•We review the effect of forest management practices on fungal diversity.•Fungal diversity is positively related with canopy cover, basal area and tree species diversity.•Diversity of deadwood size ...and decomposition stage is positively related to richness of wood-inhabiting fungi.•The higher is the forest management intensity the lower is the diversity of fungal species.•Low impact silviculture and enhancement of stand structural complexity help to conserve fungal diversity.
The influence of forest management on fungal diversity and community composition has been the subject of a wide number of studies over the last two decades. However, the difficulty of studying the complex kingdom of fungi under real forest conditions has led to rather scattered scientific knowledge. Here, we provide the current state of knowledge suggesting future research directions regarding (i) stand structure attributes (age, tree cover, stand density, tree species composition), (ii) management history (managed vs unmanaged), (iii) silvicultural treatments (thinning, clearcutting, shelterwood methods, selective cutting) and (iv) other anthropogenic disturbances (mushroom picking, salvage logging, prescribed burning, fertilization) affecting fungal diversity and community composition. The reviewed studies reported a positive correlation between fungal diversity and stand structure variables such as canopy cover, basal area of the stand and tree species diversity, particularly for mycorrhizal species. Abundance and diversity in size, tree species and decomposition stage of deadwood are reported as positively related to richness of wood-inhabiting fungi. The main findings about the effects of silvicultural practices suggest that the higher is the management intensity the lower is the diversity of ectomycorrhizal and wood-inhabiting species, at least in the short term. We have therefore reported those silvicultural practices which may reduce trade-offs between timber harvesting and fungal diversity conservation. Indeed, fungal diversity can be conserved in managed forests if (i) low impact logging operations are performed; (ii) stand structural complexity and late-successional forest characteristics are enhanced; (iii) deadwood amount and diversity is promoted, (iv) landscape heterogeneity and connectivity is improved or maintained.
Soil microclimate is a potentially important regulator of the composition of plant-associated fungal communities in climates with significant drought periods. Here, we investigated the ...spatio-temporal dynamics of soil fungal communities in a Mediterranean Pinus pinaster forest in relation to soil moisture and temperature.
Fungal communities in 336 soil samples collected monthly over 1 year from 28 long-term experimental plots were assessed by PacBio sequencing of ITS2 amplicons. Total fungal biomass was estimated by analysing ergosterol. Community changes were analysed in the context of functional traits.
Soil fungal biomass was lowest during summer and late winter and highest during autumn, concurrent with a greater relative abundance of mycorrhizal species. Intra-annual spatiotemporal changes in community composition correlated significantly with soil moisture and temperature. Mycorrhizal fungi were less affected by summer drought than free-living fungi. In particular, mycorrhizal species of the short-distance exploration type increased in relative abundance under dry conditions, whereas species of the long-distance exploration type were more abundant under wetter conditions.
Our observations demonstrate a potential for compositional and functional shifts in fungal communities in response to changing climatic conditions. Free-living fungi and mycorrhizal species with extensive mycelia may be negatively affected by increasing drought periods in Mediterranean forest ecosystems.
