Spatial variability of phyllosphere fungal assemblages: genetic distance predominates over geographic distance in a European beech stand (Fagus sylvatica)

The involvement of bark canker fungal pathogens in cypress windbreak dieback in northern Tunisia

Common cypress (Cupressus sempervirens L.) is a significant element in the Mediterranean region and Tunisia, present in both forest and agricultural windbreak for centuries. However, in recent decades, common cypresses in certain Tunisian areas have experienced dieback and mortality. Presently, many common cypress windbreaks display severe damage, possibly due to fungal pathogens. In the summer of 2022, a field survey was conducted in three regions of northern Tunisia (Menzel Bouzalfa, Morneg, El Alia) to investigate diseased common cypresses and identify the responsible pathogens: 935 trees belonging to 14 windbreaks were surveyed. Branches and twigs samples were collected from 47 affected trees showing symptoms such as yellowish-brown foliage, necrotic lesions, cankers, resin exudation and diebacks. Initially, isolates were morphologically characterized, and representative isolates were further analyzed using molecular methods. Using the traditional culture method, 41 fungal species associated with common cypress dieback were identified. Pathogenicity tests were performed on eight fungal species known as possible pathogens: Phaeobotryon cupressi, Diplodia cupressi, Diplodia olivarum, Diplodia pseudoseriata, Seiridium cardinale, Pestalotiopsis funereoides, Neofusicoccum mediterraneum, and Didymosphaeria variabile. Phaeobotryon cupressi, D. cupressi, and S. cardinale displayed the highest pathogenicity, followed by P. funereoides and D. olivarum, which caused smaller lesions. With the exception of D. cupressi, all of the identified fungal pathogens are being reported for the first time in Tunisia or in common cypress. The pathogenic action of most of the isolated fungi could have been enhanced by the prolonged droughts that have repeatedly occurred over recent years.

Invasive Buffelgrass, Cenchrus ciliaris, Balances Opportunistic Acquisition of Foliar fungi With Host and Environmental Filtering in Its Introduced Range

Plants host diverse assemblages of fungi on their foliar tissues, both in internal compartments and on exterior surfaces. When plant distributions shift, they can move with their fungal associates (i.e., co-introduction) or acquire new associates present in the novel environment (host-jumping). The fungal communities that plants acquire influence a plant's ability to establish and spread in this new environment. Here, we aimed to assess whether invasive C. ciliaris hosts similar groups of fungi in its native and introduced ranges and to evaluate community overlap of fungi associated with foliar tissue of C. ciliaris and native and non-native plants within the introduced range. In the introduced range, the majority of OTUs associated with C. ciliaris were not found in its native range, although 3.2% of OTUs were common to both ranges. Of these shared OTU, 77.6% were found on co-occurring natives and non-natives in the introduced range, whereas 22.4% were unique to C. ciliaris indicating a possible co-introduction. Fungal communities within the introduced range contained a higher proportion of generalist symbionts and increased heterogeneity of foliar communities than in its native range. Within the introduced range, host phylogenetic distance explained more variation than native status. Our findings provide evidence that non-natives acquire fungi opportunistically from their environment, although host and environmental filtering is present suggesting that successful invasive plants may be able to limit the effect of poor symbionts and select for better ones. Future experimental work will be needed to confirm the occurrence of host selection and identify its mechanisms.

Proposal of one new family, seven new genera and seventy new basidiomycetous yeast species mostly isolated from Tibet and Yunnan provinces, China

More than 2 000 yeast strains isolated from 1 200 samples mostly collected from Tibet and Yunnan provinces in China were identified as 462 species according to the internal transcribed spacer including the 5.8S rDNA (ITS) and the D1/D2 domains of the large subunit rDNA (LSU) sequence analyses. Among them, 70 new basidiomycetous yeast species were proposed based on the multi-locus phylogenetic analyses including the D1/D2 domains, the ITS, the small subunit rDNA (SSU), the largest subunit of RNA polymerase II (RPB1), the second largest subunit of RNA polymerase II (RPB2) and translation elongation factor 1-α (TEF1), as well as the phenotypic comparisons. The average nucleotide identity (ANI) analysis with the genomic metric was also used in the evaluation of the species delimitation for the genera Holtermannia, Mrakia and Takashimella that contain closely related species with low sequence heterogeneity in both ITS and D1/D2 regions. Forty-six new species belonged to 16 genera in the Agaricomycotina, 13 new species occurred in 12 genera in the Pucciniomycotina, three new species were distributed in three genera in the Ustilaginomycotina, and eight new species were classified in seven newly established genera. One new family was also proposed based on one of these new genera. The analyses revealed several inaccurate species names attributed to genomes deposited in GenBank, indicating the necessity of a more rigorous quality checks of the genomes deposited in the public databases. Taxonomic novelties: New family: Vankyiozymaceae Q.-M. Wang; New genera: Baiomyces Q.-M. Wang, Bauerozyma Q.-M. Wang, Fengyania Q.-M. Wang, Foliozyma Q.-M. Wang, Litoriozyma Q.-M. Wang, Nakaseozyma Q.-M. Wang, Vankyiozyma Q.-M. Wang; New species: Baiomyces sejilaensis Q.-M. Wang, Bauerozyma artemisiae Q.-M. Wang, Boekhoutia foliicola Q.-M. Wang, Buckleyzyma pseudoaurantiaca Q.-M. Wang, Carlosrosaea betulae Q.-M. Wang, Carlosrosaea rhododendri Q.-M. Wang, Carlosrosaea yunnanensis Q.-M. Wang, Chrysozyma quercicola Q.-M. Wang, Curvibasidium pini Q.-M. Wang, Cystobasidium cunninghamiae Q.-M. Wang, Derxomyces foliicola Q.-M. Wang, Derxomyces motuoensis Q.-M. Wang, Derxomyces orientalis Q.-M. Wang, Derxomyces paracylindricus Q.-M. Wang, Exobasidium lijiangense Q.-M. Wang, Fengyania pteridophytorum Q.-M. Wang, Foliozyma liliicola Q.-M. Wang, Halobasidium phyllophilum Q.-M. Wang, Hannaella artemisiae Q.-M. Wang, Hannaella pteridophytorum Q.-M. Wang, Hannaella urticae Q.-M. Wang, Holtermannia pseudosaccardoi Q.-M. Wang, Kockovaella cariosiligni Q.-M. Wang, Kockovaella foliicola Q.-M. Wang, Kondoa tibetensis Q.-M. Wang, Kwoniella hippophaes Q.-M. Wang, Kwoniella lonicerae Q.-M. Wang, Litoriozyma hainanensis Q.-M. Wang, Meira marina Q.-M. Wang, Microsporomyces betulae Q.-M. Wang, Microsporomyces foliicola Q.-M. Wang, Mrakia pini Q.-M. Wang, Mrakia rhododendri Q.-M. Wang, Nakaseozyma junci Q.-M.Wang, Nakaseozyma lonicerae Q.-M. Wang, Papiliotrema castaneae Q.-M. Wang, Papiliotrema catalpae Q.-M. Wang, Phaeotremella pini Q.-M. Wang, Phaffia paratasmanica Q.-M. Wang, Phaffia rhododendri Q.-M. Wang, Piskurozyma cuscutae Q.-M. Wang, Piskurozyma humicola Q.-M. Wang, Piskurozyma liliaceifoliae Q.-M. Wang, Piskurozyma linzhiensis Q.-M. Wang, Piskurozyma nanyiensis Q.-M. Wang, Piskurozyma terricola Q.-M. Wang, Pseudohyphozyma sanghuangpori Q.-M. Wang, Pseudotremella hippophaes Q.-M. Wang, Pseudotremella rhododendri Q.-M. Wang, Rhodotorula linzhiensis Q.-M. Wang, Slooffia terricola Q.-M. Wang, Takashimella corticis Q.-M. Wang, Teunia betulicola Q.-M. Wang, Teunia chimonanthi Q.-M. Wang, Teunia heritierae Q.-M. Wang, Teunia myricariae Q.-M. Wang, Teunia parabetulicola Q.-M. Wang, Teunia quercus Q.-M. Wang, Teunia rhododendri Q.-M. Wang, Ustilago foliicola Q.-M. Wang, Vankyiozyma motuoensis Q.-M. Wang, Vanrija silvicola Q.-M. Wang, Vishniacozyma catalpae Q.-M. Wang, Vishniacozyma marinae Q.-M. Wang, Vishniacozyma paravictoriae Q.-M. Wang, Vishniacozyma pini Q.-M. Wang, Vishniacozyma pyri Q.-M. Wang, Vishniacozyma sinopodophylli Q.-M. Wang, Vishniacozyma zhenxiongensis Q.-M. Wang, Yurkovia castaneae Q.-M. Wang. Citation: Jiang Y-L, Bao W-J, Liu F, Wang G-S, Yurkov AM, Ma Q, Hu Z-D, Chen X-H, Zhao W-N, Li A-H, Wang Q-M (2024). Proposal of one new family, seven new genera and seventy new basidiomycetous yeast species mostly isolated from Tibet and Yunnan provinces, China. Studies in Mycology 109: 57-153. doi: 10.3114/sim.2024.109.02.

