Andy F. S. Taylor

Towards a unified paradigm for sequence‐based identification of fungi

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third‐party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web‐based sequence management system in UNITE.

Fungal diversity in ectomycorrhizal communities: sampling effort and species detection

A number of recent review articles on ectomycorrhizal (ECM) fungal community diversity have highlighted the unprecedented increase in the number of publications on this ecologically important but neglected area. The general features of these species-rich, highly dynamic and complex communities have been comprehensively covered but one aspect crucial to our assessment of diversity, namely the sampling of ECM communities has received less attention. This is a complex issue with two principal components, the physical sampling strategy employed and the life cycle traits of the ECM fungi being examined. Combined, these two components provide the image that we perceive as ECM diversity. This contribution will focus primarily on the former of these components using a recent study from a pine forest in central Sweden to highlight some sampling problems and also to discuss some features common to ECM communities. The two commonly used elements of diversity, species richness and community evenness, present rather different problems in the assessment of ECM diversity. The applicability of using current measures of abundance (number or percentage of root tips colonised) to determine community evenness is discussed in relation to our lack of knowledge on the size of individual genets of ECM fungi. The inherent structure of most ECM communities, with a few common species and a large number of rare species, severely limits our ability to accurately assess species richness. A discussion of theoretical detection limits is included that demonstrates the importance of the sampling effort (no. of samples or tips) involved in assessing species richness. Species area abundance plots are also discussed in this context. It is suggested that sampling strategy (bulk samples versus multiple collections of single tips) may have important consequences when sampling from communities where root tip densities differ. Finally, the need for studies of the spatial distribution of ECM on roots in relation to small-scale soil heterogeneity and of the temporal aspects of ECM community dynamics is raised.

RecBCD enzyme is a DNA helicase with fast and slow motors of opposite polarity

Helicases are molecular motors that move along and unwind double-stranded nucleic acids. RecBCD enzyme is a complex helicase and nuclease, essential for the major pathway of homologous recombination and DNA repair in Escherichia coli. It has sets of helicase motifs in both RecB and RecD, two of its three subunits. This rapid, highly processive enzyme unwinds DNA in an unusual manner: the 5′-ended strand forms a long single-stranded tail, whereas the 3′-ended strand forms an ever-growing single-stranded loop and short single-stranded tail. Here we show by electron microscopy of individual molecules that RecD is a fast helicase acting on the 5′-ended strand and RecB is a slow helicase acting on the 3′-ended strand on which the single-stranded loop accumulates. Mutational inactivation of the helicase domain in RecB or in RecD, or removal of the RecD subunit, altered the rates of unwinding or the types of structure produced, or both. This dual-helicase mechanism explains how the looped recombination intermediates are generated and may serve as a general model for highly processive travelling machines with two active motors, such as other helicases and kinesins.

Defining nutritional constraints on carbon cycling in boreal forests – towards a less `phytocentric' perspective

Growing interest in possible global climate change has underlined the need for better information concerning the way in which carbon partitioning between ecosystem components is influenced by constraints on nutrient availability. Micro-organisms play a fundamental role in the cycling of carbon and nutrients in all ecosystems but the role of fungi in particular is pivotal in boreal forest ecosystems. Traditional models of nutrient cycling are based on methods and concepts developed in agricultural systems where microorganisms are considered primarily as nutrient processors providing plants with inorganic nutrients. The filamentous nature of fungi, their ability to translocate carbon and nutrients between different substrates and the capacity of ectomycorrhizal fungi to utilise organic nutrients have all been largely ignored. In this article, a new model is suggested which emphasises competition for organic nutrients between decomposer organisms and plants, with the plants depending on their associated mycorrhizal fungi for nutrient acquisition. Antagonistic interactions involving nutrient transfer between decomposer and mycorrhizal fungi are proposed as important pathways in nutrient cycling. Due to the nutrient conservative features of decomposer fungi, inorganic nutrients are considered less important for plant nutrition. The implications of the new nutrient cycling model on the carbon balance of boreal forests are discussed.

Diversity and abundance of resupinate thelephoroid fungi as ectomycorrhizal symbionts in Swedish boreal forests.

