Relationships among wood‐boring beetles, fungi, and the decomposition of forest biomass

Adaptation strategies of insects to their environment by collecting and utilizing external microorganisms

Insects adjust their adaptive capacity to biotic and abiotic stresses by collecting and utilizing microorganisms from the environment and diet.

Post-Fire Coleoptera Fauna in Central Russian Forests after the 2021 Fires (Study Using Beer Traps)

Fires can significantly impact forest ecosystems. However, studies on the effects of fires on insect communities in post-fire plots in natural forests are rare. This study presents an analysis of the Coleoptera fauna in the forests of the Mordovia State Nature Reserve (European Russia) in 2022 and 2023 after a fire. Insects were sampled from burned plots (9) in 2010 and 2021, as well as unburned (control) plots (2), and alpha diversity was compared. After processing the material, we examined a total of 12,218 Coleoptera specimens from 38 families and identified 194 species. The families Nitidulidae, Cerambycidae, Elateridae, and Scarabaeidae were the most abundant across all plots. Cerambycidae, Elateridae, Nitidulidae, Staphylinidae, Coccinellidae, and Scarabaeidae exhibited the greatest species diversity. In total, 17 species were found on all plots, including Cetonia aurata, Protaetia cuprea volhyniensis, Trogoderma glabrum, Carpophilus hemipterus, Epuraea biguttata, Glischrochilus grandis, Glischrochilus hortensis, Glischrochilus quadripunctatus, Soronia grisea, Pediacus depressus, Chrysanthia geniculata, Anastrangalia reyi, Leptura quadrifasciata, Leptura thoracica, Lepturalia nigripes, Rhagium mordax, and Anisandrus dispar. Only five species exhibited preferences for certain plots. Maximum abundance and species diversity were observed on unburned (control) plots. The plots where fires occurred in 2010 and 2021 had the lowest total abundance values for Coleoptera. These fires destroyed almost all potential sites for beetle settlement, feeding, breeding, and shelter. Traps recorded a higher abundance of Coleoptera in the first year after fires compared to the second year. The Coleoptera fauna showed the greatest similarity on the control plots.

Factors associated with seedling establishment on logs of different fungal decay types-A seed-sowing experiment

Wood decay fungi alter the abiotic and biotic properties of deadwood, which are important as nurse logs for seedling regeneration. However, the relationship between fungal decay type and seedling performance has not been evaluated experimentally. In this study, we examined the germination, growth, and survival of six arbuscular mycorrhizal (AM) and six ectomycorrhizal (ECM) tree species on three substrates (pine logs with brown and white rot and soil) by conducting seed-sowing experiments in a mixed forest dominated by Pinus densiflora and Quercus serrata. Analysis using ribosomal DNA internal transcribed spacer 1 (rDNA ITS1) sequencing revealed that the fungal community was significantly different across three substrates. The richness of operational taxonomic units (OTUs) of AM and ECM fungi was the largest on brown rot logs and soil, respectively. The substrate significantly affected the seedling performance when comparing wood decay types, but these were not consistent across the mycorrhizal status of the seedlings. Nevertheless, seedlings of some AM trees showed better growth and enhanced mycorrhizal colonization on brown rot logs than on white rot logs. The wood decay type influenced fungal communities in the logs and the performance of some seedling species partly by different mycorrhizal colonization rates. However, the effect was seedling species dependent and showed no apparent difference between AM and ECM trees.

Decomposition of Fomes fomentatius fruiting bodies - transition of healthy living fungus into a decayed bacteria-rich habitat is primarily driven by Arthropoda

Fomes fomentarius is a widespread, wood-rotting fungus of temperate, broadleaved forests. Although the fruiting bodies of F. fomentarius persist for multiple years, little is known about its associated microbiome or how these recalcitrant structures are ultimately decomposed. Here we used metagenomics and metatranscriptomics to analyse the microbial community associated with healthy living and decomposing F. fomentarius fruiting bodies to assess the functional potential of the fruiting body-associated microbiome and to determine the main players involved in fruiting body decomposition. F. fomentarius sequences in the metagenomes were replaced by bacterial sequences as the fruiting body decomposed. Most CAZymes expressed in decomposing fruiting bodies targeted components of the fungal cell wall with almost all chitin-targeting sequences, plus a high proportion of beta-glucan-targeting sequences, belonging to Arthropoda. We suggest that decomposing fruiting bodies of F. fomentarius represent a habitat rich in bacteria, while its decomposition is primarily driven by Arthropoda. Decomposing fruiting bodies thus represent a specific habitat supporting both microorganisms and microfauna.

