Fungal endophyte communities differ between chestnut galls and surrounding foliar tissues

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

Specific network and phylosymbiosis pattern in endophyte community of coastal halophytes

Halophytes colonize stressed environments of high salinity. Endophytic symbionts improve growth performance and thus adaptability of host plants in stressed environments. Nevertheless, studies focused on the distribution and assembly patterns of fungal endophyte assemblages of halophytes in high salinity environments are limited. We selected 27 common non-mangrove halophytes across 4 geographic sites along the eastern coastline of China for our investigation on endophyte assemblages. We found a significant amount of basidiomycetous fungi in the endophyte assemblage. The endophyte community compositions were significantly affected by plant species and geographic locations. Some halophyte hosts showed significant preference for endophytic fungi in host preference analysis. The network structures of host-microbe bipartite graphs at each site had low connection and were highly nested, modular and specialized. Current results also indicated significant correlation and congruency between host phylogeny and compositions of endophyte local communities and meta-community. Our research showed that host is the dominant factor shaping the fungal endophytic communities in aerial tissues of halophytes in high salinity environments, and the host influence on endophytic community relates to plant phylogeny.     

Spatial and temporal variation of fungal endophytic richness and diversity associated to the phyllosphere of olive cultivars

Fungal endophytes are micro-organisms that colonize healthy plant tissues without causing disease symptoms. They are described as plant growth and disease resistance promoters and have shown antimicrobial activity. The spatial-temporal distribution of endophytic communities in olive cultivars has been poorly explored. This study aims to investigate the richness and diversity of endophytic fungi in different seasons and sites, within the Alentejo region, Portugal. Additionally, and because the impact of some pathogenic fungi (e.g. Colletotrichum spp.) varies according to olive cultivars; three cultivars, Galega vulgar, Cobrançosa and Azeiteira, were sampled. 1868 fungal isolates were identified as belonging to 26 OTUs; 13 OTUs were identified to the genera level and 13 to species level. Cultivar Galega vulgar and season autumn showed significant higher values in terms of endophytic richness and diversity. At site level, Elvas showed the lowest fungal richness and diversity of fungal endophytes. This study reinforces the importance of exploring the combined spatio-temporal distribution of the endophytic biodiversity in different olive cultivars. Knowledge about endophytic communities may help to better understand their functions in plants hosts, such as their ecological dynamics with pathogenic fungi, which can be explored for their use as biocontrol agents.     

Temporal shifts of fungal communities in the rhizosphere and on tubers in potato fields

Soil fungal communities perform important ecological roles determining, at least in part, agricultural productivity. This study aimed at examining the fungal community dynamics in the potato rhizosphere across different development stages in two consecutive growing seasons (winter and summer). Microbial fingerprinting of rhizosphere soil samples collected at pre-planting, tuber initiation, flowering and at senescence was performed using ARISA in conjunction with Next Generation Sequencing (Illumina MiSeq). The epiphytic fungal communities on tubers at harvest were also investigated. Alpha-diversity was stable over time within and across the two seasons. In contrast, rhizospheric fungal community structure and composition were different between the two seasons and in the different plant growth stages within a given season, indicating the significance of the rhizosphere in shaping microbial communities. The phylum Ascomycota was dominant in the potato fungal rhizosphere, with Operational Taxonomic Units (OTUs) belonging to the genus Peyronellaea being the most abundant in all samples. Important fungal pathogens of potato, together with potential biological control agents and saprophytic species, were identified as indicator OTUs at different plant growth stages. These findings indicate that potato rhizosphere fungal communities are functionally diverse, which may contribute to soil health.     

Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types

The root-rhizosphere interface of Populus is the nexus of a variety of associations between bacteria, fungi, and the host plant and an ideal model for studying interactions between plants and microorganisms. However, such studies have generally been confined to greenhouse and plantation systems. Here we analyze microbial communities from the root endophytic and rhizospheric habitats of Populus deltoides in mature natural trees from both upland and bottomland sites in central Tennessee. Community profiling utilized 454 pyrosequencing with separate primers targeting the V4 region for bacterial 16S rRNA and the D1/D2 region for fungal 28S rRNA genes. Rhizosphere bacteria were dominated by Acidobacteria (31%) and Alphaproteobacteria (30%), whereas most endophytes were from the Gammaproteobacteria (54%) as well as Alphaproteobacteria (23%). A single Pseudomonas-like operational taxonomic unit (OTU) accounted for 34% of endophytic bacterial sequences. Endophytic bacterial richness was also highly variable and 10-fold lower than in rhizosphere samples originating from the same roots. Fungal rhizosphere and endophyte samples had approximately equal amounts of the Pezizomycotina (40%), while the Agaricomycotina were more abundant in the rhizosphere (34%) than endosphere (17%). Both fungal and bacterial rhizosphere samples were highly clustered compared to the more variable endophyte samples in a UniFrac principal coordinates analysis, regardless of upland or bottomland site origin. Hierarchical clustering of OTU relative abundance patterns also showed that the most abundant bacterial and fungal OTUs tended to be dominant in either the endophyte or rhizosphere samples but not both. Together, these findings demonstrate that root endophytic communities are distinct assemblages rather than opportunistic subsets of the rhizosphere.     

