Forest Age and Plant Species Composition Determine the Soil Fungal Community Composition in a Chinese Subtropical Forest

Forest Age Drives the Resource Utilization Indicators of Trees in Planted and Natural Forests in China

Specific leaf area (SLA) and leaf dry matter content (LDMC) are key leaf functional traits commonly used to reflect tree resource utilization strategies and predict forest ecosystem responses to environmental changes. Previous research on tree resource utilization strategies (SLA and LDMC) primarily focused on the species level within limited spatial scales, making it crucial to quantify the spatial variability and driving factors of these strategies. Whether there are discrepancies in resource utilization strategies between trees in planted and natural forests, and the dominant factors and mechanisms influencing them, remain unclear. This study, based on field surveys and the literature from 2008 to 2020 covering 263 planted and 434 natural forests in China, using generalized additive models (GAMs) and structural equation models (SEMs), analyzes the spatial differences and dominant factors in tree resource utilization strategies between planted and natural forests. The results show that the SLA of planted forests is significantly higher than that of natural forests (p < 0.01), and LDMC is significantly lower (p < 0.0001), indicating a "faster investment-return" resource utilization strategy. As the mean annual high temperature (MAHT) and mean annual precipitation (MAP) steadily rise, trees have adapted their resource utilization strategies, transitioning from a "conservative" survival tactic to a "rapid investment-return" model. Compared to natural forests, planted forest trees exhibit stronger environmental plasticity and greater variability with forest age in their resource utilization strategies. Overall, forest age is the dominant factor influencing resource utilization strategies in both planted and natural forests, having a far greater direct impact than climatic factors (temperature, precipitation, and sunlight) and soil nutrient factors. Additionally, as forest age increases, both planted and natural forests show an increase in SLA and a decrease in LDMC, indicating a gradual shift towards more efficient resource utilization strategies.

Stable functional structure despite high taxonomic variability across fungal communities in soils of old-growth montane forests

BACKGROUND

Major advances over the past decade in molecular ecology are providing access to soil fungal diversity in forest ecosystems worldwide, but the diverse functions and metabolic capabilities of this microbial community remain largely elusive. We conducted a field survey in montane old-growth broadleaved and conifer forests, to investigate the relationship between soil fungal diversity and functional genetic traits. To assess the extent to which variation in community composition was associated with dominant tree species (oak, spruce, and fir) and environmental variations in the old-growth forests in the Jade Dragon Snow Mountain in Yunnan Province, we applied rDNA metabarcoding. We also assessed fungal gene expression in soil using mRNA sequencing and specifically assessed the expression of genes related to organic matter decomposition and nutrient acquisition in ectomycorrhizal and saprotrophic fungi.

RESULTS

Our taxonomic profiling revealed striking shifts in the composition of the saprotrophic and ectomycorrhizal guilds among the oak-, fir-, and spruce-dominated forests. The core fungal microbiome comprised only ~ 20% of the total OTUs across all soil samples, although the overlap between conifer-associated communities was substantial. In contrast, seasonality and soil layer explained only a small proportion of the variation in community structure. However, despite their highly variable taxonomic composition, fungal guilds exhibited remarkably similar functional traits for growth-related and core metabolic pathways across forest associations, suggesting ecological redundancy. However, we found that the expression profiles of genes related to polysaccharide and protein degradation and nutrient transport notably varied between and within the fungal guilds, suggesting niche adaptation.

CONCLUSIONS

Overall, our metatranscriptomic analyses revealed the functional potential of soil fungal communities in montane old-growth forests, including a suite of specialized genes and taxa involved in organic matter decomposition. By linking genes to ecological traits, this study provides insights into fungal adaptation strategies to biotic and environmental factors, and sheds light on the importance of understanding functional gene expression patterns in predicting ecosystem functioning. Video Abstract.

Molinia caerulea alters forest Quercus petraea seedling growth through reduced mycorrhization

Oak regeneration is jeopardized by purple moor grass, a well-known competitive perennial grass in the temperate forests of Western Europe. Below-ground interactions regarding resource acquisition and interference have been demonstrated and have led to new questions about the negative impact of purple moor grass on ectomycorrhizal colonization. The objective was to examine the effects of moor grass on root system size and ectomycorrhization rate of oak seedlings as well as consequences on nitrogen (N) content in oak and soil. Oak seedlings and moor grass tufts were planted together or separately in pots under semi-controlled conditions (irrigated and natural light) and harvested 1 year after planting. Biomass, N content in shoot and root in oak and moor grass as well as number of lateral roots and ectomycorrhizal rate in oak were measured. Biomass in both oak shoot and root was reduced when planting with moor grass. Concurrently, oak lateral roots number and ectomycorrhization rate decreased, along with a reduction in N content in mixed-grown oak. An interference mechanism of moor grass is affecting oak seedlings performance through reduction in oak lateral roots number and its ectomycorrhization, observed in conjunction with a lower growth and N content in oak. By altering both oak roots and mycorrhizas, moor grass appears to be a species with a high allelopathic potential. More broadly, these results show the complexity of interspecific interactions that involve various ecological processes involving the soil microbial community and need to be explored in situ.

