Endophytic Microbiome Research Articles

Comparison of wild rice (Oryza longistaminata) tissues identifies rhizome-specific bacterial and archaeal endophytic microbiomes communities and network structures.

Compared with root-associated habitats, little is known about the role of microbiota inside other rice organs, especially the rhizome of perennial wild rice, and this information may be of importance for agriculture. Oryza longistaminata is perennial wild rice with various agronomically valuable traits, including large biomass on poor soils, high nitrogen use efficiency, and resistance to insect pests and disease. Here, we compared the endophytic bacterial and archaeal communities and network structures of the rhizome to other compartments of O. longistaminata using 16S rRNA gene sequencing. Diverse microbiota and significant variation in community structure were identified among different compartments of O. longistaminata. The rhizome microbial community showed low taxonomic and phylogenetic diversity as well as the lowest network complexity among four compartments. Rhizomes exhibited less phylogenetic clustering than roots and leaves, but similar phylogenetic clustering with stems. Streptococcus, Bacillus, and Methylobacteriaceae were the major genera in the rhizome. ASVs belonging to the Enhydrobacter, YS2, and Roseburia are specifically present in the rhizome. The relative abundance of Methylobacteriaceae in the rhizome and stem was significantly higher than that in leaf and root. Noteworthy type II methanotrophs were observed across all compartments, including the dominant Methylobacteriaceae, which potentially benefits the host by facilitating CH4-dependent N2 fixation under nitrogen nutrient-poor conditions. Our data offers a robust knowledge of host and microbiome interactions across various compartments and lends guidelines to the investigation of adaptation mechanisms of O. longistaminata in nutrient-poor environments for biofertilizer development in agriculture.

Choosing source of microorganisms and processing technology for next generation beet bioinoculant

The increase of human population and associated increasing demand for agricultural products lead to soil over-exploitation. Biofertilizers based on lyophilized plant material containing living plant growth-promoting microorganisms (PGPM) could be an alternative to conventional fertilizers that fits into sustainable agricultural technologies ideas. We aimed to: (1) assess the diversity of endophytic bacteria in sugar and sea beet roots and (2) determine the influence of osmoprotectants (trehalose and ectoine) addition during lyophilization on bacterial density, viability and salt tolerance. Microbiome diversity was assessed based on 16S rRNA amplicons sequencing, bacterial density and salt tolerance was evaluated in cultures, while bacterial viability was calculated by using fluorescence microscopy and flow cytometry. Here we show that plant genotype shapes its endophytic microbiome diversity and determines rhizosphere soil properties. Sea beet endophytic microbiome, consisting of genera characteristic for extreme environments, is more diverse and salt resistant than its crop relative. Supplementing osmoprotectants during root tissue lyophilization exerts a positive effect on bacterial community salt stress tolerance, viability and density. Trehalose improves the above-mentioned parameters more effectively than ectoine, moreover its use is economically advantageous, thus it may be used to formulate improved biofertilizers.

The Endophytic Microbiome as a Hotspot of Synergistic Interactions, with Prospects of Plant Growth Promotion.

Simple SummaryEndophytic bacteria are plant-associated bacteria that live in the internal tissues of the plant without harming the host plant. They have an important role in plant growth promotion, as they directly or indirectly promote plant growth. They do it by inhibiting the growth of plant pathogens, and/or by producing various secondary metabolites. They are used in the agricultural sector as an eco-friendly alternative tool that helps to improve crop yield. Detection of plant defense response and identification of compounds synthesized by root endophytes are an effective means for their utilization in the agriculture sector as biofertilizers. Therefore, it is important to study the diversity of root endophytic microbial community, endophyte-host plant interactions and their colonization, and their activity for successful application in agricultural lands. Here, in this review, the potential of the root endophytic microbial community, colonization, and role in the improvement of plant growth has been explained. This could mark the potential use of endophytes for the benefit of plant growth and enhanced yield. The plant root is the primary site of interaction between plants and associated microorganisms and constitutes the main components of plant microbiomes that impact crop production. The endophytic bacteria in the root zone have an important role in plant growth promotion. Diverse microbial communities inhabit plant root tissues, and they directly or indirectly promote plant growth by inhibiting the growth of plant pathogens, producing various secondary metabolites. Mechanisms of plant growth promotion and response of root endophytic microorganisms for their survival and colonization in the host plants are the result of complex plant-microbe interactions. Endophytic microorganisms also assist the host to sustain different biotic and abiotic stresses. Better insights are emerging for the endophyte, such as host plant interactions due to advancements in ‘omic’ technologies, which facilitate the exploration of genes that are responsible for plant tissue colonization. Consequently, this is informative to envisage putative functions and metabolic processes crucial for endophytic adaptations. Detection of cell signaling molecules between host plants and identification of compounds synthesized by root endophytes are effective means for their utilization in the agriculture sector as biofertilizers. In addition, it is interesting that the endophytic microorganism colonization impacts the relative abundance of indigenous microbial communities and suppresses the deleterious microorganisms in plant tissues. Natural products released by endophytes act as biocontrol agents and inhibit pathogen growth. The symbiosis of endophytic bacteria and arbuscular mycorrhizal fungi (AMF) affects plant symbiotic signaling pathways and root colonization patterns and phytohormone synthesis. In this review, the potential of the root endophytic community, colonization, and role in the improvement of plant growth has been explained in the light of intricate plant-microbe interactions.

