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

The evolutionary adaptation of wood-decay macrofungi to host gymnosperms differs from that to host angiosperms

Wood-decay macrofungi play a vital role in forest ecosystems by promoting nutrient cycling and soil structure, and their evolution is closely related to their host plants. This study investigates the potential evolutionary adaptation of wood-decay macrofungi to their host plants, focusing on whether these relationships differ between gymnosperms and angiosperms. While previous research has suggested non-random associations between specific fungi and plant deadwood, direct evidence of evolutionary adaptation has been lacking. Our study, conducted in a subtropical region, utilized metabarcoding techniques to identify deadwood species and associated fungi. We found significant evidence of evolutionary adaptation when considering all sampled species collectively. However, distinct patterns emerged when comparing angiosperms and gymnosperms: a significant evolutionary adaptation was observed of wood-decay macrofungi to angiosperms, but not to gymnosperms. This variation may be due to the longer evolutionary history and more stable species interactions of gymnosperms, as indicated by a higher modularity coefficient (r = .452), suggesting greater specialization. In contrast, angiosperms, being evolutionarily younger, displayed less stable and more coevolving interactions with fungi, reflected in a lower modularity coefficient (r = .387). Our findings provide the first direct evidence of differential evolutionary adaptation dynamics of these fungi to angiosperms versus gymnosperms, enhancing our understanding of forest ecosystem carbon cycling and resource management.

Drivers of wood-inhabiting fungal diversity in European and Oriental beech forests

The hyperdiverse wood-inhabiting fungi play a crucial role in the global carbon cycle, but often are threatened by deadwood removal, particularly in temperate forests dominated by European beech (Fagus sylvatica) and Oriental beech (Fagus orientalis). To study the impact of abiotic drivers, deadwood factors, forest management and biogeographical patterns in forests of both beech species on fungal composition and diversity, we collected 215 deadwood-drilling samples in 18 forests from France to Armenia and identified fungi by meta-barcoding. In our analyses, we distinguished the patterns driven by rare, common, and dominant species using Hill numbers. Despite a broad overlap in species, the fungal composition with focus on rare species was determined by Fagus species, deadwood type, deadwood diameter, precipitation, temperature, and management status in decreasing order. Shifting the focus on common and dominant species, only Fagus species, both climate variables and deadwood type remained. The richness of species within the deadwood objects increased significantly only with decay stage. Gamma diversity in European beech forests was higher than in Oriental beech forests. We revealed the highest gamma diversity for old-growth forests of European beech when focusing on dominant species. Our results implicate that deadwood retention efforts, focusing on dominant fungi species, critical for the decay process, should be distributed across precipitation and temperature gradients and both Fagus species. Strategies focusing on rare species should additionally focus on different diameters and on the conservation of old-growth forests.

Factors associated with seedling establishment on logs of different fungal decay types-A seed-sowing experiment

Wood decay fungi alter the abiotic and biotic properties of deadwood, which are important as nurse logs for seedling regeneration. However, the relationship between fungal decay type and seedling performance has not been evaluated experimentally. In this study, we examined the germination, growth, and survival of six arbuscular mycorrhizal (AM) and six ectomycorrhizal (ECM) tree species on three substrates (pine logs with brown and white rot and soil) by conducting seed-sowing experiments in a mixed forest dominated by Pinus densiflora and Quercus serrata. Analysis using ribosomal DNA internal transcribed spacer 1 (rDNA ITS1) sequencing revealed that the fungal community was significantly different across three substrates. The richness of operational taxonomic units (OTUs) of AM and ECM fungi was the largest on brown rot logs and soil, respectively. The substrate significantly affected the seedling performance when comparing wood decay types, but these were not consistent across the mycorrhizal status of the seedlings. Nevertheless, seedlings of some AM trees showed better growth and enhanced mycorrhizal colonization on brown rot logs than on white rot logs. The wood decay type influenced fungal communities in the logs and the performance of some seedling species partly by different mycorrhizal colonization rates. However, the effect was seedling species dependent and showed no apparent difference between AM and ECM trees.

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.

From individual leaves to forest stands: importance of niche, distance decay, and stochasticity vary by ecosystem type and functional group for fungal community composition

Community assembly is influenced by environmental niche processes as well as stochastic processes that can be spatially dependent (e.g. dispersal limitation) or independent (e.g. priority effects). Here, we sampled senesced tree leaves as unit habitats to investigate fungal community assembly at two spatial scales: (i) small neighborhoods of overlapping leaves from differing tree species and (ii) forest stands of differing ecosystem types. Among forest stands, ecosystem type explained the most variation in community composition. Among adjacent leaves within stands, variability in fungal composition was surprisingly high. Leaf type was more important in stands with high soil fertility and dominated by differing tree mycorrhizal types (sugar maple vs. basswood or red oak), whereas distance decay was more important in oak-dominated forest stands with low soil fertility. Abundance of functional groups was explained by environmental factors, but predictors of taxonomic composition within differing functional groups were highly variable. These results suggest that fungal community assembly processes are clearest for functional group abundances and large spatial scales. Understanding fungal community assembly at smaller spatial scales will benefit from further study focusing on differences in drivers for different ecosystems and functional groups, as well as the importance of spatially independent factors such as priority effects.

Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species

Deadwood provides habitat for fungi and serves diverse ecological functions in forests. We already have profound knowledge of fungal assembly processes, physiological and enzymatic activities, and resulting physico-chemical changes during deadwood decay. However, in situ detection and identification methods, fungal origins, and a mechanistic understanding of the main lignocellulolytic enzymes are lacking. This study used metaproteomics to detect the main extracellular lignocellulolytic enzymes in 12 tree species in a temperate forest that have decomposed for 8 ½ years. Mainly white-rot (and few brown-rot) Basidiomycota were identified as the main wood decomposers, with Armillaria as the dominant genus; additionally, several soft-rot xylariaceous Ascomycota were identified. The key enzymes involved in lignocellulolysis included manganese peroxidase, peroxide-producing alcohol oxidases, laccase, diverse glycoside hydrolases (cellulase, glucosidase, xylanase), esterases, and lytic polysaccharide monooxygenases. The fungal community and enzyme composition differed among the 12 tree species. Ascomycota species were more prevalent in angiosperm logs than in gymnosperm logs. Regarding lignocellulolysis as a function, the extracellular enzyme toolbox acted simultaneously and was interrelated (e.g. peroxidases and peroxide-producing enzymes were strongly correlated), highly functionally redundant, and present in all logs. In summary, our in situ study provides comprehensive and detailed insight into the enzymatic machinery of wood-inhabiting fungi in temperate tree species. These findings will allow us to relate changes in environmental factors to lignocellulolysis as an ecosystem function in the future.

Nitrogen addition increases mass loss of gymnosperm but not of angiosperm deadwood without changing microbial communities

Enhanced nitrogen (N) deposition due to combustion of fossil fuels and agricultural fertilization is a global phenomenon which has severely altered carbon (C) and N cycling in temperate forest ecosystems in the northern hemisphere. Although deadwood holds a substantial amount of C in forest ecosystems and thus plays a crucial role in nutrient cycling, the effect of increased N deposition on microbial processes and communities, wood chemical traits and deadwood mass loss remains unclear. Here, we simulated high N deposition rates by adding reactive N in form of ammonium-nitrate (40 kg N ha-1 yr-1) to deadwood of 13 temperate tree species over nine years in a field experiment in Germany. Non-treated deadwood from the same logs served as control with background N deposition. Our results show that chronically elevated N levels alters deadwood mass loss alongside respiration, enzymatic activities and wood chemistry depending on tree clade and species. In gymnosperm deadwood, elevated N increased mass loss by +38 %, respiration by +37 % and increased laccase activity 12-fold alongside increases of white-rot fungal abundance +89 % (p = 0.03). Furthermore, we observed marginally significant (p = 0.06) shifts of bacterial communities in gymnosperm deadwood. In angiosperm deadwood, we did not detect consistent effects on mass loss, physico-chemical properties, extracellular enzymatic activity or changes in microbial communities except for changes in abundance of 10 fungal OTUs in seven tree species and 28 bacterial OTUs in 10 tree species. We conclude that N deposition alters decomposition processes exclusively in N limited gymnosperm deadwood in the long term by enhancing fungal activity as expressed by increases in respiration rate and extracellular enzyme activity with minor shifts in decomposing microbial communities. By contrast, deadwood of angiosperm tree species had higher N concentrations and mass loss as well as community composition did not respond to N addition.

Fate of a biodegradable plastic in forest soil: Dominant tree species and forest types drive changes in microbial community assembly, influence the composition of plastisphere, and affect poly(butylene succinate-co-adipate) degradation

Poly(butylene succinate-co-adipate) (PBSA) degradation and its plastisphere microbiome in cropland soils have been studied; however, such knowledge is limited in the case of forest ecosystems. In this context, we investigated: i) the impact of forest types (conifer and broadleaved forests) on the plastisphere microbiome and its community assembly, ii) their link to PBSA degradation, and iii) the identities of potential microbial keystone taxa. We determined that forest type significantly affected microbial richness (F = 5.26-9.88, P = 0.034 to 0.006) and fungal community composition (R² = 0.38, P = 0.001) of the plastisphere microbiome, whereas its effects on microbial abundance and bacterial community composition were not significant. The bacterial community was governed by stochastic processes (mainly homogenizing dispersal), whereas the fungal community was driven by both stochastic and deterministic processes (drift and homogeneous selection). The highest molar mass loss was found for PBSA degraded under Pinus sylvestris (26.6 ± 2.6 to 33.9 ± 1.8 % (mean ± SE) at 200 and 400 days, respectively), and the lowest molar mass loss was found under Picea abies (12.0 ± 1.6 to 16.0 ± 0.5 % (mean ± SE) at 200 and 400 days, respectively). Important fungal PBSA decomposers (Tetracladium) and atmospheric dinitrogen (N₂)-fixing bacteria (symbiotic: Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium and Methylobacterium and non-symbiotic: Mycobacterium) were identified as potential keystone taxa. The present study is among the first to determine the plastisphere microbiome and its community assembly processes associated with PBSA in forest ecosystems. We detected consistent biological patterns in the forest and cropland ecosystems, indicating a potential mechanistic interaction between N₂-fixing bacteria and Tetracladium during PBSA biodegradation.

Principal Drivers of Fungal Communities Associated with Needles, Shoots, Roots and Adjacent Soil of Pinus sylvestris

The plant- and soil-associated microbial communities are critical to plant health and their resilience to stressors, such as drought, pathogens, and pest outbreaks. A better understanding of the structure of microbial communities and how they are affected by different environmental factors is needed to predict and manage ecosystem responses to climate change. In this study, we carried out a country-wide analysis of fungal communities associated with Pinus sylvestris growing under different environmental conditions. Needle, shoot, root, mineral, and organic soil samples were collected at 30 sites. By interconnecting the high-throughput sequencing data, environmental variables, and soil chemical properties, we were able to identify key factors that drive the diversity and composition of fungal communities associated with P. sylvestris. The fungal species richness and community composition were also found to be highly dependent on the site and the substrate they colonize. The results demonstrated that different functional tissues and the rhizosphere soil of P. sylvestris are associated with diverse fungal communities, which are driven by a combination of climatic (temperature and precipitation) and edaphic factors (soil pH), and stand characteristics.