Changes in Rhizosphere Soil Fungal Communities of Pinus tabuliformis Plantations at Different Development Stages on the Loess Plateau

The soil fungal community is an important factor in the forest ecosystems, and a better understanding of its composition and dynamic changes will contribute to the maintenance, preservation, and sustainable development of the forest ecosystems. Pinus tabuliformis has been widely planted for local ecological restoration on the Loess Plateau in China in recent decades. However, these plantations have been degraded to different degrees with increasing stand age. Hence, we tried to find the possible causes for the plantation degradation by analyzing soil environmental changes and soil fungal community composition at different stand ages. We collected rhizosphere soil samples from young (10-year-old), middle-aged (20-year-old), and near-mature (30-year-old) P. tabuliformis plantations in this region and characterized their soil properties and soil fungal community diversity and composition. Our results showed that with increasing stand age, the contents of organic carbon, ammonium nitrogen (AN) and nitrate nitrogen (NN) in the soil increased significantly, while the content of available phosphorus (AP) decreased significantly. The main factors affecting the composition of the soil fungal community were the contents of AP, AN, and NN in the soil. In addition, the genus Suillus was the dominant ectomycorrhizal (ECM) fungus in all periods of P. tabuliformis plantations in this region. The results of structural equation modeling showed that the community composition of ECM fungi was significantly correlated with stand age, soil NN, and AP contents, and that of pathogenic (PAG) fungi was significantly correlated with soil AN and AP contents. The decrease in the relative abundance of ECM fungi and the increase in the relative abundance of PAG fungi would exacerbate the degradation of P. tabulaeformis plantation. Our results illustrated that the content of soil AP is not only an important factor limiting the development of plantations, but it also significantly affects the community composition of soil fungi in the rhizosphere of the P. tabuliformis plantation. This study provides a novel insight into the degradation of P. tabuliformis plantations and builds a solid foundation for their subsequent management, restoration, and sustainable development on the Loess Plateau of China.

Ecological Drivers of the Soil Microbial Diversity and Composition in Primary Old-Growth Forest and Secondary Woodland in a Subtropical Evergreen Broad-Leaved Forest Biome in the Ailao Mountains, China

Replacement of primary old-growth forests by secondary woodlands in threatened subtropical biomes drives important changes at the level of the overstory, understory and forest floor, but the impact on belowground microbial biodiversity is yet poorly documented. In the present study, we surveyed by metabarcoding sequencing, the diversity and composition of soil bacteria and fungi in the old-growth forest, dominated by stone oaks (Lithocarpus spp.) and in the secondary Yunnan pine woodland of an iconic site for biodiversity research, the Ailaoshan National Nature Reserve (Ailao Mountains, Yunnan province, China). We assessed the effect of forest replacement and other environmental factors, including soil horizons, soil physicochemical characteristics and seasonality (monsoon vs. dry seasons). We showed that tree composition and variation in soil properties were major drivers for both bacterial and fungal communities, with a significant influence from seasonality. Ectomycorrhizal Operational Taxonomic Units (OTUs) dominated the functional fungal guilds. Species richness and diversity of the bacterial and fungal communities were higher in the pine woodland compared to the primary Lithocarpus forest, although prominent OTUs were different. The slightly lower complexity of the microbiome in the primary forest stands likely resulted from environmental filtering under relatively stable conditions over centuries, when compared to the secondary pine woodlands. In the old-growth forest, we found a higher number of species, but that communities were homogeneously distributed, whereas in the pine woodlands, there is a slightly lower number of species present but the communities are heterogeneously distributed. The present surveys of the bacterial and fungal diversity will serve as references in future studies aiming to assess the impact of the climate change on soil microbial diversity in both old-growth forests and secondary woodlands in Ailaoshan.

Advanced research tools for fungal diversity and its impact on forest ecosystem

Fungi are dominant ecological participants in the forest ecosystems, which play a major role in recycling organic matter and channeling nutrients across trophic levels. Fungal populations are shaped by plant communities and environmental parameters, and in turn, fungal communities also impact the forest ecosystem through intrinsic participation of different fungal guilds. Mycorrhizal fungi result in conservation and stability of forest ecosystem, while pathogenic fungi can bring change in forest ecosystem, by replacing the dominant plant species with new or exotic plant species. Saprotrophic fungi, being ecological regulators in the forest ecosystem, convert dead tree logs into reusable constituents and complete the ecological cycles of nitrogen and carbon. However, fungal communities have not been studied in-depth with respect to functional, spatiotemporal, or environmental parameters. Previously, fungal diversity and its role in shaping the forest ecosystem were studied by traditional and laborious cultural methods, which were unable to achieve real-time results and draw a conclusive picture of fungal communities. This review highlights the latest advances in biological methods such as next-generation sequencing and meta'omics for observing fungal diversity in the forest ecosystem, the role of different fungal groups in shaping forest ecosystem, forest productivity, and nutrient cycling at global scales.

Diversity of Microbial Communities of Pinus sylvestris var. mongolica at Spatial Scale

Soil microorganisms play an indispensable role in the forest ecosystem. It is necessary to study the soil microorganisms in Pinus sylvestris var. mongolica, which is one of the afforestation species widely planted in the northern sandy region of China. We collected soil samples of P. sylvestris at large spatial scales and analyzed bacterial and fungal community composition differences using high-throughput sequencing techniques. The results showed that: (1) the richness index of different sandy lands was significantly different. The α-diversity of bacteria was the highest in Mu Us Sandy Land, and the α-diversity of fungi was the highest in Horqin Sandy Land. (2) The dominant phyla of bacteria were Actinobacteria, Proteobacteria, Chloroflexi and Acidobacteria, while the dominant phyla of fungi were Ascomycota and Basidiomycota. The relative abundance of dominant phyla was different. (3) Temperature and precipitation were the main driving factors of bacterial and fungal community change at large spatial scale. In addition, bacteria were also affected by total nitrogen, soil organic carbon and pH content; fungal community was affected by pH. The microorganisms showed obvious differences in geographical distribution, which could provide ideas for promoting sustainable management of P. sylvestris stand.

