Phylogeny of the Rhizobium–Allorhizobium–Agrobacterium clade supports the delineation of Neorhizobium gen. nov.

The genera Agrobacterium, Allorhizobium, and Rhizobium belong to the family Rhizobiaceae. However, the placement of a phytopathogenic group of bacteria, the genus Agrobacterium, among the nitrogen-fixing bacteria and the unclear position of Rhizobium galegae have caused controversy in previous taxonomic studies. To resolve uncertainties in the taxonomy and nomenclature within this family, the phylogenetic relationships of generic members of Rhizobiaceae were studied, but with particular emphasis on the taxa included in Agrobacterium and the “R. galegae complex” (R. galegae and related taxa), using multilocus sequence analysis (MLSA) of six protein-coding housekeeping genes among 114 rhizobial and agrobacterial taxa. The results showed that R. galegae, R. vignae, R. huautlense, and R. alkalisoli formed a separate clade that clearly represented a new genus, for which the name Neorhizobium is proposed. Agrobacterium was shown to represent a separate cluster of mainly pathogenic taxa of the family Rhizobiaceae. A. vitis grouped with Allorhizobium, distinct from Agrobacterium, and should be reclassified as Allorhizobium vitis, whereas Rhizobium rhizogenes was considered to be the proper name for former Agrobacterium rhizogenes. This phylogenetic study further indicated that the taxonomic status of several taxa could be resolved by the creation of more novel genera.     

In vitro, ex vivo and in vivo models: A comparative analysis of Paracoccidioides spp. proteomic studies

Members of the Paracoccidioides complex are human pathogens that infect different anatomic sites in the host. The ability of Paracoccidioides spp. to infect host niches is putatively supported by a wide range of virulence factors, as well as fitness attributes that may comprise the transition from mycelia/conidia to yeast cells, response to deprivation of micronutrients in the host, expression of adhesins on the cell surface, response to oxidative and nitrosative stresses, as well as the secretion of hydrolytic enzymes in the host tissue. Our understanding of how those molecules can contribute to the infection establishment has been increasing significantly, through the utilization of several models, including in vitro, ex vivo and in vivo infection in animal models. In this review we present an update of our understanding on the strategies used by the pathogen to establish infection. Our results were obtained through a comparative proteomic analysis of Paracoccidioides spp. in models of infection.     

The detoxification of α-tomatine by Fusarium oxysporum f. sp. lycopersici

Fusarium oxysporum f. sp. lycopersici detoxifies α-tomatine by producing an inducible extra-cellular enzyme which cleaves the glycoalkaloid into the tetrasaccharide lycotetraose and tomatidine.     

Evolutionary relationships between Fusarium oxysporum f. sp. lycopersici and F. oxysporum f. sp. radicis-lycopersici isolates inferred from mating type, elongation factor-1α and exopolygalacturonase sequences

Fusarium oxysporum is a ubiquitous species complex of soilborne plant pathogens that comprises many different formae speciales, each characterized by a high degree of host specificity. In this study, the evolutionary relationships between different isolates of the F. oxysporum species complex have been examined, with a special emphasis on the formae speciales lycopersici and radicis-lycopersici, sharing tomato as host while causing different symptoms. Phylogenetic analyses of partial sequences of a housekeeping gene, the elongation factor-1α (EF-1α) gene, and a gene encoding a pathogenicity trait, the exopolygalacturonase (pgx4) gene, were conducted on a worldwide collection of F. oxysporum strains representing the most frequently observed vegetative compatibility groups of these formae speciales. Based on the reconstructed phylogenies, multiple evolutionary lineages were found for both formae speciales. However, different tree topologies and statistical parameters were obtained for the cladograms as several strains switched from one cluster to another depending on the locus that was used to infer the phylogeny. In addition, mating type analysis showed a mixed distribution of the MAT1-1 and MAT1-2 alleles in the F. oxysporum species complex, irrespective of the geographic origin of the tested isolates. This observation, as well as the topological conflicts that were detected between EF-1α and pgx4, are discussed in relation to the evolutionary history of the F. oxysporum species complex.     

Hidden diversity uncovered in Hygrophorus sect. Aurei (Hygrophoraceae), including the Mediterranean H. meridionalis and the North American H. boyeri, spp. nov.