Resupinate thelephoroid fungi (hereafter called tomentelloid fungi) have a world‐wide distribution and comprise ≈70 basidiomycete species with inconspicuous, resupinate sporocarps. It is only recently that their ability to form ectomycorrhizas (EM) has been realized, so their distribution, abundance and significance as mycobionts in forest ecosystems is still largely unexplored. In order to provide baseline data for future ecological studies of tomentelloid fungi, we explored their presence and abundance in nine Swedish boreal forests in which the EM communities had been analysed. Phylogenetic analyses were used to compare the internal transcribed spacer of nuclear ribosomal DNA (ITS rDNA) sequence data obtained from mycobionts on single ectomycorrhizal tips with that obtained from sporocarps of identified tomentelloid fungi. Five species of Tomentella and one species of Pseudotomentella were identified as ectomycorrhizal fungi. The symbiotic nature of Tomentella bryophila, T. stuposa, T. badia and T. atramentaria is demonstrated for the first time. T. stuposa and Pseudotomentellatristis were the most commonly encountered tomentelloid fungi, with the other species, including T. sublilacina, only being recorded from single stands. Overall, tomentelloid fungi were found in five of the studies, colonizing between 1 and 8% of the mycorrhizal root tips. Two of the five sites supported several tomentelloid species. Tomentelloid fungi appear to be relatively common ectomycorrhizal symbionts with a wide distribution in Swedish coniferous forests. The results are in accordance with accumulating data that fungal species which lack conspicuous sporocarps may be of considerable importance in EM communities.

Fungal communities in mycorrhizal roots of conifer seedlings in forest nurseries under different cultivation systems, assessed by morphotyping, direct sequencing and mycelial isolation

Fungi colonising root tips of Pinus sylvestris and Picea abies grown under four different seedling cultivation systems were assessed by morphotyping, direct sequencing and isolation methods. Roots were morphotyped using two approaches: (1) 10% of the whole root system from 30 seedlings of each species and (2) 20 randomly selected tips per plant from 300 seedlings of each species. The first approach yielded 15 morphotypes, the second yielded 27, including 18 new morphotypes. The overall community consisted of 33 morphotypes. The level of mycorrhizal colonisation of roots determined by each approach was about 50%. The cultivation system had a marked effect on the level of mycorrhizal colonisation. In pine, the highest level of colonisation (48%) was observed in bare-root systems, while in spruce, colonisation was highest in polyethylene rolls (71%). Direct internal transcribed spacer ribosomal DNA sequencing and isolation detected a total of 93 fungal taxa, including 27 mycorrhizal. A total of 71 (76.3%) fungi were identified at least to a genus level. The overlap between the two methods was low. Only 13 (13.9%) of taxa were both sequenced and isolated, 47 (50.5%) were detected exclusively by sequencing and 33 (35.5%) exclusively by isolation. All isolated mycorrhizal fungi were also detected by direct sequencing. Characteristic mycorrhizas were Phialophora finlandia, Amphinema byssoides, Rhizopogon rubescens, Suillus luteus and Thelephora terrestris. There was a moderate similarity in mycorrhizal communities between pine and spruce and among different cultivation systems.

Post-fire legacy of ectomycorrhizal fungal communities in the Swedish boreal forest in relation to fire severity and logging intensity

Swedish foresters are placing increasing reliance in burning of forestland and green tree retention, in order to enhance biodiversity in the Swedish boreal forests. However, much remains to be learned about how to optimise nature conservation goals by different logging and burning procedures. We monitored the survival of ectomycorrhizal (EM) fungi as mycorrhizas, at a clear-cut, a seed tree stand and an uncut stand of Scots pine in central Sweden, with and without burning at two levels of fire severity. The abundance of mycorrhizas and the EM fungal diversity declined with increased logging intensity and with increased depth of burn. Deep burning fires in combination with logging or fire-caused tree mortality can kill much of the existing EM community. Logging intensity, fire intensity and fire severity are all factors that can be manipulated, thus changing the effects on EM fungi and other soil biota.

Mycelial growth and substrate acidification of ectomycorrhizal fungi in response to different minerals.

