This issue of Mycological Research News features: European Mycological Association (EMA) founded; and Sudden death of soybean.

Molecular phylogenetic papers in this issue consider the relationships of Phytophthora ramorum, the circumscription of the Amphisphaeriaceae, the placement of Tholurna, comparisons between polyketide synthase gene and ITS sequences in Lecanora, the separtion of Aspergillus sect. Flavi species, the identification of Armillaria isolates in Japan, the occurrence of group 1 E introns in Gondwanamyces proteae and other fungi, and the fungi associated with Fucus serratus.

In addition, Trichoderma aggressivum f. aggressivum is shown to produce 3,4-dihydro-8-hydroxy-3-methylisocoumarin which inhibits Agaricus bisporus mycelium growth, five models designed to describe the growth of entomopathogenic fungi are tested against data from four species, and the dynamics of Rhynchosporium secalis pathotypes on different cultivars are explored.

No new scientific names are introduced in this part.

Sudden oak death has been an emerging disease problem in coastal California and has caused significant losses in forest ecosystems in some regions of the state. The causal agent of this disease has been described as Phytophthora ramorum with two other less aggressive species, P. nemorosa and P. pseudosyringae, recovered from some symptomatic plants. The phylogenetic relationship of these species with other members of the genus was examined by sequence alignment of 667 bp of the mitochondrially-encoded cytochrome oxidase II gene and the nuclear encoded rDNA internal transcribed spacer region. P. ramorum was most closely related to P. hibernalis and P. lateralis in trees from both regions, although the specific relationship among species differed depending on the tree. In the cox II tree these species were on a single clade with P. lateralis basal to a group containing P. ramorum and P. hibernalis. On the maximum parsimony ITS tree P. ramorum was most closely affiliated with P. lateralis and in the same clade as P. hibernalis, but with maximum likelihood analysis P. ramorum was basal to a grouping of P. hibernalis and P. lateralis. While bootstrap support was strong for the grouping of these species together, it was not for determining the relationship among them. In contrast to the cox II tree, the clade containing these three species grouped with P. cryptogea, P. drechsleri, P. erythroseptica, and P. syringae in the ITS tree. Since the same isolates of these species were used for both the cox II and ITS sequence analysis, this difference in species grouping suggests either a differential rate of evolutionary divergence for these two regions, incorrect assumptions about alignment of ITS sequences, or different evolutionary histories of the regions under study. Analysis of combined cox II and ITS data sets gave trees where the relationships among these species were the same as for the ITS tree alone, although the results of the partition homogeneity test (P=0.072) suggest caution should be used in interpretation of this data. All analyses supported a close relationship between P. ilicis, P. nemorosa and P. pseudosyringae, although the analysis did not clarify the evolutionary relationships among these three species. Interestingly, these three species had a unique 6 bp deletion in the cox II gene just before the termination codon. While there was some similarity in phylogenetic grouping of these species and morphological characteristics, this was not consistent across all comparisons in the genus. Data would suggest that P. ramorum, P. nemorosa and P. pseudosyringae are phylogenetically distinct new species and not the result of interspecific hybridization.

The Amphisphaeriaceae is an important family of ascomycetes within the Xylariales. There has been, however, disagreement regarding the taxonomic placement of many genera within this family and whether it should be confined to ascomycetes producing Pestalotiopsis-like anamorphs. In this study, phylogenetic relationships among members of the Amphisphaeriaceae are investigated using partial sequences of the 28S rDNA. Molecular data provided further evidence to support the association of several coelomycetous genera with the ascomycetous Amphisphaeriaceae. Phylogenetic analyses also show that all ascomycetous genera possessing Pestalotiopsis-like anamorphs are monophyletic and confirm the anamorphic-teleomorphic connections of some. There is, however, insufficient evidence to support the restriction of Amphisphaeriaceae to genera, which produce Pestalotiopsis-like anamorphs, because the phylogenetic placement of Amphisphaeria umbrina is not fully resolved and its affinities with other members received low bootstrap support. The results also indicate that Iodosphaeria and Arecophila should be excluded from the Amphisphaeriaceae. The placement of Lanceispora in the Amphisphaeriaceae is doubtful. A broad concept of the family Amphisphaeriaceae is advocated until further data are available.

