Endophytic Bacterial Community Structure Research Articles

Analysis of endophytic bacterial diversity in seeds of different genotypes of cotton and the suppression of Verticillium wilt pathogen infection by a synthetic microbial community

BackgroundIn agricultural production, fungal diseases significantly impact the yield and quality of cotton (Gossypium spp.) with Verticillium wilt posing a particularly severe threat.ResultsThis study is focused on investigating the effectiveness of endophytic microbial communities present in the seeds of disease-resistant cotton genotypes in the control of cotton Verticillium wilt. The technique of 16S ribosomal RNA (16S rRNA) amplicon sequencing identified a significant enrichment of the Bacillus genus in the resistant genotype Xinluzao 78, which differed from the endophytic bacterial community structure in the susceptible genotype Xinluzao 63. Specific enriched strains were isolated and screened from the seeds of Xinluzao 78 to further explore the biological functions of seed endophytes. A synthetic microbial community (SynCom) was constructed using the broken-rod model, and seeds of the susceptible genotype Xinluzao 63 in this community that had been soaked with the SynCom were found to significantly control the occurrence of Verticillium wilt and regulate the growth of cotton plants. Antibiotic screening techniques were used to preliminarily identify the colonization of strains in the community. These techniques revealed that the strains can colonize plant tissues and occupy ecological niches in cotton tissues through a priority effect, which prevents infection by pathogens.ConclusionThis study highlights the key role of seed endophytes in driving plant disease defense and provides a theoretical basis for the future application of SynComs in agriculture.

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.

Structure and Functions of Endophytic Bacterial Communities Associated with Sphagnum Mosses and Their Drivers in Two Different Nutrient Types of Peatlands

Sphagnum mosses are keystone plant species in the peatland ecosystems that play a crucial role in the formation of peat, which shelters a broad diversity of endophytic bacteria with important ecological functions. In particular, methanotrophic and nitrogen-fixing endophytic bacteria benefit Sphagnum moss hosts by providing both carbon and nitrogen. However, the composition and abundance of endophytic bacteria from different species of Sphagnum moss in peatlands of different nutrient statuses and their drivers remain unclear. This study used 16S rRNA gene amplicon sequencing to examine endophytic bacterial communities in Sphagnum mosses and measured the activity of methanotrophic microbial by the 13C-CH4 oxidation rate. According to the results, the endophytic bacterial community structure varied among Sphagnum moss species and Sphagnum capillifolium had the highest endophytic bacterial alpha diversity. Moreover, chlorophyll, phenol oxidase, carbon contents, and water retention capacity strongly shaped the communities of endophytic bacteria. Finally, Sphagnum palustre in Hani (SP) had a higher methane oxidation rate than S. palustre in Taishanmiao. This result is associated with the higher average relative abundance of Methyloferula an obligate methanotroph in SP. In summary, this work highlights the effects of Sphagnum moss characteristics on the endophytic bacteriome. The endophytic bacteriome is important for Sphagnum moss productivity, as well as for carbon and nitrogen cycles in Sphagnum moss peatlands.

Analysis of the difference in endophytic bacterial community structure between infected and non-infected rice plants with rice bakanae disease

Abstract. Yu Y, Liu H, Xu Z, Yan P, Wu H, Wu L. 2024. Analysis of the difference in endophytic bacterial community structure between infected and non-infected rice plants with rice bakanae disease. Biodiversitas 25: 197-204. Rice bakanae disease, caused by the main pathogen Fusarium fujikuroi, is an important fungal disease that seriously threatens rice production. This study analyzed the effect of Fusarium fujikuroi on the community structure and diversity of endophytic bacteria in different rice tissues. The total DNA of different tissues, such as root, stem, and leaf, was extracted after artificial inoculation, and the bacterial 16SrRNA gene library was constructed. The high-throughput sequencing was used to analyze the biological information of bacterial community composition, diversity and function. The results showed that a total of 467841 effective sequences were obtained. Alpha diversity analysis showed that the diversity and richness of the endophytic bacterial community in infected plants were higher than in non-infected plants. At the phylum level, Cyanobacteria, Proteobacteria, Firmicutes, Acidobacteria, Bacteroidetes, Chloroflexi, and Actinobacteria were the dominant phyla. The infection of rice seedling bacteria causes changes in the abundance of endophytic bacteria in rice. Compared with non-infected plants, the abundance of Streptophyta and Acidovorax in the root decreased by 1.29 and 0.74%, respectively. The abundance of Geobacter, Devosia, Pleomorphomonas, and Herbaspirillum increased by 1.05, 1.55, 1.28, and 1.76%, while the abundance of Streptophyta in stem decreased by 7.83%. The abundance of Xanthomonas, Acidovorax, Pseudomonas and Sphingomonas increased by 1.55, 1.49, 1.11 and 1.15%, whereas the abundance of Streptophyta in the leaf decreased by 12.03%, Actinomycetales, Pseudomonas, Sphingomonas are significant biological differences between different tissues of infected and non-infected plants. The study provides a theoretical basis for the biological control of rice bakanae disease.