Landscape context and substrate characteristics shape fungal communities of dead spruce in urban and semi-natural forests

Urban green areas are becoming increasingly recognized for their biodiversity potential. However, little is known about how urbanization shapes cryptic species communities, such as those residing in deadwood. In this study, we investigated downed Norway spruce trunks at intermediate stages of decay, in urban and semi-natural forests in southern Finland. To understand the interconnections between landscape context, deadwood characteristics and wood-inhabiting fungal communities, we studied structural characteristics, surface epiphyte cover and internal moisture and temperature conditions of the tree trunks, and fungal communities residing in the wood. Our findings showed that urban tree trunks had less epiphyte cover and lower moisture than trunks in semi-natural forests. Overall, urban forests provide less favourable habitats for a majority of the dominant wood-inhabiting fungal species and for red-listed species as a group. Yet, 33% of urban trunks hosted at least one red-listed species. While these landscape-scale effects may be driven by local climatic conditions as well as contingencies related to available species pools, our results also highlight the significance of substrate-scale variability of deadwood in shaping wood-inhabiting fungal communities. We show that epiphyte cover is a significant driver or indicator of these small-scale dynamic processes in deadwood.

Cross-kingdom interactions and functional patterns of active microbiota matter in governing deadwood decay

Microbial community members are the primary microbial colonizers and active decomposers of deadwood. This study placed sterilized standardized beech and spruce sapwood specimens on the forest ground of 8 beech- and 8 spruce-dominated forest sites. After 370 days, specimens were assessed for mass loss, nitrogen (N) content and ¹⁵N isotopic signature, hydrolytic and lignin-modifying enzyme activities. Each specimen was incubated with bromodeoxyuridine (BrdU) to label metabolically active fungal and bacterial community members, which were assessed using amplicon sequencing. Fungal saprotrophs colonized the deadwood accompanied by a distinct bacterial community that was capable of cellulose degradation, aromatic depolymerization, and N₂ fixation. The latter were governed by the genus Sphingomonas, which was co-present with the majority of saprotrophic fungi regardless of whether beech or spruce specimens were decayed. Moreover, the richness of the diazotrophic Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group was significantly correlated with mass loss, N content and ¹⁵N isotopic signature. By contrast, presence of obligate predator Bdellovibrio spp. shifted bacterial community composition and were linked to decreased beech deadwood decay rates. Our study provides the first account of the composition and function of metabolically active wood-colonizing bacterial and fungal communities, highlighting cross-kingdom interactions during the early and intermediate stages of wood decay.

Fungal Community Development in Decomposing Fine Deadwood Is Largely Affected by Microclimate

Fine woody debris (FWD) represents the majority of the deadwood stock in managed forests and serves as an important biodiversity hotspot and refuge for many organisms, including deadwood fungi. Wood decomposition in forests, representing an important input of nutrients into forest soils, is mainly driven by fungal communities that undergo continuous changes during deadwood decomposition. However, while the assembly processes of fungal communities in long-lasting coarse woody debris have been repeatedly explored, similar information for the more ephemeral habitat of fine deadwood is missing. Here, we followed the fate of FWD of Fagus sylvatica and Abies alba in a Central European forest to describe the assembly and diversity patterns of fungal communities over 6 years. Importantly, the effect of microclimate on deadwood properties and fungal communities was addressed by comparing FWD decomposition in closed forests and under open canopies because the large surface-to-volume ratio of FWD makes it highly sensitive to temperature and moisture fluctuations. Indeed, fungal biomass increases and pH decreases were significantly higher in FWD under closed canopy in the initial stages of decomposition indicating higher fungal activity and hence decay processes. The assembly patterns of the fungal community were strongly affected by both tree species and microclimatic conditions. The communities in the open/closed canopies and in each tree species were different throughout the whole succession with only limited convergence in time in terms of both species and ecological guild composition. Decomposition under the open canopy was characterized by high sample-to-sample variability, showing the diversification of fungal resources. Tree species-specific fungi were detected among the abundant species mostly during the initial decomposition, whereas fungi associated with certain canopy cover treatments were present evenly during decomposition. The species diversity of forest stands and the variability in microclimatic conditions both promote the diversity of fine woody debris fungi in a forest.

Stem traits, compartments, and tree species affect fungal communities on decaying wood

Dead wood quantity and quality is important for forest biodiversity, by determining wood‐inhabiting fungal assemblages. We therefore evaluated how fungal communities were regulated by stem traits and compartments (i.e. bark, outer‐ and inner wood) of 14 common temperate tree species. Fresh logs were incubated in a common garden experiment in a forest site in the Netherlands. After 1 and 4 years of decay, the fungal composition of different compartments was assessed using Internal Transcribed Spacer amplicon sequencing. We found that fungal alpha diversity differed significantly across tree species and stem compartments, with bark showing significantly higher fungal diversity than wood. Gymnosperms and Angiosperms hold different fungal communities, and distinct fungi were found between inner wood and other compartments. Stem traits showed significant afterlife effects on fungal communities; traits associated with accessibility (e.g. conduit diameter), stem chemistry (e.g. C, N, lignin) and physical defence (e.g. density) were important factors shaping fungal community structure in decaying stems. Overall, stem traits vary substantially across stem compartments and tree species, thus regulating fungal communities and the long‐term carbon dynamics of dead trees.

Response of Fruit Body Assemblage Color Lightness to Macroclimate and Vegetation Cover

Understanding how species relate mechanistically to their environment via traits is a central goal in ecology. Many macroecological rules were found for macroorganisms, however, whether they can explain microorganismal macroecological patterns still requires investigation. Further, whether macroecological rules are also applicable in microclimates is largely unexplored. Here we use fruit body-forming fungi to understand both aspects better. A recent study showed first evidence for the thermal-melanism hypothesis (Bogert’s rule) in fruit body-forming fungi and relied on a continental spatial scale with large grid size. At large spatial extent and grid sizes, other factors like dispersal limitation or local microclimatic variability might influence observed patterns besides the rule of interest. Therefore, we test fungal assemblage fruit body color lightness along a local elevational gradient (mean annual temperature gradient of 7°C) while considering the vegetation cover as a proxy for local variability in microclimate. Using multivariate linear modeling, we found that fungal fruiting assemblages are significantly darker at lower mean annual temperatures supporting the thermal-melanism hypothesis. Further, we found a non-significant trend of assemblage color lightness with vegetation cover. Our results support Bogert’s rule for microorganisms with macroclimate, which was also found for macroorganisms.

