Evaluating methodologies for species delimitation: the mismatch between phenotypes and genotypes in lichenized fungi (Bryoria sect. Implexae, Parmeliaceae).

In many lichen-forming fungi, molecular phylogenetic analyses lead to the discovery of cryptic species within traditional morphospecies. However, in some cases, molecular sequence data also questions the separation of phenotypically characterised species. Here we apply an integrative taxonomy approach - including morphological, chemical, molecular, and distributional characters - to re-assess species boundaries in a traditionally speciose group of hair lichens, Bryoria sect. Implexae. We sampled multilocus sequence and microsatellite data from 142 specimens from a broad intercontinental distribution. Molecular data included DNA sequences of the standard fungal markers ITS, IGS, GAPDH, two newly tested loci (FRBi15 and FRBi16), and SSR frequencies from 18 microsatellite markers. Datasets were analysed with Bayesian and maximum likelihood phylogenetic reconstruction, phenogram reconstruction, STRUCTURE Bayesian clustering, principal coordinate analysis, haplotype network, and several different species delimitation analyses (ABGD, PTP, GMYC, and DISSECT). Additionally, past population demography and divergence times are estimated. The different approaches to species recognition do not support the monophyly of the 11 currently accepted morphospecies, and rather suggest the reduction of these to four phylogenetic species. Moreover, three of these are relatively recent in origin and cryptic, including phenotypically and chemically variable specimens. Issues regarding the integration of an evolutionary perspective into taxonomic conclusions in species complexes, which have undergone recent diversification, are discussed. The four accepted species, all epitypified by sequenced material, are Bryoria fuscescens, B. glabra, B. kockiana, and B. pseudofuscescens. Ten species rank names are reduced to synonymy. In the absence of molecular data, they can be recorded as the B. fuscescens complex. Intraspecific phenotype plasticity and factors affecting the speciation of different morphospecies in this group of Bryoria are outlined.

Where are all the undescribed fungi?

ABSTRACT The hypothesis that there are 1.5 million fungal species on Earth, of which only about 70,000 are described, implies that 1.43 million remain undescribed. The recognition that many new species have yet to be found is of fundamental importance to plant pathologists, agronomists, and plant regulatory officials, among others, who continue to encounter diseases caused by previously unknown or understudied fungi. Unexplored habitats with their arsenal of unknown fungi are also of interest to those searching for novel organisms for use in biological control or for their pharmaceutical attributes. This paper presents data on the expected numbers of fungi in some relatively unexplored habitats, such as tropical forests, and those obligately associated with plants, lichens, and insects. In addition to undiscovered species, many have been collected but remain lost or hidden as named species and ignored for lack of modern characterization; others have been collected and recognized as new species but remain undescribed. Some fungal species are unrecognized within erroneously circumscribed species, often based on presumed host specificity, while others exist as biological species but remain buried within those broadly defined species for lack of gross morphological characterization. From these data, one must conclude that enormous numbers of unrecognized fungi can be found almost everywhere, including one's own backyard.

Sudden infant death syndrome (SIDS) and the toxic gas hypothesis: microbiological studies of cot mattresses.

1. Fifty infants' mattresses were studied to investigate the occurrence of viable fungal and bacterial propagules, with particular reference to Scopulariopsis brevicaulis which had been suggested to be implicated in SIDS cases. A total of 19 SIDS cases mattresses, 1 non-SIDS death, 20 used controls, and 10 new unused controls were examined. 2. Differences were found between SIDS and used controls in the variety of fungal species isolated and the numbers isolated from fillings; bacterial numbers were similar. 3. S. brevicaulis was isolated from only four mattresses, three of which were SIDS cases. It was not found in most of those on which death had occurred. 4. A number of potentially pathogenic or allergenic fungi, including Aspergillus fumigatus, were isolated more frequently from SIDS cases mattresses than new or used controls. 5. Scanning electron microscopy of mattress covers and fillings showed microbial 'biofilms' in the head areas of all SIDS cases examined. This was not seen on other samples. 6. The limited number of mattresses studied and the use of unmatched controls precludes the drawing of any general conclusions as to the significance of the biofilms or other fungi isolated. 7. Reports of the existence of a dimorphism in general growth forms of S. brevicaulis were investigated by growing and transferring authentic strains between a variety of growth media. 8. No 'slimy' state of this fungus was observed and dimorphism was not confirmed.

