Wood-inhabiting Fungal Communities Research Articles

Community Assembly Processes of Deadwood Mycobiome in a Tropical Forest Revealed by Long-Read Third-Generation Sequencing

Despite the importance of wood-inhabiting fungi on nutrient cycling and ecosystem functions, their ecology, especially related to their community assembly, is still highly unexplored. In this study, we analyzed the wood-inhabiting fungal richness, community composition, and phylogenetics using PacBio sequencing. Opposite to what has been expected that deterministic processes especially environmental filtering through wood-physicochemical properties controls the community assembly of wood-inhabiting fungal communities, here we showed that both deterministic and stochastic processes can highly contribute to the community assembly processes of wood-inhabiting fungi in this tropical forest. We demonstrated that the dynamics of stochastic and deterministic processes varied with wood decomposition stages. The initial stage was mainly governed by a deterministic process (homogenous selection), whereas the early and later decomposition stages were governed by the stochastic processes (ecological drift). Deterministic processes were highly contributed by wood physicochemical properties (especially macronutrients and hemicellulose) rather than soil physicochemical factors. We elucidated that fine-scale fungal-fungal interactions, especially the network topology, modularity, and keystone taxa of wood-inhabiting fungal communities, strongly differed in an initial and decomposing deadwood. This current study contributes to a better understanding of the ecological processes of wood-inhabiting fungi in tropical regions where the knowledge of wood-inhabiting fungi is highly limited.

Bark beetle outbreaks in Picea abies stands are associated with changes in wood-inhabiting fungal communities and seedling establishment on logs

In recent decades bark beetle outbreaks have caused high mortality in natural mountain Picea abies forests in Central Europe. This study evaluated factors affecting seedling establishment of P. abies by focusing on the role of fungal communities in decaying logs, which is an important regeneration microsite. At the control site, which was affected by lower severity disturbance, well decayed logs with moss and vegetation cover hosted many seedlings. At the disturbed site, which experienced high mortality by bark beetles, greater canopy openness suppressed vegetation on logs and lowered seedling density. Additionally, the presence of a white rot basidiomycete Phellopilus nigrolimitatus was positively associated with seedling density. In contrast, the presence of a brown rot basidiomycete Fomitopsis pinicola was negatively associated with seedling density. The relationships between these decomposer fungi and seedling density might be partly attributed to changes in wood chemical properties and associated mycorrhizal and pathogenic fungi.

Wood-inhabiting fungal communities: Opportunities for integration of empirical and theoretical community ecology

The interest in studying wood-inhabiting fungal communities has grown in recent years. This interest has mainly been motivated by the important roles of wood-inhabiting fungi in ecosystem functioning (e.g. nutrient cycling) and conservation biology (e.g. their sensitivity to forest management). In this paper, I argue that another important, but yet largely unexplored motivation for studying wood-inhabiting fungal communities, is their potential to advance fundamental community ecology. One major advantage of wood-inhabiting fungi as model systems is that they are organized as spatially well-defined metacommunities, thus conforming to the assumptions of many theoretical frameworks. Another major advantage is that they allow observations and manipulations over large numbers of local communities (habitat patches). After reviewing recent approaches in theoretical community ecology, I discuss how past empirical studies on wood-inhabiting fungal communities relate to community assembly processes, and provide future research directions on how the still unstudied assembly processes could be tackled using wood-inhabiting fungi as a model system.

Patterns of community composition and diversity in latent fungi of living Quercus serrata trunks across a range of oak wilt prevalence and climate variables in Japan

Given that forest dieback due to emerging pests is increasing under global warming, understanding the relationships between pests, climate, and forest biodiversity is an urgent priority. In Japan, mass attacks of an ambrosia beetle, vectoring a pathogenic fungus, cause oak wilt outbreaks in recent decades. Here, the associations of oak wilt and climate with wood-inhabiting fungal communities in apparently healthy Quercus serrata trunks were investigated using DNA metabarcoding in seven sites along a climatic gradient in Japan. Amplicon sequencing of the fungal internal transcribed spacer 1 region generated 1,339,958 sequence reads containing 879 fungal operational taxonomic units (OTUs) in 234 wood samples. OTU compositions were significantly different between sites with and without oak wilt. OTU richness increased with temperature and precipitation at sites where oak wilt was present, but this relationship was not observed at sites without oak wilt, possibly due to interaction between oak wilt and climate. • Oak wilt disease is correlated with fungal communities in living oak trees. • OTU richness increased with temperature and precipitation at sites with oak wilt. • OTU richness was not correlated with macroclimate at sites without oak wilt. • Oak wilt was correlated with absence of some white-rot decomposer fungi. • Precipitation had a negative correlation with the species richness of brown-rot fungi.