Local climate, air quality and leaf litter cover shape foliar fungal communities on an urban tree

Foliar fungi on urban trees are important for tree health, biodiversity and ecosystem functioning. Yet, we lack insights into how urbanization influences foliar fungal communities. We created detailed maps of Stockholm region's climate and air quality and characterized foliar fungi from mature oaks (Quercus robur) across climatic, air quality and local habitat gradients. Fungal richness was higher in locations with high growing season relative humidity, and fungal community composition was structured by growing season maximum temperature, NO2 concentration and leaf litter cover. The relative abundance of mycoparasites and endophytes increased with temperature. The relative abundance of pathogens was lowest with high concentrations of NO2 and particulate matter (PM2.5), while saprotrophs increased with leaf litter cover. Our findings show that urbanization influences foliar fungi, providing insights for developing management guidelines to promote tree health, prevent disease outbreaks and maintain biodiversity within urban landscapes.

Classes and phyla of the kingdom Fungi

Fungi are one of the most diverse groups of organisms with an estimated number of species in the range of 2–3 million. The higher-level ranking of fungi has been discussed in the framework of molecular phylogenetics since Hibbett et al., and the definition and the higher ranks (e.g., phyla) of the ‘true fungi’ have been revised in several subsequent publications. Rapid accumulation of novel genomic data and the advancements in phylogenetics now facilitate a robust and precise foundation for the higher-level classification within the kingdom. This study provides an updated classification of the kingdom Fungi, drawing upon a comprehensive phylogenomic analysis of Holomycota, with which we outline well-supported nodes of the fungal tree and explore more contentious groupings. We accept 19 phyla of Fungi, viz. Aphelidiomycota, Ascomycota, Basidiobolomycota, Basidiomycota, Blastocladiomycota, Calcarisporiellomycota, Chytridiomycota, Entomophthoromycota, Entorrhizomycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota, Sanchytriomycota, and Zoopagomycota. In the phylogenies, Caulochytriomycota resides in Chytridiomycota; thus, the former is regarded as a synonym of the latter, while Caulochytriomycetes is viewed as a class in Chytridiomycota. We provide a description of each phylum followed by its classes. A new subphylum, Sanchytriomycotina Karpov is introduced as the only subphylum in Sanchytriomycota. The subclass Pneumocystomycetidae Kirk et al. in Pneumocystomycetes, Ascomycota is invalid and thus validated. Placements of fossil fungi in phyla and classes are also discussed, providing examples.

Foraging ants affect community composition and diversity of phyllosphere fungi on a myrmecophilous plants, Mallotus japonicus

Many microorganisms inhabit the aboveground parts of plants (i.e. the phyllosphere), which mainly comprise leaves. Understanding the structure of phyllosphere microbial communities and their drivers is important because they influence host plant fitness and ecosystem functions. Despite the high prevalence of ant-plant associations, few studies have used quantitative community data to investigate the effects of ants on phyllosphere microbial communities. In the present study, we investigated the effects of ants on the phyllosphere fungal communities of Mallotus japonicus using high-throughput sequencing. Mallotus japonicus is a myrmecophilous plants that bears extrafloral nectaries, attracting several ant species, but does not provide specific ant species with nest sites like myrmecophytes do. We experimentally excluded ants with sticky resins from the target plants and collected leaf discs to extract fungal DNA. The ribosomal DNA internal transcribed spacer 1 (ITS1) regions of the phyllosphere fungi were amplified and sequenced to obtain fungal community data. Our results showed that the exclusion of ants changed the phyllosphere fungal community composition; however, the effect of ants on OTU richness was not clear. These results indicate that ants can change the community of phyllosphere fungi, even if the plant is not a myrmecophyte.

Seasonal dynamics of phyllosphere epiphytic microbial communities of medicinal plants in farmland environment

Introduction

The phyllosphere of plants is inhabited by various microorganisms, which play a crucial role in plant physiological metabolism. Currently, there is limited research on the dynamic effects of species and seasons on plant phyllosphere microbial community diversity and microbial interactions.

Methods

In this study, high-throughput sequencing technology was used to sequence the leaf surface parasitic microorganisms of five medicinal plants (Bupleurum chinense, Atractylodes lancea, Salvia miltiorrhiza, Astragalus membranaceus, and Lonicera japonica).

Results

The results showed that bacteria and fungi clustered into 3,898 and 1,572 operational taxonomic units (OTUs), respectively. Compared to host species, seasons had a more significant impact on the a diversity of bacteria and fungi. The heterogeneity of phyllosphere microbial communities was greater in winter compared to summer. Key species analysis at the OTU level and Spearman correlation analysis demonstrated significant preferences in microbial interactions under plant and seasonal backgrounds. The network connections between bacterial and fungal communities significantly increased during seasonal transitions compared to connections with plants.

Discussion

This study enhances our understanding of the composition and ecological roles of plant-associated microbial communities in small-scale agricultural environments. Additionally, it provides valuable insights for assessing the biodiversity of medicinal plants.

