The mid-domain effect in ectomycorrhizal fungi: range overlap along an elevation gradient on Mount Fuji, Japan

Host Phylogeny Is a Major Determinant of Fagaceae-Associated Ectomycorrhizal Fungal Community Assembly at a Regional Scale

Environmental filtering (niche process) and dispersal limitation (neutral process) are two of the primary forces driving community assembly in ecosystems, but how these processes affect the Fagaceae-associated ectomycorrhizal (EM) fungal community at regional scales is so far poorly documented. We examined the EM fungal communities of 61 plant species in six genera belonging to the Fagaceae distributed across Chinese forest ecosystems (geographic distance up to ∼3,757 km) using Illumina Miseq sequencing of ITS2 sequences. The relative effects of environmental filtering (e.g., host plant phylogeny, soil and climate) and dispersal limitation (e.g., spatial distance) on the EM fungal community were distinguished using multiple models. In total, 2,706 operational taxonomic units (OTUs) of EM fungi, corresponding to 54 fungal lineages, were recovered at a 97% sequence similarity level. The EM fungal OTU richness was significantly affected by soil pH and nutrients and by host phylogeny. The EM fungal community composition was significantly influenced by combinations of host phylogeny, spatial distance, soil and climate. Furthermore, host phylogeny had the greatest effect on EM fungal community. The study suggests that the assembly of the EM fungal community is governed by both environmental filtering and dispersal limitation, with host effect being the most important determinant at the regional scale.

Climate stability is more important than water-energy variables in shaping the elevational variation in species richness

Changes in climate variables have an important impact on the prediction and protection of elevational biodiversity. Gaps exist in our understanding of the elevational distribution patterns in seed plant species richness. Our study examines the importance of climate variables in shaping the elevational variation in species richness. The importance of boundary constraint was also taken into account. Model selection based on Akaike's information criterion was used to select the best explaining climate models. Variation partitioning was used to assess the independent and joint effects of water-energy, physiological tolerance, and environmental stability variables on species richness. Our results revealed that: (a) Both raw (boundary constraint unreduced) and estimated (boundary constraint reduced) species richness showed large elevational variation, with the peak species richness seen at midelevations. The environmental variables were better at explaining the distribution pattern of species richness along the elevation, when the effect of boundary constraint was reduced; (b) the physiological tolerance and environmental stability variables explained more variation in raw and estimated species richness compared with the water-energy variables. Estimated species richness was better explained (98.6%) by the environmental variables than raw species richness (94%); (c) the water-related variables generally had the highest independent effect on raw and estimated species richness and were dominant in shaping the elevational variation in species richness. Our findings quantify the influence of boundary constraint on the distribution pattern of species along an altitudinal gradient and compare the relative contributions of environmental stability and water-energy in explaining the altitude gradient distribution pattern of plant seed species.

Soil pH determines fungal diversity along an elevation gradient in Southwestern China

Fungi play important roles in ecosystem processes, and the elevational pattern of fungal diversity is still unclear. Here, we examined the diversity of fungi along a 1,000 m elevation gradient on Mount Nadu, Southwestern China. We used MiSeq sequencing to obtain fungal sequences that were clustered into operational taxonomic units (OTUs) and to measure the fungal composition and diversity. Though the species richness and phylogenetic diversity of the fungal community did not exhibit significant trends with increasing altitude, they were significantly lower at mid-altitudinal sites than at the base. The Bray-Curtis distance clustering also showed that the fungal communities varied significantly with altitude. A distance-based linear model multivariate analysis (DistLM) identified that soil pH dominated the explanatory power of the species richness (23.72%), phylogenetic diversity (24.25%) and beta diversity (28.10%) of the fungal community. Moreover, the species richness and phylogenetic diversity of the fungal community increased linearly with increasing soil pH (P<0.05). Our study provides evidence that pH is an important predictor of soil fungal diversity along elevation gradients in Southwestern China.