Unveiling the putative functional genes present in root-associated endophytic microbiome from maize plant using the shotgun approach.

To ensure food security for the ever-increasing world's population, it is important to explore other alternatives for enhancing plant productivity. This study is aimed at identifying the putative plant growth-promoting (PGP) and endophytic gene clusters in root-associated endophytic microbes from maize root and to also verify if their abundance is affected by different farming practices. To achieve this, we characterize endophytic microbiome genes involved in PGP and endophytic lifestyle inside maize root using the shotgun metagenomic approach. Our results revealed the presence of genes involved in PGP activities such as nitrogen fixation, HCN biosynthesis, siderophore, 4-hydroxybenzoate, ACC deaminase, phenazine, phosphate solubilization, butanediol, methanol utilization, acetoin, nitrogen metabolism, and IAA biosynthesis. We also identify genes involved in stress resistance such as glutathione, catalase, and peroxidase. Our results further revealed the presence of putative genes involved in endophytic behaviors such as aerotaxis, regulator proteins, motility mechanisms, flagellum biosynthesis, nitrogen regulation, regulation of carbon storage, formation of biofilm, reduction of nitric oxide, regulation of beta-lactamase resistance, type III secretion, type IV conjugal DNA, type I pilus assembly, phosphotransferase system (PTS), and ATP-binding cassette (ABC). Our study suggests a high possibility in the utilization of endophytic microbial community for plant growth promotion, biocontrol activities, and stress mitigation. Further studies in ascertaining this claim through culturing of the beneficial isolates as well as pot and field experiments are necessary.

Deciphering core-microbiome of rice leaf endosphere: Revelation by metagenomic and microbiological analysis of aromatic and non-aromatic genotypes grown in three geographical zones

We have deciphered the leaf endophytic-microbiome of aromatic (cv. Pusa Basmati-1) and non-aromatic (cv. BPT-5204) rice-genotypes grown in the mountain and plateau-zones of India by both metagenomic NGS (mNGS) and conventional microbiological methods. Microbiome analysis by sequencing V3-V4 region of ribosomal gene revealed marginally more bacterial operational taxonomic units (OTU) in the mountain zone at Palampur and Almora than plateau zone at Hazaribagh. Interestingly, the rice leaf endophytic microbiomes in mountain zone were found clustered separately from that of plateau-zone. The Bray-Curtis dissimilarity indices indicated influence of geographical location as compared to genotype per se for shaping rice endophytic microbiome composition. Bacterial phyla, Proteobacteria followed by Bacteroidetes, Firmicutes, and Actinobacteria were found abundant in all three locations. The core-microbiome analysis devulged association of Acidovorax; Acinetobacter; Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium; Aureimonas; Bradyrhizobium; Burkholderia-Caballeronia-Paraburkholderia; Enterobacter; Pantoea; Pseudomonas; Sphingomonas; and Stenotrophomonas with the leaf endosphere. The phyllosphere and spermosphere microbiota appears to have contributed to endophytic microbiota of rice leaf. SparCC network analysis of the endophytic-microbiome showed complex cooperative and competitive intra-microbial interactions among the microbial communities. Microbiological validation of mNGS data further confirmed the presence of core and transient genera such as Acidovorax, Alcaligenes, Bacillus, Chryseobacterium, Comamonas, Curtobacterium, Delftia, Microbacterium, Ochrobactrum, Pantoea, Pseudomonas, Rhizobium, Rhodococcus, Sphingobacterium, Staphylococcus, Stenotrophomonas, and Xanthomonas in the rice genotypes. We isolated, characterized and identified core-endophytic microbial communities of rice leaf for developing microbiome assisted crop management by microbiome reengineering in future.