Cadmium levels and soil pH drive structure and function differentiation of endophytic bacterial communities in Sedum plumbizincicola: A field study

Sedum plumbizincicola is a promising hyperaccumulator for heavy metal phytoremediation. It grows in heavy metal polluted soil and stores specific endophyte resources with heavy metal tolerance or growth promotion characteristics. In this study, the endophyte communities of S. plumbizincicola, growing naturally in the field (two former mining locations and one natural location) were investigated, and their structure and function were comparatively studied. The bioaccumulation and translocation characteristics of cadmium (Cd) and selenium (Se) in S. plumbizincicola were also evaluated. The results showed that the heavy metal pollution reduced the richness and diversity of endophyte communities. Soil pH and Cd concentration could be the key factors affecting the composition of the endophyte community. Co-occurrence network analysis identified that 22 keystone taxa belonging to Actinobacteriota, Firmicutes, Myxococcota and Proteobacteria were positively correlated with Cd bioaccumulation and translocation. The predicted endophyte metabolic pathways were enriched in physiological metabolism, immune system, and genetic Information processing. These findings may help to understand how endophytes assist host plants to enhance their adaptability to harsh environments, and provide a basis for further exploration of plant-endophyte interactions and improvement in phytoremediation efficiency.

Endophytic bacterial community structure and diversity of the medicinal plant Mirabilis himalaica from different locations

Endophytic bacteria play important roles in medicinal plant growth, abiotic stress, and metabolism. Mirabilis himalaica (Edgew.) Heimerl is known for its medicinal value as Tibetan traditional plant; however, little is known about the endophytic bacteria associated with this plant in different geographic conditions and vegetal tissues. To compare the endophytic bacterial community associated with this plant in different geographic conditions and vegetal tissues, we collected the leaves, stems, and roots of M. himalaica from five locations, Nongmu college (NM), Gongbujiangda (GB), Zhanang County (ZL), Lang County (LX), and Sangri County (SR), and sequenced the 16S rRNA V5-V7 region with the Illumina sequencing method. A total of 522,450 high-quality sequences and 4970 operational taxonomic units (OTUs) were obtained. The different tissues from different locations harbored unique bacterial assemblages. Proteobacteria and Actinobacteria were the dominant phyla in all the samples, while the dominant genera changed based on the different tissues. The endophytic bacterial structures in the leaf and stem tissues were different compared to root tissues. Redundancy analysis (RDA) showed that the endophytic bacterial community was significantly correlated with pH, available phosphorus (AP), total phosphorus (TP), total nitrogen (TN), and soil organic matter (SOM). These findings suggested that the geographic conditions, climate type, ecosystem type, and tissues determined the endophytic bacterial composition and relative abundances. This conclusion could facilitate an understanding of the relationship and ecological function of the endophytic bacteria associated with M. himalaica and provide valuable information for artificial planting of M. himalaica and identifying and applying functional endophytic bacteria.

Endophytic bacterial community diversity in genetically related hybrid rice seeds.