Endophytic Fungal Communities Associated with Vascular Plants in the High Arctic Zone Are Highly Diverse and Host-Plant Specific

This study assessed the diversity and distribution of endophytic fungal communities associated with the leaves and stems of four vascular plant species in the High Arctic using 454 pyrosequencing with fungal-specific primers targeting the ITS region. Endophytic fungal communities showed high diversity. The 76,691 sequences obtained belonged to 250 operational taxonomic units (OTUs). Of these OTUs, 190 belonged to Ascomycota, 50 to Basidiomycota, 1 to Chytridiomycota, and 9 to unknown fungi. The dominant orders were Helotiales, Pleosporales, Capnodiales, and Tremellales, whereas the common known fungal genera were Cryptococcus, Rhizosphaera, Mycopappus, Melampsora, Tetracladium, Phaeosphaeria, Mrakia, Venturia, and Leptosphaeria. Both the climate and host-related factors might shape the fungal communities associated with the four Arctic plant species in this region. These results suggested the presence of an interesting endophytic fungal community and could improve our understanding of fungal evolution and ecology in the Arctic terrestrial ecosystems.     

Fungal Community Analyses of Endophytic Fungi from Two Oak Species,Quercus mongolica and Quercus serrata,in Korea

Fungal endophytes have been recorded in various plant species with a richness of diversity, and their presence plays an essential role in host plant protection against biotic and abiotic stresses. This study applied the Illumina MiSeq sequencing platform based on the amplification of fungal ribosomal ITS2 region to analyze fungal endophytic communities of two oak species (Quercus mongolica and Q. serrata) with different oak wilt disease susceptibilities in Korea. The results showed a total of 230,768 sequencing reads were obtained and clustered at a 97% similarity threshold into 709 operational taxonomic units (OTUs). The OTUs of Q. serrata were higher than that of Q. mongolica with the number of 617 OTUs and 512 OTUs, respectively. Shannon index also showed that Q. serrata had a significantly higher level of fungal diversity than Q. mongolica. Total of OTUs were assigned into 5 fungal phyla, 17 classes, 60 orders, 133 families, 195 genera, and 280 species. Ascomycota was the dominant phylum with 75.11% relative abundance, followed by Basidiomycota with 5.28%. Leptosillia, Aureobasidium and Acanthostigma were the most abundant genera detected in Q. serrata with the average relative abundance of 2.85, 2.76, and 2.19%, respectively. On the other hand, Peltaster, Cladosporium and Monochaetia were the most common genera detected in Q. mongolica with the average relative abundance of 4.83, 3.03, and 2.87%, respectively. Our results indicated that fungal endophytic communities were significantly different between two oak species and these differences could influence responses of host trees to oak wilt disease caused by Raffaelea quercus-mongolicae.     

The endophytic fungal communities associated with the leaves and roots of the common reed (Phragmites australis) in Lake Trasimeno (Perugia,Italy) in declining and healthy stands

We surveyed the fungal endophytes in the leaves and roots of Phragmites australis plants along a gradient of reed decline at Lake Trasimeno (central Italy) in Oct. 2010. An integrated approach consisting of cultivation and molecular identification was used. Endophytes were recovered from 61.59 % of the samples, with a total of 1 541 isolates. On the basis of a molecular analysis of the rDNA Internal Transcribed Spacer (ITS) region, 25 operational taxonomic units (OTUs) were identified. Fusarium sp. (OTU 21) and Gibberella moniliformis (OTU 1) were the most frequently isolated fungi. Comparisons of the leaf and root samples demonstrated spatial heterogeneity in the endophyte assemblages among the plant parts and sites. In this study, we have shown that reed plants in different states of decline harbour different endophytic communities. This finding may help to understand the very complex scenario of reed die-back.     

