Life histories of hosts and pathogens predict patterns in tropical fungal plant diseases

Soil microbial communities in dry and moist tropical forests exhibit distinct shifts in community composition but not diversity with succession

Soil microbial communities are integral to ecosystem function but our understanding of how they respond to secondary succession in fragmented landscapes is limited, particularly in tropical dry forests. We used DNA metabarcoding to evaluate successional changes in soil bacteria and fungi, comparing land managed for cattle, young, and older secondary forests at moist and dry sites in the Republic of Panama. We highlight key functional groups of microbes that interact with plants, including arbuscular mycorrhizal fungi (AMF), nitrogen-fixing bacteria, and plant pathogenic fungi. Plant diversity was higher at the moist site and increased with succession as the plant communities changed at both sites. By contrast, bacterial diversity was similar across sites and successional stages, and while overall fungal diversity was higher at the moist site, it also showed no changes with succession at either site. However, microbial community composition did change, with pastures and older forests having distinct bacterial and fungal communities and young secondary forests often displaying transitional ones. Functional groups of microbes showed contrasting patterns between sites, with the dry forest having a higher diversity of Nitrogen-fixing bacteria despite lower densities of legumes, higher diversity and different communities of AMF, and a much lower incidence of putative fungal plant pathogens than the moist site. Our findings highlight the importance of looking at aboveground and belowground effects together and demonstrate that predictions generated for soil microbes in moist tropical forests may not apply to dry forests. These results may also inform the restoration of climate-resilient forests.

IMPORTANCE

Secondary forests are important components of neotropical landscapes and soil microbes help to shape these forests and the ecosystem services that they provide. This study demonstrates that soil microbial communities in moist and dry tropical forests can recover and reassemble after only 20 years of natural succession following the removal of cattle. However, successional patterns that are seen in the plant community are not always seen belowground. These patterns were more predictable at the moist than the dry site where the patchiness of the landscape likely restricts dispersal of both plants and soil microbes. We highlight the importance of preserving remaining tropical dry forests as they host unique microbial biodiversity that may help forests respond to drought conditions. As community shifts in soil microbes influence plant establishment, forest productivity, and other aspects of ecosystem functioning during the succession of tropical forest communities, our results can inform the restoration of climate-resilient forests.

Prevalent arbuscular mycorrhizae in roots and highly variable mycobiome in leaves of epiphytic subtropical fern Ophioderma pendulum

PREMISE

Endophytic and mycorrhizal fungi are crucial in facilitating plant nutrition acquisition and stress tolerance. In epiphytic habitats, plants face nutrition and water stress, but their roots are mostly nonmycorrhizal and especially lacking in arbuscular mycorrhizal associations. Ophioderma pendulum is an epiphytic fern with a partially mycoheterotrophic lifestyle, likely heavily reliant on symbiotic fungi. To characterize fungal associations in the sporophyte of O. pendulum, we focused on leaves and roots of O. pendulum, seeking to reveal the fungal communities in these organs.

METHODS

Roots and leaves from O. pendulum in a subtropical forest were examined microscopically to observe the morphology of fungal structures and determine the percentage of various fungal structures in host tissues. Fungal composition was profiled using metabarcoding techniques that targeted ITS2 of the nuclear ribosomal DNA.

RESULTS

Roots were consistently colonized by arbuscular mycorrhizal fungi (Glomeromycota), especially Acaulospora. Unlike previous findings on epiphytic ferns, dark septate endophytes were rare in O. pendulum roots. Leaves were predominantly colonized by Ascomycota fungi, specifically the classes Dothideomycetes (46.88%), Eurotiomycetes (11.51%), Sordariomycetes (6.23%), and Leotiomycetes (6.14%). Across sampling sites, fungal community compositions were similar in the roots but differed significantly in the leaves.

CONCLUSIONS

Ophioderma pendulum maintains stable, single-taxon-dominant communities in the roots, primarily featuring arbuscular mycorrhizal fungi, whereas the leaves may harbor opportunistic fungal colonizers. Our study underlines the significance of mycorrhizal fungi in the adaptation of epiphytic ferns.

Elucidating the endophytic bacterial and fungal community composition and diversity in the tree fern Alsophila spinulosa through meta-amplicon sequencing

Plant tissues harbor abundant endophytes, which are crucial for plant growth. Endophytes present in Alsophila spinulosa, which is enriched with medicinal components, have not been isolated and characterized yet. Here we employed meta-amplicon sequencing to identify endophytic species and examined their diversity in the leaves, petioles, roots and stems of A. spinulosa. Our findings revealed 1,247 operational taxonomic units (OTUs) for endophytic bacteria across 210 species and 476 OTUs for endophytic fungi across 222 species. Alpha diversity analysis showed the highest endophytic bacterial diversity in A. spinulosa roots, whereas fungal diversity was similar across the leaf, petiole and root tissues. Fungal diversity in the leaves and petioles was markedly higher than that in the stems. Furthermore, beta diversity analysis revealed similarities in the endophytic bacterial and fungal compositions between the leaves and petioles, whereas the compositions in roots and stems considerably differed from those in the leaves and petioles. At the genus level, the predominant endophytic bacteria were Methylobacterium-Methylorubrum and Pseudomonas, whereas the predominant endophytic fungi were Cutaneotrichosporon and Pseudofabraea. Linear discriminant analysis effect size revealed characteristic endophytic bacterial genera specific to each tissue type and characteristic endophytic fungal genera specifically in the leaves, petioles and roots. The co-occurrence network analysis indicated that the complexity of endophyte networks was the highest in the leaves and the lowest in the stems of A. spinulosa. Overall, this study elucidates the distribution patterns of endophytes in A. spinulosa across various tissues, offering valuable microbial resources for the development of natural products for medicinal application.

