Fungal community composition in neotropical rain forests: the influence of tree diversity and precipitation

Plant diversity is considered one factor structuring soil fungal communities because the diversity of compounds in leaf litter might determine the extent of resource heterogeneity for decomposer communities. Lowland tropical rain forests have the highest plant diversity per area of any biome. Since fungi are responsible for much of the decomposition occurring in forest soils, understanding the factors that structure fungi in tropical forests may provide valuable insight for predicting changes in global carbon and nitrogen fluxes. To test the role of plant diversity in shaping fungal community structure and function, soil (0-20?cm) and leaf litter (O horizons) were collected from six established 1-ha forest census plots across a natural plant diversity gradient on the Isthmus of Panama. We used 454 pyrosequencing and phospholipid fatty acid analysis to evaluate correlations between microbial community composition, precipitation, soil nutrients, and plant richness. In soil, the number of fungal taxa increased significantly with increasing mean annual precipitation, but not with plant richness. There were no correlations between fungal communities in leaf litter and plant diversity or precipitation, and fungal communities were found to be compositionally distinct between soil and leaf litter. To directly test for effects of plant species richness on fungal diversity and function, we experimentally re-created litter diversity gradients in litter bags with 1, 25, and 50 species of litter. After 6?months, we found a significant effect of litter diversity on decomposition rate between one and 25 species of leaf litter. However, fungal richness did not track plant species richness. Although studies in a broader range of sites is required, these results suggest that precipitation may be a more important factor than plant diversity or soil nutrient status in structuring tropical forest soil fungal communities.     

Disproportionate abundance between ectomycorrhizal root tips and their associated mycelia

Extensive knowledge of various ectomycorrhizal fungal communities has been obtained over the past 10 years based on molecular identification of the fungi colonizing fine roots. In contrast, only limited information exists about the species composition of ectomycorrhizal hyphae in soil. This study compared the ectomycorrhizal external mycelial community with the adjacent root-tip community in a Danish beech forest. Sand-filled in-growth mesh bags were used to trap external mycelia by incubating the mesh bags in the soil for 70 days. The adjacent ectomycorrhizal root-tip communities were recorded at the times of insertion and retrieval of the mesh bags. Ectomycorrhizal fungi were identified by sequencing the internal transcribed spacer region. In total, 20, 31 and 24 ectomycorrhizal species were recorded from the two root-tip harvests and from the mesh bags, respectively. Boletoid species were significantly more frequent as mycelia than as root tips, while russuloid and Cortinarius species appeared to be less dominant as mycelia than as root tips. Tomentella species were equally frequent as root tips and as mycelia. These discrepancies between the root-tip and the mycelial view of the ectomycorrhizal fungal community are discussed within the framework of ectomycorrrhizal exploration types.     

Quercus rubra-associated ectomycorrhizal fungal communities of disturbed urban sites and mature forests

The presence and quality of the belowground mycorrhizal fungal community could greatly influence plant community structure and host species response. This study tests whether mycorrhizal fungal communities in areas highly impacted by anthropogenic disturbance and urbanization are less species rich or exhibit lower host root colonization rates when compared to those of less disturbed systems. Using a soil bioassay, we sampled the ectomycorrhizal fungal (EMF) communities associating with Quercus rubra (northern red oak) seedlings in soil collected from seven sites: two mature forest reference sites and five urban sites of varying levels of disturbance. Morphological and polymerase chain reaction–restriction fragment length polymorphism analyses of fungi colonizing root tips revealed that colonization rates and fungal species richness were significantly lower on root systems of seedlings grown in disturbed site soils. Analysis of similarity showed that EMF community composition was not significantly different among several urban site soils but did differ significantly between mature forest sites and all but one urban site. We identified a suite of fungal species that occurred across several urban sites. Lack of a diverse community of belowground mutualists could be a constraint on urban plant community development, especially of late-successional woodlands. Analysis of urban EMF communities can add to our understanding of urban plant community structure and should be addressed during ecological assessment before pragmatic decisions to restore habitats are framed.     

