Environmental filtering structures fungal endophyte communities in tree bark

The factors that control the assembly and composition of endophyte communities across plant hosts remains poorly understood. This is especially true for endophyte communities inhabiting inner tree bark, one of the least studied components of the plant microbiome. Here, we test the hypothesis that bark of different tree species acts as an environmental filter structuring endophyte communities, as well as the alternative hypothesis, that bark acts as a passive reservoir that accumulates a diverse assemblage of spores and latent fungal life stages. We develop a means of extracting high‐quality DNA from surface sterilized tree bark to compile the first culture‐independent study of inner bark fungal communities. We sampled a total of 120 trees, spanning five dominant overstorey species across multiple sites in a mixed temperate hardwood forest. We find that each of the five tree species harbour unique assemblages of inner bark fungi and that angiosperm and gymnosperm hosts harbour significantly different fungal communities. Chemical components of tree bark (pH, total phenolic content) structure some of the differences detected among fungal communities residing in particular tree species. Inner bark fungal communities were highly diverse (mean of 117–171 operational taxonomic units per tree) and dominated by a range of Ascomycete fungi living asymptomatically as putative endophytes. Together, our evidence supports the hypothesis that tree bark acts as an environmental filter structuring inner bark fungal communities. The role of these potentially ubiquitous and plant‐specific fungal communities remains uncertain and merits further study.     

Using direct amplification and next-generation sequencing technology to explore foliar endophyte communities in experimentally inoculated western white pines

Fungal endophytes can influence survivability and disease severity of trees. Here we characterized the endophyte community in Pinus monticola (western white pine), an important species in the northwest USA, largely decimated by pathogenic fungi. We also assessed the ability to successfully inoculate seedlings with desirable endophytes, with the long-term goal of providing a protective microbiome and added defense from pathogens. P. monticola seedlings were inoculated in the field with potential pathogen antagonists and fungi isolated from healthy mature trees. Following inoculations direct amplification and next generation sequencing were used to characterize fungal endophyte communities, and explore interspecific competition, diversity, and co-occurrence patterns in needle tissues. Negative co-occurrence patterns between inoculated fungi and potential pathogens, as well as many other species, suggest early competitive interactions. Our study explores early endophyte community assemblage and shows that fungal inoculations may influence tree growth.     

Spatial patterns of fungal endophytes in a subtropical montane rainforest of northern Taiwan

Fungal endophytes of plants are ubiquitous and important to host plant health. Wood-inhabiting and foliar endophyte communities from multiple tree hosts were sampled at multiple spatial scales across the Fushan forest dynamics plot in northern Taiwan, using culture-free, community DNA amplicon sequencing methods. Fungal endophyte communities were distinct between leaves and wood, but the mycobiomes were highly variable across and within tree species. Despite this, host tree species was an important predictor of mycobiome community-composition. Within a single common tree species, “core” mycobiomes were characterized using co-occurrence analysis. The spatial co-occurrence patterns of these few species of fungal endophytes appear to explain the strong host effect. For wood endophytes, a consistent core mycobiome coexisted with the host across the extent of the study. For leaf endophytes, the core fungi resembled a more dynamic, “gradient” model of the core microbiome, changing across the topography and distance of the study.     

Effects of host plant environment and Ustilago maydis infection on the fungal endophyte community of maize (Zea mays)

The focus of many fungal endophyte studies has been how plants benefit from endophyte infection. Few studies have investigated the role of the host plant as an environment in shaping endophyte community diversity and composition. The effects that different attributes of the host plant, that is, host genetic variation, host variation in resistance to the fungal pathogen Ustilago maydis and U. maydis infection, have on the fungal endophyte communities in maize (Zea mays) was examined. The internal transcribed spacer (ITS) region of the rDNA was sequenced to identify fungi and the endophyte communities were compared in six maize lines that varied in their resistance to U. maydis. It was found that host genetic variation, as determined by maize line, had significant effects on species richness, while the interactions between line and U. maydis infection and line and field plot had significant effects on endophyte community composition. However, the effects of maize line were not dependent on whether lines were resistant or susceptible to U. maydis. Almost 3000 clones obtained from 58 plants were sequenced to characterize the maize endophyte community. These results suggest that the endophyte community is shaped by complex interactions and factors, such as inoculum pool and microclimate, may be important.     

