Response of wood-inhabiting fungal community to fragmentation in a beech forest landscape

Fragmentation of natural habitats has become one of the main causes of the loss of biodiversity. To assess the effects of forest fragmentation on wood-inhabiting fungal community in a beech-dominated landscape, 15 differently shaped beech forest fragments were examined in northern Spain. This work covers all the wood-inhabiting macromycetes, including Basidiomycota and Ascomycota. A modelling approach was used to examine the predictability of the fungal community in a fragmented beech forest landscape. In the beech forest patches, a large proportion of edge, low tree densities and low levels of variety of woody debris caused a decrease of wood-inhabiting fungal richness. The fungal community composition proved complex to model due to its specific traits: it is made up of many species, most of which are rare, and each fungal group responds differently to environmental variables. Nevertheless, the dead wood availability and the exposure to light significantly affected the fungal community composition.     

Taxonomic gap in wood-inhabiting fungi: identifying understudied groups by a systematic survey

Despite advances in phylogenetic research and the number of ecological studies focusing on wood-inhabiting fungi, these species still represent a taxonomically poorly known group of organisms. In this study, our overall aim was to detect and characterize the understudied wood-inhabiting fungal groups in the beech forests of Navarre (northern Spain). We present a list of 326 wood-inhabiting fungal species, out of which 36 % are first regional records. Comparing the already recorded fungal species in this territory and the list of firstly recorded species, we found that field-mycologists tend to focus on certain fungal groups, and in general rare species are less frequently encountered. Particularly, species with corticioid fruit body type have been especially overlooked in this territory. We attribute the high proportion of new regional records to the use of a systematic sampling design.     

Fungi associated with beetles dispersing from dead wood – Let's take the beetle bus!

Spore characteristics of wood-inhabiting fungi suggest that wind is their predominant dispersal vector. However, since they are restricted to ephemeral habitats, colonizing new patches should benefit from dispersal by animals with similar habitat preferences because the directed, resource-searching movement of animals increases the likelihood of reaching suitable habitats. Here we determine which fungal guilds are carried by wood-inhabiting beetles and what influences beetle-associated fungal communities. High-throughput sequencing identified >1800 fungal taxa from beetle communities that emerged from 64 experimental logs. Beetle-associated fungi included mutualistic, decomposing, pathogenic and mycorrhizal fungi; decomposers were the most diverse. Partial-procrustes analysis revealed that the total beetle-associated community and mutualists were correlated (p ≤ 0.05) with beetle community composition and decomposers were marginally correlated (p ≤ 0.10) with beetle community composition. All three groups were marginally correlated with the total fungal communities that inhabit the dead wood. Our results show that beetles carry a broad range of wood-inhabiting fungi and beetle-associated fungal communities are determined by environmental factors and the vectoring beetle community and to some degree by the fungal source community. This suggests that wood-inhabiting beetles contribute to fungal dispersal, including directed dispersal, which could affect fungal community assembly and ecosystem processes like wood decomposition.     

Effects of a great cormorant colony on wood-inhabiting fungal communities in a coastal Scots pine forest

We studied the changes in the wood-inhabiting fungal communities on dead wood of Scots pine (Pinus sylvestris) under varying duration and intensity of cormorant nesting. The activities of the birds created large amounts of dead wood, changed wood chemistry and altered stand characteristics. Analyses based on records of fruiting structures of fungi showed that fungal communities in the cormorant colony differed from communities in unaffected forest. Ornithogenic factors impacted least on generalist species and promoted the occurrence of fungi uncharacteristic of coniferous wood or wood in general. The rate of ornithogenic change was rapid: a shift in fungal assemblages was evident by the third year of expansion of the bird colony into unaffected forest. It featured the disappearance of tremelloid fungi, a decline of corticioid fungi and an increase of hyphomycetoid fungi. The proportion of coniferous wood specialists decreased and that of generalists increased. It is expected that the changes in fungal communities will persist until the forest is fully regenerated.     

