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.     

Deterministic processes have limited impacts on foliar fungal endophyte communities along a savanna-forest successional gradient

Patterns and drivers of succession provide insight into the mechanisms that govern community assembly, but remain poorly understood for microbial communities. We assess whether successional trends of trees are mirrored by foliar endophyte communities of three tree species across a deterministic woody successional gradient. Additionally, we test the relative contribution of abiotic predictors, biotic factors, and spatial distance between sites in predicting composition and richness of endophyte communities. Unlike the tree community, endophyte communities showed no consistent evidence of deterministic succession. Host identity was the most important factor structuring endophyte community composition; within hosts, spatial distance from the indigenous forest and between samples was important, while environmental predictors had small and inconsistent effects. Much variation in endophyte composition remained unexplained. In contrast, endophyte richness was well-explained by predictor variables. Host identity was most important in predicting endophyte richness, while the effect of other predictors on richness differed between host species. We conclude that deterministic succession in trees did not result in deterministic succession in endophyte communities; instead community assembly was most strongly influenced by host identity; while within hosts, neutral processes may be more important for endophyte assembly than deterministic factors.     

Fungal endophyte communities differ between chestnut galls and surrounding foliar tissues

Foliar endophytic fungi are present in almost all vascular plants. The composition of endophyte communities varies among plant individuals. Likely, but understudied, sources of this variation are the species composition of the plant community and initial attacks by insect herbivores. We addressed these issues by characterizing fungal endophyte communities on leaves of chestnut (Castanea sativa) grown in pure vs. mixed stands. We used ITS metabarcoding methods to identify endophytic fungi associated with galls caused by the invasive gall wasp, Dryocosmus kuriphilus, and with surrounding chestnut leaf tissues. We found 1378 different OTUs. The richness, diversity and composition of endophyte communities differed between galls and surrounding leaf tissues but were independent of forest stand composition. Fungal endophyte richness was lower in galls than in surrounding leaf tissues. Most differences in the composition of fungal endophyte communities between galls and foliar tissues were due to OTU turnover. These results suggest that insect-induced galls provide a particular habitat condition for endophytic microorganisms, regardless of forest species composition. A better understanding of endophyte biology is important to improve their use as biocontrol agents of galling insects.     

Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees

Processes shaping the distribution of foliar fungal endophyte species remain poorly understood. Despite increasing evidence that these cryptic fungal symbionts of plants mediate interactions with pathogens and herbivores, there remain basic questions regarding the extent to which dispersal limitation and host specificity might shape fungal endophyte community composition in rainforests. To assess the relative importance of spatial pattern and host specificity, we isolated fungi from a sample of mapped trees in lowland Papua New Guinea. Sequences of the internal transcribed spacer (ITS) region were obtained for 2079 fungal endophytes from three sites and clustered into molecular operational taxonomic units (MOTUs) at 95% similarity. Multivariate analyses suggest that host affinity plays a significant role in structuring endophyte community composition whereas there was no evidence of endophyte spatial pattern at the scale of tens to hundreds of metres. Differences in endophyte communities between sampled trees were weakly correlated with variation in foliar traits but not with tree species relatedness. The dominance of relatively few generalist endophytes and the presence of a large number of rare MOTUs was a consistent observation at three sites separated by hundreds of kilometres and regional turnover was low. Host specificity appears to play a relatively weak but more important role than dispersal limitation in shaping the distribution of fungal endophyte communities in New Guinea forests. Our results suggest that in the absence of strong ecological gradients and host turnover, beta diversity of endophyte communities could be low in large areas of contiguous forest.     

