Endophytic Community Composition Research Articles

Insight into the composition and differentiation of endophytic microbial communities in kernels via 368 maize transcriptomes

Insight into the composition and differentiation of endophytic microbial communities in kernels via 368 maize transcriptomes

High-throughput sequencing-based analysis of the composition and diversity of the endophyte community in roots of Stellera chamaejasme

Stellera chamaejasme (S. chamaejasme) is an important medicinal plant with heat-clearing, detoxifying, swelling and anti-inflammatory effects. At the same time, it is also one of the iconic plants of natural grassland degradation in northwest China, playing a key role in the invasion process. Plant endophytes live in healthy plant tissues and can synthesize substances needed for plant growth, induce disease resistance in host plants, and enhance plant resistance to environmental stress. Therefore, studying the root endophytes of S. chamaejasme is of great significance for mining beneficial microbial resources and biological prevention and control of S. chamaejasme. This study used Illumina MiSeq high-throughput sequencing technology to analyze the composition and diversity of endophytes in the roots of S. chamaejasme in different alpine grasslands (BGC, NMC and XGYZ) in Tibet. Research results show that the main phylum of endophytic fungi in the roots of S. chamaejasme in different regions is Ascomycota, and the main phyla of endophytic bacteria are Actinobacteria, Proteobacteria and Firmicutes (Bacteroidota). Overall, the endophyte diversity of the NMC samples was significantly higher than that of the other two sample sites. Principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) results showed significant differences in the composition of endophytic bacterial and fungal communities among BGC, NMC and XGYZ samples. Co-occurrence network analysis of endophytes showed that there were positive correlations between fungi and some negative correlations between bacteria, and the co-occurrence network of bacteria was more complex than that of fungi. In short, this study provides a vital reference for further exploring and utilizing the endophyte resources of S. chamaejasme and an in-depth understanding of the ecological functions of S. chamaejasme endophytes.

Global insights into endophytic bacterial communities of terrestrial plants: Exploring the potential applications of endophytic microbiota in sustainable agriculture

Endophytic microorganisms are indispensable symbionts during plant growth and development and often serve functions such as growth promotion and stress resistance in plants. Therefore, an increasing number of researchers have applied endophytes for multifaceted phytoremediation (e.g., organic pollutants and heavy metals) in recent years. With the availability of next-generation sequencing technologies, an increasing number of studies have shifted the focus from culturable bacteria to total communities. However, information on the composition, structure, and function of bacterial endophytic communities is still not widely synthesized. To explore the general patterns of variation in bacterial communities between plant niches, we reanalyzed data from 1499 samples in 30 individual studies from different continents and provided comprehensive insights. A group of bacterial genera were commonly found in most plant roots and shoots. Our analysis revealed distinct variations in the diversity, composition, structure, and function of endophytic bacterial communities between plant roots and shoots. These variations underscore the sophisticated mechanisms by which plants engage with their endophytic microbiota, optimizing these interactions to bolster growth, health, and resilience against stress. Highlighting the strategic role of endophytic bacteria in promoting sustainable agricultural practices and environmental stewardship, our study not only offers global insights into the endophytic bacterial communities of terrestrial plants but also underscores the untapped potential of these communities as invaluable resources for future research.

Glyphosate residues in soil and phosphate fertilizer affect foliar endophytic microbial community composition and phytohormone levels in potato

Glyphosate, the active ingredient of glyphosate-based herbicide (GBH) controls the growth of weeds by inhibiting shikimate pathway, thereby interrupting amino acid biosynthesis in plants. However, several microbes have shikimate pathway and the action of glyphosate on these non-target organisms are ignored. Along with other agrochemicals such as phosphate fertilizers, the action of GBH is further complicated, often varying their mode of action depending on soil type or plant species. To address the impact of GBH and phosphate fertilizer, we simulated agricultural application of GBH and phosphate fertilizer in a field study, investigating the composition of endophytic microbial communities and correlation of phytohormone concentrations with the microbial diversity of potato (Solanum tuberosum). In leaves, glyphosate residues in soil from GBH treatment alone and in combination with phosphate significantly shifted bacterial community whereas phosphate alone and in combination with glyphosate significantly altered the composition of fungal community. There were no significant changes in microbial communities in roots and tubers. Plants treated with GBH showed higher ratios of potentially glyphosate-resistant bacteria, with Xanthomonadaceae and Moraxallaceae being more abundant. Additionally, phytohormone concentrations showed various correlations with bacterial and fungal diversity in different treatments. The study highlights the impact of GBH residues in soil, particularly in combination with phosphate fertilizers on the composition of plant-associated microbial communities. Together with changes in phytohormone concentrations, plant health may be affected. Moreover, future studies could provide insights to whether these agrochemicals influence plant microbiome, leading to changes in phytohormones or vice-versa.

