This month Mycological Research News features the role of fungi in black boxes and missing sinks in global climate change research, and the collective terms suggested for the fungi present in any geographical situation or eological niche (i.e. funga, mycota, and mycobiota).

The issue includes a review of species concepts in lichen-forming fungi in the light of new molecular insights. The 15 other papers cover diverse aspects of mycology. Molecular data shows that the Peronosporomycetes comprise two main groups and the ordinal placement of some genera needs reconsideration. The generic separations in the Cystotheceae of the Erysiphales also need rethinking as molecular data are at variance with some morphological features. Alternaria and its allies have been reassessed, and at the infraspecific level molecular information on Ophiostoma novo-ulmi in North America, and Pythium irregulare from diverse sources is provided. Differences in endopolygalacturonase activity in Fusarium relate to its regulation and expression.

The biological relationships of the Dacampiaceae with its lichen hosts are examined, and the activity and metabolites of fungi from marine sponges investigated. Variation in heavy metal tolerance of ectomycorrhizas is studied in vitro, and the relationships of two ectomycorrhizal fungi with Pinus sylvestris explored by molecular and anatomical approaches.

Ultrastructural papers include ones on the development of basidiospores in Tricholosporum, and the location of chitin in the different spore stages of Cronartium ribicola.

A world monograph of Amorphomyces is presented, and the following new fungal taxa are described in this issue: Torrentispora gen. nov.; and Amorphomyces hernandoi, Dactylaria cazorlii, Hansfordia catalonica, and T. fibrosa spp. nov.

The concept of species and species complexes of lichenized fungi is reviewed in the light of recent molecular approaches. Species concepts based on chemistry, morphology, reproductive mode, photobiont choice and habitat preference provide working hypotheses from which the delimitation of species or relationships within species complexes can be tested with molecular data. In studies in which a single locus such as ITS is used, a phylogenetic species concept can be applied only when the sequence data delimits genetically discrete clades that correlate with phenotypic characters or biogeographical distribution. This will be the case when sufficient time has passed for genetic isolation to result in the coalescence of different character states among the sibling species of a complex. In the case of recently diverged species, a single locus may not accurately separate species, and is not sufficient evidence to reject putative species based on a phenotypic species concept. In such cases, several genetic loci must be used to delimit species by a phylogenetic species concept. These phylogenetic species may corroborate phenotypic characters or biogeography, or they may be cryptic for all observed characters. Molecular analyses at the species level will lead to the re-evaluation of phenotypic characters for species delimitation, and will improve the understanding of speciation in lichenized fungi. The results from new molecular approaches have implications for taxonomic revisions. Formal changes in nomenclature based solely on molecular evidence should be made conservatively, and only after studies based on a thorough sampling with sufficient data of all kinds is performed, and after the taxonomic history of the group has been reviewed. In the meantime, informal names to describe new phylogenetic hypotheses are sufficient. Formally named cryptic species cause problems in distributional studies, where old material and literature references are included, but are useful in high resolution studies such as ecophysiology, especially where phenotypic differences may exist among cryptic species.

The phylogeny of the nuclear large ribosomal subunit (LSU) rDNA from Peronosporomycetes (Oomycota) was studied. Five orders Rhipidiales, Leptomitales, Saprolegniales, Pythiales and Peronosporales were included in the study in order to reveal phylogenetic relationships within the group. Based on maximum parsimony, neighbour-joining and maximum-likelihood the Peronosporomycetes seem to have evolved as two major lineages. One lineage includes members of the Rhipidiales, Leptomitales and Saprolegniales and the other includes the members of Pythiales and Peronosporales. However, the inclusion of Rhipidiales in Saprolegniomycetidae was not well supported. Leptomitales were placed basal to the Saprolegniales in the LSU rDNA based tree. In the Saprolegniaceae sensu lato the primary zoospore seems to have been lost several times in the evolution of this family. Species of Aphanomyces were placed on the most basal branch in this family. The obligate parasite, Albugo, was placed on the most basal branch within the Peronosporomycetidae. Phytophthora showed a closer relationship to Peronospora and Peronophythora than to Pythium suggesting that this genus should be removed from Pythiales to Peronosporales.