Effects of grazing exclusion on soil properties, fungal community structure, and diversity in different grassland types

Soil fungi are involved in the decomposition of organic matter, and they alter soil structure and physicochemical properties and drive the material cycle and energy flow in terrestrial ecosystems. Fungal community assembly processes were dissimilar in different soil layers and significantly affected soil microbial community function and plant growth. Grazing exclusion is one of the most common measures used to restore degraded grasslands worldwide. However, changes in soil fungal community characteristics during grazing exclusion in different types of grasslands are unknown. Here, we investigated the effects of a 9-year grazing exclusion on soil properties, fungal community composition, and diversity in three grassland types (temperate desert, temperate steppe, and mountain meadow). The results showed that (1) in the 0-5 cm soil layer, grazing exclusion significantly increased the differences in SWC, SOC, KN, and N:P among the three grassland types, while the final pH, BD, TP, C:N, and C:P values were consistent with the results before exclusion. In the 5-10 cm soil layer, grazing exclusion significantly increased total phosphorus (TP) in temperate deserts by 34.1%, while significantly decreasing bulk density (BD) by 9.8% and the nitrogen: phosphorus ratio (N:P) by 47.1%. (2) The soil fungal community composition differed among the grassland types, For example, significant differences were found among the three grassland types for the Glomeromycota and Mucoromycota. (3) Under the influence of both grazing exclusion and grassland type, there was no significant change in soil fungal alpha diversity, but there were significant differences in fungal beta diversity. (4) Grassland type was the most important factor influencing changes in fungal community diversity, and vegetation cover and soil kjeldahl nitrogen were the main factors influencing fungal diversity. Our research provides a long-term perspective for better understanding and managing different grasslands, as well as a better scientific basis for future research on grass-soil-microbe interactions.

The interaction of climate, plant, and soil factors drives putative soil fungal pathogen diversity and community structure in dry grasslands

Soil pathogens play important roles in shaping soil microbial diversity and controlling ecosystem functions. Though climate and local environmental factors and their influences on fungal pathogen communities have been examined separately, few studies explore the relative contributions of these factors. This is particularly crucial in eco-fragile regions, which are more sensitive to environmental changes. Herein we investigated the diversity and community structure of putative soil fungal pathogens in cold and dry grasslands on the Tibetan Plateau, using high-throughput sequencing. The results showed that steppe soils had the highest diversity of all pathogens and plant pathogens; contrastingly, meadow soils had the highest animal pathogen diversity. Structural equation modelling revealed that climate, plant, and soil had similar levels of influence on putative soil fungal pathogen diversity, with total effects ranging from 52% to 59% (all p < 0.001), with precipitation exhibiting a stronger direct effect than plant and soil factors. Putative soil fungal pathogen community structure gradually changed with desert, steppe, and meadow, and was primarily controlled by the interactions of climate, plant, and soil factors rather than by distinct factors individually. This finding contrasts with most studies of soil bacterial and fungal community structure, which generally report dominant roles of individual environmental factors.

Genetic Evidence for Colletotrichum gloeosporioides Transmission Between the Invasive Plant Ageratina adenophora and Co-occurring Neighbor Plants

To understand the disease-mediated invasion of exotic plants and the potential risk of disease transmission in local ecosystems, it is necessary to characterize population genetic structure and spatio-temporal dynamics of fungal community associated with both invasive and co-occurring plants. In this study, multiple genes were used to characterize the genetic diversity of 165 strains of Colletotrichum gloeosporioides species complex (CGSC) isolated from healthy leaves and symptomatic leaves of invasive plant Ageratina adenophora, as well as symptomatic leaves of its neighbor plants from eleven geographic sites in China. The data showed that these CGSC strains had a high genetic diversity in each geographic site (all Hd > 0.67 and Pi > 0.01). Haplotype diversity and nucleotide diversity varied greatly in individual gene locus: gs had the highest haplotype diversity (Hd = 0.8972), gapdh had the highest nucleotide diversity (Pi = 0.0705), and ITS had the lowest nucleotide diversity (Pi = 0.0074). Haplotypes were not clustered by geographic site, invasive age, or isolation source. AMOVA revealed that the genetic variation was mainly from within-populations, regardless of geographic or isolation origin. Both AMOVA and neutrality tests indicated these CGSC strains occurred gene exchange among geographic populations but did not experience population expansion along with A. adenophora invasion progress. Our data indicated that A. adenophora primarily accumulated these CGSC fungi in the introduced range, suggesting a high frequency of CGSC transmission between A. adenophora and co-occurring neighbor plants. This study is valuable for understanding the disease-mediated plant invasion and the potential risk of disease transmission driven by exotic plants in local ecosystems.

Light availability and plant shade tolerance modify plant-microbial interactions and feedbacks in subtropical trees

Plant-soil feedbacks (PSFs) are an important mechanism of species coexistence in forest communities. However, evidence remains limited for how light availability regulates PSFs in species with different shade tolerance via changes in plant-microbial interactions. Here we tested in a glasshouse experiment how PSFs changed as a function of light availability and tree shade tolerance. Soil bacterial and fungal communities were profiled using the 16S rRNA and ITS2 gene sequencing, respectively. Under low light, individual PSFs were positively related to shade tolerance, while the least shade-tolerant species produced the most positive PSFs under high light. Pairwise PSFs between species with contrasting shade tolerance were strongly positive under high light but negative under low light, thereby promoting the dominance of less shade-tolerant species in forest gaps and species coexistence under closed canopy, respectively. Under high light, PSFs were related to soil microbial composition and diversity, with the relative abundance of arbuscular mycorrhizal fungi being the primary driver of PSFs. Under low light, none of soil microbial properties were significantly related to PSFs. These findings indicate PSFs and plant shade tolerance interact to promote species coexistence and improve our understanding of how soil microbes contribute to variation in PSFs.

Biotrophic Fungal Pathogens: a Critical Overview

Biotrophic fungi are one group of heterogeneous organisms and these fungi differ in their traits like mode of nutrition, types of reproduction, and dispersal systems. Generally, based on the nutritional mode, fungi are classified into three broad categories, viz. biotrophs, necrotrophs, and hemi-biotrophs. Biotrophs derive their nutrients and energy from living plant cells and survive within the interstitial space of the cells. Biotrophic fungi cause serious crop diseases but are highly challenging to investigate and develop a treatment strategy. Blumeria (Erysiphe) graminis, Uromyces fabae, Ustilago maydis, Cladosporium fulvum, Puccinia graminis, and Phytophthora infestans are some of the significant biotrophic fungi that affect mainly plants. One among the biotrophic fungus, Pneumocystis jirovecii (Taphrinomycotina subphylum of the Ascomycota) exclusively a human pathogen, can cause lung diseases such as "pneumocystis." Biotrophic fungus widely parasitizing Solanaceae family crops (Tomato and potato) has done massive damage to the crops and has led to economic impact worldwide. During infection and for nutrient absorption, biotrophs develops external appendages such as appressoria or haustoria. The hyphae or appressorium adheres to the plant cell wall and collapses the layers for their nutrient absorption. The pathogen also secretes effector molecules to escape from the plant defense mechanism. Later, plants activate their primary and secondary defense mechanisms; however, the pathogen induces virulence genes to escape the host immune responses. Obligate biotrophic fungi pathogenicity has not been fully understood at the molecular level because of the complex interaction, recognition, and signaling with the host. This review summarizes the mechanism of infection in the host, and immune response to emphasize the understanding of the biotrophic fungal biology and pathogenesis in crops. Thus, the detailed review will pave the way to design methods to overcome the resistance of biotrophic fungi and develop disease-free crops.