Beyond the surface: exploring the mycobiome of Norway spruce under drought stress and with Heterobasidion parviporum

The mycobiome, comprising fungi inhabiting plants, potentially plays a crucial role in tree health and survival amidst environmental stressors like climate change and pathogenic fungi. Understanding the intricate relationships between trees and their microbial communities is essential for developing effective strategies to bolster the resilience and well-being of forest ecosystems as we adopt more sustainable forest management practices. The mycobiome can be considered an integral aspect of a tree's biology, closely linked to its genotype. To explore the influence of host genetics and environmental factors on fungal composition, we examined the mycobiome associated with phloem and roots of Norway spruce (Picea abies (L.) Karst.) cuttings under varying watering conditions. To test the "mycobiome-associated-fitness" hypothesis, we compared seedlings artificially inoculated with Heterobasidion parviporum and control plants to evaluate mycobiome interaction on necrosis development. We aimed to 1) identify specific mycobiome species for the Norway spruce genotypes/families within the phloem and root tissues and their interactions with H. parviporum and 2) assess stability in the mycobiome species composition under abiotic disturbances (reduced water availability). The mycobiome was analyzed by sequencing the ribosomal ITS2 region. Our results revealed significant variations in the diversity and prevalence of the phloem mycobiome among different Norway spruce genotypes, highlighting the considerable impact of genetic variation on the composition and diversity of the phloem mycobiome. Additionally, specific mycobiome genera in the phloem showed variations in response to water availability, indicating the influence of environmental conditions on the relative proportion of certain fungal genera in Norway spruce trees. In the root mycobiome, key fungi such as Phialocephala fortinii and Paraphaeosphaeria neglecta were identified as conferring inhibitory effects against H. parviporum growth in Norway spruce genotypes. Furthermore, certain endophytes demonstrated greater stability in root ecosystems under low water conditions than ectomycorrhizal fungi. This knowledge can contribute to developing sustainable forest management practices that enhance the well-being of trees and their ecosystems, ultimately bolstering forest resilience.

Microbiome-Mediated Protection against Pathogens in Woody Plants

Pathogens, especially invasive species, have caused significant global ecological, economic, and social losses in forests. Plant disease research has traditionally focused on direct interactions between plants and pathogens in an appropriate environment. However, recent research indicates that the microbiome can interact with the plant host and pathogens to modulate plant resistance or pathogen pathogenicity, thereby altering the outcome of plant-pathogen interactions. Thus, this presents new opportunities for studying the microbial management of forest diseases. Compared to parallel studies on human and crop microbiomes, research into the forest tree microbiome and its critical role in forest disease progression has lagged. The rapid development of microbiome sequencing and analysis technologies has resulted in the rapid accumulation of a large body of evidence regarding the association between forest microbiomes and diseases. These data will aid the development of innovative, effective, and environmentally sustainable methods for the microbial management of forest diseases. Herein, we summarize the most recent findings on the dynamic structure and composition of forest tree microbiomes in belowground and aboveground plant tissues (i.e., rhizosphere, endosphere, and phyllosphere), as well as their pleiotropic impact on plant immunity and pathogen pathogenicity, highlighting representative examples of biological control agents used to modulate relevant tree microbiomes. Lastly, we discuss the potential application of forest tree microbiomes in disease control as well as their future prospects and challenges.

The Changes of Phyllosphere Fungal Communities among Three Different Populus spp

As an ecological index for plants, the diversity and structure of phyllosphere microbial communities play a crucial role in maintaining ecosystem stability and balance; they can affect plant biogeography and ecosystem function by influencing host fitness and function. The phyllosphere microbial communities reflect the immigration, survival, and growth of microbial colonists, which are influenced by various environmental factors and leaves' physical and chemical properties. This study investigated the structure and diversity of phyllosphere fungal communities in three different Populus spp., namely-P. × euramaricana (BF3), P. nigra (N46), and P. alba × P. glandulosa (84K). Leaves' chemical properties were also analyzed to identify the dominant factors affecting the phyllosphere fungal communities. N46 exhibited the highest contents of total nitrogen (Nt), total phosphorus (Pt), soluble sugar, and starch. Additionally, there were significant variations in the abundance, diversity, and composition of phyllosphere fungal communities among the three species: N46 had the highest Chao1 index and observed_species, while 84K had the highest Pielou_e index and Simpson index. Ascomycota and Basidiomycota are the dominant fungal communities at the phylum level. Results from typical correlation analyses indicate that the chemical properties of leaves, especially total phosphorus (Pt), total nitrogen (Nt), and starch content, significantly impact the structure and diversity of the phyllosphere microbial community. However, it is worth noting that even under the same stand conditions, plants from different species have distinct leaf characteristics, proving that the identity of the host species is the critical factor affecting the structure of the phyllosphere fungal community.

Different spatial structure of plant-associated fungal communities above- and belowground

The distribution and community assembly of above- and belowground microbial communities associated with individual plants remain poorly understood, despite its consequences for plant-microbe interactions and plant health. Depending on how microbial communities are structured, we can expect different effects of the microbial community on the health of individual plants and on ecosystem processes. Importantly, the relative role of different factors will likely differ with the scale examined. Here, we address the driving factors at a landscape level, where each individual unit (oak trees) is accessible to a joint species pool. This allowed to quantify the relative effect of environmental factors and dispersal on the distribution of two types of fungal communities: those associated with the leaves and those associated with the soil of Quercus robur trees in a landscape in southwestern Finland. Within each community type, we compared the role of microclimatic, phenological, and spatial variables, and across community types, we examined the degree of association between the respective communities. Most of the variation in the foliar fungal community was found within trees, whereas soil fungal community composition showed positive spatial autocorrelation up to 50 m. Microclimate, tree phenology, and tree spatial connectivity explained little variation in the foliar and soil fungal communities. Foliar and soil fungal communities differed strongly in community structure, with no significant concordance detected between them. We provide evidence that foliar and soil fungal communities assemble independent of each other and are structured by different ecological processes.

Environmental factors and host genotype control foliar epiphytic microbial community of wild soybeans across China

Introduction

The microbiome inhabiting plant leaves is critical for plant health and productivity. Wild soybean (Glycine soja), which originated in China, is the progenitor of cultivated soybean (Glycine max). So far, the community structure and assembly mechanism of phyllosphere microbial community on G. soja were poorly understood.

Methods

Here, we combined a national-scale survey with high-throughput sequencing and microsatellite data to evaluate the contribution of host genotype vs. climate in explaining the foliar microbiome of G. soja, and the core foliar microbiota of G. soja were identified.

Results

Our findings revealed that both the host genotype and environmental factors (i.e., geographic location and climatic conditions) were important factors regulating foliar community assembly of G. soja. Host genotypes explained 0.4% and 3.6% variations of the foliar bacterial and fungal community composition, respectively, while environmental factors explained 25.8% and 19.9% variations, respectively. We further identified a core microbiome thriving on the foliage of all G. soja populations, including bacterial (dominated by Methylobacterium-Methylorubrum, Pantoea, Quadrisphaera, Pseudomonas, and Sphingomonas) and fungal (dominated by Cladosporium, Alternaria, and Penicillium) taxa.