植物内生菌定殖检测技术及其应用

自然环境中内生菌定殖于植物体内,对宿主植物产生多种有益效应,但是内生菌定殖情况难以检测,相关研究不够深入系统。目前在该领域使用较为广泛的检测技术包括：荧光标记、抗生素标记、荧光定量PCR和高通量测序等。内生菌通过孔隙伤口和降解细胞壁等方式侵染植物,通过种子垂直传递核心内生菌。对植物内生菌定殖的侵染方式、定殖方法和检测技术进行了归纳和整理,介绍了内生菌多种侵染和迁移途径,总结了目前内生菌定殖在生物防治、促进植物生长和污染修复等方面的功能,综述了多种检测方式在应用中的特点,以期为内生菌定殖植物的相关研究及其应用提供参考依据。     

Response of fungal endophyte communities within Andropogon gerardii (Big bluestem) to nutrient addition and herbivore exclusion

Fungal endophytes may alter plant responses to the environment, but how does the environment affect the communities of fungal symbionts within plants? We examined the impact of nutrient addition and herbivore exclusion on endophyte communities of the prairie grass Andropogon gerardii in a full factorial field experiment. Fungi were cultured from stems, young leaves, and mature leaves, ITS sequences obtained, and endophyte incidence, community richness, and composition analyzed. Results indicate that in plots where nutrient addition and herbivore exclusion treatments had been applied separately, fungal endophyte incidence, community composition or evenness did not differ, but that greater species richness was observed in plots with nutrient addition and herbivore exclusion treatments applied in combination, compared to other treatments. Further, although fungal community composition was significantly different in stem and leaf tissues, OTU richness was greater in all endophyte communities in nutrient addition plus herbivore exclusion treatments, regardless of tissue type. Our results indicate the distinct fungal endophyte communities found in different plant tissues respond similarly to environmental factors.     

Effects of endophyte infection on the competitive ability of Achnatherum sibiricum depend on endophyte species and nitrogen availability

Aims The leaves of almost all terrestrial plant species are colonized by endophytic fungi. Compared to agronomic grasses, which usually harbor few endophytes, native grasses generally possess greater endophyte species diversity. Existing studies examining endophyte effects on natural grasses under competition normally considered the infection status (infected or uninfected), and rarely considered endophyte species.     

植物内生菌增强植物对生物胁迫抗性的研究进展

植物在生长发育过程中因遭遇多种逆境的威胁而出现营养流失、产量大幅下降等问题，而使用传统的化学农药调控植物抗逆作用会对环境造成严重污染甚至危及人类健康，因此需要从天然成分中寻找合适的农药代替品。生活在每种植物体内的内生菌几乎都是植物微生态系统中的天然成分，因其特殊的生态位而可能对植物具有更加积极和直接的影响。然而目前，关于内生菌在提高宿主生物胁迫抗性等方面的作用机制还知之甚少。该文就植物内生菌的来源、多样性和对生物胁迫的抗性展开叙述。首先，总结了植物内生菌传播的主要方式，即水平传播和垂直传播；其次对内生菌种类的多样性以及在植物中的分布多样性进行了归纳与分析；最后，详细阐述了植物内生菌增强植物对生物胁迫应激耐受性(抗致病菌病害、抗虫害)的基本特点与作用机制，即植物内生菌可利用生态位竞争或营养位竞争产生的诱导抗性遏制病原菌感染，或合成抗生素类、生物碱类、几丁质类等次生代谢产物抑制病原菌或线虫的生长，从而防治病虫害。此外，基于内生菌增强植物生物胁迫抗性的研究现状进行了展望，为更加环保的生物防治制剂的开发与利用提供了参考。     

