ABSTRACT
Boreal peatlands play a crucial role in global carbon cycling, acting as an important carbon reservoir. However, little information is available on how peatland microbial communities are influenced by natural variability or human-induced disturbances. In this study, we have investigated the fungal diversity and community structure of both the organic soil layer and buried wood in boreal forest soils using high-throughput sequencing of the internal transcribed spacer (ITS) region. We have also compared the fungal communities during the primary colonization of wood with those of the surrounding soils. A permutational multivariate analysis of variance (PERMANOVA) confirmed that the community composition significantly differed between soil types (P < 0.001) and tree species (P < 0.001). The distance-based linear models analysis showed that environmental variables were significantly correlated with community structure (P < 0.04). The availability of soil nutrients (Ca [P = 0.002], Fe [P = 0.003], and P [P = 0.003]) within the site was an important factor in the fungal community composition. The species richness in wood was significantly lower than in the corresponding soil (P < 0.004). The results of the molecular identification were supplemented by fruiting body surveys. Seven of the genera of Agaricomycotina identified in our surveys were among the top 20 genera observed in pyrosequencing data. Our study is the first, to our knowledge, fungal high-throughput next-generation sequencing study performed on peatlands; it further provides a baseline for the investigation of the dynamics of the fungal community in the boreal peatlands.
INTRODUCTION
Boreal and subarctic peatlands play a crucial role as carbon (C) reservoirs, because they contain approximately 15% to 30% of the world's soil C in the form of peat, though they cover less than 3% of Earth's land surface (1). Peatlands can act as a sink for atmospheric C for millennia, owing to the imbalance between their net primary production and decomposition rates (2). However, direct and indirect environmental changes caused by human activities may have serious impacts on the function of peatland ecosystems. It has been hypothesized that global warming and peatland drainage will increase the rate of decomposition in boreal peatlands, potentially causing a long-term net flux of carbon dioxide (CO2) into the atmosphere (3–5). The decomposition rate of organic material in peatland may also be influenced by microbial community composition, which in turn might be affected by environmental changes. Changes in plant communities induced by peatland drainage and other factors may have effects on the soil microbial communities. Therefore, it is important to improve our understanding of the effects of environmental factors (e.g., water level and nutrient availability) on the structure of microbial communities and improve our predictions about the effect of anthropogenic disturbances on the function of peatland ecosystems.
Fungi are key players in nutrient cycling in boreal ecosystems (6, 7). They degrade soil organic matter (SOM) due to their ability to produce and secrete a broad range of appropriate hydrolytic and oxidative enzymes (8). White-rot and brown-rot fungi of the phylum Basidiomycota play a key role in the decay of recalcitrant materials of plant origin, in particular the polymers of plant cell walls. White-rot fungi are the only organisms capable of substantial lignin decay (9).
About six hundred fungal species have been reported from different types of peatlands worldwide, with the majority of them belonging to the two dominant groups, Ascomycota and Basidiomycota (10). Most of the available data on peatland fungal diversity are based upon the results of either cultivation of fungal isolates or direct identification by microscopy (10). The impact of natural factors on the structure of fungal communities in peatlands has received little attention compared to other terrestrial ecosystems. A successional trend from mycorrhizal fungi toward saprotrophs after water level drawdown has been suggested by one of the previous studies (11). However, most of the available results were obtained using low-resolution methods. Fungal communities of forest ecosystems have been studied in more detail. The effects of different environmental factors on the structure of forest fungal communities have been assessed, and it has been demonstrated that dominant tree species have the strongest effect on the composition of fungal communities in forest litter (12).
In this paper, we present the results of our analysis of fungal community structure across different soil types (pristine and drained peatland and mineral soil) with different dominant tree species (Scots pine and Norway spruce) in a boreal forest. The comparison between pristine and drained plots should provide an insight into the potential effects of lowering the water table level. With this approach, we were aiming to address the following questions. (i) How diverse are fungal communities in different types of peat soils? (ii) Do the fungal community structure and function correlate with site-related factors, such as dominant tree species, nutrient availability, and water table level? (iii) What is the impact of environmental variables on fungal community structure in the organic soil layer versus in decaying wood?
