This issue of Mycological Research News features: Kelo trees: a vanishing fungal habitat; Polarized growth in fission yeast; Comparative genomics and functional elements in the yeast genome; When physics meets biology: high-resolution laser-based techiques to study plant–microbe interactions; and an Acknowledgement.

The largest molecular phylogenetic fungal tree yet to have been published is presented, based on 1551 sequences; this will be of interest to all concerned with fungal relationships, especially at family and higher levels. Hepatic mycorrhizas are described ultrastructurally and molecularly, and the relationships of the mycobionts determined. The cytology and behaviour of nuclei in tri- and tetraradiate conidia in coelomycetes is examined, and micronuclei are documented for the first time. Confocal laser scanning electron microscopy examines nuclei and ascospore formation using a methodology likely to have wide utility.

The conditions affecting the production of the siderophore rhodotorulic acid by Rhodotorula mucilaginosa have been investigated. The poisonous Clitocybe lactea produces phallatoxins, previously only known from Amanita spp., and its relationships are explored by molecular methods. Swainsonine, the cause of locoism in cattle etc. in the USA, is produced by endophytic fungi inside the plants consumed. The enyzmes produced by the lignin-degrading Mycena galopus and responsible for this activity have been investigated and identified.

The following new scientific names are introduced in this part: Cornutispora intermedia, C. pittii, and Furcaspora abieticola spp. nov.

A data set with 1551 fungal sequences of the small subunit ribosomal RNA has been analysed phylogenetically. Four animal sequences were used to root the tree. The parsimony ratchet algorithm in combination with tree fusion was used to find most parsimonious trees and the parsimony jackknifing method was used to establish support frequencies. The full-length consensus tree, of the most parsimonious trees, is published and jackknife frequencies above 50% are plotted on the consensus tree at supported nodes. Until recently attempts to find the most parsimonious trees for large data sets were impractical, given current computational limitations. The parsimony ratchet in combination with tree fusion was found to be a very efficient method of rapid parsimony analysis of this large data set. Parsimony jackknifing is a very fast and efficient method for establishing group support. The results show that the Glomeromycota are the sister group to a monophyletic Dikaryomycota. The majority of the species in the Glomeromycota/Dikaryomycota group have a symbiotic lifestyle – a possible synapomorphy for a group ‘Symbiomycota’. This would suggest that symbiosis between fungi and green plants evolved prior to the colonization of land by plants and not as a result of the colonization process. The Basidiomycotina and the Ascomycotina are both supported as monophyletic. The Urediniomycetes is the sister group to the rest of the Basidiomycotina successively followed in a grade by Ustilaginomycetes, Tremellomycetes, Dacrymycetales, Ceratobasidiales and Homobasidiomycetes each supported as monophyletic except the Homobasidiomycetes which are left unsupported. The ascomycete node begins with a polytomy consisting of the Pneumocystidomycetes, Schizosaccharomycetes, unsupported group with the Taphrinomycetes and Neolectales, and finally an unnamed, monophyletic and supported group including the Saccharomycetes and Euascomycetes. Within the Euascomycetes the inoperculate euascomycetes (Inoperculata) are supported as monophyletic excluding the Orbiliomycetes which are included in an unsupported operculate, pezizalean sister group together with Helvellaceae, Morchellaceae, Tuberaceae and others. Geoglossum is the sister group to the rest of the inoperculate euascomycetes. The Sordariomycetes, Dothideomycetes, Chaetothyriomycetes and Eurotiomycetes are each highly supported as monophyletic. The Leotiomycetes and the Lecanoromycetes both appear in the consensus of the most parsimonious trees but neither taxon receives any jackknife support.

