Ribosomal DNA sequences were assessed for their usefulness in distinguishing among Trichoderma isolates and for their robustness in resolving their phylogenetic relationships. DNA sequences from the D2 region of the 28S rRNA gene were determined for 50 Trichoderma isolates representing seven species. Eight distinct sequence types existed, and were mostly consistent with groupings based on morphology. Sequence variability within the D2 region alone was not sufficient to provide a reliable phylogeny. Sequences from the ITS1, 5.8S and ITS2 regions were subsequently determined for 18 of the isolates. Eight distinct ITS sequence types were detected among these 18 isolates. The ITS sequence types were generally consistent with morphology, ITS1 sequence data supported the identification of the Th3 T. harzianum group of Muthumeenakshi et al. (1994) as T. atroviride. The data also confirmed that the biocontrol strains of this study were different from those causing disease problems in the mushroom industry in Europe and North America. Results from the phylogenetic analysis stress the importance of testing the robustness of data used to predict phylogenies. Two ITS sequence data sets for the same group of isolates produced significantly different phylogenies. Congruence analysis detected that T. inhamatum (GJS90-90) was corrupting tree topologies and ‘first order pruning’ was performed by removing its sequence from the two ITS data sets. Subsequent differences in the topologies of pruned ITS1 and ITS2 trees were attributed to a lack of phylogenetic information in the ITS2 sequence region. Although ITS sequences successfully differentiated among morphologically distinct isolates within Trichoderma, it did not provide a sufficient phylogenetic signal to resolve all of their relationships.

The mycelial fatty acid profiles of several Pleurotus strains and their application in intrageneric differentiation were investigated. In the lipids produced by strains of Pleurotus abalonus, P. calyptratus, P. columbinus, P. cornucopiae, P. cystidiosus, P. ostreatus, P. pulmonarius, P. sajor-caju and P. sapidus, the predominant fatty acid was linoleic (33–68% total lipids), while in P. eryngii strains the major fatty acid was oleic (43–46%). In all strains studied, oleic and palmitic acids were present in significant concentrations (>12%), whereas stearic acid was found in lower ones. By using the ratios C18[ratio ]1/C18[ratio ]0, C18[ratio ]2/C18[ratio ]1 and ΣC18/C16[ratio ]0 as variables, Pleurotus strains were clustered into six groups. Group I (P. ostreatus); group II, divided in three sub-groups (IIa: P. columbinus, IIb: P. eryngii, IIc: P. cornucopiae), group III, divided in two sub-groups (IIIa: P. sajor-caju, IIIb: P. pulmonarius), group IV (P. sapidus), group V (P. abalonus) and group VI divided in two sub-groups (VIa: P. cystidiosus and VIb: P. calyptratus). It is concluded that the mycelial fatty acid composition of Pleurotus can be used in the intrageneric taxonomy of the genus.

Pulse-field gel electrophoresis (PFGE) was used to determine the genome size and characterize karyotypic differences in isolates of the cacao biotype of Crinipellis perniciosa (C-biotype). The karyotype analysis of four isolates from Brazil revealed that this biotype could be divided into two genotypes: one presenting six chromosomal bands and the other presenting eight. The size of the chromosomes ranged from 2.7 to 5.3 Mb. The different genotypes correlate with telomere-based PCR analysis. The isolates with six chromosomal bands had two that appeared to be doublets, as shown by densitometric analysis, indicating that the haploid chromosome number for this biotype is eight. The size of the haploid genomes was estimated at approximately 30 Mb by both PFGE and Feulgen-image analysis. DNA hybridization revealed that the rDNA sequences are clustered on a single chromosome and these sequences were located on different chromosomes in an isolate dependent manner. This is the first report of genome size and chromosomal polymorphism for the C-biotype of C. perniciosa.

This study aimed to test whether fungal community on moose (Alces alces) dung is affected by habitat. We used dung of homogenous origin, composition, and age. Dung was placed in three different habitats in north-eastern Sweden, and was checked again after 35–36 d. Of the 26 species of fungi found, 12 were new to the region, 17 had never been observed on moose dung, and two were not previously described. We found a significant difference in species composition between the habitats, with a low number of species in the spruce forest and about a threefold increase in the pine forest and the open mire. Species diversity was negatively associated with degree of insect attack. This suggests that insects feeding either on the dung or the fungi (spores, mycelia) may be an important factor explaining the observed pattern. In order to test this hypothesis we need to run experiments excluding insects.

