Search Results (41)

Evaluating forest functional indicators is essential for effective forest management planning. In this study, we conducted a metagenome-based comparative analysis of the rhizosphere soils from a natural Quercus mongolica stand and an artificial Larix kaempferi stand on Mt. Gariwang, Pyeongchang, Republic of Korea. Both stands originally belonged to the same natural forest and represent the current dominant tree species. Bacterial communities were affected more by climate than by tree species. A bacterial co-occurrence network analysis showed more complex interactions in the Q. mongolica than in L. kaempferi. Conversely, fungal communities were affected more by tree species than by climate. Specifically, the Q. mongolica stand had a high ratio of saprotrophic fungi, whereas the L. kaempferi stand exhibited a higher ratio of fungi associated with nutrient decomposition and harbored a high proportion of fungi that form ectomycorrhizae with long-distance exploration types. These fungal traits serve as indicators of soil ecological changes in Q. mongolica and L. kaempferi stands. Our comparative analysis of the microbial communities of Q. mongolica and L. kaempferi, representative plantation species in the Republic of Korea, revealed seasonal and host species–specific bacterial and fungal associations, and fungal communities were less variable than bacterial communities and more accurately reflected host tree traits. Full article

Mycorrhizal symbiosis has been the focus of research for more than a century due to the positive effect of fungi on the growth of the majority of woody plants. The extramatrical mycelium (EMM) of ectomycorrhiza (EMR) accounts for up to one-third of the total soil microbial biomass, whereas litter from this short-living pool accounts for 60% of the total litterfall mass in forest ecosystems. The functioning of EMR improves the nitrogen (N) nutrition of trees and thus contributes to the carbon (C) balance of forest soils. The model presented here is an attempt to describe these EMR functions quantitatively. It calculates the growth of EMM and the subsequent “mining” of additional nitrogen from recalcitrant soil organic matter (SOM) for EMR growth, with the associated formation of “dissolved soil carbon”. The decomposition of EMM litter is carried out by all organisms in the soil food webs, forming available ${\mathrm{N}\mathrm{H}}_4^{+}$ in the first phase and then solid-phase by-products (excretes) as a new labile SOM pool. These substances are the feedback that determines the positive role of EMR symbiosis for forest vegetation. A sensitivity analysis revealed a leading role of the C:N ratio of biotic components in the dynamics of EMM. The model validation showed a satisfactory agreement between simulated and observed data in relation to EMM respiration in larch forest plantations of different ages. Model testing within the EFIMOD3 model system allowed a quantitative assessment of the contribution of different components to forest soil and ecosystem respiration. The validation and testing of this model demonstrated the adequacy of the theoretical background used in this model, with a fast EMM decomposition cycle by all soil biota of the food webs and without direct resource exchange between plants and fungi. Full article

Moss–cyanobacteria associations serve as significant nitrogen fixers and represent the primary nitrogen sink in boreal forests. Fungi, which are essential for soil biogeochemical cycling, have community structures intrinsically linked to forest ecosystem health and productivity. Using high-throughput sequencing, we investigated differences between moss-covered and non-moss soils in two alpine forests (both plantation and natural forests) by examining soil nitrogen contents, fungal community structure, composition, and functional guilds. Results demonstrated that moss cover enhanced soil nutrient contents, including total carbon, total nitrogen, and inorganic nitrogen. It also altered fungal community characteristics, resulting in higher Chao1 and Shannon diversity indices, as well as a more complex fungal network. Notable changes in functional guilds included an increase in saprotrophic fungi abundance and a decrease in ectomycorrhizal fungi. Our findings support the concept that moss cover creates distinct soil environments: moss-covered soils attract decomposers and nutrient-mobilizing fungi (particularly saprotrophs and ectomycorrhiza), while non-moss soils favor ectomycorrhizal fungi that relieve nutrient limitation through extensional mycelial networks. These findings highlight the critical role of moss cover in sustaining forest soil health and resilience, positioning it as a cornerstone of carbon and nutrient cycling within forest ecosystems. Full article