Disturbance and diversity of wood-inhabiting fungi: effects of canopy gaps and downed woody debris

Experimental canopy gap formation and additions of coarse woody debris (CWD) are techniques intended to mimic the disturbance regime and accelerate the development of northern hardwood forests. The effects of these techniques on biodiversity and ecosystem functioning were investigated by surveying the abundance and diversity of wood-inhabiting fungi in six treatments: (i) unharvested control, (ii) control + fenced to exclude deer, (iii) gap creation + fenced to exclude deer, (iv) gap creation, (v) gap creation + CWD addition, and (vi) CWD addition under closed-canopy. A total of 1,885 fungal occurrences (polyporoid and corticoid fruiting bodies) representing 130 species were recorded on 11 tree species, with eight fungal species accounting for 52 % of all observations. A linear mixed model demonstrated significant differences in the abundance and diversity of wood-inhabiting fungi by treatment, with the gap creation + CWD addition treatment supporting the highest abundance and richness of fungal species. Non-metric multidimensional scaling demonstrated that stumps, sugar maple substrates, medium (20 to <25 cm) and large-diameter (>40 cm) substrates most strongly influenced fungal species occurrences. Rarefaction curves indicated that smaller diameter substrates (<20 cm) supported a rich fungal community, yet substrates in the largest diameter class (>40 cm) supported nearly 25 % of all fungal species detected. Rarefaction curves also highlighted the importance of well-decayed substrates and minor host tree species. A subset of fungal species was significantly more abundant in gap treatments. The results indicate that wood-inhabiting fungi are responsive to forest management intended to promote the structural attributes of old-growth northern hardwood forests.     

Application of species richness estimators for the assessment of fungal diversity

Species richness and distribution patterns of wood-inhabiting fungi and mycetozoans (slime moulds) were investigated in the canopy of a Central European temperate mixed deciduous forest. Species richness was described with diversity indices and species-accumulation curves. Nonmetrical multidimensional scaling was used to assess fungal species composition on different tree species. Different species richness estimators were used to extrapolate species richness beyond our own data. The reliability of the abundance-based coverage estimator, Chao, Jackknife and other estimators of species richness was evaluated for mycological surveys. While the species-accumulation curve of mycetozoans came close to saturation, that of wood-inhabiting fungi was continuously rising. The Chao 2 richness estimator was considered most appropriate to predict the number of species at the investigation site if sampling were continued. Gray's predictor of species richness should be used if statements of the number of species in larger areas are required. Multivariate analysis revealed the importance of different tree species for the conservation and maintenance of fungal diversity within forests, because each tree species possessed a characteristic fungal community. The described mathematical approaches of estimating species richness possess great potential to address fungal diversity on a regional, national, and global scale.     

Wood-inhabiting insects can function as targeted vectors for decomposer fungi

Most wood-inhabiting fungi are assumed to be dispersed primarily by wind, with the exception of a few species involved in mutualistic relationships with insects. In this study we tested whether several species of wood-inhabiting insects can function as dispersal vectors for non-mutualistic fungi, which would indicate that wood-inhabiting fungi can benefit from targeted animal-mediated dispersal. We sampled wood-inhabiting beetles (Coleoptera) from freshly felled wood experimentally added to forests and used DNA metabarcoding to investigate the fungal DNA carried by these insects. Staphylinid beetles rarely contained fungal DNA, while Endomychus coccineus, Glischrochilus hortensis and Glischrochilus quadripunctatus frequently carried fungal DNA with a composition specific to the insect taxon. A large proportion of the obtained fungal sequences (34%) represented decomposer fungi, including well-known wood-decay fungi such as Fomitopsis pinicola, Fomes fomentarius, Trichaptum abietinum and Trametes versicolor. Scanning electron microscopy further showed that some of the fungal material was carried as spores or yeast cells on the insect exoskeletons. Our results suggest that insect-vectored dispersal is of broader importance to wood-inhabiting fungi than previously assumed.     

Influence of Forest Management on the Species Richness and Composition of Wood-inhabiting Basidiomycetes in Swiss Forests

In order to investigate the diversity of wood-inhabiting aphyllophoroid basidiomycetes in Swiss forests, 86 plots of 50 m ² were established. They harboured a total of 3339 samples of woody debris, classified according to three categories (coarse, fine, and very fine woody debris), yielding 238 species of wood-inhabiting fungi. The selected sites cover the main forest types of Switzerland and various degrees of management intensity. A multiple linear regression analysis showed that substrate variation, i.e. differences in the quality of dead wood, including volume, age, degree of decomposition and host tree species, are the most important factors influencing diversity of wood-inhabiting fungi. In addition, a Principle Coordinate Analysis highlighted differences in the fungal communities in the different forest types. The greatest fungal species richness is found on thermophilic deciduous tree and woody shrub species. Fine and very fine woody debris, even present in intensively managed forests, often serve as important refuges for many species. Forests with a recent management intervention were found to be either species poor or species rich. Possible reasons for these differences may lay in forest size and landscape fragmentation, the distance to the nearest species pool or microclimatic factors. In Switzerland intensively managed forests harbour significantly less wood-inhabiting, aphyllophoroid fungi than non-managed or extensively managed forests. This is the case in both deciduous forests and in conifer forests. However, occasionally intensively managed forest will also harbour rare and endangered species.     

