Search Results (73)

Plant microbiomes are vital for the growth and health of their host. Tree-associated microbiomes are shaped by multiple factors, of which the host is one of the key determinants. Whether different host genotypes affect the structure and diversity of the tissue-associated microbiome and how specific taxa enriched in different tree tissues are not yet well illustrated. Chinese fir (Cunninghamia lanceolata) is an important tree species for both economy and ecosystem in the subtropical regions of Asia. In this study, we investigated the tissue-specific fungal community structure and diversity of nine different Chinese fir genotypes (39 years) grown in the same field. With non-metric multidimensional scaling (NMDS) analysis, we revealed the divergence of the fungal community from rhizosphere soil (RS), fine roots (FRs), and thick roots (TRs). Through analysis with α-diversity metrics (Chao1, Shannon, Pielou, ACE, Good‘s coverage, PD-tree, Simpson, Sob), we confirmed the significant difference of the fungal community in RS, FR, and TR samples. Yet, the overall fungal community difference was not observed among nine genotypes for the same tissues (RS, FR, TR). The most abundant fungal genera were Russula in RS, Scytinostroma in FR, and Subulicystidium in TR. Functional prediction with FUNGuild analysis suggested that ectomycorrhizal fungi were commonly enriched in rhizosphere soil, while saprotroph–parasite and potentially pathogenic fungi were more abundant in root samples. Specifically, genotype N104 holds less ectomycorrhizal and pathogenic fungi in all tissues (RS, FR, TR) compared to other genotypes. Additionally, significant correlations of several endophytic fungal taxa (Scytinostroma, Neonothopanus, Lachnum) with the growth traits (tree height, diameter, stand volume) were observed. This addresses that the interaction between tree roots and the fungal community is a reflection of tree growth, supporting the “trade-off” hypothesis between growth and defense in forest trees. In summary, we revealed tissue-specific, as well as host genotype-specific and genotype-common characters of the structure and functions of their fungal communities. Full article

Despite chemical exchange often serving as the first step in plant–microbe interactions, the specialized chemical metabolites produced by grass–Epichloë endophyte symbiosis as mediators of host growth, nutrient acquisition, and modulators of the rhizosphere community under low-nitrogen conditions are areas lacking in knowledge. In this study, we investigated the plant growth-promoting effects of the Epichloë endophyte strain and identified the growth of the Epichloë strain under different types of nitrogen source treatments. In addition to the in vitro test, we evaluated growth performance for Epichloë endophyte–infected plants (E+) and Epichloë endophyte–free plants (E−) in a pot trial under 0.01 mol/L urea treatment. Seedlings from E+ and E− groups were collected to analyze the plant bacterial microbiome and root metabolites. The E. gansuensis endophyte strain was found not to produce indoleacetic acid (IAA), pectinase, or contain ferritin. The nitrogenase gene, essential for nitrogen fixation, was also absent. These results suggest that E. gansuensis endophyte strains themselves do not contain attributes to promote plant growth. Concerning N fertilization, it was observed an increase in the colony diameter of E. gansuensis strain was observed only in the NO₃⁻-N (NN) treatment, while inhibition was observed in the urea-N (UN) treatment. E. gansuensis endophyte symbiosis significantly increased tiller number and plant dry weight. Overall, our results suggest that the E+ plants had more root forks and greater average root diameter compared to E− plants under the UN treatment. In a pot experiment using UN, data from 16S rRNA amplicon sequencing revealed that E. gansuensis endophyte infection significantly altered the bacterial community composition in shoot and root, and significantly increased Shannon (p < 0.001) and Chao 1 (p < 0.01) indexes. The relative abundance of Acidobacteriota, Actinomycetota, Cyanobacteriota, Fibrobacterota, Myxococcota, and Patescibacteria in the shoot, and Cyanobacteriota, Pseudomonadota, and Verrucomicrobiota in the root were significantly increased by E. gansuensis endophyte infection. Similarly, E. gansuensis endophyte symbiosis shifted the metabolite composition of the host plants, with the E+ plants showing a higher number of metabolites than the E− plants. In addition, co-metabolism network analysis revealed that the positive relevance between exudates and microorganisms in the root of the E+ plants is higher than that of the E− plants. These findings provide valuable insights into the knowledge of the effects of the symbiotic relationship between host plants and Epichloë endophyte on interspecific interactions of plant microbiome, beneficial for harnessing endophytic symbiosis, promoting plant growth. Full article

