Endophytic Community Structure Research Articles

Endophytic bacterial diversity of the medicinal orchid Dendrobium nobile

As a valuable medicinal epiphyte of Orchidaceae, Dendrobium nobile is widely utilized in Asian medicine. Despite the importance of Mycorrhizae in the germination of Dendrobium seeds, little is known about its endophytic microbiome. In the present study, 16S rRNA high-throughput sequencing is therefore applied to investigate the endophytic bacterial community structure associated with the different vegetative organs (roots, stems and leaves) of D. nobile. A total of 24 bacterial phyla and 448 genera of endophytes were identified, with Proteobacteria, Actinobacteria, and Acidobacteria being the dominant phyla. The relative abundance and diversity of endophytes in roots are found to be generally higher than those in stems and leaves. Most of the endophytes are predicted to be involved in nutrient metabolism, and some bacterial taxa are found to be involved in the recruitment of genera from the same phylum. Overall, the study provided important insights into the community structure and functional characteristics of endophytes in D. nobile, and lay a theoretical foundation for a better understanding of the interactive dialog between medicinal plants and their endophytes.

The Zoige pioneer plant Leymus secalinus has different endophytic bacterial community structures to adapt to environmental conditions.

Leymus secalinus is a pioneer plant grown in the Zoige desertified alpine grassland and it is also one of the dominant plant species used for environmental remediation. L. secalinus plays a large role in vegetation reconstruction in sandy land, but the abundance and diversity of its endophytes have not yet been investigated. This study was performed to investigate the changes in the endophytic bacterial community structure of L. secalinus under different ecological environments and to analyze the effects of environmental changes and different plant tissues on the L. secalinus endophytic bacteria. Leaf, stem, and root tissue samples of L. secalinus were collected from Zoige Glassland (Alpine sandy land) and an open field nursery (Control). DNA was extracted and the 16S ribosomal DNA was amplified. The sequence library was sequenced on an Illumina MiSeq platform and clustered by operational taxonomic units (OTUs). α-diversity and β-diversity analyses, species diversity analyses, functional prediction, and redundancy (RDA) analyses for the soil physicochemical properties were conducted. α-diversity and β-diversity analyses showed that the endophytic bacteria in L. secalinus varied in different areas and tissues. The abundance of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, which is related to nitrogen fixation, increased significantly in the L. secalinus found in the Zoige Grassland.Moreover, the abundance of nutrition metabolism and anti-stress abilities increased in functional prediction in the desert samples. The soil physicochemical properties had an insignificant influence on bacterial diversity. The changes in the endophytic bacterial community structure in L. secalinus were significant and were caused by environmental alterations and plant choice. The endophytic bacteria in L. secalinus grown in alpine sandy land may have greater anti-stress properties and the ability to fix nitrogen, which has potential value in environmental remediation and agricultural production.

Comparative Analysis of Rhizosphere and Endophytic Microbial Communities Between Root Rot and Healthy Root of Psammosilene tunicoides

The wild resources of Psammosilene tunicoides have decreased sharply because of the long-term mining and excavation, which has led to the increased demand for its artificial cultivation. However, root rot represents a significant obstacle leading to a poor quality and product of P. tunicoides. Previous reports have not focused on root rot in P. tunicoides. Therefore, this study explores the rhizospheric and root endophytic microbial community structure and composition of healthy and root rot P. tunicoides to understand the mechanism underlying root rot. The properties of the rhizosphere soil were assessed using physiochemical methods, and the bacterial and fungal populations were studied through amplicon sequencing of the 16S rRNA genes and ITS regions in the root and soil. Compared to healthy samples, the pH, hydrolysis N, available P, and available K were significantly decreased in the diseased samples while the organic matter and total organic carbon were significantly increased in the diseased samples. Redundancy analysis (RDA) showed that soil environmental factors are related to changes in the root and rhizosphere soil microbial community of P. tunicoides indicating that the physiochemical properties of soil affect plant health. Alpha diversity analysis showed that the microbial communities of healthy and diseased samples were similar. Some bacterial and fungal genera were significantly increased or decreased (P < 0.05) in diseased P. tunicoides, and certain microbial factors that antagonized root rot were further explored. This study provides an abundant microbial resource for future studies and contributes to improving soil quality and P. tunicoides agricultural production.