Diversity and ecology of wood-inhabiting aphyllophoroid basidiomycetes on fallen woody debris in various forest types in Switzerland

This study on the ecology of aphyllophoroid wood-inhabiting basidiomycetes in Switzerland showed a remarkably high species diversity of both saprophytes and mycorrhiza-forming species. Phlebiella vaga, a saprophytic species, and Amphinema byssoides, a mycorrhizal symbiont, were the two most abundant species. A total of 3339 samples of fungal fruitbodies in 86 plots distributed all over Switzerland belonged to 238 species. The five main biogeographical regions of Switzerland showed different pattern of fungal species richness: while the Plateau at lower altitudes was found to be rather rich, the Northern Alps and Central Alps, with the highest amount of forests cover, yielded less species. Although the Southern Alps exhibited the lowest species richness, this region harbours a specific species set. These findings encourage for further studies in Central Europe, where many species of aphyllophoroid wood-inhabiting basidiomycetes seem to be highly under-investigated.     

Fungal community dynamics in relation to substrate quality of decaying Norway spruce ( Picea abies [L.] Karst.) logs in boreal forests

Decaying wood plays an important role in forest biodiversity, nutrient cycling and carbon balance. Community structure of wood-inhabiting fungi changes with mass loss of wood, but the relationship between substrate quality and decomposers is poorly understood. This limits the extent to which these ecosystem services can be effectively managed. We studied the fungal community and physico-chemical quality (stage of decay, dimensions, density, moisture, C : N ratio, lignin and water or ethanol extractives) of 543 Norway spruce logs in five unmanaged boreal forest sites of southern Finland. Fungi were identified using denaturing gradient gel electrophoresis and sequencing of DNA extracted directly from wood samples. Macroscopic fruiting bodies were also recorded. Results showed a fungal community succession with decreasing wood density and C : N ratio, and increasing moisture and lignin content. Fungal diversity peaked in the most decayed substrates. Ascomycetes typically colonized recently fallen wood. Brown-rot fungi preferred the intermediate decay stages. White-rot fungi represented approximately one-fifth of sequenced species in all decay phases excluding the final phase, where ectomycorrhizal (ECM) fungi became dominant. Lignin content of logs with white-rot fungi was low, and ECM fungi were associated with substrates containing abundant nitrogen. Macroscopic fruiting bodies were observed for only a small number of species detected with molecular techniques.     

Trait‐dependent distributional shifts in fruiting of common British fungi

Despite the dramatic phenological responses of fungal fruiting to recent climate warming, it is unknown whether spatial distributions of fungi have changed and to what extent such changes are influenced by fungal traits, such as ectomycorrhizal (ECM) or saprotrophic lifestyles, spore characteristics, or fruit body size. Our overall aim was to understand how climate and fungal traits determine whether and how species‐specific fungal fruit body abundances have shifted across latitudes over time, using the UK national database of fruiting records. The data employed were recorded over 45 yr (1970–2014), and include 853 278 records of Agaricales, Boletales and Russulales, though we focus only on the most common species (with more than 3000 records each). The georeferenced observations were analysed by a Bayesian inference as a Gaussian additive model with a specification following a joint species distribution model. We used an offset, random contributions and fixed effects to isolate different potential biases from the trait‐specific interactions with latitude/climate and time. Our main aim was assessed by examination of the three‐way‐interaction of trait, predictor (latitude or climate) and time. The results show a strong trait‐specific shift in latitudinal abundance through time, as ECM species have become more abundant relative to saprotrophic species in the north. Along precipitation gradients, phenology was important, in that species with shorter fruiting seasons have declined markedly in abundance in oceanic regions, whereas species with longer seasons have become relatively more common overall. These changes in fruit body distributions are correlated with temperature and rainfall, which act directly on both saprotrophic and ECM fungi, and also indirectly on ECM fungi, through altered photosynthate allocation from their hosts. If these distributional changes reflect fungal activity, there will be important consequences for the responses of forest ecosystems to changing climate, through effects on primary production and nutrient cycling.     