Endophytic fungi increase the processing rate of leaves by leaf‐cutting ants (Atta)

1. Fungal endophytes are microfungi that reside asymptomatically inside of leaf tissues, increasing in density and diversity through time after leaves flush. Previous studies have suggested that the presence of fungal endophytes in the harvest material of leaf‐cutting ants (Atta colombica, Guérin‐Méneville) may negatively affect the ants and their fungal cultivar. 2. In the present study, it was tested whether the presence and diversity of fungal endophytes affected the amount of time necessary for leaf‐cutter ants to cut, process, and plant leaf material in their fungal garden. It was found that ants took 30–43% longer to cut, carry, clean, and plant leaf tissue with high relative to low endophyte abundance, and that the ants responded similarly to leaf tissue with high or low endophyte diversity. 3. It was further investigated whether the fungal cultivars' colonisation rate was greater on leaf material without fungal endophytes. No difference in the ants' cultivar colonisation rate on leaf tissue with high or low endophyte abundance was observed.     

The influence of genetics,defensive chemistry and the fungal microbiome on disease outcome in whitebark pine trees

The invasive fungal pathogen Cronartium ribicola infects and kills whitebark pine (Pinus albicaulis) throughout western North America. Whitebark pine has been proposed for listing under the Endangered Species Act in the USA, and the loss of this species is predicted to have severe impacts on ecosystem composition and function in high‐elevation forests. Numerous fungal endophytes live inside whitebark pine tissues and may influence the severity of C. ribicola infection, either directly by inhibition of pathogen growth or indirectly by the induction of chemical defensive pathways in the tree. Terpenes, a form of chemical defence in pine trees, can also influence disease. In this study, we characterized fungal endophyte communities in whitebark pine seedlings before and after experimental inoculation with C. ribicola, monitored disease progression and compared fungal community composition in susceptible vs. resistant seedlings in a common garden. We analysed the terpene composition of these same seedlings. Seed family identity or maternal genetics influenced both terpenes and endophyte communities. Terpene and endophyte composition correlated with disease severity, and terpene concentrations differed in resistant vs. susceptible seedlings. These results suggest that the resistance to C. ribicola observed in natural whitebark pine populations is caused by the combined effects of genetics, endophytes and terpenes within needle tissue, in which initial interactions between microbes and hosts take place. Tree genotype, terpene and microbiome combinations associated with healthy trees could help to predict or reduce disease severity and improve outcomes of future tree breeding programmes.     

Fungal communities living within leaves of native Hawaiian dicots are structured by landscape‐scale variables as well as by host plants

A phylogenetically diverse array of fungi live within healthy leaf tissue of dicotyledonous plants. Many studies have examined these endophytes within a single plant species and/or at small spatial scales, but landscape‐scale variables that determine their community composition are not well understood, either across geographic space, across climatic conditions, or in the context of host plant phylogeny. Here, we evaluate the contributions of these variables to endophyte beta diversity using a survey of foliar endophytic fungi in native Hawaiian dicots sampled across the Hawaiian archipelago. We used Illumina technology to sequence fungal ITS1 amplicons to characterize foliar endophyte communities across five islands and 80 host plant genera. We found that communities of foliar endophytic fungi showed strong geographic structuring between distances of 7 and 36 km. Endophyte community structure was most strongly associated with host plant phylogeny and evapotranspiration, and was also significantly associated with NDVI, elevation and solar radiation. Additionally, our bipartite network analysis revealed that the five islands we sampled each harboured significantly specialized endophyte communities. These results demonstrate how the interaction of factors at large and small spatial and phylogenetic scales shapes fungal symbiont communities.     

