Steven L. Stephenson

The Faces of Fungi database: fungal names linked with morphology, phylogeny and human impacts

Taxonomic names are key links between various databases that store information on different organisms. Several global fungal nomenclural and taxonomic databases (notably Index Fungorum, Species Fungorum and MycoBank) can be sourced to find taxonomic details about fungi, while DNA sequence data can be sourced from NCBI, EBI and UNITE databases. Although the sequence data may be linked to a name, the quality of the metadata is variable and generally there is no corresponding link to images, descriptions or herbarium material. There is generally no way to establish the accuracy of the names in these genomic databases, other than whether the submission is from a reputable source. To tackle this problem, a new database (FacesofFungi), accessible at www.facesoffungi.org (FoF) has been established. This fungal database allows deposition of taxonomic data, phenotypic details and other useful data, which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification system. In addition, the database will also allow access to comprehensive metadata including descriptions of voucher and type specimens. This database is user-friendly, providing links and easy access between taxonomic ranks, with the classification system based primarily on molecular data (from the literature and via updated web-based phylogenetic trees), and to a lesser extent on morphological data when molecular data are unavailable. In FoF species are not only linked to the closest phylogenetic representatives, but also relevant data is provided, wherever available, on various applied aspects, such as ecological, industrial, quarantine and chemical uses. The data include the three main fungal groups (Ascomycota, Basidiomycota, Basal fungi) and fungus-like organisms. The FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological expertise. The webpage has 76 curators, and with the help of these specialists, FoF will provide an updated natural classification of the fungi, with illustrated accounts of species linked to molecular data. The present paper introduces the FoF database to the scientific community and briefly reviews some of the problems associated with classification and identification of the main fungal groups. The structure and use of the database is then explained. We would like to invite all mycologists to contribute to these web pages.

Myxomycete biodiversity in four different forest types in Costa Rica

The moist chamber culture technique was used to examine patterns of biodiversity and distri- bution of myxomycetes in four different forest types in Costa Rica, focusing on the substrates represented by the bark surface of living trees and leaf litter. Rar- efaction as well as bootstrap analyses were carried out to estimate the completeness of the survey in terms of the numbers of species of myxomycetes present. Both species diversity and myxomycete abundance decreased with increasing elevation and resulting higher moisture levels of the investigated forest types. The two seasonal dry forest types accounted for 90% of the total myxomycete diversity. For bark-inhabiting myxomycetes, species richness was found to be neg- atively correlated with epiphyte (i.e., mosses, liver- worts, and lichens) coverage. For both litter and bark, a higher substrate pH tended to be positively correlated with higher species diversity. Among litter- inhabiting myxomycetes, the proportion of species with rather robust phaneroplasmodia increased with increasing elevation. All of these results indicate that the excess of moisture in continuously moist tropical forests does not favor myxomycete growth and de- velopment. Species richness and frequency patterns for both substrate types were found to be comparable with those calculated from a data set reported for a study area in the temperate zone, indicating that myxomycete biodiversity does not reach its highest

From morphology to molecular biology: can we use sequence data to identify fungal endophytes?

Isolation followed by morphological identification was the traditional basis of all earlier endophyte studies. However, the use of molecular phylogenetics has become increasingly common in the identification of fungal endophytes, and during the period of 2007–2010 there were approximately 200 publications that reported data obtained using this approach. This new methodology involves using sequence data from isolates or whole DNA from plant substrates, which are amplified using fungus- specific primers. The data obtained are compared with sequences downloaded from public databases such as GenBank and then used to construct phylogenetic trees. The major problem with this approach is that much of the sequence data in these databases has been shown to be from isolates that were incorrectly named. In some species, as much as 86% of the sequences available are not from the organism whose name has been applied to the sequence in question. The use of these GenBank sequences to identify endophytic isolates by sequence similarity simply perpetuates the problem of wrong species identification, and any lists of endophytes established by such methods are likely to be highly erroneous. It is recommended that comparisons of sequence data be made using sequences from type species, and if such sequences are not available, then the data must be treated with caution.