Decay stages of wood and associated fungal communities characterise diversity\u2013decomposition relationships

The biodiversity–ecosystem function relationship is a central topic in ecology. Fungi are the dominant decomposers of organic plant material in terrestrial ecosystems and display tremendous species diversity. However, little is known about the fungal diversity–decomposition relationship. We evaluated fungal community assemblies and substrate quality in different stages of wood decay to assess the relationships between fungal species richness and weight loss of wood substrate under laboratory conditions. Wood-inhabiting fungal communities in the early and late stages of pine log decomposition were used as a model. Colonisation with certain species prior to inoculation with other species resulted in four-fold differences in fungal species richness and up to tenfold differences in the rate of wood substrate decomposition in both early- and late-decaying fungal communities. Differences in wood substrate quality had a significant impact on species richness and weight loss of wood and the relationships between the two, which were negative or neutral. Late communities showed significantly negative species richness–decay relationships in wood at all decay stages, whereas negative relationships in early communities were significant only in the intermediate decay stage. Our results suggest that changes in fungal communities and wood quality during wood decomposition affect the fungal diversity–decomposition relationship.

Enhanced Lignocellulolytic Enzyme Activities on Hardwood and Softwood during Interspecific Interactions of White- and Brown-Rot Fungi.

Wood decomposition is a sophisticated process where various biocatalysts act simultaneously and synergistically on biopolymers to efficiently break down plant cell walls. In nature, this process depends on the activities of the wood-inhabiting fungal communities that co-exist and interact during wood decay. Wood-decaying fungal species have traditionally been classified as white-rot and brown-rot fungi, which differ in their decay mechanism and enzyme repertoire. To mimic the species interaction during wood decomposition, we have cultivated the white-rot fungus, Bjerkandera adusta, and two brown-rot fungi, Gloeophyllum sepiarium and Antrodia sinuosa, in single and co-cultivations on softwood and hardwood. We compared their extracellular hydrolytic carbohydrate-active and oxidative lignin-degrading enzyme activities and production profiles. The interaction of white-rot and brown-rot species showed enhanced (hemi)cellulase activities on birch and spruce-supplemented cultivations. Based on the enzyme activity profiles, the combination of B. adusta and G. sepiarium facilitated birch wood degradation, whereas B. adusta and A. sinuosa is a promising combination for efficient degradation of spruce wood, showing synergy in β-glucosidase (BGL) and α-galactosidase (AGL) activity. Synergistic BGL and AGL activity was also detected on birch during the interaction of brown-rot species. Our findings indicate that fungal interaction on different woody substrates have an impact on both simultaneous and sequential biocatalytic activities.

Convergence of fungal traits over time in natural and forestry-fragmented patches

Setting aside small remnant patches of high biodiversity forest within managed forest landscapes is often used as conservation measure to provide a refuge and future source population of forest biodiversity, including wood-inhabiting fungal communities. Yet little is known about the long-term fungal community assembly, how these small, isolated patches change through time and how forest management in the surrounding landscape impacts traits and community functionality housed within.We applied a joint species distribution model to compare how fungal traits and communities changed over two survey periods undertaken ~20 years apart in boreal forest set-aside and natural patches. Natural patches in naturally fragmented landscapes were considered reference forests for small, remnant, near-natural forest patches in intensively managed forest landscapes.We found the majority of fungal traits converged over time between set-aside and natural patches, without changes in overall species richness. Red-listed species occurrence was initially lower in set-aside patches, but reached a comparable level of natural patches over time as a result of opposing changes in both patch types.Functional trait changes were larger in set-aside patches, but convergence was also related to opposing changes in natural patches.This is the first study to directly measure and test wood fungal community trait-environment relationships over time in small, high-conservation value forest patches. The long-term functional trait and red-listed species values of set-asides, coupled with their capacity for old-growth recovery, make them valuable focal areas for conservation.