Wood decomposition is increased by insect diversity, selection effects, and interactions between insects and microbes

Biodiversity drives ecosystem processes, but its influence on deadwood decomposition is poorly understood. To test the effects of insect diversity on wood decomposition, we conducted a mesocosm experiment manipulating the species richness and functional diversity of beetles. We applied a novel approach using computed tomography scanning to quantify decomposition by insects and recorded fungal and bacterial communities. Decomposition rates increased with both species richness and functional diversity of beetles, but the effects of functional diversity were linked to beetle biomass, and to the presence of one large-bodied species in particular. This suggests that mechanisms behind observed biodiversity effects are the selection effect, which is linked to the occurrence probability of large species, and the complementarity effect, which is driven by functional differentiation among species. Additionally, beetles had significant indirect effects on wood decomposition via bacterial diversity, fungal community composition, and fungal biomass. Our experiment shows that wood decomposition is driven by beetle diversity and its interactions with bacteria and fungi. This highlights that both insect and microbial biodiversity are critical to maintaining ecosystem functioning.

Sapwood mycobiome varies across host, plant compartment and environments in Nothofagus forests from Northern Patagonia

Global forests are increasingly being threatened by altered climatic conditions and increased attacks by pests and pathogens. The complex ecological interactions among pathogens, microbial communities, tree hosts and the environment are important drivers of forest dynamics. Little is known about the ecology of forest pathology and related microbial communities in temperate forests of the southern hemisphere. In this study, we used next-generation sequencing to characterize sapwood-inhabiting fungal communities in North Patagonian Nothofagus forests and assessed patterns of diversity of taxa and ecological guilds across climatic, site and host variables (health condition and compartment) as a contribution to Nothofagus autecology. The diversity patterns inferred through the metabarcoding analysis were similar to those obtained through culture-dependent approaches. However, we detected additional heterogeneity and greater richness with culture-free methods. Host species was the strongest driver of fungal community structure and composition, while host health status was the weakest. The relative impacts of site, season, plant compartment and health status were different for each tree species; these differences can be interpreted as a matter of water availability. For Nothofagus dombeyi, which is distributed across a wide range of climatic conditions, site was the strongest driver of community composition. The microbiome of N. pumilio varied more with season and temperature, a relevant factor for forest conservation in the present climate change scenario. Both species carry a number of potential fungal pathogens in their sapwood, whether they exhibit symptoms or not. Our results provide insight into the diversity of fungi associated with the complex pathobiome of the dominant Nothofagus species in southern South America.

Genome and transcriptome of Ips nitidus provide insights into high-altitude hypoxia adaptation and symbiosis

Ips nitidus is a well-known conifer pest that has contributed significantly to spruce forest disturbance in the Qinghai-Tibet Plateau and seriously threatens the ecological balance of these areas. We report a chromosome-level genome of I. nitidus determined by PacBio and Hi-C technology. Phylogenetic inference showed that it diverged from the common ancestor of I. typographus ∼2.27 mya. Gene family expansion in I. nitidus was characterized by DNA damage repair and energy metabolism, which may facilitate adaptation to high-altitude hypoxia. Interestingly, differential gene expression analysis revealed upregulated genes associated with high-altitude hypoxia adaptation and downregulated genes associated with detoxification after feeding and tunneling in fungal symbiont Ophiostoma bicolor-colonized substrates. Our findings provide evidence of the potential adaptability of I. nitidus to conifer host, high-altitude hypoxia and insight into how fungal symbiont assist in this process. This study enhances our understanding of insect adaptation, symbiosis, and pest management.

Variation in Larval Thermal Tolerance of Three Saproxylic Beetle Species

Temperature is a key abiotic condition that limits the distributions of organisms, and forest insects are particularly sensitive to thermal extremes. Whereas winged adult insects generally are able to escape unfavorable temperatures, other less-vagile insects (e.g., larvae) must withstand local microclimatic conditions to survive. Here, we measured the thermal tolerance of the larvae of three saproxylic beetle species that are common inhabitants of coarse woody debris (CWD) in temperate forests of eastern North America: Lucanus elaphus Fabricius (Lucanidae), Dendroides canadensis Latreille (Pyrochroidae), and Odontotaenius disjunctus Illiger (Passalidae). We determined how their critical thermal maxima (CTmax) vary with body size (mass), and measured the thermal profiles of CWD representing the range of microhabitats occupied by these species. Average CTmax differed among the three species and increased with mass intraspecifically. However, mass was not a good predictor of thermal tolerance among species. Temperature ramp rate and time in captivity also influenced larval CTmax, but only for D. canadensis and L. elaphus respectively. Heating profiles within relatively dry CWD sometimes exceeded the CTmax of the beetle larvae, and deeper portions of CWD were generally cooler. Interspecific differences in CTmax were not fully explained by microhabitat association, but the results suggest that the distribution of some species within a forest can be affected by local thermal extremes. Understanding the responses of saproxylic beetle larvae to warming habitats will help predict shifts in community structure and ecosystem functioning in light of climate change and increasing habitat fragmentation.