Culturable endophytic fungi community structure isolated from Codonopsis pilosula roots and effect of season and geographic location on their structures

BackgroundRhizosphere soil physicochemical, endophytic fungi have an important role in plant growth. A large number of endophytic fungi play an indispensable role in promoting plant growth and development, and they can provide protection for host plants by producing a variety of secondary metabolites to resist and inhibit plant pathogens. Due to the terrain of Gansu province is north–south and longitudinal, different climatic conditions, altitude, terrain and growth environment will affect the growth of Codonopsis pilosula, and the changes in these environmental factors directly affect the quality and yield of C. pilosula in different production areas. However, In C. pilosula, the connection between soil nutrients, spatiotemporal variation and the community structure of endophytic fungi isolated from C. pilosula roots has not been well studied.ResultsSeven hundred six strains of endophytic fungi were obtained using tissue isolation and the hyphaend-purification method from C. pilosula roots that picked at all seasons and six districts (Huichuan, HC; Longxi, LX; Zhangxian, ZX; Minxian, MX; Weiyuan, WY; and Lintao, LT) in Gansu Province, China. Fusarium sp. (205 strains, 29.04%), Aspergillus sp. (196 strains, 27.76%), Alternaria sp. (73 strains, 10.34%), Penicillium sp. (58 strains, 8.22%) and Plectosphaerella sp. (56 strains, 7.93%) were the dominant genus. The species composition differed from temporal and spatial distribution (Autumn and Winter were higher than Spring and Summer, MX and LT had the highest similarity, HC and LT had the lowest). physical and chemical of soil like Electroconductibility (EC), Total nitrogen (TN), Catalase (CAT), Urease (URE) and Sucrase (SUC) had significant effects on agronomic traits of C. pilosula (P < 0.05). AK (Spring and Summer), TN (Autumn) and altitude (Winter) are the main driving factors for the change of endophytic fungal community. Moreover, geographic location (such as altitude, latitude and longitude) also has effects on the diversity of endophytic fungi.ConclusionsThese results suggested that soil nutrients and enzyme, seasonal variation and geographical locations have an impact on shaping the community structure of culturable endophytic fungi in the roots of C. pilosula and its root traits. This suggests that climatic conditions may play a driving role in the growth and development of C. pilosula.

Potential impact of polyethylene microplastics on the growth of water spinach (Ipomoea aquatica F.): Endophyte and rhizosphere effects

Microplastic contamination has received much attention, especially in agroecosystems. However, since edible crops with different genetic backgrounds may present different responses to microplastics, more research should be conducted and focused on more edible crops. In the current study, pot experiments were conducted to investigate the potential impact of polyethylene microplastic (PE) (particle sizes: 0.5 μm and 1.0 μm, addition levels: 0 (control), 0.5% and 1.0% (w/w)) addition on the physiological and biochemical variations of I. aquatica F.. The results indicated that PE addition caused an increase in the soil pH and NH4+-N and soil organic matter contents, which increased by 10.1%, 29.9% and 50.1% when PE addition at A10P0.5 level (10 g (PE) kg−1 soil, particle size: 0.5 μm). While, PE exposure resulted in a decrease in soil available phosphorus and total phosphorus contents, which decreased by 53.9% and 10.5% when PE addition at A10P0.5 level. In addition, PE addition altered the soil enzyme activities. Two-way ANOVA indicated that particle size had a greater impact on the variations in soil properties and enzyme activities than the addition level. PE addition had a strong impact on the rhizosphere microbial and root endophyte community diversity and structure of I. aquatica F.. Two-way ANOVA results indicated that the particle size and addition level significantly altered the α-diversity indices of both rhizosphere microbial and root endophyte (P < 0.05, P < 0.01 or P < 0.001). Moreover, PE was adsorbed by I. aquatica F., which was clearly observed in the transverse roots and significantly increased the H2O2, ·O2−, malondialdehyde and ascorbic acid contents in both the roots and aerial parts of I. aquatica F., leading to a decrease in I. aquatica F. biomass. Overall, the current study enriches the understanding of the effect of microplastics on edible crops.

Legacy Effects of Phytoremediation on Plant-Associated Prokaryotic Communities in Remediated Subarctic Soil Historically Contaminated with Petroleum Hydrocarbons.