The Food and Agriculture Organization of the United Nations (FAO) has identified hybrid rice as ideal for addressing food scarcity in poor nations. A comprehensive investigation of the endophytic bacteria in hybrid rice seeds is essential from a microecological perspective to illuminate the mechanisms underlying its high yield, high quality, and multi-resistance. The endophytic bacterial diversity and community structures of 11 genetically correlated hybrid rice seeds with different rice blast resistance levels were studied using high-throughput sequencing (HTS) on the Illumina MiSeq platform to reveal their "core microbiota" and explore the effect of genotypes, genetic relationships, and resistance. Proteobacteria (78.15-99.15%) represented the most abundant group in the 11 hybrid rice cultivars, while Pantoea, Pseudomonas, and Microbacterium comprised the "core microbiota." Hybrid rice seeds with different genotypes, genetic correlations, and rice blast resistance displayed endophytic bacterial community structure and diversity variation. In addition, the network relationships between the rice seed endophytic bacteria of "the same female parent but different male parents" were more complex than those from "the same male parent but different female parents." Matrilineal inheritance may be the primary method of passing on endophytic bacteria in rice from generation to generation. The endophytic bacterial interaction network in rice blast-resistant hybrid rice seed varieties was more complicated than in susceptible varieties. In summary, this study demonstrated that the genotype, genetic relationship, and rice blast resistance were important factors affecting the community structures and diversity of endophytic bacteria in hybrid rice seeds, which was vital for revealing the interaction between endophytic bacteria and the host. KEY POINTS: • Pantoea, Pseudomonas, and Microbacterium represent the main endophytic bacteria in hybrid rice seeds. • Genotype is the primary factor affecting endophytic bacterial diversity in hybrid rice seeds. • The diversity of the endophytic bacterial community in hybrid rice seeds is related to their genotypes, genetic relationships, and rice blast resistance.

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.

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.

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.

Characteristics of endophytic bacterial community structure in roots of sugarcane under different fertilizer applications

<p id="C3">To explore the beneficial endophytic bacteria in sugarcanes and their functions, we analyzed the characteristics of endophytic bacterial community structure in roots of sugarcane under different fertilizer applications. At the phylum level, the proportion of Actinobacteria in roots of sugarcanes under different fertilization levels were lower than that in the control. However, the proportion of Chloroflexi in roots of sugarcanes under different fertilization levels applications were higher than that in CK. At the genus level, <italic>Haliangium</italic>, <italic>Acidicapsa</italic>, <italic>unclassified_f__Ktedonobacteraceae</italic>, and <italic>unclassified_f__Acidobacteriaceae_ Subgroup_</italic>1 were the specific dominant endophytic bacterial genera in root of sugarcanes under conventional fertilization level (3000 kg hm^-2, H treatment); while <italic>Sphingomonas</italic> was the specific dominant endophytic bacterial genus in roots of sugarcanes under fertilization level (1500 kg hm^-2, M treatment); <italic>Mesorhizobium</italic>, <italic>norank_f__BIrii</italic>41, <italic>Glycomyces</italic>, <italic>norank_f__</italic>67-14, <italic>Reyranella</italic>, <italic>unclassified_f__Steroidobacteraceae</italic>, <italic>unclassified_f__Xanthobacteraceae</italic>, <italic>norank_f__Roseiflexaceae</italic>, and <italic>Dongia</italic> were the specific dominant endophytic bacterial genus in roots of sugarcanes under the fertilization level (300 kg hm^-2, L treatment). On the contrary, <italic>Caulobacter</italic>, <italic>Pseudonocardia</italic>, <italic>Nocardia</italic>, <italic>Kitasatospora</italic>, <italic>norank_f__norank_o__norank_c__Actinobacteria</italic>, <italic>Oceanibaculum</italic>, and <italic>Amycolatopsis</italic> were the unique dominant endophytic bacterial genera in root of sugarcane without fertilization application (control). And <italic>Actinospica</italic>, <italic>Catenulispora</italic>, <italic>Acidothermus</italic>, <italic>Dyella</italic>, and <italic>norank_f__Xanthobacteraceae</italic> were lost in root of sugarcanes under low nitrogen applications. Gene function prediction also revealed that, compared to no-fertilization treatment, both the endophytic bacterial community structure and the metabolic functions of endophytic bacteria in roots of sugarcanes were affected by different fertilizer applications. However, the structures of endophytic bacterial community in roots of sugarcane were significant differences among different fertilization treatments depending on the amounts of fertilizer applications. Compared to conventional fertilization, the yields of sugarcanes, and the structure, metabolic function of endophytic bacteria in roots of sugarcanes were not significantly changed by fertilizer application under 1500 kg hm^-2 treatment. In conclusion, the conventional fertilization at the present stage can be substituted by reducing fertilizer application from 3000 kg hm^-2 to 1500 kg hm^-2 level in sugarcane.