The data presented here contribute to a better understanding of the importance of the fungal community to ecosystem processes and function in relation to the environmental variables in boreal peatlands. The study also provides important information for estimating and modeling the response of boreal peatlands to a changing climate (13).
MATERIALS AND METHODS
Study plots.The study plots are located at Lakkasuo (61°48′N, 24°19′E, ca. 150 m above sea level), a boreal peatland complex in central Finland. The characteristics of the 10 selected study plots are shown in Table 1. Four pristine peatland (PP) plots, four drained peatland (DP) plots, and two plots lacking peat layer (named here mineral soil [MS] plots) were included. All the peatland soils had clear horizons of organic material (humus or organic layer), which were the sampled horizons. The plots Pine-DP1, Pine-DP2, and Spruce-DP4 were drained in 1965, and the ditches were again cleaned in 1988. The plot Spruce-DP3 was drained in 1928, and the ditches were cleaned in 1990. The dominant forest tree species in each plot was either Scots pine (Pinus sylvestris L.) or Norway spruce [Picea abies (L.) H. Karst], each of which naturally regenerated in all plots. A detailed description of Lakkasuo and the study plots can be found elsewhere (14, 15).
Description of the study plots
Soil sampling.Soil samples were taken from the organic layer at the beginning of August 2010. Within each plot, three replicate soil cores (3-cm diameter and 5-cm depth) were taken from the organic layer of the peat or mineral soil after removal of the litter layer. The distance between replicate core samples was 10 m. In total, 6 replications for mineral soil (MS) (2 plots), 12 replications for pristine undrained peatland (PP) (4 plots), and 12 replications for drained peatland (DP) (4 plots) were sampled. To reduce complexity in the further analysis, the samples were subdivided based on tree species, vegetation, and soil type, resulting in 10 separate plots that were geographically close to each other. The samples were stored on ice, delivered to the laboratory, and stored at −20°C until further processing.
Sampling of primary wood-colonizing fungi.Four of the 10 plots described in Table 1 were used for this experiment: two pristine peatland plots (Pine-PP2 and Spruce-PP4) and two mineral soil plots (Pine-MS and Spruce-MS). Norway spruce wood cubes (1 by 1 by 1 cm) were used in the experiment. The wood cubes were weighed; then, they were autoclaved for 30 min at 120°C and dried for 3 days at 65°C in the oven. Three preweighed wood cubes were placed into a mesh bag (mesh size, 1 mm). The mesh bags with wood cubes were buried 2 to 3 cm beneath the surface of the litter layer in the four selected plots at the beginning of June 2010. For each plot, 6 replicate mesh bags containing wood cubes were prepared and placed in pairs at 3 locations. After a 2-month incubation, one mesh bag from each location, a total of three per plot, was transported on ice to the lab, where the wood cubes were cleaned to remove all nonhyphal surface materials and particles. The cleaned wood cubes were stored at −80°C until further processing. After 4 months of incubation, the process was repeated. The fungal community of the soil sampled from nearby sites within the plot where the mesh bags were buried served as a reference population (reference soil samples were collected in August 2010).
Wood decay in peatland and mineral soil.Wood decay measurements were performed in the same way as wood colonization experiments, except that they were carried out at all 10 study plots (Table 1). Sterilized preweighed Norway spruce wood cubes were placed into mesh bags and buried 2 to 3 cm beneath the surface of the litter layer. After 4 months of incubation, the mesh bags were collected. The wood cubes were cleaned to remove all additional superficial materials and weighed after being dried for 3 days at 65°C in the oven. The total wood weight loss was calculated.
DNA extraction, amplification of internal transcribed spacer region, and pyrosequencing.The wood cube was ground in liquid nitrogen with a grinder (Kinematica, Switzerland). DNA was isolated from 0.5 g of the homogenized sample using the PowerSoil DNA isolation kit (MoBio Laboratories, Carlsbad, CA, USA), and the internal transcribed spacer (ITS) region was amplified using the fungus-specific primers ITS1-F (containing 454 pyrosequencing A-adapter and a 6-bp barcode) and ITS4 (containing 454 pyrosequencing B-adapter) (16, 17). The possible amplification of contaminants was evaluated with a negative PCR control, in which the template DNA was replaced with sterile water. These remained free of PCR amplicons. PCR amplicons were sequenced using the ITS1-F primer at the Institute of Biotechnology (University of Helsinki, Finland) using the 454 GS-FLX titanium protocol (Life Sciences/Roche Diagnostics, CT, USA), which yielded read lengths of ∼400 bp.