Eucalyptus Plantation Age and Species Govern Soil Fungal Community Structure and Function Under a Tropical Monsoon Climate in China

Fungi perform crucial roles in nutrient cycles, but there is limited information on how soil fungal communities vary with stand age and tree species. Eucalyptus has been extensively planted in China, which has caused severe soil erosion and water deficiency due to short rotation management. In this study, the fungal community structure and potential function in Eucalyptus plantations with different ages (1-5+ years) and species (Eucalyptus urophylla × Eucalyptus grandis, Eucalyptus camaldulens, and Eucalyptus pellita) under a tropical monsoon climate in China were characterized by Illumina Miseq coupled with FUNGuild analysis. The results showed that the fungal alpha diversity decreased with an increase in the age of the plantation. Plantations of different ages and species formed distinct fungal communities and potential functional structures, respectively (p < 0.05), in which the age of the plantation contributed more to the variations. At high taxonomic levels, the soil fungal community changed from the dominance of orders belonging to Ascomycota (Pleosporales, Chaetothyriales, and Eurotiales) to orders belonging to Basidiomycota (Agaricales, Sebacinales, Cantharellales, and Russulales) with increasing plantation age. The community potential function shifted from the dominance of plant pathogens to a higher abundance of saprotrophs and symbiotrophs. The organic carbon of the soil was the key environmental driver to both the fungal community and potential functional structure. The results provide useful information on the importance of fungi for the management of Eucalyptus plantations.

What shapes ground beetle assemblages in a tree species-rich subtropical forest?

As woody plants provide much of the trophic basis for food webs in forests their species richness, but also stand age and numerous further variables such as vegetation structure, soil properties and elevation can shape assemblages of ground beetles (Coleoptera: Carabidae). However, the combined impact of these numerous variables on ground beetle diversity and community structure has rarely been studied simultaneously. Therefore, ground beetles were studied in 27 plots in a highly diverse and structurally heterogeneous subtropical forest ecosystem, the Gutianshan National Park (southeast China) using pitfall traps and flight interception traps. Both trapping methods collected partly overlapping species spectra. The arboreal fauna was dominated by lebiines and to a smaller extent by tiger beetles and platynines; the epigeic fauna comprised mostly representatives of the genus Carabus and numerous tribes, especially anisodactylines, pterostichines, and sphodrines. Ground beetle species richness, abundance, and biomass of the pitfall trap catches were analyzed with generalized linear mixed models (GLMMs), fitted with seven environmental variables. Four of these variables influenced the ground beetle assemblages: Canopy cover, herb cover, pH-value of the topsoil and elevation. Contrary to our expectations, woody plant species richness and stand age did not significantly affect ground beetle assemblages. Thus, ground beetles seem to respond differently to environmental variables than ants and spiders, two other predominantly predatory arthropod groups that were studied on the same plots in our study area and which showed distinct relationships with woody plant richness. Our results highlight the need to study a wider range of taxa to achieve a better understanding of how environmental changes affect species assemblages and their functioning in forest ecosystems.

Soil Fungal Community Structure in Boreal Pine Forests: From Southern to Subarctic Areas of Finland

The boreal forest environment plays an important role in the global C cycle due to its high carbon storage capacity. However, relatively little is known about the forest fungal community at a regional scale in boreal forests. In the present study, we have re-analyzed the data from our previous studies and highlighted the core fungal community composition and potential functional groups in three forests dominated by Scots pine (Pinus sylvestris L.) in Finland, and identified the fungal generalists that appear across geographic locations despite differences in local conditions. The three forests represent subarctic, northern and southern boreal forest, and are all in an un-managed state without human interference or management. The subarctic and northern areas are subject to reindeer grazing. The results showed that the three locations formed distinct fungal community structures (P < 0.05). Compared to the two northern locations, the southern boreal forest harbored a greater abundance of Zygomycota, Lactarius, Mortierella Umbelopsis, and Tylospora, in which aspect there were no differences between the two northern forests. Cortinarius, Piloderma, and Suillus were the core fungal genera in the boreal Scots pine forest. Functionally, the southern boreal forest harbored a greater abundance of saprotroph, endophytes and fungal parasite-lichen, whereas a greater abundance of ectomycorrhizal fungi was observed in the northern boreal forests. Moreover, the pathotroph and wood saprotrophs were commonly present in these three regions. The three locations formed two distinct fungal community functional structures, by which the southern forest was clearly separated from the two northern forests, suggesting a distance–decay relationship via geographic location. This study provides useful information for better understanding the common fungal communities and functions in boreal forests in different geographical locations.

Pyrosequencing and Taxonomic Composition of the Fungal Community from Soil of Tricholoma matsutake in Gyeongju

Tricholoma matsutake is an ectomycorrhizal fungus that has a symbiotic relationship with the root of Pinus densiflora. Soil microbial communities greatly affect the growth of T. matsutake, however, few studies have examined the characteristics of these communities. In the present study, we analyzed soil fungal communities from Gyeongju and Yeongdeok using metagenomic pyrosequencing to investigate differences in fungal species diversity, richness, and taxonomic composition between the soil under T. matsutake fruiting bodies (Sample 2) and soil where the fairy ring of T. matsutake was no longer present (Sample 1). The same spot was investigated three times at intervals of four months to observe changes in the community. In the samples from Yeongdeok, the number of valid reads was lower than that at Gyeongju. The operational taxonomic units of most Sample 2 groups were less than those of Sample 1 groups, indicating that fungal diversity was low in the T. matsutakedominant soil. The soil under the T. matsutake fruiting bodies was dominated by more than 51% T. matsutake. From fall to the following spring, the ratio of T. matsutake decreased. Basidiomycota was the dominant phylum in most samples. G-F1-2, G-F2-2, and Y-F1-2 had the genera Tricholoma, Umbelopsis, Oidiodendron, Sagenomella, Cladophialophora, and Phialocephala in common. G-F1-1, G-F2-1, and Y-F1-1 had 10 genera including Umbelopsis and Sagenomella in common. From fall to the following spring, the amount of phyla Basidiomycota and Mucoromycota gradually decreased but that of phylum Ascomycota increased. We suggest that the genus Umbelopsis is positively related to T. matsutake.

