Truffle trouble: what happened to the Tuberales?

An overview of truffles (now considered to belong in the Pezizales, but formerly treated in the Tuberales) is presented, including a discussion on morphological and biological traits characterizing this form group. Accepted genera are listed and discussed according to a system based on molecular results combined with morphological characters. Phylogenetic analyses of LSU rDNA sequences from 55 hypogeous and 139 epigeous taxa of Pezizales were performed to examine their relationships. Parsimony, ML, and Bayesian analyses of these sequences indicate that the truffles studied represent at least 15 independent lineages within the Pezizales. Sequences from hypogeous representatives referred to the following families and genera were analysed: Discinaceae–Morchellaceae (Fischerula, Hydnotrya, Leucangium), Helvellaceae (Balsamia and Barssia), Pezizaceae (Amylascus, Cazia, Eremiomyces, Hydnotryopsis, Kaliharituber, Mattirolomyces, Pachyphloeus, Peziza, Ruhlandiella, Stephensia, Terfezia, and Tirmania), Pyronemataceae (Genea, Geopora, Paurocotylis, and Stephensia) and Tuberaceae (Choiromyces, Dingleya, Labyrinthomyces, Reddellomyces, and Tuber). The different types of hypogeous ascomata were found within most major evolutionary lines often nesting close to apothecial species. Although the Pezizaceae traditionally have been defined mainly on the presence of amyloid reactions of the ascus wall several truffles appear to have lost this character. The value of the number of nuclei in mature ascospores as a delimiting family character is evaluated and found to be more variable than generally assumed.     

Phylogenetic and populational study of the Tuber indicum complex

When examined using SEM, Chinese samples of Tuber indicum and T. sinense displayed the same ascospore ornamentation as that of T. pseudohimalayense, T. indicum, collected in India by Duthie in 1899, and samples renamed T. himalayense in 1988. The different authors who named the four taxa (T. indicum, T. himalayense, T. sinense, T. pseudohimalyense) described differences in the surface of the peridium which could be considered as usual variations within a single species. We consider T. indicum, T. himalayense, T. sinense and T. pseudohimalayense as one species, T. indicum. Within this T. indicum complex, according to ITS and β-tubulin sequences, there are two groups in China, which could be considered as geographical ecotypes. This study is the first to identify a genetic and phylogeographical structure within the Chinese Tuber species.     

A multivariate statistical approach to Centaurea classification using essential oil composition data of some species from Turkey

The composition of the essential oils of ten Centaurea species from Turkey, Centaurea aladaghensis, C. antiochia var. prealta, C. antitauri, C. babylonica, C. balsamita, C. cheirolepidoides, C. deflexa, C. iconiensis, C. lanigera, C. ptosimopappoides have been studied. Multivariate statistical analyses (Principal Component Analysis, Multidimensional Scaling, Hierarchical Cluster Analysis) applied to GC-MS data, seem to be very useful to investigate and establish the natural taxonomic delimitation of this very difficult genus. The groupings resulted independent from the ecological similarities (i.e. plants that live in the same habitats or share similar morphological characteristics), so it seems that the environment has no influence on the biosynthesis of the volatiles of these plants.     

Comparative seed morphology and character evolution in the genus Lysimachia (Myrsinaceae) and related taxa