Conclusion

Our study revealed the significant role of host genetic distance as a driver of the foliar microbiome of the wild progenitor of soya, as well as the effects of climatic changes on foliar microbiomes. These findings would increase our knowledge of assembly mechanisms in the phyllosphere of wild soybeans and suggest the potential to manage the phyllosphere of soya plantations by plant breeding and selecting specific genotypes under climate change.

Differential impacts of adult trees on offspring and non-offspring recruits in a subtropical forest

An important mechanism promoting species coexistence is conspecific negative density dependence (CNDD), which inhibits conspecific neighbors by accumulating host-specific enemies near adult trees. Natural enemies may be genotype-specific and regulate offspring dynamics more strongly than non-offspring, which is often neglected due to the difficulty in ascertaining genetic relatedness. Here, we investigated whether offspring and non-offspring of a dominant species, Castanopsis eyrei, suffered from different strength of CNDD based on parentage assignment in a subtropical forest. We found decreased recruitment efficiency (proxy of survival probability) of offspring compared with non-offspring near adult trees during the seedling-sapling transition, suggesting genotype-dependent interactions drive tree demographic dynamics. Furthermore, the genetic similarity between individuals of same cohort decreased in late life history stages, indicating genetic-relatedness-dependent tree mortality throughout ontogeny. Our results demonstrate that within-species genetic relatedness significantly affects the strength of CNDD, implying genotype-specific natural enemies may contribute to population dynamics in natural forests.

An Integrative View of the Phyllosphere Mycobiome of Native Rubber Trees in the Brazilian Amazon

The rubber tree, Hevea brasiliensis, is a neotropical Amazonian species. Despite its high economic value and fungi associated with native individuals, in its original area in Brazil, it has been scarcely investigated and only using culture-dependent methods. Herein, we integrated in silico approaches with novel field/experimental approaches and a case study of shotgun metagenomics and small RNA metatranscriptomics of an adult individual. Scientific literature, host fungus, and DNA databases are biased to fungal taxa, and are mainly related to rubber tree diseases and in non-native ecosystems. Metabarcoding retrieved specific phyllospheric core fungal communities of all individuals, adults, plantlets, and leaves of the same plant, unravelling hierarchical structured core mycobiomes. Basidiomycotan yeast-like fungi that display the potential to produce antifungal compounds and a complex of non-invasive ectophytic parasites (Sooty Blotch and Flyspeck fungi) co-occurred in all samples, encompassing the strictest core mycobiome. The case study of the same adult tree (previously studied using culture-dependent approach) analyzed by amplicon, shotgun metagenomics, and small RNA transcriptomics revealed a high relative abundance of insect parasite-pathogens, anaerobic fungi and a high expression of Trichoderma (a fungal genus long reported as dominant in healthy wild rubber trees), respectively. Altogether, our study unravels new and intriguing information/hypotheses of the foliar mycobiome of native H. brasiliensis, which may also occur in other native Amazonian trees.

Host genotype interacts with aerial spore communities and influences the needle mycobiome of Norway spruce

The factors shaping the composition of the tree mycobiome are still under investigation. We tested the effects of host genotype, site, host phenotypic traits, and air fungal spore communities on the assembly of the fungi inhabiting Norway spruce needles. We used Norway spruce clones and spore traps within the collection sites and characterized both needle and air mycobiome communities by high‐throughput sequencing of the ITS2 region. The composition of the needle mycobiome differed between Norway spruce clones, and clones with high genetic similarity had a more similar mycobiome. The needle mycobiome also varied across sites and was associated with the composition of the local air mycobiome and climate. Phenotypic traits such as diameter at breast height or crown health influenced the needle mycobiome to a lesser extent than host genotype and air mycobiome. Altogether, our results suggest that the needle mycobiome is mainly driven by the host genotype in combination with the composition of the local air spore communities. Our work highlights the role of host intraspecific variation in shaping the mycobiome of trees and provides new insights on the ecological processes structuring fungal communities inhabiting woody plants.

Changes in the phyllosphere and rhizosphere microbial communities of soybean in the presence of pathogens

Soybean (Glycine max L.) is host to an array of foliar- and root-infecting pathogens that can cause significant yield losses. To provide insights into the roles of microorganisms in disease development, we evaluated the bacterial and fungal communities associated with the soybean rhizosphere and phyllosphere. For this, leaf and soil samples of healthy, Phytophthora sojae-infected and Septoria glycines-infected plants were sampled at three stages during the production cycle, and then subjected to 16S and Internal Transcribed Spacer (ITS) amplicon sequencing. The results indicated that biotic stresses did not have a significant impact on species richness and evenness regardless of growth stage. However, the structure and composition of soybean microbial communities were dramatically altered by biotic stresses, particularly for the fungal phyllosphere. Additionally, we cataloged a variety of microbial genera that were altered by biotic stresses and their associations with other genera, which could serve as biological indicators for disease development. In terms of soybean development, the rhizosphere and phyllosphere had distinct microbial communities, with the fungal phyllosphere most influenced by growth stage. Overall, this study characterized the phyllosphere and rhizosphere microbial communities of soybean, and described the impact of pathogen infection and plant development in shaping these bacterial and fungal communities.

Maple and hickory leaf litter fungal communities reflect pre-senescent leaf communities

Fungal communities are known to contribute to the functioning of living plant microbiomes as well as to the decay of dead plant material and affect vital ecosystem services, such as pathogen resistance and nutrient cycling. Yet, factors that drive structure and function of phyllosphere mycobiomes and their fate in leaf litter are often ignored. We sought to determine the factors contributing to the composition of communities in temperate forest substrates, with culture-independent amplicon sequencing of fungal communities of pre-senescent leaf surfaces, internal tissues, leaf litter, underlying humus soil of co-occurring red maple (Acer rubrum) and shagbark hickory (Carya ovata). Paired samples were taken at five sites within a temperate forest in southern Michigan, USA. Fungal communities were differentiable based on substrate, host species, and site, as well as all two-way and three-way interactions of these variables. PERMANOVA analyses and co-occurrence of taxa indicate that soil communities are unique from both phyllosphere and leaf litter communities. Correspondence of endophyte, epiphyte, and litter communities suggests dispersal plays an important role in structuring fungal communities. Future work will be needed to assess how this dispersal changes microbial community functioning in these niches.