Dynamic Change of Carbon and Nitrogen Sources in Colonized Apples by Penicillium expansum

Penicillium expansum is a necrotrophic pathogen, which actively kills host cells and obtains nutrients from dead cells to achieve infection. However, few reports have elucidated the differential levels of carbon and nitrogen sources over increasing distances of the leading edge in fungal colonized fruit tissues during colonization. Our results showed that the highest consumption of sucrose and fructose, as well as the accumulation of glucose, were found in the decayed region of P. expansum-colonized ‘Delicious’ apple fruit compared with the healthy region at the leading edge and the healthy region 6 mm away from the leading edge. As nitrogen sources, the contents of methionine, glutamate, leucine, valine, isoleucine and serine were the lowest in the decayed region compared with the healthy regions during colonization. In addition, the titratable acidity, oxalic acid, citric acid, succinic acid and malic acid showed the highest accumulation in the decayed region compared with the healthy regions. P. expansum colonization induced the accumulation of saturated fatty acids in the decayed region, while the level of unsaturated fatty acids was the lowest. These changes were not observed in the healthy regions. These results indicated that P. expansum kills cells in advance of its colonization in order to obtain the nutrients of the apple tissue from the distal leading tissue of the colonized apple. It is understood that more carbon and nitrogen sources are required for fungal colonization, and a stronger defense response against colonization occurred in the fruit, causing the transit of nutrients from the distal tissue to the infected sites.

Massive genome investigations reveal insights of prevalent introgression for environmental adaptation and triterpene biosynthesis in Ganoderma

Genome introgression is one of the driving forces that can increase species and genetic diversity and facilitate the adaptive evolution of organisms and biodiversity conservation. However, the genomic introgression and its contribution to biodiversity of macrofungi are still unclear. The genus Ganoderma is a typical macrofungal group that plays crucial roles in forest ecosystem as saprophytic organisms and plant pathogens, and is also involved in human health as medicinal mushrooms. Most public Ganoderma genomes are fragmented, and reference genomes and whole-genome information of diverse germplasm resources for many Ganoderma species are lacking, thus hindering functional and evolutionary genomic investigations among Ganoderma species. In this study, we provide high-quality genomes of 10 Ganoderma species and whole-genome variants data of 224 individuals from various ecoregions, enabling us to infer the phylogeny of Ganoderma species and their historical population dynamics. Based on whole-genome variants, widespread and genome-wide introgression among Ganoderma species is revealed. Genes with significant introgression signals were related to stress response, digestive absorption, and secondary metabolite synthesis, factors that may contribute to environmental adaptation and important biocomponent metabolism. CYP512U6, an essential functional gene in the CYP450 family related to Ganoderma triterpene synthesis, was detected with significant introgression and selection signals combined with Ganoderma metabolomic analysis, indicating that both ancient gene exchange and recent domestication have contributed to the categories and content of secondary metabolites of Ganoderma. The reference genomes, whole-genome variants, and metabolite profiles could serve as abundant and valuable genetic resources for evolution, ecology, and conservation investigations of Ganoderma species and other macrofungi.

Distribution pattern of endophytic bacteria and fungi in tea plants

Endophytes are critical for plant growth and health. Tea is an economically important crop in China. However, little is known about the distribution pattern and potential functions of endophytic communities in tea trees. In this study, two genotypes (BXZ and MF) cultivated under the same conditions were selected, and endophytic bacteria and fungi were analyzed through 16S rRNA and ITS high-throughput sequencing technologies, respectively. For endophytic bacteria, root tissues harbored the most diverse endophytes, followed by stems and old leaves, and new leaves possessed the lowest diversity. In contrast, old leave tissues harbored more diverse endophytic fungi than did root and stem tissues. Most of the dominant endophytes showed obvious cultivar and tissue preferences. Tissue type played a more important role in shaping community structure than did cultivar. Nevertheless, some endophytic bacterial groups, which mainly affiliated to Chryseobacterium, Sphingomonas, Rhizobium, Morganella, Methylobacterium and Comamonadaceae, could parasitize different tissues, and the average relative abundance of endophytic bacteria was as high as 72.57%. Some endophytic fungal populations, such as Colletotrichum, Uwebraunia, Cladosporium, and Devriesia, could also parasitize tea, and the relative abundance accounted for approximately 25.70–97.26%. The cooperative relationship between endophytic bacteria and fungi in the new leaves was stronger than that in the old leaves, which can better participate in the metabolism of tea material.

Root attributes dominate the community assembly of soil fungal functional guilds across arid inland river basin

Plant attributes are increasingly acknowledged as key drivers shaping soil fungal communities, but considerable uncertainty exists over fungal community assembly mechanisms and their plant drivers based only on inferences from plant aboveground attributes. To date, empirical evidences of how root attributes are integrated into microbiome-plant linkages remain limited. Using 162 soil samples from a typical arid inland river basin in China, we assessed the drivers that regulate the distribution patterns and assembly processes of total, mycorrhizal, saprotrophic and pathotrophic fungi in surface (0-15 cm) and subsurface soils (15-30 cm). Total fungi and fungal functional guilds exhibited similar distribution patterns in arid inland river basins. Null-model and variance partitioning analysis revealed that the heterogeneous selection induced by root attributes, rather than dispersal limitation, predominated the fungal community assembly. Multiple regressions on matrices further demonstrated that specific root length were the most important predictors of fungal community assembly, which mediated the balance of assembly processes of soil fungal communities. Heterogeneous selection decreased for total, mycorrhizal and saprotrophic fungi, but increased for pathotrophic fungi with increasing specific root length. Additionally, fine-root biomass exerted important effects on fungal assembly processes in subsurface soil but not in surface soil, suggesting root attributes differently affected fungal community assembly between surface and subsurface soil. Collectively, our study highlights the importance of considering root attributes in differentiating the balance of stochastic and deterministic processes in microbial community assembly.

