygenase (8R-DOX) activities of linoleate diol synthases (LDS) are homologous heme-dependent enzymes that oxygenate fatty acids by a tyrosyl radical-mediated hydrogen abstraction and antarafacial insertion of O₂. Soybean lipoxygenase-1 (sLOX-1) contains non-heme iron and oxidizes 18:2n ? 6 with a large deuterium kinetic isotope effect (D-KIE). The aim of the present work was to obtain further mechanistic insight into the action of these enzymes by using a series of n ? 6 and n ? 9 fatty acids and by analysis of D-KIE. COX-1 oxidized C₂₀ and C₁₈ fatty acids in the following order of rates: 20:2n ? 6 > 20:1n ? 6 > 20:3n ? 9 > 20:1n ? 9 and 18:3n ? 3 ≥ 18:2n ? 6 > 18:1n ? 6. 18:2n ? 6 and its geometrical isomer (9E,12Z)18:2 were both mainly oxygenated at C-9 by COX-1, but the 9Z,12E isomer was mostly oxygenated at C-13. A cis-configured double bond in the n ? 6 position therefore seems important for substrate positioning. 8R-DOX oxidized (9Z,12E)18:2 at C-8 in analogy with 18:2n ? 6, but the 9E,12Z isomer was mainly subject to hydrogen abstraction at C-11 and oxygen insertion at C-9 by 8R-DOX of 5,8-LDS. sLOX-1 and 13R-MnLOX oxidized [11S-²H]18:2n ? 6 with similar D-KIE (~ 53), which implies that the catalytic metals did not alter the D-KIE. Oxygenation of 18:2n ? 6 by COX-1 and COX-2 took place with a D-KIE of 3–5 as probed by incubations of [11,11-²H₂]- and [11S-²H]18:2n ? 6. In contrast, the more energetically demanding hydrogen abstractions of the allylic carbons of 20:1n ? 6 by COX-1 and 18:1n ? 9 by 8R-DOX were both accompanied by large D-KIE (> 20).     

Methyl-palladium(II) complexes of pyridine-bridged bis(nucleophilic heterocyclic carbene) ligands: Substituent effects on structure,stability, and catalytic performance

A series of discrete, mononuclear palladium(II)–methyl complexes, together with several palladium(II)–chloro analogues, of pyridine-functionalised bis-NHC ligands have been prepared via ligand transmetallation from the silver(I)-NHC complexes. The reported complexes comprise examples with both the methylene-bridged 2,6-bis[(3-R-imidazolin-2-yliden-1-yl)methyl]pyridine (_RC^∧N^∧C; R = Mes, dipp, ^tBu) and planar 2,6-bis(3-R-imidazolin-2-yliden-1-yl)pyridine (_RCNC; R = Mes, dipp) ligands and, when combined with the previously reported _MeC^∧N^∧C/_MeCNC examples, cover a broad spectrum of ligand substituent steric and electronic properties, including the bulky Mes and dipp groups frequently used in catalytic applications. The palladium(II) complexes have been characterised by a variety of methods, including single crystal X-ray crystallography, with the shielding of the Pd–Me groups in the proton NMR spectra of some of the N-aryl substituted examples correlated with the proximity of the aryl rings to the methyl group in the solid state structures. The [PdMe(_RC^∧N^∧C/_RCNC)]⁺ complexes undergo thermal degradation via reductive methyl-NHC coupling to give 2-methyl-3-R-imidazolium-1-yl species with relative stabilities in the order of [PdMe(_MesC^∧N^∧C)]BF₄ > [PdMe(_MeC^∧N^∧C)]BF₄ ≈ [PdMe(_MesCNC)]BF₄ > [PdMe(_MeCNC)]BF₄ > [PdMe(_tBuC^∧N^∧C)]BF₄ ≫ [PdMe(_tBuCNC)]BF₄ (not isolable). A comparison of the activity of the complexes as precatalysts in a model Heck coupling reaction shows greatest activity in those species bearing bulkier N-substituents, with complexes bearing _RC^∧N^∧C ligands generally more efficient precatalysts than those bearing _RCNC ligands.     

