Factors related to diversity of decomposer fungi in tropical forests

Recent studies suggest that host-preferences are common among certain groups of tropical fungal decomposers but rare in others, and sometimes occur where we least expect them. Host preferences among microfungi and ascomycetes that decompose leaf litter are common but usually involve differences in relative frequencies more than presence/absence, so their diversity may be loosely correlated with species richness of host trees. Strong host-specificity appears to be rare among wood decomposer fungi, whereas characteristics of their substrata and habitat are very important for this group. Anthropogenic disturbance predisposed a tropical forest to subsequent hurricane damage, and the resulting direct and indirect effects on host diversity and habitat heterogeneity were reflected in the decomposer fungal community more than sixty years after the original disturbance. While species richness of dictyostelid slime molds and functional diversity of their bacterial prey increased with disturbance, the more diverse microfungi and ascomycetes were apparently negatively affected by disturbance.     

Phylogenetic congruence between subtropical trees and their associated fungi

Recent studies have detected phylogenetic signals in pathogen–host networks for both soil‐borne and leaf‐infecting fungi, suggesting that pathogenic fungi may track or coevolve with their preferred hosts. However, a phylogenetically concordant relationship between multiple hosts and multiple fungi in has rarely been investigated. Using next‐generation high‐throughput DNA sequencing techniques, we analyzed fungal taxa associated with diseased leaves, rotten seeds, and infected seedlings of subtropical trees. We compared the topologies of the phylogenetic trees of the soil and foliar fungi based on the internal transcribed spacer (ITS) region with the phylogeny of host tree species based on matK, rbcL, atpB, and 5.8S genes. We identified 37 foliar and 103 soil pathogenic fungi belonging to the Ascomycota and Basidiomycota phyla and detected significantly nonrandom host–fungus combinations, which clustered on both the fungus phylogeny and the host phylogeny. The explicit evidence of congruent phylogenies between tree hosts and their potential fungal pathogens suggests either diffuse coevolution among the plant–fungal interaction networks or that the distribution of fungal species tracked spatially associated hosts with phylogenetically conserved traits and habitat preferences. Phylogenetic conservatism in plant–fungal interactions within a local community promotes host and parasite specificity, which is integral to the important role of fungi in promoting species coexistence and maintaining biodiversity of forest communities.     

Host and habitat preferences of polypore fungi in Micronesian tropical flooded forests

The distribution and ecological impacts of plant-associated fungi is determined in large part by their degree of specificity for particular host species or environmental conditions. Here we evaluate the host and habitat preferences among the Aphyllophorales, a guild of wood-decay basidiomycete fungi usually considered to be host generalists. We determined the patterns of host association in three well-defined, floristically distinct, tropical wetlands — freshwater forested wetlands, saltwater mangrove forests, and peatlands with scattered trees — on the islands of Kosrae and Pohnpei in the Federated States of Micronesia. Of 33 fungal species, 20 were locally rare. Of the 11 species sufficiently common to evaluate habitat specificity, nine showed significant habitat preferences. Of eight species common enough to evaluate within-habitat host specificity, six showed strong host preferences. All except one of the nine habitat-specialized fungi showed either statistically significant host specificity or strong numerical biases toward single host species. Our results suggest that host preferences may be important in shaping the assemblages of wood-decay fungi, and that the effect of environment on the distribution of susceptible plant species, rather on the fungi themselves, may ultimately drive the apparent habitat specificity of many fungi.     

Neighboring trees regulate the root‐associated pathogenic fungi on the host plant in a subtropical forest

Root‐associated fungi and host‐specific pathogens are major determinants of species coexistence in forests. Phylogenetically related neighboring trees can strongly affect the fungal community structure of the host plant, which, in turn, will affect the ecological processes. Unfortunately, our understanding of the factors influencing fungal community composition in forests is still limited. In particular, investigation of the relationship between the phytopathogenic fungal community and neighboring trees is incomplete. In the current study, we tested the host specificity of members of the root‐associated fungal community collected from seven tree species and determined the influence of neighboring trees and habitat variation on the composition of the phytopathogenic fungal community of the focal plant in a subtropical evergreen forest. Using high‐throughput sequencing data with respect to the internal transcribed spacer (ITS) region, we characterized the community composition of the root‐associated fungi and found significant differences with respect to fungal groups among the seven tree species. The density of conspecific neighboring trees had a significantly positive influence on the relative abundance of phytopathogens, especially host‐specific pathogens, while the heterospecific neighbor density had a significant negative impact on the species richness of host‐specific pathogens, as well as phytopathogens. Our work provides evidence that the root‐associated phytopathogenic fungi of a host plant depend greatly on the tree neighbors of the host plant.     