Fungal Diversity in Multiple Post-harvest Aged Red Pine Stumps and Their Potential Influence on Heterobasidion Root Rot in Managed Stands Across Minnesota

Thinning operations that occur in managed red pine (Pinus resinosa) stands, create tree stumps that can serve as a habitat for fungi, especially Heterobasidion irregulare, the cause of a serious root disease. Different fungi can colonize stumps early and the community of fungi can change over time as initial fungal species become replaced. Samples were collected from both the native and non-native range of red pine from stumps that were cut at different time periods. Stumps that were harvested at 0-1, 2-3, 5-6, and 10-12 years before sampling were used to provide data on the diversity of fungi that colonize tree stumps and how these communities can change over time as well as how they influence colonization of H. irregulare. Traditional culturing methods and Illumina MiSeq sequencing were used to identify the fungi in the samples. Of particular interest was Phlebiopsis gigantea, which can colonize cut stumps and prevent H. irregulare from becoming established. Overall, P. gigantea was the most abundant fungus isolated and sequenced via Illumina MiSeq. Results show that Phlebiopsis gigantea was isolated from 90% of all stumps sampled for sites harvested within 3 years of sampling in the native range of red pine compared to 33% in the non-native range. For Illumina MiSeq, 5,940 total amplicon sequence variants (ASVs) were detected. P. gigantea represented 14% of the total reads and composed 19% of the reads in the native range and 8% in non-native range of red pine. Furthermore, P. gigantea represented 38% of the reads for stumps that were harvested within 3 years of sampling in the native range of red pine compared to 14% in the non-native range. These results help demonstrate that a higher amount of P. gigantea is present in the native range of red pine and could be acting as a native biological control agent. Additional fungi, including Resinicium bicolor, Hypochnicium cremicolor, Leptographium spp., and others identified at different cutting times are also discussed. Finally, different diversity indices revealed similar, but slightly higher diversity for southern sites via Shannon and Simpson Diversity indices. Beta diversity demonstrated a similar species composition in stumps harvested at different times with these stumps being grouped together based on harvesting years.

Diversity and structural characteristics of soil microbial communities in different habitats of wild Lilium regale Wilson in Wenchuan area

Lilium regale Wilson (L.regale), originated in the Minjiang River basin in Sichuan, China, has different phenotypic characteristics in different environments. To analyze the correlation between the phenotypes of L.regale and its soil micro-ecological environment, wild habitat soil of L.regale at the two altitudes were selected to analyze the diversity and community structure of microorganisms in soil, and measure the soil physicochemical factors and enzyme activities. The structural composition and diversity of fungal and bacterial communities in hillside and valley soils were significantly different (p < 0.01). Soil available potassium (AK) and soil enzyme activities such as urease (S_UE), sucrase (S_SC), and catalase (S_CAT) differed significantly different between hillsides and valleys (p < 0.01), while organic matter (OM), total phosphorus (TP), and polyphenol oxidase (S_PPO) had no great variances. Correlation analysis was conducted between the common and differential microorganisms and the morphological characteristics, soil physicochemical factors and soil enzyme activities of L.regale in both hillside and valley. The results showed that both of the fungal and bacterial could be clustered into two distinct groups by positive and negative correlations, suggesting that the representative microorganism may have structural characteristics that are directly related to soil physicochemical properties and enzyme activities, which conversely affect the phenotype of Lily. Therefore, the study on the native species of horticultural plants and the local soil microhabitat environment will benefit the conservation of wild Lily and provide theoretical guidance for the domestication and breeding of horticultural plants.

Do different growth rates of trees cause distinct habitat qualities for saproxylic assemblages?

In production forests, a common silvicultural objective is enhancing tree growth rates. The growth rate influences both mechanical and biochemical properties of wood, which may have an impact on dead wood inhabiting (i.e. saproxylic) species. In this study, we tested for the first time whether tree growth rates affect dead-wood associated assemblages in general and the occurrence of red-listed species in particular. We sampled saproxylic beetles (eclector traps) and fungi (DNA metabarcoding of wood samples) in dead trunks of Norway spruce (Picea abies), which had different growth rates within the same hemiboreal forests in Sweden. A high proportion of fungi showed a positive association to increasing tree growth. This resulted in higher fungal richness in fast-grown trees both at the trunk scale and across multiple studied trunks. Such patterns were not observed for saproxylic beetles. However, a set of species (both beetles and fungi) preferred slow-grown wood. Moreover, the total number of red-listed species was highest in slow-grown trunks. We conclude that dead wood from slow-grown trees hosts relatively fewer saproxylic species, but a part of these may be vulnerable to production forestry. It implies that slow-grown trees should be a target in nature conservation. However, where slow-grown trees are absent, for instance in forests managed for a high biomass production, increasing the volumes of dead wood from fast-grown trees may support many species.

Variation in Downed Deadwood Density, Biomass, and Moisture during Decomposition in a Natural Temperate Forest

Deadwood is a resource of water, nutrients, and carbon, as well as an important driving factor of spatial pedocomplexity and hillslope processes in forested landscapes. The applicability of existing relevant studies in mountain forests in Central Europe is limited by the low number of data, absence of precise dating, and short time periods studied. Here, we aimed to assess the decomposition pathway in terms of changes and variability in the physical characteristics of deadwood (wood density, biomass, and moisture) during the decomposition process, and to describe differences in decomposition rate. The research was carried out in the Žofínský Primeval Forest, one of the oldest forest reserves in Europe. Samples were taken from sapwood of downed logs of the three main tree species: Fagus sylvatica L., Abies alba Mill., and Picea abies (L.) Karst. The time since the death of each downed log was obtained using tree censuses repeated since 1975 and dendrochronology. The maximal time since the death of a log was species-specific, and ranged from 61–76 years. The rate of change (slope) of moisture content along the time since death in a linear regression model was the highest for F. sylvatica (b = 3.94) compared to A. alba (b = 2.21) and P. abies (b = 1.93). An exponential model showing the dependence of biomass loss on time since death revealed that F. sylvatica stems with a diameter of 50–90 cm had the shortest decomposition rate—51 years—followed by P. abies (71 years) and A. alba (72 years). Our findings can be used in geochemical models of element cycles in temperate old-growth forests, the prediction of deadwood dynamics and changes in related biodiversity, and in refining management recommendations.