Optimization of Protocol for Construction of Fungal ITS Amplicon Library for High-Throughput Illumina Sequencing to Study the Mycobiome of Aspen Leaves

High-Throughput Illumina Sequencing (HTS) can be used to study metagenomes, for example, those of importance for plant health. However, protocols must be optimized according to the plant system in question, the focal microorganisms in the samples, the marker genes selected, and the number of environmental samples. We optimized the protocol for metagenomic studies of aspen leaves, originating from varied genotypes sampled across the growing season, and consequently varying in phenolic composition and in the abundance of endo- and epiphytic fungal species. We optimized the DNA extraction protocol by comparing commercial kits and evaluating five fungal ribosomal specific primers (Ps) alone, and with extended primers that allow binding to sample-specific index primers, and we then optimized the amplification with these composite Ps for 380 samples. The fungal DNA concentration in the samples varied from 561 ng/µL to 1526 ng/µL depending on the DNA extraction kit used. However, binding to phenolic compounds affected DNA quality as assessed by Nanodrop measurements (0.63–2.04 and 0.26–2.00 absorbance ratios for 260/280 and 260/230, respectively), and this was judged to be more important in making our choice of DNA extraction kit. We initially modified the PCR conditions after determining the concentration of DNA extract in a few subsamples and then evaluated and optimized the annealing temperature, duration, and number of cycles to obtain the required amplification and PCR product bands. For three specific Ps, the extended Ps produced dimers and unexpected amplicon fragments due to nonspecific binding. However, we found that the specific Ps that targeted the ITS2 region of fungal rDNA successfully amplified this region for every sample (with and without the extension PP) resulting in the desired PCR bands, and also allowing the addition of sample-specific index primers, findings which were successfully verified in a second PCR. The optimized protocol allowed us to successfully prepare an amplicon library in order to subject the intended 380 environmental samples to HTS.

Scale-Dependent Effects of Growth Stage and Elevational Gradient on Rice Phyllosphere Bacterial and Fungal Microbial Patterns in the Terrace Field

The variation of phyllosphere bacterial and fungal communities along elevation gradients may provide a potential link with temperature, which corresponds to an elevation over short geographic distances. At the same time, the plant growth stage is also an important factor affecting phyllosphere microorganisms. Understanding microbiological diversity over changes in elevation and among plant growth stages is important for developing crop growth ecological theories. Thus, we investigated variations in the composition of the rice phyllosphere bacterial and fungal communities at five sites along an elevation gradient from 580 to 980 m above sea level (asl) in the Ziquejie Mountain at the seedling, heading, and mature stages, using high-throughput Illumina sequencing methods. The results revealed that the dominant bacterial phyla were Proteobacteria, Actinobacteria, and Bacteroidetes, and the dominant fungal phyla were Ascomycota and Basidiomycota, which varied significantly at different elevation sites and growth stages. Elevation had a greater effect on the α diversity of phyllosphere bacteria than on that phyllosphere fungi. Meanwhile, the growth stage had a great effect on the α diversity of both phyllosphere bacteria and fungi. Our results also showed that the composition of bacterial and fungal communities varied significantly along elevation within the different growth stages, in terms of both changes in the relative abundance of species, and that the variations in bacterial and fungal composition were well correlated with variations in the average elevation. A total of 18 bacterial and 24 fungal genera were significantly correlated with elevational gradient, displaying large differences at the various growth stages. Soluble protein (SP) shared a strong positive correlation with bacterial and fungal communities (p < 0.05) and had a strong significant negative correlation with Serratia, Passalora, unclassified_Trichosphaeriales, and antioxidant enzymes (R > 0.5, p < 0.05), and significant positive correlation with the fungal genera Xylaria, Gibberella, and Penicillium (R > 0.5, p < 0.05). Therefore, it suggests that elevation and growth stage might alter both the diversity and abundance of phyllosphere bacterial and fungal populations.

Analysis of microbial diversity in the root of Astragalus mongholicus

Abstract The dry root of Astragalus mongholicus has therapeutic effects such as tonifing the middle - jiao, replenishing qi, solidifing the surface, promoting diuresis, dispelling sepsis outwards and nourishing muscle. There are some slices having black spots after slicing the root of astragalus. The diversity of endophytic fungi between slices with black spots and normal slices was analysed in this paper. The endophytic fungal sequences obtained by high-throughput sequencing were 298,044 and 297,396, and the 116 OTU subsets obtained after clustering belonged to 3 phyla, 9 classes, 22 orders, 38 families and 46 genera. The dominant classes were Eurotiomycetes and Leotiomycetes. The dominant order is Eurotiales and Helotiales. The dominant families are Helotiales_fam_Incertae_sedis and Aspergillaceae. The dominant genera are Cadophora and Aspergillus. There are some peculiar fungal flora in both normal slices and spotted slices. The study on endophytic fungi diversity of astragalus slices will provide some help for drug development of this plant.

Differences between the Leaf Mycobiome of Coffea arabica and Wild Coffee Species and Their Modulation by Caffeine/Chlorogenic Acid Content

The study of microbes associated with the coffee tree has been gaining strength in recent years. In this work, we compared the leaf mycobiome of the traditional crop Coffea arabica with wild species Coffea racemosa and Coffea stenophylla using ITS sequencing for qualitative information and real-time PCR for quantitative information, seeking to relate the mycobiomes with the content of caffeine and chlorogenic acid in leaves. Dothideomycetes, Wallemiomycetes, and Tremellomycetes are the dominant classes of fungi. The core leaf mycobiome among the three Coffea species is formed by Hannaella, Cladosporium, Cryptococcus, Erythrobasidium, and Alternaria. A network analysis showed that Phoma, an important C. arabica pathogen, is negatively related to six fungal species present in C. racemosa and C. stenophylla and absent in C. arabica. Finally, C. arabica have more than 35 times the concentration of caffeine and 2.5 times the concentration of chlorogenic acid than C. stenophylla and C. racemosa. The relationship between caffeine/chlorogenic acid content, the leaf mycobiome, and genotype pathogen resistance is discussed.

Phyllosphere microbiome: Diversity and functions

Phyllosphere or aerial surface of plants represents the globally largest and peculiar microbial habitat that inhabits diverse and rich communities of bacteria, fungi, viruses, cyanobacteria, actinobacteria, nematodes, and protozoans. These hyperdiverse microbial communities are related to the host's specific functional traits and influence the host's physiology and the ecosystem's functioning. In the last few years, significant advances have been made in unravelling several aspects of phyllosphere microbiology, including diversity and microbial community composition, dynamics, and functional interactions. This review highlights the current knowledge about the assembly, structure, and composition of phyllosphere microbial communities across spatio-temporal scales, besides functional significance of different microbial communities to the plant host and the surrounding environment. The knowledge will help develop strategies for modelling and manipulating these highly beneficial microbial consortia for furthering scientific inquiry into their interactions with the host plants and also for their useful and economic utilization.

Maternal effects shape the seed mycobiome in Quercus petraea

The tree seed mycobiome has received little attention despite its potential role in forest regeneration and health. The aim of the present study was to analyze the processes shaping the composition of seed fungal communities in natural forests as seeds transition from the mother plant to the ground for establishment. We used metabarcoding approaches and confocal microscopy to analyze the fungal communities of seeds collected in the canopy and on the ground in four natural populations of sessile oak (Quercus petraea). Ecological processes shaping the seed mycobiome were inferred using joint species distribution models. Fungi were present in seed internal tissues, including the embryo. The seed mycobiome differed among oak populations and trees within the same population. Its composition was largely influenced by the mother, with weak significant environmental influences. The models also revealed several probable interactions among fungal pathogens and mycoparasites. Our results demonstrate that maternal effects, environmental filtering and biotic interactions all shape the seed mycobiome of sessile oak. They provide a starting point for future research aimed at understanding how maternal genes and environments interact to control the vertical transmission of fungal species that could then influence seed dispersal and germination, and seedling recruitment.