Endophytic fungi: understanding complex cross-talks

Although heeding and leading in the application perspective, we are lagging to address the variegated cross-talks involved in plant-endophyte interactions, the basis for the pertinence of endophytes. Endophytism represents the phenomenon in which a microbe resides asymptomatically within the plant tissues. The competency of the endophytes to penetrate, colonize, and flourish inside the plant premises by exhibiting complex multivariate interactions with the host, makes them unique. An endophyte, besides dealing with the host has to deal with the existing endospheric microbiota to make its colonization successful. However, we are at the beginning to appreciate the involvement of complex crosstalks between a plant and its endophytic microbiome and among the endophytic microbes associated with the plant. In this review, conglomerate cross-talks existing between plants and endophytes to maintain an ecological balance has been emphasized. Endophytic fungi have developed a palette of strategies to make their subsistence asymptomatic within the host. However, it is still a concern of exploration to unravel all the strategies employed by the endophytes, especially at the molecular level to accomplish this complex cross-kingdom association and making an asymptomatic existence inside the host. In recent years, the bioprospection of endophytes has received much attention, however, the differential survival strategies developed by them are poorly understood. This review summarizes currently available knowledge about the mechanisms behind the endophytic fungal colonization emphasizing the strategies employed by them in maintaining endophytism with special reference to quorum sensing and quorum quenching.

Volatile organic compounds profile synthesized and released by endophytes of tomato (Solanum lycopersici L.) and their antagonistic role.

The endophytic microbiome uses mechanisms such as the secretion of diffusible antibiotic molecules, synthesis and release of volatile organic compounds, and/or toxins to protect plants. The aim of this research was to study the volatile organic compounds (VOCs) profile as well as the diffusible secondary metabolites produced and released by endophytic bacteria isolated from tomato plants that in in-vitro assays prevented growth of pathogenic fungi. Bacteria belonging to seven genera (Acinetobacter, Arthrobacter, Bacillus, Microbacterium, Pantoea, Pseudomonas, and Stenotrophomonas) were isolated from different tissues of tomato plants with and without symptoms of Gray leaf spot, a disease provoked by Stemphylium lycopersici. In vitro, antagonistic assays were performed and the effect of volatile and soluble compounds released by endophytic bacteria on the growth of pathogenic fungi was determined. The VOCs synthesized by the endophytes were extracted, identified and quantified. These isolates representatives of seven bacterial genera inhibited the growth of three fungal pathogens of tomato S. lycopersici, Alternaria alternata and Corynespora cassiicola, which was related to the synthesis of soluble compounds as well as VOCs. Endophytes synthesize and release different VOCs, probably due to the different type of interaction that each bacterium establishes with the fungus, presenting a range of fungal growth inhibition.

Shotgun metagenomics reveals the functional diversity of root-associated endophytic microbiomes in maize plant

In this study, we used shotgun metagenomics to analyze the whole DNA from maize root planted with different fertilization and without fertilization in a bid to profile the impact of fertilizer applications on the functional diversity of endophytic microbiomes. Complete DNA extraction from roots of maize plant grown on different farming sites such as organic (FK), inorganic (NK) and no fertilizer (CK) sites was carried out, and sequenced using a shotgun metagenomic approach. The raw sequenced data obtained were analyzed using an online database called MG-RAST. Through MG-RAST analysis, endophytic microbiome sequences were identified while sequences of maize origin were discarded. The prediction of the functions of the endophytic microbiomes was done using the SEED subsystem. Our results revealed that no significant difference (P > 0.05) exist in the relative abundance of the 28 functional groups identified within the endophytic microbiomes across the sites. Also, some functional groups and metabolic pathways associated with plant growth promotion such as carbohydrate, secondary metabolism, nitrogen metabolism, iron acquisition and metabolism alongside phosphorus metabolism were observed in the endophytes across the sites. Alpha diversity study revealed no significant difference exist among the functional groups of the endophytes across the sites, while beta diversity study indicated that there was a significant difference (P = 0.01) among the functional groups of the endophytes across the fertilizer sites. Going by the high abundance of functional groups observed in this study, especially in FK samples, it is evident that different farming practices influenced the functions of endophytic microbiomes. We recommend that further studies should explore the functional genes in endophytic microbiomes with the aim of assessing their usefulness in promoting sustainable agriculture.

