Endophytic Community Structure Research Articles

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 < 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.

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.

Resistance of different ecotypes of Gastrodia elata to tuber rot

Tuber rot has become a serious problem in the large-scale cultivation of Gastrodia elata. In this study, we compared the resistance of different ecotypes of G. elata to tuber rot by field experiments on the basis of the investigation of G. elata diseases. The histological observation and transcriptome analysis were conducted to reveal the resistance differences and the underlying mechanisms among different ecotypes. In the field, G. elata f. glauca had the highest incidence of tuber rot, followed by G. elata f. viridis, and G. elata f. elata and G. elata f. glauca×G. elata f. elata showed the lowest incidence. Tuber rot showcased obvious plant source specificity and mainly occurred in the buds and bottom of G. elata plants. After infection, the pathogen spread hyphae in host cortex cells, which can change the endophytic fungal community structure in the cortex and parenchyma of G. elata. G. elata f. glauca had thinner lytic layer and more sugar lumps in the parenchyma than G. elata f. elata. The transcription of genes involved in immune defense, enzyme synthesis, polysaccharide synthesis, carbohydrate transport and metabolism, hydroxylase activity, and aromatic compound synthesis had significant differences between G. elata f. glauca and G. elata f. elata. These findings suggested that the differences in resis-tance to tuber rot among different ecotypes of G. elata may be related to the varied gene expression patterns and secondary metabolites. This study provides basic data for the prevention and control of tuber rot and the improvement of planting technology for G. elata.

Dynamic Shifts in the Root Microbiota of Cultivated Paphiopedilum armeniacum during Different Stages of Growth

Paphiopedilum armeniacum S. C. Chen et F. Y. Liu is an endangered lady’s slipper orchid species with high horticultural value. As observed for other orchids, mycorrhizal fungi and endophytic bacteria play important roles in the growth and development of P. armeniacum. In the present study, the community structure dynamics across three growth and development stages of cultivated P. armeniacum were investigated. The potential interactions between Tulasnellaceae fungi and core bacterial genera on one hand and the stability of the presumed mycorrhizal fungi communities on the other were analyzed in three growth stages of P. armeniacum to enhance our understanding of endophytic microbial community structure dynamics in the roots at different development stages. Based on sequencing, 3 and 16 phyla and 59 and 269 genera were identified in the fungal and bacterial communities, respectively. The predominant fungi and bacteria were Basidiomycota (62.90%) and Proteobacteria (43.98%), which exhibited changes in abundance and diversity depending on the growth stage of P. armeniacum. Assessment of the entire microbial communities from different growth stages showed that the seedling stage had the highest richness and diversity. The microbial communities recruited by P. armeniacum at the seedling stage were different from those recruited at the vegetative and reproductive growth stages, and the microbial communities recruited in the latter two stages overlapped. Tulasnellaceae were the only dominant fungal symbionts during P. armeniacum growth. Brevibacillus, Mycobacterium, and Sphingomonas, the three core genera, showed significant interactions with the main OTUs of Tulasnellaceae. Putative mycorrhizal fungi in P. armeniacum were relatively stable across different growth environments, and the core mycorrhizal fungi were uncultured Tulasnellaceae (OTU1). This could facilitate the ex situ conservation and commercial development of the endangered orchid.

Linking Phyllostachys edulis (moso bamboo) growth with soil nitrogen cycling and microbial community of plant-soil system: Effects of plant age and niche differentiation

Understanding the impacts of plant age on bamboo growth, soil nutrient and functional microorganism can assist in the development of management practices to maximize the benefits of nutrients and functional endophytic and soil microbes in moso bamboo plantations. In this study, moso bamboos of different ages (0.5, 2.5, 4.5 and 6.5 years) were selected. The above-ground biomass, soil properties and endophytic microbes of above-ground tissue and stump root of different age bamboos were quantified, and their interactive relationships were also examined. There were negligible differences in the heights and above-ground fresh biomass among the bamboo plants of different ages, but net nitrogen (N) mineralization and potential nitrification rates of soils were significantly affected by the bamboo ages. The soil nprA gene abundances decreased with the bamboo ages, and soil AOB amoA gene abundances of the 0.5-yr bamboo were significantly higher than those of the other older plants. Average soil urease activities of the 2.5-yr, 4.5-yr and 6.5-yr bamboos were 81.4%, 81.1% and 88.2% lower than those of the 0.5-yr bamboo, respectively. Bacterial diversity indices and richness estimators in the soils were significantly higher than those in the above-ground tissues. Endophytic microbial community structures were more sensitive to the bamboo ages than the soil counterparts, and endophytic microbial community diversities and structures in the above-ground tissues were significantly changed with the bamboo ages. Bacterial and fungal community structures in the above-ground tissues were significantly different from those in the soils. Bamboo ages significantly affected the N transformations in the soils and endophytic community structures, but niche differentiations among the above-ground tissue, stump root and soil outweighed the plant ages in shaping the whole microbial communities of plant-soil system.

