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.

The white-rot basidiomycete, Inonotus hispidus, produces a characteristic pattern of decay in naturally infected London plane (Platanus × hispanica) in which zones of severely decayed wood, traversed by relatively undegraded xylem rays, alternate with relatively undegraded, gummous ‘reaction zones’. Microscopic observations of London plane wood both naturally colonized and artificially inoculated with I. hispidus indicated that the resistance of reaction zones and xylem rays to degradation is due respectively to obstruction of cell lumina by tyloses and polyphenols, and infiltration of intercellular spaces by polyphenols. Inonotus hispidus was apparently able to circumvent these impedances by forming soft-rot like tunnels through the wood cell walls.

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.

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.

The phylogenetic relationships among fungi that cause spring dead spot disease of Bermuda grass in Australia and the United States were studied from nucleotide sequence data of the ITS region of the rDNA. High levels of sequence similarity were observed among Ophiosphaerella herpotricha, O. korrae and Leptosphaeria narmari. These species clustered into a distinct clade that was distant from other Leptosphaeria and Phaeosphaeria species. Based on sequence data and previous descriptions of the ascoma and ascospore characteristics of these species, we propose a taxonomic transfer of L. narmari to O. narmari. Oligonucleotide primers specific for O. narmari were developed from ITS1 and ITS2 regions to help identify non-sporulating isolates. These primers amplified all isolates of O. narmari, including those from the United States, but not those of O. herpotricha, O. korrae or other ectotrophic root-inhabiting fungi. This is the first report of O. narmari in North America. Two Group I introns were found in the small subunit rDNA of some isolates of O. korrae and O. narmari, but not O. herpotricha. A 425-nucleotide intron in O. narmari and O. korrae was inserted two nucleotides downstream from the ITS5 conserved primer sequence. These introns exhibited an 80% sequence identity. In addition, a second 431-nucleotide intron in O. narmari was similar in size and location to one in O. korrae.

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.

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 content of phenolic substances in freshly collected fruit bodies of several basidiomycete genera varied in the range 2·35–9·05 mg g−1, following closely the trend of a normal function.

It was necessary to use a polyphenoloxidase-inhibiting substance to obtain reliable analysis. The content of phenolics decreased, during 3 d at room temperature and following freezing at −20°C.

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.

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.

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.

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.

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.

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.

Cerato-ulmin (CU) is a low molecular weight hydrophobin protein secreted at high levels in vitro by the highly aggressive Dutch elm disease pathogen, O. novo-ulmi, but at much lower levels by the less aggressive O. ulmi. The recent discovery of an endemic Dutch elm disease fungus in the Himalayas, Ophiostoma himal-ulmi, which is a separate species from O. ulmi and O. novo-ulmi, yet like O. novo-ulmi produces high levels of CU in vitro, suggested that O. novo-ulmi may have acquired its cu gene from O. himal-ulmi. To investigate this possibility we have compared the nucleotide sequences of the cu gene isolates of O. himal-ulmi with those of O. ulmi and of the EAN and NAN races of O. novo-ulmi. Alignments of nucleotide sequences and their derived amino acid sequences are presented, allowing estimations of evolutionary relationships to be made. These comparisons indicate that the cu gene of O. himal-ulmi is less closely related to the cu gene of either O. ulmi or O. novo-ulmi than the cu gene of O. novo-ulmi is to that of O. ulmi; hence the cu gene of O. novo-ulmi is unlikely to have been acquired recently from O. himal-ulmi.

Vesicular–arbuscular (VA) mycorrhizas are described from anatomically preserved roots of the Middle Eocene taxodiaceous conifer Metasequoia milleri, and compared to those of the living species M. glyptostroboides. Virtually identical VA mycorrhizal structures occur in the root cortex of both species, where they conform to the Paris-type. Coiled hyphae are most common within cells of the inner cortical region, and these produce numerous, highly branched arbuscules. Close similarity of fungal position and structure within roots of the living and fossil Metasequoia species demonstrates that modern Paris-type VA mycorrhizal associations characterized taxodiaceous conifers by the early Tertiary.

The phylogeny of the Agyriales was investigated using nucleotide sequences of ITS1, 5.8S, and ITS2 rDNA. Sequences of these regions from 15 new sequences of 13 agyrialean fungi were aligned to those of four representatives of Ostropales used as outgroup. Six different alignments were analysed cladistically using maximum parsimony. The Agyriales were supported as a monophyletic group in the strict consensus tree and the synonymy of the Rimulariaceae and Saccomorphaceae was confirmed. The Schaereriaceae is also shown to belong to the Agyriaceae. The distribution of selected characters in the Agyriales is investigated and it is shown that the ascus type is variable within the group, while the ascoma ontogeny is invariant within the Agyriaceae. Trapelia as usually circumscribed is polyphyletic. The T. geochroa group is not closely related to Trapelia s. str. and the new genus Ainoa is described to accommodate T. geochroa and T. mooreana.

The effect of increasing culture age on cell surface hydrophobicity (CSH) and cell surface electrostatic charge (measured as zeta potential) of conidia from five isolates of Coniothyrium minitans representing three different morphological types was examined. Conidial CSH of three isolates (A2 960/1, CH1 and CH2) decreased with culture age, whereas CSH of two others (B 1300/2 and IMI 134523) remained high for the whole 42 day experimental period. In contrast, cell surface electrostatic charge decreased uniformly in conidia of all five isolates for the first 34 d and then rose slightly at 42 d. The variation in cell surface electrostatic charge (spectrum width) of the sampled conidia decreased with age for all five isolates. In all five isolates cell surface electrostatic charge of conidia became increasingly negative as the pH of the buffer used to suspend conidia was increased from pH 3·0 to 9·0. No relationship between colony morphology of C. minitans and conidial CSH and cell surface electrostatic charge was found.