Herbivory on planted oak seedlings across a habitat edge created by timber harvest

Edge habitats create environmental gradients that affect plant community composition and herbivore behavior. Silvicultural disturbance creates edge habitat with direct (via changes in light) and indirect (via changes in herbivore behavior) consequences for the growth and survival of tree seedlings, and thus, the composition of the future forest stands. Herbivores, particularly ungulates, can be a major limiting factor in oak regeneration, and silvicultural disturbance may alter the abundance or behavior of herbivores following harvest. We measured the severity of herbivory on experimentally planted white (Quercus alba) and black oak (Quercus velutina) seedlings by white-tailed deer (Odocoileus virginianus) and eastern cottontail rabbits (Sylvilagus floridanus), as well as foliar damage from insects, across gradients created by clearcuts in a deciduous forest in Indiana, USA. Overall browse pressure on oaks was low in our study. Nonetheless, spatial variation in herbivory depended on herbivore taxa; herbivory by rabbits was highest inside harvest openings, whereas foliar damage by insects peaked in the forest. Intensity of deer herbivory was constant across the edge. In addition, we observed indirect interactions among herbivore species mediated by a seedling’s browsing history. Herbivore damage by deer was positively related to past browsing by rabbits, and foliar damage from insects was positively related to past browsing by both deer and rabbits. Increasing woody plant competition reduced herbivory on seedlings by both deer and rabbits. Given the lack of spatial variability in deer herbivory and low overall herbivory by rabbits, we suspect that interactions between timber harvesting and herbivory did not have a strong impact on oak seedlings at our study sites.     

Large herbivores affect the stoichiometry of nutrients in a regenerating woodland ecosystem

Previous studies on the effects of herbivores on nutrient cycling have given little consideration to the relationship between soil nitrogen (N) and phosphorus (P) availability. Here we examined how browsing by red deer influences the relative availability of N and P in a regenerating woodland ecosystem. We found that removal of browsing by fencing for 14 years led to a shift from N toward P limitation of the dominant tree species Betula pubescens . This was evidenced by a significant increase in foliar N:P ratio of B. pubescens as a result of removal of browsing; mean N:P ratio of foliage from browsed areas was 13.2 suggesting that trees growing in browsed areas were N limited, whereas foliage from unbrowsed areas had a mean N:P ratio of 15.8, suggesting that these areas were more P limited. Further evidence of a shift toward P limitation in unbrowsed areas came from the finding that root uptake of labelled ³²P was significantly greater in roots collected from unbrowsed than browsed trees. Soil phosphatase activity did not significantly differ between browsed and unbrowsed areas. Our data indicate therefore that herbivores have the potential to significantly affect the stoichiometry of N and P in forest ecosystems.     

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.     

Unintended Consequences of Invasive Predator Control in an Australian Forest: Overabundant Wallabies and Vegetation Change

Over-abundance of native herbivores is a problem in many forests worldwide. The abundance of native macropod wallabies is extremely high at Booderee National Park (BNP) in south-eastern Australia. This has occurred because of the reduction of exotic predators through an intensive baiting program, coupled with the absence of other predators. The high density of wallabies at BNP may be inhibiting the recruitment of many plant species following fire-induced recruitment events. We experimentally examined the post-fire response of a range of plant species to browsing by wallabies in a forest heavily infested with the invasive species, bitou bush Chrysanthemoides monilifera. We recorded the abundance and size of a range of plant species in 18 unfenced (browsed) and 16 fenced (unbrowsed) plots. We found the abundance and size of bitou bush was suppressed in browsed plots compared to unbrowsed plots. Regenerating seedlings of the canopy or middle storey tree species Eucalyptus pilularis, Acacia implexa, Allocasuarina littoralis, Breynia oblongifolia and Banksia integrifolia were either smaller or fewer in number in grazed plots than treatment plots as were the vines Kennedia rubicunda, Glycine tabacina and Glycine clandestina. In contrast, the understorey fern, Pteridium esculentum increased in abundance in the browsed plots relative to unbrowsed plots probably because of reduced competition with more palatable angiosperms. Twelve months after plots were installed the community structure of the browsed and unbrowsed plots was significantly different (P = 0.023, Global R = 0.091). The relative abundance of C. monilifera and P. esculentum contributed most to the differences. We discuss the possible development of a low diversity bracken fern parkland in Booderee National Park through a trophic cascade, similar to that caused by overabundant deer in the northern hemisphere. We also discuss its implications for broad scale fox control in southern Australian forests.     