For many years, the binomial Hygrophorus hypothejus was widely applied to collections from various geographical regions in different continents, assuming a circum-boreal and circum-mediterranean distribution for this species. This hypothesis, however, had never been put to the test. To assess the diversity and species-limits within this complex of yellow-coloured waxcaps, a phylogenetic, morphological and taxonomical investigation into Hygrophorus sect. Aurei and similar species in sect. Olivaceoumbrini was carried out, including material of pan-European origin, as well as the east and west coasts of North America. Following sequencing of the ITS rDNA locus, nine lineages are confirmed in sect. Aurei, most of them highly continentalised. Of these, two are new to science, introduced here as Hygrophorus boyeri sp. nov., from Pinus banksiana and P. rigida forests in eastern North America and from P. muricata and P. contorta forests in western North America, and Hygrophorus meridionalis sp. nov., from Pinus brutia and Pinus halepensis forests in the island of Cyprus and mainland Greece. H. hypothejus is lectotypified and epitypified, and here resolved as a strictly European species, with the old forgotten taxon Hygrophorus siccipes revived as its North American vicariant. The placement of Hygrophorus fuligineus in sect. Aurei is phylogenetically confirmed and detailed comparisons between morphologically similar and phylogenetically affiliated taxa in sect. Aurei and sect. Olivaceoumbrini are provided. The chronic confusion associated with Hygrophorus fuscoalbus, a highly controversial taxon described from Germany nearly two centuries ago and variously interpreted since, is discussed, concluding that this name is too ambiguous to be applied to any currently recognized species.     

A Fusarium solani endophyte vs fungicides: Compatibility in a Fusarium oxysporum f.sp. radicis-lycopersici – tomato pathosystem

The potential of FsK, a non-pathogenic endophytic Fusarium solani strain, to be utilized as a biocontrol agent in combination with nine selected fungicides registered in tomato crops in Greece was evaluated. In vitro fungitoxicity tests revealed that FsK was insensitive to doses exceeding 100 μg/mL of thiophanate-methyl, fenhexamid, cyprodinil, boscalid and mancozeb. On the contrary, prochloraz, fludioxonil, pyraclostrobin and difenoconazole were most toxic to FsK. None of the later fungicides affected conidial production in an adverse way. Drenching of tomato plants with the above fungicides at recommended doses did not significantly affect colonization of tomato roots by FsK as revealed by in vitro isolation and Real Time PCR quantification. The disease suppressive ability of FsK against Fusarium oxysporum f.sp.radicis lycopersici (FORL) was not adversely affected by the post-inoculation application of commercial formulations of fludioxonil (Switch) and pyraclostrobin (Comet) at the recommended doses. Even more, the Comet–FsK combination resulted in enhanced disease suppression compared to either of the two treatments applied individually. In conclusion, not only biocontrol agent FsK is suitable for use in tomato integrated disease management programs that include all tested fungicides but also, some FsK –fungicide combinations can have additive effect against FORL disease incidence.     

A structure–activity relationship study of flavonoids as inhibitors of E. coli by membrane interaction effect

Flavonoids exhibit a broad range of biological activities including antibacterial activity. However, the mechanism of their antibacterial activity has not been fully investigated. The antibacterial activity and membrane interaction of 11 flavonoids (including 2 polymethoxyflavones and 4 isoflavonoids) against Escherichia coli were examined in this study. The antibacterial capacity was determined as flavonoids > polymethoxyflavones > isoflavonoids. Using fluorescence, it was observed that the 5 flavonoids rigidified the liposomal membrane, while the polymethoxyflavones and isoflavonoids increased membrane fluidity. There was a significant positive correlation between antibacterial capacity and membrane rigidification effect of the flavonoids. A quantitative structure–activity relationship (QSAR) study demonstrated that the activity of the flavonoid compounds can be related to molecular hydrophobicity (CLogP) and charges on C atom at position3 (C3). The QSAR model could be used to predict the antibacterial activity of flavonoids which could lead to natural compounds having important use in food and medical industry.     

A critical reappraisal of Phytolacca acinosa Roxb. (Phytolaccaceae) – A manganese-hyperaccumulating plant

Phytolacca acinosa Roxb. (Phytolaccaceae) was reported in 2004 to be a manganese-hyperaccumulating plant. Phytolacca americana L., growing at the same site was then independently reported in 2007 to have the same property. An apparent confusion in the taxonomy of the genus Phytolacca and interest in the Mn hyperaccumulative trait reported in P. acinosa has led to an extended field sampling, glasshouse cultivation and comparison with herbarium materials of P. americana s.l. Our specific aim was to identify and name the Mn hyperaccumulator plant correctly. P. acinosa is closely related to P. americana but it differs from the former in having an erect infructescence with usually eight distinct carpels, while from the latter has a nutant infructescence usually with 10 concrescent carpels. Our study indicated that the Mn hyperaccumulator plant P. acinosa which we first reported from the Xiangtan Mn tailings wasteland must now be reduced to P. americana as a synonym in order to prevent further confusion in identity and nomenclatural redundancy.     