Soil Microbial and Organic Carbon Legacies of Pre-Existing Plants Drive Pioneer Tree Growth during Subalpine Forest Succession

Fast-growing pioneer tree species play a crucial role in triggering late successional development in forests. Experimental evidence of the soil legacy effects of pre-existing plants on pioneer tree performance is lacking. We explored the legacy effects of soils conditioned by early successional herbs (Poa poophagorum Bor and Potentilla fragarioides L.) and mid-successional shrubs (Rhododendron fortunei Lindl. and Enkianthus quinqueflorus Lour.) on late-successional ectomycorrhizal (ECM) pioneer tree (Betula platyphylla Sukaczev) seedling growth. The soils were analyzed for soil nutrient status and fungal and bacterial compositions using ITS and 16S rRNA gene sequencing. B. platyphylla seedlings produced higher biomass in soils conditioned by shrubs. Soil organic carbon (SOC) and bacterial and fungal legacies most impacted pioneer tree seedling growth. Additionally, the partial least squares path model revealed that soil nutrients, especially SOC, indirectly affected seedling biomass by their direct effects on the bacterial and fungal communities. The changes in bacterial community composition had a stronger effect on seedling biomass than those of fungi because bacteria with shorter turnover times are generally considered to be more efficient than fungi in enhancing nutrient availability. Our study integrates soil microbial and nutrient legacies to explain the potential mechanisms of pioneer tree regeneration.

Experimental and observational evidence of negative conspecific density dependence in temperate ectomycorrhizal trees

Conspecific negative density dependence (CNDD) promotes tree species diversity by reducing recruitment near conspecific adults due to biotic feedbacks from herbivores, pathogens, or competitors. While this process is well-described in tropical forests, tests of temperate tree species range from strong positive to strong negative density dependence. To explain this, several studies have suggested that tree species traits may help predict the strength and direction of density dependence: for example, ectomycorrhizal-associated tree species typically exhibit either positive or weaker negative conspecific density dependence. More generally, the strength of density dependence may be predictably related to other species-specific ecological attributes such as shade tolerance, or the relative local abundance of a species. To test the strength of density dependence and whether it affects seedling community diversity in a temperate forest, we tracked the survival of seedlings of three ectomycorrhizal-associated species experimentally planted beneath conspecific and heterospecific adults on the Prospect Hill tract of the Harvard Forest, in Massachusetts, USA. Experimental seedling survival was always lower under conspecific adults, which increased seedling community diversity in one of six treatments. We compared these results to evidence of CNDD from observed sapling survival patterns of 28 species over approximately 8 years in an adjacent 35-hectare forest plot. We tested whether species-specific estimates of CNDD were associated with mycorrhizal association, shade tolerance, and local abundance. We found evidence of significant, negative conspecific density dependence (CNDD) in 23 of 28 species, and positive conspecific density dependence in two species. Contrary to our expectations, ectomycorrhizal-associated species generally exhibited stronger (e.g. more negative) CNDD than arbuscular mycorrhizal- associated species. CNDD was also stronger in more shade tolerant species but was not associated with local abundance. Conspecific adult trees often have a negative influence on seedling survival in temperate forests, particularly for tree species with certain traits. Here we found strong experimental and observational evidence that ectomycorrhizal-associating species consistently exhibit CNDD. Moreover, similarities in the relative strength of density dependence from experiments and observations of sapling mortality suggest a mechanistic link between negative effects of conspecific adults on seedling and sapling survival and local tree species distributions.

Tree species diversity increases with conspecific negative density dependence across an elevation gradient

Elevational and latitudinal gradients in species diversity may be mediated by biotic interactions that cause density-dependent effects of conspecifics on survival or growth to differ from effects of heterospecifics (i.e. conspecific density dependence), but limited evidence exists to support this. We tested the hypothesis that conspecific density dependence varies with elevation using over 40 years of data on tree survival and growth from 23 old-growth temperate forest stands across a 1,000-m elevation gradient. We found that conspecific-density-dependent effects on survival of small-to-intermediate-sized focal trees were negative in lower elevation, higher diversity forest stands typically characterised by warmer temperatures and greater relative humidity. Conspecific-density-dependent effects on survival were less negative in higher elevation stands and ridges than in lower elevation stands and valley bottoms for small-to-intermediate-sized trees, but were neutral for larger trees across elevations. Conspecific-density-dependent effects on growth were negative across all tree size classes and elevations. These findings reveal fundamental differences in biotic interactions that may contribute to relationships between species diversity, elevation and climate.

Environmental and plant community drivers of plant pathogen composition and richness

Interactions between individual plant pathogens and their environment have been described many times. However, the relative contribution of different environmental parameters as controls of pathogen communities remains largely unknown. Here we investigate the importance of environmental factors, including geomorphology, climate, land use, soil and plant community composition, for a broad range of aboveground and belowground fungal, oomycete and bacterial plant pathogens. We found that plant community composition is the main driver of the composition and richness of plant pathogens after taking into account all other tested parameters, especially those related to climate and soil. In the face of future changes in climate and land use, our results suggest that changes in plant pathogen community composition and richness will primarily be mediated through changes in plant communities, rather than the direct effects of climate or soils.

Soil Layers Matter: Vertical Stratification of Root-Associated Fungal Assemblages in Temperate Forests Reveals Differences in Habitat Colonization

Ectomycorrhizal and saprotrophic fungi play pivotal roles in ecosystem functioning. Here, we studied the vertical differentiation of root-associated fungi (RAF) in temperate forests. We analysed RAF assemblages in the organic and mineral soil from 150 experimental forest plots across three biogeographic regions spanning a distance of about 800 km. Saprotrophic RAF showed the highest richness in organic and symbiotrophic RAF in mineral soil. Symbiotrophic RAF exhibited higher relative abundances than saprotrophic fungi in both soil layers. Beta-diversity of RAF was mainly due to turnover between organic and mineral soil and showed regional differences for symbiotrophic and saprotrophic fungi. Regional differences were also found for different phylogenetic levels, i.e., fungal orders and indicator species in the organic and mineral soil, supporting that habitat conditions strongly influence differentiation of RAF assemblages. Important exceptions were fungal orders that occurred irrespective of the habitat conditions in distinct soil layers across the biogeographic gradient: Russulales and Cantharellales (ectomycorrhizal fungi) were enriched in RAF assemblages in mineral soil, whereas saprotrophic Polyporales and Sordariales and ectomycorrhizal Boletales were enriched in RAF assemblages in the organic layer. These results underpin a phylogenetic signature for niche partitioning at the rank of fungal orders and suggest that RAF assembly entails two strategies encompassing flexible and territorial habitat colonization by different fungal taxa.

