Influence of tree species on richness and diversity of epigeous fungal communities in a French temperate forest stand

Soil mycobiomes in native European aspen forests and hybrid aspen plantations have a similar fungal richness but different compositions, mainly driven by edaphic and floristic factors

Background

The cultivation of short-rotation tree species on non-forest land is increasing due to the growing demand for woody biomass for the future bioeconomy and to mitigate climate change impacts. However, forest plantations are often seen as a trade-off between climate benefits and low biodiversity. The diversity and composition of soil fungal biota in plantations of hybrid aspen, one of the most planted tree species for short-rotation forestry in Northern Europe, are poorly studied.

Methods

The goal of this study was to obtain baseline knowledge about the soil fungal biota and the edaphic, floristic and management factors that drive fungal richness and communities in 18-year-old hybrid aspen plantations on former agricultural soils and compare the fungal biota with those of European aspen stands on native forest land in a 130-year chronosequence. Sites were categorized as hybrid aspen (17-18-year-old plantations) and native aspen stands of three age classes (8-29, 30-55, and 65-131-year-old stands). High-throughput sequencing was applied to soil samples to investigate fungal diversity and assemblages.

Results

Native aspen forests showed a higher ectomycorrhizal (EcM) fungal OTU richness than plantations, regardless of forest age. Short-distance type EcM genera dominated in both plantations and forests. The richness of saprotrophic fungi was similar between native forest and plantation sites and was highest in the middle-aged class (30-55-year-old stands) in the native aspen stands. The fungal communities of native forests and plantations were significantly different. Community composition varied more, and the natural forest sites were more diverse than the relatively homogeneous plantations. Soil pH was the best explanatory variable to describe soil fungal communities in hybrid aspen stands. Soil fungal community composition did not show any clear patterns between the age classes of native aspen stands.

Conclusion

We conclude that edaphic factors are more important in describing fungal communities in both native aspen forest sites and hybrid aspen plantation sites than forest thinning, age, or former land use for plantations. Although first-generation hybrid aspen plantations and native forests are similar in overall fungal diversity, their taxonomic and functional composition is strikingly different. Therefore, hybrid aspen plantations can be used to reduce felling pressure on native forests; however, our knowledge is still insufficient to conclude that plantations could replace native aspen forests from the soil biodiversity perspective.

Metatranscriptomics sheds light on the links between the functional traits of fungal guilds and ecological processes in forest soil ecosystems

Soil fungi belonging to different functional guilds, such as saprotrophs, pathogens, and mycorrhizal symbionts, play key roles in forest ecosystems. To date, no study has compared the actual gene expression of these guilds in different forest soils. We used metatranscriptomics to study the competition for organic resources by these fungal groups in boreal, temperate, and Mediterranean forest soils. Using a dedicated mRNA annotation pipeline combined with the JGI MycoCosm database, we compared the transcripts of these three fungal guilds, targeting enzymes involved in C- and N mobilization from plant and microbial cell walls. Genes encoding enzymes involved in the degradation of plant cell walls were expressed at a higher level in saprotrophic fungi than in ectomycorrhizal and pathogenic fungi. However, ectomycorrhizal and saprotrophic fungi showed similarly high expression levels of genes encoding enzymes involved in fungal cell wall degradation. Transcripts for N-related transporters were more highly expressed in ectomycorrhizal fungi than in other groups. We showed that ectomycorrhizal and saprotrophic fungi compete for N in soil organic matter, suggesting that their interactions could decelerate C cycling. Metatranscriptomics provides a unique tool to test controversial ecological hypotheses and to better understand the underlying ecological processes involved in soil functioning and carbon stabilization.

The influence of tree genus, phylogeny, and richness on the specificity, rarity, and diversity of ectomycorrhizal fungi