Comparative Analysis of the Rhizosphere and Endophytic Microbiomes across Apple Rootstock Genotypes in Replant Orchard Soils

Apple replant disease (ARD), caused by a complex of soilborne pathogens, negatively impacts tree health and productivity in new orchard plantings at sites previously planted to apple. Use of new disease-tolerant apple rootstock genotypes may diminish growth-limiting effects of ARD; however, the influence of rootstock genotype on modulating the rhizosphere and endophytic microbiome to enable ARD tolerance is not fully understood. Composition of the rhizosphere and root endophytic microbiomes was characterized across a diversity of apple rootstock genotypes. A series of tolerant (G.210, G.41, G.890, and G.935) and susceptible (M.26 and M.9) rootstock cultivars were consecutively planted into orchard replant soil containing a known pathogen complex. Amplicon sequencing was used to determine simultaneously the presence of a broad taxonomic range of organisms and their relative abundance. Microbial communities exhibited significant differences in composition between the rhizosphere and endophytic environments in terms of species diversity, content, and abundance. Significant differences in composition of the endophytic and rhizosphere microbiomes were observed between rootstock genotypes. Among rootstock endophytic fungal communities, rootstock G.890 samples consistently harbored the highest percentage of arbuscular mycorrhizal fungal species (>5% of total). Ilyonectria spp., which may function as a pathogen of apple, were detected at high relative abundance in the endosphere of all genotypes, with the highest relative abundance in M.26. These results provide further insight into rhizosphere and endophytic microbial communities of apple rootstocks, which could be exploited or manipulated to improve tree fruit agricultural management practices with respect to plant nutrition and disease control.

Metagenomic Analysis Reveals Reduced Beneficial Microorganism Associations in Roots of Foot-Rot-Affected Citrus Trees

Root endophytes have been shown to influence plant growth and plant responses to pathogens. Phytophthora spp. are important pathogens of citrus that cause foot rot and fibrous root decline. We hypothesize that foot rot infection by Phytophthora spp. can result in changes of the endophytic microbial community in citrus roots. Therefore, the endophytic (including bacterial and fungal) microbiome of roots from Phytophthora foot-rot-affected and healthy citrus trees were analyzed by Illumina sequencing of 16S ribosomal RNA and internal transcribed spacer amplicons. Results indicate that the composition and structure of the endophytic bacterial and fungal communities were changed in roots of foot-rot-affected citrus trees. The populations of bacterial genera Asteroleplasma, Pseudomonas, and Streptomyces were decreased in foot-rot-affected trees. Also, the relative abundance of Exophiala pisciphila and Glomeraceae spp. was significantly decreased in citrus roots. Pseudomonas and Streptomyces spp. are considered beneficial bacteria and E. pisciphila and Glomeraceae spp. are dark septate endophytes and arbuscular mycorrhizal fungi, respectively, which are involved in citrus health and growth. This study provides a baseline to continue investigating the interactions between the citrus host, Phytophthora spp., and beneficial microbes.

Insights into the early stages of plant-endophytic bacteria interaction.

The plant holobiont is a complex entity composed of the plant and the organisms that live in and on it including its microbiota. The plant microbiota includes, among other microorganisms, bacterial endophytes, which are bacteria that can invade living plant tissues without causing symptoms of disease. The interaction between the endophytic bacterial microbiota and their plant host has profound influences on their fitness and depends on biotic and abiotic factors. For these interactions to be established, the bacteria have to be present at the right time, in the right place either colonizing the soil or the seed. In this review we summarize the current knowledge regarding the sources of the bacterial endophytic microbiome and the processes involved in the assemblage of the resulting community during the initial stages of plant development. The adaptations that allow the spatial approximation of soil- and seed-borne bacteria towards infection and colonization of the internal tissues of plants will be addressed in this review.