Scale-Dependent Influences of Distance and Vegetation on the Composition of Aboveground and Belowground Tropical Fungal Communities

Fungi provide essential ecosystem services and engage in a variety of symbiotic relationships with trees. In this study, we investigate the spatial relationship of trees and fungi at a community level. We characterized the spatial dynamics for above- and belowground fungi using a series of forest monitoring plots, at nested spatial scales, located in the tropical South Pacific, in Vanuatu. Fungal communities from different habitats were sampled using metagenomic analysis of the nuclear ribosomal ITS1 region. Fungal communities exhibited strong distance-decay of similarity across our entire sampling range (3-110,000 m) and also at small spatial scales (< 50 m). Unexpectedly, this pattern was inverted at an intermediate scale (3.7-26 km). At large scales (80-110 km), belowground and aboveground fungal communities responded inversely to increasing geographic distance. Aboveground fungal community turnover (beta diversity) was best explained, at all scales, by geographic distance. In contrast, belowground fungal community turnover was best explained by geographic distance at small scales and tree community composition at large scales. Fungal communities from various habitats respond differently to the influences of habitat and geographic distance. At large geographic distances (80-110 km), community turnover for aboveground fungi is better explained by spatial distance, whereas community turnover for belowground fungi is better explained by plant community turnover. Future syntheses of spatial dynamics among fungal communities must explicitly consider geographic scale to appropriately contextualize community turnover.

Divergence of Phyllosphere Microbial Communities Between Females and Males of the Dioecious Populus cathayana

Females and males of dioecious plants have evolved sex-specific characteristics in terms of their morphological and physiological properties. However, the differentiation of phyllosphere microbiota in dioecious plants remains largely unexplored. Here, the diversity and composition of female and male Populus cathayana phyllosphere bacterial and fungal communities were investigated using 16S rRNA/ITS1 gene-based MiSeq sequencing. The divergences of bacterial and fungal community compositions occurred between females and males. Both females and males had their unique phyllosphere bacterial and fungal microbiota, such as bacterial Gemmata spp. (5.41%) and fungal Pringsheimia spp. (0.03%) in females and bacterial Chitinophaga spp. (0.009%) and fungal Phaeococcomyces spp. (0.02%) in males. Significant differences in the relative abundance of phyla Proteobacteria and Planctomycetes bacteria and phyla Ascomycota and Basidiomycota fungi (P < 0.05) were also found between females and males. Some bacterial species of genera Spirosoma and Amnibacterium and fungal genera Venturia, Suillus, and Elmerina spp. were significantly enriched in males (P < 0.05). In contrast, levels of fungal genera Phoma and Aureobasidium spp. were significantly higher in females than in males (P < 0.05). The mineral, inorganic, and organic nutrients content contributed differently to the divergence of female and male phyllosphere microbial communities, with 87.08 and 45.17% of the variations being explained for bacterial and fungal communities, respectively. These results highlight the sexual discrimination of phyllosphere microbes on the dioecious plants and provide hints on the potential host-associated species in phyllosphere environments.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Foliar mycoendophytome of an endemic plant of the Mediterranean biome (Myrtus communis) reveals the dominance of basidiomycete woody saprotrophs

The true myrtle, Myrtus communis, is a small perennial evergreen tree that occurs in Europe, Africa, and Asia with a circum-Mediterranean geographic distribution. Unfortunately, the Mediterranean Forests, where M. communis occurs, are critically endangered and are currently restricted to small fragmented areas in protected conservation units. In the present work, we performed, for the first time, a metabarcoding study on the spatial variation of fungal community structure in the foliar endophytome of this endemic plant of the Mediterranean biome, using bipartite network analysis as a model. The local bipartite network of Myrtus communis individuals and their foliar endophytic fungi is very low connected, with low nestedness, and moderately high specialization and modularity. Similar network patterns were also retrieved in both culture-dependent and amplicon metagenomics of foliar endophytes in distinct arboreal hosts in varied biomes. Furthermore, the majority of putative fungal endophytes species were basidiomycete woody saprotrophs of the orders Polyporales, Agaricales, and Hymenochaetales. Altogether, these findings suggest a possible adaptation of these wood-decaying fungi to cope with moisture limitation and spatial scarcity of their primary substrate (dead wood), which are totally consistent with the predictions of the viaphytism hypothesis that wood-decomposing fungi inhabit the internal leaf tissue of forest trees in order to enhance dispersal to substrates on the forest floor, by using leaves as vectors and as refugia, during periods of environmental stress.

Crop-Zone Weed Mycobiomes of the South-Western Australian Grain Belt

In the absence of a primary crop host, secondary plant hosts may act as a reservoir for fungal plant pathogens of agricultural crops. Secondary hosts may potentially harbor heteroecious biotrophs (e.g., the stripe rust fungus Puccinia striiformis) or other pathogens with broad host ranges. Agricultural grain production tends toward monoculture or a limited number of crop hosts over large regions, and local weeds are a major source of potential secondary hosts. In this study, the fungal phyllospheres of 12 weed species common in the agricultural regions of Western Australia (WA) were compared through high-throughput DNA sequencing. Amplicons of D2 and ITS were sequenced on an Illumina MiSeq system using previously published primers and BLAST outputs analyzed using MEGAN. A heatmap of cumulative presence-absence for fungal taxa was generated, and variance patterns were investigated using principal components analysis (PCA) and canonical correspondence analysis (CCA). We observed the presence of several major international crop pathogens, including basidiomycete rusts of the Puccinia spp., and ascomycete phytopathogens of the Leptosphaeria and Pyrenophora genera. Unrelated to crop production, several endemic pathogen species including those infecting Eucalyptus trees were also observed, which was consistent with local native flora. We also observed that differences in latitude or climate zones appeared to influence the geographic distributions of plant pathogenic species more than the presence of compatible host species, with the exception of Brassicaceae host family. There was an increased proportion of necrotrophic Ascomycete species in warmer and drier regions of central WA, compared to an increased proportion of biotrophic Basidiomycete species in cooler and wetter regions in southern WA.

Host tree organ is the primary driver of endophytic fungal community structure in a hemiboreal forest

Despite numerous studies on plant endophytes, little is known about fungal communities associated with different aboveground tissues of living trees. We used high-throughput sequencing to compare the diversity and community structure of fungi inhabiting leaves, branches and trunks of Alnus incana and Corylus avellana growing at three hemiboreal forest sites. Our analysis revealed that tree organs are the main determinants of the structure of fungal communities, whereas the effects of host species and locality remained secondary and negligible, respectively. The structure of fungal communities in trunks was the most distinct compared to that in leaves and branches. The foliar fungal communities were more similar within than between individual trees, implying that certain fungi may grow through parts of the tree crown. The weak effect of locality compared to host organs and species identity suggests that the structural variation of fungal communities in the aboveground parts of trees depends mainly on deterministic factors rather than dispersal limitation.