Summary We investigated seed morphology in 34 species of the genus Lysimachia and in 14 species and two subspecies of six additional genera (Anagallis, Ardisiandra, Asterolinon, Glaux, Pelletiera, Trientalis), which have been shown to be closely related to, or are placed within Lysimachia in previous molecular studies. We studied seed shape, seed coat structure, and seed coat surface patterns. Three major types of seed shape were identified: (1) sectoroid, (2) polyhedral, and (3) coarsely rugose with concave hilar area. In addition, seeds may be keeled or winged. The outer layer of the seed coat is either sponge-like and adhering only loosely to the inner seed coat or it is thin and tightly adhering to the underlying tissue. Seed surface patterns can be divided into six main types: (1) reticulate, (2) tuberculate, (3) vesiculose, (4) colliculate, (5) undulate, or (6) poroid-alveolate. Seed surface patterns are mostly congruent with molecular phylogenetic relationships. A reticulate surface pattern is diagnostic of, e.g. Lysimachia subgenera Palladia and Hawaiian Lysimachiopsis. Mapping seed characters onto a recent phylogenetic tree, reveals that they provide potentially synapomorphic character states for various subclades of Lysimachia. Salient examples include a rugose seed shape, which turns out to be synapomorphic for the clade comprising the genus Pelletiera plus Asterolinon linum-stellatum and a sponge-like outer seed coat layer, which characterizes a clade with Lysimachia vulgaris, L. thyrsiflora, and L. terrestris, with an analogue that apparently evolved in parallel in Trientalis europaea. We also discuss possible habitat factors that may have favored the independent evolution of particular seed types such as winged seeds in various lineages.     

基于ITS序列的中国外来苋属植物系统关系分析

通过ITS序列对21种中国外来苋属植物进行系统进化关系研究。通过ITS序列种间、种内遗传距离分析,发现苋属种间变异为0~0.055 1,种内变异为0~0.009 2。使用TAXON DNA软件分析ITS序列种间、种内变异的分布图看出规律,结果表明苋属ITS序列的种间变异适中,种间变异明显大于种内变异。采用最大似然法(ML)构建的系统树将中国苋属分为5或6个进化支(根据自展支持率取值不同)。异株苋亚属长芒苋和苋亚属刺苋聚类在一起,西部苋和糙果苋单独成为一个进化支。苋亚属中苋组苋亚组反枝苋和绿穗苋亚组鲍氏苋有着更近的亲缘关系,苋组苋亚组尾穗苋和绿穗苋亚组绿穗苋、繁穗苋等亲缘关系更近。白苋亚属分为2或3个类群,根据自展支持率取值不同,合被苋可以和白苋、北美苋并为一支,也可以单独成为一支。综上所述,该文认为苋属经典分类体系中3亚属或2~3组的分类地位不成立,建议中国苋属采取5组2亚组或6组2亚组的分类体系。5组2亚组分别由长芒苋组、糙果苋组、苋组(苋亚组和绿穗苋亚组)、白苋组和凹头苋组组成。其中,合被苋也可从白苋组分出,单独构成1组,形成6组2亚组的分类体系。表明该序列对苋属大部分种类分类效果较好,对西部苋和糙果苋复合群,绿穗苋复合群以及白苋亚属的分类价值不高。     

Low sequence similarity and gene content of symbiotic clusters of Bradyrhizobium sp. WM9 (Lupinus) indicate early divergence of “lupin” lineage in the genus Bradyrhizobium

Two sequenced nodulation regions of lupin Bradyrhizobium sp. WM9 carried the majority of genes involved in the Nod factor production. The nod region I harbored: nolA, nodD, nodA, nodB, nodC, nodS, nodI, nodJ, nolO, nodZ, fixR, nifA, fixA, nodM, nolK and noeL. This gene arrangement resembled that found in the nodulation region of Bradyrhizobium japonicum USDA110, however strain WM9 harbored only one nodD gene copy, while the nodM, nolK and noeL genes had no counterparts in the 410 kb symbiotic region of strain USDA110. Region II harbored nolL and nodW, but lacked an nodV gene. Both regions carried ORFs that lacked similarity to the published USDA110 sequences, though they had homologues in symbiotic regions of Rhizobium etli, Sinorhizobium sp. NGR234 and Mesorhizobium loti. These differences in gene content, as well as a low average sequence identity (70%) of symbiotic genes with respect to B. japonicum USDA110 were in contrast with the phylogenetic relationship of USDA110 and WM9 revealed by the analysis of 16S rDNA and dnaK sequences. This most likely reflected an early divergence of symbiotic loci, and possible co-speciation with distinct legumes. During this process the loss of a noeI gene and the acquisition of a nolL gene could be regarded as an adaptation towards these legumes that responded to Nod factors carrying 4-O-acetylfucose rather than 2-O-methylfucose. This explained various responses of lupins and serradella plants to infection by mutants in nodZ and nolL genes, knowing that serradella is a stringent legume while lupins are more promiscuous legumes. This revised version was published online in August 2006 with corrections to the Cover Date.     