Timing of Resource Addition Affects the Migration Behavior of Wood Decomposer Fungal Mycelia

Studies of fungal behavior are essential for a better understanding of fungal-driven ecological processes. Here, we evaluated the effects of timing of resource (bait) addition on the behavior of fungal mycelia when it remains in the inoculum and when it migrates from it towards a bait, using cord-forming basidiomycetes. Experiments allowed mycelium to grow from an inoculum wood across the surface of a soil microcosm, where it encountered a new wood bait 14 or 98 d after the start of growth. After the 42-d colonization of the bait, inoculum and bait were individually moved to a dish containing fresh soil to determine whether the mycelia were able to grow out. When the inoculum and bait of mycelia baited after 14 d were transferred to new soil, there was 100% regrowth from both inoculum and bait in Pholiota brunnescens and Phanerochaete velutina, indicating that no migration occurred. However, when mycelium was baited after 98 d, 3 and 4 out of 10 replicates of P. brunnescens and P. velutina, respectively, regrew only from bait and not from inoculum, indicating migration. These results suggest that prolonged periods without new resources alter the behavior of mycelium, probably due to the exhaustion of resources.

Successional Development of Fungal Communities Associated with Decomposing Deadwood in a Natural Mixed Temperate Forest

Deadwood represents an important carbon stock and contributes to climate change mitigation. Wood decomposition is mainly driven by fungal communities. Their composition is known to change during decomposition, but it is unclear how environmental factors such as wood chemistry affect these successional patterns through their effects on dominant fungal taxa. We analysed the deadwood of Fagus sylvatica and Abies alba across a deadwood succession series of >40 years in a natural fir-beech forest in the Czech Republic to describe the successional changes in fungal communities, fungal abundance and enzymatic activities and to link these changes to environmental variables. The fungal communities showed high levels of spatial variability and beta diversity. In young deadwood, fungal communities showed higher similarity among tree species, and fungi were generally less abundant, less diverse and less active than in older deadwood. pH and the carbon to nitrogen ratio (C/N) were the best predictors of the fungal community composition, and they affected the abundance of half of the dominant fungal taxa. The relative abundance of most of the dominant taxa tended to increase with increasing pH or C/N, possibly indicating that acidification and atmospheric N deposition may shift the community composition towards species that are currently less dominant.

Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus Pycnoporus

White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here, we combined comparative genomics, transcriptomics and secretome proteomics to identify conserved enzymatic signatures at the onset of wood-decaying activity within the Basidiomycota genus Pycnoporus. We observed a strong conservation in the genome structures and the repertoires of protein-coding genes across the four Pycnoporus species described to date, despite the species having distinct geographic distributions. We further analysed the early response of P. cinnabarinus, P. coccineus and P. sanguineus to diverse (ligno)-cellulosic substrates. We identified a conserved set of enzymes mobilized by the three species for breaking down cellulose, hemicellulose and pectin. The co-occurrence in the exo-proteomes of H₂O₂-producing enzymes with H₂O₂-consuming enzymes was a common feature of the three species, although each enzymatic partner displayed independent transcriptional regulation. Finally, cellobiose dehydrogenase-coding genes were systematically co-regulated with at least one AA9 lytic polysaccharide monooxygenase gene, indicative of enzymatic synergy in vivo. This study highlights a conserved core white-rot fungal enzymatic mechanism behind the wood-decaying process.

Temperature Sensitivity of CO2 and CH4 Fluxes from Coarse Woody Debris in Northern Boreal Forests

Carbon dioxide (CO2) and methane (CH4) are recognized as the main greenhouse gases causing climate warming. In forest ecosystems, the death of trees leads to the formation of coarse woody debris (CWD) that is one of the sources of greenhouse gas emissions due to wood decomposition. We quantified the CO2 and CH4 fluxes from CWD of larch (Larix gmelinii (Rupr.)) and birch (Betula tortuosa Ledeb.) collected in the northern boreal forests of Central Siberia. The CWD samples were incubated at +5, +15 and +25 °C. The CO2 and CH4 fluxes showed strong correlations with temperature, moisture, decomposition stage and the type of wood’s rot. The temperature coefficient Q10 indicated higher temperature sensitivity of CO2 flux within the temperature interval from +5 to +15 °C than from +15 to +25 °C. Methane flux had higher temperature sensitivity within the interval from +15 to +25 °C. It was found that, in boreal forests, CWD of early decay stage can serve as a source of methane to the atmosphere when air temperatures increased above +15 °C. Strong positive correlation between CH4 production and CO2 emission indicated a biological source and supported findings on aerobic origin of the main process contributing to the CH4 flux from decomposing CWD.

Decay stages of wood and associated fungal communities characterise diversity-decomposition 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.

Sapwood and heartwood affect differentially bacterial and fungal community structure and successional dynamics during Quercus petraea decomposition

In forests, bacteria and fungi are key players in wood degradation. Still, studies focusing on bacterial and fungal successions during the decomposition process depending on the wood types (i.e. sapwood and heartwood) remain scarce. This study aimed to understand the effect of wood type on the dynamics of microbial ecological guilds in wood decomposition. Using Illumina metabarcoding, bacterial and fungal communities were monitored every 3 months for 3 years from Quercus petraea wood discs placed on forest soil. Wood density and microbial enzymes involved in biopolymer degradation were measured. We observed rapid changes in the bacterial and fungal communities and microbial ecological guilds associated with wood decomposition throughout the experiment. Bacterial and fungal succession dynamics were very contrasted between sapwood and heartwood. The initial microbial communities were quickly replaced by new bacterial and fungal assemblages in the sapwood. Conversely, some initial functional guilds (i.e. endophytes and yeasts) persisted all along the experiment in heartwood and finally became dominant, possibly limiting the development of saprotrophic fungi. Our data also suggested a significant role of bacteria in nitrogen cycle during wood decomposition.