Osmotrophic eukaryotes with a cell wall during the assimilative phase are ‘fungi’: the term ‘fungus’ is an essentially physiological concept, thus flagellate fungi conforming to this definition are not ‘pseudofungi’. But mycologists may also work with flagellate organisms which are phagotrophic or lack a plasmodial cell wall and, therefore, are not strictly ‘fungi’. In fungi the flagellate stage is confined to planonts (asexual zoospores and gametes).

Flagellar form and function have many conserved characteristics, but although ultrastructural diversity, particularly in kinetosome/flagellar root structure, has been intensively studied, other morphological features of the zoospore have been less thoroughly explored. The numbers, lengths, orientations and structural ornaments of flagella all provide data for biodiversity assessments at the species and ecological levels. The structural and functional biodiversity of fungal flagella and zoospores are reviewed, particularly with respect to the isokont/anisokont flagellar lengths and the isokont/heterokont flagellar ornaments of the zoospore. The straminipilous ornamentation has particular functional significance.

Correlations between molecular biology and flagellar ultrastructure indicate that several independent phylogenetic lines have evolved flagellate fungi. The strengths and weaknesses of the databases for these phylogenies are discussed in historical and current contexts.

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.

Eleven cultures representing eight genera of five families of Loculoascomycetes were obtained from ATCC and IMI. Partial 18S and 28S nuclear ribosomal DNA (rDNA) were amplified using PCR and sequenced. About 1100 bps of 18S rDNA (NS1/NS4 region) and 459 bps of 28S rDNA (F63/R635 region) for each taxon were subject to phylogenetic analysis using parsimony. The reconstructed phylogenetic trees supported the separation of two monophyletic groups, containing the type genera of the Leptosphaeriaceae and the Pleosporaceae, respectively. The members of the Leptosphaeriaceae (sensu Barr) consisted of the paraphyletic clade in the phylogenetic trees. The members of the Pleosporaceae (sensu Barr) plus Pyrenophora trichostoma formed a monophyletic clade. The results generally supported the separation of the Leptosphaeriaceae from Pleosporaceae and the placement of P. trichostoma, and Comoclathris baccata in the Pleosporaceae. The taxonomic position of Pleospora betae, whose coelomycetous anamorph is more closely related to Leptosphaeriaceae, was not well resolved because of low bootstrap values and decay indices. Leptosphaeria bicolor, whose ascospore morphology is not congeneric with the type of the genus, L. doliolum, does not belong to Leptosphaeria based on the 18S sequence data. The taxonomic disposition of Lewia, Pyrenophora, and Comoclathris based on the phylogenetic analyses are discussed.

A panel of monoclonal antibodies (MAbs) was raised to Botrytis cinerea using four different immunogens. Co-immunization with cross-reactive monoclonal antibodies helped to increase the percentage of specific hybridoma cell lines produced. The abilities of the MAbs to detect fungal antigens in extracts from infected tissue was correlated with their taxonomic specificities and with the localization of the antigens on the surfaces of the hyphae and conidia. Four distinct groups were identified: taxonomically unrelated, near-genus-, genus- and near-isolate-specific. Genus-specific antibodies gave the highest absorbance values in ELISAs with extracts from infected plant tissues. MAbs from this group all recognized heat-stable epitopes on antigens expressed along the length of the extracellular matrix of the hyphae and surface of the conidia. Antibodies from this group were all IgG1 antibodies.

Sterile dematiaceous fungi are commonly isolated from plant roots. They are often assigned to Mycelium radicis atrovirens, a name originally proposed for black, sterile, fast-growing, pseudomycorrhizal fungi. Dematiaceous fungi isolated from roots may be mutualists, commensalists, or pathogens and, in the absence of sporulation, identification is not possible. Forty-six isolates of dematiaceous fungi from the roots of different hosts and locations were characterized using restriction site mapping of polymerase chain reaction amplified nuclear ribosomal DNA internal transcribed spacers. The restriction site maps were compared to identified dematiaceous mycorrhizal and pseudomycorrhizal fungi. Computer generated trees (UPGMA and parsimony analysis) characterized two unknown isolates as Phialophora finlandia, an ectendomycorrhizal fungus. The majority of the isolates were characterized as Phialocephala fortinii-like. Phialocephala fortinii has been reported as both pathogenic and non-pathogenic in a number of hosts. There was variation within the P. fortinii-like group suggesting intraspecific variation or a species complex.