Genetic differentiation of metallicolous and non-metallicolous Armeria maritima (Mill.) Willd. taxa (Plumbaginaceae) in Central Europe

This study investigates the genetic differentiation within the Central European Armeria maritima (Mill.) Willd. complex with special reference to the metallicolous populations using AFLP markers. Our sampling comprised all metallicolous (ssp. halleri, hornburgensis, bottendorfensis, eifeliaca, calaminaria), and non-metallicolous taxa (ssp. maritima, elongata, alpina). Geographical and genetic distances between populations were moderately positively correlated. Genetic variability of metallicolous and non-metallicolous populations was not significantly different. Lowland populations were clearly differentiated from the alpine populations. Within the lowland group metallicolous and non-metallicolous populations were not genetically differentiated. All lowland populations show a regional differentiation and close relationships to ssp. elongata. Thus, the metallicolous taxa should not be maintained as subspecies. Likewise, their treatment as varieties of a ssp. halleri s.l. is critical because this taxon cannot be consistently characterized throughout its geographical range and may be an artefact itself. If a taxonomical recognition should be considered necessary it is advisable to treat the microendemics as varieties of ssp. elongata.     

Isolation and characterization of arsenite-oxidizing bacteria from arsenic-contaminated soils in Thailand

Two hundred and eighty-eight arsenic-resistant bacteria were isolated by an enrichment culture method from a total of 69 arsenic-contaminated soil-samples collected from Dantchaeng district in Suphanburi province (47 samples), and from Ron Phiboon district in Nakhon Sri Thammarat province (22 samples), in Central and Southern Thailand, respectively. Twenty-four of the 288 isolated arsenic-resistant bacteria were found to be arsenite-oxidizing bacteria. On the basis of their morphological, cultural, physiological, biochemical and chemotaxonomic characteristics, and supported by phylogenetic analysis based upon their 16S rRNA gene sequences, they were divided into five groups, within the genera Acinetobacter, Flavobacterium, Pseudomonas, Sinorhizobium and Sphingomonas, respectively. Within genera, phylogenetic analysis using the 16S rRNA gene sequences suggested that they were comprised of at least ten species, five isolates being closely related to known bacteria (Acinetobacter calcoaceticus NCCB 22016^T, Pseudomonas plecoglossicida FPC951^T, Ps. knackmussii B13^T, Sinorhizobium morelense Lc04^T, and Sphingomonas subterranea IFO16086^T). The other five proposed species are likely to be new species closely related to Flavobacterium johnsoniae, Sinorhizobium morelense, Acinetobacter calcoaceticus and Pseudomonas plecoglossicida, but this awaits further characterization for confirmation of the taxonomic status. No overlap in isolated species or strains was observed between the two sites. The strain distribution and characterization are described.     

Phylogenetic relationships of graminicolous downy mildews based on cox2 sequence data

Graminicolous downy mildews (GDM) are an understudied, yet economically important, group of plant pathogens, which are one of the major constraints to poaceous crops in the tropics and subtropics. Here we present a first molecular phylogeny based on cox2 sequences comprising all genera of the GDM currently accepted, with both lasting (Graminivora, Poakatesthia, and Viennotia) and evanescent (Peronosclerospora, Sclerophthora, and Sclerospora) sporangiophores. In addition, all other downy mildew genera currently accepted, as well as a representative sample of other oomycete taxa, have been included. It was shown that all genera of the GDM have had a long, independent evolutionary history, and that the delineation between Peronosclerospora and Sclerospora is correct. Sclerophthora was found to be a particularly divergent taxon nested within a paraphyletic Phytophthora, but without support. The results confirm that the placement of Peronosclerospora and Sclerospora in the Saprolegniomycetidae is incorrect. Sclerophthora is not closely related to Pachymetra of the family Verrucalvaceae, and also does not belong to the Saprolegniomycetidae, but shows close affinities to the Peronosporaceae. In addition, all GDM are interspersed throughout the Peronosporaceae s lat., suggesting that a separate family for the Sclerosporaceae might not be justified.     