Phytoremediation of petroleum hydrocarbons in subarctic regions relies on the successful establishment of plants that stimulate petroleum-degrading microorganisms, which can be challenging due to the extreme climate, limited nutrients, and difficulties in maintaining sites in remote locations. A long-term phytoremediation experiment was initiated in Alaska in 1995 with the introduction of grasses and/or fertilizer to petroleum hydrocarbon (PHC)-contaminated soils that were subsequently left unmanaged. In 2011, the PHC concentrations were below detection limits in all soils tested and the originally planted grasses had been replaced by volunteer plant species that had colonized the site. Here, we sought to understand how the original treatments influenced the structure of prokaryotic communities associated with plant species that colonized the soils and to assess the interactions between the rhizospheric and endophytic communities of the colonizing vegetation 20 years after the experiment was established. Metataxonomic analysis performed using 16S rRNA gene sequencing revealed that the original type of contaminated soil and phytoremediation strategy influenced the structure of both rhizospheric and endophytic communities of colonizing plants, even 20 years after the treatments were applied and following the disappearance of the originally planted grasses. Our findings demonstrate that the choice of initial phytoremediation strategy drove the succession of microorganisms associated with the colonizing vegetation. The outcome of this study provides new insight into the establishment of plant-associated microbial communities during secondary succession of subarctic areas previously contaminated by PHCs and indicates that the strategies for restoring these ecosystems influence the plant-associated microbiota in the long term. IMPORTANCE Subarctic ecosystems provide key services to local communities, yet they are threatened by pollution caused by spills and disposal of petroleum waste. Finding solutions for the remediation and restoration of subarctic soils is valuable for reasons related to human and ecosystem health, as well as environmental justice. This study provides novel insight into the long-term succession of soil and plant-associated microbiota in subarctic soils that had been historically contaminated with different sources of PHCs and subjected to distinct phytoremediation strategies. We provide evidence that even after the successful removal of PHCs and the occurrence of secondary succession, the fingerprint of the original source of contamination and the initial choice of remediation strategy can be detected as a microbial legacy in the rhizosphere, roots, and shoots of volunteer vegetation even 2 decades after the contamination had occurred. Such information needs to be borne in mind when designing and applying restoration approaches for PHC-contaminated soils in subarctic ecosystems.

Cadmium stimulated cooperation between bacterial endophytes and plant intrinsic detoxification mechanism in Lonicera japonica thunb

Due to the intimate association between plant physiology and metabolism, the internal colonizing microbe (endophytes) community must be adjusted to support plant productivity in response to cell damage in plants under stress. However, how endophytes coordinate their activities with plant intrinsic mechanisms such as antioxidative systems and detoxification pathways during Cd accumulation remains unknown. In this hydroponic pot study, we investigated how exposure of Lonicera japonica. thunb. to different levels of Cd (0.5, 2.5, 5, 10, and 20 mg kg−1) affected plant growth, metabolic pathways, and endophyte community structure and function. Although Cd accumulation increased at 5 mg kg−1 Cd, the biomass and height of L. japonica increased in association with elevated endophyte-involved plant detoxification activities. Endophytes, such as Sphingomonas, Klenkia, and Modestobacter, expressed major antioxidative regulators (superoxide dismutase and ascorbate acid) to detoxify Cd in L. japonica. Furthermore, L. japonica and its endophytes synergistically regulated the toxic effects of Cd accumulation via multiple plant metabolic defensive pathways to increase resistance to metal-induced stress.

Abiotic factors and endophytes co-regulate flavone and terpenoid glycoside metabolism in Glycyrrhiza uralensis

Recently, endorhizospheric microbiota is realized to be able to promote the secondary metabolism in medicinal plants, but the detailed metabolic regulation metabolisms and whether the promotion is influenced by environmental factors are unclear yet. Here, the major flavonoids and endophytic bacterial communities in various Glycyrrhiza uralensis Fisch. roots collected from seven distinct places in northwest China, as well as the edaphic conditions, were characterized and analyzed. It was found that the soil moisture and temperature might modulate the secondary metabolism in G. uralensis roots partially through some endophytes. One rationally isolated endophyte Rhizobium rhizolycopersici GUH21 was proved to promote the accumulation of isoliquiritin and glycyrrhizic acid significantly in roots of the potted G. uralensis under the relatively high-level watering and low temperature. Furthermore, we did the comparative transcriptome analysis of G. uralensis seedling roots in different treatments to investigate the detailed mechanisms of the environment-endophyte-plant interactions and found that the low temperature went hand in hand with the high-level watering to activate the aglycone biosynthesis in G. uralensis, while GUH21 and the high-level watering cooperatively promoted the in planta glucosyl unit production. Our study is of significance for the development of methods to rationally promote the medicinal plant quality.Key points• Soil temperature and moisture related to isoliquiritin contents in Glycyrrhiza uralensis Fisch.• Soil temperature and moisture related to the hosts’ endophytic bacterial community structures.• The causal relation among abiotic factors—endophytes—host was proved through the pot experiment.