Foliar nutrients shape fungal endophyte communities in Western white pine (Pinus monticola) with implications for white-tailed deer herbivory

Asymptomatic fungal endophytes colonize tissues of woody plants worldwide, with largely unknown ecological effects. Using culture-based methods and ITS1-5.8S-ITS2 rDNA sequence analysis, we investigated differences between foliar endophyte communities in disease-resistant hybrid and wild-type Pinus monticola (Western white pine) trees with observed variation in tree growth, vigor, and browsing damage by white-tailed deer (Odocoileus virginianus). We isolated 69 phylotypes of endophytic fungi in at least 39 genera, including 26 that have not previously been reported in P. monticola. Principal components analysis revealed that endophyte communities differed between browsed seedlings, unbrowsed seedlings, and unbrowsed adult trees. Sulfur, nitrate and calcium concentrations correlated with endophyte community differences among tree groups based on a distance-based redundancy analysis. Our results indicate that foliar nutrient variation influences endophyte community assembly and deer herbivory in P. monticola on a small landscape scale (80 hectares).     

Comparison of fungal communities associated with spruce seedling roots and bryophyte carpets on logs in an old-growth subalpine coniferous forest in Japan

Fungal communities associated with plant tissues were compared between two bryophyte species dominating decaying logs (Scapania bolanderi and Pleurozium schreberi), and roots of spruce seedlings growing on the bryophytes and in the ground soil, to evaluate the contribution of fungal communities to seedling regeneration. Using high-throughput DNA sequencing, a total of 1233 fungal operational taxonomic units (OTUs) were detected. Saprotrophic Ascomycota were dominant in bryophytes, whereas ectomycorrhizal (ECM) Basidiomycota were dominant in spruce roots. Fungal communities were significantly different between the two bryophyte species. In addition, fungal communities of spruce seedlings were significantly affected by the substrates on which they were growing. Some ECM fungi were detected from both of the bryophytes and the spruce seedlings growing on them; however, the dominant OTU identities differed between the two bryophyte systems. The possible effects of functional differences between dominant fungal OTUs on spruce seedling regeneration are discussed.     

Fungal Endophytes of Alpinia officinarum Rhizomes: Insights on Diversity and Variation across Growth Years,Growth Sites,and the Inner Active Chemical Concentration

In the present study, the terminal-restriction fragment length polymorphism (T-RFLP) technique, combined with the use of a clone library, was applied to assess the baseline diversity of fungal endophyte communities associated with rhizomes of Alpinia officinarum Hance, a medicinal plant with a long history of use. A total of 46 distinct T-RFLP fragment peaks were detected using HhaI or MspI mono-digestion-targeted, amplified fungal rDNA ITS sequences from A. officinarum rhizomes. Cloning and sequencing of representative sequences resulted in the detection of members of 10 fungal genera: Pestalotiopsis, Sebacina, Penicillium, Marasmius, Fusarium, Exserohilum, Mycoleptodiscus, Colletotrichum, Meyerozyma, and Scopulariopsis. The T-RFLP profiles revealed an influence of growth year of the host plant on fungal endophyte communities in rhizomes of this plant species; whereas, the geographic location where A. officinarum was grown contributed to only limited variation in the fungal endophyte communities of the host tissue. Furthermore, non-metric multidimensional scaling (NMDS) analysis across all of the rhizome samples showed that the fungal endophyte community assemblages in the rhizome samples could be grouped according to the presence of two types of active indicator chemicals: total volatile oils and galangin. Our present results, for the first time, address a diverse fungal endophyte community is able to internally colonize the rhizome tissue of A. officinarum. The diversity of the fungal endophytes found in the A. officinarum rhizome appeared to be closely correlated with the accumulation of active chemicals in the host plant tissue. The present study also provides the first systematic overview of the fungal endophyte communities in plant rhizome tissue using a culture-independent method.     

荒漠植物黑沙蒿嫩枝与成熟枝内生菌群落结构差异

[背景]黑沙蒿是我国北方沙漠地区分布广泛、抗旱性能优良的固沙灌木,对稳定沙漠地区生态系统有至关重要的作用.[目的]内生菌在植物生命过程中扮演着重要角色,认识植物生长发育阶段幼嫩和成熟组织内生菌群的结构变化,对于理解菌群间的相互作用及保护宿主植物抵御生物和非生物胁迫具有积极意义.[方法]以宁夏拉巴湖林场黑沙蒿为研究对象,...     

Factors influencing communities of foliar fungal endophytes in riparian woody plants

Riparian areas within a given arid region frequently contain broadly similar plant communities despite substantive geographic separation. Whether they also harbor similar communities of fungal symbionts, or feature assemblages unique to each riparian zone, is unknown. We examined fungal endophytes in foliage of woody angiosperms in six riparian areas in Arizona. Abundance and diversity differed among host species according to leaf longevity and phytochemistry, and among sites as a function of rainfall. Community composition varied among sites and host species. Comparison with regional data revealed that riparian areas harbor different subsets of the regional mycota rather than a consistent group of riparian taxa. Overall a high species- and phylogenetic richness of endophytes was recovered, especially among Mycosphaerella and affiliated anamorphs. Variation in endophyte communities across sites despite the relative consistency of plant communities underscores the importance of riparian zones both singly and in combination for harboring fungal biodiversity.     