Patterns in the distribution of myctophid fish in the northern Scotia Sea ecosystem

The mesopelagic fish community of the northern Scotia Sea was investigated during the austral autumn using multi-frequency acoustics, opening and closing nets and pelagic trawls fished from the surface to 1,000 m. The Family Myctophidae (15 species in 5 genera) dominated the ichthyofauna, with larval notothenids caught over the South Georgia shelf and bathylagids and stomiids abundant in deeper hauls. The biomass of myctophids was estimated to be 2.93 g wet weight 1,000 m⁻³, with Electrona carlsbergi, E. antarctica, Protomyctophum bolini, P. choriodon, Gymnoscopelus braueri, G. fraseri, G. nicholsi and Krefftichthys anderssoni, being the most abundant species. Analysis of community structure indicated a high level of depth stratification within the myctophids, with evidence of diurnal vertical migration in some, but not all, species. Length-frequencies of G. braueri, G. nicholsi, E. antarctica and K. anderssoni were multimodal, suggesting that all life stages may be present in the northern Scotia Sea. In contrast, P. choriodon, P. bolini, G. fraseri and E. carlsbergi had unimodal distributions despite having multi-year lifecycles, indicating that they probably migrate into the region from warmer areas to the north.     

An attempt to clarify taxonomic relationships in ``Verwandtschaftskreis der Gattung Ligusticum' (Umbelliferae-Apioideae) by molecular analysis

Relationships among the taxa of Umbelliferae, presumably close to Ligusticum and Selinum were investigated by two independent molecular taxonomic methods. 134 ITS 1-2 sequences were analyzed (29 new and 2 reinvestigated species) and immunochemical comparison of storage seed proteins for 38 species of Apioideae of Ligusticum affinity was performed, eight reference systems (antisera) were used. Both approaches yield similar results, showing the extremely polyphyletic nature of this group and some large genera (Ligusticum s.l., Selinum s.l., Pachypleurum) in the Umbelliferae. The independent status of the genera Magadania, Sphaenolobium, Arafoe, Lomatocarpa, Dimorphosciadium and some other segregates of Ligusticum, Cnidium and Selinum have been confirmed, but Cnidium proved to be unnatural even as currently circumscribed. In the group of East Asian taxa the genera Oreocome, Ligusticopsis, Cortia and Cortiella appeared to be closely related. Haplosphaera was shown to be a genus of Hansenia-Notopterygium group.     

Host range of an NPV and a GV isolated from the common cutworm, Agrotis segetum: pathogenicity within the cutworm complex

The term cutworm covers a range of species with a similar life history that can be very damaging pests on a wide range of crops. Attacks by cutworms are often made up of more than one species; thus, the most cost effective microbial control agent needs to be pathogenic for multiple species within this complex. In this study we investigate the host range of Agrotis segetum NPV and A. segetum GV for other cutworm species and closely related Noctuinae. Eight species, A. segetum, Agrotis ipsilon, Agrotis exclamationis, Agrotis puta, Noctua comes, Peridroma saucia, Xestia sexstrigata, and Xestia xanthographa, were clearly susceptible to AgseNPV, which was confirmed by DNA analysis. Aglais urticae, Diarsia rubi, Noctua pronuba, and Xestia c-nigrum were not susceptible to AgseNPV at the doses used. Noctua fimbriata, Noctua janthina, and Ochroplura plecta gave ambivalent results: larvae died of NPV infection when they were challenged with AgseNPV, but these individuals only produced weak positives in a squash blot analysis and there was insufficient DNA for confirmation by restriction endonuclease profiling. These ambivalent results could suggest either a weak infection by AgseNPV or partial homology between their own virus and AgseNPV. The untreated control insects of several species died of NPV infection, which indicates that these field-collected insects were probably carrying a vertically transmitted NPV. Fewer species were tested with AgseGV and only N. pronuba and N. comes were susceptible. N. fimbriata and Helicoverpa armigera were not susceptible to AgseGV.     