Wood-colonizing fungal community response to forest restoration thinnings in a Pinus tabuliformis plantation in northern China

Forest restoration thinning in Chinese pine (Pinus tabuliformis) plantations can alter stand structure and soil abiotic properties, which have the potential to change biotic properties such as wood-inhabiting fungal community structure. Therefore, three thinning treatments (30%, 41% and 53% of the standing biomass removed) and an unthinned control stand were established at stand age 35 to determine the effects on surface and mineral soil wood-inhabiting fungi. Chinese pine, loblolly pine (Pinus taeda), and trembling aspen (Populus tremuloides) wood stakes were placed horizontally on the soil surface and inserted vertically into the mineral soil and sampled over 3 years. Fungal species were identified using high-throughput amplicon sequencing (HTAS) of DNA barcode regions. Across all wood stake species on the soil surface, operational taxonomic unit (OTU) richness averaged 138 OTUs per thinning treatment. Significantly greater OTU richness (p < 0.01) on both surface pine species stakes was observed in the unthinned control as compared to the moderate and heavily thinned plots. In the mineral soil, wood stakes averaged only 91 OTUs, with no clear OTU pattern for thinning treatment or sampling time for richness. However, aspen stakes had significantly lower (p < 0.01) OTU richness than both pine species stakes on the surface and in mineral soil. Although richness was not strongly affected, fungal community composition in the mineral soil was significantly altered by thinning treatments, wood stake species, and sampling time. This study extends our knowledge of the long-term effects of stand thinning on fungal communities’ richness and composition.

Rare species of wood-inhabiting fungi are not local.

Wood-inhabiting fungal communities are a diverse and ecologically critical part of forest ecosystems, yet the spatial structure of fungal biodiversity in these ecosystems is largely unknown. Legislation allowed harvesting of deadwood from temperate rainforests on conservation lands in New Zealand following Cyclone Ita in 2014. Harvesting guidelines specified widely spread harvesting, on the assumption that rare fungal species may be highly spatially restricted, but were not based on quantitative assessment. We sampled fungi in and on logs of Dacrydium cupressinum (Podocarpaceae) a long-lived, common, canopy tree in lowland New Zealand forests. DNA was extracted from 81 logs varying in decay state across a 40km long region of West Coast (South Island) forests, and sequenced using general fungal primers for metabarcoding to identify OTUs (operational taxonomic units). We examined three axes of rarity: occupancy, dominance when present, and niche breadth (as spatial extent and decay state specialization). Low-occupancy fungi were common, including a group of infrequently occurring but dominant when present fungi, the majority of which were Ascomycota. Despite this, there was an overall positive relationship between occupancy and dominance. Widespread, dominant fungi were most commonly Basidiomycota. Testing all fungal OTUs, there were no more fungi with maximum range sizes<4km than would be expected at random. Of the 351 low-occupancy OTUs found two to four times, only 12 had maximum range sizes<900m, and there was no more spatial restriction at scales<900m than would be expected by random chance, although there was some evidence of niche breadth restriction based on decay state similarity. The results show that fungal communities in deadwood are highly diverse, and include many rare taxa. Nonetheless, the lack of fungal OTUs with spatial restriction at scales<900m suggests that spatially dispersed timber harvesting will not mitigate risks of harvesting to rare fungal biodiversity.

Morphological traits predict host-tree specialization in wood-inhabiting fungal communities

Abstract Tree species is one of the most important determinants of wood-inhabiting fungal community composition, yet its relationship with fungal reproductive and dispersal traits remains poorly understood. We studied fungal communities (total of 657 species) inhabiting broadleaved and coniferous dead wood (total of 192 logs) in 12 semi-natural boreal forests. We utilized a trait-based hierarchical joint species distribution model to examine how the relationship between dead wood quality and species occurrence correlates with reproductive and dispersal morphological traits. Broadleaved trees had higher species richness than conifers, due to discomycetoids and pyrenomycetoids specializing in them. Resupinate and pileate species were generally specialized in coniferous dead wood. Fungi inhabiting broadleaved trees had larger and more elongated spores than fungi in conifers. Spore size was larger and spore shape more spherical in species occupying large dead wood units. These results indicate the selective effect of dead wood quality, visible not only in species diversity, but also in reproductive and dispersal traits.

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. • The impact of cormorant nesting on wood-inhabiting fungal communities was studied. • Fungal communities under bird impact differed from those in unaffected forest. • Fungi not normally associated with coniferous wood were observed on pine woody debris. • Generalist species and hyphomycetous fungi were more tolerant of bird impact. • A shift in fungal assemblages was recorded three years after the start of bird impact.