Root presence modifies the long-term decomposition dynamics of fungal necromass and the associated microbial communities in a boreal forest

Recent studies have highlighted that dead fungal mycelium represents an important fraction of soil carbon (C) and nitrogen (N) inputs and stocks. Consequently, identifying the microbial communities and the ecological factors that govern the decomposition of fungal necromass will provide critical insight into how fungal organic matter (OM) affects forest soil C and nutrient cycles. Here, we examined the microbial communities colonising fungal necromass during a multiyear decomposition experiment in a boreal forest, which included incubation bags with different mesh sizes to manipulate both plant root and microbial decomposer group access. Necromass-associated bacterial and fungal communities were taxonomically and functionally rich throughout the 30 months of incubation, with increasing abundances of oligotrophic bacteria and root-associated fungi (i.e., ectomycorrhizal, ericoid mycorrhizal and endophytic fungi) in the late stages of decomposition in the mesh bags to which they had access. Necromass-associated β-glucosidase activity was highest at 6 months, while leucine aminopeptidase peptidase was highest at 18 months. Based on an asymptotic decomposition model, root presence was associated with an initial faster rate of fungal necromass decomposition, but resulted in higher amounts of fungal necromass retained at later sampling times. Collectively, these results indicate that microbial community composition and enzyme activities on decomposing fungal necromass remain dynamic years after initial input, and that roots and their associated fungal symbionts result in the slowing of microbial necromass turnover with time.

Evolution of Fungal Carbohydrate-Active Enzyme Portfolios and Adaptation to Plant Cell-Wall Polymers

The postindustrial era is currently facing two ecological challenges. First, the rise in global temperature, mostly caused by the accumulation of carbon dioxide (CO₂) in the atmosphere, and second, the inability of the environment to absorb the waste of human activities. Fungi are valuable levers for both a reduction in CO₂ emissions, and the improvement of a circular economy with the optimized valorization of plant waste and biomass. Soil fungi may promote plant growth and thereby increase CO₂ assimilation via photosynthesis or, conversely, they may prompt the decomposition of dead organic matter, and thereby contribute to CO₂ emissions. The strategies that fungi use to cope with plant-cell-wall polymers and access the saccharides that they use as a carbon source largely rely on the secretion of carbohydrate-active enzymes (CAZymes). In the past few years, comparative genomics and phylogenomics coupled with the functional characterization of CAZymes significantly improved the understanding of their evolution in fungal genomes, providing a framework for the design of nature-inspired enzymatic catalysts. Here, we provide an overview of the diversity of CAZyme enzymatic systems employed by fungi that exhibit different substrate preferences, different ecologies, or belong to different taxonomical groups for lignocellulose degradation.

Wood construction more strongly shapes deadwood microbial communities than spatial location over 5 years of decay

Diverse communities of fungi and bacteria in deadwood mediate wood decay. While rates of decomposition vary greatly among woody species and spatially distinct habitats, the relative importance of these factors in structuring microbial communities and whether these shift over time remains largely unknown. We characterized fungal and bacterial diversity within pieces of deadwood that experienced 6.3-98.8% mass loss while decaying in common garden 'rotplots' in a temperate oak-hickory forest in the Ozark Highlands, MO, USA. Communities were isolated from 21 woody species that had been decomposing for 1-5 years in spatially distinct habitats at the landscape scale (top and bottom of watersheds) and within stems (top and bottom of stems). Microbial community structure varied more strongly with wood traits than with spatial locations, mirroring the relative role of these factors on decay rates on the same pieces of wood even after 5 years. Co-occurring fungal and bacterial communities persistently influenced one another independently from their shared environmental conditions. However, the relative influence of wood construction versus spatial locations differed between fungi and bacteria, suggesting that life history characteristics of these clades structure diversity differently across space and time in decomposing wood.

Functional Genomics, Transcriptomics, and Proteomics Reveal Distinct Combat Strategies Between Lineages of Wood-Degrading Fungi With Redundant Wood Decay Mechanisms

Wood-degrading fungi vary in their strategies for deconstructing wood, and their competitive successes shape the rate and fate of carbon released from wood, Earth’s largest pool of aboveground terrestrial carbon. In this study, one-on-one interspecific interactions between two model brown rot (carbohydrate-selective) fungi, Gloeophyllum trabeum and Rhodonia (Postia) placenta, were studied on wood wafers where a clearly resolved interaction zone (IZ) could be generated, reproducibly. Comparative RNAseq and proteomics between the IZ and non-interacting hyphae of each species identified combative strategies for each fungus. Glycoside hydrolases were a relatively smaller portion of the interaction secretome compared to non-interacting hyphae. The interaction zone showed higher pectinase specific activity than all other sampling locations, and higher laminarinase specific activity (branched β-glucan proxy) was seen in the IZ secretome relative to equivalent hyphae in single-species cultures. Our efforts also identified two distinct competitive strategies in these two fungi with a shared nutritional mode (brown rot) but polyphyletic ancestral lineages. Gloeophyllum trabeum (Gloeophyllum clade) upregulated more secondary metabolite (SM) synthesis genes in response to a competitor than did R. placenta. R. placenta (Antrodia clade) upregulated a larger variety of uncharacterized oxidoreductases in interacting hyphae, suggesting that these may play a role in mediating competitor response in this fungus. Both species produced several hypothetical proteins exclusively in the interaction zone, leaving questions as to the function of these proteins. This work supports the existence of multiple interaction strategies among brown rot fungi and highlights the functional diversity among wood decay fungi.