Endophytic fungi reduce leaf-cutting ant damage to seedlings

Our study examines how the mutualism between Atta colombica leaf-cutting ants and their cultivated fungus is influenced by the presence of diverse foliar endophytic fungi (endophytes) at high densities in tropical leaf tissues. We conducted laboratory choice trials in which ant colonies chose between Cordia alliodora seedlings with high (E_high) or low (E_low) densities of endophytes. The E_high seedlings contained 5.5 times higher endophyte content and a greater diversity of fungal morphospecies than the E_low treatment, and endophyte content was not correlated with leaf toughness or thickness. Leaf-cutting ants cut over 2.5 times the leaf area from E_low relative to E_high seedlings and had a tendency to recruit more ants to E_low plants. Our findings suggest that leaf-cutting ants may incur costs from cutting and processing leaves with high endophyte loads, which could impact Neotropical forests by causing variable damage rates within plant communities.     

Can Epichloë endophytes enhance direct and indirect plant defence?

Induced or constitutive production of secondary metabolites is a successful plant defence strategy against herbivores which can be mediated by plant associated micro-organisms. Several grass species can be associated with an endophytic fungus of the genus Epichloë which produces herbivore toxic or deterring alkaloids. Besides these direct defences, herbivorous insects are controlled via indirect plant defence mechanisms by attracting predators. Recent studies indicate that Epichloë endophytes can improve the grass emitted volatile organic compounds towards herbivore deterrence. Due to their defensive mutualistic function, we hypothesize that Epichloë altered plant volatiles can attract aphid predators and contribute to an increased indirect plant defence. With a common garden study, we show that hoverfly (Syrphidae) larvae and pupae were more abundant on endophyte-infected plants compared to uninfected plants. Our results indicate that the Epichloë endophyte provides, besides direct defence (alkaloid), indirect plant defence by improving the plant odor attracting more olfactory foraging aphid predators. Future research is needed in order to understand: (I) whether endophyte-mediated changes in plant volatiles are induced herbivore specific, (II) whether there is a trade-off between endophyte-mediated direct and indirect plant defence, (III) whether the endophyte produces volatiles or induces a change in plant-derived volatiles, (IV) the role of plant signals in endophyte-mediated plant defence.     

Site‐specific responses of foliar fungal microbiomes to nutrient addition and herbivory at different spatial scales

The plant microbiome can affect host function in many ways and characterizing the ecological factors that shape endophytic (microbes living inside host plant tissues) community diversity is a key step in understanding the impacts of environmental change on these communities. Phylogenetic relatedness among members of a community offers a way of quantifying phylogenetic diversity of a community and can provide insight into the ecological factors that shape endophyte microbiomes. We examined the effects of experimental nutrient addition and herbivory exclusion on the phylogenetic diversity of foliar fungal endophyte communities of the grass species Andropogon gerardii at four sites in the Great Plains of the central USA. Using amplicon sequencing, we characterized the effects of fertilization and herbivory on fungal community phylogenetic diversity at spatial scales that spanned within‐host to between sites across the Great Plains. Despite increasing fungal diversity and richness, at larger spatial scales, fungal microbiomes were composed of taxa showing random phylogenetic associations. Phylogenetic diversity did not differ systematically when summed across increasing spatial scales from a few meters within plots to hundreds of kilometers among sites. We observed substantial shifts in composition across sites, demonstrating distinct but similarly diverse fungal communities were maintained within sites across the region. In contrast, at the scale of within leaves, fungal communities tended to be comprised of closely related taxa regardless of the environment, but there were no shifts in phylogenetic composition among communities. We also found that nutrient addition (fertilization) and herbivory have varying effects at different sites. These results suggest that the direction and magnitude of the outcomes of environmental modifications likely depend on the spatial scale considered, and can also be constrained by regional site differences in microbial diversity and composition.     