First experimental evidence for active farming in ambrosia beetles and strong heredity of garden microbiomes

Fungal cultivation is a defining feature for advanced agriculture in fungus-farming ants and termites. In a third supposedly fungus-farming group, wood-colonizing ambrosia beetles, an experimental proof for the effectiveness of beetle activity for selective promotion of their food fungi over others is lacking and farming has only been assumed based on observations of social and hygienic behaviours. Here, we experimentally removed mothers and their offspring from young nests of the fruit-tree pinhole borer, Xyleborinus saxesenii. By amplicon sequencing of bacterial and fungal communities of nests with and without beetles we could show that beetles are indeed able to actively shift symbiont communities. Although being consumed, the Raffaelea food fungi were more abundant when beetles were present while a weed fungus (Chaetomium sp.) as well as overall bacterial diversity were reduced in comparison to nests without beetles. Core symbiont communities were generally of low diversity and there were strong signs for vertical transmission not only for the cultivars, but also for secondary symbionts. Our findings verify the existence of active farming, even though the exact mechanisms underlying the selective promotion and/or suppression of symbionts need further investigation.

Which Is the Best Substrate to Regenerate? A Comparative Pot Experiment for Tree Seedling Growth on Decayed Wood and in Soil

Dead wood is an important microsite for seedling regeneration in forest ecosystems. Although recent studies have found important associations between fungal wood decay type (white rot and brown rot) and both density and species composition of regenerating seedlings, its abiotic and biotic mechanisms are unknown. In the present study, pot experiments were conducted with the seedlings of two ectomycorrhizal tree species (Abies veitchii and Betula ermanii) and two arbuscular mycorrhizal tree species (Chamaecyparis obtusa and Cryptomeria japonica) to evaluate their growth using three substrates: brown rot wood, white rot wood, and soil. Results showed that the shoot growth of B. ermanii grown in white rot wood was greater than in other substrates, but this effect disappeared in sterilized substrates, suggesting some biotic positive effects occur in white rot wood. The seedling weights of Cr. japonica and Ch. obtusa were found to be greater in soil than in wood, and this may be partly attributable to the high mycorrhizal rate of their roots in soil. Colonization of arbuscular and ectomycorrhizal fungi was restricted to the seedlings in unsterilized soil. These results demonstrate the importance of the biological mechanisms affecting seedlings’ preferences for a variety of regeneration microsites and illustrate the need for future experiments to include larger sets of seedling species.

Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers

Full taxonomic characterisation of fungal communities is necessary for establishing ecological associations and early detection of pathogens and invasive species. Complex communities of fungi are regularly characterised by metabarcoding using the Internal Transcribed Spacer (ITS) and the Large-Subunit (LSU) gene of the rRNA locus, but reliance on a single short sequence fragment limits the confidence of identification. Here we link metabarcoding from the ITS2 and LSU D1-D2 regions to characterise fungal communities associated with bark beetles (Scolytinae), the likely vectors of several tree pathogens. Both markers revealed similar patterns of overall species richness and response to key variables (beetle species, forest type), but identification against the respective reference databases using various taxonomic classifiers revealed poor resolution towards lower taxonomic levels, especially the species level. Thus, Operational Taxonomic Units (OTUs) could not be linked via taxonomic classifiers across ITS and LSU fragments. However, using phylogenetic trees (focused on the epidemiologically important Sordariomycetes) we placed OTUs obtained with either marker relative to reference sequences of the entire rRNA cistron that includes both loci and demonstrated the largely similar phylogenetic distribution of ITS and LSU-derived OTUs. Sensitivity analysis of congruence in both markers suggested the biologically most defensible threshold values for OTU delimitation in Sordariomycetes to be 98% for ITS2 and 99% for LSU D1-D2. Studies of fungal communities using the canonical ITS barcode require corroboration across additional loci. Phylogenetic analysis of OTU sequences aligned to the full rRNA cistron shows higher success rate and greater accuracy of species identification compared to probabilistic taxonomic classifiers.

