Linking wood-decay fungal communities to decay rates: Using a long-term experimental manipulation of deadwood and canopy gaps

Decomposition transfers carbon (C) from detrital organic matter to soil and atmospheric pools. In forested ecosystems, deadwood accounts for a large proportion of the detrital C pool and is primarily decomposed by wood-inhabiting fungi (WIF). Deadwood reductions linked to forest harvesting may alter WIF richness and composition, thus indirectly influencing the persistence of deadwood and its contribution to C and nutrient cycling. Forest structure was enhanced via canopy gap creation and coarse woody debris (CWD) addition that mimic natural disturbance by windfall within a deciduous northern hardwood forest (Wisconsin, USA) to examine its effect on deadwood-associated biodiversity and function. Experimental sugar maple (Acer saccharum) logs were sampled, for DNA extraction, ten years after placement to determine the assembly of fungal community composition and its relationship to wood decay rates.Our findings suggest that the WIF community responded to gap disturbance by favoring species able to persist under more extreme microclimates caused by gaps. CWD addition under closed canopy tended to favor a different species assemblage from gap creation treatments and the control, where canopy was undisturbed and CWD was not added. This was presumably due to consistent microclimatic conditions and the abundance of CWD substrates for host specialists. Fungal OTU richness was significantly and inversely related to CWD decay rates, likely due to competition for resources. In contrast, fungal OTU composition was not significantly related to CWD decay rates, canopy openness or CWD addition amounts. Our study site represents a diverse fungal community in which complex interactions among wood-inhabiting organisms and abiotic factors are likely to slow CWD decomposition, which suggests that maintaining a biodiverse and microsite-rich ecosystem may enhance the capacity for C storage within temperate forests.     

Linking taxonomical and functional biodiversity of saproxylic fungi and beetles in broad‐leaved forests in southern Italy with varying management histories

Abstract

The fundamental ecological significance of deadwood decomposition in forests has been highlighted in several reviews, some conclusions regarding silviculture being drawn. Old‐growth forests are natural centres of biodiversity. Saproxylic fungi and beetles, which are vital components of these ecosystems, occupy a variety of spatial and trophic niches. Fungal and beetle diversity on coarse woody debris (CWD) was analysed in 36 forest sites in the Cilento and Vallo di Diano National Park, Italy. The data were analysed by DCA and Spearman’s rank correlation. The results provide empirical evidence of the existence of a pattern of joint colonization of the woody substrate by fungi and beetles, which includes an assemblage of reciprocal trophic roles within fungal/beetle communities. These organisms act together to form a dynamic taxonomical and functional ecosystem component within the complex set of processes involved in wood decay. The variables most predictive of correlations between management‐related structural attributes and fungal/beetle species richness and their trophic roles for old‐growth forest are: number of logs, number of decay classes and CWD total volume. Deadwood spatio‐temporal continuity should be the main objective of forest planning to stop the loss of saproxylic fungal and insect biodiversity.     

Spatial structure and the effects of host and soil environments on communities of ectomycorrhizal fungi in wooded savannas and rain forests of Continental Africa and Madagascar

Mycorrhizal fungi play a key role in mineral nutrition of terrestrial plants, but the factors affecting natural distribution, diversity and community composition of particularly tropical fungi remain poorly understood. This study addresses shifts in community structure and species frequency of ectomycorrhizal (EcM) fungi in relation to host taxa, soil depth and spatial structure in four contrasting African ecosystems. We used the rDNA and plastid trnL intron sequence analysis for identification of fungi and host plants, respectively. By partitioning out spatial autocorrelation in plant and fungal distribution, we suggest that African EcM fungal communities are little structured by soil horizon and host at the plant species and family levels. These findings contrast with patterns of vegetation in these forests and EcM fungal communities in other tropical and temperate ecosystems. The low level of host preference indirectly supports an earlier hypothesis that pioneer Phyllanthaceae may facilitate the establishment of late successional Fabaceae and potentially other EcM host trees by providing compatible fungal inoculum in deforested and naturally disturbed ecosystems of tropical Africa.     