American ginseng (AG) cultivation suffers from severe diseases, requiring heavy pesticide use. This study aimed to explore whether companion planting with maize (AG-maize) or Perilla frutescens (AG-perilla) could enhance AG growth and alter rhizosphere/root microbiomes in a root rot-infested field. Compared to monoculture (CK), companion planting significantly improved AG growth and survival rate at wither stage, with AG-maize showing the superior efficacy- increasing root length and fresh weight, and plant height by 39.04%, 46.10%, and 48.69%, respectively, while raising survival rate from 1.51% to 14.54%. Microbial analysis revealed that companion planting increased microbiome diversity and network complexity. At green fruit stage, AG-perilla increased rhizosphere fungal Chao1 index by 42.6%, while AG-maize and AG-perilla elevated endophytic fungal Shannon indices by 46.68% and 74.84%, respectively. At wither stage, AG-maize notably enriched beneficial microbes (e.g., soil Pseudomonas +108.49%, Bacillus +200.73%) while reducing pathogens (soil Fusarium −20.04%, root endophytic Alternaria −54.55%). Structural equation model indicated AG-maize improved AG survival via core species-driven antibiosis and nutrient regulation, with keystone species Lysobacter sp. RHLT3-4 and Verrucomicrobium sp. IMCC25902 significantly correlating with AG health. The AG-maize system fostered synergistic microbial networks, enriching beneficial taxa and suppressing pathogens. These findings provide a foundation for developing eco-friendly disease management and high-yield AG cultivation strategies. Full article

Root endophytic microbial communities play a key role in plant health and productivity, yet the extent to which these communities vary across different crop species remains underexplored. This study aimed to investigate the root endophytic bacterial diversity of two important crops—hybrid tomato (Lycopersicon esculentum Mill. var. TNAU CO3) and finger millet (Eleusine coracana L. var. TNAU CO13)—to understand how crop-specific microbiomes contribute to agricultural sustainability and productivity. Targeted 16S rDNA amplicon sequencing was performed on tomato and finger millet root samples. A total of 165,772 and 181,327 16S rRNA gene sequences were generated from tomato and finger millet roots, respectively. These sequences were processed to identify amplicon sequence variants (ASVs), which were then classified taxonomically to assess community composition and functional prediction. Across the two hybrid crops, 1400 ASVs were detected in tomato and 1838 in finger millet. Proteobacteria (52.61–62.09%) were the dominant phylum in both, followed by Actinobacteria, Firmicutes, Bacteroidota, unidentified bacteria, Myxococcota, Verrucomicrobiota, Acidobacteriota, Fusobacteriota, and Chloroflexi. Finger millet roots harbored a more diverse and robust microbial assemblage, particularly enriched with nitrogen-fixing and oxidative stress-mitigating bacteria. In contrast, tomato roots showed a higher abundance of phosphate-solubilizing and biofilm-forming taxa, potentially enhancing resilience to environmental stress. These findings highlight the crop-specific nature of endophytic bacterial communities and their diverse functional capabilities. By revealing distinct microbial profiles in tomato and finger millet, this work provides a valuable foundation for developing strategies to optimize soil health, crop performance, and abiotic stress tolerance. Full article

Microbial symbioses deal with the symbiotic interactions between a given microorganism and another host. The most widely known and investigated microbial symbiosis is the association between leguminous plants and nitrogen-fixing rhizobia. It is one of the best-studied plant–microbe interactions that occur in the soil rhizosphere and one of the oldest plant–microbe interactions extensively studied for the past several decades globally. Until recently, it used to be a common understanding among scientists in the field of rhizobia and microbial ecology that the root nodules of thousands of leguminous species only contain nitrogen-fixing symbiotic rhizobia. With the advancement of molecular microbiology and the coming into being of state-of-the-art biotechnology innovations, including next-generation sequencing, it has now been revealed that rhizobia living in the root nodules of legumes are not alone. Microbiome studies such as metagenomics of the root nodule microbial community showed that, in addition to symbiotic rhizobia, other bacteria referred to as non-rhizobial endophytes (NREs) exist in the nodules. This review provides an insight into the occurrence of non-rhizobial endophytes in the root nodules of several legume species and the beneficial roles of the tripartite interactions between the legumes, the rhizobia and the non-rhizobial endophytes (NREs). Full article