Botanical microbiomes on the cheap: Inexpensive molecular fingerprinting methods to study plant-associated communities of bacteria and fungi

High-throughput sequencing technologies have revolutionized the study of plant-associated microbial populations, but they are relatively expensive. Molecular fingerprinting techniques are more affordable, yet yield considerably less information about the microbial community. Does this mean they are no longer useful for plant microbiome research? In this paper, we review the past 10 years of studies on plant-associated microbiomes using molecular fingerprinting methodologies, including single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), amplicon length heterogeneity PCR (LH-PCR), ribosomal intergenic spacer analysis (RISA) and automated ribosomal intergenic spacer analysis (ARISA), and terminal restriction fragment length polymorphism (TRFLP). We also present data juxtaposing results from TRFLP methods with those generated using Illumina sequencing in the comparison of rhizobacterial populations of Brazilian maize and fungal surveys in Canadian tomato roots. In both cases, the TRFLP approach yielded the desired results at a level of resolution comparable to that of the MiSeq method, but at a fraction of the cost. Community fingerprinting methods (especially TRFLP) remain relevant for the identification of dominant microbes in a population, the observation of shifts in plant microbiome community diversity, and for screening samples before their use in more sensitive and expensive approaches.

Tissue age, orchard location and disease management influence the composition of fungal and bacterial communities present on the bark of apple trees

Plants host microbial communities that can be affected by environmental conditions and agronomic practices. Despite the role of bark as a reservoir of plant pathogens and beneficial microorganisms, no information is available on the effects of disease management on the taxonomic composition of the bark-associated communities of apple trees. We assessed the impact of disease management strategies on fungal and bacterial communities on the bark of a scab-resistant apple cultivar in two orchard locations and for two consecutive seasons. The amplicon sequencing revealed that bark age and orchard location strongly affected fungal and bacterial diversity. Microbiota dissimilarity between orchards evolved during the growing season and showed specific temporal series for fungal and bacterial populations in old and young bark. Disease management did not induce global changes in the microbial populations across locations and seasons, but specifically affected the abundance of some taxa according to bark age, orchard location and sampling time. Therefore, the disease management applied to scab-resistant cultivars, which is based on a limited use of fungicides, partially changed the taxonomic composition of bark-associated fungal and bacterial communities, suggesting the need for a more accurate risk assessment regarding possible pathogen outbreaks.

Genotypic variation in Norway spruce correlates to fungal communities in vegetative buds

The taxonomically diverse phyllosphere fungi inhabit leaves of plants. Thus, apart from the fungi's dispersal capacities and environmental factors, the assembly of the phyllosphere community associated with a given host plant depends on factors encoded by the host's genome. The host genetic factors and their influence on the assembly of phyllosphere communities under natural conditions are poorly understood, especially in trees. Recent work indicates that Norway spruce (Picea abies) vegetative buds harbour active fungal communities, but these are hitherto largely uncharacterized. This study combines internal transcribed spacer sequencing of the fungal communities associated with dormant vegetative buds with a genome-wide association study (GWAS) in 478 unrelated Norway spruce trees. The aim was to detect host loci associated with variation in the fungal communities across the population, and to identify loci correlating with the presence of specific, latent, pathogens. The fungal communities were dominated by known Norway spruce phyllosphere endophytes and pathogens. We identified six quantitative trait loci (QTLs) associated with the relative abundance of the dominating taxa (i.e., top 1% most abundant taxa). Three additional QTLs associated with colonization by the spruce needle cast pathogen Lirula macrospora or the cherry spruce rust (Thekopsora areolata) in asymptomatic tissues were detected. The identification of the nine QTLs shows that the genetic variation in Norway spruce influences the fungal community in dormant buds and that mechanisms underlying the assembly of the communities and the colonization of latent pathogens in trees may be uncovered by combining molecular identification of fungi with GWAS.

Effects of nutrient supply, herbivory, and host community on fungal endophyte diversity

The microbes contained within free-living organisms can alter host growth, reproduction, and interactions with the environment. In turn, processes occurring at larger scales determine the local biotic and abiotic environment of each host that may affect the diversity and composition of the microbiome community. Here, we examine variation in the diversity and composition of the foliar fungal microbiome in the grass host, Andropogon gerardii, across four mesic prairies in the central United States. Composition of fungal endophyte communities differed among sites and among individuals within a site, but was not consistently affected by experimental manipulation of nutrient supply to hosts (A. gerardii) or herbivore reduction via fencing. In contrast, mean fungal diversity was similar among sites but was limited by total plant biomass at the plot scale. Our work demonstrates that distributed experiments motivated by ecological theory are a powerful tool to unravel the multiscale processes governing microbial community composition and diversity.

Differences in the fungal communities nursed by two genetic groups of the alpine cushion plant, Silene acaulis

Foundation plants shape the composition of local biotic communities and abiotic environments, but the impact of a plant's intraspecific variations on these processes is poorly understood. We examined these links in the alpine cushion moss campion (Silene acaulis) on two neighboring mountain ranges in the French Alps. Genotyping of cushion plants revealed two genetic clusters matching known subspecies. The exscapa subspecies was found on both limestone and granite, while the longiscapa one was only found on limestone. Even on similar limestone bedrock, cushion soils from the two S. acaulis subspecies deeply differed in their impact on soil abiotic conditions. They further strikingly differed from each other and from the surrounding bare soils in fungal community composition. Plant genotype variations accounted for a large part of the fungal composition variability in cushion soils, even when considering geography or soil chemistry, and particularly for the dominant molecular operational taxonomic units (MOTUs). Both saprophytic and biotrophic fungal taxa were related to the MOTUs recurrently associated with a single plant genetic cluster. Moreover, the putative phytopathogens were abundant, and within the same genus (Cladosporium) or species (Pyrenopeziza brassicae), MOTUs showing specificity for each plant subspecies were found. Our study highlights the combined influences of bedrock and plant genotype on fungal recruitment into cushion soils and suggests the coexistence of two mechanisms, an indirect selection resulting from the colonization of an engineered soil by free-living saprobes and a direct selection resulting from direct plant-fungi interactions.

Leaves of Indoor Ornamentals Are Biodiversity and Functional Hotspots for Fungi

Leaf-inhabiting fungi are an important, but often overlooked component of molecular biodiversity studies. To understand their diversity and function in relation to plant species and climate, the phyllospheres of 14 phylogenetically diverse ornamental plant species were analyzed under different controlled greenhouse conditions. We found unexpectedly high fungal diversity (H' = 2.8-6.5), OTU numbers (449-1050) and abundances (103-106 CFU cm-2 leaf surface) associated with all plants studied indoors. Despite experimental limitations, the composition of fungal communities were inclined toward a plant species-dependent pattern compared to the ambient climatic variables. Most detected fungi were patho- and saprotrophs showing a yeast-like growth morphology and were associated to the groups of endophytes and potential plant pathogens in a plant species-specific manner. A representative strain collection showed that 1/3 of the tested fungi (mainly Penicillium, Cladosporium, and Cryptococcus spp.) were able to inhibit mycelial growth and 2/3 inhibit sporulation of the plant pathogen Botrytis cinerea by the production of antifungal volatile organic compounds (VOCs) completely. This study indicates that plant leaves harbor a stable phyllosphere fungal diversity in diverse microclimates and enrich distinctive functional guilds.