Bacterial endophytic community composition varies by hemp cultivar in commercially sourced seed.

The seed-endophytic bacterial community is a potentially beneficial and heritable fraction of the plant microbiome. Its utilization as a sustainable crop improvement strategy could be especially valuable for species such as hemp, where production is being scaled up and new challenges will be faced in managing crop productivity and health. However, little is known about the makeup and variation of the hemp seed microbiome. This study profiled the endophytic bacterial communities harboured by 16 hemp cultivars sourced from commercial suppliers in Europe. A 16S rDNA amplicon sequencing approach identified 917 amplicon sequence variants across samples. Taxonomic classification of sequences revealed 4 phyla and 87 genera to be represented in the dataset. Several genera were widespread while some were specific to one or a few cultivars. Flavobacterium, Pseudomonas, and Pantoea were notable in their high overall abundance and prevalence, but community composition was variable and no one taxon was universally abundant, suggesting a high degree of flexibility in community assembly. Taxonomic composition and alpha diversity differed among cultivars, though further work is required to understand the relative influence of hemp genetic factors on community structure. The taxonomic profiles presented here can be used to inform further work investigating the functional characteristics and potential plant-growth-promoting traits of seed-borne bacteria in hemp.

The host sex contributes to the endophytic bacterial community in Sargassum thunbergii and their receptacles.

Endophytic bacteria have a complex coevolutionary relationship with their host macroalgae. Dioecious macroalgae are important producers in marine ecosystems, but there is still a lack of research on how sex influences their endophytic bacteria. In this study, the endophytic bacterial communities in male and female S. thunbergii and their reproductive tissues (receptacles) were compared using culture methods and high-throughput sequencing. The endophytic bacterial communities detected by the two methods were different. Among the 78 isolated strains, the dominant phylum, genus, and species were Bacillota, Alkalihalobacillus, and Alkalihalobacillus algicola, respectively, in the algal bodies, while in the receptacles, they were Bacillota, Vibrio, and Vibrio alginolyticus. However, 24 phyla and 349 genera of endophytic bacteria were identified by high-throughput sequencing, and the dominant phylum and genus were Pseudomonadota and Sva0996_ Marine_ Group, respectively, in both the algal body and the receptacles. The two methods showed similar compositions of endophytic bacterial communities between the samples of different sexes, but the relative abundances of dominant and specific taxa were different. The high-throughput sequencing results showed more clearly that the sex of the host alga had an effect on its endophyte community assembly and a greater effect on the endophytic bacterial community in the receptacles. Moreover, most specific bacteria and predicted functional genes that differed between the samples from the males and females were related to metabolism, suggesting that metabolic differences are the main causes of sex differences in the endophytic bacterial community. Our research is the first to show that host sex contributes to the composition of endophytic bacterial communities in dioecious marine macroalgae. The results enrich the database of endophytic bacteria of dioecious marine macroalgae and pave the way for better understanding the assembly mechanism of the endophytic bacterial community of algae.