Arnebia euchroma (Royle) Johnst. has high medicinal and economic value, but in recent years, wild resources of this species have been depleted and the quality of artificially cultivated A. euchroma has been poor. The endophyte community of medicinal plants is rich, serving as an internal resource that promotes the growth of medicinal plants and the accumulation of secondary metabolites, and has important potential application value in improving the quality of medicinal materials. A. euchroma cultivars and wild varieties contain abundant endophyte communities and metabolites in different tissues. However, the relationships between A. euchroma endophytes and metabolites with different growth patterns and different tissue sites remain unclear. In this study, microbiome analysis and metabolomics were used to analyze the diversity of endophytes in the root and leaf tissues of cultivated and wild A. euchroma and their correlations with metabolites. The results revealed that the diversity of endophytes in A. euchroma was different from that in wild A. euchroma and that there was tissue specificity among different tissues. A species composition analysis revealed that the dominant endophytic fungi belonged to Ascomycota and Basidiomycota, and the dominant endophytic bacteria belonged to Proteobacteria and Cyanobacteria. A total of 248 metabolites, including quinones, flavonoids, alkaloids, organic acids, sugars, amino acids, coumarins, sterols, terpenoids, polyphenols, fatty ketones, and their derivatives, were identified in positive ion mode via LC–MS/MS. According to their different growth patterns and associated tissue parts, 9 differentially abundant metabolites were screened between AEZ-L (cultivated leaf tissue of A. euchroma) and AEY-L (wild leaf tissue of A. euchroma), 6 differentially abundant metabolites were screened between AEZ-R (cultivated root tissue of A. euchroma) and AEY-R (wild root tissue of A. euchroma), and 104 differentially abundant metabolites were screened between AEZ-R and AEZ-L. Eighty-two differentially abundant metabolites were screened between AEY-R and AEY-L. The contents of eight naphthoquinones in AEZ-R and AEY-R were determined via HPLC. The contents of β,β’-dimethylacrylylakanin in wild A. euchroma were greater than those in cultivated A. euchroma. A correlation analysis revealed that the dominant endophytes in the four groups were significantly correlated with a variety of metabolites, and the eight naphthoquinones in the root tissue were also significantly correlated with the dominant endophytes. The diversity of the A. euchroma endophyte community differed across different growth patterns and different tissue parts. There were significant differences in the relative contents of A. euchroma metabolites in different tissues. A correlation analysis verified the correlation between A. euchroma endophytes and metabolites. Full article

Plants inhabiting environments with suboptimal growth conditions often have a more pronounced capacity to attract and sustain microbial communities that improve nutrient absorption and expand abiotic stress tolerance. Rhodiola rosea L. is a succulent plant of the Crassulaceae family adapted to survive in sandy or rocky soils or dry tundra. The aim of the present study was to investigate the diversity and plant growth-stimulating potential of R. rosea endophytic microbiota. Metataxonomic analysis of the bacterial diversity in the rhizome of R. rosea revealed 108 families. Among these, three families were found exclusively in the core microbiome of 1-year-old plants, while nine families were unique to the core microbiome of mature plants grown in the field for more than 4 years. Seventy-three endophytic bacteria isolates were obtained from the rhizome of R. rosea plants and were assigned into 14 distinct bacterial genera of Firmicutes (26%) or Proteobacteria (74%) phyla. Screening for functional genes related to the nitrogen cycle, phosphorus mineralisation or dissolution, and traits associated with nitrogen fixation (56% of isolates), siderophore production (40%), inorganic phosphorus solubilisation (30%), and production of indole-related compounds (51%) led to the classification of the isolates into 16 distinct clusters. Co-cultivation of 45 selected isolates with germinating Arabidopsis seedlings revealed 18 and 5 isolates that resulted in more than a 20% increase in root or shoot growth, respectively. The study results established the complexity of the succulent R. rosea endophytic microbiome and identified isolates for potential plant growth-stimulating applications. Full article