Knowing your neighbourhood-the effects of Epichloë endophytes on foliar fungal assemblages in perennial ryegrass in dependence of season and land-use intensity

Epichloë endophytes associated with cool-season grass species can protect their hosts from herbivory and can suppress mycorrhizal colonization of the hosts' roots. However, little is known about whether or not Epichloë endophyte infection can also change the foliar fungal assemblages of the host. We tested 52 grassland study sites along a land-use intensity gradient in three study regions over two seasons (spring vs. summer) to determine whether Epichloë infection of the host grass Lolium perenne changes the fungal community structure in leaves. Foliar fungal communities were assessed by Next Generation Sequencing of the ITS rRNA gene region. Fungal community structure was strongly affected by study region and season in our study, while land-use intensity and infection with Epichloë endophytes had no significant effects. We conclude that effects on non-systemic endophytes resulting from land use practices and Epichloë infection reported in other studies were masked by local and seasonal variability in this study's grassland sites.

Distinct Communities of Poplar Endophytes on an Unpolluted and a Risk Element-Polluted Site and Their Plant Growth-Promoting Potential In Vitro

Numerous studies demonstrated that endophytic microbes can promote plant growth and increase plant stress resistance. We aimed at isolating poplar endophytes able to increase their hosts' fitness both in nutrient-limited and polluted environments. To achieve this goal, endophytic bacteria and fungi were isolated from roots and leaves of hybrid poplars (Populus nigra × P. maximowiczii clone Max-4) on an unpolluted and a risk element-polluted site in the Czech Republic and subsequently screened by a number of in vitro tests. Bacterial communities at the unpolluted site were dominated by Gammaproteobacteria with Pseudomonas sp. as the prominent member of the class, followed by Bacilli with prevailing Bacillus sp., whereas Alphaproteobacteria, mostly Rhizobium sp., prevailed at the polluted site. The fungal endophytic community was dominated by Ascomycetes and highly distinct on both sites. Dothideomycetes, mostly Cladosporium, prevailed at the non-polluted site while unclassified Sordariomycetous fungi dominated at the polluted site. Species diversity of endophytes was higher at the unpolluted site. Many tested endophytic strains solubilized phosphate and produced siderophores, phytohormones, and antioxidants. Some strains also exhibited ACC-deaminase activity. Selected bacteria showed high tolerance and the ability to accumulate risk elements, making them promising candidates for use in inocula promoting biomass production and phytoremediation. Graphical Abstract ᅟ.

Tissue age and plant genotype affect the microbiota of apple and pear bark

Plant tissues host complex fungal and bacterial communities, and their composition is determined by host traits such as tissue age, plant genotype and environmental conditions. Despite the importance of bark as a possible reservoir of plant pathogenic microorganisms, little is known about the associated microbial communities. In this work, we evaluated the composition of fungal and bacterial communities in the pear (Abate and Williams cultivars) and apple (Golden Delicious and Gala cultivars) bark of three/four-year-old shoots (old bark) or one-year-old shoots (young bark), using a meta-barcoding approach. The results showed that both fungal and bacterial communities are dominated by genera with ubiquitous attitudes, such as Aureobasidium, Cryptococcus, Deinococcus and Hymenobacter, indicating intense microbial migration to surrounding environments. The shoot age, plant species and plant cultivar influenced the composition of bark fungal and bacterial communities. In particular, bark communities included potential biocontrol agents that could maintain an equilibrium with potential plant pathogens. The abundance of fungal (e.g. Alternaria, Penicillium, Rosellinia, Stemphylium and Taphrina) and bacterial (e.g. Curtobacterium and Pseudomonas) plant pathogens was affected by bark age and host genotype, as well as those of fungal genera (e.g. Arthrinium, Aureobasidium, Rhodotorula, Sporobolomyces) and bacterial genera (e.g. Bacillus, Brevibacillus, Methylobacterium, Sphingomonas and Stenotrophomonas) with possible biocontrol and plant growth promotion properties.

A confidence interval analysis of sampling effort, sequencing depth, and taxonomic resolution of fungal community ecology in the era of high-throughput sequencing

High-throughput sequencing technology has helped microbial community ecologists explore ecological and evolutionary patterns at unprecedented scales. The benefits of a large sample size still typically outweigh that of greater sequencing depths per sample for accurate estimations of ecological inferences. However, excluding or not sequencing rare taxa may mislead the answers to the questions ‘how and why are communities different?’ This study evaluates the confidence intervals of ecological inferences from high-throughput sequencing data of foliar fungal endophytes as case studies through a range of sampling efforts, sequencing depths, and taxonomic resolutions to understand how technical and analytical practices may affect our interpretations. Increasing sampling size reliably decreased confidence intervals across multiple community comparisons. However, the effects of sequencing depths on confidence intervals depended on how rare taxa influenced the dissimilarity estimates among communities and did not significantly decrease confidence intervals for all community comparisons. A comparison of simulated communities under random drift suggests that sequencing depths are important in estimating dissimilarities between microbial communities under neutral selective processes. Confidence interval analyses reveal important biases as well as biological trends in microbial community studies that otherwise may be ignored when communities are only compared for statistically significant differences.

Comparing diversity of fungi from living leaves using culturing and high-throughput environmental sequencing

High-throughput sequencing technologies using amplicon approaches have changed the way that studies investigating fungal distribution are undertaken. These powerful and time-efficient technologies have the potential for the first time to accurately map fungal distributions across landscapes or changes in diversity across ecological or biological gradients of interest. There is no requirement for a fungus to form a fruiting body to be detected, and both culturable and nonculturable organisms can be detected. Here we use high-throughput amplicon sequencing from bulk DNA extracts to test the impact that biases associated with culture-based methods had on an earlier study that compared the influence of site and host on fungal diversity in Nothofagaceae forests in New Zealand. Both detection methods sampled tissue from the same set of symptomless, living leaves. We found that both the culturing and high-throughput approaches show that host is a stronger driver of fungal community structure than site, but that both methods have some taxonomic biases. We also found that the individual trees selected for high-throughput sampling can impact the alpha-diversity detected and through this could potentially affect subsequent analyses based on a comparison of this diversity.

Distance decay relationships in foliar fungal endophytes are driven by rare taxa

Foliar fungal endophytes represent a diverse and species-rich plant microbiome. Their biogeography provides essential clues to their cryptic relationship with hosts and the environment in which they disperse. We present species composition, diversity, and dispersal patterns of endophytic fungi associated with needles of Pinus taeda trees across regional scales in the absence of strong environmental gradients as well as within individual trees. An empirical designation of rare and abundant taxa enlightens us on the structure of endophyte communities. We report multiple distance-decay patterns consistent with effects of dispersal limitation, largely driven by community changes in rare taxa, those taxonomic units that made up less than 0.31% of reads per sample on average. Distance-decay rates and community structure also depended on specific classes of fungi and were predominantly influenced by rare members of Dothideomycetes. Communities separated by urban areas also revealed stronger effects of distance on community similarity, confirming that host density and diversity plays an important role in symbiont biogeography, which may ultimately lead to a mosaic of functional diversity as well as rare species diversity across landscapes.