Unveiling Endophytic Bacterial Community Structures of Different Rice Cultivars Grown in a Cadmium-Contaminated Paddy Field.

Endophytic bacteria play potentially important roles in the processes of plant adaptation to the environment. Understanding the composition and dynamics of endophytic bacterial communities under heavy metal (HM) stress can reveal their impacts on host development and stress tolerance. In this study, we investigated root endophytic bacterial communities of different rice cultivars grown in a cadmium (Cd)-contaminated paddy field. These rice cultivars are classified into low (RBQ, 728B, and NX1B) and high (BB and S95B) levels of Cd-accumulating capacity. Our metagenomic analysis targeting 16S rRNA gene sequence data reveals that Proteobacteria, Firmicutes, Actinobacteria, Acidobacteria, Bacteroidetes, and Spirochaetes are predominant root endophytic bacterial phyla of the five rice cultivars that we studied. Principal coordinate analysis shows that the developmental stage of rice governs a larger source of variation in the bacterial communities compared to that of any specific rice cultivar or of the root Cd content. Endophytic bacterial communities during the reproductive stage of rice form a more highly interconnected network and exhibit higher operational taxonomic unit numbers, diversities, and abundance than those during the vegetative stage. Forty-five genera are significantly correlated with Cd content in rice root, notably including positive-correlating Geobacter and Haliangium; and negative-correlating Pseudomonas and Streptacidiphilus. Furthermore, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States analysis shows that functional pathways, such as biosynthesis of siderophore and type II polyketide products, are significantly enhanced during the reproductive stage compared to those during the vegetative stage under Cd stress. The isolated endophytic bacteria from the Cd-contaminated rice roots display high Cd resistance and multiple traits that may promote plant growth, suggesting their potential application in alleviating HM stress on plants. This study describes in detail for the first time the assemblage of the bacterial endophytomes of rice roots under Cd stress and may provide insights into the interactions among endophytes, plants, and HM contamination.

Bacterial community structure of the sunflower (Helianthus annuus) endosphere

ABSTRACT Agrochemical applications on farmland aim to enhance crop yield; however, the consequence of biodiversity loss has caused a reduction in ecological functions. The positive endosphere interactions and crop rotation systems may function in restoring a stable ecosystem. Employing culture-independent techniques will help access the total bacteria community in the sunflower endosphere. Limited information is available on the bacteria diversity in sunflower plants cultivated under different agricultural practices. Hence, this study was designed to investigate the endophytic bacterial community structure of sunflower at the growing stage. Plant root and stem samples were sourced from two locations (Itsoseng and Lichtenburg), for DNA extraction and sequenced on the Illumina Miseq platform. The sequence dataset was analyzed using online bioinformatics tools. Saccharibacteria and Acidobacteria were dominant in plant roots, while the stem is dominated by Proteobacteria, Bacteriodetes, and Gemmatimonadetes across the sites. Bacterial genera, Acidovorax, Flavobacterium, Hydrogenophaga, and Burkholderia-Paraburkhoderia were found dominant in the root, while the stem is dominated by Streptomyces. The diverse bacterial community structure at phyla and class levels were significantly different in plant organs across the sites. The influence of soil physical and chemical parameters analyzed was observed to induce bacterial distribution across the sites. This study provides information on the dominant bacteria community structure in sunflowers at the growing stage and their predictive functions, which suggest their future exploration as bioinoculants for improved agricultural yields.