To understand the evolutionary history of Erysiphaceae tribe Cystotheceae, phylogentic trees were constructed from the nucleotide sequences of the ribosomal DNA internal transcribed spacer of 28 taxa of the fungal ingroup and two outgroup taxa. The first split of the ingroup taxa occurred between a clade composed of the genus Cystotheca and a clade composed of the genera Podosphaera and Sphaerotheca. Podosphaera and Sphaerotheca did not separate into clades. Instead, Podosphaera species parasitic to Prunus and Sphaerotheca section Magnicellulatae grouped together, with the remaining Podosphaera species and Sphaerotheca section Sphaerotheca forming another subclade. Since the first splits were shared by Podosphaera species in both subclades, it was assumed the ancestral features of both subclades were Podosphaera-like and the genus Sphaerotheca derived from a Podosphaera-like ancestral taxon on at least two independent occasions. The results of this study suggest that ancestral fungi of the tribe Cystotheceae were originally arbor-parasitic, and transition from arbor-parasitism to herb-parasitism may have occurred at least twice independently, accompanied by a morphological change of appendages. The mycelioid appendage of the genus Sphaerotheca and other herb-parasitic genera seems to have evolved convergently at multiple times as an adaptation to herb-parasitism.

To elucidate relationships among Alternaria, Ulocladium, and Stemphylium species, nuclear internal transcribed spacer (ITS) and mitochondrial small subunit (SSU) ribosomal DNA (rDNA) sequences from 18 Alternaria, four Ulocladium and four Stemphylium spp. were determined and compared. Phylogenetic analysis of the ITS and SSU rDNA sequences, performed by the neighbour joining and maximum parsimony methods, revealed that the Stemphylium spp. were phylogenetically distinct from the Alternaria and Ulocladium spp. Most Alternaria spp. and the Ulocladium spp. were placed together in a large Alternaria/Ulocladium clade. Within this large clade, the Alternaria spp. clustered into several distinct species-clades, most of which correlated with species-groups previously established based upon morphological characteristics. The Ulocladium spp. were placed into two species-clades, each of which also included Alternaria spp. A. longissima was distantly related to the other Alternaria spp., as well as the Ulocladium and Stemphylium spp. Based upon ITS and nuclear 18S rDNA sequence identities, A. longissima was most closely related to Leptosphaeria.

275 isolates of Ophiostoma novo-ulmi, sampled across the southern Great Lakes region of North America from Wisconsin to Ohio in 1996, were analysed for vegetative compatibility (vc) types. Over 60% of the sample was a clonal vc component, comprising only two vc types (the AMSG and EUSG); the remainder of the sample was highly heterogeneous for vc types. Vc diversity was highest in Indiana and Michigan; close to where NAN O. novo-ulmi probably first appeared in North America. Each vc clone exhibited a uniform RAPD haplotype and a lower frequency of the A compared with the B mating type. This is consistent with the clones being mainly asexually spread, but with a potential for inbreeding, an unusual feature in a ‘genetic clone’. The heterogeneous component, however, exhibited diverse RAPD haplotypes and a near 1[ratio ]1 ratio of A[ratio ]B mating types, indicating that the mainly novel vc types of this component arise via sexual recombination. In Europe, dominant vc clones have been quickly replaced by novel vc types. In the Great Lakes region, however, vc clones appear to have survived for over 50 years despite a high potential for emergence of new vc types via sexual recombination. No differences were found between the clonal and heterogeneous components with regard to growth rate and pathogenicity, two important fitness parameters. Two other factors, a low level of selection imposed by deleterious d-factor viruses and a density dependent effect associated with vegetative incompatibility, may have favoured prolonged survival of the clones in North America.