Drought stress has a significant impact on agricultural productivity, affecting key crops such as soybeans, the second most widely cultivated crop in the United States. Endophytic and rhizospheric microbial diversity analyses were conducted with soybean plants cultivated during the 2023 growing season amid extreme weather conditions of prolonged high temperatures and drought in Louisiana. Specifically, surviving and non-surviving soybean plants were collected from two plots of a Louisiana soybean field severely damaged by extreme heat and drought conditions in 2023. Although no significant difference was observed between surviving and non-surviving plants in microbial diversity of the rhizosphere, obvious differences were found in the structure of the endophytic microbial community in root tissues between the two plant conditions. In particular, the bacterial genera belonging to Proteobacteria, Pseudomonas and Pantoea, were predominant in the surviving root tissues, while the bacterial genus Streptomyces was conspicuously dominant in the non-surviving (dead) root tissues. Co-occurrence patterns and network centrality analyses enabled us to discern the intricate characteristics of operational taxonomic units (OTUs) within endophytic and rhizospheric networks. Additionally, we isolated and identified bacterial strains that enhanced soybean tolerance to drought stresses, which were sourced from soybean plants under a drought field condition. The 16S rDNA sequence analysis revealed that the beneficial bacterial strains belong to the genera Acinetobacter, Pseudomonas, Enterobacter, and Stenotrophomonas. Specific bacterial strains, particularly those identified as Acinetobacter pittii and Pseudomonas sp., significantly enhanced plant growth metrics and reduced drought stress indices in soybean plants through seed treatment. Overall, this study advances our understanding of the soybean-associated microbiome structure under drought stress, paving the way for future research to develop innovative strategies and biological tools for enhancing soybean resilience to drought. Full article

Drought is an increasingly critical global challenge, significantly impacting agricultural productivity, food security, and ecosystem stability. As climate change intensifies the frequency and severity of drought events, innovative strategies are essential to enhance plant resilience and sustain agricultural systems. This review explores the vital role of beneficial microbes in conferring drought tolerance, focusing on Plant Growth-Promoting Rhizobacteria (PGPR), mycorrhizal fungi, endophytes, actinomycetes, and cyanobacteria. These microorganisms mitigate drought stress through diverse mechanisms, including osmotic adjustment, enhancement of root architecture, modulation of phytohormones, induction of antioxidant defenses, and regulation of stress-responsive gene expression. Ecological and agricultural innovations leveraging these beneficial microbes have demonstrated significant potential in bolstering drought resilience. Strategies such as soil microbiome engineering, bioaugmentation, and the integration of microbial synergies within pest management frameworks enhance ecosystem resilience and agricultural sustainability. Additionally, advancements in agricultural practices, including seed coating, soil amendments, the development of microbial consortia, and precision agriculture technologies, have validated the effectiveness and scalability of microbial interventions in diverse farming systems. Despite promising advancements, several challenges hinder the widespread adoption of microbial solutions. Environmental variability can affect microbial performance, necessitating the development of robust and adaptable strains. Scale-up and commercialization hurdles, economic constraints, and regulatory and safety considerations also pose significant barriers. Furthermore, the complex interactions between microbes, plants, and their environments require a deeper understanding to optimize microbial benefits consistently. Future research should focus on integrating cutting-edge technologies such as genomics, synthetic biology, and precision agriculture to refine and enhance microbial interventions. Collaborative efforts among academia, industry, and government are essential to bridge the gap between research and practical implementation. By addressing these challenges and harnessing microbial innovations, it is possible to develop resilient and sustainable agricultural systems capable of thriving in an increasingly water-scarce world. Full article