Wood-decay type and fungal guild dominance across a North American log transplant experiment

We incubated 196 large-diameter aspen (Populus tremuloides), birch (Betula papyrifera), and pine (Pinus taeda) logs on the FACE Wood Decomposition Experiment encompassing eight climatically-distinct forest sites in the United States. We sampled dead wood from these large-diameter logs after 2 to 6 y of decomposition and determined wood rot type as a continuous variable using the lignin loss/density loss ratio (L/D) and assessed wood-rotting fungal guilds using high-throughput amplicon sequencing (HTAS) of the ITS-2 marker. We found L/D values in line with a white rot dominance in all three tree species, with pine having lower L/D values than aspen and birch. Based on HTAS data, white rot fungi were the most abundant and diverse wood-rotting fungal guild, and soft rot fungi were more abundant and diverse than brown rot fungi in logs with low L/D values. For aspen and birch logs, decay type was related to the wood density at sampling. For the pine logs, decay type was associated with the balance between white and brown/soft rot fungi abundance and OTU richness. Our results demonstrate that decay type is governed by biotic and abiotic factors, which vary by tree species.     

辽东次生林木腐菌的物种多样性及其分布特征

2013年7—9月,以清原林场、老秃顶子国家级自然保护区和宽甸白石砬子自然保护区为研究区域,对辽东次生林中木腐菌的物种多样性及其分布特征进行了研究.经过野外调查,共采集和记录木腐菌1062份,经鉴定为92种,隶属于48个属;其中白石砬子国家级自然保护区木腐真菌物种最丰富,Shannon多样性指数为4.04.从物种的地理成分来看,辽东地区的木腐菌以世界性广布和北温带分布为主,具有明显的北温带特征.白腐真菌是该地区倒木的主要分解者;该地区的木腐菌主要生长在腐烂等级为2、3的倒木上,主要优势寄主为槭属倒木,有243份真菌采集于槭属倒木,占总数的23.2%.     

尖峰岭热带山地雨林根部真菌-植物互作网络结构特征

不同功能群的根部真菌可能会与植物差异性地互作, 并进一步影响地下真菌与植物群落构建。本研究采用Illumina Miseq测序方法检测了海南尖峰岭热带山地雨林中常见植物的根部真菌; 采用网络分析法比较了丛枝菌根(AM)真菌、外生菌根(ECM)真菌, 以及所有根部真菌与植物互作的二分网络(bipartite networks)结构特性。从槭树科、番荔枝科、夹竹桃科、冬青科、棕榈科、壳斗科、樟科和木犀科等8科植物的根系中, 检测到297,831条真菌ITS1序列, 这些序列被划为1,279个真菌分类单元(OTUs), 其中子囊菌门748个、担子菌门354个、球囊菌亚门80个, 以及未知真菌97个。核心根部真菌群落(420个OTUs)中, 至少有三类不同生态功能的真菌常见, 即丛枝菌根真菌(40个OTUs, 占总序列数23.4%)、外生菌根真菌(48个OTUs, 13.9%)和腐生型真菌(83个OTUs, 19.8%)。尖峰岭山地雨林根部真菌-植物互作网络结构特性的指标普遍显著高于/低于假定物种随机互作的零模型期待值。在群落水平, 不同功能型的根部真菌-植物互作网络表现出不同或相反的结构特性, 如丛枝菌根互作网络表现为比零模型预测值高的嵌套性和连接性, 以及比零模型低的专一性, 而外生菌根互作网络呈现出比零模型预测值低的嵌套性和连接性, 以及比零模型高的专一性。在功能群水平, 植物的生态位重叠度在AM互作网络高, 而ECM互作网络低; 真菌的生态位宽度在ECM互作网络窄, 而在AM互作网络较宽。共现(co-occurrence)网络分析进一步揭示, ECM群落的物种对资源的高度种间竞争(植物、真菌高C-score), 以及AM群落的物种无明显种间竞争(低C-score), 可能分别是形成反嵌套ECM互作网络及高嵌套AM互作网络结构的原因。上述结果说明, 尖峰岭山地雨林中至少有两种及以上的种间互作机制调节群落构建: 驱动AM互作网络冗余(nestedness)及ECM互作网络的高生态位分化(专一性)。本研究在同一个森林内探讨了不同功能型的真菌-植物互作特性, 对深入理解热带森林的物种共存机制和生态恢复具有重要意义。     

Accumulation and decay dynamics of coarse woody debris in a Japanese old-growth subalpine coniferous forest