α-N-acetyl-indole-3-acetyl-ε-L-lysine: A metabolite of indole-3-acetic acid from Pseudomonas syringae pv. savastanoi

A product of indole-3-acetic acid (IAA) metabolism having an auxin-like activity has been isolated from liquid cultures of Pseudomonas syringae pv. savastanoi. By spectral data and chemical correlations the compound has been identified as α-N-acetyl-indole-3-acetyl-ε-l-lysine (Ac-IAA-Lys). The IAA-derivative was detected in culture filtrates of oleander strains but not in culture filtrates of olive strains. The physiological effects of Ac-IAA-Lys on hypocotyl elongation in wheat, leaf chlorosis in oleander and bean and the hypertrophic response of potato tuber discs were compared with those of IAA. The results indicated that Ac-IAA-Lys was approximately 60 % less active than IAA.     

Hypoxyvermelhotins A–C,new pigments from Hypoxylon lechatii sp. nov

A new species of Hypoxylon was discovered, based on material collected in French Guiana and recognised on the basis of new combination of morpholological characters in comparison with type and authentic material of macroscopically similar taxa. These findings were corroborated by the rather isolated positions of its ITS-nrDNA and beta-tubulin DNA sequences in molecular phylogenies. However, the most salient feature of this fungus only became evident by a comparison of its stromatal HPLC profile, revealing several secondary metabolites that were hitherto not observed in stromata of any other member of the Xylariaceae. Part of the stromata were subsequently extracted to isolate these apparently specific components, using preparative chromatography. Five metabolites were obtained in pure state, and their chemical structures were elucidated by means of high resolution mass spectrometry and nuclear magnetic resonance spectroscopy. They turned out to be tetramic acid derivatives of the so-called vermelhotin type. Aside from vermelhotin, previously isolated from cultures of endophytic fungi, we identified three novel congeners, for which the trivial names hypoxyvermelhotins A–C were proposed. Like vermelhotin, they constitute orange-red pigments and a preliminary biological characterisation revealed them to have rather strong cytotoxic and moderate to weak antimicrobial effects. These results further illustrate the high diversity of unique secondary metabolites in stromata of the hypoxyloid Xylariaceae, a family in which biological diversity seems to parallel the chemical diversity of their bioactive principles to a great extent.     

Chara baltica Bruzelius 1824 and Chara intermedia A. Braun 1859—Distinct species or habitat specific modifications?

Species separation in charophytes is primarily based on vegetative morphology, but the taxonomic delineation at species level worldwide is inconsistent. Here we compare ecophysiological characteristics of selected Chara species with vegetative morphological traits and genetic data. Four populations of the Chara baltica-Chara intermedia species cluster from locations along a north-south gradient through Europe were investigated. Physiological differences indicate habitat-specific adaptations. The Baltic Sea population from Hiddensee was found to be separated from a freshwater river population close to Munich with respect to light and salinity acclimation capabilities. However, a population from a brackish Mediterranean pool near Montpellier and one from the continental brackish water lake “Salziger See” near Halle, Germany, show intermediate ecophysiological characteristics, suggesting a continuum. Genetic analyses using AFLP (amplified fragment length polymorphism) match the results of the physiological analyses. The individuals of the Mediterranean and the Salziger See neither cluster to the typical C. baltica from the Baltic Sea nor to the C. intermedia from the freshwater habitat, but instead take an intermediate position. These results are stable against the background of a larger AFLP dataset on charophytes. Morphological analysis revealed no distinct groups and we therefore conclude that the C. baltica-C. intermedia cluster forms a physiological, morphological and genetic continuum.     