Soybean Microbiome Recovery After Disruption is Modulated by the Seed and Not the Soil Microbiome

Endophytic microbiomes of healthy seed form a symbiotic relationship with their host. Seed and environment are sources of microbes that colonize the developing plant; however, the influence of each remains unclear. Here, using irradiation combined with surface sterilization to generate near-axenic seed with disrupted and reduced microbiomes, we contrasted the colonization potential of seed and soil microbiomes. We hypothesized that the seed microbiome would be the primary colonizer of the plant endophytic compartments. Our experimental design comprised four treatments, using soybean as a model plant: (i) nearly axenic seed growing in a sterile environment, (ii) nonaxenic seed inoculated with a microbial soil extract, (iii) nearly axenic seed inoculated with a microbial seed extract, and (iv) nearly axenic seed inoculated with a microbial soil extract. After 14 days of growth, plants were harvested, and DNA was extracted from the shoot, roots, and rhizosphere and subjected to 16S ribosomal RNA gene amplicon sequencing, quantitative PCR quantification of the total community, and functional genes involved in the N cycle. Community dynamics were similar for most treatments within their respective compartments, except for the soil treatment, where rhizosphere and root microbiomes differed from other treatments, suggesting that the soil microbiome colonizes the belowground compartment efficiently only when the seed microbiome is severely disrupted. For the shoot, all treatments resembled the seed microbiome treatment, suggesting that the seedborne bacteria colonize the aboveground compartment preferentially. Our results highlight the primacy of the seed microbiome over the soils during early colonization, putting seed microbes as potential candidates of microbiome engineering efforts.

Molecular Barcoding Reveals the Genus Streptomyces as Associated Root Endophytes of Apple (Malus domestica) Plants Grown in Soils Affected by Apple Replant Disease

Apple replant disease (ARD) occurs when apple is repeatedly planted at the same site, leading to growth reductions and losses in fruit yield and quality. Up to now, the etiology has been poorly understood; however, soil (micro)biota are known to be involved. Because endophytes often colonize plants via the rhizosphere, this study aimed at comparing the bacterial endophytic root microbiome in plants growing in ARD-affected and unaffected soils from three different sites based on greenhouse biotests using a molecular barcoding approach. The initial endophytic microbiome of the starting material (in vitro propagated plants of the apple rootstock M26) did not significantly affect the overall richness and diversity of the endophytic community in plants after 8 weeks of growth in the respective soils but some genera of the initial microbiome managed to establish in apple roots. Proteobacteria was the dominant phylum in all samples. No differences in diversity or number of amplicon sequence variants (ASVs) between plants grown in ARD soil and unaffected soil was observed. However, several ASVs of high abundance uniquely found in plants grown in ARD-affected soils were Streptomyces spp. In soil from all three sites, these Streptomyces spp. were negatively correlated with plant growth parameters. Future inoculation experiments using selected Streptomyces isolates have to prove whether bacteria from this genus are opportunists or part of the ARD complex. For the first time, the bacterial endophytic community of apple roots grown in ARD-affected soils was characterized, which will help us to understand the etiology of ARD and develop countermeasures. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .

Coupling the endophytic microbiome with the host transcriptome in olive roots

The connection between olive genetic responses to environmental and agro-climatic conditions and the composition, structure and functioning of host-associated, belowground microbiota has never been studied under the holobiont conceptual framework. Two groups of cultivars growing under the same environmental, pedological and agronomic conditions, and showing highest (AH) and lowest (AL) Actinophytocola relative abundances, were earlier identified. We aimed now to: i) compare the root transcriptome profiles of these two groups harboring significantly different relative abundances in the above-mentioned bacterial genus; ii) examine their rhizosphere and root-endosphere microbiota co-occurrence networks; and iii) connect the root host transcriptome pattern to the composition of the root microbial communities by correlation and co-occurrence network analyses. Significant differences in olive gene expression were found between the two groups. Co-occurrence networks of the root endosphere microbiota were clearly different as well. Pearson’s correlation analysis enabled a first portray of the interaction occurring between the root host transcriptome and the endophytic community. To further identify keystone operational taxonomic units (OTUs) and genes, subsequent co-occurrence network analysis showed significant interactions between 32 differentially expressed genes (DEGs) and 19 OTUs. Overall, negative correlation was detected between all upregulated genes in the AH group and all OTUs except of Actinophytocola. While two groups of olive cultivars grown under the same conditions showed significantly different microbial profiles, the most remarkable finding was to unveil a strong correlation between these profiles and the differential gene expression pattern of each group. In conclusion, this study shows a holistic view of the plant-microbiome communication.