Forty-seven isolates of Pythium irregulare from different hosts and geographic origins were compared from molecular, morphological and physiological viewpoints. They were divided into four groups (I–IV) based on ITS-RFLP analysis and RAPD analysis. Groups I and II included 32 and eight isolates, respectively, collected from diverse hosts and geographic origins, and groups III and IV comprised seven isolates derived from sugar beet and sugar beet field soil. Group I had smaller oogonia and oospores than did the other three groups. In groups I and II, a significantly higher percentage of the oogonia produced multiple projections compared to groups III and IV which occasionally produced one projection. The growth rate of the four groups was similar at 5–30 °C. At 33°, many isolates of group I grew rapidly but most of the isolates of other groups grew slowly, and at 35°, the former grew but the latter did not. In phylogenetic analysis based on sequences of the ITS region, four groups of P. irregulare were included in one cluster with P. sylvaticum. Groups I–II and III–IV clustered more tightly in the same branch, respectively. The genetic divergence between I–II and III–IV was higher than between each group (I–II and III–IV) and P. sylvaticum, indicating that groups I–II and III–IV may represent two different species.

Polygalacturonase (PG) synthetized by Fusarium spp. is a polymorphic enzyme with complex isoform patterns influenced by culture conditions and which are variable at the intra- and inter-specific levels. The partial sequence of an endopolygalacturonase coding gene (endopg) has been analyzed in isolates of seven species of Fusarium, most of them associated with Pinus pinea. The genomic fragment analyzed, 740 bp long, included two introns and the exon 4, which contained most of the amino acid motifs conserved in PGs from different origins. The high similarity of the amino acid sequences found among the isolates would indicate that differences in amino acid composition are not probably the main reason of the variability of this enzyme. Therefore, differences in the gene expression and regulation patterns of endopg gene among the isolates should be considered. Both types of sequences, the coding and the two intron sequences contained in the endopg fragment, were compared among the isolates to evaluate their potential use for phylogenetic studies. The different levels of variability of these sequences and the similar results obtained from the phylogenetic analyses when the three sequences (coding, intron and amino acid sequences) were used indicate that this endopg region would be very useful for phylogenetic analysis in the genus Fusarium.

The biological relationships of lichenicolous fungi and their hosts are studied in four members of the Dacampiaceae. Infections of the lichenicolous species Dacampia engeliana induce in its host Solorina a thallus morphology similar to that found in the lichenized D. hookeri. D. engeliana, however, differs microscopically by hyphae growing inside those of Solorina in the algal layer and the medulla. Pyrenidium actinellum develops short haustorial structures into the hyphae of the host. These haustoria are characterised by finger-like outgrowths into the host cells. Clypeococcum hypocenomycis forms dense brown mycelia in the upper cortex of the host, which is progressively destroyed. These lichenicolous parasites have a preference for the fungal symbiont of the host lichen and, in contrast to several other lichenicolous fungi, the algal partner is not primarily affected. The various types of infection modes found in the family Dacampiaceae suggest that a great variation of infection modes may exist in further groups of lichenicolous fungi. Other infection types are included in the discussion.

The diversity, biological activity and secondary metabolite production of fungi associated with marine sponges were investigated in order to assess the potential of these fungi for the production of novel biologically active secondary metabolites. 681 fungal strains were isolated from 16 sponge species from six different locations, representing 13 genera of Ascomycota, 2 of Zygomycota, 37 of mitosporic fungi, and 37 strains of sterile mycelium. The spectrum of fungi from each location was dominated by a few genera of mainly mitosporic fungi that are also commonly encountered in terrestrial habitats.

A high proportion of culture extracts of sponge-associated fungi was biologically active in tests to detect antifungal, antialgal, and antibacterial activity, cytotoxicity and inhibition of reverse-transcriptase and tyrosine kinase. The corresponding chemistry was structurally diverse and related to that of terrestrial fungi. From the biologically active culture extracts of five fungal strains, nine pure compounds were isolated in addition to 18 previously reported.

Thirty-nine ectomycorrhizal isolates of Paxillus involutus, Pisolithus tinctorius, Suillus bovinus, S. luteus and S. variegatus were tested on cadmium, copper, nickel and zinc amended media to determine their in vitro tolerance, measured as inhibition of biomass production. Twenty-one isolates were from heavy metal polluted sites, whereas the others were from non-contaminated soils. There was a strong interspecific variation in metal tolerance. S. luteus, S. variegatus and P. tinctorius were more tolerant of Cu, Cd and Zn when compared with P. involutus, whereas the reverse was true for Ni. A high intraspecific heterogeneity in metal tolerance was also found. EC50 values for isolates originating from polluted sites were not statistically different from EC50 values for isolates originating from non-contaminated sites. The findings are discussed in relation to the potential benefits of ectomycorrhizal fungi in protecting their host plants from metal contamination.