Sequencing of leaf endophytic fungal communities of Carya illinoinensis revealed a dominance of pathogenic fungi

Understanding the composition of leaf endophytic fungal communities could have important implications for orchard management. The planted area of pecan trees, Carya illinoinensis, is increasing in China. Leaf diseases of pecan trees cause huge economic losses and have incidence ofabout 50%–90%. However, little is known about whether the pathogens mainly persist on leaf surfaces, in the soil or in the air, or live within leaves as endophytes. In this study, pecan leaves were sampled from 2-, 3-, 6-, and 10-year old trees in the subtropical humid monsoon climate of China, and leaf endophytic fungal communities were characterized using high throughput sequencing. Leaf endophytic fungal OTUs (operational taxonomic units) mainly belonged to Ascomycota, with a much smaller fraction in the Basidiomycota. Ramularia was the dominant genus across all four tree ages. Plant pathogens were found to be the dominant functional guild by functional group annotation using FUNGuild. Three known disease agents of pecan (Trichomerium dioscoreae, Phaeosphaeria fuckelii and Alternaria alternata), were detected as leaf endophytes. To our knowledge, this is the first report of leaf fungal pathogens occurring as dominant endophytes in pecan leaves.

Effects of different dwarfing interstocks on the rhizosphere, endophytic bacteria, and drought resistance of apple trees

Rootstock is commonly used to enhance plant resistance to drought stress. However, it is necessary to investigate the effects of different rootstock, interstock, and scion combinations on rhizosphere and root endophytic bacteria under drought stress. We conducted a pot experiment to investigate how interstock [SH40, Jizhen 1 (J1), and Jizhen 2 (J2)] affects the drought tolerance and nitrogen (N) uptake and utilization of apple trees under drought stress. The results showed that the total dry weight, total chlorophyll content, carotenoid content, photosynthesis rate, and N absorption and utilization efficiency of apple trees decreased significantly, whereas relative electrolyte leakage increased significantly under drought stress. Membership function analysis showed that the apple plants with the J1 interstock had the greatest drought resistance. In addition, drought treatment significantly affected the diversity and composition of rhizosphere and root endophytic communities in all three rootstock/interstock/scion combinations. Further analysis revealed that the relative abundance of the plant pathogen Ralstonia was significantly increased in J2 drought-treated roots, compared to the other groups, whereas those of some potentially beneficial bacteria (0134_terrestrial_group, Phenylobacterium, Ellin6067, Kribbella, Chloronema, and Streptomyces) increased significantly in the J1 drought-treated sample. Co-occurrence network analysis showed that some potentially beneficial bacteria (Ellin6067, S0134_terrestrial_group, Pedomicrobium, and Subgroup_10) were significantly positively correlated with N content. These modifications of the rhizosphere and endophytic bacterial communities may influence the drought resilience and N uptake efficiency of different combinations of interstocks and scions. This study is a much-needed step towards understanding the stress response mechanism of scion–rootstock combinations.

Effects of Different Heavy Metal Stressors on the Endophytic Community Composition and Diversity of Symphytum officinale.

Endophytes play an important role in helping plants resist heavy metal stress. However, little is known about the effects of different heavy metals on the diversity and composition of endophyte communities. In this study, we used 16S and ITS amplicon sequencing to reveal the structure and function of endophytes in Symphytum officinale under different heavy metal stressors. The results showed that the endophytic fungal diversity decreased compared with the control under the different heavy metals stressors, while the diversity of endophytic bacteria showed an increasing trend. The biomarker analysis indicated that Zn and Pb stress led to obvious branches. Specific OTUs analysis showed that there were 1224, 597, and 1004 OTUs specific under Zn, Pb, and Cd stress in the bacterial community and 135, 81, and 110 OTUs specific under Zn, Pb, and Cd stress in the fungal community. The co-occurrence network showed changes in microbial interactions under heavy metal contamination conditions, suggesting that endophytic bacteria play an important role in the resistance of host plants. The Spearman analysis showed that the correlation between endophytic bacteria and endophytic fungi in relation to heavy metal transport exhibited variations. Our results expand the knowledge of the relationships of plant-microbe interactions and offer pivotal information to reveal the role of endophytes under different heavy metal stress conditions.

Melatonin alleviates cadmium toxicity by regulating root endophytic bacteria community structure and metabolite composition in apple.