Effects of environmental variables on vesicular‐arbuscular mycorrhizal abundance in wild populations of Vangueria infausta

Abstract. Vesicular‐arbuscular endomycorrhizal fungi include among its members some of the most widespread root symbiont species. It is not known whether these fungal species show environmental or host preferences. In 13 semi‐arid savanna sites in Botswana, we found positive correlations between individual environmental factors and the abundance of VAM associations in the roots of an important host, the indigenous fruit tree Vangueria infausta (Rubiaceae). The concentration of phosphorus in the leaves of the host was positively correlated with both phosphorus in the soil and the abundance of VAM associations in its roots, indicating direct benefits to the host of this association. Abundance of VAM associations was significantly different between the studied sites and between seasons and was positively correlated with the mean annual rainfall. In addition, there was a negative correlation with phosphorus concentration in the soil. The differences between the summer and winter abundance of VAM associations were positively correlated with the density of bush cover and the amount of grazing. The apparent correlation found between the abundance of VAM in V. infausta and bush and tree community composition is presumably related to correlations between these two parameters and environmental conditions.     

Sharing of Diverse Mycorrhizal and Root-Endophytic Fungi among Plant Species in an Oak-Dominated Cool–Temperate Forest

Most terrestrial plants interact with diverse clades of mycorrhizal and root-endophytic fungi in their roots. Through belowground plant–fungal interactions, dominant plants can benefit by interacting with host-specific mutualistic fungi and proliferate in a community based on positive plant–mutualistic fungal feedback. On the other hand, subordinate plant species may persist in the community by sharing other sets (functional groups) of fungal symbionts with each other. Therefore, revealing how diverse clades of root-associated fungi are differentially hosted by dominant and subordinate plant species is essential for understanding plant community structure and dynamics. Based on 454-pyrosequencing, we determined the community composition of root-associated fungi on 36 co-occurring plant species in an oak-dominated forest in northern Japan and statistically evaluated the host preference phenotypes of diverse mycorrhizal and root-endophytic fungi. An analysis of 278 fungal taxa indicated that an ectomycorrhizal basidiomycete fungus in the genus Lactarius and a possibly endophytic ascomycete fungus in the order Helotiales significantly favored the dominant oak (Quercus) species. In contrast, arbuscular mycorrhizal fungi were generally shared among subordinate plant species. Although fungi with host preferences contributed to the compartmentalization of belowground plant–fungal associations, diverse clades of ectomycorrhizal fungi and possible root endophytes were associated not only with the dominant Quercus but also with the remaining plant species. Our findings suggest that dominant-ectomycorrhizal and subordinate plant species can host different subsets of root-associated fungi, and diverse clades of generalist fungi can counterbalance the compartmentalization of plant–fungal associations. Such insights into the overall structure of belowground plant–fungal associations will help us understand the mechanisms that facilitate the coexistence of plant species in natural communities.     

Host Associations Between Fungal Root Endophytes and Boreal Trees

Fungal root endophytes colonize root tissue concomitantly with mycorrhizal fungi, but their identities and host preferences are largely unknown. We cultured fungal endophytes from surface-sterilized Cenococcum geophilum ectomycorrhizae of Betula papyrifera, Abies balsamea, and Picea glauca from two boreal sites in eastern Canada. Isolates were initially grouped on the basis of cultural morphology and then identified by internal transcribed spacer ribosomal DNA sequencing or by PCR restriction fragment length polymorphism. Phylogenetic analysis of the sequence data revealed 31 distinct phylotypes among the isolates, comprising mainly members of the ascomycete families Helotiaceae, Dermateaceae, Myxotrichaceae, and Hyaloscyphaceae, although other fungi were also isolated. Multivariate analyses indicate a clear separation among the endophyte communities colonizing each host tree species. Some phylotypes were evenly distributed across the roots of all three host species, some were found preferentially on particular hosts, and others were isolated from single hosts only. The results indicate that fungal root endophytes of boreal trees are not randomly distributed, but instead form relatively distinct assemblages on different host tree species.     