Birch family and environmental conditions affect endophytic fungi in leaves

We investigated whether variation in foliar endophyte frequency among mountain birch trees from different maternal families was due in part to genetic differences among trees. The effect of different environmental conditions on the susceptibility of these mountain birch families to foliar endophytes was tested. The 3-year study was conducted in two tree gardens (altitudinal difference 180 m) with ten families of mountain birch. The frequency of the commonest endophytic fungus in mountain birch leaves, Fusicladium sp., was significantly affected by mountain birch family, with the ranking of families relative to Fusicladium sp. frequency being consistent from environment to environment. Variation in the frequency of Melanconium sp. was difficult to interpret because of significant family × garden × year interaction. Fusicladium sp. and Melanconium sp. endophytes were most frequent in different tree individuals, families and gardens. We conclude that mountain birch trees show heritable variation in their foliar endophyte frequency, and thus one of the conditions necessary for foliar endophytes of mountain birch trees to be able to affect the evolution of their host plant is fulfilled. However, the effect of mountain birch family on the frequency of endophytic fungi varies depending on the endophytic genera in question and partially also on environmental conditions. Received: 28 March 1998 / Accepted: 14 October 1998     

Geographic locality greatly influences fungal endophyte communities in Cephalotaxus harringtonia

Although endophytes of conifers have been extensively studied, few data are available on Cephalotaxaceae. We examined foliar and stem endophytes of Cephalotaxus harringtonia, within its natural range in Japan and outside its natural range in France to study the effect of geography on endophyte community composition. In Japan, rapidly growing endophytes were dominant and may have masked the real diversity, in comparison to France where most endophytes were growing slowly. Analyses of ITS rDNA revealed 104 different Blast Groups among 554 isolates. Almost no overlap between endophyte assemblages of C. harringtonia from the two countries was observed. It seems that Japanese C. harringtonia trees, which should be well adapted to their native site, would host a specific, endemic endophyte community, while trees that have been introduced recently to a foreign site, in France, should have captured existing cosmopolitan and more generalist taxa. In Japan the majority of xylariaceous taxa, which dominated the communities, were unknown and, although closely related to Asian taxa, may be new to science. Dothideomycetes were more prevalent in France. Locally, urban environment, particularly in Japan, may have introduced some perturbations in the native endophyte community of C. harringtonia, with an abundance of generalist fungi such as Nigrospora and Colletotrichum.     

Crown closure affects endophytic leaf mycobiome compositional dynamics over time in Pseudotsuga menziesii var. menziesii

Old-growth Pseudotsuga menziesii var. menziesii forests produce complex environmental and spatial gradients along which biota assemble. Given this, it has been proposed that changes in the crown microenvironment are associated with different community assembly outcomes for needle fungi. Using high-throughput sequencing, the endophytic mycobiomes of needles were characterized for increasing ages of needles sampled along the boles of eight coastal Douglas-fir trees. Leveraging airborne light detection and ranging (LiDAR) data to create three-dimensional “point cloud” representations of tree crowns revealed that crown closure accounted for more fungal compositional variation than height in crown, and fungal richness and diversity were positively correlated with increasing crown closure. Supplementing the point clouds of each climbed tree with clouds from >5,000 randomly selected trees in the study area showed that fungal communities from closed portions of the crown were increasingly structured with needle age. These findings highlight the importance of the crown microenvironment in the development of foliar fungal communities for a foundation tree species.     

Canopy tree species and openness affect foliar endophytic fungal communities of understory seedlings

There is growing evidence demonstrating the diversity of foliar endophytic fungi and their ecological roles in the survival of tree seedlings. However, the factors that shape fungal communities in tree seedlings within natural forest ecosystems remain poorly understood. Here, we evaluated the composition of foliar endophytic fungi growing in current-year seedlings of Cornus controversa and Prunus grayana in a cool temperate deciduous forest through a seed-sowing experiment and fungal isolation. The composition of endophytic fungi was affected by canopy tree species, canopy openness, and time after germination. In total, 27 and 22 fungal taxa were isolated from C. controversa and P. grayana seedlings, respectively. The dominant fungal taxa in both seedling species were Colletotorichum spp., and their isolation frequencies were higher under C. controversa canopies than under P. grayana canopies; the frequencies also increased with time after germination. These results suggest that overstory tree species strongly influences the endophytic fungal communities of understory seedlings.     