Soil bacterial communities and their associated functions for forest restoration on a limestone mine in northern Thailand

Opencast mining removes topsoil and associated bacterial communities that play crucial roles in soil ecosystem functioning. Understanding the community composition and functioning of these organisms may lead to improve mine-rehabilitation practices. We used a culture-dependent method, combined with Illumina sequencing, to compare the taxonomic richness and composition of living bacterial communities in opencast mine substrates and young mine-rehabilitation plots, with those of soil in adjacent remnant forest at a limestone mine in northern Thailand. We further investigated the effects of soil physico-chemical factors and ground-flora cover on the same. Although, loosened subsoil, brought in to initiate rehabilitation, improved water retention and facilitated plant re-establishment, it did not increase the population density of living microbes substantially within 9 months. Planted trees and sparse ground flora in young rehabilitation plots had not ameliorated the micro-habitat enough to change the taxonomic composition of the soil bacteria compared with non-rehabilitated mine sites. Viable microbes were significantly more abundant in forest soil than in mine substrates. The living bacterial community composition differed significantly, between the forest plots and both the mine and rehabilitation plots. Proteobacteria dominated in forest soil, whereas Firmicutes dominated in samples from both mine and rehabilitation plots. Although, several bacterial taxa could survive in the mine substrate, soil ecosystem functions were greatly reduced. Bacteria, capable of chitinolysis, aromatic compound degradation, ammonification and nitrate reduction were all absent or rare in the mine substrate. Functional redundancy of the bacterial communities in both mine substrate and young mine-rehabilitation soil was substantially reduced, compared with that of forest soil. Promoting the recovery of microbial biomass and functional diversity, early during mine rehabilitation, is recommended, to accelerate soil ecosystem restoration and support vegetation recovery. Moreover, if inoculation is included in mine rehabilitation programs, the genera: Bacillus, Streptomyces and Arthrobacter are likely to be of particular interest, since these genera can be cultivated easily and this study showed that they can survive under the extreme conditions that prevail on opencast mines.

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.

Metabarcoding on both environmental DNA and RNA highlights differences between fungal communities sampled in different habitats

In recent years, metabarcoding has become a key tool to describe microbial communities from natural and artificial environments. Thanks to its high throughput nature, metabarcoding efficiently explores microbial biodiversity under different conditions. It can be performed on environmental (e)DNA to describe so-called total microbial community, or from environmental (e)RNA to describe active microbial community. As opposed to total microbial communities, active ones exclude dead or dormant organisms. For what concerns Fungi, which are mostly filamentous microorganisms, the relationship between DNA-based (total) and RNA-based (active) communities is unclear. In the present study, we evaluated the consequences of performing metabarcoding on both soil and wood-extracted eDNA and eRNA to delineate molecular operational taxonomic units (MOTUs) and differentiate fungal communities according to the environment they originate from. DNA and RNA-based communities differed not only in their taxonomic composition, but also in the relative abundances of several functional guilds. From a taxonomic perspective, we showed that several higher taxa are globally more represented in either “active” or “total” microbial communities. We also observed that delineation of MOTUs based on their co-occurrence among DNA and RNA sequences highlighted differences between the studied habitats that were overlooked when all MOTUs were considered, including those identified exclusively by eDNA sequences. We conclude that metabarcoding on eRNA provides original functional information on the specific roles of several taxonomic or functional groups that would not have been revealed using eDNA alone.

Relationship between Species Richness, Biomass and Structure of Vegetation and Mycobiota along an Altitudinal Transect in the Polar Urals

Aboveground species richness patterns of vascular plants, aphyllophoroid macrofungi, bryophytes and lichens were compared along an altitudinal gradient (80–310 m a.s.l.) on the Slantsevaya mountain at the eastern macroslope of the Polar Urals (Russia). Five altitudinal levels were included in the study: (1) Northern boreal forest with larch-spruce in the Sob’ river valley habitats; (2–3) two levels of closed, northern boreal, larch-dominated forests on the slopes; (4) crook-stemmed forest; (5) tundra habitats above the timberline. Vascular plant or bryophyte species richness was not affected by altitudinal levels, but lichen species richness significantly increased from the river valley to the tundra. For aphyllophoroid macrofungi, species richness was highest at intermediate and low altitudes, and poorest in the tundra. These results indicate a positive ecotone effect on aphyllophoroid fungal species richness. The species richness of aphyllophoroid fungi as a whole was neither correlated to mortmass stocks, nor to species richness of vascular plants, but individual ecological or morphological groups depended on these parameters. Poroid fungal species richness was positively correlated to tree age, wood biomass and crown density, and therefore peaked in the middle of the slope and at the foot of the mountain. In contrast, clavarioid fungal species richness was negatively related to woody bio- and mortmass, and therefore peaked in the tundra. This altitudinal level was characterized by high biomass proportions of lichens and mosses, and by high litter mortmass. The proportion of corticoid fungi increased with altitude, reaching its maximum at the timberline. Results from the different methods used in this work were concordant, and showed significant patterns. Tundra communities differ significantly from the forest communities, as is also confirmed by nonmetric multidimensional scaling (NMDS) analyses based on the spectrum of morphological and ecological groups of aphyllophoroid fungi.