The phylogenetic relationships of Tholurna dissimilis were investigated in relation to a phylogeny of twenty-three species in Caliciaceae and eighteen species from Physciaceae. ITS and LSU regions of the nuclear ribosomal DNA were used for the reconstruction of phylogenies by maximum parsimony methods. Calicium adaequatum was shown to be the closest relative of and possibly congeneric with Tholurna. Calicium is thus not monophyletic unless Tholurna is included. Calicium in the molecular phylogeny contains several distinct clades, which to some extent can be characterized morphologically. Cyphelium in a traditional sense is probably not monophyletic. Cyphelium s. str. has immersed apothecia, large smooth spores and a very thin excipulum throughout. C. inquinans and C. karelicum, which form a distinct and highly supported clade, may be accommodated in Acolium, possibly along with other Cyphelium and Calicium species. The phylogenies presented here do not support the recognition of neither Physciaceae nor Caliciaceae in a narrow sense, but they also do not exclude this. Numerous spliceosomal and unclassified insertions were found in the LSU sequences. They to some extent offered phylogenetic information both with respect to location and by their sequence similarities.

The ketosynthase domains of putative polyketide synthase (PKS) genes from 15 species in the lichenized genus Lecanora as well as three representatives of other genera were amplified and sequenced using conserved primers. A phylogenetic analysis was carried out with the corresponding amino acid sequences, including those of non-lichenized fungi. The phylogenetic hypothesis places all PKS sequences from Lecanora and the other genera in a clade of PKSs that produce complex aromatic compounds. The PKSs from Lecanora are found in two distinct clades. One of these forms a monophyletic group with PKSs producing precursors of dihydroxy naphthalenes from non-lichenized species. This includes PKSs from the L. rupicola group and several other species which are not closely related. The other clade represents at least one functionally different protein and has no close relationships with known PKSs from other fungi. A comparison between an ITS phylogeny of the species with their DNA sequences of ketosynthase domains reveals similar PKS genes in certain closely related species. Coevolution was unapparent in other clades, suggesting the presence of paralogous genes.

Twenty-four isolates of Aspergillus sojae, A. parasiticus, A. oryzae and A. flavus, including a number that have the capacity to produce aflatoxin, have been compared using amplified fragment length polymorphisms (AFLPs). Based on analysis of 12 different primer combinations, 500 potentially polymorphic fragments have been identified. Analysis of the AFLP data consistently and clearly separates the A. sojae/A. parasiticus isolates from the A. oryzae/A. flavus isolates. Furthermore, there are markers that can be used to distinguish the A. sojae isolates from those of A. parasiticus, which form the basis for species-specific markers. However, whilst there were many polymorphisms between isolates within the A. oryzae/A. flavus subgroup, no markers could be identified that distinguish between the two species. Sequencing of the ribosomal DNA ITS (internal transcribed spacers) from selected isolates also separated the A. sojae/A. parasiticus subgroup from the A. oryzae/A. flavus subgroup, but was unable to distinguish between the A. sojae and A. parasiticus isolates. Some ITS variation was found between isolates within the A. oryzae/A. flavus subgroup, but did not correlate with the species classification, indicating that it is difficult to use molecular data to separate the two species. In addition, sequencing of ribosomal ITS regions and AFLP analysis suggested that some species annotations in public culture collections may be inaccurate.

Polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) analysis of the first intergenic region (IGR1) of nuclear ribosomal DNA was used to clarify the relationship between IGR1 variations and six Japanese biological species of Armillaria: A. gallica, A. nabsnona, A. ostoyae, A. cepistipes, A. mellea and Nagasawa's E (Nag. E: taxonomically unknown species). The procedure was then used to identify Armillaria species associated with Wynnea species (W. americana and W. gigantea) and Entoloma abortivum. By combining the RFLP patterns obtained using three endonucleases, HaeIII, HinfI and MspI, the IGR1s from 18 isolates of six Armillaria species were assigned to nine different RFLP phenotypes and the six species were distinguished from each other. Each of the RFLP phenotypes from the Armillaria isolates associated with Wynnea species or E. abortivum matched a corresponding phenotypes observed among the six Armillaria species. Based on this, all four isolates from W. gigantea were identified as A. mellea, two from W. americana as A. cepistipes, and all three from E. abortivum as Nag. E. These results provide new information on the biological species of Armillaria associated with Wynnea and E. abortivum.

During a phylogenetic study of ophiostomatoid fungi, a group I intron-like sequence was noted in the SSU rDNA gene of Gondwanamyces proteae. Secondary structure and sequence characteristics assigned the intron to the I E class. We then examined 27 related Group I-like sequences deposited in GenBank, and as a result 15 additional and previously uncategorized I E rDNA introns were identified. This study, with other recent publications, suggests that the I E class might represent a major family of group I introns that are located within the nuclear SSU and, to some extent LSU, genes in fungi.