The level of cadmium (Cd) accumulation in orchard soils is increasing, and excess Cd will cause serious damage to plants. Melatonin is a potent natural antioxidant and has a potential role in alleviating Cd stress. This study aimed to investigate the effects of exogenous melatonin on a root endophyte bacteria community and metabolite composition under Cd stress. The results showed that melatonin significantly scavenged the reactive oxygen species and restored the photosynthetic system (manifested by the improved photosynthetic parameters, total chlorophyll content and the chlorophyll fluorescence parameters (Fv/Fm)), increased the activity of antioxidant enzymes (the activities of catalase, superoxide dismutase, peroxidase and ascorbate oxidase) and reduced the concentration of Cd in the roots and leaves of apple plants. High-throughput sequencing showed that melatonin increased the endophytic bacterial community richness significantly and changed the community structure under Cd stress. The abundance of some potentially beneficial endophytic bacteria (Ohtaekwangia, Streptomyces, Tabrizicola and Azovibrio) increased significantly, indicating that the plants may absorb potentially beneficial microorganisms to resist Cd stress. The metabolomics results showed that melatonin significantly changed the composition of root metabolites, and the relative abundance of some metabolites decreased, suggesting that melatonin may resist Cd stress by depleting root metabolites. In addition, co-occurrence network analysis indicated that some potentially beneficial endophytes may be influenced by specific metabolites. These results provide a theoretical basis for studying the effects of melatonin on the endophytic bacterial community and metabolic composition in apple plants.

Interdomain ecological network analysis infers the endophytic bacteria protect against Fusarium root rot invasion

Fungi and bacteria coexist assembling complex communities in plant rhizosphere and endosphere that are important for plant health and agricultural productivity, however, the influence of root rot pathogen on bacterial-fungal interactions in plant ecological settings remains unclear. Here, bacterial communities from soil to endophyte of tobacco during Fusarium root rot invasion were comprehensively investigated. The bacterial community diversity and composition of stem endophytes were significantly altered by Fusarium root rot invasion. Molecular ecological network analysis revealed that the interactions among bacterial microbes in infected plant soils exhibit more intricate network structures compared to those found in healthy plants. The pathogens invasion led to changes in the crucial species within both the rhizosphere soil and plant endophytic bacterial communities. Furthermore, the interactions among fungal and bacterial species indicated that diseased samples, encompassing both the rhizosphere and endosphere, exhibited more complicated interdomain networks compared to their healthy counterparts. Importantly, the endophytic bacterial species Bacillus, Paenibacillus, Lactococcus, and two unclassified bacteria (OTU11999 and OTU730) from infected roots, and Bacillus, Raoultella, Leminorella, Pseudomonas, and three unclassified bacteria (OTU12058, OTU3 and OTU11435) from infected stems were negatively correlated with the pathogen Fusarium oxysporum f sp. psidii. It suggested that these endophytic bacteria may be associated with anantagonist effect and resistant against Fusarium root rot.

Floral Volatile Organic Compounds Change the Composition and Function of the Endophytic Fungal Community in the Flowers of Osmanthus fragrans.

Endophytic fungi in flowers influence plant health and reproduction. However, whether floral volatile organic compounds (VOCs) affect the composition and function of the endophytic fungal community remains unclear. Here, gas chromatography-mass spectrometry (GC-MS) and high-throughput sequencing were used to explore the relationship between floral VOCs and the endophytic fungal community during different flower development stages in Osmanthus fragrans 'Rixiang Gui'. The results showed that the composition of the endophytic fungal community and floral VOCs shifted along with flowering development. The highest and lowest α diversity of the endophytic fungal community occurred in the flower fading stage and full blooming stage, respectively. The dominant fungi, including Dothideomycetes (class), Pleosporales (order), and Neocladophialophora, Alternaria, and Setophoma (genera), were enriched in the flower fading stage and decreased in the full blooming stage, demonstrating the enrichment of the Pathotroph, Saprotroph, and Pathotroph-Saprotroph functions in the flower fading stage and their depletion in the full blooming stage. However, the total VOC and terpene contents were highest in the full blooming stage and lowest in the flower fading stage, which was opposite to the α diversity of the endophytic fungal community and the dominant fungi during flowering development. Linalool, dihydro-β-ionone, and trans-linalool oxide(furan) were key factors affecting the endophytic fungal community composition. Furthermore, dihydro-β-ionone played an extremely important role in inhibiting endophytic fungi in the full blooming stage. Based on the above results, it is believed that VOCs, especially terpenes, changed the endophytic fungal community composition in the flowers of O. fragrans 'Rixiang Gui'. These findings improve the understanding of the interaction between endophytic fungi and VOCs in flowers and provide new insight into the mechanism of flower development.