Biodiversity of endophytic fungi in different leaf ages of Calotropis procera and their antimicrobial activity

Calotropis procera has many important medicinal properties with proven pharmacological potential. Some of these properties may be mediated by its fungal endophytes. This study analyzed, for the first time, the community of endophytic fungi of C. procera outside its region of origin. A total of 156 fungal isolates distributed across 19 taxa were obtained from 468 fragments of C. procera leaves at different stages of maturation. The rate of endophyte colonization increased with the leaf age/development. The dominant species of endophytic fungi of C. procera introduced in Northeast Brazil were different from those found in studies on the same species and other species of the same genus in native regions. The dominant endophyte was Phaeoramularia calotropidis (63.5 %), followed by Guignardia bidwellii (21.1 %). Six isolates of endophytic fungi showed antimicrobial activity against human pathogenic micro-organisms and one plant pathogenic fungus. The antibacterial activity was more intense than the antifungal activity. The endophytic Curvularia pallescens (URM 6048) stood out inhibited Gram-positive bacteria, Staphylococcus aureus, Streptococcus pyogenes, the plant pathogenic fungus Colletotrichum dematium. Ecological and biotechnological aspects of endophytic mycota are discussed.     

Influences of Plant Species,Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants

Bacteria are known to be associated endophytically with plants. Research on endophytic bacteria has identified their importance in food safety, agricultural production and phytoremediation. However, the diversity of endophytic bacterial communities and the forces that shape their compositions in non-cultivated plants are largely uncharacterized. In this study, we explored the diversity, community structure, and dynamics of endophytic bacteria in different plant species in the Tallgrass Prairie Preserve of northern Oklahoma, USA. High throughput sequencing of amplified segments of bacterial rDNA from 81 samples collected at four sampling times from five plant species at four locations identified 335 distinct OTUs at 97% sequence similarity, representing 16 phyla. Proteobacteria was the dominant phylum in the communities, followed by the phyla Bacteriodetes and Actinobacteria. Bacteria from four classes of Proteobacteria were detected with Alphaproteobacteria as the dominant class. Analysis of molecular variance revealed that host plant species and collecting date had significant influences on the compositions of the leaf endophytic bacterial communities. The proportion of Alphaproteobacteria was much higher in the communities from Asclepias viridis than from other plant species and differed from month to month. The most dominant bacterial groups identified in LDA Effect Size analysis showed host-specific patterns, indicating mutual selection between host plants and endophytic bacteria and that leaf endophytic bacterial compositions were dynamic, varying with the host plant’s growing season in three distinct patterns. In summary, next generation sequencing has revealed variations in the taxonomic compositions of leaf endophytic bacterial communities dependent primarily on the nature of the plant host species.     

Fungal Epiphytes and Endophytes of Coffee Leaves (Coffea arabica)

Plants harbor diverse communities of fungi and other microorganisms. Fungi are known to occur both on plant surfaces (epiphytes) and inside plant tissues (endophytes), but the two communities have rarely been compared. We compared epiphytic and endophytic fungal communities associated with leaves of coffee (Coffea arabica) in Puerto Rico. We asked whether the dominant fungi are the same in both communities, whether endophyte and epiphyte communities are equally diverse, and whether epiphytes and endophytes exhibit similar patterns of spatial heterogeneity among sites. Leaves of naturalized coffee plants were collected from six sites in Puerto Rico. Epiphytic and endophytic fungi were isolated by placing leaf pieces on potato dextrose agar without and with surface sterilization, respectively. A total of 821 colonies were isolated and grouped into 131 morphospecies. The taxonomic affinities of the four most common nonsporulating fungi were determined by sequencing the nuclear ribosomal internal transcribed spacer (ITS) region: two grouped with Xylaria and one each with Botryosphaeria and Guignardia. Of the most common genera, Pestalotia and Botryosphaeria were significantly more common as epiphytes; Colletotrichum, Xylaria, and Guignardia were significantly more common as endophytes. Suprisingly, more morphospecies occurred as endophytes than as epiphytes. Differences among sites in number of fungi per plant were significant. Thus epiphytic and endophytic communities differed greatly on a single leaf, despite living only millimeters apart, and both communities differed from site to site. Significant correlations between occurrence of fungal morphospecies suggested that fungi may have positive or negative effects on their neighbors. This is the first quantitative comparison of epiphytic and endophytic fungal floras in any plant, and the first to examine endophytic fungi or epiphytic fungi in leaves of coffee, one of the world’s most valuable crops.     