Tree species identity and diversity drive fungal richness and community composition along an elevational gradient in a Mediterranean ecosystem

Ecological and taxonomic knowledge is important for conservation and utilization of biodiversity. Biodiversity and ecology of fungi in Mediterranean ecosystems is poorly understood. Here, we examined the diversity and spatial distribution of fungi along an elevational gradient in a Mediterranean ecosystem, using DNA metabarcoding. This study provides novel information about diversity of all ecological and taxonomic groups of fungi along an elevational gradient in a Mediterranean ecosystem. Our analyses revealed that among all biotic and abiotic variables tested, host species identity is the main driver of the fungal richness and fungal community composition. Fungal richness was strongly associated with tree richness and peaked in Quercus-dominated habitats and Cistus-dominated habitats. The highest taxonomic richness of ectomycorrhizal fungi was observed under Quercus ilex, whereas the highest taxonomic richness of saprotrophs was found under Pinus. Our results suggest that the effect of plant diversity on fungal richness and community composition may override that of abiotic variables across environmental gradients.

Root-associated fungal communities in three Pyroleae species and their mycobiont sharing with surrounding trees in subalpine coniferous forests on Mount Fuji, Japan

Pyroleae species are perennial understory shrubs, many of which are partial mycoheterotrophs. Most fungi colonizing Pyroleae roots are ectomycorrhizal (ECM) and share common mycobionts with their Pyroleae hosts. However, such mycobiont sharing has neither been examined in depth before nor has the interspecific variation in sharing among Pyroleae species. Here, we examined root-associated fungal communities in three co-existing Pyroleae species, including Pyrola alpina, Pyrola incarnata, and Orthilia secunda, with reference to co-existing ECM fungi on the surrounding trees in the same soil blocks in subalpine coniferous forests. We identified 42, 75, and 18 fungal molecular operational taxonomic units in P. alpina, P. incarnata, and O. secunda roots, respectively. Mycobiont sharing with surrounding trees, which was defined as the occurrence of the same mycobiont between Pyroleae and surrounding trees in each soil block, was most frequent among P. incarnata (31 of 44 plants). In P. alpina, sharing was confirmed in 12 of 37 plants, and the fungal community was similar to that of P. incarnata. Mycobiont sharing was least common in O. secunda, found in only 5 of 32 plants. Root-associated fungi of O. secunda were dominated by Wilcoxina species, which were absent from the surrounding ECM roots in the same soil blocks. These results indicate that mycobiont sharing with surrounding trees does not equally occur among Pyroleae plants, some of which may develop independent mycorrhizal associations with ECM fungi, as suggested in O. secunda at our research sites.

Convergence and contrast in the community structure of Bacteria, Fungi and Archaea along a tropical elevation-climate gradient

Changes in species richness along climatological gradients have been instrumental in developing theories about the general drivers of biodiversity. Previous studies on microbial communities along climate gradients on mountainsides have revealed positive, negative and neutral richness trends. We examined changes in richness and composition of Fungi, Bacteria and Archaea in soil along a 50-1000 m elevation, 280-3280 mm/yr precipitation gradient in Hawai'i. Soil properties and their drivers are exceptionally well understood along this gradient. All three microbial groups responded strongly to the gradient, with community ordinations being similar along axes of environmental conditions (pH, rainfall) and resource availability (nitrogen, phosphorus). However, the form of the richness-climate relationship varied between Fungi (positive linear), Bacteria (unimodal) and Archaea (negative linear). These differences were related to resource-ecology and limiting conditions for each group, with fungal richness increasing most strongly with soil carbon, ammonia-oxidizing Archaea increasing with nitrogen mineralization rate, and Bacteria increasing with both carbon and pH. Reponses to the gradient became increasingly variable at finer taxonomic scales and within any taxonomic group most individual OTUs occurred in narrow climate-elevation ranges. These results show that microbial responses to climate gradients are heterogeneous due to complexity of underlying environmental changes and the diverse ecologies of microbial taxa.