The Nitschkiaceae has been placed in the Coronophorales or the Sordariales in recent years. Most recently it was accepted in the Coronophorales and placed in the Hypocreomycetidae based on sequence data from large subunit nrDNA. To confirm and corroborate the taxonomic placement and monophyly of the Coronophorales, additional taxa representing the diversity of the group were targeted for phylogenetic analysis using partial sequences of the large subunit nrDNA (LSU). Based on molecular data, the Coronophorales is found to be monophyletic and its placement in the Hypocreomycetidae is maintained. The order is a coherent group with morphologies that include superficial, often turbinate, often collabent ascomata that may or may not contain a quellkorper and asci that are often stipitate and at times polysporous. Three species with accepted Nitschkia names, together with Fracchiaea broomeiana and Acanthonitschkea argentinensis, comprise the paraphyletic nitschkiaceous complex. Two new families, Chaetosphaerellaceae and Scortechiniaceae fams nov., are described for the clades containing Chaetosphaerella and Crassochaeta and the taxa having a quellkorper (Euacanthe, Neofracchiaea and Scortechinia) respectively. The Bertiaceae is accepted for the clade containing Bertia species. Three new species are described: Bertia tropicalis, Lasiobertia portoricensis, and Nitschkia meniscoidea spp. nov.

Fungal colonies sporulating on 71 kinds of leaves that fell during the dry season in the Tai National Park (Ivory Coast) were analysed. A consistent connection between certain fungal species and their substrata was detected among the 184 fungal species that were identified. Each fungal species was characterized according to morphological and ecological features. Multidimensional scaling showed that certain ubiquitous and common species have morphological characters distinguishing them from specialised species.

Five species of pathogenic fungi belong to Neofabraea. One of these, N. krawtzewii (syn. N. populi), is responsible for bark lesions on poplar (Populus) trees. The other four species cause post-harvest bull's eye rot of pome fruits, and at least two of these also cause bark cankers on pome fruit trees. Morphological variation among these species is slight, and overlap in geographic range sometimes occurs. As a consequence, identification based on conventional criteria can be tenuous. PCR primers with putative species specificity were developed following genetic analysis of the β-tubulin gene for isolates of each of the five species of Neofabraea. PCR conditions required to achieve specificity of the primer sets were determined, and a multiplex PCR protocol was developed to optimize their diagnostic utility on apple fruits. A protocol with higher annealing temperatures in the initial PCR cycles followed by lower temperatures in later cycles gave complete species-specificity when the primer sets were used individually and in multiplex, resulting in successful detection of the pathogens from axenic culture and infected apple fruits.

The patterns of mycelial development (length and branching) of five strains of Fusarium oxysporum were measured in the vicinity of tomato and wheat roots. Two strains were of f. sp. lycopersici, two of f. sp. radicis-lycopersici and the fifth was a non-pathogenic strain currently used as a biocontrol agent. Hyphal extension and branching were measured microscopically using a CCD camera and an image analyser. Furthermore, the role of soluble root exudates, insoluble root materials, glucose supply, and nitrogen supply (casamino acids) on mycelial development was investigated. Each strain had its own pattern of development in the absence of a root. Fungal development of all five strains was stimulated in the vicinity of roots irrespective of plant species but there was no chemotropic response towards or away from the root. Both pathogenic and non-pathogenic F. oxysporum populations exhibited their own characteristic growth and development features which were not related to their pathogenicity. Growth stimulation was mainly related to the presence of organic nitrogen in the soluble exudates. It is proposed that signalling and recognition mechanisms between the host plant and the pathogenic or non-pathogenic strains are likely to occur on or in the root rather than external to the root.

Sooty moulds are described and illustrated from European amber dating back to 22–54 Myr. All the fossils are fragments of superficial subicula composed of brown moniliform hyphae with markedly tapering distal ends. The subglobose cells are identical to those of extant Metacapnodium (Metacapnodiaceae, Capnodiales) species. Also other preserved features, like the type of apical growth, wide-angled branching and the production of two distinctive conidial states, supports a placement in this genus. The fossils demonstrate that Metacapnodium hyphae have remained unchanged for tens of millions of years. This confirms that hyphal morphology and conidial states should be accorded considerable classificatory significance in this group of fungi. The following nomenclatural change is made: Metacapnodium succinum comb. nov. (syn. Rosaria succina). The type specimen was initially described as a filamentous cyanobacterium, due to similarities with Rosaria ramosa. Also the systematic position of this attribute is shortly discussed.

