Adam W. Rollins

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.

Myxomycetes associated with grasslands of the western central United States

The assemblages of myxomycetes associated with the three types of temperate grasslands (tall grass, mixed grass and short grass) found across the western central United States were examined by collecting samples for isolation of these organisms from nine study sites. Samples consisted of two types of ground litter, two types of aerial litter (dead but still attached plant parts) and dung. These were brought back to the laboratory and used to prepare a series of moist chamber cultures. These cultures yielded 1,301 collections of myxomycetes representing 59 species in 18 genera. Some collections could be identified only to genus and one in particular (Lepidoderma sp.) appears to be an undescribed taxon. Physarum spectabile was recorded for the first time in North America. Overall, only eight species (Badhamia melanospora, Didymium anellus, D. difforme, D. squamulosum, Perichaena depressa, Physarum cinereum, P. pusillum, and Stemonitis fusca) were recovered from all nine study sites and thus are considered to represent a core component of the myxomycete biota of temperate grasslands.

Changes in Forest Composition and Structure across the Red Spruce-Hardwood Ecotone in the Central Appalachians

Abstract During the period of 1992 to 1994, ten belt transects, each consisting of a series of contiguous 10 × 10 m (100 m2) quadrats, were established and sampled at seven study sites in southwestern Virginia and eastern central West Virginia. Each transect extended from a red spruce-dominated community through the ecotone and into the adjacent hardwood community. In 2004 and 2005, these same transects were resampled in order to assess changes that had occurred. As a general trend, red spruce either maintained its ecological status or increased in number in all size classes, with noticeable expansion into the hardwood community at some study sites.

Dictyostelid cellular slime molds associated with grasslands of the central and western United States

Dictyostelid cellular slime molds (dictyostelids) associated with grassland ecosystems of the central and western United States were investigated at nine sites that included examples of the three major ecological types of grasslands (tall grass, mixed grass and short grass) generally recognized for the region. Samples of soil/humus collected from each site were examined with the Cavender method of isolating dictyostelids. For each of those six sites with well developed gallery forests present, an additional set of forest soil/humus samples was collected. A more intensive sampling effort was carried out at one site (Konza LTER) to assess the possible effects of burning and grazing on dictyostelid diversity and density. Twelve species of dictyostelids were recovered from grassland sites, whereas gallery forest sites yielded only nine species. Four cosmopolitan species (Dictyostelium giganteum, D. mucoroides, D. sphaerocephalum and Polysphondylium pallidum) were represented by the greatest densities of clones, with D. sphaerocephalum particularly common. The general pattern across all sites was that both species richness and density of dictyostelids decreased with decreasing precipitation. Samples collected from ungrazed grassland plots yielded higher numbers of both species and clones as compared to grazed plots, and the general pattern was for both values to increase as the interval between fires increased. For numbers of clones this correlation was statistically significant.

New small dictyostelids from seasonal rainforests of Central America

Ten small dictyostelids isolated from samples collected from the surface humus layer of seasonal rainforests of Belize and Guatemala were studied morphologically, and nine were found to represent distinct species, all with an average height of < 2 mm (0.5–3.5 mm). Although their fruiting bodies (sorocarps) closely resemble one another, the nine species differ in their patterns of aggregation, stream pattern, branching development, formation of microcysts, spore shape, presence or absence of spore granules and their distribution, as well as in the shapes and behavior of their sorogens and myxamoebae. These stable morphological features were sufficient to recognize nine new species of small dictyostelids, one with two varieties. SSU rDNA sequences were generated for all these new isolates, and phylogenetic analyses of these sequences show these new isolates belong to Dictyostelid group 3. As a result of this and other recent studies, the concept of what constitutes a species in the dictyostelids has become much more restricted and well defined, in as much as some of the morphological and behavioral patterns now being observed were overlooked in the past. The extent, flow direction and conformation of streaming within the group varies from simple aggregation mounds with no streams to short streams, to somewhat longer streams and finally to well developed streams. Each of these is characterized by a particular set of distinguishing features.