The association of ascomycetes with Fucus serratus was investigated by comparing the broad-based molecular and cultural diversities of healthy and dead fronds. Four PCR primer pairs were used to amplify the 18S (primers NS1-FR1; NS1-EF3) or 28S rRNA (primers NL209-NL912; NL359-NL912) genes directly from the DNA of algal thalli. Two novel primer pairs, NL209-NL912 and NL359-NL912 giving product sizes of 700 and 559 bp respectively, were designed to amplify the 28S rDNA from ascomycetes specifically. All primer combinations amplified DNA from 33 reference taxa isolated from Fucus serratus, and the products generated by primers NS1-FR1GC and NL359-NL912GC were separated in 18–38% and 38–60% denaturant gradients respectively after DGGE. The 18S rDNA DGGE system resolved eight bands from algal DNA, but many of the sequences separated were not fungal, whereas the 28S rDNA system resolved seven bands that were all identified as ascomycetes. Phylogenetic analysis and BLAST search results of environmental sequences revealed the presence of four main ascomycete groups: (1) the Halosphaeriales, (2) the Hypocreales, (3) an unidentified Lulworthiales complex, and (4) the Pleosporales. Few fungal isolates were detected molecularly suggesting that fungal colonisation of fronds was limited, mainly to species in dead casts.

Trichoderma harzianum is a ubiquitously distributed asexual soil fungus that produces a variety of antibiotic compounds. Colonisation of soil inhabited by competing microbiota is facilitated by the antibiotic activity of these compounds. In addition, T. harzianum produces hydrolytic enzymes that degrade the cell wall components of many microorganisms, which can then be used as a source of nutrients. Recently, biotypes of T. harzianum differing morphologically from those originally described by Rifai were isolated on commercial mushroom (Agaricus bisporus) farms. These ‘aggressive’ biotypes cause devastating crop loss on mushroom farms. The aggressive biotype in North America was originally known as ‘Th4’ but has been recently renamed Trichoderma aggressivum f. aggressivum. In contrast, ‘non-aggressive’ biotypes, have no noticeable effect on the crop, are similar to T. harzianum and are commonly found on mushroom farms. The mechanism of disease establishment is unknown. We have identified a metabolite produced by T. aggressivum isolates in vitro that inhibits growth of A. bisporus and other fungi. This antifungal compound is not produced by ‘non-aggressive’ T. harzianum isolates under the culture conditions tested and is identified as 3,4-dihydro-8-hydroxy-3-methylisocoumarin. Another compound was isolated from both liquid culture and infested compost. Although its chemical structure could not be precisely determined, this compound also inhibits A. bisporus growth, is predominant in infested compost and likely has a inhibitory effect on the mycelia present in mushroom compost, resulting in devastating crop loss.

Five non-linear models with three to five parameters, built to quantify the effect of temperature on insect development and microbial growth, were tested to describe the influence of temperature on in vitro-measured growth rates of entomopathogenic hyphomycetes. Data from two isolates of each of the four fungal species, Paecilomyces fumosoroseus, Beauveria bassiana, Metarhizium anisopliae, Metarhizium flavoviride, were used to assess the features of each model. Criteria for model evaluation included the statistical quality of parameters estimates, the goodness of fit to data, as well as the ability to provide estimates of several key parameters: the upper and lower development thresholds, the thermal optimum and the maximal growth rate at thermal optimum. The second model proposed by Brière et al. (1999) was found to be the best, and Ratkowsky's model (1983) also exhibited good features.

Rhynchosporium secalis isolates E97-2 and H97-2, represented the major pathotypes in populations on barley in Alberta, Canada, but differed widely in their virulence. Following greenhouse co-inoculation with the two pathotypes, E97-2, originally isolated from resistant cv. ‘CDC Earl’, predominated over H97-2, isolated from the susceptible cv. ‘Harrington’, from the first to the last of four infection cycles on both ‘CDC Earl’ and ‘Harrington’. These results indicated that the host can rapidly influence pathotype composition and that pathotype E97-2 may have a competitive advantage over H97-2 on these cultivars. DNA polymorphisms were found between isolates from single or mixed inoculations on cvs ‘CDC Earl’ and ‘Harrington’ for four successive cycles. Co-inoculation with the two isolates resulted in a shift to a molecular phenotype more similar to E97-2 than H97-2. The competitive advantage of E97-2 over H97-2, combined with the selective pressure exerted by the host, would explain the increased susceptibility of cv. ‘CDC Earl’ and other cultivars with similar sources of scald resistance, in fields across Alberta. However, H97-2 will likely remain one of the major pathotypes in Alberta due to the relatively large acreage of cv. ‘Harrington’ in this province.

In the paper by M. Morretti, A. Arnoldi, A. D'Agostina, G. Farina & F. Gozzo on the ‘Characterization of field isolates and derived DMI-resistant strains of Cercospora beticola’, in Fig. 2 there is an error in the formula of 14α-methyl-3,6-diol: an -OH group was omitted in the C6 position.