Pyrosequencing data processing.The sequence data were analyzed using the mothur pipeline v. 1.31.2 (18), following a modified standard operation procedure (19). In summary, the raw reads were subjected to quality control, and each sequence was screened for a match to the sequencing primer (ITS1-F) and valid DNA tag. Sequences were removed if they contained (i) ambiguous (N) bases; (ii) homopolymers longer than eight nucleotides; or (iii) an average Phred quality score lower than 25. Due to the lack of reference templates for sequence alignment, each sequence that passed the quality filtering was truncated to a 250-bp length after the primer (ITS1-F) and tag were removed. To remove sequences that were likely due to pyrosequencing errors, the remaining sequences were preclustered within a distance of 1 bp using a pseudosingle linkage algorithm implemented in mothur. All potentially chimeric sequences were identified using the mothur-embedded uchime de novo algorithm (20) and removed. Unique sequences were pairwise aligned with the Needleman method (21), and the aligned distance matrices were clustered into operational taxonomic units (OTUs) using the average neighbor-joining algorithm at 97% similarity. All global singletons (OTUs containing only one sequence across all samples) were omitted due to their uncertain origin (22). Observed and estimated species richness Chao 1 (23), a diversity index (inverse Simpson's complement), and Good's coverage (complement of the ratio between local singleton OTUs and the total sequence count) were estimated.
To correct for differences in survey effort and ensure comparable estimators across samples, the number of sequences of the smallest size (1,000 reads/sample) among all samples was randomly subsampled (rarefaction) and used for calculation of estimators and for fungal structure comparison between communities.
To determine the taxonomic affinities, the whole sequence data set was phylogenetically classified using a mothur-formatted copy of the full UNITE + INSD data sets version 6 (24) with an 80% confidence threshold in mothur (18). Nonfungal sequences were removed using the remove lineage command in mothur.
Field inventory of fungal fruiting bodies.Three circular plots of 50 m2 (radius, 3.99 m), 10 m apart, were placed in the plots so that the center of the plot was located approximately at the site where the sample for pyrosequencing was collected. All fruiting bodies within the plots were documented. The majority of fruiting bodies were photographed and collected for further identification. The survey was carried out twice, on 20 August 2010 and on 20 September 2010. The survey was designed to complement the pyrosequencing results rather than to provide an exhaustive overview of the fungi present in the study area.
Statistical analysis.After the assumptions of data normality and constant variance were checked, the permutational multivariate analysis of variance (PERMANOVA) package (25) in PRIMER 6 (26) was used to test the difference in species richness, diversity, and community structure between samples. The soil types were used as the first factor, and the tree species were used as the second factor. The data from mineral soils were excluded, because there was no replication within treatment combinations. The principal coordinate analysis (PCoA) in PERMANOVA was used to visualize the community structure based on the OTU abundance from each plot. The OTU abundances were transformed by taking the square root prior to the PCoA. The environmental variables were plotted in PCoA with a Spearman correlation, and the distance-based linear models (DistLM) were performed to calculate the correlations between environmental variables and community structure. The community structure in wood and in the corresponding soil based on the OTU abundance was visualized by PCoA in PERMANOVA.
The Jaccard index (presence/absence) (27) was used to calculate the dendrogram describing the dissimilarity between communities based on the number of shared and unique OTUs in mothur. To determine whether clustering within the tree was statistically significant, a parsimony test of similarity (28) was performed.
Nucleotide sequence accession number.The raw sequence data are available in the European Nucleotide Archive at the European Bioinformatics Institute under accession number PRJEB6211 (http://www.ebi.ac.uk/ena/data/view/PRJEB6211).