Root-associated (rhizosphere and endosphere) microbiomes of the Miscanthus sinensis and their response to the heavy metal contamination

The plant root-associated microbiomes, including both the rhizosphere and the root endosphere microbial community, are considered as a critical extension of the plant genome. Comparing to the well-studied rhizosphere microbiome, the understanding of the root endophytic microbiome is still in its infancy. Miscanthus sinensis is a pioneering plant that could thrive on metal contaminated lands and holds the potential for phytoremediation applications. Characterizing its root-associated microbiome, especially the root endophytic microbiome, could provide pivotal knowledge for phytoremediation of mine tailings. In the current study, M. sinensis residing in two Pb/Zn tailings and one uncontaminated site were collected. The results demonstrated that the metal contaminant fractions exposed strong impacts on the microbial community structures. Their influences on the microbial community, however, gradually decreases from the bulk soil through the rhizosphere soil and finally to the endosphere, which resulting in distinct root endophytic microbial community structures compared to both the bulk and rhizosphere soil. Diverse members affiliated with the order Rhizobiales was identified as the core microbiome residing in the root of M. sinensis. In addition, enrichment of plant-growth promoting functions within the root endosphere were predicted, suggesting the root endophytes may provide critical services to the host plant. The current study provides new insights into taxonomy and potential functions of the root-associated microbiomes of the pioneer plant, M. sinensis, which may facilitate future phytoremediation practices.

Succession of the fungal endophytic microbiome of wheat is dependent on tissue-specific interactions between host genotype and environment

Fungi living inside plants affect many aspects of plant health, but little is known about how plant genotype influences the fungal endophytic microbiome. However, a deeper understanding of interactions between plant genotype and biotic and abiotic environment in shaping the plant microbiome is of significance for modern agriculture, with implications for disease management, breeding and the development of biocontrol agents.For this purpose, we analysed the fungal wheat microbiome from seed to plant to seeds and studied how different potential sources of inoculum contributed to shaping of the microbiome. We conducted a large-scale pot experiment with related wheat cultivars over one growth-season in two environments (indoors and outdoors) to disentangle the effects of host genotype, abiotic environment (temperature, humidity, precipitation) and fungi present in the seed stock, air and soil on the succession of the endophytic fungal communities in roots, flag leaves and seeds at harvest. The communities were studied with ITS1 metabarcoding and environmental climate factors were monitored during the experimental period.Host genotype, tissue type and abiotic factors influenced fungal communities significantly. The effect of host genotype was mostly limited to leaves and roots, and was location-independent. While there was a clear effect of plant genotype, the relatedness between cultivars was not reflected in the microbiome. For the phyllosphere microbiome, location-dependent weather conditions factors largely explained differences in abundance, diversity, and presence of genera containing pathogens, whereas the root communities were less affected by abiotic factors. Our findings suggest that airborne fungi are the primary inoculum source for fungal communities in aerial plant parts whereas vertical transmission is likely to be insignificant.In summary, our study demonstrates that host genotype, environment and presence of fungi in the environment shape the endophytic fungal community in wheat over a growing season.

The Dynamics of Endophytic Bacterial Community Structure in Rice Roots under Different Field Management Systems

The structure of endophytic bacteria is important to plant health and stress tolerance, but little is known about the impacts of farming systems on temporal changes in diversity of endophytic bacteria. In this study, we investigated the endophytic microbiome in rice roots under organic and conventional farming systems at the seedling and tillering stages over two consecutive cropping seasons using 16S rRNA gene sequencing. Although the composition of the microbiome was significantly influenced by a field management system, growth stage, and interaction between the two factors, the growth stage alone explained more than 40% of variance. Soil pH and organic matter content also partially influenced the endophytic bacterial community composition. In addition, through indicator species analysis and the functional profiles predicted by phylogenetic analysis, we revealed the selection force of rice roots at the tillering stage to recruit endophytes, which are beneficial to plant growth. In summary, our data show that the dynamics of rice root bacterial composition are mainly influenced by the plant growth stage. Our findings offer new insights regarding the control of the root microbiome by host plants and the influence of farming systems.