Precipitation increases the abundance of fungal plant pathogens in Eucalyptus phyllosphere

Understanding the current and future distributions of plant pathogens is critical to predict the plant performance and related economic benefits in the changing environment. Yet, little is known about the roles of environmental drivers in shaping the profiles of fungal plant pathogens in phyllosphere, an important habitat of microbiomes on Earth. Here, using a large-scale investigation of Eucalyptus phyllospheric microbiomes in Australia and the multiple linear regression model, we show that precipitation is the most important predictor of fungal taxonomic diversity and abundance. The abundance of fungal plant pathogens in phyllosphere exhibited a positive linear relationship with precipitation. With this empirical dataset, we constructed current and future atlases of phyllosphere plant pathogens to estimate their spatial distributions under different climate change scenarios. Our atlases indicate that the abundance of fungal plant pathogens would increase especially in the coastal regions with up to 100-fold increase compared with the current abundance. These findings advance our understanding of the distributions of fungal plant pathogens in phyllospheric microbiomes under the climate change, which can improve our ability to predict and mitigate their impacts on plant productivity and economic losses.

Virulence and community dynamics of fungal species with vertical and horizontal transmission on a plant with multiple infections

The virulence evolution of multiple infections of parasites from the same species has been modeled widely in evolution theory. However, experimental studies on this topic remain scarce, particularly regarding multiple infections by different parasite species. Here, we characterized the virulence and community dynamics of fungal pathogens on the invasive plant Ageratina adenophora to verify the predictions made by the model. We observed that A. adenophora was highly susceptible to diverse foliar pathogens with mixed vertical and horizontal transmission within leaf spots. The transmission mode mainly determined the pathogen community structure at the leaf spot level. Over time, the pathogen community within a leaf spot showed decreased Shannon diversity; moreover, the vertically transmitted pathogens exhibited decreased virulence to the host A. adenophora, but the horizontally transmitted pathogens exhibited increased virulence to the host. Our results demonstrate that the predictions of classical models for the virulence evolution of multiple infections are still valid in a complex realistic environment and highlight the impact of transmission mode on disease epidemics of foliar fungal pathogens. We also propose that seedborne fungi play an important role in structuring the foliar pathogen community from multiple infections within a leaf spot.

A growing number of examples indicate that many plant diseases are caused by multiple taxa of microbes. Therefore, how virulence evolves in the context of multiple infections by different species with both vertical and horizontal transmission modes represents an important area of pathogen ecology and evolution, but there is a lack of experimental study. Here, we employ a naturally occurring host-parasite system, the invasive plant Ageratina adenophora and its foliar pathogens, to verify that theoretical predictions of classical models for virulence evolution are still valid in a complex realistic environment, i.e., the transmission mode determines the dynamics of the virulence and pathogen community under multiple infections. Moreover, we propose that seedborne fungi are important in structuring the foliar pathogen community consisting of multiple infections within a leaf spot. Our findings provide valuable information for understanding how multiple infections affect the key components, i.e., the virulence evolution and pathogen community dynamics, of host-pathogen interactions in the field.

Fungal foraging behaviour and hyphal space exploration in micro-structured Soil Chips

How do fungi navigate through the complex microscopic maze-like structures found in the soil? Fungal behaviour, especially at the hyphal scale, is largely unknown and challenging to study in natural habitats such as the opaque soil matrix. We monitored hyphal growth behaviour and strategies of seven Basidiomycete litter decomposing species in a micro-fabricated "Soil Chip" system that simulates principal aspects of the soil pore space and its micro-spatial heterogeneity. The hyphae were faced with micrometre constrictions, sharp turns and protruding obstacles, and the species examined were found to have profoundly different responses in terms of foraging range and persistence, spatial exploration and ability to pass obstacles. Hyphal behaviour was not predictable solely based on ecological assumptions, and our results obtained a level of trait information at the hyphal scale that cannot be fully explained using classical concepts of space exploration and exploitation such as the phalanx/guerrilla strategies. Instead, we propose a multivariate trait analysis, acknowledging the complex trade-offs and microscale strategies that fungal mycelia exhibit. Our results provide novel insights about hyphal behaviour, as well as an additional understanding of fungal habitat colonisation, their foraging strategies and niche partitioning in the soil environment.

Plant Defense Responses to Biotic Stress and Its Interplay With Fluctuating Dark/Light Conditions

Plants are subjected to a plethora of environmental cues that cause extreme losses to crop productivity. Due to fluctuating environmental conditions, plants encounter difficulties in attaining full genetic potential for growth and reproduction. One such environmental condition is the recurrent attack on plants by herbivores and microbial pathogens. To surmount such attacks, plants have developed a complex array of defense mechanisms. The defense mechanism can be either preformed, where toxic secondary metabolites are stored; or can be inducible, where defense is activated upon detection of an attack. Plants sense biotic stress conditions, activate the regulatory or transcriptional machinery, and eventually generate an appropriate response. Plant defense against pathogen attack is well understood, but the interplay and impact of different signals to generate defense responses against biotic stress still remain elusive. The impact of light and dark signals on biotic stress response is one such area to comprehend. Light and dark alterations not only regulate defense mechanisms impacting plant development and biochemistry but also bestow resistance against invading pathogens. The interaction between plant defense and dark/light environment activates a signaling cascade. This signaling cascade acts as a connecting link between perception of biotic stress, dark/light environment, and generation of an appropriate physiological or biochemical response. The present review highlights molecular responses arising from dark/light fluctuations vis-à-vis elicitation of defense mechanisms in plants.

Pineapple Mycobiome Related to Fruitlet Core Rot Occurrence and the Influence of Fungal Species Dispersion Patterns

Fruitlet Core Rot (FCR) is a fungal disease that negatively impacts the quality of pineapple, in particular the 'Queen Victoria' cultivar. The main FCR causal agent has been identified as Fusariumananatum. This study focused on the correlation between FCR disease occurrence, fungal diversity, and environmental factors. FCR incidence and fungal species repartition patterns were spatially contextualized with specific surrounding parameters of the experimental plots. The mycobiome composition of healthy and diseased fruitlets was compared in order to search for potential fungal markers. A total of 240 pineapple fruits were sampled, and 344 fungal isolates were identified as belonging to 49 species among 17 genera. FCR symptom distribution revealed a significant gradient that correlated to that of the most abundant fungal species. The association of wind direction and the position of proximal cultivated crops sharing pathogens constituted an elevated risk of FCR incidence. Five highly represented species were assayed by Koch's postulates, and their pathogenicity was confirmed. These novel pathogens belonging to Fusariumfujikuroi and Talaromycespurpureogenus species complexes were identified, unravelling the complexity of the FCR pathosystem and the difficulty of apprehending the pathogenesis over the last several decades. This study revealed that FCR is an airborne disease characterized by a multi-partite pathosystem.