Diversity of Ophiostomatoid Fungi Associated with Dendroctonus armandi Infesting Pinus armandii in Western China

Pinus armandii (P. armandii) is extensively abundant in western China and, as a pioneer tree, and prominently influences local ecology. However, pine forests in this region have been significantly damaged by Dendroctonus armandi (D. armandi) infestations, in close association with ophiostomatoid fungi. This study aimed to identify the diversity of ophiostomatoid fungi associated with D. armandi infesting P. armandii in western China. A total of 695 ophiostomatoid fungal strains were isolated from 1040 tissue pieces from D. armandi galleries and 89 adult beetles at four sites. In this study, based on multiloci DNA sequence data, as well as morphological and physiological characteristics, seven species belonging to five genera were identified including three known species, Esteyea vermicola, Graphium pseudormiticum and L. wushanense, two novel taxa, Graphilbum parakesiyea and Ophiostoma shennongense, and an unidentified Ophiostoma sp. 1. A neotype of Leptographium qinlingense. Ophiostoma shennongense was the dominant taxon (78.99%) in the ophiostomatoid community. This study provides a valuable scientific theoretical basis for the occurrence and management of D. armandi in the future.

Understudied, underrepresented, and unknown: Methodological biases that limit detection of early diverging fungi from environmental samples

Metabarcoding is an important tool for understanding fungal communities. The internal transcribed spacer (ITS) rDNA is the accepted fungal barcode but has known problems. The large subunit (LSU) rDNA has also been used to investigate fungal communities but available LSU metabarcoding primers were mostly designed to target Dikarya (Ascomycota + Basidiomycota) with little attention to early diverging fungi (EDF). However, evidence from multiple studies suggests that EDF comprise a large portion of unknown diversity in community sampling. Here, we investigate how DNA marker choice and methodological biases impact recovery of EDF from environmental samples. We focused on one EDF lineage, Zoopagomycota, as an example. We evaluated three primer sets (ITS1F/ITS2, LROR/LR3, and LR3 paired with new primer LR22F) to amplify and sequence a Zoopagomycota mock community and a set of 146 environmental samples with Illumina MiSeq. We compared two taxonomy assignment methods and created an LSU reference database compatible with AMPtk software. The two taxonomy assignment methods recovered strikingly different communities of fungi and EDF. Target fragment length variation exacerbated PCR amplification biases and influenced downstream taxonomic assignments, but this effect was greater for EDF than Dikarya. To improve identification of LSU amplicons we performed phylogenetic reconstruction and illustrate the advantages of this critical tool for investigating identified and unidentified sequences. Our results suggest much of the EDF community may be missed or misidentified with "standard" metabarcoding approaches and modified techniques are needed to understand the role of these taxa in a broader ecological context.

Novel Symbiotic Association Between Euwallacea Ambrosia Beetle and Fusarium Fungus on Fig Trees in Japan

Ficus carica plantations in Japan were first reported to be infested by an ambrosia beetle species, identified as Euwallacea interjectus, in 1996. The purpose of this study was to determine the symbiotic fungi of female adults of E. interjectus emerging from F. carica trees infected with fig wilt disease (FWD). Dispersal adults (51 females) of E. interjectus, which were collected from logs of an infested fig tree in Hiroshima Prefecture, Western Japan, were separated into three respective body parts (head, thorax, and abdomen) and used for fungal isolation. Isolated fungi were identified based on the morphological characteristics and DNA sequence data. Over 13 species of associated fungi were detected, of which a specific fungus, Fusarium kuroshium, was dominant in female head (including oral mycangia). The plant-pathogenic fungus of FWD, Ceratocystis ficicola, was not observed within any body parts of E. interjectus. We further discussed the relationship among E. interjectus and its associated fungi in fig tree.