Comparison of Rhizospheric and Endophytic Bacterial Compositions between Netted and Oriental Melons.

To elucidate the biological mechanism of formation of the netted pattern in melons, the characteristics of the soil bacterial community structure in the rhizosphere and of the endophytic bacteria in the stems of netted melons were analyzed. High-throughput sequencing technology was used for the analysis of plant stem and soil samples collected from netted melons (NM) and oriental melons (OM). At the phylum level, Acidobacteria, Dependentiae, and Chloroflexi were the dominant endophytic bacteria in the stems of NM only. In addition, at the genus level, the soil bacteria enriched in the rhizospheres of NM and OM were different. Five unique dominant bacterial genera, including Gaiella, Actinoplanes, norank_f__Gemmatimonadaceae, Devosia, and Bradyrhizobium, were the dominant soil bacteria unique to the rhizosphere of NM. In contrast, Mycobacterium and unclassified_f__Acetobacteraceae were the dominant soil bacteria in the rhizosphere of OM. Moreover, Hyphomicrobium, Nocardioides, norank_f__norank_o__Gaiellales, Bryobacter, unclassified_f__Pseudonocardiaceae, Pseudolabrys, norank_f__Micropepsaceae, Ideonella, Mizugakiibacter, norank_f__Vermiphilaceae, unclassified_f__Xanthobacteraceae, Bacillus, and Pseudaminobacter were the dominant endophytic bacteria in the stems of NM. In contrast, Flavobacterium, Stenotrophomonas, unclassified_f__Burkholderiaceae, Paenibacillus, Bordetella, Hephaestia, and Ideonella were the dominant endophytic bacteria in the stems of OM. The specific substances (enzymes, proteins, endogenous hormones, etc.) secreted by unique rhizospheric and endophytic bacteria, such as Bacillus and Bradyrhizobium, may activate the promoters of genes. Therefore, the expression of genes can be regulated by unique rhizospheric and endophytic bacteria for formation or nonformation of netting in melons. IMPORTANCE The study of the differential structures and functions of rhizospheric and endophytic bacterial communities between netted melon and oriental melon treatments is investigated. Our findings make a significant contribution to the literature because they are the first step in coupling the study of rhizospheric and endophytic microbial community structure to reticulation formation in netted melon. Further, we believe that this research appears to be meaningful because it provides new insights into the mechanisms of reticulation formation in netted melon in modern agricultural production.

Can Sugarcane Yield and Health Be Altered with Fully Mechanized Management?

At present, fully mechanized cultivation (FMC) has begun to be utilized in commercial sugarcane production in China. To provide new insights into whether cane yield and health are altered by fully mechanized cultivations, the cane yield and endophytic microbial community structure in stems of sugarcane that underwent fully mechanized cultivation (FMC) and conventional artificial cultivation (CAC) were compared. The results showed that the diversity and richness of endophytic microorganisms, except for the bacterial richness in the stems of sugarcane, could be significantly increased by using FMC. Meanwhile, in comparison with CAC, the relative abundance of Proteobacteria and Ascomycota increased under FMC. Moreover, some dominant endophytic bacterial genera, such as Acidovorax, Microbacterium, and Paenibacillus, and some dominant endophytic fungal genera, such as Scleroramularia, Tetraplosphaeria, and Dinemasporium, were found to be significantly enriched in cane stems under FMC treatments. Additionally, the endophytic microbial functions in sugarcane stems were not significantly altered by FMC treatments. Our results suggest that cane growth, yield, and health are not significantly altered by FMC. The results also indicate that fully mechanized management can be developed as a sustainable method in sugarcane production.

Root endophytic bacterial community composition of Aconitum carmichaelii debx. from three main producing areas in China.