The distribution and behaviour of nuclei in conidia of 11 coelomycete species with tri- and tetraradiate conidia and belonging to five genera has been investigated: Cornutispora (C. ciliata, C. intermedia, C. lichenicola, C. limaciformis, and C. pittii), Eriosporella (E. calami), Furcaspora (F. abieticola, F. pinicola), Suttoniella (S. eriobotryae, S. gaubae), and Tetranacrium (T. gramineum). They have been studied by the HCl-Giemsa technique using dried, preserved material including holotypes and isotypes with ages ranging from 3 to 116 yr. Conidia of Cornutispora species showed different ploidy levels, and C. limaciformis showed a very high (>90%) frequency of stable and viable micronuclei with an unusual type of ploidy level, occurring naturally. Frequency of ploidy levels in nuclei within conidia of Cornutispora species appeared to be associated with changes in gross conidial morphology. This is the first report of micronuclei in coelomycetes. The types of appendages on arms or parts of conidia have been studied using various stains including erythrosin in ammonia and a modified Leifson's flagella staining technique. In Furcaspora species the apical and basal conidial appendages are cellular maintaining protoplasmic continuity with the arms on which they are sited. The results have been compared with those of Crucellisporium species which have tetraradiate conidia. The new species, Cornutispora intermedia, C. pittii and Furcaspora abieticola spp. nov. are described, and illustrated, and a key to all known Cornutispora species is provided.

Rhodotorula mucilaginosa produces the siderophore rhodotorulic acid (RA) when grown in iron-limited conditions. R. mucilaginosa grew at rates between 0.10 and 0.19 h−1 in iron-restricted conditions, depending on the carbon source, and at 0.23 h−1 in iron-sufficient conditions. In bioreactors inoculated with iron-starved pre-cultures, initial specific growth rates in batch culture were dependent on the iron concentration. The critical dilution rate (Dcrit, at which steady state cultures cannot be sustained) in continuous cultures was also dependent on the iron concentration and was lower than μmax in batch culture. Sucrose was the best carbon source for RA production [287±11 μmol (g biomass)−1] and production could be further increased by supplementing the medium with the precursors acetate [460±13 μmol (g biomass)−1], ornithine [376±6 μmol (g biomass)−1], or both [539±15 μmol (g biomass)−1]. Citric acid was an effective suppresser of RA production. RA was produced in a growth rate dependent manner and was optimally produced at pH 6.5.

In order to evaluate substrate dependence of the symbiotic fungal associations in leafy liverworts (Jungermanniopsida), 28 species out of 12 families were investigated by transmission electron microscopy and molecular methods. Samples were obtained from the diverse substrates: from naked soil, from the forest floor on needle litter, from between peat moss, from rotten bark of standing trees, and from stumps and rotten wood. Associations with ascomycetes were found in most of the specimens independent from the substrate. Seven species sampled from soil were found to contain basidiomycete hyphae. Ultrastructure consistently showed dolipores with imperforate parenthesomes. Molecular phylogenetic studies revealed that three specimens belonging to the Jungermanniales were associated with members of Sebacinaceae, while Aneura pinguis (Metzgeriales) was associated with a Tulasnella species. These taxa are so far the only basidiomycetes known to be symbiotically associated with leafy liverworts. The probability that the associations with Sebacinaceae are evolutionary old, but the Tulasnella associations more derived is discussed. The sebacinoid mycobionts form a similar interaction type with the jungermannialian leafy liverworts as do the associated ascomycetes. The term ‘jungermannioid mycorrhiza’ is proposed for this distinctive symbiotic interaction type.

Conocybe lactea was examined as part of a larger study on the distribution of amatoxins and phallotoxins in fungi, and the taxonomic relationships between these fungi. As amatoxins are present in the congener C. filaris, the locally abundant C. lactea was examined using HPLC and mass spectroscopy. Amatoxins were not found in C. lactea, but the related phallotoxins were present in small quantities making it the first fungus outside of the genus Amanita in which phallotoxins have been detected. Despite the presence of a related toxin, C. lactea was found not to be taxonomically close to C. filaris. Phylogenetic analyses using nuclear ribosomal RNA genes indicated that North American specimens of C. lactea were conspecific with North American specimens of C. crispa in Conocybe sect. Candidae. European C. crispa was a distinct taxon. The implications of the use of the name C. albipes for these taxa are discussed. Nucleotide data confirmed placement of the sequestrate taxon Gastrocybe lateritia in sect. Candidae, but as a distinct taxon. It is hypothesized that the unique sequestrate morphology of G. lateritia may be caused by a bacterial infection.