Soil fungi are fundamental drivers of forest ecosystem processes. Soil physico-chemical parameters and vegetation features such as host type or stand structure can affect soil fungal communities. ...However, there is a lack of comprehensive studies describing the relative importance of niche processes (soil physico-chemistry and forest structural drivers) versus neutral processes (geographical distance) driving soil fungal community assemblages, especially in less-studied drought-prone ecosystems such as Mediterranean forests. In this study, we performed Pacific Biosciences sequencing of internal transcribed spacer 2 amplicons to characterize the soil fungal community composition and diversity of 42 forests dominated by either pure Pinus nigra, Pinus halepensis or Pinus sylvestris or a P. nigra–P. halepensis or P. nigra–P. sylvestris mixture. Our specific aims were to identify and disentangle the relative importance of the main soil characteristics and the spatial and forest structural factors that accounted for the greatest proportion of fungal community variation along a regional gradient in the Mediterranean Pre-Pyrenees. Soil parameters accounted for the greatest significant proportion of the total variance in the overall fungal community (25%), in the mycorrhizal (23%) and saprotrophic (22%) communities, while geographical distance accounted for 14% of the variance in the overall fungal community, 7% in the mycorrhizal and 22% in the saprotrophic communities. Conversely, forest structure did not significantly affect the soil fungal community, as fungal composition and diversity did not differ significantly among the pine hosts. Moreover, pH, followed by P and the C:N ratio explained the largest differences in the composition of the overall fungal community and in the mycorrhizal fungal community. By contrast, the largest proportion of differences in saprotrophic composition were explained by geographical distance, closely followed by the C:N ratio and N. Our results show that, in these Mediterranean pine forests, soil parameters are the most important driving forces shaping soil fungal communities at the regional scale given that ectomycorrhizal and saprotrophic fungi were more influenced by soil physico-chemical parameters or geographical distance than by Pinus species or forest structural variables. Finally, P content in soils also emerged as a significant factor driving differences in mycorrhizal communities.
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•Soil fungal communities were profiled in 42 pure and mixed pine forests.•Soil chemistry significantly influenced variation in soil fungal communities.•Pine species and stand structure had no effect on the soil fungal communities.•pH, P and CN ratio were the strongest predictors shaping fungal communities.
Mycorrhizal fungi can help plants to cope with drought, but research on the fungal communities that are more resistant to drought or alleviate drought stress of trees is still scarce. In this study, ...we investigated effects of drought on soil fungal communities and explored potential fungal traits related to drought resistance under greenhouse conditions. We manipulated water availability in pine seedlings belonging to three Spanish Pinus pinaster populations from geographical areas subjected to contrasting summer drought. A set of plant ecophysiological traits were quantified and soil fungi was quantified and profiled using ergosterol and Pacific Biosciences sequencing. Abundance of ectomycorrhizal (ECM) fungi in plants subjected to drought was lower than in well-watered plants. Most ECM taxa in plants surviving drought had long exploration types and were taxa typically forming rhizomorphs and hydrophobic mycelia. By contrast, ECM taxa in well-watered plants had wider range of distinct exploration types. No differences in fungal communities were found among P. pinaster populations. No associations between ECM fungi and plant ecophysiological traits were found, but significant interactions between drought treatments and belowground plant biomass were found for the relative abundances of ECM fungi, particularly ECM with long exploration types. Plants subjected to drought may benefit by associating to ECM taxa previously shown to transport water efficiently.
•Drought decreased the relative abundances of ectomycorrhizal fungi.•Fungi with long exploration types dominated under drought conditions.•Plant population identity did not influence soil fungal communities.•Plants from mesic populations had higher soil fungal biomass.
• Recent studies have questioned the use of high-throughput sequencing of the nuclear ribosomal internal transcribed spacer (ITS) region to derive a semi-quantitative representation of fungal ...community composition. However, comprehensive studies that quantify biases occurring during PCR and sequencing of ITS amplicons are still lacking.
• We used artificially assembled communities consisting of 10 ITS-like fragments of varying lengths and guanine-cytosine (GC) contents to evaluate and quantify biases during PCR and sequencing with Illumina MiSeq, PacBio RS II and PacBio Sequel I technologies.
• Fragment length variation was the main source of bias in observed community composition relative to the template, with longer fragments generally being under-represented for all sequencing platforms. This bias was three times higher for Illumina MiSeq than for PacBio RS II and Sequel I. All 10 fragments in the artificial community were recovered when sequenced with PacBio technologies, whereas the three longest fragments (> 447 bases) were lost when sequenced with Illumina MiSeq. Fragment length bias also increased linearly with increasing number of PCR cycles but could be mitigated by optimization of the PCR setup. No significant biases related to GC content were observed.
• Despite lower sequencing output, PacBio sequencing was better able to reflect the community composition of the template than Illumina MiSeq sequencing.