Endophyte communities vary in the needles of Norway spruce clones

Endophytic fungi show no symptoms of their presence but can influence the performance and vitality of host trees. The potential use of endophytes to indicate vitality has been previously realized, but a standard protocol has yet to be developed due to an incomplete understanding of the factors that regulate endophyte communities. Using a culture-free molecular approach, we examined the extent to which host genotype influences the abundance, species richness, and community composition of endophytic fungi in Norway spruce needles. Briefly, total DNA was extracted from the surface-sterilized needles of 30 clones grown in a nursery field and the copy number of the fungal internal transcribed spacer (ITS) region of ribosomal DNA was estimated by quantitative PCR. Fungal species richness and community composition were determined by denaturing gradient gel electrophoresis and DNA sequencing. We found that community structure and ITS copy number varied among spruce clones, whereas species richness did not. Host traits interacting with endophyte communities included needle surface area and the location of cuttings in the experimental area. Although Lophodermium piceae is considered the dominant needle endophyte of Norway spruce, we detected this species in only 33 % of samples. The most frequently observed fungus (66 %) was the potentially pathogenic Phoma herbarum. Interestingly, ITS copy number of endophytic fungi correlated negatively with the richness of ectomycorrhizal fungi and thus potential interactions between fungal communities and their influence on the host tree are discussed. Our results suggest that in addition to environmental factors, endophyte communities of spruce needles are determined by host tree identity and needle surface area.     

Environmental factors and host genetic variation shape the fungal endophyte communities within needles of Scots pine (Pinus sylvestris)

To determine the role of environmental and host genetic factors in shaping fungal endophyte communities we used culturing and metabarcoding techniques to quantify fungal taxa within healthy Scots pine (Pinus sylvestris) needles in a 7-y old provenance-progeny trial replicated at three sites. Both methods revealed a community of ascomycete and basidiomycete taxa dominated by the needle pathogen Lophodermium seditiosum. Differences in fungal endophyte taxon composition and diversity indices were highly significant among trial sites. Within two sites, fungal endophyte communities varied significantly among provenances. Furthermore, the communities differed significantly among maternal families within provenances in 11/15 and 7/15 comparisons involving culture and metabarcoding data respectively. We conclude that both environmental and host genetic variation shape the fungal endophyte community of P. sylvestris needles.     

Horizontal transmission of the Picea glauca foliar endophyte Phialocephala scopiformis CBS 120377

We have studied the presence of the foliar endophtye of Picea glauca (white spruce) Phialocephala scopiformis CBS 120377 and its affect on the growth of Choristoneura fumiferana (spruce budworm). Here we examine the transmission of this fungus from 50 trees planted in a test field site to 250 P. glauca seedlings planted under the emerging canopies. After 3 y, the endophyte spread to 40 % of these trees (now 20–30 cm) with an average rugulosin (an anti-insect toxin) concentration of 1 μg g^?1. All woody plants within 2 m of the test trees were collected. These were all shown to be negative for P. scopiformis except for some spruce seedlings that arose from seeds (natural generation). This is positive evidence for the horizontal transmission of P. scopiformis and its apparent specificity to P. glauca under field conditions.     

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.     

Species-specific characteristics of trees can determine the litter macroinvertebrate community and decomposition process below their canopies