危害松树的小蠹虫与其伴生菌的相互关系

危害健康松属植物的小蠹虫经常与一些特殊的真菌相联系。在小蠹虫危害松属植物的过程中,这些真菌被小蠹虫的一些特殊结构或者体表携带到松属植物上。小蠹虫与其伴生菌的联系表明小蠹虫和其伴生菌之间是一种互惠互利的关系。伴生菌随小蠹虫扩散而被带到新的寄主树木。而伴生菌或作为小蠹虫的食物来源,但更重要的是,有些伴生菌能够通过其菌丝渗透寄主组织,释放毒素,致死寄主树木,以帮助小蠹虫降低寄主抗性。许多研究致力于探索小蠹虫/伴生菌联合体与寄主树木之间关系的特征和确定小蠹虫与其伴生菌相互关系在生态学上的意义。然而,不同小蠹虫和其伴生菌所组成的共生体系,不同小蠹虫的种群数量,和不同环境条件下同种小蠹虫与其伴生菌相互作用方式的差异使我们在研究小蠹虫和其伴生菌这个共生体系时,对它们各自在成功聚集寄主树木过程中所发挥的重要作用的概括变得非常困难。     

Comparison of Degradative Ability, Enzymatic Activity, and Palatability of Aquatic Hyphomycetes Grown on Leaf Litter

Stream fungi have the capacity to degrade leaf litter and, through their activities, to transform it into a more palatable food source for invertebrate detritivores. The objectives of the present study were to characterize various aspects of fungal modification of the leaf substrate and to examine the effects these changes have on leaf palatability to detritivores. Fungal species were grown on aspen leaves for two incubation times. Leaves were analyzed to determine the weight loss, the degree of softening of the leaf matrix, and the concentrations of ATP and nitrogen associated with leaves. The activities of a protease and 10 polysaccharide-degrading enzymes produced by each fungus were also determined. Most fungi caused similar changes in physicochemical characteristics of the leaves. All fungi exhibited the capability to depolymerize pectin, xylan, and cellulose. Differences among fungi were found in their capabilities to produce protease and certain glycosidases. Leaf palatability was assessed by offering leaves of all treatments to larvae of two caddisfly shredders (Trichoptera). Feeding preferences exhibited by the shredders were similar and indicated that they perceived distinct differences among fungi. Two fungal species were highly consumed, some moderately and others only slightly. No relationships were found between any of the fungal characteristics measured and detritivore feeding preferences. Apparently, interspecific differences among fungi other than parameters associated with biomass or degradation of structural polysaccharides influence fungal palatability to caddisfly detritivores.     

Specificity of assemblage,not fungal partner species,explains mycorrhizal partnerships of mycoheterotrophic Burmannia plants

Mycoheterotrophic plants (MHPs) growing on arbuscular mycorrhizal fungi (AMF) usually maintain specialized mycorrhizal associations. The level of specificity varies between MHPs, although it remains largely unknown whether interactions with mycorrhizal fungi differ by plant lineage, species, and/or by population. Here, we investigate the mycorrhizal interactions among Burmannia species (Burmanniaceae) with different trophic modes using high-throughput DNA sequencing. We characterized the inter- and intraspecific dynamics of the fungal communities by assessing the composition and diversity of fungi among sites. We found that fully mycoheterotrophic species are more specialized in their fungal associations than chlorophyllous species, and that this specialization possibly results from the gradual loss of some fungal groups. In particular, although many fungal species were shared by different Burmannia species, fully MHP species typically host species-specific fungal assemblages, suggesting that they have a preference for the selected fungi. Although no apparent cophylogenetic relationship was detected between fungi and plants, we observe that evolutionarily closely related plants tend to have a greater proportion of shared or closely related fungal partners. Our findings suggest a host preference and specialization toward fungal assemblages in Burmannia, improving understanding of interactions between MHPs and fungi.Subject terms: Fungi, Plant sciences, Evolution     

A narrowly endemic photosynthetic orchid is non‐specific in its mycorrhizal associations

Mycorrhizal association is a common characteristic in a majority of land plants, and the survival and distribution of a species can depend on the distribution of suitable fungi in its habitat. Orchidaceae is one of the most species‐rich angiosperm families, and all orchids are fully dependent on fungi for their seed germination and some also for subsequent growth and survival. Given this obligate dependence, at least in the early growth stages, elucidating the patterns of orchid–mycorrhizal relationships is critical to orchid biology, ecology and conservation. To assess whether rarity of an orchid is determined by its specificity towards its fungal hosts, we studied the spatial and temporal variability in the host fungi associated with one of the rarest North American terrestrial orchids, Piperia yadonii. The fungal internal transcribed spacer region was amplified and sequenced by sampling roots from eight populations of P. yadonii distributed across two habitats, Pinus radiata forest and maritime chaparral, in California. Across populations and sampling years, 26 operational taxonomic units representing three fungal families, the Ceratobasidiaceae, Sebacinaceae and Tulasnellaceae, were identified. Fungi belonging to the Sebacinaceae were documented in orchid roots only at P. radiata forest sites, while those from the Ceratobasidiaceae and Tulasnellaceae occurred in both habitats. Our results indicate that orchid rarity can be unrelated to the breadth of mycorrhizal associations. Our data also show that the dominance of various fungal families in mycorrhizal plants can be influenced by habitat preferences of mycorrhizal partners.     