Simple febrile convulsions: evidence for best practice.

Febrile convulsions are common in early childhood and may be the first sign of an illness. Witnessing the convulsion and experiencing the subsequent admission is extremely stressful for parents. Children's nurses need to identify the evidence for best practice in the management of febrile convulsions. Parent education is an essential component of the management of care.

Roselliniella revealed as an overlooked genus of Hypocreales, with the description of a second species on parmelioid lichens.

Based on newly obtained 28S rDNA sequences from Roselliniella atlantica and R. euparmeliicola sp. nov., the genus Roselliniella has to be placed in Hypocreales and not in Sordariales; however, the family placement could not be resolved from the sequences obtained. The mature ascospores are single-celled and brown, but young ascospores are hyaline and sometimes have a median septum. The new species occurs on a Parmelia s.str. species in China, and differs in 24 nucleotide substitution positions in the nu-LSU rDNA region and ascospore size from R. atlantica. In this case, small variations in ascospore sizes and shape prove to be phylogenetically and taxonomically informative. The two species occur in the same clade with 95 % jack-knife support. Roselliniella atlantica occurs on Xanthoparmelia and Melanohalea species in Europe, whereas R. euparmeliicola was found on the species of Parmelia s.str. DNA was successfully recovered from a dried specimen of R. atlantica collected in 1992. Two unidentified fungi were also recovered from the Chinese specimen, and these belong to Sordariomycetidae and Dothideomycetes; whether these two are additional fungi living endolichenically in the lichen host, saprobes, or contaminants could not be ascertained.

Recent changes in the international rules affecting the nomenclature of fungi.

Major changes in the rules governing the nomenclature of fungi were enacted at the XIIIth International Botanical Congress in 1981. The effects of these, and the reasons why changes were made, are reviewed with particular emphasis on those concerned with the starting-point date and fungi with pleomorphic life cycles.

[Fungi and biodiversity: international incentives]. / Hongos y biodiversidad: iniciativas internacionales.

Interest in biodiversity has spawned international actions both political and scientific, many of which are relevant to mycologists. The political initiatives include the Convention on Biological Diversity and Biodiversity Action Plans, and the scientific: the Global Biodiversity Assessment, Species 2000, Systematics Agenda 2000 International, BioNet International, Diversitas, All Taxa Biodiversity Inventory, and Biodiversity Methods Manuals. Mycologists need to contribute to such programmes, maintain an enhance profile, and remain flexible to respond to new challenges.

The API ZYM enzyme testing system as an aid to the rapid identification of Penicillium isolates.

The API ZYM strip is a commercially available, rapid, enzyme testing system. It has been demonstrated to be a useful method in certain areas of bacterial identification. Its suitability for the identification of filamentous fungi was evaluated, with encouraging results being obtained.

Studies on a species of Monosporascus isolated from Triticum.

A species of Monosporascus isolated from darkened stem bases of Triticum in Libya is compared with the two known species of the genus: M. cannonballus and M. eutypoides. The isolate resembles M. cannonballus in the type of ostiole developed but M. eutypoides in having mainly two-spored asci. It differs from M. eutypoides in having a reduced ostiole but this may be a response to growth in culture as this species has only previously been reported from infected tissues. In addition to having mainly two-spored and not one-spored asci, the isolate differs from M. cannonballus in that the spores pass through a stage in which a reticulum is visible when viewed by SEM. SEM photographs of the spores of both M. cannonballus and M. eutypoides, to which species this fungus is tentatively referred, are included. On germination the ascospores of the Triticum isolate produce 5--10 germ tubes. A growth curve for cultures is provided showing that the optimum temperature for growth is in the range 25--35 degrees C. Subcultures held at 48 degrees and 55 degrees C for five days failed to grow when transferred to 30 degrees C but ones held at 45 degrees for the same period grew normally when the temperature was reduced to 30 degrees C. The appearance of the colonies at different temperatures is also described.