Ecology and Distribution of Myxomycetes

Abstract In this chapter, the results obtained from recent studies of myxomycete ecology are discussed, with special emphasis on their distribution patterns in particular habitats, the relationships that exist between myxomycetes and other organisms and the effect of disturbance events on myxomycete communities. It is important to note that most of the available data are based on collections of fruiting bodies, which probably represent (in a literal sense) only the tip of the iceberg because it is possible that these reflect only a minor fraction of the real diversity of myxomycetes in a particular habitat. Therefore, it appears unlikely that a single method will be universally applicable for assessing myxomycete diversity in all habitats and on all substrates. The approaches, techniques, and their potential limitations are discussed herein, along with recent advances (e.g., moist chamber cultures, environmental PCR, metagenomics and barcoding attempts) that have been applied to studies of myxomycete ecology and will undoubtedly increase our understanding of myxomycete communities in the future.

Dictyostelid Cellular Slime Molds of Arkansas

Abstract During the period of 2003 to 2008, samples for isolation of dictyostelid cellular slime molds (dictyostelids) were collected from 17 localities throughout the state of Arkansas. The localities sampled included at least two examples in each of the six natural regions (Arkansas River Valley, Ozark Plateau, Ouachita Mountains, Gulf Coastal Plain, Crowleys Ridge and Mississippi Alluvial Plain) recognized for the State. The 167 samples collected from the 17 localities yielded a total of 2,082 individual clones representing 13 different species plus one form that could not be assigned to any described species. Six of the species recovered are reported from Arkansas for the first time, bringing the total number known from the State to 16. Polysphondylium pallidum was by far the most abundant species, comprising almost 50% of all isolates. Three other species (Dictyostelium minutum, P. violaceum and D. purpureum) made up approximately 30% of all remaining isolates, and the nine other species recovered were uncommon to rare. Two isolates of what appears to be Dictyostelium rhizopodium, a species in which the sorocarps have crampon bases, represent one of the northernmost known occurrences of a dictyostelid with this feature, which is characteristically found in species associated with tropical and subtropical regions of the world. Two species (D. caveatum and D. rosarium) reported previously from Arkansas were not isolated in the present study.

Ectomycorrhizal Fungi Associated with American Chestnut at a Site in Tennessee, USA

ABSTRACT  The ectomycorrhizal fungi associated with American chestnut (Castanea dentata) were characterized using DNA extracted from the root-tips of naturally occurring saplings from a forest in northeastern Tennessee. A total of 18 taxa were recorded, although one of these (Oidiodendron maius) was surprising because it has been reported previously to form what appear to be mycorrhizal associations only with members of the Ericaceae. One-third of the recorded taxa were representatives of the genera Russula or Lactarius (both members of the family Russulaceae), and three other genera (Cortinarius, Tomentella, and Tricholoma, each represented by two species). The data presented herein at least suggest that members of the Russulaceae are among the most common and widespread ectomycorrhizal fungi associated with naturally occurring individuals of American chestnut in the forests of eastern North America in which it was once dominant. However, it should be pointed out that our data are limited and thus are best considered as preliminary.

Methods for Sampling and Analyzing Wetland Fungi

Most fungi are terrestrial, but representatives of all major groups of fungi along with three groups of fungus-like organisms (water molds, slime molds and lichens), usually studied by mycologists, can be found in wetlands. The primary ecological role of the fungi and water molds in wetland habitats is to decompose dead plant material—both woody and herbaceous debris as well as dead bryophytes. Although sometimes present in wetlands, slime molds and lichens occur almost exclusively on emergent (dry) substrates. Because the vast majority of fungi and fungus-like organisms associated with wetlands are microscopic, efforts to document their distribution and patterns of occurrence often pose a real challenge to ecologists. This chapter reviews some of the more useful and effective methods that can be used to study these organisms in wetland habitats. These include collecting specimens directly in the field, isolating specimens from substrate samples placed in moist chamber cultures and obtaining specimens on various types of organic baits.

Myxomycete Assemblages Recovered from Experimental Grass and Forb Microhabitats Placed Out and Then Recollected in the Tallgrass Prairie Preserve, OK

Abstract Results obtained in studies of grassland myxomycetes (plasmodial slime molds or myxogastrids), based on the species appearing in moist-chamber cultures, have indicated that forb microhabitats yield considerably more collections than grass microhabitats. We experimentally evaluated this pattern at the Tall Grass Prairie Preserve in Oklahoma by using litterbags prepared with autoclaved samples of grasses and forbs. We obtained a total of 162 collections representing 20 species; Perichaena pedata and Diderma effusum were the dominant species present. Total number of collections, species richness, and species diversity were significantly higher for forb microhabitats when compared to grass microhabitats. These results corroborate previous reports and demonstrate the utility of using litterbags as an experimental approach to assess myxomycete diversity and to confirm or refute observations from previous ecological studies.