Partner specificity is a well-documented phenomenon in biotic interactions, yet the factors that determine specificity in plant-fungal associations remain largely unknown. By utilizing composite soil samples, we identified the predictors that drive partner specificity in both plants and fungi, with a particular focus on ectomycorrhizal associations. Fungal guilds exhibited significant differences in overall partner preference and avoidance, richness, and specificity to specific tree genera. The highest level of specificity was observed in root endophytic and ectomycorrhizal associations, while the lowest was found in arbuscular mycorrhizal associations. The majority of ectomycorrhizal fungal species showed a preference for one of their partner trees, primarily at the plant genus level. Specialist ectomycorrhizal fungi were dominant in belowground communities in terms of species richness and relative abundance. Moreover, all tree genera (and occasionally species) demonstrated a preference for certain fungal groups. Partner specificity was not related to the rarity of fungi or plants or environmental conditions, except for soil pH. Depending on the partner tree genus, specific fungi became more prevalent and relatively more abundant with increasing stand age, tree dominance, and soil pH conditions optimal for the partner tree genus. The richness of partner tree species and increased evenness of ectomycorrhizal fungi in multi-host communities enhanced the species richness of ectomycorrhizal fungi. However, it was primarily the partner-generalist fungi that contributed to the high diversity of ectomycorrhizal fungi in mixed forests.

Differential effects of tree species identity on rhizospheric bacterial and fungal community richness and composition across multiple trace element-contaminated sites

Soil microbial communities play a key role in plant nutrition and stress tolerance. This is particularly true in sites contaminated by trace metals, which often have low fertility and stressful conditions for woody plants in particular. However, we have limited knowledge of the abiotic and biotic factors affecting the richness and composition of microbial communities inhabiting the rhizosphere of plants in contaminated sites. Using high-throughput amplicon sequencing, we studied the rhizospheric bacterial and fungal community structures of 14 woody plant families planted in three contrasting sites contaminated by metals (Pb, Cd, Zn, Mn, Fe, S). The rhizospheric bacterial communities in the given sites showed no significant difference between the various woody species but did differ significantly between sites. The Proteobacteria phylum was dominant, accounting for over 25 % of the overall relative abundance, followed by Actinobacteria, Bacteroidetes and Gemmatimonadetes. Site was also the main driver of fungal community composition, yet unlike bacteria, tree species identity significantly affected fungal communities. The Betulaceae, Salicaceae and Fagaceae families had a high proportion of Basidiomycota, particularly ectomycorrhizal fungi, and the lowest diversity and richness. The other tree families and the unplanted soil harboured a greater abundance of Ascomycota and Mucoromycota. Consequently, for both bacteria and fungi, the site effect significantly impacted their community richness and composition, while the influence of plants on the richness and composition of rhizospheric microbial communities stayed consistent across sites and was dependent on the microbial kingdom. Finally, we highlighted the importance of considering this contrasting response of plant rhizospheric microbial communities in relation to their host identity, particularly to improve assisted revegetation efforts at contaminated sites.

Diversity and Distribution of Macrofungi in Protected Mountain Forest Habitats in Serbia and Its Relation to Abiotic Factors

Fungal diversity is one of the most important indicators of overall forest biodiversity and its health. However, scarce information exists on the state of macrofungal communities of mountain forests in Serbia, making it one of the countries with the least-published mycological data in the Mediterranean and Balkan region of Europe. This paper presents the results of the first comprehensive, long-term study of macrofungal communities in some of the most important mountain forest ecosystems in Serbia (Tara, Kopaonik and Vidlič). In the course of three consecutive years, the sampling of five permanent experimental plots resulted in 245 species of macrofungi, classified into three functional groups (terricolous saprothrophs, lignicolous, and mycorrhizal fungi). Special attention was given to protected and indicator species, which point out the great value of studied forest habitats and the importance of their conservation. It was found that precipitation, habitat humidity, and temperature significantly influence the occurrence and distribution, primarily of mycorrhizal and lignicolous group of fungi. Thus, the continuation of long-term monitoring is crucial in order to more precisely determine which groups/species of macrofungi would, and to what extent they would, adapt to a rapidly changing climate.

Co-occurring Fungal Functional Groups Respond Differently to Tree Neighborhoods and Soil Properties Across Three Tropical Rainforests in Panama

Abiotic and biotic drivers of co-occurring fungal functional guilds across regional-scale environmental gradients remain poorly understood. We characterized fungal communities using Illumina sequencing from soil cores collected across three Neotropical rainforests in Panama that vary in soil properties and plant community composition. We classified each fungal OTU into different functional guilds, namely plant pathogens, saprotrophs, arbuscular mycorrhizal (AM), or ectomycorrhizal (ECM). We measured soil properties and nutrients within each core and determined the tree community composition and richness around each sampling core. Canonical correspondence analyses showed that soil pH and moisture were shared potential drivers of fungal communities for all guilds. However, partial the Mantel tests showed different strength of responses of fungal guilds to composition of trees and soils. Plant pathogens and saprotrophs were more strongly correlated with soil properties than with tree composition; ECM fungi showed a stronger correlation with tree composition than with soil properties; and AM fungi were correlated with soil properties, but not with trees. In conclusion, we show that co-occurring fungal guilds respond differently to abiotic and biotic environmental factors, depending on their ecological function. This highlights the joint role that abiotic and biotic factors play in determining composition of fungal communities, including those associated with plant hosts.