The tree-associated microbiome is vital for both individual trees and the forest ecosystem. The microbiome is dynamic; however, it is influenced by the developmental stages and environmental stresses experienced by host trees. Chinese fir (Cunninghamia lanceolata) is an economically important tree species in the subtropical regions of China. This study investigated the diversity of microbial communities, including bacteria and fungi, in the roots and bulk soil of young (2 years old) and old (46 years old) Chinese fir. It specifically examined the functional characteristics of these microbial communities. Through a non-metric multidimensional scaling (NMDS) analysis, we examined differences in microbial community structures among root and soil samples of Chinese fir. Evaluations using α-diversity metrics (Chao1, Shannon, Pielou, etc.) confirmed significant differences in diversity and structure between soil and root samples but high similarity between young and old tree samples. A network analysis identified key bacterial and fungal genera, such as Burkholderia and Russula, which play pivotal roles in the microbiome structure. We also demonstrated significant variations in microbial metabolic functions, such as dioxin and benzoic acid degradation metabolic pathways, which might relate to stress alleviation for tree fitness. Additionally, for the detection of endophytic microorganisms in Chinese fir seeds, only small amounts (less than 10%) of fungal endophytes and bare bacterial endophytes were identified. In summary, this study revealed that the stable structure of the rhizosphere microbiome was established in the early stage of tree life in Chinese fir, which mostly originated from surrounding soil rather than seed endophytes. The associated microbial metabolic activity naturally decreased with tree aging, implicating the tree microbial dynamics and the need for the addition of an actively functional synthetic community for tree fitness. Full article

Verticillium wilt caused by Verticillium dahliae Kleb. is a lethal soil-borne fungal disease of Cotinus coggygria. The plant endophytic microbiome plays an important role in maintaining plant health and disease resistance, but it is unclear how the endophytic microbiome of C. coggygria roots varies in response to Verticillium wilt occurrence. In this study, the endophytic microbial diversity, community composition, dominant species, and co-occurrence network of C. coggygria under Verticillium wilt-affected and healthy conditions were assessed using Illumina sequencing. Compared with healthy plants, the bacterial alpha diversity indices of Verticillium wilt-affected plants decreased significantly, while the fungal alpha diversity indices showed obvious increases. The relative abundance of dominant taxa including Proteobacteria, Actinobacteriota, Ascomycota, and Basidiomycota at the phylum level, as well as Gammaproteobacteria, Thermoleophilia, Dothideomycetes, and Agaricomycetes at the class level, differed significantly between Verticillium wilt-affected and healthy plants. Co-occurrence networks revealed that the fungal network of Verticillium wilt-affected roots was denser with more negative interactions, which may be relevant to functional changes from reciprocity to competition in the microbial community, in response to V. dahliae infection. The results enhanced our understanding on the relationships between the endophytic microbiome and Verticillium wilt, which could provide information for the management of this disease in C. coggygria. Full article

The objective of the present study was to isolate endophytes from the roots of the halophyte Sesuvium portulacastrum, which is applied for aquatic phytoremediation. From these endophytes, siderophore-producing bacteria were specifically isolated for their potential capacity to promote plant growth. The siderophore production capacity of the isolated bacteria was quantified, and a high-yield siderophore-producing strain was selected for further investigation. A total of 33 endophytic bacteria were successfully isolated and identified using a culturable approach. Of these, 10 siderophore-producing bacteria were identified using the selective agar assay, displaying siderophore unit (SU) values ranging from 11.90% to 80.39%. It is noteworthy that Erwinia sp. QZ-E9 exhibited the highest siderophore production capacity, achieving an SU of 80.39%. A microcosm co-cultivation experiment was conducted with the strain QZ-E9 in iron-deficient conditions (2 μmol/L Fe³⁺). The results demonstrated that strain QZ-E9 significantly enhanced the growth of S. portulacastrum, by increases in both fresh weight (1.41 g) and root length (18.7 cm). Furthermore, fluorescence in situ hybridization (FISH) was utilized to ascertain the colonization pattern of strain QZ-E9 within the plant roots. The analysis demonstrated that strain QZ-E9 exhibited extensive colonization of the epidermal and outer cortical cells of S. portulacastrum roots, as well as the intercellular spaces and vascular tissues. This colonization indicated that Erwinia sp. QZ-E9 plays a crucial role in promoting the growth of S. portulacastrum, presumably through its siderophore-mediated iron acquisition mechanism. Full article