Trait-based variation in host contribution to pathogen transmission across species and resource supplies

Two key knowledge gaps currently limit the development of more predictive and general models of pathogen transmission: (1) the physiological basis of heterogeneity in host contribution to pathogen transmission (reservoir potential) remains poorly understood and (2) a general means of integrating the ecological dynamics of host communities has yet to emerge. If the traits responsible for differences in reservoir potential also modulate host community dynamics, these traits could be used to predict pathogen transmission as host communities change. In two greenhouse experiments, across 23 host species and two levels of resource supply, the reservoir potential of plant hosts increased significantly along the Leaf Economics Spectrum, a global axis of plant physiological trait covariation that features prominently in models of plant community ecology. This indicates that the traits of the Leaf Economics Spectrum underlie broad differences in reservoir potential across host species and resource supplies. Therefore, host traits could be used to integrate epidemiological models of pathogen transmission with ecological models of host community change.

Quantifying the sharing of foliar fungal pathogens by the invasive plant Ageratina adenophora and its neighbours

Local pathogens can accumulate as asymptomatic endophytes, making it difficult to detect the impacts of invasive species as propagators of disease in the invaded range. We used the invasive plant Ageratina adenophora to assess such accumulation. We intensively collected foliar fungal endophytes and leaf spot pathogens of A. adenophora and co-occurring neighbours and performed an inoculation experiment to evaluate their pathogenicity and host range. Ageratina adenophora harboured diverse necrotrophic pathogens; its communities of endophytes and leaf spot pathogens were different in composition and shared only a small number of fungal species. In the pathogen communities of local plant hosts, 21% of the operational taxonomic units (OTUs), representing 50% of strains, also occurred as leaf spot pathogens and/or endophytes of A. adenophora. The local pathogen community was more similar to the endophytes than to the pathogens of A. adenophora. The inoculation experiment showed that local pathogens could infect A. adenophora leaves asymptomatically and that local plant hosts were susceptible to both A. adenophora endophytes and pathogens. Ageratina adenophora is a highly competent host for local pathogens, and its asymptomatic latent pathogens are fungi primarily shared with local neighbours. This poses challenges for understanding the long-term ecological consequences of plant invasion.

Abundance, origin, and phylogeny of plants do not predict community-level patterns of pathogen diversity and infection

Pathogens have the potential to shape plant community structure, and thus, it is important to understand the factors that determine pathogen diversity and infection in communities. The abundance, origin, and evolutionary relationships of plant hosts are all known to influence pathogen patterns and are typically studied separately. We present an observational study that examined the influence of all three factors and their interactions on the diversity of and infection of several broad taxonomic groups of foliar, floral, and stem pathogens across three sites in a temperate grassland in the central United States. Despite that pathogens are known to respond positively to increases in their host abundances in other systems, we found no relationship between host abundance and either pathogen diversity or infection. Native and exotic plants did not differ in their infection levels, but exotic plants hosted a more generalist pathogen community compared to native plants. There was no phylogenetic signal across plants in pathogen diversity or infection. The lack of evidence for a role of abundance, origin, and evolutionary relationships in shaping patterns of pathogens in our study might be explained by the high generalization and global distributions of our focal pathogen community, as well as the high diversity of our plant host community. In general, the community-level patterns of aboveground pathogen infections have received less attention than belowground pathogens, and our results suggest that their patterns might not be explained by the same drivers.

Characterization of the fungal community in the canopy air of the invasive plant Ageratina adenophora and its potential to cause plant diseases

Airborne fungi and their ecological functions have been largely ignored in plant invasions. In this study, high-throughput sequencing technology was used to characterize the airborne fungi in the canopy air of the invasive weed Ageratina adenophora. Then, representative phytopathogenic strains were isolated from A. adenophora leaf spots and their virulence to A.adenophora as well as common native plants in the invaded range was tested. The fungal alpha diversities were not different between the sampling sites or between the high/low part of the canopy air, but fungal co-occurrences were less common in the high than in the low part of the canopy air. Interestingly, we found that the phytopathogenic Didymellaceae fungi co-occurred more frequently with themselves than with other fungi. Disease experiments indicated that all 5 Didymellaceae strains could infect A. adenophora as well as the 16 tested native plants and that there was large variation in the virulence and host range. Our data suggested that the diverse pathogens in the canopy air might be a disease infection source that weakens the competition of invasive weeds, a novel phenomenon that remains to be explored in other invasive plants.

Discovery of antitumor lectins from rainforest tree root transcriptomes

Glycans are multi-branched sugars that are displayed from lipids and proteins. Through their diverse polysaccharide structures they can potentiate a myriad of cellular signaling pathways involved in development, growth, immuno-communication and survival. Not surprisingly, disruption of glycan synthesis is fundamental to various human diseases; including cancer, where aberrant glycosylation drives malignancy. Here, we report the discovery of a novel mannose-binding lectin, ML6, which selectively recognizes and binds to these irregular tumor-specific glycans to elicit potent and rapid cancer cell death. This lectin was engineered from gene models identified in a tropical rainforest tree root transcriptome and is unusual in its six canonical mannose binding domains (QxDxNxVxY), each with a unique amino acid sequence. Remarkably, ML6 displays antitumor activity that is >105 times more potent than standard chemotherapeutics, while being almost completely inactive towards non-transformed, healthy cells. This activity, in combination with results from glycan binding studies, suggests ML6 differentiates healthy and malignant cells by exploiting divergent glycosylation pathways that yield naïve and incomplete cell surface glycans in tumors. Thus, ML6 and other high-valence lectins may serve as novel biochemical tools to elucidate the glycomic signature of different human tumors and aid in the rational design of carbohydrate-directed therapies. Further, understanding how nature evolves proteins, like ML6, to combat the changing defenses of competing microorganisms may allow for fundamental advances in the way we approach combinatorial therapies to fight therapeutic resistance in cancer.

Tree species traits affect which natural enemies drive the Janzen-Connell effect in a temperate forest

A prominent tree species coexistence mechanism suggests host-specific natural enemies inhibit seedling recruitment at high conspecific density (negative conspecific density dependence). Natural-enemy-mediated conspecific density dependence affects numerous tree populations, but its strength varies substantially among species. Understanding how conspecific density dependence varies with species’ traits and influences the dynamics of whole communities remains a challenge. Using a three-year manipulative community-scale experiment in a temperate forest, we show that plant-associated fungi, and to a lesser extent insect herbivores, reduce seedling recruitment and survival at high adult conspecific density. Plant-associated fungi are primarily responsible for reducing seedling recruitment near conspecific adults in ectomycorrhizal and shade-tolerant species. Insects, in contrast, primarily inhibit seedling recruitment of shade-intolerant species near conspecific adults. Our results suggest that natural enemies drive conspecific density dependence in this temperate forest and that which natural enemies are responsible depends on the mycorrhizal association and shade tolerance of tree species.