The black truffle (
Tuber melanosporum
Vittad.) and the summer truffle (
Tuber aestivum
Vittad.) are two of the most appreciated edible fungi worldwide. The natural distributions of both species ...partially overlap. However, the interspecific interactions between these truffles and how irrigation and mulching techniques impact the dynamics between them are still unknown. Here, an experimental truffle plantation with
Quercus ilex
was established in Maials (Catalonia, Spain), combining three soil mulch treatments (white mulch, black mulch and bare soil as a control) and two irrigation regimes (irrigated and non-irrigated as a control) to investigate truffle mycelial dynamics in soil when both truffle species co-occur. The development of truffle mycelium in two different seasons (spring and autumn) in two consecutive years (2017 and 2018) was quantified using qPCR. Truffle mycelia of both species showed greatest development under white mulch. When mycelia of both truffle species co-occurred in soil, irrigation combined with white mulch resulted in greater quantities of
T. melanosporum
mycelial biomass, whereas the control irrigation treatment favoured the development of
T. aestivum
. Mulch treatments were also advantageous for seedling growth, which was expressed as root collar diameter and its increment during the study period. Significant relationships between root collar diameter and root growth and the amount of mycelial biomass in the soil were observed for both truffle species. Our results indicate the potential advantages of using white mulch to support irrigation in truffle plantations located in areas with dry Mediterranean climatic conditions to promote the development of
Tuber
mycelium.
Black truffle plantations are established on the basis that Tuber melanosporum Vittad. spreads from artificially inoculated trees. Although truffle cultivation has progressed tremendously over the ...past 30 years, the ecological processes underlying T. melanosporum mycelium expansion and its interactions with the rest of the fungal community over time are not completely understood. Controversy exists on how mating type distribution evolves with time and its incidence on truffle production. We studied the soil fungal community and mating type distribution in plantations before truffle production (3, 5 and 7 years and after plantation establishment) and during the production period (10, 14 and 20 years) at three distances from the tree stem: 40, 100 and 200 cm. We found that T. melanosporum developed steadily over the years as extraradical mycelium, first at the nearest part of the tree and later up to 200 cm. T. melanosporum development was not correlated with changes in other ectomycorrhizal fungi and was negatively correlated with lower relative abundance of arbuscular mycorrhizal fungi and of non-root associated guilds such as moulds, yeasts and plant pathogens. Mating type frequency did not change across years. Twenty years after establishment no signs of replacement of T. melanosporum by other fungi nor biases in mating type abundance were observed in soil mycelia, indicating that T. melanosporum can colonize and dominate the surrounding soil in mature Quercus ilex L. plantations.
•T. melanosporum mycelium developed steadily in a 20-year chronosequence.•T. melanosporum development is not limited by other ECM fungi.•T. melanosporum development was correlated with lower abundance of other guilds.•Mating type frequency did not change across the years in T. melanosporum orchards.•Fruiting body production is not limited by unbalances in the mating types.
Understanding soil dynamics and nutrient cycling is crucial for the sustainable management of Japanese forests covering 70 % of the national land area. These forests are dominated by tree species ...with contrasting traits, influencing soil dynamics differently. We investigated how changes in soil characteristics across different forest stands shift in composition and functioning of fungal communities. Four different forest stands dominated by two different mycorrhizal types were selected: Fagus crenata and Larix kaempferi, representing ectomycorrhizal (ECM) types, and Cryptomeria japonica and Robinia pseudoacacia, representing arbuscular mycorrhizal (AM) types. In total, 62 composite topsoil samples from two depths were analyzed for their physicochemical properties and fungal communities were profiled by DNA sequencing. Ectomycorrhizal fungi dominated soils of Fagus crenata and Larix kaempferi forests, while fungal saprotrophs were more abundant in Cryptomeria japonica and Robinia pseudoacacia forests. Forest stand type rather than soil depth determined the composition and structure of soil fungal communities. Soil pH was positively correlated with abundances of saprotrophic fungi (P < 0.05) and negatively with ECM fungi. Soil C:N ratio was positively correlated, and nitrate was negatively correlated with relative abundances of root-associated fungi, primarily ECM fungi. No links between C nor N stocks with fungal guilds were found across the dataset. Observed links between soil C:N ratio and relative abundances of root-associated fungi and saprotrophs stress the importance of these guilds for influencing nutrient cycling economy across contrasting forest types. The lack of correlation between fungal communities and soil C and N stocks suggests distinct mechanisms driving stocks in these soils.