In-vitro anti-<Emphasis Type="Italic">Vibrio</Emphasis> spp. activity and chemical composition of some Tunisian aromatic plants

The chemical composition of five aromatic plants (Mentha longifolia, M. pulegium, Eugenia caryophyllata, Thymus vulgaris and Rosmarinus officinalis) frequently used in food preparation in Tunisia was analysed by GC-MS. The antimicrobial effect of the essential oils obtained from these plants was tested against Vibrio alginolyticus, Vibrio parahaemolyticus, Vibrio vulnificus and Vibrio fluvialis strains. Thyme oil exhibited a high level of antimicrobial activities against Vibrio spp. strains. The diameter of the zones of growth inhibition for V. parahaemolyticus species was interestingly high (ranging from 14.66 to 28 mm). The MIC and MBC values were interestingly low for thyme oil (MIC 0.078–0.156 mg/ml) and (MBC >0.31–1.25 mg/ml). These results showed that these plants especially thyme and clove, can be to be used for seafood preparation to protect against contamination by Vibrio spp. strains. An erratum to this article can be found at     

A study on the effects of some laboratory-derived genetic mutations on biofilm formation by Listeria monocytogenes

Biofilms formed by the human pathogen Listeria monocytogenes in food-processing environments can be a potential source of contamination. In this study, we investigated the ability of L. monocytogenes wild type and its laboratory-derived isogenic mutants in cwhA, prfA, agrA, flaA, degU, ami and sigB to adhere to and form biofilms on abiotic surfaces. The results suggest that inactivation of the two component regulatory system degU completely abolished biofilm formation, while inactivation of the flagellar gene flaA, two component response regulator agrA and the autolysin-adhesin gene ami lead to severe impairment of initial attachment and the subsequent development of a mature biofilm by L. monocytogenes. Mutants in the global regulator of virulence prfA and the alternative sigma factor sigB were unaffected and formed biofilms similar to wild type L. monocytogenes.     

Molecular phylogeny and systematics of Genista (Leguminosae) and related genera based on nucleotide sequences of nrDNA (ITS region) and cpDNA (trnL-trnF intergenic spacer)

Phylogenetic relationships of Genista and related genera (Teline, Chamaespartium, Pterospartum, Echinospartum, Ulex, Stauracanthus and Retama) were assessed by the analysis of sequences of the nrDNA internal transcribed spacer (ITS region), and the cpDNA trnL-trnF intergenic spacer. The tree obtained by combining both sets of data indicates the existence of three lines of diversification within Genista, that correspond to three subgenera: Genista, Phyllobotrys and Spartocarpus, however, each of these lineages encompass also species of the related genera Echinospartum, Teline, Retama, Chamaespartium, Pterospartum, Ulex, Stauracanthus. The molecular data do not support division of these subgenera into taxonomical units at the sectional level; only sections Genista and Spartocarpus are monophyletic groups. The sequences of both regions are also informative at the specific level, grouping morphologically related species (e.g. the G. cinerea aggregate). The molecular data have also helped to clarify the position of taxa whose relationships were not well established (e.g. G. valdes-bermejoi). The relationships of related genera that belong to the Genista lines of diversification have also been investigated. Echinospartum splits into two separate clades matching the separation of two ecological and caryological differentiated groups. Teline also forms two groups, both placed near to Genista subgenus Genista, but that separated from the main core of the group. Retama, morphologically well differentiated from Genista, is close to Genista subgenus Spartocarpus. Chamaespartium and Pterospartum do not form a monophyletic group. Chamaespartium is closer to Genista subgenus Genista, whereas Pterospartum stands close to: 1) Genista subgenus Spartocarpus (particularly, sect. Cephalospartum); and 2) the Ulex-Stauracanthus clade (a terminal derivative of Genista subgenus Spartocarpus). Cases of incongruence (e.g. Echinospartum, Chamaespartium, Teline) between the trees obtained from the two molecular markers, may be indicating hybridisation and/or introgression between different lines of Genisteae.     