The Janzen-Connell hypothesis posits that seedlings may be less likely to establish near conspecifics due to shared natural enemies. Here, Jia et al. show that tree species traits determine whether fungal pathogens or insect herbivores inhibit seedling recruitment and survival in a temperate forest.

Deeply conserved susceptibility in a multi-host, multi-parasite system

Variation in susceptibility is ubiquitous in multi-host, multi-parasite assemblages, and can have profound implications for ecology and evolution in these systems. The extent to which susceptibility to parasites is phylogenetically conserved among hosts can be revealed by analysing diverse regional communities. We screened for haemosporidian parasites in 3983 birds representing 40 families and 523 species, spanning ~ 4500 m elevation in the tropical Andes. To quantify the influence of host phylogeny on infection status, we applied Bayesian phylogenetic multilevel models that included a suite of environmental, spatial, temporal, life history and ecological predictors. We found evidence of deeply conserved susceptibility across the avian tree; host phylogeny explained substantial variation in infection status, and results were robust to phylogenetic uncertainty. Our study suggests that susceptibility is governed, in part, by conserved, latent aspects of anti-parasite defence. This demonstrates the importance of deep phylogeny for understanding present-day ecological interactions.

Phylogenetic imprint of woody plants on the soil mycobiome in natural mountain forests of eastern China

Recent studies have detected strong phylogenetic signals in tree-fungus associations for diseased leaves and mycorrhizal symbioses. However, the extent of plant phylogenetic constraints on the free-living soil mycobiome remains unknown, especially at broad geographic scales. Here, 343 soil samples were collected adjacent to individual tree trunks, representing 58 woody plant species located in five mountain forests of eastern China. Integrating plant species identity and phylogenetic information, we aimed to unravel the relative contributions of phylogenetic relationships among tree species, abiotic environmental filtering, and geographic isolation to the geographic distribution of soil mycobiome. We found that the community dissimilarities of total fungi and each dominant guild (viz. saprotrophs, plant pathogens, and ectomycorrhizal fungi) significantly increased with increasing plant phylogenetic distance. Plant phylogenetic eigenvectors explained 11.4% of the variation in community composition, whereas environmental and spatial factors explained 24.1% and 7.2% of the variation, respectively. The communities of ectomycorrhizal fungi and plant pathogens were relatively more strongly affected by plant phylogeny than those of saprotrophs (13.7% and 10.4% vs. 8.5%). Overall, our results demonstrate how plant phylogeny, environment, and geographic space contribute to forest soil fungal distributions and suggest that the influence of plant phylogeny on fungal association may differ by guilds.

Comparative transcriptome analysis of two citrus germplasms with contrasting susceptibility to Phytophthora nicotianae provides new insights into tolerance mechanisms

Host perception of Phytophthora nicotianae switching to necrotrophy is fundamental for disease tolerance of citrus. It involves an HR-like response, strengthening of the cell wall structure and hormonal signaling. Stem rot caused by P. nicotianae is a worldwide disease of several important crops, including citrus. Given the growing awareness of chemical fungicides drawbacks, genetic improvement of citrus rootstocks remains the best alternative. However, the molecular basis underlying the successful response of resistant and/or tolerant genotypes remains poorly understood. Therefore, we performed a transcriptomic analysis to examine the differential defense response to P. nicotianae of two germplasms-tolerant sour orange (SO, Citrus aurantium) and susceptible Madam Vinous (MV, C. sinensis)-in both the biotrophic and necrotrophic phases of host-pathogen interaction. Our results revealed the necrotrophic phase as a decisive turning point, since it included stronger modulation of a number of genes implicated in pathogen perception, signal transduction, HR-like response, transcriptional reprogramming, hormone signaling, and cell wall modifications. In particular, the pathogen perception category reflected the ability of SO to perceive the pathogen even after its switch to necrotrophy, and thus to cope successfully with the infection, while MV failed. The concomitant changes in genes involved in the remaining functional categories seemed to prevent pathogen spread. This investigation provided further understanding of the successful defense mechanisms of C. aurantium against P. nicotianae, which might be exploited in post-genomic strategies to develop resistant Citrus genotypes.

Fungi reduce preference and performance of insect herbivores on challenged plants

Although insect herbivores and fungal pathogens frequently share the same individual host plant, we lack general insights in how fungal infection affects insect preference and performance. We addressed this question in a meta-analysis of 1,113 case studies gathered from 101 primary papers that compared preference or performance of insect herbivores on control vs. fungus challenged plants. Generally, insects preferred, and performed better on, not challenged plants, regardless of experimental conditions. Insect response to fungus infection significantly differed according to fungus lifestyle, insect feeding guild, and the spatial scale of the interaction (local/distant). Insect performance was reduced on plants challenged by biotrophic pathogens or endophytes but not by necrotrophic pathogens. For both chewing and piercing-sucking insects, performance was reduced on challenged plants when interactions occurred locally but not distantly. In plants challenged by biotrophic pathogens, both preference and performance of herbivores were negatively impacted, whereas infection by necrotrophic pathogens reduced herbivore preference more than performance and endophyte infection reduced only herbivore performance. Our study demonstrates that fungi could be important but hitherto overlooked drivers of plant-herbivore interactions, suggesting both direct and plant-mediated effects of fungi on insect's behavior and development.

Biotrophy-necrotrophy switch in pathogen evoke differential response in resistant and susceptible sesame involving multiple signaling pathways at different phases

Infection stages of charcoal rot fungus Macrophomina phaseolina in sesame revealed for the first time a transition from biotrophy via BNS (biotrophy-to-necrotrophy switch) to necrotrophy as confirmed by transcriptional studies. Microscopy using normal and GFP-expressing pathogen showed typical constricted thick intercellular bitrophic hyphae which gave rise to thin intracellular necrotrophic hyphae during BNS and this stage was delayed in a resistant host. Results also show that as the pathogen switched its strategy of infection, the host tailored its defense strategy to meet the changing situation. Less ROS accumulation, upregulation of ROS signaling genes and higher antioxidant enzyme activities post BNS resulted in resistance. There was greater accumulation of secondary metabolites and upregulation of secondary metabolite-related genes after BNS. A total of twenty genes functioning in different aspects of plant defense that were monitored over a time course during the changing infection phases showed a coordinated response. Experiments using phytohormone priming and phytohormone inhibitors showed that resistance resulted from activation of JA-ET signaling pathway. Most importantly this defense response was more prompt in the resistant than the susceptible host indicating that a resistant host makes different choices from a susceptible host during infection which ultimately influences the severity of the disease.