The interactive effects of environmental heterogeneity caused by forest gaps and ectomycorrhizae on fungal community characteristics remain insufficiently explored. To address this knowledge gap, we established a three-year field manipulation experiment in a Picea asperata (Picea asperata Mast.) plantation located in the subalpine region of western Sichuan, China. Growth bags with three mesh sizes—1000 μm (allowing ectomycorrhizae and hyphae), 48 μm (excluding ectomycorrhizae), and 1 μm (excluding both)—were placed across forest gaps (closed canopy, gap edge, and gap center) to investigate how gap disturbances influence soil fungal communities via changes in ectomycorrhizal and hyphal turnover alongside soil physicochemical properties. Soil fungal α-diversity was significantly lower under closed-canopy conditions than at forest gap centers and remained unaffected by ectomycorrhizal and hyphal treatments. Particularly, species diversity increased by 9%, and phylogenetic diversity increased by 10% in forest gap centers compared to the closed canopy. In contrast, soil fungal β-diversity responded to both ectomycorrhizal/hyphal treatments (R² = 0.061; p = 0.001) and forest gap positions (R² = 0.033; p = 0.003). Pairwise comparative analyses revealed significant distinctions between treatments, concurrently excluding ectomycorrhizal and hyphal treatments versus other experimental treatments, as well as between closed-canopy conditions and forest gap centers. The fungal community was dominated by four major phyla: Ascomycota (25.6%–71.0%), Basidiomycota (17.7%–43.7%), Mortierellomycota (1.4%–24.5%), and Rozellomycota (0.4%–2.9%), the relative abundances of which were unaffected by either ectomycorrhizal/hyphal treatments or forest gap positions. The biomass of ectomycorrhizal and saprotrophic fungi showed no significant response to ectomycorrhizal/hyphal treatments. Notably, the exclusion of ectomycorrhizae and hyphae enhanced the significant correlations between fungal community characteristics and soil physicochemical properties. Hierarchical partitioning analysis revealed that the soil water content (SWC) and dissolved organic carbon content were the key determinants of soil fungal community characteristics beneath closed-canopy conditions. In contrast, at forest gap edges and centers, the fungal communities were predominantly shaped by the SWC and dissolved carbon and nitrogen contents. This study highlights the impacts of forest gap disturbances and ectomycorrhizal treatments on soil fungal communities, offering valuable insights for the sustainable management and biodiversity conservation of subalpine forest ecosystems. Full article

Nanopore raw read accuracy has improved to over 99%, making it a potential tool for metabarcoding. For broad adoption, guidelines on quality filtering are needed to ensure reliable taxonomic unit recovery. This study aims to provide those guidelines for a fungal metabarcoding context and to apply them to a case study of ectomycorrhizae in the decaying bark of Fagus sylvatica. We introduce the eNano pipeline to test two standard metabarcoding approaches: (1) Reference-based mapping leveraging UNITE’s species hypothesis system (SH approach); (2) Constructing 98% OTUs (OTU approach). Our results demonstrate that both approaches are effective with Nanopore data. When using a reference database, we recommend strict mapping criteria rather than Phred-based filtering. Leveraging the SH-system further enhances reproducibility and facilitates cross-study communication. For the 98% OTUs, filtering reads at ≥Q25 is recommended. Our case study reveals that the decay gradient is a primary determinant of community composition and that specific mycorrhizal fungi colonize decaying bark. Complementing our metabarcoding results with root tip morphotypification, we identify Laccaria amethystina and Tomentella sublilacina as key ectomycorrhizae of saplings on decaying logs. These findings demonstrate that Nanopore sequencing can provide valuable ecological insights and support its broader use in fungal metabarcoding as read quality continues to improve. Full article

Ectomycorrhizal fungi employ different strategies for mycelial growth and host colonization under varying nutrient conditions. However, key genes associated with mycorrhizal interaction should be influenced solely by the inoculation treatment and not by nutrient variations. To utilize subtle nutrient differences and rapidly screen for key genes related to the interaction between Suillus luteus and Pinus massoniana, we performed an inoculation experiment using culture bottles containing high- and low-nutrient media. Interestingly, S. luteus LS88 promoted the growth of P. massoniana seedlings without mature ectomycorrhiza, and the impact of LS88 inoculation on P. massoniana roots was greater than that of nutrient changes. In this study, the resequenced genome of the LS88 strain was utilized for transcriptome analysis of the strain. The analysis indicated that a unique gene encoding glutathione S-transferase (GST) in LS88 is likely involved in colonizing P. massoniana roots. In this study, the GST gene expression was independent of nutrient levels. It was probably induced by P. massoniana and could be used as a marker for S. luteus colonization degree. Full article