Contrasted ecological niches shape fungal and prokaryotic community structure in mangroves sediments

Mangroves are forest ecosystems located at the interface between land and sea where sediments presented a variety of contrasted environmental conditions (i.e. oxic/anoxic, non-sulfidic/sulfidic, organic matter content) providing an ideal ecosystem to study microbial communities with niche differentiation and distinct community structures. In this work, prokaryotic and fungal compositions were investigated during both wet and dry seasons in New Caledonian mangrove sediments, from the surface to deeper horizons under the two most common tree species in this region (Avicennia marina and Rhizophora stylosa), using high-throughput sequencing. Our results showed that Bacteria and Archaea communities were mainly shaped by sediment depth while the fungal community was almost evenly distributed according to sediment depth, vegetation cover and season. A detailed analysis of prokaryotic and fungal phyla showed a dominance of Ascomycota over Basidiomycota whatever the compartment, while there was a clear shift in prokaryotic composition. Some prokaryotic phyla were enriched in surface layers such as Proteobacteria, Euryarchaeota while others were mostly associated with deeper layers as Chloroflexi, Bathyarchaeota, Aminicenantes. Our results highlight the importance of considering fungal and prokaryotic counterparts for a better understanding of the microbial succession involved in plant organic matter decomposition in tropical coastal sediments.

Aboveground overyielding in a mixed temperate forest is not explained by belowground processes

The relationship between forest productivity and tree species diversity has been described in detail, but the underlying processes have yet to be identified. One important issue is to understand which processes are at the origin of observed aboveground overyielding in some mixed forests. We used a beech-maple plantation exhibiting aboveground overyielding to test whether belowground processes could explain this pattern. Soil cores were collected to determine fine root (FR) biomass and vertical distribution. Correlograms were used to detect spatial arrangement. Near-infrared reflectance spectroscopy was used to identify the tree species proportion in the FR samples and spatial root segregation. An isotopic approach was used to identify water acquisition patterns. The structure and the composition of the ectomycorrhizal fungal community were determined by high-throughput sequencing of DNA in the soil samples. We found no spatial pattern for FR biomass or for its vertical distribution along the gradients. No vertical root segregation was found, as FR density for both species decreased with depth in a similar way. The two species displayed similar vertical water acquisition profiles as well, mainly absorbing water from shallow soil layers; hence, niche differentiation for water acquisition was not highlighted here. Significant alterations in the fungal community compositions were detected in function of the percentage of maple in the vicinity of beech. Our findings do not support the commonly suggested drivers of aboveground overyielding in species-diverse forests and suggest that competition reduction or between-species facilitation of belowground resource acquisition may not explain the observed aboveground overyielding.

Ectomycorrhizal fungal communities in high mountain conifer forests in central Mexico and their potential use in the assisted migration of Abies religiosa

Abies religiosa forests in central Mexico are the only overwinter refuge of the monarch butterfly and provide important ecosystem services. These forests have lost 55% of their original area and as a consequence, diversity and biotic interactions in these ecosystems are in risk. The aim of this study was to compare the soil fungal diversity and community structure in the Abies religiosa forests and surrounding Pinus montezumae, Pinus hartwegii, and coniferous mixed forest plant communities to provide data on ecology of mycorrhizal interactions for the assisted migration of A. religiosa. We sampled soil from five coniferous forests, extracted total soil DNA, and sequenced the ITS2 region by Illumina MiSeq. The soil fungi community was integrated by 1746 taxa with a species turnover ranging from 0.280 to 0.461 between sampling sites. In the whole community, the more abundant and frequent species were Russula sp. (aff. olivobrunnea), Mortierella sp.1, and Piloderma sp. (aff. olivacearum). The ectomycorrhizal fungi were the more frequent and abundant functional group. A total of 298 species (84 ectomycorrhizal) was shared in the five conifer forests; these widely distributed species were dominated by Russulaceae and Clavulinaceae. The fungal community composition was significantly influenced by altitude and the lowest species turnover happened between the two A. religiosa forests even though they have different soil types. As Pinus montezumae forests have a higher altitudinal distribution adjacent to A. religiosa and share the largest number of ectomycorrhizal fungi with it, we suggest these forests as a potential habitat for new A. religiosa populations.

Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities

The impacts of plant species on the microbial communities and physico-chemical characteristics of soil are well documented for many herbs, grasses and legumes but much less so for tree species. Here, we investigate by rRNA and ITS amplicon sequencing the diversity of microorganisms from the three domains of life (Archaea, Bacteria and Eukaryota:Fungi) in soil samples taken from the forest experimental site of Breuil-Chenue (France). We discovered significant differences in the abundance, composition and structure of the microbial communities associated with two phylogenetically distant tree species of the same age, deciduous European beech (Fagus sylvatica) and coniferous Norway spruce (Picea abies Karst), planted in the same soil. Our results suggest a significant effect of tree species on soil microbiota though in different ways for each of the three microbial groups. Fungal and archaeal community structures and compositions are mainly determined according to tree species, whereas bacterial communities differ to a great degree between rhizosphere and bulk soils, regardless of the tree species. These results were confirmed by quantitative PCR, which revealed significant enrichment of specific bacterial genera, such as Burkholderia and Collimonas, known for their ability to weather minerals within the tree root vicinity.

Ectomycorrhizal fungal assemblages of Abies alba Mill. outside its native range in Poland

Abies alba (Mill.) is an important forest tree species, native to the mountainous regions of Europe but has been also widely introduced in the lowlands outside its native range. Like most forest tree species, A. alba forms obligate mutualisms with ectomycorrhizal (ECM) fungi. This investigation sought to examine ECM fungal communities of A. alba when the species grows 400 km north of its native range in the region of Pomerania in Poland. We surveyed for ECM fungi by sampling live roots from four mature forest stands where the A. alba component ranged from 20 to 100%. Ectomycorrhizal fungal symbionts were identified based on morphotyping and sequencing of the internal transcribed spacer (ITS) of nuclear ribosomal DNA (rDNA). Thirty-five ECM fungal taxa were distinguished on root tips of A. alba from all tested stands with 22 to 27 ECM fungal taxa in the individual stand. The diversity and similarity metrics revealed a lack of statistical differences in the structure of the ECM fungal community between stands varying in overstory tree composition. Cenococcum geophilum was the most common fungal species at all investigated A. alba stands, with an abundance of 50 to 70%. The ECM community was characterized by the lack of Abies-specific fungal symbionts and a rich and diverse suite of host-generalist mycobionts that seem to be sufficient for successful growth and development of A. alba outside of its native range.

Litter quality indirectly influences community composition, reproductive mode and trophic structure of oribatid mite communities: a microcosm experiment

Our knowledge of the assembly processes of species-rich oribatid mite communities is fairly limited. Also, very little information is available on the effects of habitat factors on these processes. In this paper, the role of litter quality in pattern formation was investigated in a microcosm experiment using the "home-field advantage" approach. Native (home) and foreign (away) types of microarthropod assemblages were extracted from three types of litter samples (Turkey oak, Scots pine and black locust tree), and transferred alive into 'home' and 'away' samples, which have been defaunated and reinoculated with microorganisms to form microcosms. Microarthropods were extracted from the microcosms after incubation for 3-12 months. In addition to species identification and abundance records, some chemical properties of the litter were measured. We hypothesized that oribatid mite communities deteriorate, the proportion of parthenogenetic individuals decreases and the proportion of omnivorous individuals increases in 'away' microcosms in contrast to 'home' systems. Pine and oak litter were favourable for all the three types of oribatid communities since their community traits in these types of litter were found to be similar to 'home' litter. Black locust litter was favourable only for its native oribatid community in the long run. The proportion of parthenogenetic individuals partly supported our hypothesis, mainly in black locust litter. The relative abundance of omnivorous individuals did not differ significantly between treatments. Litter quality is likely to influence oribatid mite assemblages only indirectly.