Microbial Diversity During Cellulose Decomposition in Different Forest Stands: I. Microbial Communities and Environmental Conditions

We studied the effect of forest tree species on a community of decomposers that colonize cellulose strips. Both fungal and bacterial communities were targeted in a native forest dominated by beech and oak and 30-year-old beech and spruce plantations, growing in similar ecological conditions in the Breuil-Chenue experimental forest site in Morvan (France). Microbial ingrowths from the 3rd to 10th month of strip decomposition (May to December 2004) were studied. Community composition was assessed using temperature gradient gel electrophoresis with universal fungal (ITS1F, ITS2) and bacterial (1401r, 968f) primers. Soil temperature and moisture as well as fungal biomass were also measured to give additional information on decomposition processes. Changing the dominant tree species had no significant influence in the number of decomposer species. However, decomposer community composition was clearly different. If compared to the native forest, where community composition highly differed, young monocultures displayed similar species structure for fungi and bacteria. Both species numbers and community composition evolved during the decay process. Time effect was found to be more important than tree species. Nevertheless, the actual environmental conditions and seasonal effect seemed to be even more determining factors for the development of microbial communities. The course and correlations of the explored variables often differed between tree species, although certain general trends were identified. Fungal biomass was high in summer, despite that species richness (SR) decreased and conversely, that high SR did not necessarily mean high biomass values. It can be concluded that the growth and development of the microbiological communities that colonized a model material in situ depended on the combination of physical and biological factors acting collectively and interdependently at the forest soil microsite.     

Effects of arbuscular mycorrhiza on community composition and seedling recruitment in temperate forest understory

Arbuscular mycorrhizal (AM) fungal communities can influence the species composition of plant communities. This influence may result from effects of AM on seedling recruitment, although the existing evidence is limited to experimental systems. We addressed the impact of AM fungi on the plant community composition and seedling recruitment of two species – Oxalis acetosella and Prunella vulgaris – in a temperate forest understory. We established a field experiment over two years in which soil fertility (using fertilizer to enhance and sucrose to decrease fertility) and the activity of AM fungi (using fungicide) was manipulated in a factorial design. Species richness, diversity and community composition of understory plants were not influenced by soil fertility or AM fungal activity treatments. However, plant community composition was marginally significantly affected by the interaction of these treatments as the effect of AM fungal activity became evident under enhanced soil fertility. Suppression of AM fungal activity combined with decreased soil fertility increased the number of shoots of herbaceous plants. Unchanged activity of AM fungi enhanced the growth of O. acetosella seedlings under decreased soil fertility, but did not influence the growth of P. vulgaris seedlings. We conclude that the role of AM fungi in structuring plant communities depends on soil fertility. AM fungi can have a strong influence on seedling recruitment, especially for those plants that are characteristic of the habitat.     

Restoration of belowground fungal communities in reclaimed landscapes of the Canadian boreal forest

The trajectory of forests establishing on reclaimed oil sands mines in the Canadian boreal forest is uncertain. Soil microbes, namely mycorrhizal fungi, partly underlie successional trajectories of plant communities, yet their role in restoration is often overlooked. Here, we tested the relative importance of common management tools used in restoration—species planted and soil placement—on the recovery of ectomycorrhizal fungal communities over 4 years. Importantly, we further compared the community assembly of fungi on reclaimed landscapes to that in reference ecosystems disturbed to different degrees. This latter test addresses whether disturbance intensity is more important than common management interventions to restore fungal communities in these ecosystems. Three main findings emerged. (1) The effect of tree species planted and soil placement on ectomycorrhizal fungal communities establishing on reclaimed landscapes was dynamic through time. (2) Disturbances that remove or disrupt the organic layer of soils substantially affect the composition of ectomycorrhizal fungal communities. (3) Shifts in the community composition of ectomycorrhizal fungi were driven to a greater extent by disturbance severity than either tree species planted or soil placement.     

Fungal Growth and Biomass Development is Boosted by Plants in Snow-Covered Soil

Soil microbial communities follow distinct seasonal cycles which result in drastic changes in processes involving soil nutrient availability. The biomass of fungi has been reported to be highest during winter, but is fungal growth really occurring in frozen soil? And what is the effect of plant cover on biomass formation and on the composition of fungal communities? To answer these questions, we monitored microbial biomass N, ergosterol, and the amount of fungal hyphae during summer and winter in vegetated and unvegetated soils of an alpine primary successional habitat. The winter fungal communities were identified by rDNA ITS clone libraries. Winter soil temperatures ranged between -0.6°C and -0.1°C in snow-covered soil. We found distinct seasonal patterns for all biomass parameters, with highest biomass concentrations during winter in snow-covered soil. The presence of plant cover had a significant positive effect on the amount of biomass in the soil, but the type of plant cover (plant species) was not a significant factor. A mean hyphal ingrowth of 5.6 m g(-1) soil was detected in snow-covered soil during winter, thus clearly proving fungal growth during winter in snow-covered soil. Winter fungal communities had a typical species composition: saprobial fungi were dominating, among them many basidiomycete yeasts. Plant cover had no influence on the composition of winter fungal communities.     