Far less is known about the coarse woody debris (CWD) stock and decay process in temperate Asia compared with that in boreal and temperate Europe and North America. We estimated coniferous CWD stock (logs and snags), decay rate and process, and fungal species responsible for the decay process in a Japanese subalpine coniferous forest. The CWD mass was 42.4 Mg ha^?1, which was the greatest among the previous data recorded in temperate Asia. The decay rate calculated using the annual input of CWD divided by CWD accumulation was 0.036 year^?1, whereas the decay rate when measured chronosequentially was 0.020–0.023 year^?1. The decay process was divided into two phases characterized by different dominant organic chemical constituents. In the first phase, both acid-unhydrolyzable residue and holocellulose decayed simultaneously, suggestive of the white-rot process. In the second phase, holocellulose was selectively decomposed and AUR accumulated, suggestive of the brown-rot process. Nutrients (N, P, K, Na, Mg, and Ca) were mineralized in the first phase but immobilized in the second phase. The fruiting bodies of 26 taxa of fungi were recorded as occurring on CWD in the study area. Trichaptum abietinum and T. fuscoviolaceum, which dominated in the first phase and are known as white-rot fungi, were assumed to be the main decomposers of lignocellulose in the first phase. Although no known strong wood decomposers dominated the second phase, Laetiporus sulphureus and Oligoporus caesius, known as brown-rot fungi, were expected to participate in the selective decomposition of holocellulose in the second phase.     

Ectomycorrhizal-Dominated Boreal and Tropical Forests Have Distinct Fungal Communities,but Analogous Spatial Patterns across Soil Horizons

Fungi regulate key nutrient cycling processes in many forest ecosystems, but their diversity and distribution within and across ecosystems are poorly understood. Here, we examine the spatial distribution of fungi across a boreal and tropical ecosystem, focusing on ectomycorrhizal fungi. We analyzed fungal community composition across litter (organic horizons) and underlying soil horizons (0–20 cm) using 454 pyrosequencing and clone library sequencing. In both forests, we found significant clustering of fungal communities by site and soil horizons with analogous patterns detected by both sequencing technologies. Free-living saprotrophic fungi dominated the recently-shed leaf litter and ectomycorrhizal fungi dominated the underlying soil horizons. This vertical pattern of fungal segregation has also been found in temperate and European boreal forests, suggesting that these results apply broadly to ectomycorrhizal-dominated systems, including tropical rain forests. Since ectomycorrhizal and free-living saprotrophic fungi have different influences on soil carbon and nitrogen dynamics, information on the spatial distribution of these functional groups will improve our understanding of forest nutrient cycling.     

Host plant genus-level diversity is the best predictor of ectomycorrhizal fungal diversity in a Chinese subtropical forest

Microbial diversity is generally far higher than plant diversity, but the relationship between microbial diversity and plant diversity remains enigmatic. To shed light on this problem, we examined the diversity of a key guild of root-associated microbes, that is, ectomycorrhizal (EM) fungi along a plant diversity gradient in a Chinese subtropical forest. The results indicated that EM fungal diversity was positively correlated with host plant diversity. Furthermore, this relationship was best predicted by host genus-level diversity, rather than species-level diversity or family-level diversity. The generality of this finding was extended beyond our study system through the analyses of 100 additional studies of EM fungal communities from tropical and temperate forests. Here as well, EM fungal lineage composition was significantly affected by EM plant diversity levels, and some EM fungal lineages were co-associated with some host plant genera. These results suggest a general diversity maintenance mechanism for host-specific microbes based on higher order host plant phylogenetic diversity.     

A comparison of fungal endophytic community diversity in tree leaves of rural and urban temperate forests of Kanto district,eastern Japan

To clarify the effects of forest fragmentation and a change in tree species composition following urbanization on endophytic fungal communities, we isolated fungal endophytes from the foliage of nine tree species in suburban (Kashiwa City, Chiba) and rural (Mt. Wagakuni, Ibaraki; Mt. Takao, Tokyo) forests and compared the fungal communities between sites and host tree species. Host specificity was evaluated using the index of host specificity (Si), and the number of isolated species, total isolation frequency, and the diversity index were calculated. From just one to several host-specific species were recognized in all host tree species at all sites. The total isolation frequency of all fungal species on Quercus myrsinaefolia, Quercus serrata, and Chamaecyparis obtusa and the total isolation frequency of host-specific species on Q. myrsinaefolia, Q. serrata, and Eurya japonica were significantly lower in Kashiwa than in the rural forests. The similarity indices (nonmetric multidimensional scaling (NMS) and C_MH) of endophytic communities among different tree species were higher in Kashiwa, as many tree species shared the same fungal species in the suburban forest. Endophytic fungi with a broad host range were grouped into four clusters suggesting their preference for conifer/broadleaves and evergreen/deciduous trees. Forest fragmentation and isolation by urbanization have been shown to cause the decline of host-specific fungal species and a decrease in β diversity of endophytic communities, i.e., endophytic communities associated with tree leaves in suburban forests were found to be depauperate.     