Traits mediate drought effects on wood carbon fluxes

CO₂ fluxes from wood decomposition represent an important source of carbon from forest ecosystems to the atmosphere, which are determined by both wood traits and climate influencing the metabolic rates of decomposers. Previous studies have quantified the effects of moisture and temperature on wood decomposition, but these effects were not separated from the potential influence of wood traits. Indeed, it is not well understood how traits and climate interact to influence wood CO₂ fluxes. Here, we examined the responses of CO₂ fluxes from dead wood with different traits (angiosperm and gymnosperm) to 0%, 35%, and 70% rainfall reduction across seasonal temperature gradients. Our results showed that drought significantly decreased wood CO₂ fluxes, but its effects varied with both taxonomical group and drought intensity. Drought-induced reduction in wood CO₂ fluxes was larger in angiosperms than gymnosperms for the 35% rainfall reduction treatment, but there was no significant difference between these groups for the 70% reduction treatment. This is because wood nitrogen density and carbon quality were significantly higher in angiosperms than gymnosperms, yielding a higher moisture sensitivity of wood decomposition. These findings were demonstrated by a significant positive interaction effect between wood nitrogen and moisture on CO₂ fluxes in a structural equation model. Additionally, we ascertained that a constant temperature sensitivity of CO₂ fluxes was independent of wood traits and consistent with previous estimates for extracellular enzyme kinetics. Our results highlight the key role of wood traits in regulating drought responses of wood carbon fluxes. Given that both climate and forest management might extensively modify taxonomic compositions in the future, it is critical for carbon cycle models to account for such interactions between wood traits and climate in driving dynamics of wood decomposition.

Fungal communities and their association with nitrogen-fixing bacteria affect early decomposition of Norway spruce deadwood

Deadwood decomposition is relevant in nature and wood inhabiting fungi (WIF) are its main decomposers. However, climate influence on WIF community and their interactions with bacteria are poorly understood. Therefore, we set up an in-field mesocosm experiment in the Italian Alps and monitored the effect of slope exposure (north- vs. south-facing slope) on the decomposition of Picea abies wood blocks and their microbiome over two years. Unlike fungal richness and diversity, we observed compositional and functional differences in the WIF communities as a function of exposure. Wood-degrading operational taxonomic units (OTUs) such as Mycena, and mycorrhizal and endophytic OTUs were characteristic of the south-facing slope. On the north-facing one, Mucoromycota, primarily Mucor, were abundant and mixotrophic basidiomycetes with limited lignin-degrading capacities had a higher prevalence compared to the southern slope. The colder, more humid conditions and prolonged snow-coverage at north exposure likely influenced the development of the wood-degrading microbial communities. Networks between WIF and N2-fixing bacteria were composed of higher numbers of interacting microbial units and showed denser connections at the south-facing slope. The association of WIF to N2-fixing Burkholderiales and Rhizobiales could have provided additional competitive advantages, especially for early wood colonization.

A trait-based understanding of wood decomposition by fungi

As the primary decomposers of organic material in terrestrial ecosystems, fungi are critical agents of the global carbon cycle. Yet our ability to link fungal community composition to ecosystem functioning is constrained by a limited understanding of the factors accounting for different wood decomposition rates among fungi. Here we examine which traits best explain fungal decomposition ability by combining detailed trait-based assays on 34 saprotrophic fungi from across North America in the laboratory with a 5-y field study comprising 1,582 fungi isolated from 74 decomposing logs. Fungal growth rate (hyphal extension rate) was the strongest single predictor of fungal-mediated wood decomposition rate under laboratory conditions, and accounted for up to 27% of the in situ variation in decomposition in the field. At the individual level, decomposition rate was negatively correlated with moisture niche width (an indicator of drought stress tolerance) and with the production of nutrient-mineralizing extracellular enzymes. Together, these results suggest that decomposition rates strongly align with a dominance-tolerance life-history trade-off that was previously identified in these isolates, forming a spectrum from slow-growing, stress-tolerant fungi that are poor decomposers to fast-growing, highly competitive fungi with fast decomposition rates. Our study illustrates how an understanding of fungal trait variation could improve our predictive ability of the early and midstages of wood decay, to which our findings are most applicable. By mapping our results onto the biogeographic distribution of the dominance-tolerance trade-off across North America, we approximate broad-scale patterns in intrinsic fungal-mediated wood decomposition rates.

The Effect of Size of Black Cherry Stumps on the Composition of Fungal Communities Colonising Stumps

We investigated fungal communities colonising black cherry stumps. We tested the hypothesis that black cherry stumps of greater diameter should be characterised by more diverse fungal communities than stumps of smaller diameter. The material for analyses came from Podanin Forest District. DNA was extracted using a Plant Genomic DNA purification kit. The results were subjected to bioinformatic analysis and statistical analysis. The OTU sequences were compared using the BLAST algorithm with reference sequences from the UNITE database. In total, 8192 raw sequences were obtained from samples of black cherry stumps applying the Illumina sequencing technique. The results of the statistical analysis indicate a trend towards increased diversity in bigger black cherry stumps. The dominant share of fungi associated with wood decomposition indicates the progressing process of decomposition in stumps. Identification of the role and functions of the individual components of fungal communities colonising stumps may provide insight into the overall ecology of these organisms and provide a basis for improved plant protection, with a view to limiting the occurrence of black cherries in the future in undesirable locations outside their natural range.