Reference strains of Rhizoctonia solani from AG-1 1A, -1–1B, 1–1C, 2–1, 2–2, and 3 to 9, isolates of AG-1 1A from various rice growing countries and field isolates from a paddy rice field experiment in Côte d'Ivoire were analysed by pectin enzyme analysis. A subset of these isolates was also analysed by A+T-rich DNA (AT-DNA) RFLPs, both with the objectives to study the diversity at various taxonomic levels and to obtain a clearer picture of the relationships between these isolates. Field isolates were submitted to simple sequence repeat PCR (SSR-PCR). Pectin enzyme analysis as well as AT-DNA RFLP showed that isolates of different anastomosis groups generated very distinct patterns. Isolates of AG-1 1A from various countries had a lower degree of variability in zymogram patterns and AT-DNA RFLPS, while zymograms and AT-DNA RFLPs of field isolates obtained from one field experiment consisted of one identical pattern. However, these isolates showed variation in RFLPs obtained through SSR-PCR, indicating that they were not clones sensu stricto.

A new Claviceps species that causes ergot in sorghum and Sudan grass in Japan is described. The new species is distinct from C. sorghi and C. africana, from India and Africa, respectively, in the colour and texture of sclerotia, colour and morphology of stromata arising from the sclerotia, and size of ascospores and conidia. The pathogen infected only Sorghum in inoculation tests using 11 gramineous plants. Hyphal growth of C. sorghicola was 1 mm d−1 on PDA at 25 °C. Production of a different ergoline alkaloid in the sclerotia was suggested.

Maple leaf disks were exposed in a softwater stream for two weeks and then aerated for 2 d in water to induce spore production by aquatic hyphomycetes. Sporulation was inhibited by the addition of yeast extract or leaf leachate (up to 2·5 g l−1) to the sporulation water. With leaf leachate, but not with yeast extract, this effect was neutralized by the addition of 50 mg l−1 of CaCl2. Sporulation increased at intermediate concentrations of several inorganic compounds (CaCl2; KH2PO4/K2HPO4; NaNO3; NaCl). It increased at low concentrations (1–3 g l−1) of an artificial seasalt mixture, was much reduced at 7·5 g l−1 and absent at 15 g l−1.

Genetic relationships of twenty strains of Scedosporium, Petriella and Pseudallescheria were studied by sequencing a 370 bp part of the gene which encodes the large subunit ribosomal RNA (LSU rDNA). This study confirms and specifies earlier results from the small subunit ribosomal RNA gene (SSU rDNA).

It was confirmed that the pathogenic Scedosporium prolificans is closely related to Petriella, as is Graphium tectonae. Petriella setifera, which includes clinically isolated Scedosporium strains, can be divided into several groups inside the same genus.

The main part of Pseudallescheria is clearly distinguished from Petriella. Pseudallescheria is heterogeneous, however: Ps. africana is referred to Petriella and Ps. fimeti is more closely related to Microascus.

Didymella bryoniae (anamorph Phoma cucurbitacearum) is an ascomycete that causes gummy stem blight, a foliar disease that occurs on cucurbits in greenhouses and fields throughout the world. In a previous study using RAPD analysis, little genetic diversity was found among isolates of D. bryoniae from New York and South Carolina, USA. Here we report the use of amplified fragment length polymorphism (AFLP) analysis to assess the genetic variation within a worldwide collection of D. bryoniae. 102 field and greenhouse isolates from ten states in the USA (California, Delaware, Florida, Georgia, Indiana, Maryland, Michigan, Oklahoma, South Carolina, and Texas) and seven other countries (Australia, Canada, China, Greece, Israel, Sweden, and The Netherlands) were examined. Seven different AFLP primer-pair combinations generated 450 bands, of which 134 were polymorphic (30%). Using cluster analysis, two groups and a total of seven subgroups were delineated. Representative isolates varied in their virulence on muskmelon and watermelon seedlings, but the degree of virulence was not strongly associated with AFLP groupings. However, isolates from the northern USA grouped separately from isolates originating from the southern USA.

DNA was extracted from dried specimens of nine taxa of the Cantharellaceae. Approximately 325 bases near the 5′ end of the nuclear 28S ribosomal gene were sequenced, and the sequences were compared. Sequence analyses demonstrated that Cantharellus and Craterellus should be treated as distinct genera. The phylogeny generated using parsimony suggests that Cantharellus tubaeformis and Pseudocraterellus sinuosus should be considered species of Craterellus. As a result of this study, we recognize the first placement of these two species in Craterellus by Fries and Quélet. A reassessment of the morphological characters used to separate Cantharellus and Craterellus is indicated.