Aconitum carmichaelii Debx. is famous for the bioactive aconitum alkaloids as traditional Chinese medicine. Endophytic bacteria play vital roles in plant growth, health, and the production of secondary metabolites such as alkaloids. In this study, we employed 16 S rRNA amplicon high-throughput sequencing to determine the root endophytic bacterial community of A. carmichaelii Debx. collected from three main producing areas including the geo-authentic area in China, high performance liquid chromatography to measure the contents of six bioactive alkaloids and correlation analysis to explore the relationship among environmental factors, alkaloids contents, and endophytic bacterial community. The results indicated that the root core microbiota of A. carmichaelii Debx. was dominated by Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Root endophytic bacterial community in the geo-authentic area was distinct from the other two regions. Soil nitrogen contents, organic matter, and temperature were the main factors contributing to the endophytic bacterial community structure. Significant correlation was found between alkaloids contents and some bacterial genera. Particularly, the abundance of Lactobacillus was positively correlated with the contents of benzoyl-mesaconitine and benzoyl-aconine. This study provided the first insight into the root endophytic bacterial community composition of A. carmichaelii Debx., and can direct further isolation of functional bacterial strains.

Identification and antibacterial activity of Thamnolia vermicularis and Thamnolia subuliformis

Thamnolia vermicularis (Tv) and Thamnolia subuliformis (Ts) are two species from the same habitat with such similar external morphological characteristics that researchers often confuse the two in their scientific work and do not distinguish between them. This study applies three different methods to distinguish them. The diversity of endophytic fungi was also compared and their antibacterial activity in vitro was evaluated. The results show that all three methods can distinguish Tv and Ts, and can be used to cross-validate each other. The ultraviolet fluorescence method and the chemical colour change method are simpler strategies, while thin-layer chromatography is relatively complicated but can more clearly distinguish the chemical composition of the two species. In the analysis of the endophytic fungi community structure of Tv and Ts, it was found that the diversity of endophytic fungi in Tv was more abundant and had wider antibacterial activity and better inhibitory activity against gram-positive bacteria in vitro.

Seed coating with fungicide causes a beneficial shift in root‐associated microbiomes of mature soybean

AbstractWhile seed coating with fungicide is commonly used to control diseases in conventional soybean culture, the impact of fungicide seed coating on root‐associated microbial communities remains largely understudied. This hinders our assessment of the potential ecological and environmental risks of fungicide seed coating and our ability to improve plant health by using appropriate disease control practices. Here, we examined the diversity and composition of bacterial and fungal communities across root–soil compartments collected from a field experiment sown with fungicide‐coated or untreated seeds. The community structures significantly differed among the root–soil compartments. Fungicide seed coating demonstrated a greater effect on the structure of endophytic communities, including root endosphere and nodule, than the rhizosphere communities. A number of plant beneficial microbes responded positively to fungicide seed coating. Meanwhile, seed coating increased the absolute abundance of the nifH gene related to nitrogen fixation, especially in the root endosphere, from 2.63 to 18.30 ×108 copies g–1 dry root. Root‐associated microbes with coatings had a higher complexity of the microbial interkingdom cooccurrence network than those without coatings. Altogether, soybean [Glycine max (L.) Merr.] root‐associated microbiomes may have a high resilience under fungicide seed coating. At the mature stage of soybean, seed coating did not show any negative impact of residual fungicide on the root‐associated microecology, and it may pose a lower environmental risk than we have envisaged. Our results took a step forward in the responses of root‐associated microbiomes to the environment for legumes that have rarely been studied and provided new evidence of the eco‐friendly advantages of seed coatings in addition to agricultural output.

Changes of endophytic microbial community in Rhododendron simsii roots under heat stress and its correlation with leaf physiological indicators.

The response mechanism of Rhododendron simsii and its endophytic microorganism to heat stress is still unclear. The light incubator was used to set the temperature gradients, and the control (CK) was (day/night: 14/10 h) 25/22°C, the moderate-heat-stress (MHS) was 35/30°C and the high-heat-stress (HHS) was 40/35°C. Compared with CK, MHS significantly increased the contents of malondialdehyde, hydrogen peroxide, proline, and soluble sugar, as well as the activities of catalase and peroxidase in leaf, while HHS increased the activities of ascorbate peroxidase, and decreased chlorophyll content. Compared with CK, MHS reduced soil available nitrogen (N) content. Both heat stress changed the endophytic microbial community structure in roots. MHS enriched Pezicula and Paracoccus, while HHS significantly enriched Acidothermus and Haliangium. The abundance of Pezicula positively correlated with the contents of chlorophyll a and proline in leaf, and negatively correlated with soil ammonium N content. The abundance of Pezicula and Haliangium positively correlated with soluble sugar and malondialdehyde contents, respectively. Our results suggest that root endophytic microorganisms play an important role in helping Rhododendron resisting heat stress, mainly by regulating soil N content and plant physiological characteristics.