Dynamics of vesicular-arbuscular mycorrhizae during old field succession

Summary The species composition of vesicular-arbuscular mycorrhizal (VAM) fungal communities changed during secondary succession of abandoned fields based on a field to forest chronosequence. Twenty-five VAM fungal species were identified. Seven species were clearly early successional and five species were clearly late successional. The total number of VAM fungal species did not increase with successional time, but diversity as measured by the Shannon-Wiener index tended to increase, primarily because the community became more even as a single species, Glomus aggregatum, became less dominant in the older sites. Diversity of the VAM fungal community was positively correlated with soil C and N. The density of VAM fungi, as measured by infectivity and total spore count, first increased with time since abandonment and then decreased in the late successional forest sites. Within 12 abandoned fields, VAM fungal density increased with increasing soil pH, H₂O soluble soil C, and root biomass, but was inversely related to extractable soil P and percent cover of non-host plant species. The lower abundance of VAM fungi in the forest sites compared with the field sites agrees with the findings of other workers and corresponds with a shift in the dominant vegetation from herbaceous VAM hosts to woody ectomycorrhizal hosts.     

Soil Organism and Plant Introductions in Restoration of Species-Rich Grassland Communities

Soil organisms can strongly affect competitive interactions and successional replacements of grassland plant species. However, introduction of whole soil communities as management strategy in grassland restoration has received little experimental testing. In a 5-year field experiment at a topsoil-removed ex-arable site ( receptor site ), we tested effects of (1) spreading hay and soil, independently or combined, and (2) transplanting intact turfs on plant and soil nematode community development. Material for the treatments was obtained from later successional, species-rich grassland ( donor site ). Spreading hay affected plant community composition, whereas spreading soil did not have additional effects. Plant species composition of transplanted turfs became less similar to that in the donor site. Moreover, most plants did not expand into the receiving plots. Soil spreading and turf transplantation did not affect soil nematode community composition. Unfavorable soil conditions (e.g., low organic matter content and seasonal fluctuations in water level) at the receptor site may have limited plant and nematode survival in the turfs and may have precluded successful establishment outside the turfs. We conclude that introduction of later successional soil organisms into a topsoil-removed soil did not facilitate the establishment of later successional plants, probably because of the "mismatch" in abiotic soil conditions between the donor and the receptor site. Further research should focus on the required conditions for establishment of soil organisms at restoration sites in order to make use of their contribution to grassland restoration. We propose that introduction of organisms from "intermediate" stages will be more effective as management strategy than introduction of organisms from "target" stages.     

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...     

Influence of long-term repeated prescribed burning on mycelial communities of ectomycorrhizal fungi

To demonstrate the efficacy of direct DNA extraction from hyphal ingrowth bags for community profiling of ectomycorrhizal (ECM) mycelia in soil, we applied the method to investigate the influence of long-term repeated prescribed burning on an ECM fungal community. DNA was extracted from hyphal ingrowth bags buried in forest plots that received different prescribed burning treatments for 30 yr, and denaturing gradient gel electrophoresis (DGGE) profiles of partial fungal rDNA internal transcribed spacer (ITS) regions were compared. Restriction fragment length polymorphism (RFLP) and sequence analyses were also used to compare clone assemblages between the treatments. The majority of sequences derived from the ingrowth bags were apparently those of ECM fungi. DGGE profiles for biennially burned plots were significantly different from those of quadrennially burned and unburned control plots. Analysis of clone assemblages indicated that this reflected altered ECM fungal community composition. The results indicate that hyphal ingrowth bags represent a useful method for investigation of ECM mycelial communities, and that frequent long-term prescribed burning can influence below-ground ECM fungal communities.     