Correlating Mushroom Habitats and Geology in Grevena Prefecture (Greece) with the Use of Geographic Information Systems (GIS)

The aim of this study is to assess the relationship between geological background and habitats of mushrooms. The study area is Grevena, a Prefecture of Greece well known for the great variety of the fungal flora and its distinctive geology. Thematic maps of the study area were produced with the use of GIS, taking under consideration geological formations, elevation, ecosystems and land use. Findings provide evidence that certain mushrooms are more likely to be found in specific ecosystems. The connection between forest ecosystems and the geology of the study area is more apparent, as certain forest types are related with specific geological formations; due to the insignificant presence of grasslands and riverine settings in the study area, it is not possible to assess the role of the geological formation for these mushroom habitats.

Mycorrhizal ecology and evolution: the past, the present, and the future

Almost all land plants form symbiotic associations with mycorrhizal fungi. These below-ground fungi play a key role in terrestrial ecosystems as they regulate nutrient and carbon cycles, and influence soil structure and ecosystem multifunctionality. Up to 80% of plant N and P is provided by mycorrhizal fungi and many plant species depend on these symbionts for growth and survival. Estimates suggest that there are c. 50 000 fungal species that form mycorrhizal associations with c. 250 000 plant species. The development of high-throughput molecular tools has helped us to better understand the biology, evolution, and biodiversity of mycorrhizal associations. Nuclear genome assemblies and gene annotations of 33 mycorrhizal fungal species are now available providing fascinating opportunities to deepen our understanding of the mycorrhizal lifestyle, the metabolic capabilities of these plant symbionts, the molecular dialogue between symbionts, and evolutionary adaptations across a range of mycorrhizal associations. Large-scale molecular surveys have provided novel insights into the diversity, spatial and temporal dynamics of mycorrhizal fungal communities. At the ecological level, network theory makes it possible to analyze interactions between plant-fungal partners as complex underground multi-species networks. Our analysis suggests that nestedness, modularity and specificity of mycorrhizal networks vary and depend on mycorrhizal type. Mechanistic models explaining partner choice, resource exchange, and coevolution in mycorrhizal associations have been developed and are being tested. This review ends with major frontiers for further research.

PCR primers to study the diversity of expressed fungal genes encoding lignocellulolytic enzymes in soils using high-throughput sequencing

Plant biomass degradation in soil is one of the key steps of carbon cycling in terrestrial ecosystems. Fungal saprotrophic communities play an essential role in this process by producing hydrolytic enzymes active on the main components of plant organic matter. Open questions in this field regard the diversity of the species involved, the major biochemical pathways implicated and how these are affected by external factors such as litter quality or climate changes. This can be tackled by environmental genomic approaches involving the systematic sequencing of key enzyme-coding gene families using soil-extracted RNA as material. Such an approach necessitates the design and evaluation of gene family-specific PCR primers producing sequence fragments compatible with high-throughput sequencing approaches. In the present study, we developed and evaluated PCR primers for the specific amplification of fungal CAZy Glycoside Hydrolase gene families GH5 (subfamily 5) and GH11 encoding endo-β-1,4-glucanases and endo-β-1,4-xylanases respectively as well as Basidiomycota class II peroxidases, corresponding to the CAZy Auxiliary Activity family 2 (AA2), active on lignin. These primers were experimentally validated using DNA extracted from a wide range of Ascomycota and Basidiomycota species including 27 with sequenced genomes. Along with the published primers for Glycoside Hydrolase GH7 encoding enzymes active on cellulose, the newly design primers were shown to be compatible with the Illumina MiSeq sequencing technology. Sequences obtained from RNA extracted from beech or spruce forest soils showed a high diversity and were uniformly distributed in gene trees featuring the global diversity of these gene families. This high-throughput sequencing approach using several degenerate primers constitutes a robust method, which allows the simultaneous characterization of the diversity of different fungal transcripts involved in plant organic matter degradation and may lead to the discovery of complex patterns in gene expression of soil fungal communities.

Tree diversity does not always improve resistance of forest ecosystems to drought

Climate models predict an increase in the intensity and frequency of drought episodes in the Northern Hemisphere. Among terrestrial ecosystems, forests will be profoundly impacted by drier climatic conditions, with drastic consequences for the functions and services they supply. Simultaneously, biodiversity is known to support a wide range of forest ecosystem functions and services. However, whether biodiversity also improves the resistance of these ecosystems to drought remains unclear. We compared soil drought exposure levels in a total of 160 forest stands within five major forest types across Europe along a gradient of tree species diversity. We assessed soil drought exposure in each forest stand by calculating the stand-level increase in carbon isotope composition of late wood from a wet to a dry year (Δδ(13)CS). Δδ(13)CS exhibited a negative linear relationship with tree species diversity in two forest types, suggesting that species interactions in these forests diminished the drought exposure of the ecosystem. However, the other three forest types were unaffected by tree species diversity. We conclude that higher diversity enhances resistance to drought events only in drought-prone environments. Managing forest ecosystems for high tree species diversity does not necessarily assure improved adaptability to the more severe and frequent drought events predicted for the future.