Effects of Hericium erinaceus Hedgehog mushroom on the endophytic microbial community of the host plant.

Hedgehog mushroom is a Hericium erinaceus associated with fagaceae and pinaceae trees in the northern hemisphere. It is still unknown whether this symbiotic relationship will affect the endophytic microbial community of the host plants. In this study, the endophytic microbial communities of different Quercus aliena tissues (root, stem, and leaf) with or without H. erinaceus partner were analyzed by bar-coded pyrosequencing. About 29,000 clean reads were obtained per sample representing 28 phyla of bacteria and 6 phyla of fungi. A total of 26,838 operational taxonomic units (OTUs) of bacteria and 4323 OTUs of fungi were observed at a 97% similarity level. Three bacterial phyla, Proteobacteria, Cyanobacteria and Bacteroidetes, and fungal phylum Ascomycota were dominant in all tissues. The relative abundance of these dominant communities showed significantly differences between Q. aliena tissues with or without H. erinaceus. Bacterial genus Pseudomonas and fungal genus Cryptosporiopsis were species-rich in Q. aliena root infected by H. erinaceus hyphae. This study demonstrated that the endophytic microbial community structure and dominant species varied in Q. aliena mycorrhized with H. erinaceus.

The Endophytic Fungi Diversity, Community Structure, and Ecological Function Prediction of Sophora alopecuroides in Ningxia, China.

Sophora alopecuroides L. has great medicinal and ecological value in northwestern China. The host and its microbiota are mutually symbiotic, collectively forming a holobiont, conferring beneficial effects to the plant. However, the analysis of diversity, mycobiota composition, and the ecological function of endophytic fungi in the holobiont of S. alopecuroides is relatively lacking. In this article, the fungal community profiling of roots, stems, leaves, and seeds of S. alopecuroides (at the fruit maturity stage) from Huamachi and Baofeng in Ningxia, China were investigated based on the ITS1 region, using high-throughput sequencing technology. As a result, a total of 751 operational taxonomic units (OTUs) were obtained and further classified into 9 phyla, 27 classes, 66 orders, 141 families, 245 genera, and 340 species. The roots had the highest fungal richness and diversity, while the stems had the highest evenness and pedigree diversity. There also was a significant difference in the richness of the endophytic fungal community between root and seed (p &lt; 0.05). The organ was the main factor affecting the community structure of endophytic fungi in S. alopecuroides. The genera of unclassified Ascomycota, Tricholoma, Apiotrichum, Alternaria, and Aspergillus made up the vast majority of relative abundance, which were common in all four organs as well. The dominant and endemic genera and biomarkers of endophytic fungi in four organs of S. alopecuroides were different and exhibited organ specificity or tissue preference. The endophytic fungi of S. alopecuroides were mainly divided into 15 ecological function groups, among which saprotroph was absolutely dominant, followed by mixotrophic and pathotroph, and the symbiotroph was the least. With this study, we revealed the diversity and community structure and predicted the ecological function of the endophytic fungi of S. alopecuroides, which provided a theoretical reference for the further development and utilization of the endophytic fungi resources of S. alopecuroides.

Towards defining the core Saccharum microbiome: input from five genotypes

BackgroundPlant microbiome and its manipulation inaugurate a new era for plant biotechnology with the potential to benefit sustainable crop production. Here, we used the large-scale 16S rDNA sequencing analysis to unravel the dynamic, structure, and composition of exophytic and endophytic microbial communities in two hybrid commercial cultivars of sugarcane (R570 and SP80–3280), two cultivated genotypes (Saccharum officinarum and Saccharum barberi) and one wild species (Saccharum spontaneum).ResultsOur analysis identified 1372 amplicon sequence variants (ASVs). The microbial communities’ profiles are grouped by two, root and bulk soils and stem and leave when these four components are compared. However, PCoA-based data supports that endophytes and epiphytes communities form distinct groups, revealing an active host-derived mechanism to select the resident microbiota. A strong genotype-influence on the assembly of microbial communities in Saccharum ssp. is documented. A total of 220 ASVs persisted across plant cultivars and species. The ubiquitous bacteria are two potential beneficial bacteria, Acinetobacter ssp., and Serratia symbiotica.ConclusionsThe results presented support the existence of common and cultivar-specific ASVs in two commercial hybrids, two cultivated canes and one species of Saccharum across tissues (leaves, stems, and roots). Also, evidence is provided that under the experimental conditions described here, each genotype bears its microbial community with little impact from the soil conditions, except in the root system. It remains to be demonstrated which aspect, genotype, environment or both, has the most significant impact on the microbial selection in sugarcane fields.