Plant–microbe interactions are key to nutrient-use efficiency. Root microbes are influenced by rhizosphere soil and plant cultivars. The impact of cultivar-by-nitrogen (N) interactions on the maize-root microbiome remains unclear, yet it is crucial for understanding N use efficiency in maize. This study evaluated the effects of maize cultivars and N forms, along with their interactions, on the diversity and composition of root bacteria and fungi. Additionally, we examined correlations between soil microbes and root metabolites. The maize cultivar Zhengdan 958 (ZD958) showed a positive response to the mixture of nitrate and ammonium N, resulting in increased in biomass, grain yield, shoot N content, grain N content, and root area. In contrast, the cultivar Denghai605 (DH605) did not exhibit a similar response. The diversity and composition of root bacteria and fungi differed between ZD958 and DH605. The N form primarily affected the community structure of rhizospheric fungi in ZD958 and rhizospheric bacteria in DH605, rather than endophytic microbes. A mixed N supply increased the relative abundance of Basidiomycota, which was positively correlated with ZD958 yield. For DH605, a mixed N treatment enhanced nitrification functions involving Bacteroidetes and Proteobacteria, while it reduced the effects of ammonium N supply. The dominant rhizospheric microbes in DH605 showed a stronger response to changes in root metabolites compared to those in ZD958. A mixed N supply increased the content of palmitoleic acid in ZD958 root exudates, facilitating the recruitment of beneficial rhizospheric microbes, which promotes maize growth. In DH605, a mixed N supply decreased the concentration of sphinganine, which is significantly correlated with Acidobacteria (negatively), Proteobacteria (negatively), Bacteroidetes (positively), and TM7 (positively). Our findings suggest that different maize cultivars respond differently to N forms, causing distinct rhizospheric microbial effects, and that root metabolites send metabolic signals to regulate and recruit key bacterial and fungal communities. Full article

Biological invasions are now seen as one of the main threats to the Antarctic ecosystem. An example of such an invasion is the recent colonization of the H. Arctowski Polish Antarctic Station area by the non-native grass Poa annua. This site was previously occupied only by native plants like the Antarctic hair grass Deschampsia antarctica. To adapt successfully to new conditions, plants interact with soil microorganisms, including fungi. The aim of this study was to determine how the newly introduced grass P. annua established an interaction with fungi compared to resident grass D. antarctica. We found that fungal diversity in D. antarctica roots was significantly higher compared with P. annua roots. D. antarctica managed a biodiverse microbiome because of its ability to recruit fungal biocontrol agents from the soil, thus maintaining a beneficial nature of the endophyte community. P. annua relied on a set of specific fungal taxa, which likely modulated its cold response, increasing its competitiveness in Antarctic conditions. Cultivated endophytic fungi displayed strong chitinolysis, pointing towards their role as phytopathogenic fungi, nematode, and insect antagonists. This is the first study to compare the root mycobiomes of both grass species by direct culture-independent techniques as well as culture-based methods. Full article

Clubroot is a soilborne disease of canola (Brassica napus) and other crucifers caused by the obligate parasite Plasmodiophora brassicae. In western Canada, clubroot is usually managed by planting-resistant cultivars, but the emergence of resistance-breaking pathotypes of P. brassicae represents a major threat to sustainable canola production. The rhizosphere and root contain beneficial microorganisms that can improve plant health. In this study, we evaluated the effect of two P. brassicae isolates (termed A and B) with different levels of virulence on the root and rhizosphere microbiomes of clubroot-resistant and clubroot-susceptible canola. Additionally, potential biocontrol microorganisms were identified based on taxa antagonistic to clubroot. Although both P. brassicae isolates were classified as pathotype 3A, isolate A caused a higher disease severity index in the resistant canola genotype compared with isolate B. Metabarcoding analysis indicated a shift in the bacterial and fungal communities in response to inoculation with either field isolate. Root endophytic bacterial and fungal communities responded to changes in inoculation, isolate type, sampling time, and canola genotype. In contrast, fungal communities associated with the rhizosphere exhibited significant differences between sampling times, while bacterial communities associated with the rhizosphere exhibited low variability. Full article