RESULTS
Impact of soil type and dominant tree species on fungal diversity and community structure.All of the sequence reads that passed the quality control were assigned to the domain Fungi, and 94% of them were classified below the domain level. They were clustered in 967 OTUs (1,742 OTUs with singletons included), which were further classified into four fungal phyla, i.e., Ascomycota, Basidiomycota, former Zygomycota, and Chytridiomycota. The Ascomycota group was the most species rich, whereas Basidiomycota dominated the sequence counts (Fig. 1; see Fig. S1 and S2 in the supplemental material). More than 35% of the identified OTUs (342 OTUs) were assigned down to the genus or species level. Of these, 86 OTUs (which accounted for 3% of the total sequence reads) belonged to the Ascomycota phylum, and 234 OTUs (which accounted for 56% of the reads) belonged to the Basidiomycota phylum.
Bar charts showing identification to the phylum level of operational taxonomic units (OTUs) as number of OTUs and as sequence reads from all 10 plots (total of 967 OTUs and 53,975 reads) (A) and from woods (total of 512 OTUs and 55,704 reads) (C), and the relative proportion of OTUs and sequence reads from all 10 plots (B) and from woods (D).
The OTUs identified in our sequencing effort were assigned to 135 fungal genera. The most abundant genera were the ectomycorrhizal (ECM) basidiomycetes Cortinarius, Russula, Piloderma, and Tomentella (Table 2; Fig. 2). Among the soil saprotrophs, the most abundant were the genera Mortierella, Mycena, and Syzygospora (Table 2; Fig. 2). Of the top 20 most abundant genera in soil, ECM fungi comprised 60% of the genera, whereas saprotrophs made up only 30%. The genus Meliniomyces (Ascomycota), which is able to form both ericoid-type mycorrhiza (ErM) and ectomycorrhiza, was also found among the most abundant genera (Table 2; Fig. 2).
Top 20 fungal genera in peatland soil during wood colonization and in decayed logs based on relative abundance of reads
The relative abundance of the top 20 genera of fungal ITS sequences classified (A) and fungi identified in fruiting bodies surveys (B) from the mineral and peat soil forest plots. Sequence proportions were calculated based on the sequences classified with an 80% confidence threshold. A description of each plot is presented in Table 1.
In pine-dominated plots, we identified 652 OTUs. Only 11% of them were shared by the three soil types (MS, DP, and PP), whereas the fraction of unique OTUs in each soil type ranged from 13% to 29% (Fig. 3A). In the spruce-dominated plots, 696 OTUs were detected; 17% of them were common to all three soil types, whereas the percentage of OTUs unique to a given soil type ranged from 8.5% to 29% (Fig. 3B).
Venn diagrams showing unique and shared OTUs in mineral soil (MS), pristine peat (PP), and drained peat (DP) in pine-dominated (A) and spruce-dominated (B) plots.
The sampled soils showed great variation in fungal diversity and species richness (see Table S1 in the supplemental material). The PERMANOVA analysis demonstrated that neither soil type nor tree species had a significant effect on fungal diversity (inverse Simpson's complement) or species richness (Chao 1). However, the interaction effect between soil and tree species significantly influenced the fungal species richness (P < 0.02).
PCoA separated the communities between spruce- and pine-dominated plots and between pristine and drained peat plots (Fig. 4). The PERMANOVA confirmed that the community composition significantly differed between soil types (P < 0.001) and tree species (P < 0.001). The interaction between soil type and tree species also had significant effects on community structure (P < 0.001). The DistLM analysis showed that the environmental variables were significantly correlated with community structure (Fig. 4) (r2 = 0.5425, P < 0.04). The availabilities of soil nutrients (Ca [r2 = 0.2314, P = 0.002], Fe [r2 = 0.3375, P = 0.003], and P [r2 = 0.2092, P = 0.003]) within the site were important factors in the fungal community composition. The water depth in each plot also had a significant effect on the community composition (r2 = 0.2114, P = 0.003), but it explained only 8.8% of the total variation. The effect of other tested factors on community structure was not statistically significant.
Principal coordinate (PCO) analysis based on the OTU abundance showing the fungal community structure with environmental variables in pristine and drained peat soils.