A comparative biogeographical study of myxomycetes in the mid-Appalachians of eastern North America and two regions of India

Although species lists for particular localities have been compiled by numerous workers, relatively few biogeographical studies of myxomycetes (plasmodial slime moulds) have been carried out. In the present study, the data represented by a total of 3788 collections of myxomycetes made during the period of 1954-90 from two study areas in the midAppalachians of eastern North America and study areas in northwestern and southern India were analysed to obtain information on the biogeographical relationships and patterns of occurrence of these organisms. The climate of the study area in southern India is tropical/subtropical, whereas both study areas in eastern North America and the one in north western India have a temperate climate. Based on coefficient of community indices calculated for all possible combinations of the four different data sets, southern India had the lowest overall similarity (mean index = 0.322) to the other study areas. Members of the Physarales made up a much greater proportion (63%) of the collections from southern India than elsewhere, whereas members of the Liceales were conspicuously under-represented when compared to the other study areas. The majority of collections ( > 63%) from southern India occurred on leaf litter and other types of non-woody plant debris, whereas > 80% of all collections from eastern North America and north western India were made from woody substrates. These results suggest that myxomycetes show recognizable patterns of latitudinal variation not unlike those described for many other groups of organisms. Not only is the assemblage of species found in tropical/subtropical regions of the world distinctly different from that of temperate regions, but the species present also exhibit quite different patterns of distribution with respect to the types of substrates upon which they typically occur.

Myxomycete diversity and distribution from the fossil record to the present

The myxomycetes (plasmodial slime molds or myxogastrids) are a group of eukaryotic microorganisms usually present and sometimes abundant in terrestrial ecosystems. Evidence from molecular studies suggests that the myxomycetes have a significant evolutionary history. However, due to the fragile nature of the fruiting body, fossil records of the group are exceedingly rare. Although most myxomycetes are thought to have very large distributional ranges and many species appear to be cosmopolitan or nearly so, results from recent studies have provided evidence that spatial distribution patterns of these organisms can be successfully related to (1) differences in climate and/or vegetation on a global scale and (2) the ecological differences that exist for particular habitats on a local scale. A detailed examination of the global distribution of four examples (Barbeyella minutissima, Ceratiomyxa morchella, Leocarpus fragilis and Protophysarum phloiogenum) demonstrates that these species have recognizable distribution patterns in spite of the theoretical ability of their spores to bridge continents.

The present distribution of chestnut in the upland forest communities of Virginia

STEPHENSON, S. L., H. S. ADAMS AND M. L. LIPFORD (Department of Biology, Fairmont State College, Fairmont, WV 26554, Division of Arts and Sciences, Dabney S. Lancaster Community College, Clifton Forge, VA 24422, and Division of Natural Heritage, Department of Conservation and Recreation, Richmond, VA 23219). The present distribution of chestnut in the upland forest communities of Virginia. Bull. Torrey Bot. Club 118: 24-32. 1991.-The present distribution of American chestnut (Castanea dentata [Marsh.] Borkh.) as a component of upland forest communities in the mid-Appalachians was investigated in three different areas of western Virginia. Two of these (Alleghany County and the Mountain Lake area of Giles County) are within the Ridge and Valley physiographic province and the third (Shenandoah National Park) is in the Blue Ridge province. Quantitative data on composition and structure of the vegetation and various topographic variables were analyzed using correlation analysis and DCA ordination. The results of these analyses indicate that the present distribution of chestnut is strongly correlated with elevation and site moisture conditions. In general, chestnut was much less abundant (only 192 stems/ha) in Alleghany County (mean elevation of 39 stands = 645 m) than in either Shenandoah National Park (532 stems/ha) or Giles County (770 stems/ha), where sampled stands occur at mean elevations of 882 m (20 stands) and 1079 m (43 stands), respectively. Maximum density of chestnut (>2500 stems/ha for some stands) occurred on subxeric sites, particularly midto upper slope positions on southern exposures. In all three areas, chestnut was conspicuously absent from most mesic sites.