Leaf and root-associated fungal assemblages do not follow similar elevational diversity patterns

The diversity of fungi along environmental gradients has been little explored in contrast to plants and animals. Consequently, environmental factors influencing the composition of fungal assemblages are poorly understood. The aim of this study was to determine whether the diversity and composition of leaf and root-associated fungal assemblages vary with elevation and to investigate potential explanatory variables. High-throughput sequencing of the Internal Transcribed Spacer 1 region was used to explore fungal assemblages along three elevation gradients, located in French mountainous regions. Beech forest was selected as a study system to minimise the host effect. The variation in species richness and specific composition was investigated for ascomycetes and basidiomycetes assemblages with a particular focus on root-associated ectomycorrhizal fungi. The richness of fungal communities associated with leaves or roots did not significantly relate to any of the tested environmental drivers, i.e. elevation, mean temperature, precipitation or edaphic variables such as soil pH or the ratio carbon∶nitrogen. Nevertheless, the ascomycete species richness peaked at mid-temperature, illustrating a mid-domain effect model. We found that leaf and root-associated fungal assemblages did not follow similar patterns of composition with elevation. While the composition of the leaf-associated fungal assemblage correlated primarily with the mean annual temperature, the composition of root-associated fungal assemblage was explained equally by soil pH and by temperature. The ectomycorrhizal composition was also related to these variables. Our results therefore suggest that above and below-ground fungal assemblages are not controlled by the same main environmental variables. This may be due to the larger amplitude of climatic variables in the tree foliage compared to the soil environment.

Functional profiling and distribution of the forest soil bacterial communities along the soil mycorrhizosphere continuum

An ectomycorrhiza is a multitrophic association between a tree root, an ectomycorrhizal fungus, free-living fungi and the associated bacterial communities. Enzymatic activities of ectomycorrhizal root tips are therefore result of the contribution from different partners of the symbiotic organ. However, the functional potential of the fungus-associated bacterial communities remains unknown. In this study, a collection of 80 bacterial strains randomly selected and isolated from a soil-ectomycorrhiza continuum (oak-Scleroderma citrinum ectomycorrhizas, the ectomycorrhizosphere and the surrounding bulk soil) were characterized. All the bacterial isolates were identified by partial 16S rRNA gene sequences as members of the genera Burkholderia, Collimonas, Dyella, Mesorhizobium, Pseudomonas, Rhizobium and Sphingomonas. The bacterial strains were then assayed for β-xylosidase, β-glucosidase, N-acetyl-hexosaminidase, β-glucuronidase, cellobiohydrolase, phosphomonoesterase, leucine-aminopeptidase and laccase activities, chitin solubilization and auxin production. Using these bioassays, we demonstrated significant differences in the functional distribution of the bacterial communities living in the different compartments of the soil-ectomycorrhiza continuum. The surrounding bulk soil was significantly enriched in bacterial isolates capable of hydrolysing cellobiose and N-acetylglucosamine. In contrast, the ectomycorrhizosphere appeared significantly enriched in bacterial isolates capable of hydrolysing glucopyranoside and chitin. Notably, chitinase and laccase activities were found only in bacterial isolates belonging to the Collimonas and Pseudomonas genera. Overall, the results suggest that the ectomycorrhizal fungi favour specific bacterial communities with contrasting functional characteristics from the surrounding soil.