Assessment of fungal diversity in soil rhizosphere associated with Rhazya stricta and some desert plants using metagenomics

This study aimed to compare the fungal rhizosphere communities of Rhazya stricta, Enneapogon desvauxii, Citrullus colocynthis, Senna italica, and Zygophyllum simplex, and the gut mycobiota of Poekilocerus bufonius (Orthoptera, Pyrgomorphidae, "Usherhopper"). A total of 164,485 fungal reads were observed from the five plant rhizospheres and Usherhopper gut. The highest reads were in S. italica rhizosphere (29,883 reads). Species richness in the P. bufonius gut was the highest among the six samples. Ascomycota was dominant in all samples, with the highest reads in E. desvauxii (26,734 reads) rhizosphere. Sordariomycetes and Dothideomycetes were the dominant classes detected with the highest abundance in C. colocynthis and E. desvauxii rhizospheres. Aspergillus and Ceratobasidium were the most abundant genera in the R. stricta rhizosphere, Fusarium and Penicillium in the E. desvauxii rhizosphere and P. bufonius gut, Ceratobasidium and Myrothecium in the C. colocynthis rhizosphere, Aspergillus and Fusarium in the S. italica rhizosphere, and Cochliobolus in the Z. simplex rhizosphere. Aspergillus terreus was the most abundant species in the R. stricta and S. italica rhizospheres, Fusarium sp. in E. desvauxii rhizosphere, Ceratobasidium sp. in C. colocynthis rhizosphere, Cochliobolus sp. in Z. simplex rhizosphere, and Penicillium sp. in P. bufonius gut. The phylogenetic results revealed the unclassified species were related closely to Ascomycota and the species in E. desvauxii, S. italica and Z. simplex rhizospheres were closely related, where the species in the P. bufonius gut, were closely related to the species in the R. stricta, and C. colocynthis rhizospheres.

Comparative Analysis of Fungal Diversity in Rhizospheric Soil from Wild and Reintroduced Magnolia sinica Estimated via High-Throughput Sequencing

Magnolia sinica is a critically endangered species and considered a “plant species with extremely small populations” (PSESP). It is an endemic species in southeastern Yunnan Province, China, with reproductive barriers. Rhizosphere fungi play a crucial role in plant growth and health. However, the composition, diversity, and function of fungal communities in wild and reintroduced M. sinica rhizospheres remain unknown. In this study, Illumina sequencing of the internal transcribed spacer 2 (ITS2) region was used to analyze rhizospheric soil samples from wild and reintroduced M. sinica. Thirteen phyla, 45 classes, 105 orders, 232 families, and 433 genera of fungi were detected. Basidiomycota and Ascomycota were dominant across all samples. The fungal community composition was similar between the wild and reintroduced rhizospheres, but the fungal taxa relative abundances differed. The fungal community richness was higher in the reintroduced rhizosphere than in the wild rhizosphere, but the diversity showed the opposite pattern. Soil nutrients and leaf litter significantly affected the fungal community composition and functional diversity. Here, the composition, structure, diversity, and ecological functions of the fungal communities in the rhizospheres of wild and reintroduced M. sinica were elucidated for the first time, laying a foundation for future research and endangered species protection.

Forest Soil Fungal Community Elevational Distribution Pattern and Their Ecological Assembly Processes

Soil fungi play vital roles in natural ecosystems, however, their community distribution patterns along different environmental gradients and ecological assembly processes remain unclear. In this study, Illumina MiSeq sequencing was used to investigate the soil fungal community structures of five different forest types along an elevational gradient, and a framework based on a null model was adopted to quantify the relative contribution of deterministic and stochastic ecological assembly processes. The results showed that the majority of soil fungal OTUs were derived from Zygomycota, Basidiomycota, and Ascomycota. Soil fungal community structure differed significantly among the five sites (P < 0.01), and the fungal α-diversity decreased as elevation increased (P < 0.01). The null model showed that the relative contribution of stochastic processes (37.78-73.33%) was higher than that of deterministic processes (26.67-62.22%) within the same forest type, while that of deterministic processes (35.00-93.00%) was higher than stochastic processes (7.00-65.00%) between forest types. These results suggest that forest soil fungal diversity decreased significantly with increasing elevation, and that deterministic processes may be key factors influencing soil fungal community assemblies among forest types. The results of this study provide new insight into soil fungal distribution patterns and community assembly processes in natural forest ecosystems.

Ectomycorrhizal Community on Norway Spruce Seedlings Following Bark Beetle Infestation

Ectomycorrhizal (ECM) fungi importantly influence seedling growth, nutrition, and survival and create an extensive mycelial network interconnecting tree species and enabling resource redistribution. Due to their symbiotic relationship with trees, they are impacted by forest disturbances, which are of increasing relevance due to climate change. The effect of disturbance on seedling colonization and their morphology is still largely unknown. Seedling growth parameters and the ECM fungal assemblage on the roots of Norway spruce (Picea abies (L.) H. Karst.) seedlings were assessed in mature spruce forests attacked and destroyed by bark beetle and in a mature non-attacked forest as a reference. We did not detect significant differences in number of ECM species on seedling roots among forest types, but ECM species composition changed; Tylospora fibrillosa (Burt) Donk, Meliniomyces variabilis Hambl. & Sigler, and Phialocephala fortinii C.J.K. Wang & H.E. Wilcox were characteristic species in the forest destroyed by bark beetle, whereas Lactarius, Cortinarius, and Russula were in the mature forest. Forest type further significantly influenced the height, root length, and root collar thickness of seedlings and the proportion of exploration types of mycorrhizae.

Different revegetation types alter soil physical-chemical characteristics and fungal community in the Baishilazi Nature Reserve

The effects of different revegetation types on soil physical-chemical characteristics and fungal community diversity and composition of soils sampled from five different revegetation types (JM, Juglans mandshurica; QM, Quercus mongolica; conifer-broadleaf forest (CB); LG, Larix gmelinii; PK, Pinus koraiensis) in the Baishilazi Nature Reserve were determined. Soil fungal communities were assessed employing ITS rRNA Illunima Miseq high-throughput sequencing. Responses of the soil fungi community to soil environmental factors were assessed through canonical correspondence analysis (CCA) and Pearson correlation analysis. The coniferous forests (L. gmelinii, P. koraiensis) and CB had reduced soil total carbon (C), total nitrogen (N), and available nitrogen (AN) values compared with the broadleaf forest (J. mandshurica, Q. mongolica). The average fungus diversity according to the Shannon, ACE, Chao1, and Simpson index were increased in the J. mandshurica site. Basidiomycota, Ascomycota, Zygomycota, and Rozellomycota were the dominant fungal taxa in this region. The phylum Basidiomycota was dominant in the Q. mongolica, CB, L. gmelinii, and P. koraiensis sites, while Ascomycota was the dominant phylum in the J. mandshurica site. The clear differentiation of fungal communities and the clustering in the heatmap and in non-metric multidimensional scaling plot showed that broadleaf forests, CB, and coniferous forests harbored different fungal communities. The results of the CCA showed that soil environmental factors, such as soil pH, total C, total N, AN, and available phosphorus (P) greatly influenced the fungal community structure. Based on our results, the different responses of the soil fungal communities to the different revegetation types largely dependent on different forest types and soil physicochemical characteristic in Baishilazi Nature Reserve.