The ectomycorrhizal fungal communities associated with Quercus liaotungensis in different habitats across northern China

Quercus liaotungensis is a major tree species in deciduous broad-leaved forests in northern China. In this study, we investigated ectomycorrhizal (ECM) communities associated with Q. liaotungensis from five typical habitats across northern China. We used internal transcribed spacer-polymerase chain reaction and DNA sequencing to identify ECM fungi, and we detected 220 operational taxonomic units. In general, at the regional scale, the dominant ECM lineages were /tomentella-thelephora, /cenococcum, /russula-lactarius, and /inocybe. Analysis of variance demonstrated significant differences in alpha diversity among these ECM communities, and the ECM fungal richness was positively correlated with elevation and soil organic matter. Analysis of similarity and a nonmetric multidimensional scaling analysis revealed that there were significant differences in community composition, and the geographical distance was correlated with the ECM fungal communities. Among the environmental factors we studied, soil parameters and climate factors were the primary direct driving factors of the ECM fungal communities. Our study primarily advances our understanding of environmental factors affecting ECM fungal communities at regional scale.

Diversity and community structure of ectomycorrhizal fungi associated with Larix chinensis across the alpine treeline ecotone of Taibai Mountain

Alpine treeline ecotones represent ecosystems that are vulnerable to climate change. We investigated the ectomycorrhizal (ECM) community, which has potential to stabilize alpine ecosystems. ECM communities associated with Larix chinensis were studied in four zones along a natural ecotone from a mixed forest stand over pure forest stands, the timberline, and eventually, the treeline (3050-3450 m) in Tabai Mountain, China. Sixty operational taxonomic units (OTUs) of ECM fungi were identified by sequencing the rDNA internal transcribed spacer of ECM tips. The richness of ECM species increased with elevation. The soil C/N ratio was the most important factor explaining ECM species richness. The treeline zone harbored some unique ECM fungi whereas no unique genera were observed in the timberline and pure forest zone. Elevation and topography were equally important factors influencing ECM communities in the alpine region. We suggest that a higher diversity of the ECM fungal community associated with L. chinensis in the treeline zone could result from niche differentiation.

Changes in richness and community composition of ectomycorrhizal fungi among altitudinal vegetation types on Mount Kinabalu in Borneo

The distribution patterns of tropical ectomycorrhizal (ECM) fungi along altitudinal gradients remain largely unknown. Furthermore, despite being an iconic site for biodiversity research, virtually nothing is known about the diversity and spatial patterns of fungi on Mt Kinabalu and neighbouring mountain ranges. We carried out deep DNA sequencing of soil samples collected between 425 and 4000 m above sea level to compare richness and community composition of ECM fungi among altitudinal forest types in Borneo. In addition, we tested whether the observed patterns are driven by habitat or by geometric effect of overlapping ranges of species (mid-domain effect). Community composition of ECM fungi was strongly correlated with elevation. In most genera, richness peaked in the mid-elevation montane forest zone, with the exception of tomentelloid fungi, which showed monotonal decrease in richness with increasing altitude. Richness in lower-mid- and mid-elevations was significantly greater than predicted under the mid-domain effect model. We provide the first insight into the composition of ECM fungal communities and their strong altitudinal turnover in Borneo. The high richness and restricted distribution of many ECM fungi in the montane forests suggest that mid-elevation peak richness is primarily driven by environmental characteristics of this habitat and not by the mid-domain effect.

Soil nematodes show a mid-elevation diversity maximum and elevational zonation on Mt. Norikura, Japan

Little is known about how nematode ecology differs across elevational gradients. We investigated the soil nematode community along a ~2,200 m elevational range on Mt. Norikura, Japan, by sequencing the 18S rRNA gene. As with many other groups of organisms, nematode diversity showed a high correlation with elevation, and a maximum in mid-elevations. While elevation itself, in the context of the mid domain effect, could predict the observed unimodal pattern of soil nematode communities along the elevational gradient, mean annual temperature and soil total nitrogen concentration were the best predictors of diversity. We also found nematode community composition showed strong elevational zonation, indicating that a high degree of ecological specialization that may exist in nematodes in relation to elevation-related environmental gradients and certain nematode OTUs had ranges extending across all elevations, and these generalized OTUs made up a greater proportion of the community at high elevations – such that high elevation nematode OTUs had broader elevational ranges on average, providing an example consistent to Rapoport’s elevational hypothesis. This study reveals the potential for using sequencing methods to investigate elevational gradients of small soil organisms, providing a method for rapid investigation of patterns without specialized knowledge in taxonomic identification.