Soil fungal communities reflect aspect-driven environmental structuring and vegetation types in a Pannonian forest landscape

In temperate regions, slope aspect is one of the most influential drivers of environmental conditions at landscape level. The effect of aspect on vegetation has been well studied, but virtually nothing is known about how fungal communities are shaped by aspect-driven environmental conditions. I carried out DNA metabarcoding of fungi from soil samples taken in a selected study area of Pannonian forests in northern Hungary to compare richness and community composition of taxonomic and functional groups of fungi between slopes of predominantly southerly vs. northerly aspect. The deep sequence data presented here (i.e. 980 766 quality-filtered sequences) indicate that both niche (environmental filtering) and neutral (stochastic) processes shape fungal community composition at landscape level. Fungal community composition correlated strongly with aspect, with many fungi showing preference for either south-facing or north-facing slopes. Several taxonomic and functional groups showed significant differences in richness between north- and south-facing slopes and strong compositional differences were observed in all functional groups. The effect of aspect on fungal communities likely is mediated through contrasting mesoclimatic conditions, that in turn influence edaphic processes as well as vegetation. The compositional differences observed in fungi are largely consistent with the coenologically described forest types, which indicates the usefulness of these habitat types as a framework to better understand environmental differences that influence fungal community composition at landscape level. Finally, the data presented here provide unprecedented insights into the diversity and landscape-level community dynamics of fungi in the Pannonian forests.     

Communities of wood-inhabiting fungi in dead pine logs along a geographical gradient in Japan

Fungi are the main agents of coarse woody debris decomposition in forest ecosystems. We examined the associations of environmental variables with fungal community structures in dead pine logs at 12 geographically distant sites using amplicon pyrosequencing of fungal ITS rDNA. A total of 575 operational taxonomic units (OTUs) were identified based on clustering at 97% similarity. Among the known fungal ecological groups, saprotrophic fungi generally showed highest frequency of occurrence and were positively associated with mean annual temperature (MAT) and log diameter. Wood decay fungi with unknown decay type were positively associated with pine wilt disease and negatively associated with log diameter. Ordination analysis of the 42 most prevalent OTUs showed that MAT and annual precipitation significantly explained the observed fungal community structure. These results suggested that climate conditions and site history differentially effect structure fungal communities in pine logs among different ecological groups.     

森林生态系统中木腐真菌群落形成机理及生态功能

在森林生态系统中,枯死木是一个重要的组成部分,为很多生物提供栖息地,有助于养分循环以及碳和水的储存.木材分解是森林生态系统养分循环、土壤形成和碳收支的决定性过程,越来越受到森林生态学家、病理学家和管理者的重视.在此过程中,木腐真菌通过分泌多种酶降解木材主要成分,实现生态系统中的物质循环,具有极为关键和重要的作用.木腐真...     

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

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

Soil propagule banks of ectomycorrhizal fungi share many common species along an elevation gradient

We conducted bioassay experiments to investigate the soil propagule banks of ectomycorrhizal (EM) fungi in old-growth forests along an elevation gradient and compared the elevation pattern with the composition of EM fungi on existing roots in the field. In total, 150 soil cores were collected from three forests on Mt. Ishizuchi, western Japan, and subjected to bioassays using Pinus densiflora and Betula maximowicziana. Using molecular analyses, we recorded 23 EM fungal species in the assayed propagule banks. Eight species (34.8 %) were shared across the three sites, which ranged from a warm–temperate evergreen mixed forest to a subalpine conifer forest. The elevation pattern of the assayed propagule banks differed dramatically from that of EM fungi on existing roots along the same gradient, where only a small proportion of EM fungal species (3.5 %) were shared across sites. The EM fungal species found in the assayed propagule banks included many pioneer fungal species and composition differed significantly from that on existing roots. Furthermore, only 4 of 23 species were shared between the two host species, indicating a strong effect of bioassay host identity in determining the propagule banks of EM fungi. These results imply that the assayed propagule bank is less affected by climate compared to EM fungal communities on existing roots. The dominance of disturbance-dependent fungal species in the assayed propagule banks may result in higher ecosystem resilience to disturbance even in old-growth temperate forests.     