A colorimetric method was developed to permit semi-quantitative measurement of substrate acidification by different ectomycorrhizal and one saprotrophic fungus growing on media containing one of five different minerals. Overall, substrate acidification differed between fungal species and the degree of variation in acidification in response to different minerals was highly species-dependent. Mycena galopus and Cortinarius glaucopus produced the least biomass of all tested species and produced the highest amount of acidification per unit mycelial density. Substrate acidification by C. glaucopus was inversely related to mycelial density, with particularly high acidification at low mycelial density on medium enriched with tri-calcium phosphate. Substrate acidification by M. galopus was constant irrespective of mycelial density and varied only according to mineral treatment, with higher substrate acidification on tri-calcium phosphate compared to the other minerals.

Effects of Acidification and its Mitigation with Lime and Wood Ash on Forest Soil Processes: A Review

Anthropogenic acid deposition causes forest soil acidification and perturbation of the soil forming processes. The impact of soil acidification on tree growth is discussed in view of the role of mycorrhizal fungi in weathering and nutrient uptake. A review has been carried out of experiments involving treatments of forest soil by lime and wood ash, where soil properties and soil solution composition have been investigated. Results from these experiments in Europe and North America are summarized. In general, the content of C in the mor layer decreased as a result of treatment due to higher microbial activity and soil respiration as well as increased leakage of DOC. In addition, the content of N in the mor layer, in general, decreased after treatment and there are occasional peaks of high NO3concentrations in soil solution. In nearly all reviewed investigations the pH of the deep mineral soil solution decreased and Al, SO4and NO3concentrations increased after treatment. These effects are probably due to the high ionic strength and increased microbial activity as a consequence of the treatments. In the soil, pH, CEC and base saturation increased in the upper horizons, but decreases in the upper mineral soil are also reported. In general, there was no increase in tree growth as a result of these treatments. The positive effects of the treatments on soil processes and tree growth are therefore questionable. In view of these conclusions, an investigation was carried out on the soil and soil solution chemistry and the role of mycorrhizal fungi in a spruce stand treated with two doses of lime and another treated with lime/ash in southern Sweden. The results of this investigation is reported in this volume.

Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses

BackgroundMany fungi are obligate biotrophs of plants, growing in live plant tissues, gaining direct access to recently photosynthesized carbon. Photosynthate within plants is transported from source to sink tissues as sucrose, which is hydrolyzed by plant glycosyl hydrolase family 32 enzymes (GH32) into its constituent monosaccharides to meet plant cellular demands. A number of plant pathogenic fungi also use GH32 enzymes to access plant-derived sucrose, but less is known about the sucrose utilization ability of mutualistic and commensal plant biotrophic fungi, such as mycorrhizal and endophytic fungi. The aim of this study was to explore the distribution and abundance of GH32 genes in fungi to understand how sucrose utilization is structured within and among major ecological guilds and evolutionary lineages. Using bioinformatic and PCR-based analyses, we tested for GH32 gene presence in all available fungal genomes and an additional 149 species representing a broad phylogenetic and ecological range of biotrophic fungi.ResultsWe detected 9 lineages of GH32 genes in fungi, 4 of which we describe for the first time. GH32 gene number in fungal genomes ranged from 0–12. Ancestral state reconstruction of GH32 gene abundance showed a strong correlation with nutritional mode, and gene family expansion was observed in several clades of pathogenic filamentous Ascomycota species. GH32 gene number was negatively correlated with animal pathogenicity and positively correlated with plant biotrophy, with the notable exception of mycorrhizal taxa. Few mycorrhizal species were found to have GH32 genes as compared to other guilds of plant-associated fungi, such as pathogens, endophytes and lichen-forming fungi. GH32 genes were also more prevalent in the Ascomycota than in the Basidiomycota.ConclusionWe found a strong signature of both ecological strategy and phylogeny on GH32 gene number in fungi. These data suggest that plant biotrophic fungi exhibit a wide range of ability to access plant-synthesized sucrose. Endophytic fungi are more similar to plant pathogens in their possession of GH32 genes, whereas most genomes of mycorrhizal taxa lack GH32 genes. Reliance on plant GH32 enzyme activity for C acquisition in these symbionts supports earlier predictions of possible plant control over C allocation in the mycorrhizal symbiosis.