By incubating the soil without living roots in situ at two spruce forest sites, we simulated the effects of tree dieback and interrupted mycorrhizal associations following forest disturbance on the soil microbiome and phosphorus leaching. We observed the retreat of ectomycorrhizal fungi and increased proportion of saprotrophs without changes in community richness and the Shannon diversity index. This was accompanied by a pronounced decomposition of organic matter, associated with an increased activity of carbon-mining hydrolases and acid phosphatase. The nonexistent phosphorus uptake and immobilization by ectomycorrhizal associations led to its substantial increase in the soil, in the labile fractions, such as microbial biomass and water-soluble reactive phosphorus, but also in the fraction bound to organometallics (extractable by oxalate), and caused considerable phosphate leaching, as estimated using ion-exchange resin traps. The results show that the retreat of the root-specific environment, characterized by the input of available carbon and effective nutrient uptake and by the specific microbiome, has profound effects on phosphorus dynamics and loss. Furthermore, we suggest that ectomycorrhiza plays an equally important role in controlling phosphorus-mining from organic matter and subsequent immobilization and/or leaching from soils concurrently to its known role in nitrogen cycling and immobilization in spruce forests. Full article

Mycoparasite secondary metabolites control fungal infections or diseases in agriculture and human health. Among genes involved in synthesizing secondary metabolites, cytochrome P450 monooxygenases (CYPs/P450s) play a key role in synthesizing and attributing diversity to the secondary metabolites. Despite the importance of P450s, a comparative analysis of P450s in mycoparasites has yet to be reported. This study is aimed at addressing this research gap. Genome-wide analysis of P450s in 43 fungi representing six fungal phyla and three distinct lifestyles, such as mycoparasitic (24 species), saprophytic (5 species), and ectomycorrhizal (14 species), revealed the expansion of P450s in Pezizomycete mycoparasites for the synthesis of secondary metabolites. The number of P450s and their families and subfamilies, the number of secondary-metabolite biosynthetic gene clusters (SMBGCs), and the number of P450s that are part of these SMBGCs were found to be highest in Pezizomycete mycoparasites compared to their counterparts of saprophytes and ectomycorrhiza, indicating P450s also play a key role in mycoparasitism. An analysis of P450 location as part of SMBGCs and the available literature on Pezizomycete P450s revealed that P450s play a key role in the synthesis of anti-fungal secondary metabolites such as trichothecene sesquiterpene, harzianum A, heptelidic acid, and gliotoxin. The mycoparasite Trichoderma virens Tv29.8 P450 CYP68Q3 is found to be a bifunctional enzyme with epoxidation and oxidation capability, and CYP5117A3 performs a Baeyer–Villiger oxidation reaction with regioselectivity. This study serves as a reference for future annotation of P450s in mycoparasites. Full article

Fungi of the genus Tuber are famous for their hypogeous ascomata (truffles), many of which possess noteworthy organoleptic properties. T. aestivum shows a wide geographic distribution, has many plant symbionts and is well adapted to various climatic conditions. In this study, five Quercus taxa native to Greece (i.e., Q. coccifera, Q. ilex, Q. ithaburensis subsp. macrolepis, Q. pubescens and Q. trojana subsp. trojana) were inoculated with spore suspensions obtained from a single ascoma of T. aestivum. The fungal colonization of oak roots was evaluated at three, seven and 12 months after inoculation; the respective colonization rates for each time period were as follows: low to medium (17–41%) for Q. pubescens, Q. ithaburensis subsp. macrolepis and Q. trojana subsp. trojana, medium to relatively high (58–80%) for Q. ithaburensis subsp. macrolepis, Q. ilex, Q. pubescens and Q. trojana subsp. trojana, and medium to high (45–87%) for all oak species examined. Positive correlations were assessed between the number of colonized root tips and the total root tips number, but no significant differences were detected between the inoculated plants and the respective control as regards plant growth. The ectomycorrhizae formed by T. aestivum with Q. ithaburensis subsp. macrolepis and Q. trojana subsp. trojana are described for the first time. The outcome of the study evidences the feasibility of generating the seedlings of various indigenous oak species (covering a large range of diverse habitats) successfully inoculated with autochthonous truffles to be readily used for cultivation purposes. Full article