Identification of cellulose-responsive bacterial and fungal communities in geographically and edaphically different soils by using stable isotope probing

Many bacteria and fungi are known to degrade cellulose in culture, but their combined response to cellulose in different soils is unknown. Replicate soil microcosms amended with [(13)C]cellulose were used to identify bacterial and fungal communities responsive to cellulose in five geographically and edaphically different soils. The diversity and composition of the cellulose-responsive communities were assessed by DNA-stable isotope probing combined with Sanger sequencing of small-subunit and large-subunit rRNA genes for the bacterial and fungal communities, respectively. In each soil, the (13)C-enriched, cellulose-responsive communities were of distinct composition compared to the original soil community or (12)C-nonenriched communities. The composition of cellulose-responsive taxa, as identified by sequence operational taxonomic unit (OTU) similarity, differed in each soil. When OTUs were grouped at the bacterial order level, we found that members of the Burkholderiales, Caulobacteriales, Rhizobiales, Sphingobacteriales, Xanthomonadales, and the subdivision 1 Acidobacteria were prevalent in the (13)C-enriched DNA in at least three of the soils. The cellulose-responsive fungi were identified as members of the Trichocladium, Chaetomium, Dactylaria, and Arthrobotrys genera, along with two novel Ascomycota clusters, unique to one soil. Although similarities were identified in higher-level taxa among some soils, the composition of cellulose-responsive bacteria and fungi was generally unique to a certain soil type, suggesting a strong potential influence of multiple edaphic factors in shaping the community.     

Long-term dynamics of aboveground fungal communities in a subalpine Norway spruce forest under elevated nitrogen input

As anthropogenic N deposition has been suspected to be the main reason for the decline of macromycetous sporocarp production in forest ecosystems, various N-fertilization experiments were started in the mid 1990s. The dynamics of ectomycorrhizal (root-inhabiting) and terricolous saprobic (litter-inhabiting) fungal communities were studied by exhaustive sporocarp inventories in a substitution Norway spruce (Picea abies) forest in two 256-m² plots sampled for periods of 1 week at 1-m² resolution between 1994 and 2007. N was added to the soil twice per year in one plot from the fourth year onwards. The effects of N input and time on aboveground fungal communities were assessed using redundancy analysis, principal response curves and non-parametric multivariate ANOVA. Results of this long-term experiment revealed that both ectomycorrhizal and saprobic fungal communities responded to an increase in soil N input. The ectomycorrhizal community reacted by a fast decrease in sporocarp production and in species richness, whereas the saprobic community was less affected. The response was highly species specific, especially for the saprobic community. The difference in species composition between control and fertilized plots was significant after 1 year of N addition for ectomycorrhizal fungi and only after 3 years for saprobic fungi. An aging effect affected sporocarp production in the whole area. For both communities, this unidirectional drift in species composition was as important as the treatment effect. This result highlights the importance of considering the respective role of treatment and year effects in long-term field experiments on fungal communities.     

Afforested fields benefit nutrient‐demanding fungi

Impaired ecosystems are converted back to natural ecosystems or some other target stage by means of restoration and management. Due to their agricultural legacy, afforested fields might be valuable compensatory habitats for rare fungal species that require nutrient‐rich forest soils. Using a large‐scale field experiment in Finland, we studied community composition of macrofungi (agarics and boletes) on former fields, which had been afforested as monocultures 20 years ago using native spruce Picea abies, pine Pinus sylvestris, and birch Betula pendula. We studied the effect of soil quality, tree species, and site on community composition and structure. Many nutrient‐demanding as well as rare fungal species were recorded, particularly from pine and spruce plots. Pine plots supported more nutrient‐demanding fungi than birch plots. There was no relationship between soil pH, bulk density, P, N, or Ca, and species richness of nutrient‐demanding fungi. Fungal community composition was more similar within sites than among sites for all tree species. Among sites, spruce plots had the smallest fungal species turnover, and birch plots largest. Within sites, however, fungal species turnover from plot to plot was similar among tree species. Our results indicate that tree species has a relatively mild influence on species composition of fungi after 20 years of succession. Interestingly, the results show that afforested fields can be valuable complementary habitats for rare, red‐listed, and nutrient‐demanding fungal species. Field afforestation is a potential conservation tool that could be used to complement the poor representation of rare habitat types in highly fragmented protected area networks.     

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.     

The annual invasive plant Impatiens glandulifera reduces hyphal biomass of soil fungi in deciduous forests

Soil fungi play a crucial role in ecosystem functioning and there is increasing evidence that exotic plants invading forests can affect soil fungal communities. We examined potential effects of the invasive plant Impatiens glandulifera on hyphal biomass of ectomycorrhizal fungi, their genetic diversity and the diversity of other soil fungi in deciduous forests in Switzerland. We compared invaded patches with patches where I. glandulifera had been removed, by establishing pairs of 3-m long transect lines at the edge of seven areas of either type. Along the transects we assessed the length of ectomycorrhizal fungal hyphae using the ‘ingrowth mesh bag method’, and used terminal restriction fragment length polymorphism (T-RFLP) analysis to examine fungal genetic diversity. The invasive plant reduced fungal hyphal biomass by 30–80%: the reduction was largest in the centre of the patch. I. glandulifera did not alter fungal richness, but affected the composition of fungal communities. This is probably the result of a decrease of mycorrhizal fungi, coupled with an increase of saprotrophic fungi. Our findings demonstrate the adverse impacts of an annual invasive plant species on both fungal hyphal biomass and the composition of soil fungal communities. This may negatively affect forest nutrient and carbon cycling, soil stability and the functionality of the fungal community, with major consequences for forest ecosystem functioning.     