Effect of Bursaphelenchus xylophilus infection on the endophytic bacterial community structure in different parts of Pinus massoniana seedlings

Objective  With an investigation of the structural changes of the endophytic bacterialflora of pine stems, pine needles and pine roots, this study is aimed to fully explore the endophytic bacterial resources of Pinus massoniana. Method  DGGE and high-throughput sequencing technology was employed in the exploration of the structural changes of endophyticbacterial flora of three-year-old P. massoniana trees upon the infection of Bursaphelenchus xylophilus disease. Result  (1) There was a significant diversity in the endophytic bacterial community structure in different parts of P. massoniana trees with the diversity decreasing from the pine stem to pine needles and to the root system. (2) There was significant increase in parts of the bacterial genera in pine stems after 15 days of infection, whereas there were no symptoms shown on the surface of the seedlings. (3) Of the 442 genera of endophytic bacteria detected in P. massoniana that fall into 35 phyla, 49 classes, 110 order and 210 families, the relative abundance of Methylobacterium, Sphingomonas, Hymenobacter, Pantoea, Sphingomonas and Curtobacterium in pine stems and pine needles varies greatly throughout the infection process. Conclusion  The effect of the infection of B. xylophilus disease on the structure of the endophytic bacterial flora varies from none to pretty significant to extremely significant in roots, pine needles and pine stems respectively. And some endophytic bacteria may have potential biocontrol effects on B. xylophilus disease, which is conducive to the excavation of later biocontrol strains. In addition, real-time monitoring of changes in the bacterial community structure of pine stems during the peak period of infection is helpful to the early diagnosis of B. xylophilus disease. [Ch, 5 fig. 1 tab. 25 ref.]

Endophytic bacteria associated with the enhanced cadmium resistance in NHX1- overexpressing tobacco plants

Human industrial activities have left large area of land polluted with cadmium (Cd), which poses tremendous threat to ecosystem. Na+/H+ antiporter 1 (NHX1) was a transporter located on vacuoles, which mediated the compartmentation of Na+ into vacuole and transportation of H+ into the cytoplasm. And the overexpressing of its code gene (NHX1 gene) was previously identified to enhance Cd resistance in tobacco (Nicotiana tabacum) plants possibly by maintaining the change of ion content. However, the mechanisms of Cd resistance in NHX1-overexpressing plants have not been well elucidated yet. In this study, the endophytic bacteria communities, the activities of soil enzymes and the antioxidant enzymes were characterized to explore possible mechanisms of the enhanced Cd resistance in NHX1-overeexpressing tobacco plants. Some differences in the endophytic bacterial community structure in roots of transgenic and WT tobaccos under Cd stress were observed, in which, Sphingomonas, Steroidobacter and Actinoplanes were proposed as vital endophytic bacteria for enhancing Cd resistance of transgenic tobacco plants. In addition, the soil enzymes were increased in the rhizospheric soil around the transgenic tobacco plants compared to WT plants under Cd stress. Under Cd exposure, the SOD and CAT activities were 1.65 times and 1.88 times of that in WT plants, respectively. The content of MDA and H2O2 were also observed to be 35 % and 28 % lower in transgenic tobacco roots compared to WT plants under Cd stress. Moreover, the Cd content of transgenic plants decreased by 38 % under Cd stress compared to WT plants. These findings suggested that the endophytic bacteria communities associated with the NHX1-overexpressing plants might lead to the increased Cd resistance by enhancing the rhizosphere soil enzyme activities, strengthening the antioxidative defense system, and better maintaining of the ion changes. Taken together, this study suggested that the enhanced Cd resistance was observed in transgenic tobacco plants associated with the increase of soil enzyme activities and changes of endophytic bacteria community, and the possible mechanisms involved in this process were also discussed.

Diversity of Endophytic Bacteria in Cardamine hupingshanensis and Potential of Culturable Selenium-Resistant Endophytes to Enhance Seed Germination Under Selenate Stress

The endophytic bacterial communities of Se hyperaccumulator Cardamine hupingshanensis collected from greenhouse and seleniummining area in Enshi City were investigated by Illumina sequencing technology. In addition, 14 culturable endophytic selenium-resistant strains were isolated and their selenium tolerance and plant growth promotion abilities were studied. The results showed that phylum Proteobacteria predominated in all the plants (> 70%) regardless of their habitats, with most of the OTUs related to Betaproteobacteria, Alphaproteobacteria, and Gammaproteobacteria. Roots harbored many more OTUs and showed higher alpha diversities than the leaves. Both growing environment and specific microflora selection of plants were found to have noticeable effects on endophytic bacterial community structure. The 14 culturable endophytes belonging to 11 bacterial genera were able to resist different levels of selenite and selenate, with their MIC ranges of 10-120mM and 100-600mM. Among them, Oceanobacillus and Terribacillus genera were firstly reported for the selenium-tolerant properties of their members. Inoculation experiment revealed that three endophytic strains (CHP07, CHP08, and CHP14) with excellent plant growth-promoting traits were beneficial for growth of Brassica chinensis seeds at germination stage under 0.19mM selenate stress.