Identification of fungal species by fruiting body surveys.The fruiting body surveys were performed to complement the results of molecular analysis. In total, we identified members of 32 fungal genera based on collected sporocarps (see Table S2 in the supplemental material). The top 20 genera are shown in Figure 2. Most of the identified genera belonged to Basidiomycota, with the exception of three genera of Ascomycota: Cudonia (Helotiales), Hypomyces (Hypocreales) and Otidea (Pezizales). The order Agaricales (Basidiomycota) was the most diverse and the most abundant group in our surveys, as indicated by the number of identified genera and by total number of collected sporocarps. Cortinarius appeared to be the most common genus by sporocarp number, which is consistent with the results of molecular analysis. The number of saprotrophs among identified genera was slightly higher than the number of mycorrhiza formers, but the mycorrhiza formers were better represented in the numbers of collected sporocarps.
Influence of soil type and dominant tree species on fungal diversity and community structure during primary wood colonization.We documented 512 OTUs across all the wood samples. The fungal diversity index and richness (Chao 1 estimator) in wood cubes differed between the 2-month and 4-month incubation periods (see Table S3 in the supplemental material). The species richness in wood was significantly lower than that of the corresponding soil (P < 0.004) (see Tables S1 and S3).
PCoA distinguished the fungal community structures of pine- and spruce-dominated plots and of mineral and peat soil (Fig. 5). PERMANOVA confirmed a significant difference between tree species (P < 0.01) and between soil types (P < 0.02). Neither the soil type nor the dominant tree species had a significant effect on wood decay rate under experimental conditions (see Fig. S3 in the supplemental material).
Principal coordinate (PCO) analysis based on the OTU abundance showing the fungal community structure in wood after 2 and 4 months of incubation in pristine peat and mineral soil (A) and the fungal community structure between wood cubes and the corresponding soils (B).
Pairwise analysis showed that, in mineral soil, the relative abundance of Ascomycota and Basidiomycota in wood significantly differed from that in the corresponding soil (P < 0.02 and P < 0.03, respectively). The Ascomycota were more abundant in wood, whereas Basidiomycota were more abundant in the soil.
Between the two incubation periods, a shift in relative abundance of dominant taxa was observed. The relative abundance of Ascomycota increased, whereas the Basidiomycota abundance decreased (see Fig. S4 in the supplemental material). The analysis of variance (ANOVA) of sequences showed a significant shift in community composition in wood cubes between incubation intervals within each plot (P < 0.001). Within each plot, the two incubation periods formed separate fungal clusters (see Fig. S5). Among plots, spruce and pine also formed distinct fungal community in both pristine and mineral soils.
The OTUs in the wood chips were classified into phyla Ascomycota, Basidiomycota, and former Zygomycota (Fig. 1). More than 45% of the total OTUs belonged to the Ascomycota phylum (233 OTUs), accounting for half of the total reads (55,704). Basidiomycota (162 OTUs) represented 32% of the total OTUs, covering 32% of the total reads. Former Zygomycota and unknown phyla made up 4% and 19% of the OTUs, respectively, and accounted for 1% and 17% of the sequence count, respectively. Of the OTUs, 29%, representing 32% of the total sequences, were further assigned to the genus or species level. Of these, most belonged to Basidiomycota (15%) and Ascomycota (11%).
At the genus level, the sequences were classified into 87 genera. The most abundant genus in wood cube was the ascomycete Meliniomyces (5.6% of reads). It was followed by a diverse range of soil saprotrophs and one ECM genus, Lactarius (Fig. 6). The two incubation periods in each plot shared a considerable fraction of the genera (∼43%) (see Fig. S6 in the supplemental material).
Relative abundance of fungal genera (top 20) in wood cubes after 2 and 4 months of incubation in each plot. Proportions were calculated based on the sequences classified with an 80% confidence threshold. The number after the plot indicates 2 or 4 months after incubation. MS, mineral soil; PP, pristine peat.
DISCUSSION
The boreal soil and peatland investigated in this study possessed a diverse fungal community with high variation across the sampled plots. We identified more fungal species (if OTUs are regarded as proxy for species) than all previous studies combined (10). Similar to some previously published works (30, 31), we found no correlation between the fungal diversity (inverse Simpson's complement) and the dominant tree species. One reason that could at least partly explain the absence of such a correlation is the high variability of the fungal diversity across the studied plots.