Thelephora ganbajun Zang, a rare wild macrofungus, has significant culinary and medicinal value. However, it also has a high cost attributed to its inability to achieve artificial cultivation and its strict environmental requirements. To reveal the intricacies of its development, we conducted a comprehensive analysis of the proteome and metabolome in three pivotal developmental stages: the mycelium, the primordium, and the fruiting body. In our investigation, genes exhibiting various expression levels across multi-omics analyses were identified as potential candidates implicated in growth, development, or metabolic regulation. The aim of this study was to provide a clearer direction for understanding the fundamental metabolic activities and growth stages of this species. Label-free proteomic sequencing revealed a critical juncture in ectomycorrhiza formation, particularly during the transition from the mycelium to the primordium. Secreted proteins, signaling proteins, membrane proteins, and proteins with unidentified functions were rapidly synthesized, with certain amino acids contributing to the synthesis of proteins involved in signaling pathways or hormone precursor substances. In the metabolomics analysis, the classification of secondary metabolites revealed a noteworthy increase in lipid substances and organic acids, contributing to cell activity. The early mycelial development stage exhibited vigorous cell metabolism, contrasting with a decline in cell division activity during fruiting body formation. In our findings, the integration of metabolomic and transcriptomic data highlighted the potential key role of folate biosynthesis in regulating early ectomycorrhiza development. Notably, the expression of alkaline phosphatase and dihydrofolate synthase genes within this pathway was significantly up-regulated in the mycelium and fruiting body stages but down-regulated in the primordium stage. This regulation primarily influences dihydrofolate reductase activity and B vitamin synthesis. Full article

Suillus bovinus is a wild edible ectomycorrhizal fungus with important economic and ecological value, which often forms an ectomycorrhiza with pine trees. We know little about the mechanisms associated with the metabolism and symbiosis of S. bovinus and its effects on the nutritional value. In this study, the whole-genome sequencing of S. bovinus was performed using Illumina, HiFi, and Hi-C technologies, and the sequencing data were subjected to genome assembly, gene prediction, and functional annotation to obtain a high-quality chromosome-level genome of S. bovinus. The final assembly of the S. bovinus genome includes 12 chromosomes, with a total length of 43.03 Mb, a GC content of 46.58%, and a contig N50 size of 3.78 Mb. A total of 11,199 coding protein sequences were predicted from genome annotation. The S. bovinus genome contains a large number of small secreted proteins (SSPs) and genes that encode enzymes related to carbohydrates, as well as genes related to terpenoids, auxin, and lipochitooligosaccharides. These genes may contribute to symbiotic processes. The whole-genome sequencing and genetic information provide a theoretical basis for a deeper understanding of the mechanism of the mycorrhizal symbiosis of S. bovinus and can serve as a reference for comparative genomics of ectomycorrhizal fungi. Full article

In the present study, the mycobiomes of two soils with different ecological conditions located in Benin (West Africa) were investigated by environmental sequencing (Illumina MiSeq) of the ITS2-region of ribosomal DNA to gain information about the influence of pedological stratification on fungal diversity. For each soil depth and horizon, fungal diversity and community composition were analyzed as well as the potential impact of site characteristics, like vegetation, on these traits. The retrieved sequences revealed in all their replicates high similarities between fungal communities of samples from the same site and soil horizon, but differed within one site in their horizons. It was possible to assign a saprotrophic, symbiotrophic, or parasitic lifestyle to 24% of the recorded fungal mOTUs. Plant parasites were found in all samples in similar proportions. The presence of ectomycorrhizal fungi in one site could be linked to the presence of ectomycorrhizal trees. Overall, it was observed that fungal diversity decreased with increasing depth if only one horizon was present, whereas a deeper horizon present at one site contained communities with a distinct composition regarding the taxonomical affiliations and lifestyles of the fungi found compared to the upper layer. Hence, soil horizonation seems to drive differences in the composition of fungal communities, and should be regarded with more attention when analyzing soil mycobiomes. Full article