Interaction between the endophytic fungus Epichloe bromicola and the grass bromus erectus: effects of endophyte infection, fungal concentration and environment on grass growth and flowering

Epichloe bromicola is an endophytic fungal species that systemically and perennially colonizes intercellular spaces of leaf blades, leaf sheaths and culms of Bromus grass species. E. bromicola causes choke disease in B. erectus, suppressing maturation of most, if not all, host inflorescences. In an investigation of the interaction between fungus and host, we used a quantitative polymerase chain reaction technique to estimate the amount of fungal DNA, and thereby fungal concentration, in host plants. Fungal concentration was directly correlated with vegetative vigour of the plant, as measured by longest leaf length, number of tillers and vegetative above-ground biomass, suggesting that, during vegetative growth, the endophytic fungus is most beneficial for the plant when present in high concentrations. In contrast, the reproduction of the plant, as measured by the number of functional inflorescences, was inversely correlated with fungal concentration: the majority of infected plants, and all that were associated with high concentrations of fungi, were diseased. Thus, the benefit of endophyte infection for the plant is coupled with the disadvantages of infertility. Fungal concentration was shown to be at least in part genetically determined because fungal concentration differed significantly in different plant-endophyte genotype combinations (symbiotum). In a field experiment with normal and CO2-enriched environments, elevated CO2 levels favoured fungal reproductive vigour over host reproductive vigour, suggesting that these plant endophytes would be at a selective advantage in a corresponding environmental-change scenario. We conclude that a dynamic and complex relationship between fungal endophyte infection, fungal concentration, genotype and environment affects growth and fecundity of B. erectus and should contribute to the evolution of these plant-fungal interactions.     

Mycobiota diversity and its vertical transmission in plants along an elevation gradient in mountains

Plants are colonized by fungal endophytes. In this study we tested the hypothesis that endophyte communities in mountain plants changes along the elevation gradient. We identified fungal endophytes in aboveground parts and seeds of five plant species at altitudes of 1000–1750 m in the Tatra National Park. Endophytes isolated from them were grouped into morphotypes on the basis of macroscopic features, such as mycelium shape and colour. Isolates representing individual morphotypes were identified using molecular markers ITS1 and ITS2. When comparing species composition, we used Bray-Curtis distance matrices, calculated on the basis of frequency of the given fungal species. We identified 16 species of fungal endophytes. Five taxa were absent from seeds in spite of their occurrence in mother plant leaves. Differences in altitude were not significantly correlated with fungal species composition observed at a given sampling site. There was also no significant correlation between the species composition of leaf and seed mycobiota. This suggests imperfect vertical transmission in the studied plant species.     

Insect oviposition preference between Epichloë‐symbiotic and Epichloë‐free grasses does not necessarily reflect larval performance

Variation in plant communities is likely to modulate the feeding and oviposition behavior of herbivorous insects, and plant‐associated microbes are largely ignored in this context. Here, we take into account that insects feeding on grasses commonly encounter systemic and vertically transmitted (via seeds) fungal Epichloë endophytes, which are regarded as defensive grass mutualists. Defensive mutualism is primarily attributable to alkaloids of fungal origin. To study the effects of Epichloë on insect behavior and performance, we selected wild tall fescue (Festuca arundinacea) and red fescue (Festuca rubra) as grass–endophyte models. The plants used either harbored the systemic endophyte (E+) or were endophyte‐free (E?). As a model herbivore, we selected the Coenonympha hero butterfly feeding on grasses as larvae. We examined both oviposition and feeding preferences of the herbivore as well as larval performance in relation to the presence of Epichloë endophytes in the plants. Our findings did not clearly support the female's oviposition preference to reflect the performance of her offspring. First, the preference responses depended greatly on the grass–endophyte symbiotum. In F. arundinacea, C. hero females preferred E+ individuals in oviposition‐choice tests, whereas in F. rubra, the endophytes may decrease exploitation, as both C. hero adults and larvae preferred E? grasses. Second, the endophytes had no effect on larval performance. Overall, F. arundinacea was an inferior host for C. hero larvae. However, the attraction of C. hero females to E+ may not be maladaptive if these plants constitute a favorable oviposition substrate for reasons other than the plants' nutritional quality. For example, rougher surface of E+ plant may physically facilitate the attachment of eggs, or the plants offer greater protection from natural enemies. Our results highlight the importance of considering the preference of herbivorous insects in studies involving the endophyte‐symbiotic grasses as host plants.     