Structure and Function of Rhizosphere Soil and Root Endophytic Microbial Communities Associated With Root Rot of Panax notoginseng.

Panax notoginseng (Burk.) F. H. Chen is a Chinese medicinal plant of the Araliaceae family used for the treatment of cardiovascular and cerebrovascular diseases in Asia. P. notoginseng is vulnerable to root rot disease, which reduces the yield of P. notoginseng. In this study, we analyzed the rhizosphere soil and root endophyte microbial communities of P. notoginseng from different geographical locations using high-throughput sequencing. Our results revealed that the P. notoginseng rhizosphere soil microbial community was more diverse than the root endophyte community. Rhodopseudomonas, Actinoplanes, Burkholderia, and Variovorax paradoxus can help P. notoginseng resist the invasion of root rot disease. Ilyonectria mors-panacis, Pseudomonas fluorescens, and Pseudopyrenochaeta lycopersici are pathogenic bacteria of P. notoginseng. The upregulation of amino acid transport and metabolism in the soil would help to resist pathogens and improve the resistance of P. notoginseng. The ABC transporter and gene modulating resistance genes can improve the disease resistance of P. notoginseng, and the increase in the number of GTs (glycosyltransferases) and GHs (glycoside hydrolases) families may be a molecular manifestation of P. notoginseng root rot. In addition, the complete genomes of two Flavobacteriaceae species and one Bacteroides species were obtained. This study demonstrated the microbial and functional diversity in the rhizosphere and root microbial community of P. notoginseng and provided useful information for a better understanding of the microbial community in P. notoginseng root rot. Our results provide insights into the molecular mechanism underlying P. notoginseng root rot and other plant rhizosphere microbial communities.

Vertical Stratification of Microbial Communities in Woody Plants

Bacterial and fungal endophytes form diverse communities and contribute to the performance and health of their host plants. Recent evidence suggests that both host-related factors and environmental conditions determine the community structure of plant endophytes. However, we know little about their distribution patterns and underlying community assembly mechanisms across plant compartments. Here, we analyzed the structure of bacterial and fungal communities associated with tree compartments as well as their underlying soils across 12 tree individuals in boreal forests. We found that the structure of bacterial and fungal communities depends more strongly on the vertical location of tree compartments rather than the locality, species, and individuals of host trees. Microbial communities showed much stronger host specificity in aboveground than belowground compartments. Compared with fungal communities, the composition and diversity of bacterial communities were markedly more distinct between below- and aboveground components but not between hosts, reflecting the greater importance of environmental conditions rather than dispersal limitation and host identity in their community assembly. Our data suggest that spatial distance from soil as a major microbiome source contributes to the formation of microbiomes in plants, and that bacterial and fungal communities may follow contrasting assembly processes in associating with a single individual tree.

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.

Plant Growth Promotion Diversity in Switchgrass-Colonizing, Diazotrophic Endophytes.

Endophytic nitrogen-fixing (diazotrophic) bacteria are essential members of the microbiome of switchgrass (Panicum virgatum), considered to be an important commodity crop in bioenergy production. While endophytic diazotrophs are known to provide fixed atmospheric nitrogen to their host plant, there are many other plant growth-promoting (PGP) capabilities of these organisms to be demonstrated. The diversity of PGP traits across different taxa of switchgrass-colonizing endophytes is understudied, yet critical for understanding endophytic function and improving cultivation methods of important commodity crops. Here, we present the isolation and characterization of three diazotrophic endophytes: Azospirillum agricola R1C, Klebsiella variicola F10Cl, and Raoultella terrigena R1Gly. Strains R1C and F10Cl were isolated from switchgrass and strain R1Gly, while isolated from tobacco, is demonstrated herein to colonize switchgrass. Each strain exhibited highly diverse genomic and phenotypic PGP capabilities. Strain F10Cl and R1Gly demonstrated the highest functional similarity, suggesting that, while endophyte community structure may vary widely based on host species, differences in functional diversity are not a clearly delineated. The results of this study advance our understanding of diazotrophic endophyte diversity, which will allow us to design robust strategies to improve cultivation methods of many economically important commodity crops.