Culturable fungi associated with wood decay of Picea abies in subalpine forest soils: a field-mesocosm case study

Abstract: Fungi are the principal wood decomposers in forest ecosystems and their activity provides wood necromass to other living organisms. However, the wood decay mechanisms and the associated microbial community are largely unknown, especially in Alpine areas. In this study, the culturable fraction of fungal communities associated with the decomposition of Norway spruce (Picea abies [L.] Karst) deadwood in subalpine forest soils were determined using microbiological methods coupled with molecular identification. Fungal communities were evaluated using in-field mesocosms after one year of exposition of P. abies wood blocks along an altitudinal gradient ranging from 1200 up to 2000 m a.s.l. comprising eight subalpine sites, four of them located at north- and other four at south-facing slopes. Although many saprotrophic species were isolated from the wood blocks, several white-rot species as the pathogenic fungi Armillaria cepistipes and Heterobasidion annosum, along with soft-rot fungi such as Lecytophora sp. were identified. Our results further indicated that the wood-inhabiting fungal community was mainly influenced by topographic features and by the chemical properties of the wood blocks, providing first insights into the effect of different slope exposure on the deadwood mycobiome in the subalpine forest ecosystem.

A continuum of dead wood with various habitat elements maintains the diversity of wood-inhabiting fungi in an old-growth boreal forest

Evidence on habitat associations of threatened wood-inhabiting species in boreal forests may contribute to a better understanding of their ecology and conservation needs. We examined the diversity of wood-inhabiting fungal communities in an old-growth boreal forest with high substrate availability and continuity based on repeated surveys of fruit bodies. The number of species in morphological and functional groups in relation to coarse woody debris (CWD) attributes was estimated with generalized linear models. Additionally, we calculated species interaction networks of CWD attributes and fungal species. The composition of fungal communities was analysed using a non-metric multidimensional scaling with subsequent environmental fitting. Old conifer (especially spruce) logs and large aspen logs with branches represented the most important substrates for the red-listed species and the indicator species of old-growth boreal forests. Among “dynamic” CWD attributes such as time since tree death, decay class and stage of epixylic succession, the latter was the most important indicator of diversity of all species and their morphological and functional groups. The interaction network provided evidence of the importance of tree species diversity for fungal diversity. The composition of fungal communities was tree species specific and related to dynamic attributes, bark cover and diameter of logs. Our results suggest the importance of a continuum of dead wood from different tree species with a variety of niches such as branches, exposed wood, fragmented and complete cover of bark and patches of epixylic vegetation to maintain the assemblages of wood-inhabiting fungi in an old-growth boreal forest.

Fungal community structure of fallen pine and oak wood at different stages of decomposition in the Qinling Mountains, China

Historically, intense forest hazards have resulted in an increase in the quantity of fallen wood in the Qinling Mountains. Fallen wood has a decisive influence on the nutrient cycling, carbon budget and ecosystem biodiversity of forests, and fungi are essential for the decomposition of fallen wood. Moreover, decaying dead wood alters fungal communities. The development of high-throughput sequencing methods has facilitated the ongoing investigation of relevant molecular forest ecosystems with a focus on fungal communities. In this study, fallen wood and its associated fungal communities were compared at different stages of decomposition to evaluate relative species abundance and species diversity. The physical and chemical factors that alter fungal communities were also compared by performing correspondence analysis according to host tree species across all stages of decomposition. Tree species were the major source of differences in fungal community diversity at all decomposition stages, and fungal communities achieved the highest levels of diversity at the intermediate and late decomposition stages. Interactions between various physical and chemical factors and fungal communities shared the same regulatory mechanisms, and there was no tree species-specific influence. Improving our knowledge of wood-inhabiting fungal communities is crucial for forest ecosystem conservation.

Interactions between soil- and dead wood-inhabiting fungal communities during the decay of Norway spruce logs

We investigated the interaction between fungal communities of soil and dead wood substrates. For this, we applied molecular species identification and stable isotope tracking to both soil and decaying wood in an unmanaged boreal Norway spruce-dominated stand. Altogether, we recorded 1990 operational taxonomic units, out of which more than 600 were shared by both substrates and 589 were found to exclusively inhabit wood. On average the soil was more species-rich than the decaying wood, but the species richness in dead wood increased monotonically along the decay gradient, reaching the same species richness and community composition as soil in the late stages. Decaying logs at all decay stages locally influenced the fungal communities from soil, some fungal species occurring in soil only under decaying wood. Stable isotope analyses suggest that mycorrhizal species colonising dead wood in the late decay stages actively transfer nitrogen and carbon between soil and host plants. Most importantly, Piloderma sphaerosporum and Tylospora sp. mycorrhizal species were highly abundant in decayed wood. Soil- and wood-inhabiting fungal communities interact at all decay phases of wood that has important implications in fungal community dynamics and thus nutrient transportation.

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

Abstract 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.