Competitiveness of endophytic Phialocephala fortinii s.l. – Acephala applanata strains in Norway spruce roots

Dark septate endophytes of the Phialocephala fortinii s.l. – Acephala applanata species complex (PAC) are presumed to be the most abundant root colonizing endophytes of conifers across the Northern hemisphere. To test the competitiveness of different PAC strains, PAC-free Picea abies saplings were inoculated with five different PAC strains by planting them in pre-colonized substrates. Saplings were left to grow for six weeks and then transplanted crosswise into a substrate colonized by one of the other four strains for a further two weeks. PAC were isolated and genotyped using microsatellite markers. The power of colonization, i.e. the ability of colonizing roots already colonized by another PAC strain, and the power of retention, i.e. the ability of a resident strain of not being suppressed by an invading PAC strain, were calculated for each strain in every combination. The experiment was run twice under two different climatic conditions. Our results show that PAC strains differ (1) in their ability to colonize PAC-free, non-sterile roots, (2) in resistance against being suppressed by another PAC strain and (3) in their ability to invade roots already colonized by another PAC strain. In addition, both the PAC–PAC and the PAC-host interactions depend on the climatic conditions.     

Alcaloïdes d'Alstonia vitiensis var. Novo ebudica monachino

Five alkaloids have been isolated from Alstonia vitiensis: pleïocarpamine, vincorine, cabucraline, alstovine (11-methoxycompactinervine) and quaternoxine; the latter two are new alkaloids.     

E. coli sabotages the in vivo production of O-linked β-N-acetylglucosamine-modified proteins

The O-linked β-N-acetylglucosamine (O-GlcNAc) post-translational modification is an important, regulatory modification of cytosolic and nuclear enzymes. To date, no 3-dimensional structures of O-GlcNAc-modified proteins exist due to difficulties in producing sufficient quantities with either in vitro or in vivo techniques. Recombinant co-expression of substrate protein and O-GlcNAc transferase in Escherichia coli was used to produce O-GlcNAc-modified domains of human cAMP responsive element-binding protein (CREB1) and Abelson tyrosine-kinase 2 (ABL2). Recombinant expression in E. coli is an advantageous approach, but only small quantities of insoluble O-GlcNAc-modified protein were produced. Adding β-N-acetylglucosaminidase inhibitor, O-(2-acetamido-2-dexoy-d-glucopyranosylidene)amino-N-phenylcarbamate (PUGNAc), to the culture media provided the first evidence that an E. coli enzyme cleaves O-GlcNAc from proteins in vivo. With the inhibitor present, the yields of O-GlcNAc-modified protein increased. The E. coli β-N-acetylglucosaminidase was isolated and shown to cleave O-GlcNAc from a synthetic O-GlcNAc-peptide in vitro. The identity of the interfering β-N-acetylglucosaminidase was confirmed by testing a nagZ knockout strain. In E. coli, NagZ natively cleaves the GlcNAc-β1,4-N-acetylmuramic acid linkage to recycle peptidoglycan in the cytoplasm and cleaves the GlcNAc-β-O-linkage of foreign O-GlcNAc-modified proteins in vivo, sabotaging the recombinant co-expression system.     

A study of the pollen grains of Amaranthus spinosus Linné and A. Dubius Mart ex Thellung and their hybrids

A pollen-morphology study of Amaranthus spinosus, A. dubius, and their hybrids has been carried out. Three pollen types have been observed, namely (1) Type A: micrograins; (2) Type B: grains with smaller pores; and (3) Type C: grains with larger pores. Type B is characteristic of A. spinosus, Type C of A. dubius, and the micrograins of the hybrids. Pollen size range, and frequency of the various morphotypes serve to throw light on the biosystematics of the plants studied.     

On barriers to hybridization between Strongylocentrotus droebachiensis (O.F. Müller) and S. Pallidus (G.O. Sars)

Strongylocentrotus droebachiensis (O. F. Müller) and Strongylocentrotus pallidus (G. O. Sars) occur together over much of their ranges in both the Atlantic and Pacific Oceans and remain distinct species, but no strong barrier to genetic exchange has been found in a study in the San Juan Islands. Co-occurrence of embryos of both species in the plankton indicates similar times of spawning. Ova of S. droebachiensis are fertilized by sperm of S. pallidus but the reciprocal cross gives a percent fertilization near zero. Hybrids of both crosses are viable with pigmentation resembling S. pallidus in the larval stage and S. droebachiensis in the adult stage. Ova of first generation female hybrids are more readily fertilized by sperm of S. pallidus, so that gene flow through female hybrids is more likely to be from S. droebachiensis to S. pallidus than the reverse. Male hybrids were not tested. S. droebachiensis and S. pallidus from deeper waters have lower fecundity than shallow water S. droebachiensis, which suggests that in the deeper waters individuals are food limited. The hypothesis that S. pallidus uses the sterile male technique to reduce reproductive output of S. droebachiensis is considered and rejected.