"Breeding on Mountains" Resulted in the Reorganization of Endophytic Fungi in Asexually Propagated Plants (Ligusticum chuanxiong Hort.).

“Breeding on mountains, cultivation in dam areas” is a unique propagation method for the vegetatively propagated plant Ligusticum chuanxiong, including two transplants between the mountain and the dam area. It is well known that the environment can influence the endophytic community structure of plants. However, the change of host endophytic flora caused by transplanting in different places and its influence on asexual reproduction are still poorly understood. We carried out three cycles of cultivation experiments on L. chuanxiong and collected stem nodes (LZ), immature rhizomes (PX), medicinal rhizomes (CX), and rhizosphere. High-throughput sequencing was performed to analyze the endophytic fungi in all samples. We observed that the diversity and richness of endophytic fungi in L. chuanxiong increased as a result of transplanting cultivation from dam areas to mountains. Local transplantation caused minor changes in the endophytic fungus structure of L. chuanxiong, while remote transplantation caused significant changes. Compared with LZ after breeding in the dam area, the LZ after breeding on mountains has more abundant Gibberella, Phoma, Pericona, Paraphoma, and Neocosmospora. The regular pattern of the relative abundance of endophytic fungi is consistent with that of the fungus in the soil, while there are also some cases that the relative abundance of endophytic fungi is the opposite of that of soil fungi. In addition, there is a significant correlation among certain kinds of endophytic fungi whether in the soil or the plants. We have isolated more gibberellin-producing and auxin-producing fungi in the LZ cultivated in the mountains than that in the LZ cultivated in the dam area. The results of pot experiments showed that the three fungi isolated from LZ cultivated in mountainous areas can promote the development of shoots, stem nodes, and internodes of LZ, and increase the activity of plant peroxidase, catalase, phenylalanine ammonia lyase, and other enzymes. We can conclude that transplantation leads to the recombination of the host endophytic fungus, the more significant the difference in the environment is, the greater the reorganization caused by transplanting. Reorganization is determined by the soil environment, hosts, and the interaction of microorganisms. Remote transplantation is a crucial opportunity to reshuffle the micro-ecological structure of the asexual reproduction of plants, and regulate the growth, development, and resistance of plants, and prevent germplasm degradation caused by asexual reproduction.

Bacterial epiphyte and endophyte communities of seagrass Thalassia hemprichii: the impact of feed extract solution.

The global seagrass bed ecosystem acts as a natural ecological barrier in the littoral coastal zone. In recent years, this ecosystem has suffered from serious eutrophication and destruction caused by the continuous expansion of aquaculture. However, our understanding of the influence of aquaculture on the bacterial community remains limited. In this study, we used 16S amplicon sequencing to evaluate the impact of aquaculture feed extract solution on the composition and function of bacterial epiphytes and endophyte communities of the core seagrass from the seagrass bed ecosystem in Hainan, Thalassia hemprichii. The feed extract solution was the main factor that significantly affected the bacterial epiphyte and endophyte community structure of seagrass leaves but had no marked effect on alpha diversity was observed. Additionally, the bacterial epiphyte and endophyte community of the T. hemprichii leaves alleviated the effects of organic matter, sulfide, and nutrients caused by aquaculture wastewater. The feed extract solution promoted the proliferation of Bacteroidales, Vibrio, Desulfobulbaceae, Desulfobacteraceae, Pseudoalteromonas, Paludibacter, Marinomonas, and Pseudomonas in the leaves and root of T. hemprichii, which can effectively improve the digestibility of eutrophication. In fact, Desulfobacteraceae and Desulfobulbaceae can reduce sulfate to sulfide and oxidize sulfide to sulfur within seagrass, indicating that the increase in Desulfobulbaceae and Desulfobacteraceae facilitated the accumulation of sulfide with the treatment of feed extract solution, which may be the reason for the degradation of seagrass caused by aquaculture wastewater containing high concentrations of organic pollutants. These results suggest that although seagrass beds can withstand low concentrations of aquaculture pollutants, sulfide emissions should be minimized.