Fungi have important ecological functions in the soil of forests, where they decompose organic matter, provide plants with nutrients, increase plant water uptake, and improve plant resistance to adversity, disease, and disturbance. A forest fire presents a serious disturbance of the local ecosystem and can be considered an important component affecting the function of ecosystem biomes; however, the response of soil fungi to fire disturbance is largely unknown. To investigate the effects of fire disturbance on the community composition and diversity of soil fungi in a taiga forest, we collected soil from plots that had undergone a light, moderate, and heavy fire 10 years previously, with the inclusion of a fire-free control. The present soil fungi were characterized using Illumina MiSeq technology, and the sequences were analyzed to identify differences in the community composition and diversity in response to the changed soil physicochemical properties. The results showed that the Chao1 index, which characterizes the alpha diversity of the fungi, did not change significantly. In contrast, the Shannon index increased significantly (p < 0.05) and the Simpson index decreased significantly (p < 0.05) following a light or heavy fire disturbance compared to the control. The relative abundance of Basidiomycota was significantly higher in the soil of the fire sites than that in the control (p < 0.01), and the relative abundance of Ascomycota was significantly lower (p < 0.01). The results of principal coordinates analyses (PCoAs) showed that fire disturbance highly significantly affected the beta diversity of soil fungi (p < 0.001), while the results of canonical correlation analysis (CCA) indicated that the available nitrogen (AN), moisture content (MC), pH, available potassium (AK), and total nitrogen (TN) contents of the soil significantly affected the compositional structure and diversity of the soil fungal communities. The results of functional prediction showed that the majority of the detected soil fungi were symbiotrophs, followed by saprotrophs and saprotroph–symbiotrophs, with ectomycorrhiza being the dominant functional taxon. Fire disturbance significantly reduced the relative abundance of ectomycorrhiza (p < 0.05). This study illustrates that fire disturbance alters the structural composition, diversity, dominance, and relative abundance of the guilds of soil fungal communities in taiga forest, and strongly affected the beta diversity of soil fungi, with AN, MC, pH, AK, and TN being the most important factors affecting their community structure. The results may provide a useful reference for the restoration and rehabilitation of taiga forests after fire disturbance. Full article

Bareroot European beech (Fagus sylvatica L.) seedlings are frequently used in reforestation programs in Central Europe. However, beech outplanting is often unsuccessful due to drought stress. In this study, the effects of a simulated water deficit and of a hydrogel and ectomycorrhizal fungi (EMF) application were estimated on the development of 1 + 1 beech seedlings. The roots of 1-year-old bareroot seedlings were treated with the additives at the time of transplanting to pots in spring and then exposed to the whole growing season under different watering regimes: (i) full watering (FW; volumetric water content 70%), (ii) reduced watering (RW; 40%), (iii) periodic watering (PW; substrate rewetted to 70% after drying), and (iv) no watering (NW). Almost all FW seedlings survived the whole growing season, whereas all NW seedlings died after 17 weeks of desiccation. The survival and growth of FW and NW seedlings were significantly higher and lower, respectively, than those under both PW and RW treatments. The additives significantly increased survival in RW seedlings only but had no effect on growth. A promoting effect of FW on the chlorophyll a fluorescence parameters was found. The number and EMF colonization of the short roots were significantly lower in FW seedlings compared to the other watering treatments. The additives did not affect these parameters. The occurrence of neither treatment-specific EMF root morphotype nor fungi applied in the inoculum and traced by molecular analysis indicated the formation of ectomycorrhizas with native EMF in all treatments. The seedlings in the water-deficient treatments exhibited higher foliar nutrient concentrations than FW seedlings. The additives increased the concentration of nutrients in PW and phosphorus in NW seedlings. The results suggest the significant effect of the water supply, but a weaker effect of the additives tested on beech seedling development under experimental conditions. Full article

The mycorrhizal type affects the structure and functions of tree roots. Therefore, the mechanical traits of the roots of tree species with different types of mycorrhizal fungi may be linked to different root functional traits. Fine roots, in particular, are closely related to the root structure and are also important for slope protection. However, the relationship among the mycorrhizal types of trees, root mechanical traits, and root structure remains unclear. This study aims to investigate the link between fine root tensile strength (Tr) and root morphological and/or structural traits in temperate trees with different mycorrhizal types. We investigated the seedlings of 15 dominant tree species in the cool temperate forests of northern Japan. For each species, fine root Tr and other five common root morphological and structural traits were measured. There was a significant positive correlation between total fine root biomass and fine root Tr consistently, even in the analysis of mycorrhizal types (arbuscular mycorrhizal (AM), and ectomycorrhizae (EM)). Our findings indicate that the root structural trait is an important driver of fine root Tr, especially for AM and EM species, and suggest that including a plant-mycorrhizal framework in future work offers great potential to improve our understanding of forest restoration. Full article