Seasonal dynamics of Boletus edulis and Lactarius deliciosus extraradical mycelium in pine forests of central Spain

The annual belowground dynamics of extraradical soil mycelium and sporocarp production of two ectomycorrhizal fungi, Boletus edulis and Lactarius deliciosus, have been studied in two different pine forests (Pinar Grande and Pinares Llanos, respectively) in Soria (central Spain). Soil samples (five per plot) were taken monthly (from September 2009 to August 2010 in Pinar Grande and from September 2010 to September 2011 in Pinares Llanos) in eight permanent plots (four for each site). B. edulis and L. deliciosus extraradical soil mycelium was quantified by real-time polymerase chain reaction, with DNA extracted from soil samples, using specific primers and TaqMan® probes. The quantities of B. edulis soil mycelium did not differ significantly between plots, but there was a significant difference over time with a maximum in February (0.1576 mg mycelium/g soil) and a minimum in October (0.0170 mg mycelium/g soil). For L. deliciosus, significant differences were detected between plots and over time. The highest amount of mycelium was found in December (1.84 mg mycelium/g soil) and the minimum in February (0.0332 mg mycelium/g soil). B. edulis mycelium quantities were positively correlated with precipitation of the current month and negatively correlated with the mean temperature of the previous month. Mycelium biomass of L. deliciosus was positively correlated with relative humidity and negatively correlated with mean temperature and radiation. No significant correlation between productivity of the plots with the soil mycelium biomass was observed for any of the two species. No correlations were found between B. edulis sporocarp production and weather parameters. Sporocarp production of L. deliciosus was positively correlated with precipitation and relative humidity and negatively correlated with maximum and minimum temperatures. Both species have similar distribution over time, presenting an annual dynamics characterized by a seasonal variability, with a clear increase on the amounts of biomass during the coldest months of the year. Soil mycelial dynamics of both species are strongly dependent on the weather.

Structural and functional variation in soil fungal communities associated with litter bags containing maize leaf

Soil fungi are key players in the degradation of recalcitrant organic matter in terrestrial ecosystems. To examine the organisms and genes responsible for complex organic matter degradation in soil, we tracked changes in fungal community composition and expressed genes in soil adjacent to mesh bags containing maize leaves undergoing decomposition. Using high-throughput sequencing approaches, changes in fungal community composition were determined by targeting 18S rRNA gene sequences, whereas community gene expression was examined via a metatranscriptomic approach. The majority of the 93 000 partial 18S rRNA gene sequences generated, were affiliated with the Ascomycota and Basidiomycota. Fungal diversity was at least 224 operational taxonomic units at the 97% similarity cutoff level. During litter degradation, the relative proportion of Basidiomycota increased, with a decrease in Ascomycota : Basidiomycota ratios over time. The most commonly detected decomposition-associated fungi included Agaricomycetes and Tremellales as well as unclassified Mucoromycotina. The majority of protein families found in the metatranscriptomic data were affiliated to fungal groups described to degrade plant-derived cellulose, such as Mucoraceae, Chaetomiaceae, Sordariaceae, Sebacinaceae, Tremellaceae, Psathyrellaceae and Schizophyllaceae. The combination of high-throughput rRNA gene-based and metatranscriptomic approaches provided perspectives into the organisms and genes involved in complex organic matter in soil.

Functional assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation

In temperate ecosystems, acidic forest soils are among the most nutrient-poor terrestrial environments. In this context, the long-term differentiation of the forest soils into horizons may impact the assembly and the functions of the soil microbial communities. To gain a more comprehensive understanding of the ecology and functional potentials of these microbial communities, a suite of analyses including comparative metagenomics was applied on independent soil samples from a spruce plantation (Breuil-Chenue, France). The objectives were to assess whether the decreasing nutrient bioavailability and pH variations that naturally occurs between the organic and mineral horizons affects the soil microbial functional biodiversity. The 14 Gbp of pyrosequencing and Illumina sequences generated in this study revealed complex microbial communities dominated by bacteria. Detailed analyses showed that the organic soil horizon was significantly enriched in sequences related to Bacteria, Chordata, Arthropoda and Ascomycota. On the contrary the mineral horizon was significantly enriched in sequences related to Archaea. Our analyses also highlighted that the microbial communities inhabiting the two soil horizons differed significantly in their functional potentials according to functional assays and MG-RAST analyses, suggesting a functional specialisation of these microbial communities. Consistent with this specialisation, our shotgun metagenomic approach revealed a significant increase in the relative abundance of sequences related glycoside hydrolases in the organic horizon compared to the mineral horizon that was significantly enriched in glycoside transferases. This functional stratification according to the soil horizon was also confirmed by a significant correlation between the functional assays performed in this study and the functional metagenomic analyses. Together, our results suggest that the soil stratification and particularly the soil resource availability impact the functional diversity and to a lesser extent the taxonomic diversity of the bacterial communities.