Stimuli responsive polymorphism of C12NO/DOPE/DNA complexes: Effect of pH,temperature and composition

N,N-dimethyldodecylamine-N-oxide (C₁₂NO) is a surfactant that may exist either in a neutral or cationic protonated form depending on the pH of aqueous solutions. Using small angle X-ray diffraction (SAXD) we observe the rich structural polymorphism of pH responsive complexes prepared due to DNA interaction with C₁₂NO/dioleoylphosphatidylethanolamine (DOPE) vesicles and discuss it in view of utilizing the surfactant for the gene delivery vector of a pH sensitive system. In neutral solutions, the DNA uptake is low, and a lamellar L_α phase formed by C₁₂NO/DOPE is prevailing in the complexes at 0.2 ≤ C₁₂NO/DOPE < 0.6 mol/mol. A maximum of ~ 30% of the total DNA volume in the sample is bound in a condensed lamellar phase L_α^C at C₁₂NO/DOPE = 1 mol/mol and pH 7.2. In acidic conditions, a condensed inverted hexagonal phase H_II^C was observed at C₁₂NO/DOPE = 0.2 mol/mol. Commensurate lattice parameters, a_HC ≈ d_LC, were detected at 0.3 ≤ C₁₂NO/DOPE ≤ 0.4 mol/mol and pH = 4.9–6.4 suggesting that L_α^C and H_II^C phases were epitaxially related. While at the same composition but pH ~ 7, the mixture forms a cubic phase (Pn3m) when the complexes were heated to 80 °C and cooled down to 20 °C. Finally, a large portion of the surfactant (C₁₂NO/DOPE > 0.5) stabilizes the L_α^C phase in C₁₂NO/DOPE/DNA complexes and the distance between DNA strands (d_DNA) is modulated by the pH value. Both the composition and pH affect the DNA binding in the complexes reaching up to ~ 95% of the DNA total amount at acidic conditions.     

Paenibacillus ihbetae sp. nov., a cold-adapted antimicrobial producing bacterium isolated from high altitude Suraj Tal Lake in the Indian trans-Himalayas

The assessment of bacterial diversity and bioprospection of the high-altitude lake Suraj Tal microorganisms for potent antimicrobial activities revealed the presence of two Gram-stain-variable, endospore-forming, rod-shaped, aerobic bacteria, namely IHBB 9852^T and IHBB 9951. Phylogenetic analysis based on 16S rRNA gene sequence showed the affiliation of strains IHBB 9852^T and IHBB 9951 within the genus Paenibacillus, exhibiting the highest sequence similarity to Paenibacillus lactis DSM 15596^T (97.8% and 97.7%) and less than 95.9% similarity to other species of the genus Paenibacillus. DNA-DNA relatedness among strains IHBB 9852^T and IHBB 9951 was 90.2%, and with P. lactis DSM 15596^T, was 52.7% and 52.4%, respectively. The novel strains contain anteiso-C_15:0, iso-C_15:0, C_16:0 and iso-C_16:0 as major fatty acids, and phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol were predominant polar lipids. The DNA G+C content for IHBB 9852T and IHBB 9951 was 52.1 and 52.2 mol%. Based on the results of phenotypic and genomic characterisations, we concluded that strains IHBB 9852^T and IHBB 9951 belong to a novel Paenibacillus species, for which the name Paenibacillus ihbetae sp. nov. is proposed. The type strain is IHBB 9852^T (=MTCC 12459^T = MCC 2795^T = JCM 31131^T = KACC 19072^T; DPD TaxonNumber TA00046) and IHBB 9951 (=MTCC 12458 = MCC 2794 = JCM 31132 = KACC 19073) is a reference strain.     