Host Specificity and Seasonal Variation in the Colonization of Tubakia sensu lato Associated with Evergreen Oak Species in Eastern Japan.

Foliar fungal endophytes are ubiquitous and hyperdiverse, and tend to be host-specific among dominant forest tree species. The fungal genus Tubakia sensu lato is comprised of foliar pathogens and endophytes that exhibit host preference for Quercus and other Fagaceae species. To clarify interspecific differences in ecological characteristics among Tubakia species, we examined the endophyte communities of seven evergreen Quercus spp. at three sites in eastern Japan during summer and winter. Host tree species was the most significant factor affecting endophyte community composition. Tubakia species found at the study sites were divided into five specialists and three generalists according to their relative abundance in each host species and their host ranges. Specialists were dominant on their own host in summer, and their abundance declined in winter. To test the hypothesis that generalists are more widely adapted to their environment than specialists, we compared their spore germination rates at different temperatures. Spores of generalist Tubakia species were more tolerant of colder temperatures than were spores of specialist Tubakia species, supporting our hypothesis. Seasonal and site variations among Tubakia species were also consistent with our hypothesis. Host identity and ecology were significantly associated with endophyte community structure.

Root-Associated Microbiota Response to Ecological Factors: Role of Soil Acidity in Enhancing Citrus Tolerance to Huanglongbing.

The citrus orchards in southern China are widely threatened by low soil pH and Huanglongbing (HLB) prevalence. Notably, the lime application has been used to optimize soil pH, which is propitious to maintain root health and enhance HLB tolerance of citrus; however, little is known about the interactive effects of soil acidity on the soil properties and root-associated (rhizoplane and endosphere) microbial community of HLB-infected citrus orchard. In this study, the differences in microbial community structures and functions between the acidified and amended soils in the Gannan citrus orchard were investigated, which may represent the response of the host-associated microbiome in diseased roots and rhizoplane to dynamic soil acidity. Our findings demonstrated that the severity of soil acidification and aluminum toxicity was mitigated after soil improvement, accompanied by the increase in root activity and the decrease of HLB pathogen concentration in citrus roots. Additionally, the Illumina sequencing-based community analysis showed that the application of soil amendment enriched functional categories involved in host-microbe interactions and nitrogen and sulfur metabolisms in the HLB-infected citrus rhizoplane; and it also strongly altered root endophytic microbial community diversity and structure, which represented by the enrichment of beneficial microorganisms in diseased roots. These changes in rhizoplane-enriched functional properties and microbial composition may subsequently benefit the plant's health and tolerance to HLB disease. Overall, this study advances our understanding of the important role of root-associated microbiota changes and ecological factors, such as soil acidity, in delaying and alleviating HLB disease.

An Overview: Interaction between Microbial Endophytes and Root Exudates

Bacterial endophytes of rhizosphere were able to reside in different plant tissues as a microbiome and from there they positively induce plant growth. Endophytic community structure in plant tissues is active and is altered by various biotic and abiotic stresses such as soil parameters, crop locations, plant verities, microbe–microbe interactions and plant–microbe interactions, both at local and larger scales. Root exudates include soluble organic substances, constitutes sugars, amino acids, organic acids, enzymes, and other substances. Apart from these compounds, the root surroundings contains lysates of cells, which released when root cortex cells are subjected mechanical damage, microbial graze, infection, or the natural pores formed in the process of lateral roots emergence. Since root exudates have abundance roles in plant growth promotion at different stages of plant life cycle. In recent times, the nature of compounds released by plant roots could attract group of microorganisms (beneficial) and particularly focus is more attracted towards the endophytic bacteria moved towards root surfaces and their entry into the plant tissues. In view of this hypothesis, the present review has attempted to describe the various functions of root exudates and their interactions with microbial community present with in the plant tissues and their positive effects on plant health.