Influence of soil pathogens on early regeneration success of tropical trees varies between forest edge and interior

Soil fungi are key mediators of negative density-dependent mortality in seeds and seedlings, and the ability to withstand pathogens in the shaded understory of closed-canopy forests could reinforce light gradient partitioning by tree species. For four species of tropical rainforest trees-two shade-tolerant and two shade-intolerant-we conducted a field experiment to examine the interactive effects of fungal pathogens, light, and seed density on germination and early seedling establishment. In a fully factorial design, seeds were sown into 1 m² plots containing soil collected from underneath conspecific adult trees, with plots assigned to forest edge (high light) or shaded understory, high or low density, and fungicide or no fungicide application. We monitored total seed germination and final seedling survival over 15 weeks. Shade-intolerant species were strongly constrained by light; their seedlings survived only at the edge. Fungicide application significantly improved seedling emergence and/or survival for three of the four focal species. There were no significant interactions between fungicide and seed density, suggesting that pathogen spread with increased aggregation of seeds and seedlings did not contribute to pathogen-mediated mortality. Two species experienced significant edge-fungicide interactions, but fungicide effects in edge vs. interior forest varied with species and recruitment stage. Our results suggest that changes to plant-pathogen interactions could affect plant recruitment in human-impacted forests subject to fragmentation and edge-effects.

Impact of salicylic acid- and jasmonic acid-regulated defences on root colonization by Trichoderma harzianum T-78

We recently found that the beneficial fungus Trichoderma harzianum T-78 primes tomato plants for salicylic acid (SA)- and jasmonic acid (JA)-regulated defenses, resulting in enhanced resistance against the root knot nematode Meloidogyne incognita. By using SA- and JA-impaired mutant lines and exogenous hormonal application, here we investigated whether the SA- and JA-pathways also have a role in T-78 root colonization of Arabidopsis thaliana. Endophytic colonization by T-78 was faster in the SA-impaired mutant sid2 than in the wild type. Moreover, elicitation of SA-dependent defenses by SA application reduced T-78 colonization, indicating that the SA-pathway affects T-78 endophytism. In contrast, elicitation of the JA-pathway, which antagonized SA-dependent defenses, resulted in enhanced endophytic colonization by T-78. These findings are in line with our previous observation that SA-dependent defenses are repressed by T-78, which likely aids colonization by the endophytic fungus.

Reduced susceptibility of tomato stem to the necrotrophic fungus Botrytis cinerea is associated with a specific adjustment of fructose content in the host sugar pool

Background and aims

Plant soluble sugars, as main components of primary metabolism, are thought to be implicated in defence against pathogenic fungi. However, the function of sucrose and hexoses remains unclear. This study aimed to identify robust patterns in the dynamics of soluble sugars in sink tissues of tomato plants during the course of infection by the necrotrophic fungus Botrytis cinerea . Distinct roles for glucose and fructose in defence against B. cinerea were hypothesized.

Methods

We examined sugar contents and defence hormonal markers in tomato stem tissues before and after infection by B. cinerea , in a range of abiotic environments created by various nitrogen and water supplies.

Key Results

Limited nitrogen or water supplies increased tomato stem susceptibility to B. cinerea . Glucose and fructose contents of tissues surrounding infection sites evolved differently after inoculation. The fructose content never decreased after inoculation with B. cinerea , while that of glucose showed either positive or negative variation, depending on the abiotic environment. An increase in the relative fructose content (defined as the proportion of fructose in the soluble sugar pool) was observed in the absence of glucose accumulation and was associated with lower susceptibility. A lower expression of the salicylic acid marker PR1a , and a lower repression of a jasmonate marker COI1 were associated with reduced susceptibility. Accordingly, COI1 expression was positively correlated with the relative fructose contents 7 d after infection.

Conclusions

Small variations of fructose content among the sugar pool are unlikely to affect intrinsic pathogen growth. Our results highlight distinct use of host glucose and fructose after infection by B. cinerea and suggest strongly that adjustment of the relative fructose content is required for enhanced plant defence.

Forest health in a changing world

Forest pathology, the science of forest health and tree diseases, is operating in a rapidly developing environment. Most importantly, global trade and climate change are increasing the threat to forest ecosystems posed by new diseases. Various studies relevant to forest pathology in a changing world are accumulating, thus making it necessary to provide an update of recent literature. In this contribution, we summarize research at the interface between forest pathology and landscape ecology, biogeography, global change science and research on tree endophytes. Regional outbreaks of tree diseases are requiring interdisciplinary collaboration, e.g. between forest pathologists and landscape ecologists. When tree pathogens are widely distributed, the factors determining their broad-scale distribution can be studied using a biogeographic approach. Global change, the combination of climate and land use change, increased pollution, trade and urbanization, as well as invasive species, will influence the effects of forest disturbances such as wildfires, droughts, storms, diseases and insect outbreaks, thus affecting the health and resilience of forest ecosystems worldwide. Tree endophytes can contribute to biological control of infectious diseases, enhance tolerance to environmental stress or behave as opportunistic weak pathogens potentially competing with more harmful ones. New molecular techniques are available for studying the complete tree endobiome under the influence of global change stressors from the landscape to the intercontinental level. Given that exotic tree diseases have both ecologic and economic consequences, we call for increased interdisciplinary collaboration in the coming decades between forest pathologists and researchers studying endophytes with tree geneticists, evolutionary and landscape ecologists, biogeographers, conservation biologists and global change scientists and outline interdisciplinary research gaps.

Light regulation of plant defense

Precise allocation of limited resources between growth and defense is critical for plant survival. In shade-intolerant species, perception of competition signals by informational photoreceptors activates shade-avoidance responses and reduces the expression of defenses against pathogens and insects. The main mechanism underlying defense suppression is the simultaneous downregulation of jasmonate and salicylic acid signaling by low ratios of red:far-red radiation. Inactivation of phytochrome B by low red:far-red ratios appears to suppress jasmonate responses by altering the balance between DELLA and JASMONATE ZIM DOMAIN (JAZ) proteins in favor of the latter. Solar UVB radiation is a positive modulator of plant defense, signaling through jasmonate-dependent and jasmonate-independent pathways. Light, perceived by phytochrome B and presumably other photoreceptors, helps plants concentrate their defensive arsenals in photosynthetically valuable leaves. The discovery of connections between photoreceptors and defense signaling is revealing novel mechanisms that control key resource allocation decisions in plant canopies.