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.

High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of upland rice

Upland rice is an ecotype crop resulting from the long-term domestication and evolution of rice in dry land without a water layer. Generally, the stems and leaves are thick and luxuriant, while the leaves also typically broad and light. The root system is developed with abundant root hair, and the osmotic pressure of the root and cell juice concentration in the leaves is high, while this plant is drought-resistant, heat-resistant, and water absorbent. This study aims to reveal the "core flora" of the endophytes in upland rice seeds by examining their diversity and community structures. It further intends to reveal the impact of the soil environment on the formation of endophyte community structures in upland rice seeds by comparing the environmental soil microorganisms in upland rice habitats. In this study, high-throughput sequencing technology based on the Illumina Hiseq 2500 platform was used to investigate the structure and diversity of endophytic bacterial communities using upland rice varieties collected from different locations and soil samples from unified planting sites as materials. Here, 42 endophytic OTUs were found to coexist in the 14 samples. At the phylum level, the first dominant phyla in all the samples were Proteobacteria (93.81-99.99%). At the genus level, Pantoea (8.77-87.77%), Pseudomonas (1.15-61.58%), Methylobacterium (0.40-4.64%), Sphingomonas (0.26-3.85%), Microbacterium (0.01-4.67%) and Aurantimonas (0.04-4.34%), which represent the core microflora in upland rice seeds, served as the dominant genera that coexisted in all the upland rice seeds tested. This study significant for the isolation, screening, functional evaluation, and re-action of various functional microorganisms in upland rice to improve its agronomic traits. It also provides a specific reference for the interaction between microorganisms and plants.

Root-associated endophytic bacterial community composition and structure of three medicinal licorices and their changes with the growing year

BackgroundThe dried roots and rhizomes of medicinal licorices are widely used worldwide as a traditional medicinal herb, which are mainly attributed to a variety of bioactive compounds that can be extracted from licorice root. Endophytes and plants form a symbiotic relationship, which is an important source of host secondary metabolites.ResultsIn this study, we used high-throughput sequencing technology and high-performance liquid chromatography to explore the composition and structure of the endophytic bacterial community and the content of bioactive compounds (glycyrrhizic acid, liquiritin and total flavonoids) in different species of medicinal licorices (Glycyrrhiza uralensis, Glycyrrhiza glabra, and Glycyrrhiza inflata) and in different planting years (1–3 years). Our results showed that the contents of the bioactive compounds in the roots of medicinal licorices were not affected by the species, but were significantly affected by the main effect growing year (1–3) (P < 0.05), and with a trend of stable increase in the contents observed with each growing year. In 27 samples, a total of 1,979,531 effective sequences were obtained after quality control, and 2432 effective operational taxonomic units (OTUs) were obtained at 97% identity. The phylum Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes, and the genera unified-Rhizobiaceae, Pseudomonas, Novosphingobium, and Pantoea were significantly dominant in the 27 samples. Distance-based redundancy analysis (db-RDA) showed that the content of total flavonoids explained the differences in composition and distribution of endophytic bacterial communities in roots of cultivated medicinal liquorices to the greatest extent. Total soil salt was the most important factor that significantly affected the endophytic bacterial community in soil factors, followed by ammonium nitrogen and nitrate nitrogen. Among the leaf nutrition factors, leaf water content had the most significant effect on the endophytic bacterial community, followed by total phosphorus and total potassium.ConclusionsThis study not only provides information on the composition and distribution of endophytic bacteria in the roots of medicinal licorices, but also reveals the influence of abiotic factors on the community of endophytic bacteria and bioactive compounds, which provides a reference for improving the quality of licorice.