Wood-inhabiting fungal communities in woody debris of Norway spruce (Picea abies (L.) Karst.), as reflected by sporocarps, mycelial isolations and T-RFLP identification

Wood-inhabiting fungi play a key role in forest ecosystems and constitute an essential part of forest biodiversity. We therefore examined the composition and abundance of wood-inhabiting fungi by three methods: sporocarp counts, mycelial culturing and direct amplification of internal transcribed spacer terminal restriction fragment length polymorphism from wood combined with sequencing of reference rDNA. Seven-year-old slash piles left after a thinning were analyzed in a 50-year-old Norway spruce plantation. Fifty-eight fungal species were detected from the piled branches and treetops. More species were revealed by sporocarp counts and cultured mycelia than by direct amplification from wood. In principle, sporocarp monitoring may reveal all fruiting taxa, but it poorly reflects their relative abundance in the wood. In contrast, terminal restriction fragment length polymorphism will record the most frequent fungal taxa in the wood, but it may overlook uncommon taxa. Culturing mycelia from wood gives a bias towards species favoured by the cultural medium. The results demonstrate the advantage and the limitations of these methods to be considered in analyses of fungal communities in wood.     

Topography-specific emergence of fungal fruiting bodies in warm temperate evergreen broad-leaved forests on Yakushima Island,Japan

We conducted line route censuses of fungal fruiting bodies from August to September in 2005 and 2006 along ridges and valleys and compared the differences in the encounter rates of fungal fruiting bodies (= fruiting bodies seen per census kilometer) between types of topography and between fungal functional groups (i.e., ectomycorrhizal and saprobic fungi) in warm temperate evergreen broad-leaved forests on Yakushima Island, Japan. We found 251 fungal fruiting bodies (26 families, 50 genera, and 65 species) in total, including 51 bodies from Tricholomataceae, 41 from Russulaceae, 25 from Boletaceae, and 19 from Amanitaceae. The encounter rate of ectomycorrhizal fungi was greater at the ridge route (26.7 unit/km) than at the valley route (8.7 unit/km) and that of saprobic fungi was greater at the valley route (25.0 unit/km) than at the ridge route (12.5 unit/km). In addition, we conducted 7-year intermittent sampling and identified 40 families, 96 genera, and 142 species. The topography-specific emergence pattern of the intermittent sampling method was similar to that of the line census method. The fungal species composition in this study was possibly affected by a topographic gradient for both fungal functional groups through soil moisture, nutrient availability, and host tree distribution.     

The importance of timing and number of surveys in fungal biodiversity research

Practical conservation of biological diversity is dependent on reliable knowledge about what kind, how much, and where the diversity is. To obtain such knowledge three questions, why, what, and how, must be answered before commencing any biodiversity survey. While the questions why and what are often value decisions and thus determined outside the realm of scientific research, the question about how the surveys are conducted lies in the heart of science. Here, we report an intensive repeated survey of wood-inhabiting fungi with the aim of determining the optimal timing and number of the surveys for reliable estimation of the diversity of this species group. The research focusing on the ecology of wood-inhabiting fungi has been increasing but little is known about the reliability of the methods. The variation in the estimates of diversity among surveys was high and the results varied between studied species groups. The site-scale detectability for species belonging to different groups varied from 10 to 95% depending on the survey month and the species group. We conclude that because detectability of many fungi turned out to be poor even when surveys were conducted at an optimal time, the common practice of using a single fruit body survey to estimate fungal diversity of any given area is not enough. We suggest that multiple surveys at an optimal time should be a norm in fungal diversity studies. Improper methodology results in unreliable outcomes that have potential to hamper our goal of conserving the biological diversity.     

Cryptogam communities on decaying deciduous wood – does tree species diversity matter?

Bryophyte and fungal communities were investigated on fallen trees representing seven deciduous tree species in a mixed near natural nemoral forest. Bryophytes were represented by 41 taxa, including several very frequent species. Of the 296 fungal species, most were recorded with very low frequency and the share of high frequent species was much lower than among the bryophytes. Species turnover was bigger in the fungal communities, compared to the bryophyte communities, and related to a higher extent to measured differences in environmental conditions. Tree species diversity was found to be an important factor for fungal species composition, while only small differences in bryophyte species composition were found between the different tree species. On the other hand bryophyte species richness showed distinct relations to tree species and microclimatic variables, a tendency which was not evident for fungal diversity. It is concluded that the two organism groups to some extent differ in their conservation demands. Thus, conservation of wood-inhabiting bryophytes requires prioritising of large, coherent forest stands in which a stable humid microclimate and a reasonable supply of dead wood is secured. Successful conservation of fungi requires that substantial amounts of dead wood are left for natural decay in a variety of natural forest environments representing different tree species, so that heterogeneity in dead wood types is secured.     