Determinants of Soil Bacterial and Fungal Community Composition Toward Carbon-Use Efficiency Across Primary and Secondary Forests in a Costa Rican Conservation Area

Tropical secondary forests currently represent over half of the world's remaining tropical forests and are critical candidates for maintaining global biodiversity and enhancing potential carbon-use efficiency (CUE) and, thus, carbon sequestration. However, these ecosystems can exhibit multiple successional pathways, which have hindered our understanding of the soil microbial drivers that facilitate improved CUE. To begin to address this, we examined soil % C; % N; C:N ratio; soil microbial biomass C (C_mic); NO₃^-; NH₄⁺; pH; % moisture; % sand, silt, and clay; and elevation, along with soil bacterial and fungal community composition, and determined which soil abiotic properties structure the soil C_mic and the soil bacterial and fungal communities across a primary forest, 33-year-old secondary forest, and 22-year-old young secondary in the Northern Zone of Costa Rica. We provide evidence that soil microbial communities were mostly distinct across the habitat types and that these habitats appear to have affected the soil ectomycorrhizal fungi and the soil microbial groups associated with the degradation of complex carbon compounds. We found that soil C_mic levels increased along the management gradient from young, to old secondary, to primary forest. In addition, the changes in soil C_mic and soil fungal community structure were significantly related to levels of soil NO₃^-. Our analyses showed that even after 33 years of natural forest regrowth, the clearing of tropical forests can have persistent effects on soil microbial communities and that it may take a longer time than we realized for secondary forests to develop carbon-utilization efficiencies similar to that of a primary forest. Our results also indicated that forms of inorganic N may be an important factor in structuring soil C_mic and the soil microbial communities, leading to improved CUE in regenerating secondary forests. This study is the first in the region to highlight some of the factors which appear to be structuring the soil C_mic and soil microbial communities such that they are more conducive for enhanced CUE in secondary forests.

Belowground fungal community diversity and composition associated with Norway spruce along an altitudinal gradient

Altitudinal gradients provide valuable information about the effects of environmental variables on changes in species richness and composition as well as the distribution of below ground fungal communities. Since most knowledge in this respect has been gathered on aboveground communities, we focused our study towards the characterization of belowground fungal communities associated with two different ages of Norway spruce (Picea abies) trees along an altitudinal gradient. By sequencing the internal transcribed spacer (ITS) region on the Illumina platform, we investigated the fungal communities in a floristically and geologically relatively well explored forest on the slope of Mt. Iseler of the Bavarian Alps. From fine roots and rhizosphere of a total of 90 of Norway spruce trees from 18 plots we detected 1285 taxa, with a range of 167 to 506 (average 377) taxa per plot. Fungal taxa are distributed over 96 different orders belonging to the phyla Ascomycota, Basidiomycota, Chrytridiomycota, Glomeromycota, and Mucoromycota. Overall the Agaricales (438 taxa) and Tremellales (81 taxa) belonging to the Basidiomycota and the Hypocreales (65 spp.) and Helotiales (61 taxa) belonging to the Ascomycota represented the taxon richest orders. The evaluation of our multivariate generalized mixed models indicate that the altitude has a significant influence on the composition of the fungal communities (p < 0.003) and that tree age determines community diversity (p < 0.05). A total of 47 ecological guilds were detected, of which the ectomycorrhizal and saprophytic guilds were the most taxon-rich. Our ITS amplicon Illumina sequencing approach allowed us to characterize a high fungal community diversity that would not be possible to capture with fruiting body surveys alone. We conclude that it is an invaluable tool for diverse monitoring tasks and inventorying biodiversity, especially in the detection of microorganisms developing very ephemeral and/or inconspicuous fruiting bodies or lacking them all together. Results suggest that the altitude mainly influences the community composition, whereas fungal diversity becomes higher in mature/older trees. Finally, we demonstrate that novel techniques from bacterial microbiome analyses are also useful for studying fungal diversity and community structure in a DNA metabarcoding approach, but that incomplete reference sequence databases so far limit effective identification.

Experimental Evidence of Functional Group-Dependent Effects of Tree Diversity on Soil Fungi in Subtropical Forests

Deconvoluting the relative contributions made by specific biotic and abiotic drivers to soil fungal community compositions facilitates predictions about the functional responses of ecosystems to environmental changes, such as losses of plant diversity, but it is hindered by the complex interactions involved. Experimental assembly of tree species allows separation of the respective effects of plant community composition (biotic components) and soil properties (abiotic components), enabling much greater statistical power than can be achieved in observational studies. We therefore analyzed these contributions by assessing, via pyrotag sequencing of the internal transcribed spacer (ITS2) rDNA region, fungal communities in young subtropical forest plots included in a large experiment on the effects of tree species richness. Spatial variables and soil properties were the main drivers of soil fungal alpha and beta-diversity, implying strong early-stage environmental filtering and dispersal limitation. Tree related variables, such as tree community composition, significantly affected arbuscular mycorrhizal and pathogen fungal community structure, while differences in tree host species and host abundance affected ectomycorrhizal fungal community composition. At this early stage of the experiment, only a limited amount of carbon inputs (rhizodeposits and leaf litter) was being provided to the ecosystem due to the size of the tree saplings, and persisting legacy effects were observed. We thus expect to find increasing tree related effects on fungal community composition as forest development proceeds.