Mushroom biomass and diversity are driven by different spatio-temporal scales along Mediterranean elevation gradients

Mushrooms are important non-wood-forest-products in many Mediterranean ecosystems, being highly vulnerable to climate change. However, the ecological scales of variation of mushroom productivity and diversity, and climate dependence has been usually overlooked due to a lack of available data. We determined the spatio-temporal variability of epigeous sporocarps and the climatic factors driving their fruiting to plan future sustainable management of wild mushrooms production. We collected fruiting bodies in Pinus sylvestris stands along an elevation gradient for 8 consecutive years. Overall, sporocarp biomass was mainly dependent on inter-annual variations, whereas richness was more spatial-scale dependent. Elevation was not significant, but there were clear elevational differences in biomass and richness patterns between ectomycorrhizal and saprotrophic guilds. The main driver of variation was late-summer-early-autumn precipitation. Thus, different scale processes (inter-annual vs. spatial-scale) drive sporocarp biomass and diversity patterns; temporal effects for biomass and ectomycorrhizal fungi vs. spatial scale for diversity and saprotrophic fungi. The significant role of precipitation across fungal guilds and spatio-temporal scales indicates that it is a limiting resource controlling sporocarp production and diversity in Mediterranean regions. The high spatial and temporal variability of mushrooms emphasize the need for long-term datasets of multiple spatial points to effectively characterize fungal fruiting patterns.

First detection of Endogone ectomycorrhizas in natural oak forests

The order Endogonales in Mucoromycotina, an early divergent lineage of fungi, includes ectomycorrhizal (EM) fungi. This order is therefore considered a key taxon for elucidation of the evolution of EM associations. Recent studies have revealed high diversity of EM lineages of Basidiomycota and Ascomycota; however, EM associations of Endogonales and its relatives remain largely unknown. In this study, EM root tips with a unique fungal sheath, with aseptate and highly branched hyphae of variable widths, were identified in Quercus acutissima and Quercus crispula forests in the temperate zone of Japan. The mycobionts were confirmed as Endogone sp., which were placed as a sister clade of Endogone pisiformis, based on phylogenetic analyses of the small and large subunits of the nuclear ribosomal RNA and elongation factor-1α genes. This is the first report of EM of Endogone in natural forests of the Northern Hemisphere and the first finding on Quercus.

Pyrola japonica, a partially mycoheterotrophic Ericaceae, has mycorrhizal preference for russulacean fungi in central Japan

Mycorrhizal symbiosis often displays low specificity, except for mycoheterotrophic plants that obtain carbon from their mycorrhizal fungi and often have higher specificity to certain fungal taxa. Partially mycoheterotrophic (or mixotrophic, MX) plant species tend to have a larger diversity of fungal partners, e.g., in the genus Pyrola (Monotropoideae, Ericaceae). Preliminary evidence however showed that the Japanese Pyrola japonica has preference for russulacean fungi based on direct sequencing of the fungal internal transcribed spacer (ITS) region from a single site. The present study challenges this conclusion using (1) sampling of P. japonica in different Japanese regions and forest types and (2) fungal identification by ITS cloning. Plants were sampled from eight sites in three regions, in one of which the fungal community on tree ectomycorrhizal (ECM) tips surrounding P. japonica was also analyzed. In all, 1512 clone sequences were obtained successfully from 35 P. japonica plants and 137 sequences from ECM communities. These sequences were collectively divided into 74 molecular operational taxonomic units (MOTUs) (51 and 33 MOTUs, respectively). MOTUs from P. japonica involved 36 ECM taxa (96 % of all clones), and 17 of these were Russula spp. (76.2 % of all clones), which colonized 33 of the 35 sampled plants. The MOTU composition significantly differed between P. japonica and ECM tips, although shared species represented 26.3 % of the ECM tips community in abundance. This suggests that P. japonica has a preference for russulacean fungi.

Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient

Mountain elevation gradients are invaluable sites for understanding the effects of climate change on ecosystem function, community structure and distribution. However, relatively little is known about the impact on soil microbial communities, in spite of their importance for the functioning of the soil ecosystem. Previous studies of microbial diversity along elevational gradients were often limited by confounding variables such as vegetation, pH, and nutrients. Here, we utilised a transect in the Pyrenees established to minimise variation in such parameters, to examine prokaryotic, fungal, protist and metazoan communities throughout three consecutive years. We aimed to determine the influences of climate and environmental parameters on soil microbial community structure; as well as on the relationships between those microbial communities. Further, functional diversity of heterotrophic bacteria was determined using Biolog. Prokaryotic and fungal community structure, but not alpha-diversity, correlated significantly with elevation. However, carbon-to-nitrogen ratio and pH appeared to affect prokaryotic and protist communities more strongly. Both community structure and physicochemical parameters varied considerably between years, illustrating the value of long-term monitoring of the dynamic processes controlling the soil ecosystem. Our study also illustrates both the challenges and strengths of using microbial communities as indicators of potential impacts of climate change.

Belowground responses to elevation in a changing cloud forest

Few studies have investigated how soil fungal communities respond to elevation, especially within TMCF (tropical montane cloud forests). We used an elevation gradient in a TMCF in Costa Rica to determine how soil properties, processes, and community composition of fungi change in response to elevation and across seasons. As elevation increased, soil temperature and soil pH decreased, while soil moisture and soil C:N ratios increased with elevation. Responses of these properties varied seasonally. Fungal abundance increased with elevation during wet and dry seasons. Fungal community composition shifted in response to elevation, and to a lesser extent by season. These shifts were accompanied by varying responses of important fungal functional groups during the wet season and the relative abundance of certain fungal phyla. We suggest that elevation and the responses of certain fungal functional groups may be structuring fungal communities along this elevation gradient. TMCF are ecosystems that are rapidly changing due to climate change. Our study suggests that these changes may affect how fungal communities are structured.

Soil propagule banks of ectomycorrhizal fungi share many common species along an elevation gradient

We conducted bioassay experiments to investigate the soil propagule banks of ectomycorrhizal (EM) fungi in old-growth forests along an elevation gradient and compared the elevation pattern with the composition of EM fungi on existing roots in the field. In total, 150 soil cores were collected from three forests on Mt. Ishizuchi, western Japan, and subjected to bioassays using Pinus densiflora and Betula maximowicziana. Using molecular analyses, we recorded 23 EM fungal species in the assayed propagule banks. Eight species (34.8 %) were shared across the three sites, which ranged from a warm-temperate evergreen mixed forest to a subalpine conifer forest. The elevation pattern of the assayed propagule banks differed dramatically from that of EM fungi on existing roots along the same gradient, where only a small proportion of EM fungal species (3.5 %) were shared across sites. The EM fungal species found in the assayed propagule banks included many pioneer fungal species and composition differed significantly from that on existing roots. Furthermore, only 4 of 23 species were shared between the two host species, indicating a strong effect of bioassay host identity in determining the propagule banks of EM fungi. These results imply that the assayed propagule bank is less affected by climate compared to EM fungal communities on existing roots. The dominance of disturbance-dependent fungal species in the assayed propagule banks may result in higher ecosystem resilience to disturbance even in old-growth temperate forests.

Disentangling the relative importance of host tree community, abiotic environment and spatial factors on ectomycorrhizal fungal assemblages along an elevation gradient

Recent studies have shown that changes in community compositions of ectomycorrhizal (ECM) fungi along elevation gradients are mainly affected by changes in host tree communities and/or in abiotic environments. However, few studies have taken the effects of processes related to fungal dispersal (i.e. spatial processes) into account and distinguished the effects of host community, abiotic environment and spatial processes on community composition along elevation gradients. This has left unclear the relative importance of these factors in structuring the ECM community assemblages. To address this, we investigated the community composition of ECM fungi along an elevation gradient in northern Japan with 454 meta-barcoding. We found that the community composition of ECM fungi changed along the elevation and that all three factors jointly affected the compositional changes. We separated the magnitude of importance of the three factors in structuring ECM fungal communities and found that most of the spatial variation in ECM fungal community was explained by host communities and abiotic environments. Our results suggest that while biotic and/or abiotic environments can be important factors in determining the ECM fungal community composition along an elevation gradient, spatial processes may also be a primary determinant.