Limited initial impacts of biomass harvesting on composition of wood-inhabiting fungi within residual stumps

Growing pressures linked to global warming are prompting governments to put policies in place to find alternatives to fossil fuels. In this study, we compared the impact of tree-length harvesting to more intensive full-tree harvesting on the composition of fungi residing in residual stumps 5 years after harvest. In the tree-length treatment, a larger amount of residual material was left around the residual stumps in contrast to the full-tree treatment where a large amount of woody debris was removed. We collected sawdust from five randomly selected residual stumps in five blocks in each of the tree-length and full-tree treatments, yielding a total of 50 samples (25 in each treatment). We characterized the fungal operational taxonomic units (OTUs) present in each stump using high-throughput DNA sequencing of the fungal ITS region. We observed no differences in Shannon diversity between tree-length and full-tree harvesting. Likewise, we observed few differences in the composition of fungal OTUs among tree-length and full-tree samples using non-metric multidimensional scaling. Using the differential abundance analysis implemented with DESeq2, we did, however, detect several associations between specific fungal taxa and the intensity of residual biomass harvest. For example, Peniophorella pallida (Bres.) KH Larss. and Tephromela sp. were found mainly in the full-tree treatment, while Phlebia livida (Pers.) Bres. and Cladophialophora chaetospira (Grove) Crous & Arzanlou were found mainly in the tree-length treatment. While none of the 20 most abundant species in our study were identified as pathogens we did identify one conifer pathogen species Serpula himantioides (Fr.) P. Karst found mainly in the full-tree treatment.

Home-Field Advantage in Wood Decomposition Is Mainly Mediated by Fungal Community Shifts at "Home" Versus "Away"

The home-field advantage (HFA) hypothesis has been used intensively to study leaf litter decomposition in various ecosystems. However, the HFA in woody substrates is still unexplored. Here, we reanalyzed and integrated existing datasets on various groups of microorganisms collected from natural deadwood of two temperate trees, Fagus sylvatica and Picea abies, from forests in which one or other of these species dominates but where both are present. Our aims were (i) to test the HFA hypothesis on wood decomposition rates of these two temperate tree species, and (ii) to investigate if HFA hypothesis can be explained by diversity and community composition of bacteria and in detail N-fixing bacteria (as determined by molecular 16S rRNA and nifH gene amplification) and fungi (as determined by molecular ITS rRNA amplification and sporocarp surveys). Our results showed that wood decomposition rates were accelerated at "home" versus "away" by 38.19% ± 20.04% (mean ± SE). We detected strong changes in fungal richness (increase 36-50%) and community composition (R_ANOSIM = 0.52-0.60, P < 0.05) according to HFA hypothesis. The changes of fungi were much stronger than for total bacteria and nitrogen fixing for both at richness and community composition levels. In conclusion, our results support the HFA hypothesis in deadwood: decomposition rate is accelerated at home due to specialization of fungal communities produced by the plant community above them. Furthermore, the higher richness of fungal sporocarps and nitrogen-fixing bacteria (nifH) may stimulate or at least stabilize wood decomposition rates at "home" versus "away."

Good neighbors aplenty: fungal endophytes rarely exhibit competitive exclusion patterns across a span of woody habitats

Environmental forces and biotic interactions, both positive and negative, structure ecological communities, but their relative roles remain obscure despite strong theory. For instance, ecologically similar species, based on the principle of limiting similarity, are expected to be most competitive and show negative interactions. Specious communities that assemble along broad environmental gradients afford the most power to test theory, but the communities often are difficult to quantify. Microbes, specifically fungal endophytes of wood, are especially suited for testing community assembly theory because they are relatively easy to sample across a comprehensive range of environmental space with clear axes of variation. Moreover, endophytes mediate key forest carbon cycle processes, and although saprophytic fungi from dead wood typically compete, endophytic fungi in living wood may enhance success through cooperative symbioses. To classify interactions within endophyte communities, we analyzed fungal DNA barcode variation across 22 woody plant species growing in woodlands near Richmond, New South Wales, Australia. We estimated the response of endophytes to the measured wood environment (i.e., 11 anatomical and chemical wood traits) and each other using latent-variable models and identified recurrent communities across wood environments using model-based classification. We used this information to evaluate whether (1) co-occurrence patterns are consistent with strong competitive exclusion, and (2) a priori classifications by trophic mode and phylum distinguish taxa that are more likely to have positive vs. negative associations under the principle of limiting similarity. Fungal endophytes were diverse (mean = 140 taxa/sample), with differences in community composition structured by wood traits. Variation in wood water content and carbon concentration were associated with especially large community shifts. Surprisingly, after accounting for wood traits, fungal species were still more than three times more likely to have positive than negative co-occurrence patterns. That is, patterns consistent with strong competitive exclusion were rare, and positive interactions among fungal endophytes were more common than expected. Confirming the frequency of positive vs. negative interactions among fungal taxa requires experimental tests, and our findings establish clear paths for further study. Evidence to date intriguingly suggests that, across a wide range of wood traits, cooperation may outweigh combat for these fungi.

Changes in the Microbial Community of Pinus arizonica Saplings After Being Colonized by the Bark Beetle Dendroctonus rhizophagus (Curculionidae: Scolytinae)

The death of trees is an ecological process that promotes regeneration, organic matter recycling, and the structure of communities. However, diverse biotic and abiotic factors can disturb this process. Dendroctonus bark beetles (Curculionidae: Scolytinae) are natural inhabitants of pine forests, some of which produce periodic outbreaks, killing thousands of trees in the process. These insects spend almost their entire life cycle under tree bark, where they reproduce and feed on phloem. Tunneling and feeding of the beetles result in the death of the tree and an alteration of the resident microbiota as well as the introduction of microbes that the beetles vector. To understand how microbial communities in subcortical tissues of pines change after they are colonized by the bark beetle Dendroctonus rhizophagus, we compare both the bacterial and fungal community structures in two colonization stages of Pinus arizonica (Arizona pine) employing Illumina MiSeq. Our findings showed significant differences in diversity and the dominance of bacterial community in the two colonization stages with Shannon (P = 0.004) and Simpson (P = 0.0006) indices, respectively, but not in species richness with Chao1 (P = 0.19). In contrast, fungal communities in both stages showed significant differences in species richness with Chao1 (P = 0.0003) and a diversity with Shannon index (P = 0.038), but not in the dominance with the Simpson index (P = 0.12). The β-diversity also showed significant changes in the structure of bacterial and fungal communities along the colonization stages, maintaining the dominant members in both cases. Our results suggest that microbial communities present in the Arizona pine at the tree early colonization stage by bark beetle change predictably over time.