This paper tests whether individual trees in a mature forest stand influence the process of litter decomposition and the macroinvertebrate communities in the soil underneath their canopies, as a result of species-specific characteristics. A field decomposition experiment was performed in a mature forest stand of tropical montane cloud forest in Mexico. The areas under the canopies of Quercus laurina Humbl. & Bompl., Oreopanax xalapensis (Kunth) Decne. & Planchon and Beilschmedia ovalis (Blake) C. K. Allen trees were used as experimental units. The natural soil and litter macroinvertebrate communities were monitored and compared to the community that invaded decomposition boxes with reciprocally transplanted leaf litter. The abundances of four macroinvertebrate taxa in natural litter differed among tree species independently of season. No differences were found in the soil community. The response to experimental litter by macroinvertebrate taxa suggests that the production of a specific quality of litter is an important mechanism by which a tree influences the litter macroinvertebrate community that develops under its canopy. However, not all differences in community composition naturally found between tree species can be explained by differences in litter quality during the first year of decomposition. Differences in nutrient release that occur after the first year, and physical properties of litter also probably play an important role. Independently of the canopy tree, the initial chemical quality (N, P, Ca, Mg and lignin) of experimental litter largely determined the decomposition rate and nutrient dynamics of decomposing leaves. However, it was found that under O. xalapensis trees the breakdown of lignin from the litter produced by the same species of tree was particularly effective. This suggests that a feedback has developed between this tree species and the decomposer community prevailing under its canopy.     

Linking deer browsing and terpene production among genetic identities in Chamaecyparis nootkatensis and Thuja plicata (Cupressaceae)

To investigate whether differential herbivore browsing reflects genetic variation in plant defense expression, variation in needle terpenes and damage caused by black-tailed deer (Odocoileus hemionus) was analyzed on yellow-cedar (Chamaecyparis nootkatensis) and western redcedar (Thuja plicata). In a 100-genet yellow-cedar population, three genets that were heavily browsed and had extremely low levels of monoterpenes (0-0.36% dry matter), sesquiterpenes, and diterpenes were compared to unbrowsed genets (0.85-3.83% monoterpenes in dry matter). These differences were maintained in individuals protected from browsing, suggesting genetically based variation in constitutive terpene production. In western redcedar, heavily browsed trees had significantly lower total monoterpene concentrations (1.69% dry matter) than lightly browsed trees (3.32% dry matter). One heavily browsed tree expressed no monoterpenes. No differences were found for diterpenes. In both species, the genotypes with extremely low monoterpene concentrations came from the same open-pollinated families.     

Role of mycorrhizal networks and tree proximity in ectomycorrhizal colonization of planted seedlings

The importance of mycorrhizal network (MN)-mediated colonization under field conditions between trees and seedlings was investigated. We also determined the combined influences of inoculum source and distance from trees on the ectomycorrhizal (EM) community of seedlings. On six sites, we established trenched plots around 24 residual Pseudotsuga menziesii var. glauca trees and then planted seedlings at four distances (0.5, 1.0, 2.5, and 5.0 m) from the tree into four mesh treatments that served to restrict inoculum access (i.e., planted into mesh bags with 0.5, 35, 250 μm pores or directly into soil). Ectomycorrhizal communities were identified after two growing seasons using morphological and molecular techniques. Mesh treatments had no effect on seedling mycorrhizal colonization, richness, or diversity, suggesting that MN-mediated colonization, was not an essential mechanism by which EM communities were perpetuated to seedlings. Instead, wind-borne and soil inoculum played an important role in seedling colonization. The potential for MNs to form in these forests was not dismissed, however, because trees and seedlings shared 83 % of the abundant EM. Seedlings furthest from trees had a simpler EM community composition and reduced EM richness and diversity compared to seedlings in closer proximity.     

Host phylogeny is the primary determinant of ectomycorrhizal fungal community composition in the permafrost ecosystem of eastern Siberia at a regional scale

Ectomycorrhizal (EM) fungal communities have been studied worldwide; however, those in the very cold and dry continental climate zone of northern Eurasia remain understudied. We investigated EM fungal community structure on plant roots and its determinants in eastern Siberia. We identified 291 EM fungal taxa belonging to 37 fungal genera from nine sites spanning 2100 km. In a variation partitioning analysis, host plant phylogeny was the primary factor that explained variation in fungal community composition, followed by spatial distance, soil, and climate. Host specificity and preference were attributed to differences in EM fungal community composition among host plants. The EM fungal community on Larix cajanderi, the dominant canopy tree in the region, was characterized by a high proportion of Suillus and Rhizopogon species. This implies that these specialist fungal symbionts have a close ecological relationship with pioneer Larix trees to adapt to the harsh continental climate of Siberia.