Notes onOrdus chiayiensis in Tsukuba

Ordus chiayiensis isolated from discolored red pine needles is redescribed and illustrated.     

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.     

A molecular phylogeny of Hebeloma species from Europe

In order to widen the scope of existing phylogenies of the ectomycorrhizal agaric genus Hebeloma a total of 53 new rDNA ITS sequences from that genus was generated, augmented by sequences retrieved from GenBank, and analysed using Bayesian, strict consensus and neighbour joining methods. The lignicolous Hebelomina neerlandica, Gymnopilus penetrans, and two species of Galerina served as outgroup taxa. Anamika indica, as well as representatives of the genera Hymenogaster and Naucoria, were included to test the monophyly of Hebeloma, which is confirmed by the results. Hebeloma, Naucoria, Hymenogaster and Anamika indica cluster in a strongly supported monophyletic hebelomatoid clade. All trees largely reflect the current infrageneric classification within Hebeloma, and divide the genus into mostly well-supported monophyletic groups surrounding H. crustuliniforme, H. velutipes, H. sacchariolens, H. sinapizans, and H. radicosum, with H. sarcophyllum being shown at an independent position; however this is not well supported. The section Indusiata divides with strong support into three groups, the position of the pleurocystidiate Hebeloma cistophilum suggests the possible existence of a third subsection within sect. Indusiata. Subsection Sacchariolentia is raised to the rank of section.     

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.     

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.     

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.     

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.     

Phylogeny of cardinalfishes (Teleostei: Gobiiformes: Apogonidae) and the evolution of visceral bioluminescence

The cardinalfishes (Apogonidae) are a diverse clade of small, mostly reef-dwelling fishes, for which a variety of morphological data have not yielded a consistent phylogeny. We use DNA sequence to hypothesize phylogenetic relationships within Apogonidae and among apogonids and other acanthomorph families, to examine patterns of evolution including the distribution of a visceral bioluminescence system. In conformance with previous studies, Apogonidae is placed in a clade with Pempheridae, Kurtidae, Leiognathidae, and Gobioidei. The apogonid genus Pseudamia is recovered outside the remainder of the family, not as sister to the superficially similar genus Gymnapogon. Species sampled from the Caribbean and Western Atlantic (Phaeoptyx, Astrapogon, and some Apogon species) form a clade, as do the larger-bodied Glossamia and Cheilodipterus. Incidence of visceral bioluminescence is found scattered throughout the phylogeny, independently for each group in which it is present. Examination of the fine structure of the visceral bioluminescence system through histology shows that light organs exhibit a range of morphologies, with some composed of complex masses of tubules (Siphamia, Pempheris, Parapriacanthus) and others lacking tubules but containing chambers formed by folds of the visceral epithelium (Acropoma, Archamia, Jaydia, and Rhabdamia). Light organs in Siphamia, Acropoma, Pempheris and Parapriacanthus are distinct from but connected to the gut; those in Archamia, Jaydia, and Rhabdamia are simply portions of the intestinal tract, and are little differentiated from the surrounding tissues. The presence or absence of symbiotic luminescent bacteria does not correlate with light organ structure; the tubular light organs of Siphamia and chambered tubes of Acropoma house bacteria, those in Pempheridae and the other Apogonidae do not.     

Die GattungKarschia — Bindeglied zwischen bitunicaten Ascomyceten und lecanoralen Flechtenpilzen?

The genusKarschia, in the earlier sense, including saprophytes and parasites on lichens, has been thought to be a non-lichenized parallel genus of the lichen genusBuellia. Modern workers included it on the one hand inBuellia, on the other hand combined it with bitunicate ascomycetes. It is now proved thatKarschia is heterogeneous and contains but superficially similar members both of the genusBuellia of theLecanorales and of typical or masked bitunicateAscomycetes. Therefore, it can not be regarded as a link betweenLecanorales andDothideales. The type species ofKarschia belongs to theDothideales.

     

Phylogeny and classification ofFumariaceae, with emphasis onDicentra s. l., based on the plastid generps16 intron

The phylogeny ofFumariaceae, as inferred fromrps16 intron sequences, is compared with morphological data, and nrDNA-ITS. The different data sets are largely congruent and indicate that (1)Dicentra and the tribeCorydaleae as hitherto circumscribed are polyphyletic, (2)Lamprocapnos (=Dicentra spectabilis) is sister group to the rest of subfam.Fumarioideae, (3)Ehrendorferia, gen. nov. (=Dicentra chrysantha andD. ochroleuca) is basal in the latter group, (4) the morphologically aberrantIchtyoselmis, gen. nov. (=Dicentra macrantha) groups withDicentra s. str., (5) the genusCysticapnos should be included in the tribeFumarieae, (6)Dactylicapnos (=Dicentra subg.Dactylicapnos) is sister group toCorydalis, (7) the genusCorydalis is monophyletic, and consists of three subgenera:Chremnocapnos, stat. nov.,Sophorocapnos, stat. nov., andCorydalis. The following new combinations are validated:Ehrendorferia chrysantha, E. ochroleuca, Ichtyoselmis macrantha, andLamprocapnos spectabilis. Dedicated to emer. Univ.-Prof. DrFriedrich Ehrendorfer on the occasion of his 70th birthday     