Differences in the Endophytic Microbiome of Olive Cultivars Infected by Xylella fastidiosa across Seasons.

The dynamics of Xylella fastidiosa infections in the context of the endophytic microbiome was studied in field-grown plants of the susceptible and resistant olive cultivars Kalamata and FS17. Whole metagenome shotgun sequencing (WMSS) coupled with 16S/ITS rRNA gene sequencing was carried out on the same trees at two different stages of the infections: In Spring 2017 when plants were almost symptomless and in Autumn 2018 when the trees of the susceptible cultivar clearly showed desiccations. The progression of the infections detected in both cultivars clearly unraveled that Xylella tends to occupy the whole ecological niche and suppresses the diversity of the endophytic microbiome. However, this trend was mitigated in the resistant cultivar FS17, harboring lower population sizes and therefore lower Xylella average abundance ratio over total bacteria, and a higher α-diversity. Host cultivar had a negligible effect on the community composition and no clear associations of a single taxon or microbial consortia with the resistance cultivar were found with both sequencing approaches, suggesting that the mechanisms of resistance likely reside on factors that are independent of the microbiome structure. Overall, Proteobacteria, Actinobacteria, Firmicutes, and Bacteriodetes dominated the bacterial microbiome while Ascomycota and Basidiomycota those of Fungi.

Fungal endophyte diversity in table grapes.

Plant fungal endophytes are diverse microbial sources that reside inside plants. Grapes (Vitis vinifera) are rich in polyphenols that have beneficial health effects, and recent research has shown that fungal endophytes in grapes may contribute to the production of these polyphenols and may serve as biocontrol agents. In this study, we determined the fungal microbial endophyte diversity in North American table grapes found at a Winnipeg, Manitoba, market. The amplicon internal transcribed spacer (ITS) metagenomics approach was used to profile the fungal communities of the fruit endophyte microbiome of three table grape types. The data supported endophyte diversity in different table grapes, including possible bioactive, saprophytic, and pathogenic fungi. Culturable endophytes were isolated and identified by morphology and ITS amplicon sequencing. The majority of the isolated culturable strains included Alternaria spp. and Cladosporium spp. The results provided evidence of the existence of diverse fungal endophytes isolated and identified from the fruit of the table grapes. These fungal endophytes may have potential in agricultural, industrial, and pharmaceutical applications.

Bacterial Blight Induced Shifts in Endophytic Microbiome of Rice Leaves and the Enrichment of Specific Bacterial Strains With Pathogen Antagonism.

The endophytic microbiome plays an important role in plant health and pathogenesis. However, little is known about its relationship with bacterial blight (BB) of rice caused by Xanthomonas oryzae pv. oryzae (Xoo). The current study compared the community compositional structure of the endophytic microbiota in healthy and BB symptomatic leaves of rice through a metabarcoding approach, which revealed BB induced a decrease in the alpha-diversity of the fungal communities and an increase in the bacterial communities. BB-diseased rice leaves were enriched with saprophytic fungi that are capable of decomposing plant cell walls (e.g. Khuskia spp. and Leptosphaerulina spp.), while healthy rice leaves were found to be significantly more abundant with plant pathogens or mycotoxin-producing fungi (e.g. Fusarium, Magnaporthe, and Aspergillus). The endophytic bacterial communities of BB-diseased leaves were significantly enriched with Pantoea, Pseudomonas, and Curtobacterium, strains. Pantoea sp. isolates from BB leaves are identified as promising candidates for the biocontrol of BB for their ability to inhibit in vitro growth of Xoo, suppress the development of rice BB disease, and possess multiple PGP characteristics. Our study revealed BB-induced complexed changes in the endophytic fungal and bacterial communities of rice leaves and demonstrated that BB-associated enrichment of some endophytic bacterial taxa, e.g. Pantoea sp. isolates, may play important roles in suppressing the development of BB disease in rice.