Toward a methodical framework for comprehensively assessing forest multifunctionality

Biodiversity-ecosystem functioning (BEF) research has extended its scope from communities that are short-lived or reshape their structure annually to structurally complex forest ecosystems. The establishment of tree diversity experiments poses specific methodological challenges for assessing the multiple functions provided by forest ecosystems. In particular, methodological inconsistencies and nonstandardized protocols impede the analysis of multifunctionality within, and comparability across the increasing number of tree diversity experiments. By providing an overview on key methods currently applied in one of the largest forest biodiversity experiments, we show how methods differing in scale and simplicity can be combined to retrieve consistent data allowing novel insights into forest ecosystem functioning. Furthermore, we discuss and develop recommendations for the integration and transferability of diverse methodical approaches to present and future forest biodiversity experiments. We identified four principles that should guide basic decisions concerning method selection for tree diversity experiments and forest BEF research: (1) method selection should be directed toward maximizing data density to increase the number of measured variables in each plot. (2) Methods should cover all relevant scales of the experiment to consider scale dependencies of biodiversity effects. (3) The same variable should be evaluated with the same method across space and time for adequate larger-scale and longer-time data analysis and to reduce errors due to changing measurement protocols. (4) Standardized, practical and rapid methods for assessing biodiversity and ecosystem functions should be promoted to increase comparability among forest BEF experiments. We demonstrate that currently available methods provide us with a sophisticated toolbox to improve a synergistic understanding of forest multifunctionality. However, these methods require further adjustment to the specific requirements of structurally complex and long-lived forest ecosystems. By applying methods connecting relevant scales, trophic levels, and above- and belowground ecosystem compartments, knowledge gain from large tree diversity experiments can be optimized.

Comparative metagenomics approaches to characterize the soil fungal communities of western coastal region, Saudi Arabia

A total of 145007 reads were obtained from pyrosequencing for all the 4 samples. The total count ranged from 11,301,014 (Mecca old road) to 23,503,512 bp (Thuwal). A total of 460 fungal species belonging to 133 genera, 58 families, 33 orders, 13 classes and 4 phyla was identified across the four sites. The most abundant phylum at all four sites was Ascomycota followed by Basidiomycota. Four phyla (Ascomycota—99.31%, Basidiomycota—0.59%, Chytridiomycota—0.04%, Glomeromycota—0.03%) were detected in Khulais. Except for Glomeromycota, all phyla were detected at Mecca old road (Ascomycota—74.26%, Basidiomycota—25.71%, Chytridiomycota—0.01%) and Thuwal (Ascomycota—99.59%, Basidiomycota—0.40%, Chytridiomycota—0.002%); while only Ascomycota—90.98% and Basidiomycota—9.01% were detected in Asfan road. At the class level, Sordariomycetes was predominantly observed at Asfan road—59.88%, Khulais—68.26% and Thuwal—94.84%; while Pezizomycetes was dominant at Mecca old road—56.01%, was absent at Asfan road. Agaricomycetes was present only at Mecca old road—25.73%; while Tremellomycetes—5.77%, Malasseizomycetes—2.13% and Microbotryomycetes—1.10% were found only at Asfan road. The phylogenetic trees revealed that clear genus level differences are visible across all the four sites, with an overall predominance of Thielavia followed by Madurella, Aspergillus, and Gelasinospora. Chaetomium sp., Aspergillus caespitosus and Aspergillus sp. were found in moderate (Mecca old road and Thuwal) to abundant (Asfan road and Khulais) quantities. Thielavia sp., Thielavia hyalocarpa and Madurella sp. are found in moderate quantities at Khulais and Mecca old road, while in abundant levels at Asfan road and Thuwal. Fusarium equisati and F. oxysporum were detected at Thuwal and Khulais. Sordaria araneosa was present at Khulais, while Malasseiza globosa species was detected in moderate quantities across all sites except Khulais.

Belowground top-down and aboveground bottom-up effects structure multitrophic community relationships in a biodiverse forest

Ecosystem functioning and human well-being critically depend on numerous species interactions above- and belowground. However, unraveling the structure of multitrophic interaction webs at the ecosystem level is challenging for biodiverse ecosystems. Attempts to identify major relationships between trophic levels usually rely on simplified proxies, such as species diversity. Here, we propose to consider the full information on species composition across trophic levels, using Procrustes correlation and structural equation models. We show that species composition data of a highly diverse subtropical forest―with 5,716 taxa across 25 trophic groups― reveal strong interrelationships among plants, arthropods, and microorganisms, indicating complex multitrophic interactions. We found substantial support for top-down effects of microorganisms belowground, indicating important feedbacks of microbial symbionts, pathogens, and decomposers on plant communities. In contrast, aboveground pathways were characterized by bottom-up control of plants on arthropods, including many non-trophic links. Additional analyses based on diversity patterns revealed much weaker interrelationships. Our study suggests that multitrophic communities in our forest system are structured via top-down effects of belowground biota on plants, which in turn affect aboveground arthropod communities across trophic levels. Moreover, the study shows that the consequences of species loss will be more complex than indicated by studies based solely on diversity.