Saproxylic moths reveal complex within-group and group-environment patterns

We investigated saproxylic moths of the family Tineidae, a neglected group inhabiting wood-decaying fungi and dead wood, within the Bia?owie?a Primeval Forest in Poland. Study data were obtained from the collection of 280 fruiting bodies of wood-decaying fungi and the subsequent rearing of adults. Spatial and statistical distribution of saproxylic moths, relationship among species and the influence of environment reflected by interaction with tree and fungal species together with tree and stand level characteristics were studied. Fifteen species and 533 individuals of saproxylic moths were reared. The fungal species, number of fruiting bodies and standing position of a tree influenced species richness. Moth abundance was influenced by fungal species, coniferous trees, increasing tree diameter, number of fruiting bodies and brown rot. Moth abundance was also enhanced by standing dead trees located in managed forests with higher canopy closure. Analyses indicate that several moth species favor a particular rot type and that some fungi host a richer fauna than others. Furthermore, our results indicate mutually independent fungal colonization events by saproxylic moth species, and thus a possible mechanism exists for competition avoidance with other saproxylic moths. Saproxylic moths revealed complex within-group patterns that responded differently to environmental variables. Thus, potential conservation of these organisms requires various approaches including ecosystem management, especially in the context of addressing their diverse habitat requirements.     

Habitat association in two genetic groups of the insect-pathogenic fungus metarhizium anisopliae: uncovering cryptic species?

Strains of insect-pathogenic fungi with high virulence toward certain pest insects have great potential for commercial biological control applications. Identifying such strains has been a central theme in using fungi for biological control. This theme is supported by a persistent paradigm in insect pathology which suggests that the host insect is the predominant influence on the population genetics of insect-pathogenic fungi. In this study, a population genetics analysis of the insect-pathogenic fungus Metarhizium anisopliae from forested and agricultural habitats in Ontario, Canada, showed a nonrandom association of alleles between two distinct, reproductively isolated groups (index of multilocus association = 1.2). Analyses of the mitochondrial DNA showed no differences between the groups. The two groups were associated with different habitat types, and associations with insect hosts were not found. The group from forested areas showed an ability for cold-active growth (i.e., 8 degrees C), while the group from the agricultural area showed an ability for growth at high temperatures (i.e., 37 degrees C) and resilience to UV exposure. These results represent a significant paradigm shift; habitat selection, not host insect selection, drives the population structure of these insect-pathogenic deuteromycetous fungi. With each group we observed recombining population structures as well as clonally reproducing lineages. We discuss whether these groups may represent cryptic species. Worldwide, M. anisopliae may be an assembly of cryptic species, each adapted to certain environmental conditions. The association of fungal genotypes with habitat but not with host insects has implications on the criteria for utility of this, and perhaps other, fungal biocontrol agents.     

Arbuscular mycorrhizal communities in tropical forests are affected by host tree species and environment

Arbuscular mycorrhizal (AM) fungi are mutualists with plant roots that are proposed to enhance plant community diversity. Models indicate that AM fungal communities could maintain plant diversity in forests if functionally different communities are spatially separated. In this study we assess the spatial and temporal distribution of the AM fungal community in a wet tropical rainforest in Costa Rica. We test whether distinct fungal communities correlate with variation in tree life history characteristics, with host tree species, and the relative importance of soil type, seasonality and rainfall. Host tree species differ in their associated AM fungal communities, but differences in the AM community between hosts could not be generalized over life history groupings of hosts. Changes in the relative abundance of a few common AM fungal species were the cause of differences in AM fungal communities for different host tree species instead of differences in the presence and absence of AM fungal species. Thus, AM fungal communities are spatially distinguishable in the forest, even though all species are widespread. Soil fertility ranging between 5 and 9 Mg/ha phosphorus did not affect composition of AM fungal communities, although sporulation was more abundant in lower fertility soils. Sampling soils over seasons revealed that some AM fungal species sporulate profusely in the dry season compared to the rainy season. On one host tree species sampled at two sites with vastly different rainfall, relative abundance of spores from Acaulospora was lower and that of Glomus was relatively higher at the site with lower and more seasonal rainfall.     