Late Quaternary climate change explains soil fungal community composition rather than fungal richness in forest ecosystems

The dramatic climate fluctuations of the late Quaternary have influenced the diversity and composition of macroorganism communities, but how they structure belowground microbial communities is less well known. Fungi constitute an important component of soil microorganism communities. They play an important role in biodiversity maintenance, community assembly, and ecosystem functioning, and differ from many macroorganisms in many traits. Here, we examined soil fungal communities in Chinese temperate, subtropical, and tropic forests using Illumina MiSeq sequencing of the fungal ITS1 region. The relative effect of late Quaternary climate change and contemporary environment (plant, soil, current climate, and geographic distance) on the soil fungal community was analyzed. The richness of the total fungal community, along with saprotrophic, ectomycorrhizal (EM), and pathogenic fungal communities, was influenced primarily by the contemporary environment (plant and/or soil) but not by late Quaternary climate change. Late Quaternary climate change acted in concert with the contemporary environment to shape total, saprotrophic, EM, and pathogenic fungal community compositions and with a stronger effect in temperate forest than in tropic–subtropical forest ecosystems. Some contemporary environmental factors influencing total, saprotrophic, EM, and pathogenic fungal communities in temperate and tropic–subtropical forests were different. We demonstrate that late Quaternary climate change can help to explain current soil fungal community composition and argue that climatic legacies can help to predict soil fungal responses to climate change.     

Wildfire severity reduces richness and alters composition of soil fungal communities in boreal forests of western Canada

Wildfire is the dominant disturbance in boreal forests and fire activity is increasing in these regions. Soil fungal communities are important for plant growth and nutrient cycling postfire but there is little understanding of how fires impact fungal communities across landscapes, fire severity gradients, and stand types in boreal forests. Understanding relationships between fungal community composition, particularly mycorrhizas, and understory plant composition is therefore important in predicting how future fire regimes may affect vegetation. We used an extreme wildfire event in boreal forests of Canada's Northwest Territories to test drivers of fungal communities and assess relationships with plant communities. We sampled soils from 39 plots 1 year after fire and 8 unburned plots. High‐throughput sequencing (MiSeq, ITS) revealed 2,034 fungal operational taxonomic units. We found soil pH and fire severity (proportion soil organic layer combusted), and interactions between these drivers were important for fungal community structure (composition, richness, diversity, functional groups). Where fire severity was low, samples with low pH had higher total fungal, mycorrhizal, and saprotroph richness compared to where severity was high. Increased fire severity caused declines in richness of total fungi, mycorrhizas, and saprotrophs, and declines in diversity of total fungi and mycorrhizas. The importance of stand age (a surrogate for fire return interval) for fungal composition suggests we could detect long‐term successional patterns even after fire. Mycorrhizal and plant community composition, richness, and diversity were weakly but significantly correlated. These weak relationships and the distribution of fungi across plots suggest that the underlying driver of fungal community structure is pH, which is modified by fire severity. This study shows the importance of edaphic factors in determining fungal community structure at large scales, but suggests these patterns are mediated by interactions between fire and forest stand composition.     

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.     

High richness of ectomycorrhizal fungi and low host specificity in a coastal sand dune ecosystem revealed by network analysis

Ectomycorrhizal (EM) fungi are ubiquitous in temperate and boreal forests, comprising over 20,000 species forming root symbiotic associations with Pinaceae and woody angiosperms. As much as 100 different EM fungal species can coexist and interact with the same tree species, forming complex multispecies networks in soils. The degree of host specificity and structural properties of these interaction networks (e.g., nestedness and modularity) may influence plant and fungal community assembly and species coexistence, yet their structure has been little studied in northern coniferous forests, where trees depend on EM fungi for nutrient acquisition. We used high‐throughput sequencing to characterize the composition and diversity of bulk soil and root‐associated fungal communities in four co‐occurring Pinaceae in a relic foredune plain located at Îles de la Madeleine, Québec, Canada. We found high EM fungal richness across the four hosts, with a total of 200 EM operational taxonomic units (OTUs), mainly belonging to the Agaricomycetes. Network analysis revealed an antinested pattern in both bulk soil and roots EM fungal communities. However, there was no detectable modularity (i.e., subgroups of interacting species) in the interaction networks, indicating a low level of specificity in these EM associations. In addition, there were no differences in EM fungal OTU richness or community structure among the four tree species. Limited shared resources and competitive exclusion typically restrict the number of taxa coexisting within the same niche. As such, our finding of high EM fungal richness and low host specificity highlights the need for further studies to determine the mechanisms enabling such a large number of EM fungal species to coexist locally on the same hosts.