The fungal community structure was significantly influenced by the dominant tree species and the soil type, as confirmed by PCoA and by PERMANOVA (Fig. 4). This observation agrees with the results of previous studies, demonstrating the profound influence of the dominant tree species on the structure of the fungal community in soil and litter (11, 32). Trees affect the composition of soil microbial communities in different ways, for example, by influencing the chemical composition of litter and root exudates but also by creating a spatially heterogeneous environment and by influencing understory vegetation and fauna (11). Additionally, many fungal root symbionts are tree specific (33), and dominant tree species have a particularly strong effect in ECM-dominated fungal communities.
Soil microbial communities may be influenced by soil chemistry and nutrient availability, such as the soil pH, C-to-N ratio, and nitrogen and phosphorus content, and by the precipitation amount and the physical soil properties (31, 34–37). In our study, we have identified the availability of Ca, Fe and P as the factors driving the fungal community structure. However, there are also reports showing no significant effect of soil chemistry on fungal communities (11), suggesting that the role of these factors might vary between sites. It is possible that chemical elements present at growth-limiting concentrations have the strongest effect on the microbial soil communities.
The level of the water table also had a statistically significant effect on the fungal community structure in our experiment, indicating that drainage might influence fungal communities in peatlands, though it explained only 8.8% of total variation. The percentage of observed variation agrees with the findings of previous work performed on the same field plots, which showed that water level has only a minor impact on microbial community structure (12). However, the water table level might have an effect on functional activities of soil microbial communities, which merits further investigation.
Among the top 20 fungal genera most abundant in soil, the mycorrhizal fungi were represented by 15 genera, whereas only 5 genera belonged to soil saprotrophic fungi (Table 2). Mycorrhizal fungi were also the most prominent group based on the number of sequence reads. Specialized wood-degrading fungi were scarcely represented in our samples, e.g., the entire order Polyporales accounted for less than 0.4% of reads, confirming earlier observations that this ecological group is relatively uncommon in peatlands (10). Previous studies have demonstrated that soil saprotrophic fungal taxa are more abundant in the litter horizon of the forest floor, whereas mycorrhizal fungi increase in abundance with soil depth (31, 38). The increased abundance of ECM fungi in late summer or autumn has been reported previously (39–41). Our samples were collected at the beginning of autumn and only from the organic soil layer. Thus, the sampling time and strategy may have biased our results in favor of the mycorrhiza-forming species.
Results of molecular identification were supplemented by sporocarp surveys. Seven of the genera of Agaricomycotina identified in our surveys were among the top 20 genera according to pyrosequencing data. Cortinarius was the most abundant genus based both on number of sequence reads and on sporocarp surveys. It is one of the largest genera among agaricoids, and the largest genus of ECM fungi (42). The high numbers of species of Agaricales and Boletales identified in the surveys correlate with their abilities to produce easily detectable macroscopic fruiting bodies (mushrooms). At the same time, basidiomycetes with resupinate fruiting bodies and ascomycetes were clearly underrepresented in the fruiting body surveys, as those species are often difficult to spot in the field. This was probably the main reason why some of the genera from the top 20 list (e.g., Piloderma, Tomentella, Tylospora, and Amphinema) were not collected during the sporocarp surveys. Additionally, the absence of microscopic fungi, such as Mortierella and Meliniomyces, in the fruiting body surveys is not unexpected. At the same time, 9 genera identified in the surveys were not detected by molecular methods. This is an important result, showing that even relatively common taxa (e.g., Marasmiellus) can escape detection by molecular methods. Possible explanations include the great spatial heterogeneity of soil fungal communities and certain biases during sampling. In our case, we collected samples from organic soil layer after removing the litter and so probably excluded some of litter-degrading species. For example, this could explain the absence of the genus Marasmiellus from fungal taxa identified by next-generation sequencing, since members of this genus are specialized decomposers of spruce needles, and they are probably present in the very top litter layer only. Though the results of our fruiting body inventory are suggestive, they reflect the outcomes of most of previous studies of fungal diversity in forests of the Northern Hemisphere (43–45).