Biodiversity: measurement and estimation.

In introducing a series of 11 papers on the measurement and estimation of biodiversity, eight crucial questions are posed: What is 'biodiversity'? Is biodiversity just the number of species in an area? If biodiversity is more than the number of species how can it be measured? Are all species of equal weight? Should biodiversity measures include infraspecific genetic variance? Do some species contribute more than others to the biodiversity of an area? Are there useful indicators of areas where biodiversity is high? And can the extent of biodiversity in taxonomic groups be estimated by extrapolation? In addition, the modern concept of biological diversity is attributed to Elliot R. Norse and his colleagues.

International Commission on the Taxonomy of Fungi (ICTF). Code of practice for systematic mycologists.

Fourteen points which mycologists dealing with the systematics of fungi (including yeasts) are encouraged to adhere to in their work are presented as a Code of Practice for Systematic Mycologists. Adoption of these will encourage both stability in nomenclature and uniformity in approaches to the descriptions of fungi.

International Commission on the Taxonomy of Fungi code of practice for systematic mycologists.

Fourteen points which mycologists dealing with the systematics of fungi (including yeasts) are encouraged to adhere to in their work are presented as a Code of Practice for Systematic Mycologists. Adoption of these will encourage both stability in nomenclature and uniformity in approaches to the descriptions of fungi.

Theoretical and practical aspects of the quantification of biodiversity among microorganisms.

The quantification of biodiversity among microorganisms has to address both theoretical and practical aspects. Species concepts are often at variance with those applied in macroorganisms, and satisfactory concepts suitable for general use in bacteria and fungi have yet to be formulated. Molecular approaches have not yet provided a universal solution to this key issue. Quantification in habitats such as soil is difficult as isolation procedures yield only a small and skewed selection of the microorganisms present. Indices of taxonomic or phylogenetic diversity have potential in the quantification of microbial diversity at a range of ranks, but the non-equivalence of ranks and representatives of the taxa detected have to be addressed. Chemical and molecular methods have immense potential in the quantification of microbial diversity in environmental samples; 16S rRNA has shown particular promise with bacteria, but as yet the fungi lack a universal probe. A greater awareness of the limitations of existing approaches and methodologies used by microbiologists is needed, but significant progress can be anticipated as new technologies are developed and become more widely adopted.

A reappraisal of the terverticillate penicillia using biochemical, physiological and morphological features. III. An evaluation of pectinase and amylase isoenzymes for species characterization.

Polyacrylamide gel electrophoresis of extracellular pectinase and amylase isozymes of 170 mainly terverticillate Penicillium strains was undertaken. The data were coded and subjected to numerical analysis. Variation in intensity of isozymes was observed in repeat analyses of some strains, although most were consistent. Variation was also observed between some representative strains of species. P. viridicatum was more variable than P. brevicompactum and P. hordei for intensity of pectinase activity. There was a correlation between the grouping of the strains on the basis of the isozymes and the species concepts only in some cases. The method proved useful for the identification of strains producing intense activity which provided clear patterns, for example, P. brevicompactum and P. chrysogenum and to a lesser extent P. solitum var. crustosum and P. hordei. The method was also exclusionary in that some species were restricted to a particular cluster or subcluster. Amylase patterns confirmed that strains referred to as single species are not all homogeneous genetically, and that some strains are not simply haploid homokaryons. The genetic heterogeneity of the strains explains some of the problems in the systematics of the terverticillate penicillia.

A reappraisal of the terverticillate penicillia using biochemical, physiological and morphological features. II. Identification.