Local adaptation in migrated interior Douglas-fir seedlings is mediated by ectomycorrhizas and other soil factors

Separating edaphic impacts on tree distributions from those of climate and geography is notoriously difficult. Aboveground and belowground factors play important roles, and determining their relative contribution to tree success will greatly assist in refining predictive models and forestry strategies in a changing climate. In a common glasshouse, seedlings of interior Douglas-fir (Pseudotsuga menziesii var. glauca) from multiple populations were grown in multiple forest soils. Fungicide was applied to half of the seedlings to separate soil fungal and nonfungal impacts on seedling performance. Soils of varying geographic and climatic distance from seed origin were compared, using a transfer function approach. Seedling height and biomass were optimized following seed transfer into drier soils, whereas survival was optimized when elevation transfer was minimised. Fungicide application reduced ectomycorrhizal root colonization by c. 50%, with treated seedlings exhibiting greater survival but reduced biomass. Local adaptation of Douglas-fir populations to soils was mediated by soil fungi to some extent in 56% of soil origin by response variable combinations. Mediation by edaphic factors in general occurred in 81% of combinations. Soil biota, hitherto unaccounted for in climate models, interacts with biogeography to influence plant ranges in a changing climate.

Strong effect of climate on ectomycorrhizal fungal composition: evidence from range overlap between two mountains

Separating the effects of environmental factors and spatial distance on microbial composition is difficult when these factors covary. We examined the composition of ectomycorrhizal (EM) fungi along elevation gradients on geographically distant mountains to clarify the effect of climate at the regional scale. Soil cores were collected from various forest types along an elevation gradient in southwestern Japan. Fungal species were identified by the internal transcribed spacer regions of the rDNA using direct sequencing. The occurrence of fungal species in this study was compared with a previous study conducted on a mountain separated by ∼550 km. In total, we recorded 454 EM fungi from 330 of 350 soil cores. Forty-seven fungal species (∼20% of the total excluding singletons) were shared between two mountains, mostly between similar forest types on both mountains. Variation partitioning in redundancy analysis revealed that climate explained the largest variance in EM fungal composition. The similarity of forest tree composition, which is usually determined by climatic conditions, was positively correlated with the similarity of the EM fungal composition. However, the lack of large host effects implied that communities of forest trees and EM fungi may be determined independently by climate. Our data provide important insights that host plants and mutualistic fungi may respond to climate change idiosyncratically, potentially altering carbon and nutrient cycles in relation to the plant-fungus associations.

Strong altitudinal partitioning in the distributions of ectomycorrhizal fungi along a short (300 m) elevation gradient

Changes in species richness and distributions of ectomycorrhizal (ECM) fungal communities along altitudinal gradients have been attributed to changes in both host distributions and abiotic variables. However, few studies have considered altitudinal relationships of ECM fungi associated with a single host to identify the role of abiotic drivers. To address this, ECM fungal communities associated with one host were assessed along five altitudinal transects in Scotland. Roots of Scots pine (Pinus sylvestris) were collected from sites between 300 and 550-600 m altitude, and ECM fungal communities were identified by 454 pyrosequencing of the fungal internal transcribed spacer (ITS) region. Soil moisture, temperature, pH, carbon : nitrogen (C : N) ratio and organic matter content were measured as potential predictors of fungal species richness and community composition. Altitude did not affect species richness of ECM fungal communities, but strongly influenced fungal community composition. Shifts in community composition along the altitudinal gradient were most clearly related to changes in soil moisture and temperature. Our results show that a 300 m altitudinal gradient produced distinct shifts in ECM fungal communities associated with a single host, and that this pattern was strongly related to climatic variables. This finding suggests significant climatic niche partitioning among ECM fungal species.