Many intimate associations between different species of ectomycorrhizal fungi are inferred on the basis of the consistent co-occurrence of their fruit bodies. Suillus bovinus and Gomphidius roseus, where the latter never occurs without the former, is one example. This association was examined with PCR identification and light microscopy. S. bovinus and G. roseus were unambiguously separated on the basis of RFLPs of the PCR-amplified ITS region of ribosomal DNA. Tuberculate mycorrhizas of Pinus sylvestris sampled under fruit bodies of G. roseus and S. bovinus were investigated and the majority were identified as mixed associations involving both G. roseus and S. bovinus. Tuberculate mycorrhizas, which macroscopically resemble the ones of Suillus species, contained typical chlamydospores of G. roseus and they had haustoria where G. roseus hyphae penetrated the cortical root cells. Pine seedlings collected near the fruit bodies of the two species were mainly colonised by S. bovinus. Mycelial rhizomorphs collected under the fruit bodies of G. roseus were identified as S. bovinus, while both fungal species were present at the base of G. roseus fruit bodies. The significance of these observations and the possibility that G. roseus acts as a parasite are discussed.

The genus Tricholosporum is characterised by cruciate spores. The formation of these basidiospores and their subsequent growth until release from the sterigmata, is described from a sequence of SEM photographs. The spores on a basidium form either a diad, a triad or a tetrad during their development. The outer cell wall layer of the basidiospore enlarges, resulting in the cruciate shape of the spores and the ultimate calyptrate appearance after release when desiccated. The spores are seceded sequentially.

Ultrathin sections of five spore stages of C. ribicola were incubated with wheat germ agglutinin (WGA), which binds to chitin, followed by an ovomucoid-gold complex, which binds to WGA and examined by TEM. Labelling experiments showed the presence of chitin in all five stages of the fungus, although the distribution of chitin varied among spore stages. Competitive inhibition studies with triacetyl chitotriose showed that WGA bound to cell walls of basidiospores much more strongly than other spore types, requiring a 10-fold increase in concentration over that required for the other spore types to achieve complete inhibition.

A revision of Amorphomyces was carried out based on an examination of the author's and type material. Detailed study of the development of the female thallus of Amorphomyces italicus revealed a small, lobate, free, external primary appendage. A free appendage appeared to be lacking in all other known species of the genus. The generic circumscription of Amorphomyces is therefore emended. The new species A. hernandoi, parasitizing the marine aleocharid Diglotta mersa, is described from Portugal. Amorphomyces stipitatus and A. trogophloei are synonymized with A. italicus. With additions and changes, Amorphomyces currently includes ten species. All taxa are illustrated with photographs and line drawings, and a key for their determination is provided.

Torrentispora fibrosa gen. sp. nov. (Ascomycota, Annulatascaceae) is described based on specimens from submerged wood collected from streams in Tai Po Kau Forest Reserve, Hong Kong. T. fibrosa is characterized by immersed to superficial ascomata with a peridium of black cells arranged in irregular rows, wide septate paraphyses, long cylindrical asci with a relatively massive refractive apical ring, and unicellular ascospores with a fibrillar sheath. Illustrations from light and scanning electron microscopy are provided. It is compared with species in the genus Annulatascus, from which it differs in ascoma peridium and ascospore sheath morphology, and with other aquatic ascomycetes possessing ascospores with a similar fibrillar sheath structure.

Dactylaria cazorlii sp. nov. and Hansfordia catalonica sp. nov. from plant debris collected in different localities of Spain are described and illustrated. The first species is characterized by its hyaline, usually 4–6-septate, ellipsoid or subclavate conidia. The second one is distinguished by its brown, smooth, thick-walled, broadly obovoid, turbinate or ellipsoid conidia.