Origin and evolution of fungus farming in wood-boring Coleoptera - a palaeontological perspective

Insect-fungus mutualism is one of the better-studied symbiotic interactions in nature. Ambrosia fungi are an ecological assemblage of unrelated fungi that are cultivated by ambrosia beetles in their galleries as obligate food for larvae. Despite recently increased research interest, it remains unclear which ecological factors facilitated the origin of fungus farming, and how it transformed into a symbiotic relationship with obligate dependency. It is clear from phylogenetic analyses that this symbiosis evolved independently many times in several beetle and fungus lineages. However, there is a mismatch between palaeontological and phylogenetic data. Herein we review, for the first time, the ambrosia system from a palaeontological perspective. Although largely ignored, families such as Lymexylidae and Bostrichidae should be included in the list of ambrosia beetles because some of their species cultivate ambrosia fungi. The estimated origin for some groups of ambrosia fungi during the Cretaceous concurs with a known high diversity of Lymexylidae and Bostrichidae at that time. Although potentially older, the greatest radiation of various ambrosia beetle lineages occurred in the weevil subfamilies Scolytinae and Platypodinae during the Eocene. In this review we explore the evolutionary relationship between ambrosia beetles, fungi and their host trees, which is likely to have persisted for longer than previously supposed.

Habitat Quality Determines Dispersal Decisions and Fitness in a Beetle – Fungus Mutualism

Delayed dispersal of sexually mature offspring is a fundamental component of cooperative breeding. In ambrosia beetles, female offspring temporarily remain in their natal nest and refrain from reproduction, instead investing in alloparental care. Previous work has demonstrated a link between helping behaviour and the increased need for pathogen defence, arising from their close association with fungal cultivars. In the ambrosia beetle Xyleborinus saxesenii, mature female offspring can effectively fight pathogen infections and manage the microbial composition within the nest by adjusting the frequency of different hygienic and nest maintenance behaviours. This suggests a potential to respond flexibly to the ecology of their nest, which calls for a better understanding of the connection between behaviour and the microbial community thriving within their nests. Here, we studied the significance of the mutualistic fungus garden composition for the beetles’ nest ecology and fitness by experimentally varying substrate quality. We found that the vertically transmitted ambrosia fungus garden is composed of at least two fungus mutualist species and a wide variety of other microbes varying in their relative abundance. This is strongly affected by the moisture content of the substrate, which in nature depends on the age and type of wood. We found that the mutualist fungi complement each other in terms of dryness-resistance, allowing the beetles to utilise a broad range of substrates over prolonged time during which the wood gradually desiccates. Under suboptimal humidity conditions, the interaction between host and multiple fungus species has important ramifications for the behaviour of philopatric helpers, including their alloparental investment, sibling cannibalism and the timing of dispersal. Rearing five generations of beetles consecutively in dry substrate resulted in transgenerational effects on philopatry and alloparental care, probably mediated through the dominance of a particular fungus species that was driven by the experimental habitat condition. Interestingly, the nests of these selection lines produced much more offspring after five generations than any first-generation nest, which may have reflected increased egg laying by non-dispersing daughters. Our study highlights the importance of considering the interactions between the microbial community and their insect hosts for understanding social evolution in cooperatively breeding beetles.

Decay stages of wood and associated fungal communities characterise diversity-decomposition relationships

The biodiversity–ecosystem function relationship is a central topic in ecology. Fungi are the dominant decomposers of organic plant material in terrestrial ecosystems and display tremendous species diversity. However, little is known about the fungal diversity–decomposition relationship. We evaluated fungal community assemblies and substrate quality in different stages of wood decay to assess the relationships between fungal species richness and weight loss of wood substrate under laboratory conditions. Wood-inhabiting fungal communities in the early and late stages of pine log decomposition were used as a model. Colonisation with certain species prior to inoculation with other species resulted in four-fold differences in fungal species richness and up to tenfold differences in the rate of wood substrate decomposition in both early- and late-decaying fungal communities. Differences in wood substrate quality had a significant impact on species richness and weight loss of wood and the relationships between the two, which were negative or neutral. Late communities showed significantly negative species richness–decay relationships in wood at all decay stages, whereas negative relationships in early communities were significant only in the intermediate decay stage. Our results suggest that changes in fungal communities and wood quality during wood decomposition affect the fungal diversity–decomposition relationship.

Crystallicutis gen. nov. (Irpicaceae, Basidiomycota), including C. damiettensis sp. nov., found on Phoenix dactylifera (date palm) trunks in the Nile Delta of Egypt