Strict substrate requirements alongside rapid substrate turnover may indicate an early colonization: A case study of Pleurotus calyptratus (Agaricales,Basidiomycota)

Pleurotus calyptratus is a wood-inhabiting oyster mushroom associated with Populus tremula and P. alba. This fungus is rather common in Ukraine, but considered rare in many other European countries. Aiming to find causes for variation in rarity, we conducted habitat mapping and repeated surveys to understand the substrate requirements and fruiting dynamics of P. calyptratus. We showed that fruiting is strictly associated with older trees and early decay stages, and not with physical properties of a tree trunk like volume or position. This timespan of substrate suitability lasts for 1–3 y, determining rapid substrate turnover. We also detected DNA of P. calyptratus in living tissues of visually healthy trees, meaning its latent presence in the hosts, which places the fungus in a position to be a pioneer in a fungal succession. Despite the high spatial and temporal variation in fruiting, five annual surveys demonstrated no significant trends in P. calyptratus population's dynamics, and supported the assumption of random variation in fruiting, driven mostly by dynamics of forest stands. Therefore, we hypothesize that P. calyptratus' relative abundance in Ukraine is explained by continuous substrate supply from large homogenous aspen stands that are rare in the rest of Europe due to intensive management.     

Understanding the distribution of wood-inhabiting fungi in European beech reserves from species-specific habitat models

We assessed how environmental drivers influence the occurrences of wood-inhabiting macrofungi in European beech forests, using an extensive dataset of fruit body records collected in 53 reserves across twelve European countries. We found that the 105 species included in this study varied greatly in their responses to covariates related to resource quality, climate and forest connectivity, both in the strength and direction of the observed effects. Climate was the most important driver for some species, while others responded more to connectivity, or simply to the presence of high quality substrates within the reserves. Species occurrences varied also across geographical regions, especially between the UK and the rest of Europe. Our results show that wood-inhabiting fungi in European beech forests respond individualistically to habitat filters and differ in their biogeographical distribution patterns, and they thus provide a detailed perspective of how wood-inhabiting fungal communities are structured across Europe.     

Fungi ahoy! Diversity on marine wooden substrata in the high North

Marine fungi are severely understudied in the polar regions. We used molecularly identified cultures to study fungi inhabiting 50 intertidal and sea-floor logs along the North Norwegian coast. The aim was to explore the taxonomic and ecological diversity and to examine factors shaping the marine wood-inhabiting fungal communities. The 577 pure cultures analyzed clustered into 147 operational taxonomic units (OTUs) based on 97 % ITS sequence similarity. Ascomycota dominated, but OTUs belonging to Basidiomycota, Mucoromycotina and Chytridiomycota were also isolated. Nine OTUs could not be assigned to any fungal phylum. Almost half of the OTUs were considered non-marine. The western and eastern part of the Norwegian Barents Sea coast hosted different communities. Geography, substratum and site level variables contributed to shaping these communities. We characterized a previously overlooked fungal community in a poorly studied area, discovered high diversity and report many taxa for the first time from the marine environment.     

Impact of white-rot fungi on numbers and community composition of bacteria colonizing beech wood from forest soil

White-rot fungi are important wood-decomposing organisms in forest ecosystems. Their ability to colonize and decompose woody resources may be strongly influenced by wood-inhabiting bacteria that grow on easily utilizable compounds e.g. oligomers of wood-polymers released by fungal enzymes. However, so far, it is not known how white-rot fungi deal with the presence of potential competing bacteria. Here, the effects of two white-rot fungi, Hypholoma fasciculare and Resinicium bicolor, on the numbers and composition of bacteria colonizing sterile beech wood blocks from forest soil are reported. Both total numbers (microscopic counts) and the numbers of cultivable wood-inhabiting bacteria were considerably lower in wood blocks that became colonized by the white-rot fungi than in control blocks. This points to the fungi out-competing the opportunistic bacteria. The presence of white-rot fungi resulted in a change in the relative abundance of families of cultivable bacteria in wood and also in a change of denaturing gradient gel electrophoresis patterns of directly amplified 16S rRNA gene fragments. Analysis of the bacterial community structure in soil adhering to exploratory mycelium (cords) indicated that fungal species-specific effects on bacterial community composition were also apparent in this fungal growth phase.