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•Soil pH, nitrate and C:N correlate with fungal community composition and structure•Soil C:N positively correlated with relative abundances of root-associated fungi•Nitrate negatively correlated with relative abundances of root-associated fungi•No links between C nor N stocks with fungal guilds were found•Links between soil C:N and fungal community influence nutrient cycling economy
Forest disturbances have a strong effect on soil fungal communities and associated ecosystem processes. However, little is known about the response of mycelial biomass to disturbances, and how fungi ...reallocate carbon into different fungal structures under environmental stressors. We investigated above- and below-ground fungal biomass shifts in response to different intensities of forest management in Mediterranean Pinus pinaster forests. Soil fungal biomass was estimated by ergosterol quantification and production of sporocarps was estimated from repeated field samplings during 5 years in 26 experimental plots. Abundance of mycorrhizal and saprotrophic fungi belowground was determined using Pacific Biosciences sequencing of fungal ITS2 amplicons. Thinning had a prolonged negative effect belowground, inter- and intra-annually, on total fungal biomass and on the biomass of ectomycorrhizal fungi, but not on saprotrophic fungi. Total and ectomycorrhizal mushroom yields were negatively correlated with the total and the ectomycorrhizal mycelial biomass, respectively. Thinning also correlated positively with the aboveground/belowground ratio of both total and ectomycorrhizal fungal biomass. We show potential short-term shifts in resource allocation of fungi from below-to above-ground structures under disturbances such as forest thinning. Ectomycorrhizal fungi may respond to disturbances by increasing reproduction rather than colonizing the surrounding soil.
•Forest thinning reduced total and ectomycorrhizal soil fungal biomass.•Thinning effects were observed both inter- and intra-annually.•No thinning effect was detected on saprotrophic fungal biomass belowground.•Sporocarp productivity and mycelium biomass were negatively correlated.•Thinning may result in carbon allocation from mycelia to sporocarps.
•T. melanosporum dominate irrespective of the distance from the forest.•Fungal community changed with distance to the forest.•Fungal community was less affected by the proximity to the forest in ...larger trees.•EcM other-than-T. melanosporum were more abundant in smaller trees near forests.
Black truffles are a highly valued non-wood forest product. The success of truffle plantations is raising the interest to establish orchards within forest settings. One main concern is that the forest may act as a source of ectomycorrhizal fungi that could displace Tuber melanosporum in plantations and impair truffle production. We studied the effects of host tree distance to the surrounding forest on T. melanosporum development and on the root-associated fungal community. Our research was carried out in a 5-year old holm oak (Quercus ilex) plantation established in an abandoned pasture surrounded by a Q. ilex forest in the Pyrenees. The spatial distribution of different fungal guilds as well as of T. melanosporum mycelium quantity and mating types frequency was correlated with the distance to the forest and the diameter of the trees. We found a higher relative abundance of non-T. melanosporum EcM fungi associated with the trees closer to the forest. Larger root collar diameter trees had greater biomass of T. melanosporum mycelium and whose fungal community was less affected by the distance to the forest. No association between the biomass of T. melanosporum mycelium in the soil and the distance to the forest or the abundance of non-T. melanosporum EcM fungi were observed. Our results indicate that T. melanosporum inoculated oaks planted in areas surrounded by forests may be colonised by other ectomycorrhizal species, and develop a distinct microbial community from those usually established in agricultural lands. Further investigations should be carried out to determine whether a different fungal community may affect truffle production in the future, but to date, truffle mycelium does not seem to be impaired.
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