Consumption of locoweeds, legumes endemic in arid western USA, has long been associated with locoism, a disease of ruminant animals. To explore the relationship between fungi associated with locoweed and locoweed toxicity, 11 locoweed populations from various sites in New Mexico were assessed for endophytic fungi. Endophytes were isolated from the leaves, stems, seeds, and flowers of eight populations of the toxic locoweeds Astragalus mollissimus, Oxytropis lambertii, and O. sericea. Fungal cultures grew very slowly and sporadically produced subcylindrical conidia with very dark transverse septa. All cultured endophytes produced the alkaloid swainsonine, which causes locoism. Endophyte-infected locoweed populations produced swainsonine, and the swainsonine level of endophyte strains in vitro was highly correlated with the swainsonine level of their host plant populations. The rDNA ITS from mycelia from four endophyte isolates and β-tubulin encoding regions from mycelia of 18 fungal endophyte isolates were amplified using PCR and the nucleic acid sequences were analyzed. The nucleic acid sequences of the β-tubulin encoding regions were essentially identical among all the endophytes regardless of plant genus and locations. Morphological evidence and sequence analysis of the ITS region suggest that the endophytes are most closely related to Embellisia. However, with the paucity of Embellisia species represented in sequence databases, precise taxonomic placement will await further study.

A method for visualization of fungal nuclear structures using the DNA specific fluorochrome SYTOX Green and confocal laser scanning microscopy is presented. The staining procedure detects nuclei in different cell types with high contrast. Furthermore, the method permits generation of high-resolution confocal image stacks using optimised scanning conditions. This approach significantly improved visualization of stained fungal nuclear structures. The technique was applied to some lichenized fungi, but can also be used to study similar detail in non-lichenized fungi. In certain cases, incompletely separated chromosome-like structures, heterochromatic material as well as weakly stained nucleolar regions can be seen. In Xanthoria parietina, variation in the nuclear division was observed in developing ascospores. Delayed division after the formation of endospore thickening resulted in the exchange of nuclear material through a narrow isthmus.

Mycena galopus is among the most important leaf litter decomposers in UK coniferous and angiosperm woodlands, having the potential to utilise all the major constituents of plant litter. Even so, the enzyme or combination of enzymes produced by M. galopus responsible for lignin depolymerisation was previously unknown. A range of media from liquid and semi-solid cultures to more natural substrata was tested to determine whether laccase was produced by an isolate of M. galopus, M9053. Malt extract liquid medium (MEL) with 2,5-xylidine favoured laccase production as compared with the same medium containing the inducers veratryl alcohol, veratryl aldehyde, veratric acid, homoveratric acid, vanillic acid or p-anisic acid. A semi-solid medium of cereal bran in phosphate buffer and a solid medium of Picea sitchensis F1 horizon needle litter were also not as effective as MEL with 2,5-xylidine as an inducer. Compared with six other isolates of the same species grown in MEL without inducers, M9053 exhibited rates of laccase activity fairly typical for M. galopus. An isolate from a dark coloured basidiome of M. galopus, but not var. nigra, exhibited the greatest activity while var. candida showed relatively low laccase activity. Marasmius androsaceus exhibited peak laccase production several days later than M. galopus. In addition, a manganese-dependent peroxidase that was responsible for 15% (in MEL culture fluid) and 39% (in needle litter extract III) of ligninolytic activity was produced by M9053. A further peroxidase was found to be the major ligninolytic constituent in MEL extracts (53%), and had a similar contribution to total activity (29%) as laccase (32%) in needle litter fraction III. Mycena galopus produced water- and buffer-extractable mannases and xylanases when grown on needle litter.