Microbial pathogens with impaired ability to acquire host iron

Successful microbial pathogens must be adept in obtaining growth-essential iron from healthy hosts. Some potential pathogens, however, are sufficiently impaired in iron acquisition ability so as to be dangerous mainly in hosts with such iron loading conditions as alcoholism, asplenia, hemochromatosis, -thalassemia major, or tobacco smoking. The association of six impaired pathogens (Capnocytophaga canimorsis, Yersinia enterocolitica and Y. pseudotuberculosis, Vibrio vulnificus, Tropheryma whippelii, and Legionella pneumophila) with iron loaded humans is described.     

Taxonomic and phylogenetic analysis of Saprolegniaceae (Oomycetes) inferred from LSU rDNA and ITS sequence comparisons

The aim of this study was to improve our knowledge about the taxonomy and phylogeny of the family Saprolegniaceae, a group of water molds including several pathogens of plants, fish and crustacea. ITS and LSU rDNA were sequenced for representatives of forty species corresponding to ten genera (Achlya, Aphanomyces, Brevilegnia, Dictyuchus, Leptolegenia, Plectospira, Pythiopsis, Saprolegnia, Thraustotheca). Phenetic and cladistic analyses were then carried out. The species Brevilegnia bispora does not appear to belong to the family Saprolegniaceae. Plectospira myrianda clusters with Aphanomyces spp. and they constitute an ancestral group. (Thraustotheca clavata is closely related to the eccentric species of the genus Achlya. The genus Achlya appears polyphyletic, corroborating more or less the three known subgroups, defined by their sexual spore type (eccentric, centric and subcentric). The achlyoid type of spore dehiscence, shared by Aphanomyces and Achlya genera, is shown to be an ancestral character. The saprolegnioid, dictyoid and thraustothecoid types of spore dehiscence are derived characters but their relative evolutionary positions are not resolved.     

Hybridisation,genomic constitution and generic delimitation inElymus s. l. (Poaceae: Triticeae)

Intergeneric crosses were made between representatives of the genomically-defined generaElymus, Agropyron, Elytrigia, Pseudoroegneria, andThinopyrum. The genomic constitution ofElytrigia repens, the type species ofElytrigia, is shown to be SSH, a genomic combination otherwise found only inElymus. The S genome ofPseudoroegneria has almost always a dominant influence on the morphology of the taxa of which it is a component.Wang (1989) showed that the J genome inThinopyrum and the S genome have considerable homoeology, with a mean c-value of 0.35 in diploid SJ hybrids. A genetic coherence from S to SJ^e, J^e, J^eJ^b, and J^b can be expected, agreeing with the continuous morphologic variation pattern observed. Because of the absence of morphological discontinuities between the taxa,Pseudoroegneria (S),Elymus (SH, SY, sometimes with additional genomes),Elytrigia (SSH, SSHX), andThinopyrum (SJ, SJJ, J) are best treated as a single genus,Elymus, following the generic concept ofMelderis in Flora Europaea and Flora of Turkey. The basic genomic constituents ofElymus will then be the S and/or J genomes.Agropyron, with diploids, tetraploids, and hexaploids based on the P genome is morphologically distinct from other genera inTriticeae. In a few species ofElymus andPseudoroegneria, a P genome is an additional constituent. In these cases the P genome has a negligible morphological influence. Therefore, it seems reasonable to maintainAgropyron as a separate genus.