Afforested fields benefit nutrient‐demanding fungi

Impaired ecosystems are converted back to natural ecosystems or some other target stage by means of restoration and management. Due to their agricultural legacy, afforested fields might be valuable compensatory habitats for rare fungal species that require nutrient‐rich forest soils. Using a large‐scale field experiment in Finland, we studied community composition of macrofungi (agarics and boletes) on former fields, which had been afforested as monocultures 20 years ago using native spruce Picea abies, pine Pinus sylvestris, and birch Betula pendula. We studied the effect of soil quality, tree species, and site on community composition and structure. Many nutrient‐demanding as well as rare fungal species were recorded, particularly from pine and spruce plots. Pine plots supported more nutrient‐demanding fungi than birch plots. There was no relationship between soil pH, bulk density, P, N, or Ca, and species richness of nutrient‐demanding fungi. Fungal community composition was more similar within sites than among sites for all tree species. Among sites, spruce plots had the smallest fungal species turnover, and birch plots largest. Within sites, however, fungal species turnover from plot to plot was similar among tree species. Our results indicate that tree species has a relatively mild influence on species composition of fungi after 20 years of succession. Interestingly, the results show that afforested fields can be valuable complementary habitats for rare, red‐listed, and nutrient‐demanding fungal species. Field afforestation is a potential conservation tool that could be used to complement the poor representation of rare habitat types in highly fragmented protected area networks.     

EVOLUTION OF HABITAT PREFERENCE AND NUTRITION MODE IN A COSMOPOLITAN FUNGAL GENUS WITH EVIDENCE OF INTERKINGDOM HOST JUMPS AND MAJOR SHIFTS IN ECOLOGY

Host jumps by microbial symbionts are often associated with bursts of species diversification driven by the exploitation of new adaptive zones. The objective of this study was to infer the evolution of habitat preference (decaying plants, soil, living fungi, and living plants), and nutrition mode (saprotrophy and mycoparasitism) in the fungal genus Trichoderma to elucidate possible interkingdom host jumps and shifts in ecology. Host and ecological role shifts were inferred by phylogenetic analyses and ancestral character reconstructions. The results support several interkingdom host jumps and also show that the preference for a particular habitat was gained or lost multiple times. Diversification analysis revealed that mycoparasitism is associated with accelerated speciation rates, which then suggests that this trait may be linked to the high number of species in Trichoderma. In this study it was also possible to infer the cryptic roles that endophytes or soil inhabitants play in their hosts by evaluating their closest relatives and determining their most recent ancestors. Findings from this study may have implications for understanding certain evolutionary processes such as species radiations in some hyperdiverse groups of fungi, and for more applied fields such as the discovery and development of novel biological control strategies.     

Spatial Community Structure of Mountain Pine Beetle Fungal Symbionts Across a Latitudinal Gradient

Symbiont redundancy in obligate insect–fungal systems is thought to buffer the insect host against symbiont loss and to extend the environmental conditions under which the insect can persist. The mountain pine beetle is associated with at least three well-known and putatively obligate ophiostomatoid fungal symbionts that vary in their environmental tolerances. To better understand the spatial variation in beetle–fungal symbiotic associations, we examined the community composition of ophiostomatoid fungi associated with the mountain pine beetle as a function of latitude and elevation. The region investigated represents the leading edge of a recent outbreak of mountain pine beetle in western Canada. Using regression and principal components analysis, we identified significant spatial patterns in fungal species abundances that indicate symmetrical replacement between two of the three fungi along a latitudinal gradient and little variation in response to elevation. We also identified significant variation in the prevalence of pair-wise species combinations that occur within beetle galleries. Frequencies of pair-wise combinations were significantly different from what was expected given overall species abundances. These results suggest that complex processes of competitive exclusion and coexistence help determine fungal community composition and that the consequences of these processes vary spatially. The presence of three fungal symbionts in different proportions and combinations across a wide range of environmental conditions may help explain the success of mountain pine beetle attacks across a broad geographic range.     