Indirect effects of an unspecialized endophytic fungus on specialized plant – herbivorous insect interactions

The effects of Acremonium alternatum Gams (Ascomycotina, Clavicipitacea) on the development and nutrition of diamondback moth larvae Plutella xylostella L. (Lepidoptera, Plutellidae) were studied in the laboratory. All experiments were conducted before the endophyte reached the green parts of the plants; thus P. xylostella, a folivore, was not in direct contact with the endophyte. Larvae feeding on leaves of previously inoculated plants suffered from increased mortality, especially during the first 10 days of development. Likewise, during early development surviving larvae had a reduced relative growth rate (RGR), which, however, did not result in reduced pupal or adult weight. We found sexual differences in the food utilization efficiency; female P. xylostella progeny reacted more sensitively to endophytic infection of cabbage than male larvae. Female larvae feeding on leaves of endophyte-infested plants responded to reduced efficiency of conversion of ingested food (ECI) by increasing their relative consumption rate (RCR). The underlying mechanisms for these results are discussed in relation to changes in plant phytosterol metabolism which could account for reduced larval growth on inoculated cabbage plants. Our data suggest that unspecialized, soil-borne endophytic fungi, even when their association with the host plant is weak, can influence aboveground herbivore development and should be considered when investigating plant-insect interactions. Received: 3 November 1997 / Accepted 29 December 1997     

Antagonism between Byssochlamys spectabilis (anamorph Paecilomyces variotii) and plant pathogens: Involvement of the bioactive compounds produced by the endophyte

Fungal endophytes can be part of the defensive system of plants against multiple pathogens by competing for resources, hyperparasitism or producing bioactive compounds with antimicrobial properties. There is an ever‐increasing interest for obtaining new and environmentally friendly products to use in the fight against pathogens. With this purpose, Byssochlamys spectabilis (anamorph Paecilomyces variotii), which is a fungal species that commonly occurs, was evaluated as an antagonistic organism towards three phytopathogens (Biscogniauxia mediterranea, Fusarium moniliforme and Phytophthora cinnamomi). First, an in vitro experiment was designed to test the effect that the endophyte filtrate had on the three pathogens. The endophyte filtrate decreased the radius growth rate of F. moniliforme by nearly 10%. Consequently, the antagonism between B. spectabilis and F. moniliforme was evaluated in Lolium rigidum plants under greenhouse conditions by means of co‐inoculations. The endophyte produced a decrease of 50–75% in the disease severity caused by the pathogen in the earliest infection stages. Crude extracts of B. spectabilis were obtained to determine the secondary metabolites responsible for such an effect. The bioactivity‐guided chromatography and HPLC‐MS (high performance liquid chromatography coupled with mass spectrometry) of the active fraction suggested that the antibiotic activity was caused by viriditoxin. In conclusion, the fungal endophyte B. spectabilis and/or its bioactive compounds showed antagonism towards several phytopathogens and deserves further study to investigate its actual potential for use as a biocontrol agent.     

植物内生菌研究进展

内生菌由于生长于植物体内且不引起植物病害所以不易被发现,它是一类具有高实用价值的植物内生微生物。经过人们的不断研究,越来越多的植物内生菌被发现,其活性代谢产物的优势也得到了更多研究者的认可。综述了国内外有关植物内生菌研究的主要成果和进展,并从植物内生菌的发现、研究历史、多样性、生理生化特性以及植物内生菌与宿主植物间的作用关系等多个层次进行了概述,以期为植物内生菌相关研究提供参考。