Distribution patterns of endophytic fungi in different intertidal plant communities within a tropical mangrove forest in South China

Fungi play a crucial role in the growth of mangrove plants in various intertidal zones. However, our knowledge of the endophytic fungi in mangroves is limited. In this study, we analyzed the distribution patterns of endophytic fungi in true mangroves (TM), mangrove associates (MA), and other plants (OP) in a tropical mangrove forest. The results showed that Lulwoana, Fusarium, and Aspergillus were the predominant endophytic fungal taxa in TM, MA, and OP, respectively. Non-metric multidimensional scaling demonstrated significant differences in the endophytic fungal community structure among different intertidal plant communities, highlighting the plant-mediated selection of endophytic fungi. In addition, tides and plant species may affect endophytic fungal communities by altering soil properties. The colonization of arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSE) was higher in MA, possibly because of variations in soil pH and available phosphorus content. Phylogenetic analyses indicated that family Diversisporaceae and Par1 (Paraglomeraceae) were exclusively found in the mangrove associates, whereas Glome4 (Glomeraceae) and Par2 (Paraglomeraceae) were observed only in the TM. These results support the high variation in AMF communities among the different intertidal plant communities. This study emphasizes the critical role of tides and plant species in shaping the composition of endophytic fungal communities, which has significant implications for the conservation and restoration of mangrove ecosystems.

Structure and function of microbiomes in the rhizosphere and endosphere response to temperature and precipitation variation in Inner Mongolia steppes.

Owing to challenges in the study of complex rhizosphere and endophytic microbial communities, the composition and function of such microbial communities in steppe ecosystems remain elusive. Here, we studied the microbial communities of the rhizosphere and endophytic microbes of the dominant plant species across the Inner Mongolian steppes using metagenomic sequencing and investigated their relationships with changes in mean annual temperature (MAT) and mean annual precipitation (MAP). Metagenomic sequencing based on Illumina high-throughput sequencing, using the paired end method to construct a small fragment library for sequencing. Adaptation of root systems to the environment affected the composition and function of rhizosphere and endophytic microbial communities. However, these communities exhibited distinct community assembly and environmental adaptation patterns. Both rhizosphere and endophytic microbial communities can be divided into two unrelated systems based on their ecological niches. The composition and function of the rhizosphere microbial communities were mainly influenced by MAT, while those of the endophytic microbial communities were mainly influenced by MAP. MAT affected the growth, reproduction, and lipid decomposition of rhizosphere microorganisms, whereas MAP affected reverse transcription and cell wall/membrane/envelope biogenic functions of endophytic microorganisms. Our findings reveal the composition and function of the rhizosphere and endophytic microbial communities in response to changes in MAP and MAT, which has important implications for future biogeography and climate change research.

Endophytic bacterial communities in ungerminated and germinated seeds of commercial vegetables

Chile is a prominent seed exporter globally, but the seed microbiome of vegetables (46% of seeds) and its role in the early stages of plant growth have remained largely unexplored. Here, we employed DNA metabarcoding analysis to investigate the composition and putative functions of endophytic bacterial communities in ungerminated and germinated seeds of the commercial vegetables Apiaceae (parsley and carrot), Asteraceae (lettuce), Brassicaceae (cabbage and broccoli), and Solanaceae (tomato). Bacterial quantification showed 104 to 108 copies of the 16S rRNA gene per gram of ungerminated and germinated seeds. Alpha diversity analysis (e.g., Chao1, Shannon, and Simpson indices) did not indicate significant differences (Kruskal–Wallis test) between ungerminated and germinated seeds, except for Solanaceae. However, beta diversity (PCoA) analysis showed distinctions (Adonis test) between ungerminated and germinated seeds, except Apiaceae. Pseudomonadota and Bacillota were identified as the dominant and specialist taxa in both ungerminated and germinated seed samples. Chemoheterotrophy and fermentation were predicted as the main microbial functional groups in the endophytic bacterial community. Notably, a considerable number of the 143 isolated endophytic strains displayed plant growth-promoting traits (10 to 64%) and biocontrol activity (74% to 82%) against plant pathogens (Xanthomonas and Pseudomonas). This study revealed the high variability in the abundance, diversity, composition, and functionality of endophytic bacteria between ungerminated and germinated seeds in globally commercialized vegetables. Furthermore, potential beneficial endophytic bacteria contained in their seed microbiomes that may contribute to the microbiome of the early stages, development, growth and progeny of vegetables were found.

