Multiscale assemblage of an ectomycorrhizal fungal community: the influence of host functional traits and soil properties in a 10-ha miombo forest

A Stronger Rhizosphere Impact on the Fungal Communities Compared to the Bacterial Communities in Pecan Plantations

Understanding microbial communities associated with bulk and rhizosphere soils will benefit the maintenance of forest health and productivity and the sustainable development of forest ecosystems. Based on MiSeq sequencing, we explored the differences between the bulk soil and the rhizosphere soil on bacterial and fungal communities of pecan plantation. Results suggested that rhizosphere-associated fungal rather than bacterial community structures differed from bulk soil, and rhizosphere soil had lower fungal diversity than bulk soil. Actinobacteria and Cantharellales were the bacterial and fungal biomarkers of the rhizosphere soil of pecan plantation, respectively. In addition, Pleosporales, which are mainly involved in saprophylaxis and plant pathogenic processes, was identified as one of the most important fungal biomarkers for the bulk soil, and the FunGuild predicted a higher relative abundance of pathogenic fungi in bulk soil compared to rhizosphere soil. The pH, ammonium nitrogen (NH4+-N), nitrate nitrogen (NO3--N), and total carbon (TC) contents drove microbial community structure and composition. The bacterial network was simpler in the rhizosphere soil than in the bulk soil. However, fungi showed the opposite network pattern. Keystone species in bacterial and fungal networks were mostly involved in nutrient cycling and the C cycling, and were found to be enriched in the rhizosphere soil. Overall, in terms of bacterial and fungal communities, the rhizosphere soil behaves more healthily than the bulk soil and has a higher potential for nutrient cycling.

Similarities and Differences among Soil Fungal Assemblages in Managed Forests and Formerly Managed Forest Reserves

Unlike the numerous works concerning the effect of management on the forest mycobiome, only a few studies have addressed how fungi from different trophic groups recover from natural and anthropogenic disturbances and develop structural features typical of unmanaged old-growth forests. Our objective is to compare the soil fungal assemblages represented by different functional/trophic groups in protected and managed stands located in European mixed forests dominated by Scots pine. Fungal communities were analyzed using high-throughput Illumina MiSeq sequencing of fungal internal transcribed spacer 1 (ITS1) amplicons. Formerly managed forest reserves (established around 50 years ago) and forests under standard forest management appeared to be similar in terms of total and mean species richness of all fungal operational taxonomic units (OTUs), as well as OTUs assigned to different functional trophic groups. Among the 599 recorded OTUs, 497 (83%) were shared between both management types, whereas 9.5% of taxa were unique to forest reserves and 7.5% were unique to managed stands. Ascomycota and Basidiomycota were the predominant phyla, comprising 88% of all identified fungi. The main functional components of soil fungal assemblages consisted of saprotrophic (42% fungal OTUs; 27% reads) and ectomycorrhizal fungi (16%; 47%). Two-way analysis of similarities (ANOSIM) revealed that both site and management strategy influenced the species composition of soil fungal communities, with site being a primary effect for saprotrophic and ectomycorrhizal fungi. Volume of coarse and very fine woody debris and soil pH significantly influenced the ectomycorrhizal fungal community, whereas saprotrophic fungi were influenced primarily by volume of coarse woody debris and soil nitrate concentration. Among the identified fungal OTUs, 18 red-listed fungal species were identified from both forest reserves and managed forests, comprising two ECM fungi and four saprotrophs from the category of endangered species. Our results suggest that the transformation of fungal diversity after cessation of forest management is rather slow, and that both forest reserves and managed forests help uphold fungal diversity.

Three new species of Inosperma (Agaricales, Inocybaceae) from Tropical Africa

Here, we describe three new species of Inosperma from Tropical Africa: Inospermaafricanum, I.bulbomarginatum and I.flavobrunneum. Morphological and molecular data show that these species have not been described before, hence need to be described as new. The phylogenetic placements of these species were inferred, based on molecular evidence from sequences of 28S and RPB2. Additional analysis using ITS dataset shows interspecific variation between each species. Phylogenetic analyses resolve I.flavobrunneum in Old World Tropical clade 1 with weak support, I.bulbomarginatum is sister of Old World Tropical clade 1 and I.africanum is indicated as sister to the rest of Inosperma. Complete description and illustrations, including photographs and line drawings, are presented for each species. A new combination of Inocybeshawarensis into Inosperma is also proposed.

Generalized Linear Models outperform commonly used canonical analysis in estimating spatial structure of presence/absence data

Background

Ecological communities tend to be spatially structured due to environmental gradients and/or spatially contagious processes such as growth, dispersion and species interactions. Data transformation followed by usage of algorithms such as Redundancy Analysis (RDA) is a fairly common approach in studies searching for spatial structure in ecological communities, despite recent suggestions advocating the use of Generalized Linear Models (GLMs). Here, we compared the performance of GLMs and RDA in describing spatial structure in ecological community composition data. We simulated realistic presence/absence data typical of many β-diversity studies. For model selection we used standard methods commonly used in most studies involving RDA and GLMs.

Methods

We simulated communities with known spatial structure, based on three real spatial community presence/absence datasets (one terrestrial, one marine and one freshwater). We used spatial eigenvectors as explanatory variables. We varied the number of non-zero coefficients of the spatial variables, and the spatial scales with which these coefficients were associated and then compared the performance of GLMs and RDA frameworks to correctly retrieve the spatial patterns contained in the simulated communities. We used two different methods for model selection, Forward Selection (FW) for RDA and the Akaike Information Criterion (AIC) for GLMs. The performance of each method was assessed by scoring overall accuracy as the proportion of variables whose inclusion/exclusion status was correct, and by distinguishing which kind of error was observed for each method. We also assessed whether errors in variable selection could affect the interpretation of spatial structure.