Micromonospora musae sp. nov., an endophytic actinomycete isolated from roots of Musa species

Two novel actinobacterial strains, MS1-9^T and NGC1-4, were isolated from roots of Musa (ABB) cv. ‘Kluai Namwa’, collected from Chachoengsao province, and Musa (ABB) cv. ‘Kluai Chang’, from Suphan Buri province, Thailand, respectively. Comparative analysis of 16S rRNA gene (98.0 to 98.9% similarity), gyrase subunit B (gyrB) gene and whole-genome sequences emphasised that the strains MS1-9^T and NGC1-4 showed closely related with Micromonospora peucetia DSM 43363^T, M. krabiensis JCM 12869^T and M. avicenniae DSM 45758^T, respectively. Strains MS1-9^T and NGC1-4 contained meso-diaminopimelic acid in cell-wall peptidoglycan. Whole-cell sugars were glucose, xylose, mannose, and ribose. The acyl type of peptidoglycan was glycolyl. MK-10(H₆), MK-9(H₆), and MK-10(H₈) were presented as the major menaquinones. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and phosphatidylinositol were detected as predominant phospholipid profiles. The major cellular fatty acids consisted of iso-C_15:0, anteiso-C_15:0, anteiso-C_17:0, iso-C_17:0 and C_17:0. The DNA G + C content of strains MS1-9^T and NGC1-4 were 72.2 and 72.3 mol%, respectively. Draft genome sequences indicated by ANI values and digital DNA-DNA hybridisation analysis asserted that the strains MS1-9^T and NGC1-4 should be represented as a novel species within the genus Micromonospora for which the name Micromonospora musae sp. nov. is proposed. The type strain is MS1-9^T (=JCM 32149^T = TISTR 2659^T).     

Salinivibrio kushneri sp. nov., a moderately halophilic bacterium isolated from salterns

Ten Gram-strain-negative, facultatively anaerobic, moderately halophilic bacterial strains, designated AL184^T, IB560, IB563, IC202, IC317, MA421, ML277, ML318, ML328A and ML331, were isolated from water ponds of five salterns located in Spain. The cells were motile, curved rods and oxidase and catalase positive. All of them grew optimally at 37 °C, at pH 7.2–7.4 and in the presence of 7.5% (w/v) NaCl. Based on phylogenetic analyses of the 16S rRNA, the isolates were most closely related to Salinivibrio sharmensis BAG^T (99.6–98.2% 16S rRNA gene sequence similarity) and Salinivibrio costicola subsp. costicola ATCC 35508^T (99.0–98.1%). According to the MLSA analyses based on four (gyrB, recA, rpoA and rpoD) and eight (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA and topA) concatenated gene sequences, the most closely relatives were S. siamensis JCM 14472^T (96.8–95.4% and 94.9–94.7%, respectively) and S. sharmensis DSM 18182^T (94.0–92.6% and 92.9–92.7%, respectively). In silico DNA–DNA hybridization (GGDC) and average nucleotide identity (ANI) showed values of 23.3–44.8% and 80.2–91.8%, respectively with the related species demonstrating that the ten isolates constituted a single novel species of the genus Salinivibrio. Its pangenome and core genome consist of 6041 and 1230 genes, respectively. The phylogeny based on the concatenated orthologous core genes revealed that the ten strains form a coherent phylogroup well separated from the rest of the species of the genus Salinivibrio. The major cellular fatty acids of strain AL184^T were C_16:0 and C_18:1. The DNA G + C content range was 51.9–52.5 mol% (T_m) and 50.2–50.9 mol% (genome). Based on the phylogenetic-phylogenomic, phenotypic and chemotaxonomic data, the ten isolates represent a novel species of the genus Salinivibrio, for which the name Salinivibrio kushneri sp. nov. is proposed. The type strain is AL184^T (= CECT 9177^T = LMG 29817^T).