Response strategies of stem/leaves endophyte communities to nano-plastics regulate growth performance of submerged macrophytes

Research on the toxicity effects of nano-plastics on submerged macrophytes has been increasing over the past several years. However, how the endophytic bacteria of submerged macrophytes respond to nano-plastics remains unknown, although they have been widely shown to help terrestrial plants cope with various environmental stressors. Here, a microcosm experiment was performed to unravel the effects of high concentration of nano-plastics (20 mg/L) on three submerged macrophyte (Vallisneria natans, Potamogeton maackianus, Myriophyllum spicatum) and their endophytic bacterial communities. Results indicated that nano-plastics induced antioxidative stress in plants, but significantly reduction in relative growth rate (RGR) only occurred in V. natans (from 0.0034 to −0.0029 day-1), accompanied by change in the stem/leaves endophyte community composition. Further analysis suggested nano-plastics caused a reduction in environmental nutrient availability and the proportion of positive interactions between endophyte communities (43%), resulting in the lowest RGR of V. natans. In contrast, endophytes may help P. maackianus and M. spicatum cope with nano-plastic stress by increasing the proportion of positive correlations among communities (70% and 75%), leaving their RGR unaffected. Collectively, our study elucidates the species-specific response strategies of submerged macrophyte-endophyte to nano-plastics, which helps to reveal the different phytoremediation potential of submerged macrophytes against nano-plastic pollution.

The Difference in Diversity between Endophytic Microorganisms in White and Grey Zizania latifolia.

The Zizania latifolia is usually infected by the obligate parasitic fungus Ustilago esculenta to form an edible fleshy stem which is an aquatic vegetable called Jiaobai in China. The infection by the teliospore (T) strain of U. esculenta induces Z. latifolia forming gray fleshy stems, while the mycelia-teliospore (MT) strain of U. esculenta induces white fleshy stems which are more suitable for edibility than gray fleshy stems. The mechanism of this phenomenon is still largely unknown. One of the possible causes is the diversity of endophytic microbial communities between these two fleshy stems. Therefore, we utilized fungal ITS1 and bacterial 16S rDNA amplicon sequencing to investigate the diversity of endophytic microbial communities in the two different fleshy stems of Z. latifolia. The results revealed that the α diversity and richness of endophytic fungi in white Z. latifolia were significantly greater than in gray Z. latifolia. The dominant fungal genus in both fleshy stems was U. esculenta, which accounted for over 90% of the endophytic fungi. The community composition of endophytic fungi in gray and white Z. latifolia was different except for U. esculenta, and a negative correlation was observed between U. esculenta and other endophytic fungi. In addition, the dominant bacterial genus in gray Z. latifolia was Alcaligenaceae which is also negatively correlated with other bacterium communities. Additionally, the co-occurrence network of white Z. latifolia was found to have a stronger scale, connectivity, and complexity compared to that of gray Z. latifolia. And the detected beneficial bacteria and pathogens in the stems of Z. latifolia potentially compete for resources. Furthermore, the function of endophytic bacteria is more abundant than endophytic fungi in Z. latifolia. This research investigated the correlation between the development of Z. latifolia fleshy stems and endophytic microbial communities. Our findings indicate that the composition of endophytic microbial communities is closely related to the type of Z. latifolia fleshy stems. This research also suggests the potential utilization of specific microbial communities to enhance the growth and development of Z. latifolia, thereby contributing to the breeding of Z. latifolia.