Similar taxonomic richness but different communities of ectomycorrhizas in native forests and non-native plantation forests

This investigation sought to examine if there was a difference between the ectomycorrhizal (ECM) communities in plots of native oak and introduced Scots pine and Sitka spruce forest. The ECM communities in four plots of each forest type were described, from five soil cores collected in each plot, by morphotyping, internal transcribed spacer (ITS)-restriction fragment length polymorphism matching of mycorrhizas and sporocarps and ITS sequencing. Fifty-one distinct taxa were distinguished; 25 were identified to species level, 11 to genus and 15 remained unidentified. Seventy-one ECM species were recorded as sporocarps from the forest plots; most (43 species) were found in the Sitka spruce plots. The below-ground ECM communities of the different forest types did not differ significantly with respect to species richness of taxa on roots, but differed in species composition. Multivariate analysis produced a clear separation of the communities of the different forest types using below-ground data, but the above-ground sporocarp data did not separate the forest types. Moreover, results of a Mantel test found no relationship between the above- and below-ground similarity matrices. The oak plots had the most distinctive ECM community, with Laccaria amethystina and Elaphomyces granulatus being frequent. The Sitka spruce plots showed the lowest intra-forest type similarity and were often dominated by "nursery type" ectomycorrhizas. There was only 10% similarity between the above- and below-ground ECM species in these plots, different colonisation methods of ectomycorrhizal taxa and insufficient below-ground sampling being possible reasons for this disparity. Our results indicate that plantations of non-native Sitka spruce can support similar levels of ECM diversity as native forests.

Edible sporocarp production by age class in a Scots pine stand in Northern Spain

With the aim of increasing knowledge of community structure, dynamics and production of ectomycorrhizal fungi, edible sporocarp yields were monitored between 1995 and 2004 in a Pinus sylvestris stand in the northeast zone of the Iberian Peninsula. A random sampling design was performed by stand age class according to the forest management plan: 0-15, 16-30, 31-50, 51-70 and over 71-years-old. Eighteen 150 m plots were established and sampled weekly every year from September to December. One hundred and nineteen taxa belonging to 51 genera were collected, 40 of which were edible and represented 74% of the total biomass. Boletus edulis, Lactarius deliciosus, Cantharellus cibarius and Tricholoma portentosum sporocarps, which are considered to be of high commercial value, represented 34% of the total production. B. edulis and L. deliciosus were the most remarkable and abundant species, and both were collected in more than 60% of the samplings. B. edulis fructified every year of the experiment; its mean production was 40 kg/ha and year and its maximum productivity was more than 94 kg/ha in 1998. The age class with the largest production of this taxa was the fourth (51-70 years), with 70 kg/ha. L. deliciosus only failed to fructify one autumn (2000); its mean production was almost 10 kg/ha and its maximum productivity close to 30 kg/ha in 1997. The maximum productivity of this species was found in the second (16-30 years) and fifth (71-90 years) stand age classes, with 18 and 16 kg/ha, respectively. Advances in this field can certainly offer new insights into factors affecting sporocarp production.

Multiple markers pyrosequencing reveals highly diverse and host-specific fungal communities on the mangrove trees Avicennia marina and Rhizophora stylosa

Fungi are important actors in ecological processes and trophic webs in mangroves. Although saprophytic fungi occurring in the intertidal part of mangrove have been well studied, little is known about the diversity and structure of the fungal communities in this ecosystem or about the importance of functional groups like pathogens and mutualists. Using tag-encoded 454 pyrosequencing of the ITS1, ITS2, nu-ssu-V5 and nu-ssu-V7 regions, we studied and compared the fungal communities found on the marine and aerial parts of Avicennia marina and Rhizophora stylosa trees in a mangrove in New Caledonia. A total of 209,544 reads were analysed, corresponding to several thousand molecular operational taxonomic units (OTU). There is a marked zonation in the species distribution, with most of the OTU being found specifically in one of the microhabitat studied. Ascomycetes are the dominant phylum (82%), Basidiomycetes are very rare (3%), and 15% of the sequences correspond to unknown taxa. Our results indicate that host specificity is a key factor in the distribution of the highly diverse fungal communities, in both the aerial and intertidal parts of the trees. This study also validates the usefulness of multiple markers in tag-encoded pyrosequencing to consolidate and refine the assessment of the taxonomic diversity.