Ecological characterization of a tropical myxomycete assemblage—Maquipucuna Cloud Forest Reserve, Ecuador

The assemblage of myxomycetes (plasmodial slime molds) associated with cloud forests of the Maquipucuna Cloud Forest Reserve in the western Andes was investigated. Within three study sites located along a gradient extending from 1200 to 2700 m above sea level, a clear pattern of decreasing myxomycete diversity and productivity with elevation was apparent. As such, these data conform to the pattern of “reverse diversity” for myxomycetes in the neotropics, with higher diversity for less mesic forest types than for more mesic forest types. Canonical correspondence analysis of myxomycete abundances in relation to microhabitat parameters revealed three major ecological assemblages: wood-, litter- and inflorescence-inhabiting species. All three assemblages include a number of specialized species, with the assemblage associated with litter being the most diverse and the one associated with inflorescences being the most distinctive. In addition, samples from the microhabitat represented by the cover of epiphyllic liverworts on living leaves regularly produce myxomycetes in moist chamber culture but with few sporocarps and no evidence of any specialized species. At least near ground level, bark-inhabiting (corticolous) myxomycetes are uncommon in the cloud forests sampled in the present study.

From morphological to molecular: studies of myxomycetes since the publication of the Martin and Alexopoulos (1969) monograph

Myxomycetes (plasmodial slime molds or myxogastrids) are a group of eukaryotic microorganisms usually present and sometimes abundant in terrestrial ecosystems. Because they produce aerial spore-bearing structures that resemble those of certain fungi and also typically occur in some of the same types of ecological situations as fungi, myxomycetes have been traditionally studied by mycologists, and this continued to be the case for the greater part of the twentieth century. However, there is now abundant molecular data to confirm that they are amoebozoans and not fungi. Efforts are currently underway to develop the first molecular phylogeny for myxomycetes, and several recent studies have used molecular techniques to detect the presence of these organisms in nature by means of direct environmental sampling.

Mycorrhizal Assessment of Vascular Plants from Subantarctic Macquarie Island

Roots of 40 taxa of vascular plants from subantarctic Macquarie Island were examined to determine their mycorrhizal status. Samples comprised 36 flowering plant taxa (Spermatophyta) from 16 families, and 4 nonflowering plant taxa (Pteridophyta) from 4 families. No arbutoid, ericoid, or ectomycorrhizae were observed, nor did we collect the fruiting bodies of any fungi whose presence would indicate or suggest the presence of ectomycorrhizal associations. Fifteen of the plants examined showed vesicles, but vesicles and arbuscles were observed in only three plants: Hydrocotyle novae-zeelandiae (Apiaceae), Pleurophyllum hook

Taxonomic revision of true morels (Morchella) in Canada and the United States

Recent molecular phylogenetic studies have revealed the existence of at least 50 species of Morchella worldwide and demonstrated a high degree of continental endemism within the genus. Here we describe 19 phylogenetic species of Morchella from North America, 14 of which are new (M. diminutiva, M. virginiana, M. esculentoides, M. prava, M. cryptica, M. frustrata, M. populiphila, M. sextelata, M. septimelata, M. capitata, M. importuna, M. snyderi, M. brunnea and M. septentrionalis). Existing species names (M. rufobrunnea, M. tomentosa, M. punctipes and M. angusticeps) are applied to four phylogenetic species, and formal description of one species (M. sp. “Mel-8”) is deferred pending study of additional material. Methods for assessing morphological features in Morchella are delineated, and a key to the known phylogenetic species of Morchella in North America is provided. Type studies of M. crassistipa, M. hotsonii, M. angusticeps and M. punctipes are provided. Morchella crassistipa is designated nomen dubium.