Hyphomorpha als Phycobiont in Flechten

Hyphomorpha, a genus of theStigonematales, is confirmed to be a phycobiont in twoSpilonema species (Coccocarpiaceae). The morphology of the symbiotic algae inSpilonema dendroides andS. schmidtii is described. The phycobiont inS. dendroides is possiblyHyphomorpha antillarum, the alga inS. schmidtii might be a species related toH. perrieri. New localities for the rare lichens are reported: Alaska forS. dendroides and Ceylon forS. schmidtii.

     

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 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.     

Nomenclatural changes in <Emphasis Type="Italic">Lithospermum</Emphasis> (Boraginaceae) and related taxa following a reassessment of phylogenetic relationships

Lithospermum (Boraginaceae) comprises approximately 40 species in both the Old and New Worlds, with a center of diversity in the southwestern United States and Mexico. Using ten cpDNA regions, a phylogeny of Lithospermum and related taxa was reconstructed. Lithospermum (including New World and Old World species) and related New World members of Lithospermeae form a monophyletic group, with Macromeria, Onosmodium, Nomosa, Lasiarrhenum, and Psilolaemus nested among species of Lithospermum. New World Lithospermeae also is a monophyletic group, with Eurasian species of Lithospermum sister to this group. Because Lithospermum is not monophyletic without the inclusion of the other New World genera, species from these genera are transferred to Lithospermum, and appropriate nomenclatural changes are made. New combinations are Lithospermum album, Lithospermum barbigerum, Lithospermum dodrantale, Lithospermum exsertum, Lithospermum helleri, Lithospemum leonotis, Lithospermum notatum, Lithospermum oaxacanum, Lithospermum pinetorum, Lithospermum rosei, Lithospermum trinverium, and Lithospermum unicum; new names are Lithospermum chiapense, Lithospermum johnstonii, Lithospermum macromeria, Lithospermum onosmodium, Lithospermum rzedowskii, and Lithospermum turneri.     

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.     

Interaction dynamics between saprobic lignicolous fungi and Armillaria in controlled environments: Exploring the potential for competitive exclusion of Armillaria on peach

Armillaria root rot, caused by Armillaria tabescens and Armillaria mellea, is a major cause of premature tree death in peach orchards in the southeastern United States. The root systems of infected trees can become entirely colonized by Armillaria, serving as an inoculum source for adjacent trees and providing massive inoculum levels in replant situations. If dead or dying trees could be colonized by an effective competitor of Armillaria before their removal, the extent of root colonization by the pathogen could be reduced, thus decreasing the threat to adjacent trees and/or subsequent plantings. Interactions between five species of saprobic lignicolous fungi (Ganoderma lucidum, Hypholoma fasciculare, Phanerochaete velutina, Schizophyllum commune, and Xylaria hypoxylon) and the two Armillaria species were examined in controlled conditions to provide proof of concept for competitive exclusion of Armillaria from peach roots. On agar-coated glass slides, all five potential antagonists induced detrimental reactions in >58% of the Armillaria hyphae observed, with the majority resulting in hyphal swelling or granulation. On poplar wood blocks, all antagonists consistently either overgrew Armillaria colonies or—in the case of S. commune—engaged in deadlock reactions; in all cases, the viability of Armillaria colonies was reduced to <30% of that of unchallenged controls. When inoculated simultaneously onto opposite ends of peach root segments, all antagonists consistently reduced growth and viability of Armillaria on and under the bark, whereby reduction of pathogen growth underneath the bark, Armillaria’s primary ecological niche, was most pronounced for G. lucidum, S. commune, and X. hypoxylon. When root segments were allowed to be colonized entirely by Armillaria before being inoculated with the antagonists, the latter were able to overgrow the pathogen on the root surface but unable to pre-empt it from underneath the bark. In summary,G. lucidum, S. commune, and X. hypoxylon caused strong hyphal and mycelial interference reactions and the most pronounced reductions in growth of Armillaria above and below the bark, indicating that they would be the most promising candidates for field-scale evaluations to restrict colonization of dead or dying peach trees by Armillaria in the orchard.