The taxonomy of Polyporales is complicated by the variability in key morphological characters across families and genera, now being gradually resolved through molecular phylogenetic analyses. Here a new resupinate species, Crystallicutis damiettensis sp. nov. found on the decayed trunks of date palm (Phoenix dactylifera) trees in the fruit orchards of the Nile Delta region of Egypt is reported. Multigene phylogenetic analyses based on ITS, LSU, EF1α, RPB1 and RPB2 loci place this species in Irpicaceae, and forming a distinct clade with Ceraceomyces serpens and several other hitherto unnamed taxa, which we also incorporate into a new genus Crystallicutis. We name two of these species, Crystallicutis huangshanensis sp. nov. and Crystallicutis rajchenbergii sp. nov. The distinctive feature of Crystallicutis gen. nov. is the presence of crystal-encrusted hyphae in the hymenium and subiculum. Basidiomes are usually honey-yellow with white margins but there is variability in the presence of clamp connections and cystidia, as noted for other genera within Irpicacae. C. damiettensis is hitherto consistently associated with date palms killed by the red palm weevil Rhynchophorus ferrugineus, a highly damaging and invasive pest, recently spread to the Mediterranean region. C. damiettensis causes rapid wood decay by a potentially unusual white-rot mechanism and may play a role in the damage caused by R. ferrugineus.

Phylogenetic Position of Geosmithia spp. (Hypocreales) Living in Juniperus spp. Forests (Cupressaceae) with Bark Beetles of Phloeosinus spp. (Scolytinae) from the Northeast of Mexico

Geosmithia members are mitosporic filamentous fungi commonly recorded and isolated from bark beetles of the Scolytinae subfamily and their respective host’s species. This genus includes 18 species formally described and 38 phylogenetic species recorded in several localities from Africa, Asia, Australia, Europe, and North and South America, where they exhibit frequent associations with phloeophagous and wood-boring bark beetles. Among phloephagous bark beetle species, specifically, in members of the genus Phloeosinus Chapuis, almost 10% of Geosmithia strains have been isolated. By its physiographic elements and high bark beetle and conifer species richness, Mexico is a potential region to host a high diversity of Geosmithia species and potential new species. In the present study, we systematically sampled and isolated, cultured, and molecularly identified members of the Geosmithia species associated with Phloeosinus spp. and their Juniperus spp. host trees at the north of Sierra Madre Oriental, at Nuevo Leon State, Mexico. Phylogenetic analyses based on 378 internal transcribed spacer region (ITS) sequences supported the presence of strains from Geosmithia langdonii-Geosmithia sp. 32 clade associated with Phloeosinus serratus vector and with Juniperus coahuilensis (JC) host, and the presence of strains from Geosmithia sp. 21-Geosmithia xerotolerans clade with Phloeosinusdeleoni and Juniperus flaccida (JF) in this geographical region. The genetic and morphological differences found in our strains with respect to those previously described in the species from both clades (Geosmithia langdonii-Geosmithia sp. 32 and Geosmithia sp. 21-G. xerotolerans) suggest that both Geosmithia lineages from Nuevo Leon correspond to two potential new species in the genus.

Epibiotic Fungal Communities of Three Tomicus spp. Infesting Pines in Southwestern China

The association between insects and fungi has evolved over millions of years and is ubiquitous in nature. This symbiotic relationship holds critical implications for both partners, the insects and the associated microbes. Numerous fungi are externally allied with bark beetles and form a close symbiosis, but the community structures of these fungi are largely unknown. In Yunnan Province in southwestern China, the beetles Tomicus yunnanensis, T. minor, and T. brevipilosus are major forest pests that cause large losses of two indigenous pines, Pinus yunnanensis and P. kesiya. In this study, we used the Illumina MiSeq PE300 platform to process 48 samples of epibiotic fungal communities pooled from 1348 beetles; the beetles were collected during both the branch- and trunk-infection sections from five locations across Yunnan Province. Considerably greater species richness was detected using high-throughput sequencing of amplified internal transcribed spacer 1 (ITS1) ribosomal DNA (rDNA) libraries than previously documented by using culture-dependent methods. In total, 1,413,600 reads were generated, and a 97% sequence-similarity cutoff produced eight phyla, 31 classes, 83 orders, 181 families, 331 genera, 471 species, and 1157 operational taxonomic units (OTUs), with 659, 621, and 609 OTUs being confined to T. yunnanensis, T. minor, and T. brevipilosus, respectively. Tomicus yunnanensis, T. minor, and T. brevipilosus had the similar OTUs richness and evenness of fungal communities in Yunnan Province; nevertheless, the two fungal community compositions associated with T. yunnanensis and T. minor were structurally similar to each other but distinct from that associated with T. brevipilosus. Lastly, the results of principal co-ordinates analysis suggested that epibiotic fungal community structures of the three Tomicus spp. were conditioned strongly by the locations and pine hosts but weakly by beetle species and infection sections. Our findings provide baseline knowledge regarding the epibiotic fungal communities of three major Tomicus spp. in southwestern China.