Implications of reserve size and forest connectivity for the conservation of wood-inhabiting fungi in Europe

Among the factors that affect the conservation efficiency of protected areas, lack of connectivity is considered as one of the main problems. In this study, we assessed the influence of connectivity of European beech forest reserves on wood-inhabiting fungal communities, compared to the influence of local factors. To address this topic, we used a data matrix consisting of 344 fungal species on 1571 resource units (i.e. fallen beech logs, including their standing snags) sampled in 42 European beech forest reserves. Our results show that connectivity has significant effects on wood-inhabiting fungal communities in European beech forest reserves, and that the effectiveness of reserves for maintaining the wood-inhabiting fungal diversity is compromised by habitat fragmentation. Connectivity at small scales (measured as the area of the reserve) had a strong influence on the occurrence of indicator species and was also critical for the number of species at a resource. Connectivity at larger scales (connectivity to surrounding beech forests) seemed to be particularly critical for the community composition both at resource and reserve levels. In line with previous research, we found other covariates such as size of the resource units and annual temperature range to positively influence wood-inhabiting fungal species richness. The effects of habitat fragmentation were especially strong in western and northern European regions where the smallest and more isolated reserves were located. We propose that an effective conservation strategy for wood-inhabiting fungi should focus on increasing the areas of the present reserves as well as conserving new reserves in the proximity of the existing ones.

Linking molecular deadwood-inhabiting fungal diversity and community dynamics to ecosystem functions and processes in Central European forests

Fungi playvital roles in thedecomposition of dead- wood due to their secretion of various enzymes that break down plant cell-wall complexes. The compositions of wood- inhabiting fungal (WIF) communities change over the course of the decomposition process as the remaining mass of wood decreases and both abiotic and biotic conditions of the wood significantly change. It is currently not resolved which substrate-related factors govern these changes in WIF com- munities and whether such changes influence the deadwood decomposition rate. Here we report a study on fungal richness and community structure in deadwood of Norway spruce and European beech in temperate forest ecosystems using 454 pyrosequencing. Our aims were to disentangle the factors that correspondtoWIF community composition and to investigate the links between fungal richness, taxonomically-resolved fungal identity, and microbial-mediated ecosystem functions and processes by analyzing physico-chemical wood proper- ties, lignin-modifying enzyme activities and wood decompo- sition rates. Unlike fungal richness, we found significant dif- ferences in community structure between deadwood of differ- ent tree species. The composition of WIF communities was related to the physico-chemical properties of the deadwood substrates. Decomposition rates and the activities of lignin- modifying enzymes were controlled by the succession of the fungal communities and competition scenarios rather than fungal OTU richness. Our results provide further insights into links between fungal community structure and microbial- mediated ecosystem functions and processes.

Wood-inhabiting dematiaceous Hyphomycetes in the Kampinos National Park

In this work the results of investigations of wood-inhabiting fungal communities in several forest associations arę presented. The populations of these fungi on the wood of &lt;i&gt;Carpinus betulus, Quercus robur, Betula verrucosa, Tilia cordata&lt;/i&gt; and &lt;i&gt;Pinus sylvestris&lt;/i&gt; are also analyzed.

Community turnover of wood-inhabiting fungi across hierarchical spatial scales.

For efficient use of conservation resources it is important to determine how species diversity changes across spatial scales. In many poorly known species groups little is known about at which spatial scales the conservation efforts should be focused. Here we examined how the community turnover of wood-inhabiting fungi is realised at three hierarchical levels, and how much of community variation is explained by variation in resource composition and spatial proximity. The hierarchical study design consisted of management type (fixed factor), forest site (random factor, nested within management type) and study plots (randomly placed plots within each study site). To examine how species richness varied across the three hierarchical scales, randomized species accumulation curves and additive partitioning of species richness were applied. To analyse variation in wood-inhabiting species and dead wood composition at each scale, linear and Permanova modelling approaches were used. Wood-inhabiting fungal communities were dominated by rare and infrequent species. The similarity of fungal communities was higher within sites and within management categories than among sites or between the two management categories, and it decreased with increasing distance among the sampling plots and with decreasing similarity of dead wood resources. However, only a small part of community variation could be explained by these factors. The species present in managed forests were in a large extent a subset of those species present in natural forests. Our results suggest that in particular the protection of rare species requires a large total area. As managed forests have only little additional value complementing the diversity of natural forests, the conservation of natural forests is the key to ecologically effective conservation. As the dissimilarity of fungal communities increases with distance, the conserved natural forest sites should be broadly distributed in space, yet the individual conserved areas should be large enough to ensure local persistence.