The fungal communities colonizing the wood showed pronounced differences compared to those of the surrounding soils. The composition of the soil fungal community with respect to species diversity is more limited even than that of the community in the wood, but it has greater number of unique species. The community structure of wood-inhabiting fungi differed between the two incubation time points, probably as a result of the early steps of natural succession of wood colonizers that result from changes in nutrient availability and competition between species. The fungal community structure also differed between plots dominated either by pine or spruce. Species of Ascomycota prevailed over Basidiomycota in the analyzed wood samples. This was most likely because the 4-month incubation period used in our study represents the very early stage of decay, when ascomycetes prevail over basidiomycetes (46–48). Our results agree with the previous observations that ascomycetes (Geomyces, Penicillium, and Oidiodendron) and zygomycetes (Mucor) were among the fungal taxa most frequently recovered from spruce wood blocks buried beneath the peat surface for 8 to 12 months (49).
The 20 most abundant genera from soil and wood samples have only 4 genera in common (Table 2), confirming earlier observations that the structure of the wood-inhabiting fungal community does not necessarily reflect the fungal community in the surrounding soil (48).
From the functional point of view, wood-colonizing fungal communities were significantly enriched in saprotrophic species, whereas the frequency of ECM fungi was lower than that in soil samples. This might be explained by the reduced ability of ECM fungi to degrade plant cell wall polymers due to a decrease in the number of glycosyl hydrolases and other carbohydrate-acting enzymes (50, 51) and due to species succession in decomposing wood (52).
We have shown that ECM fungi are the dominant component of the fungal community in the organic soil layer along the boreal peatland gradient. Their role in providing their plant hosts with nitrogen and phosphorus, the limiting nutrients in many boreal ecosystems, is generally accepted (53). On the global scale, ECM fungi contribute to the long-term carbon sequestration in a boreal zone (7). Remarkably, some species of ECM fungi may be able to efficiently decompose plant litter while mobilizing nitrogen from soil organic matter (54). Saprotrophic species were less abundant than ECM fungi in the analyzed samples. It is possible that the lower abundance of saprotrophs in the organic soil layer could be due to limited nutrient availability, lower oxygen content, and competition with other soil microorganisms. The low abundance of saprotrophic fungi in the organic soil layer observed in our experiment agrees well with the results of previous studies, which have demonstrated that saprotrophic communities are largely confined to litter layers and that saprotrophic and root-associated microbial soil communities are vertically separated (30, 38, 55, 56).
Specialized fungal species known as white and brown rotters (52) play the primary role in wood decomposition. These species are commonly found in dead logs and other types of decaying wood material (29), but their abundance in soil is low. Our results also show that wood-degrading fungi constitute a minor fraction of fungal community in the organic soil layer of peatland soils, but their abundance may increase under favorable conditions. The most probable factors limiting the spread of wood-degrading fungi in soils are their specialization for certain microenvironments and low competitiveness compared to other soil microorganisms. For example, ectomycorrhizal fungi obtain carbohydrates directly from their symbiotic host tree and therefore have a competitive advantage over decomposers that need to obtain all of their energy from the decomposition of low-energy carbon compounds. It has been shown that white rot fungi are poor peat decomposers (57), which might be an additional factor limiting their spread in peatlands. At the same time, different species of ascomycetes may efficiently contribute to the process of Sphagnum peat decomposition (58).
The presented results show the strong effect of the dominant tree species and availability of certain nutrients (Ca, P, and Fe) on the composition of fungal communities in boreal peatland forests. Our study provides a baseline for the investigation of the dynamics of the fungal community in the boreal peatland in Finland. Establishing the link between the fungal community structure and its functional properties constitutes an important challenge for the future research of microbial communities in boreal forests.
ACKNOWLEDGMENTS
We thank The Academy of Finland for research funding. Eeva Terhonen thanks the Biological Interaction Graduate School (BIOINT) and Finnish Cultural Foundation (Pehr August and Saga Stenius Foundation grant 00110952) for a doctoral student scholarship. Hui Sun thanks the Priority Academic Program Development (PAPD) of Jiangsu Higher Education Institutions for research funding and for the Jiangsu Specially Appointed Professorship Program (2015-2018). We also thank Pauli Rainio for assistance in the field work and Dmitry Schigel and Hsiao-Che Kuo for their help during the field trip for fruiting body surveys.
FOOTNOTES
- Received 30 November 2015.
- Accepted 15 February 2016.
- Accepted manuscript posted online 19 February 2016.
Supplemental material for this article may be found at http://dx.doi.org/10.1128/AEM.03858-15.
- Copyright © 2016, American Society for Microbiology. All Rights Reserved.