Root-associated ectomycorrhizal fungi shared by various boreal forest seedlings naturally regenerating after a fire in interior alaska and correlation of different fungi with host growth responses

The role of common mycorrhizal networks (CMNs) in postfire boreal forest successional trajectories is unknown. We investigated this issue by sampling a 50-m by 40-m area of naturally regenerating black spruce (Picea mariana), trembling aspen (Populus tremuloides), and paper birch (Betula papyrifera) seedlings at various distances from alder (Alnus viridis subsp. crispa), a nitrogen-fixing shrub, 5 years after wildfire in an Alaskan interior boreal forest. Shoot biomasses and stem diameters of 4-year-old seedlings were recorded, and the fungal community associated with ectomycorrhizal (ECM) root tips from each seedling was profiled using molecular techniques. We found distinct assemblages of fungi associated with alder compared with those associated with the other tree species, making the formation of CMNs between them unlikely. However, among the spruce, aspen, and birch seedlings, there were many shared fungi (including members of the Pezoloma ericae [Hymenoscyphus ericae] species aggregate, Thelephora terrestris, and Russula spp.), raising the possibility that these regenerating seedlings may form interspecies CMNs. Distance between samples did not influence how similar ECM root tip-associated fungal communities were, and of the fungal groups identified, only one of them was more likely to be shared between seedlings that were closer together, suggesting that the majority of fungi surveyed did not have a clumped distribution across the small scale of this study. The presence of some fungal ribotypes was associated with larger or smaller seedlings, suggesting that these fungi may play a role in the promotion or inhibition of seedling growth. The fungal ribotypes associated with larger seedlings were different between spruce, aspen, and birch, suggesting differential impacts of some host-fungus combinations. One may speculate that wildfire-induced shifts in a given soil fungal community could result in variation in the growth response of different plant species after fire and a shift in regenerating vegetation.     

High richness of ectomycorrhizal fungi and low host specificity in a coastal sand dune ecosystem revealed by network analysis

Ectomycorrhizal (EM) fungi are ubiquitous in temperate and boreal forests, comprising over 20,000 species forming root symbiotic associations with Pinaceae and woody angiosperms. As much as 100 different EM fungal species can coexist and interact with the same tree species, forming complex multispecies networks in soils. The degree of host specificity and structural properties of these interaction networks (e.g., nestedness and modularity) may influence plant and fungal community assembly and species coexistence, yet their structure has been little studied in northern coniferous forests, where trees depend on EM fungi for nutrient acquisition. We used high‐throughput sequencing to characterize the composition and diversity of bulk soil and root‐associated fungal communities in four co‐occurring Pinaceae in a relic foredune plain located at Îles de la Madeleine, Québec, Canada. We found high EM fungal richness across the four hosts, with a total of 200 EM operational taxonomic units (OTUs), mainly belonging to the Agaricomycetes. Network analysis revealed an antinested pattern in both bulk soil and roots EM fungal communities. However, there was no detectable modularity (i.e., subgroups of interacting species) in the interaction networks, indicating a low level of specificity in these EM associations. In addition, there were no differences in EM fungal OTU richness or community structure among the four tree species. Limited shared resources and competitive exclusion typically restrict the number of taxa coexisting within the same niche. As such, our finding of high EM fungal richness and low host specificity highlights the need for further studies to determine the mechanisms enabling such a large number of EM fungal species to coexist locally on the same hosts.     

Soil microbial communities associated with giant sequoia: How does the world's largest tree affect some of the world's smallest organisms?

Giant sequoia (Sequoiadendron giganteum) is an iconic conifer that lives in relict populations on the western slopes of the California Sierra Nevada. In these settings, it is unusual among the dominant trees in that it associates with arbuscular mycorrhizal fungi rather than ectomycorrhizal fungi. However, it is unclear whether differences in microbial associations extend more broadly to nonmycorrhizal components of the soil microbial community. To address this question, we used next‐generation amplicon sequencing to characterize bacterial/archaeal and fungal microbiomes in bulk soil (0–5 cm) beneath giant sequoia and co‐occurring sugar pine (Pinus lambertiana) individuals. We did this across two groves with distinct parent material in Yosemite National Park, USA. We found tree‐associated differences were apparent despite a strong grove effect. Bacterial/archaeal richness was greater beneath giant sequoia than sugar pine, with a core community double the size. The tree species also harbored compositionally distinct fungal communities. This pattern depended on grove but was associated with a consistently elevated relative abundance of Hygrocybe species beneath giant sequoia. Compositional differences between host trees correlated with soil pH and soil moisture. We conclude that the effects of giant sequoia extend beyond mycorrhizal mutualists to include the broader community and that some but not all host tree differences are grove‐dependent.