The data from an integrated numerical classification was used to construct identification schemes for some fasciculate penicillia. The identification schemes were presented as a synoptic key and a frequency matrix for computer-assisted identification. Statistical testing of the frequency matrix showed that although character separation values were generally low, only four pairs of taxa showed overlap greater than that expected for a rectangular distribution. The identification schemes were tested practically with 52 previously studied strains and 51 further cultures. A synoptic key based on 10 and 90% cutoff limits was used to correctly identify 44 of the 51 additional strains, although this proved very sensitive to single test discrepancies. The frequency matrix was used to correctly identify 45 of the additional strains with a Willcox probability score and this was compared to identifications based on the modal likelihood fraction.

Structuring strain data for storage and retrieval of information on fungi and yeasts in MINE, the Microbial Information Network Europe.

A distributed Microbial Information Network Europe (MINE) is being constructed by a number of major microbial culture collections in countries of the European Community, with the support of the Biotechnology Action Programme (BAP) of the Commission of the European Community. The representatives of the collections participating in MINE have agreed to adopt a general format for the computer storage and retrieval of strain data. This uniform format will facilitate the electronic combination and exchange of data from different collections in order to produce integrated catalogues and the use of identical commands to search the different databases. It is recommended to other collections who may wish to contribute data to the MINE network or between themselves. Three kinds of records can be linked to the leading 'species records': strain records, synonym records, and alternative morphonym records. A minimum data set of 30 fields (similar to the fields used for producing catalogues) is defined that facilitates the exchange of data between the national nodes and serves as a directory to strains available at other nodes. It is suggested that the full strain record comprise 99 fields, grouped in 12 blocks: internal administration--name--strain administration--status--environment and history--biological interactions--sexuality--properties (cytology, biomolecular data)--genotype and genetics--growth conditions--chemistry and enzymes--practical applications. Several fields are divided into subfields of different ranks. Delimiters are used either to separate a range of entries that have to be indexed or to divide an entry from the reference to its source or remarks that should not be indexed. The contents and structure of the fields proposed for filamentous fungi and yeasts are described and in some cases illustrated by examples. Uniformity of input is essential for indexed fields and desirable for non-indexed fields. Seven thesaurus files are envisaged to ensure consistency.

A reappraisal of the terverticillate penicillia using biochemical, physiological and morphological features. I. Numerical taxonomy.

Three-hundred-and-forty-eight strains representing the major species of terverticillate penicillia, and including representatives of other closely and distantly related species, were included in a numerical taxonomic study. One-hundred characters were derived from morphological features, physiological and biochemical activities and SEM micrographs. Strains were compared by both Gower's coefficient and Pattern difference, and clustered using the average linkage algorithm. Thirty-seven species or species-complex clusters were recovered at approximately 70% similarity; they generally corresponded to existing taxonomic concepts. Several species were shown to contain variants or chemotypes which were often supported by differences in conidial shape and ornamentation. The use of different types of characters enabled a number of new and previously accepted species to be shown to be either variants or deteriorated examples of other species. Variation in properties both between and within species was considered, particularly in relation to strain stability.

Pneumocystis carinii shows DNA homology with the ustomycetous red yeast fungi.

Pneumocystis carinii causes life-threatening pneumonia in T-lymphocyte-immunodeficient subjects in transplant and oncology units or with acquired immune deficiency syndrome (AIDS). Recent DNA homology studies show P. carinii to be a fungus. To investigate the biology and epidemiology of this parasite further, we elected to determine for it a more precise taxonomic assignment within the fungal kingdom. We screened a wide range of organisms representing the major orders of fungi using DNA amplification and subsequently sequenced a portion of the mitochondrial gene encoding the large subunit ribosomal RNA. Our data show that the opportunistic pulmonary pathogen P. carinii is closely related to the ustomycetous red yeast fungi, a group which includes organisms that are extensively distributed throughout the environment and which release many widely dispersed airborne spores.