Results

Overall GLM with AIC-based model selection (GLM/AIC) performed better than RDA/FW in selecting spatial explanatory variables, although under some simulations the methods performed similarly. In general, RDA/FW performed unpredictably, often retaining too many explanatory variables and selecting variables associated with incorrect spatial scales. The spatial scale of the pattern had a negligible effect on GLM/AIC performance but consistently affected RDA’s error rates under almost all scenarios.

Conclusion

We encourage the use of GLM/AIC for studies searching for spatial drivers of species presence/absence patterns, since this framework outperformed RDA/FW in situations most likely to be found in natural communities. It is likely that such recommendations might extend to other types of explanatory variables.

The ability of a host plant to associate with different symbiotic partners affects ectomycorrhizal functioning

Some plants that associate with ectomycorrhizal (ECM) fungi are also able to simultaneously establish symbiosis with other types of partners. The presence of alternative partners that may provide similar benefits may affect ECM functioning. Here we compared potential leucine-aminopeptidase (LA) and acid phosphatase (AP) enzyme activity (involved in N and P cycling, respectively) in ECM fungi of three hosts planted under the same conditions but differing in the type of partners: Pinus (ECM fungi only), Eucalyptus (ECM and arbuscular mycorrhizal -AM- fungi) and Acacia (ECM, AM fungi and rhizobial bacteria). We found that the ECM community on Acacia and Eucalyptus had higher potential AP activity than the Pinus community. The ECM community in Acacia also showed increased potential LA activity compared to Pinus. Morphotypes present in more than one host showed higher potential AP and LA activity when colonizing Acacia than when colonizing another host. Our results suggest that competition with AM fungi and rhizobial bacteria could promote increased ECM activity in Eucalyptus and Acacia. Alternatively, other host-related differences such as ECM community composition could also play a role. We found evidence for ECM physiological plasticity when colonizing different hosts, which might be key for adaptation to future climate scenarios.

Ectomycorrhizal Fungal Communities and Their Functional Traits Mediate Plant-Soil Interactions in Trace Element Contaminated Soils

There is an increasing consensus that microbial communities have an important role in mediating ecosystem processes. Trait-based ecology predicts that the impact of the microbial communities on ecosystem functions will be mediated by the expression of their traits at community level. The link between the response of microbial community traits to environmental conditions and its effect on plant functioning is a gap in most current microbial ecology studies. In this study, we analyzed functional traits of ectomycorrhizal fungal species in order to understand the importance of their community assembly for the soil-plant relationships in holm oak trees (Quercus ilex subsp. ballota) growing in a gradient of exposure to anthropogenic trace element (TE) contamination after a metalliferous tailings spill. Particularly, we addressed how the ectomycorrhizal composition and morphological traits at community level mediate plant response to TE contamination and its capacity for phytoremediation. Ectomycorrhizal fungal taxonomy and functional diversity explained a high proportion of variance of tree functional traits, both in roots and leaves. Trees where ectomycorrhizal fungal communities were dominated by the abundant taxa Hebeloma cavipes and Thelephora terrestris showed a conservative root economics spectrum, while trees colonized by rare taxa presented a resource acquisition strategy. Conservative roots presented ectomycorrhizal functional traits characterized by high rhizomorphs formation and low melanization which may be driven by resource limitation. Soil-to-root transfer of TEs was explained substantially by the ectomycorrhizal fungal species composition, with the highest transfer found in trees whose roots were colonized by Hebeloma cavipes. Leaf phosphorus was related to ectomycorrhizal species composition, specifically higher leaf phosphorus was related to the root colonization by Thelephora terrestris. These findings support that ectomycorrhizal fungal community composition and their functional traits mediate plant performance in metal-contaminated soils, and have a high influence on plant capacity for phytoremediation of contaminants. The study also corroborates the overall effects of ectomycorrhizal fungi on ecosystem functioning through their mediation over the plant economics spectrum.

Soil abiotic variables are more important than Salicaceae phylogeny or habitat specialization in determining soil microbial community structure

Predicting the outcome of interspecific interactions is a central goal in ecology. The diverse soil microbes that interact with plants are shaped by different aspects of plant identity, such as phylogenetic history and functional group. Species interactions may also be strongly shaped by abiotic environment, but there is mixed evidence on the relative importance of environment, plant identity and their interactions in shaping soil microbial communities. Using a multifactor, split-plot field experiment, we tested how hydrologic context, and three facets of Salicaceae plant identity-habitat specialization, phylogenetic distance and species identity-influence soil microbial community structure. Analysis of microbial community sequencing data with generalized dissimilarity models showed that abiotic environment explained up to 25% of variation in community composition of soil bacteria, fungi and archaea, while Salicaceae identity influenced <1% of the variation in community composition of soil microbial taxa. Multivariate linear models indicated that the influence of Salicaceae identity was small, but did contribute to differentiation of soil microbes within treatments. Moreover, results from a microbial niche breadth analysis show that soil microbes in wetlands have more specialized host associations than soil microbes in drier environments-showing that abiotic environment changed how plant identity correlated with soil microbial communities. This study demonstrates the predominance of major abiotic factors in shaping soil microbial community structure; the significance of abiotic context to biotic influence on soil microbes; and the utility of field experiments to disentangling the abiotic and biotic factors that are thought to be most essential for soil microbial communities.