Characterization of Unexplored Deadwood Mycobiome in Highly Diverse Subtropical Forests Using Culture-independent Molecular Technique

The deadwood mycobiome, also known as wood-inhabiting fungi (WIF), are among the key players in wood decomposition, having a large impact on nutrient cycling in forest soils. However, our knowledge of WIF richness and distribution patterns in different forest biomes is limited. Here, we used pyrotag sequencing of the fungal internal transcribed spacer (ITS2) region to characterize the deadwood mycobiome of two tree species with greatly different wood characteristics (Schima superba and Pinus massoniana) in a Chinese subtropical forest ecosystem. Specifically, we tested (i) the effects of tree species and wood quality properties on WIF OTU richness and community composition; (ii) the role of biotic and abiotic factors in shaping the WIF communities; and (iii) the relationship between WIF OTU richness, community composition and decomposition rates. Due to different wood chemical properties, we hypothesized that the WIF communities derived from the two tree species would be correlated differently with biotic and abiotic factors. Our results show that deadwood in subtropical forests harbors diverse fungal communities comprising six ecological functional groups. We found interesting colonization patterns for this subtropical biome, where Resinicium spp. were highly detected in both broadleaved and coniferous deadwood. In addition, the members of Xylariales were frequently found in Schima. The two deadwood species differed significantly in WIF OTU richness (Pinus > Schima) and community composition (P < 0.001). Variations in WIF community composition of both tree species were significantly explained by wood pH and ecological factors (biotic: deadwood species, basal area and abiotic: soil pH), but the WIF communities derived from each tree species correlated differently with abiotic factors. Interestingly, we found that deadwood decomposition rate significantly correlated with WIF communities and negatively correlated with WIF OTU richness. We conclude that the pattern of WIF OTU richness and community composition are controlled by multiple interacting biotic and abiotic factors. Overall, our study provides an in-depth picture of the deadwood mycobiome in this subtropical forest. Furthermore, by comparing our results to results from temperate and boreal forests we contribute to a better understanding of patterns of WIF communities across different biomes and geographic locations.

Tree species, tree genotypes and tree genotypic diversity levels affect microbe-mediated soil ecosystem functions in a subtropical forest

Tree species identity and tree genotypes contribute to the shaping of soil microbial communities. However, knowledge about how these two factors influence soil ecosystem functions is still lacking. Furthermore, in forest ecosystems tree genotypes co-occur and interact with each other, thus the effects of tree genotypic diversity on soil ecosystem functions merit attention. Here we investigated the effects of tree species, tree genotypes and genotypic diversity levels, alongside soil physicochemical properties, on the overall and specific soil enzyme activity patterns. Our results indicate that tree species identity, tree genotypes and genotypic diversity level have significant influences on overall and specific soil enzyme activity patterns. These three factors influence soil enzyme patterns partly through effects on soil physicochemical properties and substrate quality. Variance partitioning showed that tree species identity, genotypic diversity level, pH and water content all together explained ~30% variations in the overall patterns of soil enzymes. However, we also found that the responses of soil ecosystem functions to tree genotypes and genotypic diversity are complex, being dependent on tree species identity and controlled by multiple factors. Our study highlights the important of inter- and intra-specific variations in tree species in shaping soil ecosystem functions in a subtropical forest.

Enhancing our understanding of anatomical diversity in Tomentella ectomycorrhizas: characterization of six new morphotypes

Ectomycorrhizas (ECM) formed by Tomentella species (Thelephorales, Basidiomycota) were collected in beech forests of Hungary and studied using anatomical and molecular phylogenetic methods. The mycobionts were identified by analysing the sequences of nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) regions together with sequences obtained from public databases. At the sampling plots, we found the occurrence of 11 Tomentella morphotypes. Among these, six morphotypes (four identified, Tomentella atroarenicolor, Tomentella bryophila, Tomentella lapida, Tomentella subclavigera, and two unidentified) were morpho-anatomically characterized for the first time. Although the six morphotypes differed anatomically from each other and from Tomentella ectomycorrhizas described previously, they shared anatomical features common to tomentelloid ectomycorrhizas fungi. These results expand our understanding of the diversity of this widely distributed ectomycorrhizal genus.

Diversity and spatial structure of belowground plant-fungal symbiosis in a mixed subtropical forest of ectomycorrhizal and arbuscular mycorrhizal plants

Plant-mycorrhizal fungal interactions are ubiquitous in forest ecosystems. While ectomycorrhizal plants and their fungi generally dominate temperate forests, arbuscular mycorrhizal symbiosis is common in the tropics. In subtropical regions, however, ectomycorrhizal and arbuscular mycorrhizal plants co-occur at comparable abundances in single forests, presumably generating complex community structures of root-associated fungi. To reveal root-associated fungal community structure in a mixed forest of ectomycorrhizal and arbuscular mycorrhizal plants, we conducted a massively-parallel pyrosequencing analysis, targeting fungi in the roots of 36 plant species that co-occur in a subtropical forest. In total, 580 fungal operational taxonomic units were detected, of which 132 and 58 were probably ectomycorrhizal and arbuscular mycorrhizal, respectively. As expected, the composition of fungal symbionts differed between fagaceous (ectomycorrhizal) and non-fagaceous (possibly arbuscular mycorrhizal) plants. However, non-fagaceous plants were associated with not only arbuscular mycorrhizal fungi but also several clades of ectomycorrhizal (e.g., Russula) and root-endophytic ascomycete fungi. Many of the ectomycorrhizal and root-endophytic fungi were detected from both fagaceous and non-fagaceous plants in the community. Interestingly, ectomycorrhizal and arbuscular mycorrhizal fungi were concurrently detected from tiny root fragments of non-fagaceous plants. The plant-fungal associations in the forest were spatially structured, and non-fagaceous plant roots hosted ectomycorrhizal fungi more often in the proximity of ectomycorrhizal plant roots. Overall, this study suggests that belowground plant-fungal symbiosis in subtropical forests is complex in that it includes "non-typical" plant-fungal combinations (e.g., ectomycorrhizal fungi on possibly arbuscular mycorrhizal plants) that do not fall within the conventional classification of mycorrhizal symbioses, and in that associations with multiple functional (or phylogenetic) groups of fungi are ubiquitous among plants. Moreover, ectomycorrhizal fungal symbionts of fagaceous plants may "invade" the roots of neighboring non-fagaceous plants, potentially influencing the interactions between non-fagaceous plants and their arbuscular-mycorrhizal fungal symbionts at a fine spatial scale.