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

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

Community analysis of Persian oak fungal microbiome under dust storm conditions

Dust storms have major effects on terrestrial ecosystems through the long-distance transport and deposition of particulate matter. It is unclear how dust deposition affects plant-associated microbiomes in downwind ecosystems. Here we show that dust deposition may negatively influence the isolation, richness, and diversity of endophytic fungal communities of Persian oak. We used culture-based methods paired with Sanger sequencing to examine these effects on fungal assemblages isolated from leaf, branch and deposited dust. Increased amounts of dust deposition led to decreased endophytic fungal diversity in plant tissues but increased fungal diversity in deposited dust layers on leaves. Dust deposition decreased the abundance of a dominant endophyte in branches with promising biocontrol properties. Endophytic fungal communities found in leaves were more similar to fungal assemblages of deposited dust in comparison to branch endophytes. Our results suggest that dust storms may have ecosystem-wide effects by altering the fungal microbiomes of forest-forming trees.     

Pyrosequencing Reveals a Highly Diverse and Cultivar-Specific Bacterial Endophyte Community in Potato Roots

In this study, we examined the bacterial endophyte community of potato (Solanum tuberosum) cultivar/clones using two different molecular-based techniques (bacterial automated ribosomal intergenic spacer analysis (B-ARISA) and pyrosequencing). B-ARISA profiles revealed a significant difference in the endophytic community between cultivars (perMANOVA, p < 0.001), and canonical correspondence analysis showed a significant correlation between the community structure and plant biomass (p = 0.001). Pyrosequencing detected, on average, 477 ± 71 bacterial operational taxonomic units (OTUs, 97% genetic similarity) residing within the roots of each cultivar, with a Chao estimated total OTU richness of 1,265 ± 313. Across all cultivars, a total of 238 known genera from 15 phyla were identified. Interestingly, five of the ten most common genera (Rheinheimera, Dyadobacter, Devosia, Pedobacter, and Pseudoxanthomonas) have not, to our knowledge, been previously reported as endophytes of potato. Like the B-ARISA analysis, the endophytic communities differed between cultivar/clones (∫-libshuff, p < 0.001) and exhibited low similarities on both a presence/absence (0.145 ± 0.019) and abundance (0.420 ± 0.081) basis. Seventeen OTUs showed a strong positive (r > 0.600) or negative (r < −0.600) correlation with plant biomass, suggesting a possible link between plant production and endophyte abundance. This study represents one of the most comprehensive assessments of the bacterial endophytic communities to date, and similar analyses in other plant species, cultivars, or tissues could be utilized to further elucidate the potential contribution(s) of endophytic communities to plant physiology and production.     

Endophytic fungi from Peruvian highland and lowland habitats form distinctive and host plant-specific assemblages

Biodiversity and biogeography of leaf-inhabiting endophytic fungi have not been resolved yet. This is because host specificity, life cycles and species concepts, in this heterogeneous ecological guild of plant-associated microfungi, are far from being understood. Even though it is known that culture-based collection techniques are often biased, this has been the method of choice for studying fungal endophytes. Isolation of fungal endophytes only through culture-based methods could potentially mask slow growing species as well as species with low prevalence, preventing the capture of the communities’ real diversity and composition. This bias can be partially resolved by the use of cultivation-independent approaches such as direct sequencing of plant tissue by next generation techniques. Irrespective of the chosen sampling method, an efficient analysis of community ecology is urgently needed in order to evaluate the driving forces acting on fungal endophytic communities. In the present study, endophytic ascomyceteous fungi from three different plant genera (Vasconcellea microcarpa, Tillandsia spp., and Hevea brasiliensis) distributed in Peru, were isolated through culture-based sampling techniques and sequenced for their ITS rDNA region. These data sets were used to assess host preferences and biogeographic patterns of endophytic assemblages. This study showed that the effect of the host’s genetic background (identity) has a significant effect on the composition of the fungal endophytic community. In other words, the composition of the fungal endophytic community was significantly related to their host’s taxonomic identity. However, this was not true for all endophytic groups, since we found some endophytic groups (e.g. Xylariales and Pleosporales) occurring in more than one host genus. Findings from this study promote the formulation of hypotheses related to the effect of altitudinal changes on the endophytic communities along the Eastern Andean slopes. These hypotheses and perspectives for fungal biodiversity research and conservation in Peru are addressed and discussed.