Contrasting Effects of Grazing in Shaping the Seasonal Trajectory of Foliar Fungal Endophyte Communities on Two Semiarid Grassland Species.

Fungal endophytes are harboured in the leaves of every individual plant host and contribute to plant health, leaf senescence, and early decomposition. In grasslands, fungal endophytes and their hosts often coexist with large herbivores. However, the influence of grazing by large herbivores on foliar fungal endophyte communities remains largely unexplored. We conducted a long-term (18 yr) grazing experiment to explore the effects of grazing on the community composition and diversity of the foliar fungal endophytes of two perennial grassland species (i.e., Artemisia capillaris and Stipa bungeana) across one growing season. Grazing significantly increased the mean fungal alpha diversity of A. capillaris in the early season. In contrast, grazing significantly reduced the mean fungal alpha diversity of endophytic fungi of S. bungeana in the late season. Grazing, growing season, and their interactions concurrently structured the community composition of the foliar fungal endophytes of both plant species. However, growing season consistently outperformed grazing and environmental factors in shaping the community composition and diversity of both plant species. Overall, our findings demonstrate that the foliar endophytic fungal community diversity and composition differed in response to grazing between A. capillaris and S. bungeana during one growing season. The focus on this difference will enhance our understanding of grazing's impact on ecological systems and improve land management practices in grazing regions. This variation in the effects of leaf nutrients and plant community characteristics on foliar endophytic fungal community diversity and composition may have a pronounced impact on plant health and plant-fungal interactions.

Leaf Endophyte Community Composition and Network Structures Differ Between Tolerant and Susceptible English Boxwood

Differential tolerance of English boxwood to boxwood blight has been linked to the ratio of culturable bacterial and fungal dominance in the leaf tissue of representative samples. To further understand how the whole endophyte communities may involve the tolerance of large samples, we extracted DNA from healthy leaf tissue of previously identified 28 tolerant (T), 41 moderately tolerant (M), and 21 susceptible (S) English boxwood plants, then sequenced associated bacterial and fungal amplicons using the Nanopore MinION platform. The endophyte community did not differ in diversity among the T, M, and S plants but differed in the abundance of bacteria and fungi, particularly between T and S samples. The bacterial genera Brevundimonas and Ammonifex had higher relative abundance in the T and M communities than in the S community, in which the fungal genera Botrytis and Thermothelomyces and family Chaetomiaceae were more dominant. The same results were obtained when mother and daughter samples in the T community were compared with controls in the S community, suggesting bacteria as a work force in the T community. Cooccurrence network analyses revealed that the T network had more fungal hubs but was less complex, with more positive connections than the S network, suggesting that the T community was supported by a healthier network. The resistance of English boxwood to blight is likely attributed to bacteria dominance and a synergic community network. This study is foundational to constructing synthetic communities and using whole communities of tolerant plants through vegetative propagation for microbe-modulated immunity.

Divergent rainforest tree microbiomes between phases of the monsoon cycle, host plants and tissues.

The Australian Monsoon Tropics (AMT) contain some of the most biodiverse forests on the continent. Little is known about the dynamics of rainforest plant microbiomes in general, and there have been no community-level studies on Australian rainforest endophytes, their seasonality, tissue and host specificity. We tested whether community composition of tropical tree endophytes (fungi and bacteria) differs: (i) at different points during a monsoon cycle, (ii) between leaf and stem tissues, (iii) between forest microclimates (gully/ridge), and between (iv) host plant species, and (v) host plant clade, using amplicon sequencing of the bacterial 16S and fungal ITS2 gene regions. Results indicated that the composition of rainforest plant microbiomes differs between wet and dry seasons, which may be explained by physiological shifts in host plants due to annual climate fluctuations from mesic to xeric. Endophyte microbiomes differed between leaves and stems. Distinct fungal communities were associated with host species and clades, with some trees enriched in a number of fungal taxa compared to host plants in other clades. Diversity of bacterial endophytes in plant stems increased in the dry season. We conclude that the microbiomes of tropical plants are responsive to monsoonal climate variation, are highly compartmentalised between plant tissues, and may be partly shaped by the relatedness of their host plants.