Fungal Community Shifts in Structure and Function across a Boreal Forest Fire Chronosequence

Forest fires are a common natural disturbance in forested ecosystems and have a large impact on the microbial communities in forest soils. The response of soil fungal communities to forest fire is poorly documented. Here, we investigated fungal community structure and function across a 152-year boreal forest fire chronosequence using high-throughput sequencing of the internal transcribed spacer 2 (ITS2) region and a functional gene array (GeoChip). Our results demonstrate that the boreal forest soil fungal community was most diverse soon after a fire disturbance and declined over time. The differences in the fungal communities were explained by changes in the abundance of basidiomycetes and ascomycetes. Ectomycorrhizal (ECM) fungi contributed to the increase in basidiomycete abundance over time, with the operational taxonomic units (OTUs) representing the genera Cortinarius and Piloderma dominating in abundance. Hierarchical cluster analysis by using gene signal intensity revealed that the sites with different fire histories formed separate clusters, suggesting differences in the potential to maintain essential biogeochemical soil processes. The site with the greatest biological diversity had also the most diverse genes. The genes involved in organic matter degradation in the mature forest, in which ECM fungi were the most abundant, were as common in the youngest site, in which saprotrophic fungi had a relatively higher abundance. This study provides insight into the impact of fire disturbance on soil fungal community dynamics.     

秦岭火地塘真菌群落海拔分布格局

土壤真菌在自然生态系统的养分循环和土壤碳储存方面起重要作用。秦岭火地塘林区在不同海拔分布着不同的优势树种,但其相应的土壤特征及微生物群落的海拔分布格局仍不明晰。本研究分析了5个海拔处(1500、1700、1900、2100和2300 m)的土壤特征变化趋势,并在高通量测序基础上研究了真菌群落格局。结果表明: 土壤有效磷含量、pH值随海拔的增加而显著增加,土壤水分则呈下降趋势。土壤真菌Shannon多样性指数随海拔升高呈下降趋势,而ACE丰度指数相反;真菌优势门为担子菌门(68.2%)、子囊菌门(19.8%)和球囊菌门(1.7%),且随海拔升高整体呈现出“U”型或“单峰”变化格局;真菌优势纲为伞菌纲(64.2%)、粪壳菌纲(5.8%)和锤舌菌纲(4.1%)。冗余分析(RDA)表明,土壤特性解释了土壤真菌群落总变异的89.1%,其中土壤有效磷含量、pH和海拔是土壤真菌群落海拔梯度变化的主要驱动因子。在秦岭火地塘林区,土壤特征在海拔梯度上的差异性影响了土壤真菌群落组成。     

Emerging from the ice-fungal communities are diverse and dynamic in earliest soil developmental stages of a receding glacier

We used amplicon sequencing and isolation of fungi from in-growth mesh bags to identify active fungi in three earliest stages of soil development (SSD) at a glacier forefield (0–3, 9–14, 18–25 years after retreat of glacial ice). Soil organic matter and nutrient concentrations were extremely low, but the fungal diversity was high [220 operational taxonomic units (OTUs)/138 cultivated OTUs]. A clear successional trend was observed along SSDs, and species richness increased with time. Distinct changes in fungal community composition occurred with the advent of vascular plants. Fungal communities of recently deglaciated soil are most distinctive and rather similar to communities typical for cryoconite or ice. This indicates melting water as an important inoculum for native soil. Moreover, distinct seasonal differences were detected in fungal communities. Some fungal taxa, especially of the class Microbotryomycetes, showed a clear preference for winter and early SSD. Our results provide insight into new facets regarding the ecology of fungal taxa, for example, by showing that many fungal taxa might have an alternative, saprobial lifestyle in snow-covered, as supposed for a few biotrophic plant pathogens of class Pucciniomycetes. The isolated fungi include a high proportion of unknown species, which can be formally described and used for experimental approaches.