Search Results (395)

One of the important traits of many plant growth-promoting rhizobacteria (PGPR) is the biocontrol of phytopathogens. Some PGPR metabolize phytohormone abscisic acid (ABA); however, the role of this trait in plant–microbe interactions is scarcely understood. Phytopathogenic fungi produce ABA and use this property as a negative regulator of plant resistance. Therefore, interactions between ABA-producing necrotrophic phytopathogen Botrytis sp. BA3 with ABA-metabolizing rhizobacterium Rhodococcus sp. P1Y were studied in a batch culture and in gnotobiotic hydroponics with sunflower seedlings. Rhizobacterium P1Y possessed no antifungal activity against BA3 and metabolized ABA, which was synthesized by BA3 in vitro and in associations with sunflower plants infected with this fungus. Inoculation with BA3 and the application of exogenous ABA increased the root ABA concentration and inhibited root and shoot growth, suggesting the involvement of this phytohormone in the pathogenesis process. Strain P1Y eliminated negative effects of BA3 and exogenous ABA on root ABA concentration and plant growth. Both microorganisms significantly modulated the hormonal status of plants, affecting indole-3-acetic, salicylic, jasmonic and gibberellic acids, as well as cytokinins concentrations in sunflower roots and/or shoots. The hormonal effects were complex and could be due to the production of phytohormones by microorganisms, changes in ABA concentrations and multiple levels of crosstalk in hormone networks regulating plant defense. The results suggest the counteraction of rhizobacteria to ABA-producing phytopathogenic fungi through the metabolism of fungal ABA. This expands our understanding of the mechanisms related to the biocontrol of phytopathogens by PGPR. Full article

Ericoid mycorrhizal fungi (EMF) enhance plant fitness and metabolic regulations in nutrient-poor soils, though the mechanisms diving these interactions require further elucidation. This study investigated the physiological and metabolic responses of blueberry seedlings following 2- and 3-weeks inoculation with Oidiodendron maius H14. The results indicated that EMF could significantly increases plant biomass, improve the accumulation of osmoregulatory substances in leaves. Additionally, the colonization rate of EMF are 26.18% and 30.22% after 2- and 3-weeks, respectively. The Metabolomics analysis identified 758 (593 up- and 165 down-regulated) and 805 (577 up- and 228 down-regulated) differential metabolites in roots at 2- and 3-weeks inoculation with O. maius H14, respectively. KEGG pathway annotation revealed that O. maius H14 triggered various amino acid metabolism pathways, including tryptophan metabolism and arginine and proline metabolism. These findings suggested that O. maius H14 stimulated root-specific biosynthesis of growth-promoting compounds and antimicrobial compounds. Concomitant downregulation of stress-associated genes and upregulation of glutamine synthetase suggest EMF modulates host defense responses to facilitate symbiosis. Thus, our results demonstrated that O. maius H14 orchestrates a metabolic reprogramming in blueberry roots, enhancing growth and stress tolerance through coordinated changes in primary and specialized metabolism, which could inform strategies for improving symbiosis and metabolic engineering in horticultural practices. Full article

The soil-borne fungi, Setophoma terrestris and Fusarium spp., are often associated with pink root, although the etiology of the disease remains doubtful. While recognized as the primary inoculum, studies show conflicting views on the formation of chlamydospores and microsclerotia in Setophoma. Therefore, this study aims to clarify the etiology of the pink root of garlic and onion and the formation of chlamydospores and microsclerotia in Setophoma. The isolates were obtained from symptomatic tissues of garlic, leeks, brachiaria, onions, chives, and maize collected from seven different states in Brazil. Representative isolates were selected for pathogenicity tests. Sequence comparison of the tubulin gene showed Setophoma (n = 50) and Fusarium clades (n = 25). Garlic and onion plants inoculated with Setophoma showed pink root symptoms, while plants inoculated with different Fusarium isolates remained asymptomatic. Multigene analysis of pathogenic isolates confirms that only Setophoma terrestris causes pink root in garlic and onion. In addition, brachiaria, chives, and leeks are newly identified hosts of this pathogen in Brazil. To our knowledge, the main sources of primary inoculum of the disease are chlamydospores, pycnidia, colonized roots of garlic, onion, and plant debris of susceptible crops. The new information obtained in this study will be fundamental for researchers in the development of genotypes that are resistant to pink root and will help the efficient management of the disease. Full article

Ecological restoration in the cold and high-altitude mining areas of the Qinghai–Tibet Plateau is faced with dual challenges of extreme environments and insufficient microbial adaptability. This study aimed to screen local microbial resources with both extreme environmental adaptability and plant-growth-promoting functions. Local fungi (DK; F18-3) and commercially available bacteria (B0) were used as materials to explore their regulatory mechanisms for plant growth, soil physicochemical factors, microbial communities, and metabolic profiles in the field. Compared to bacterial treatments, local fungi treatments exhibited stronger ecological restoration efficacy. In addition, the DK and F18-3 strains, respectively, increased shoot and root biomass by 23.43% and 195.58% and significantly enhanced soil nutrient content and enzyme activity. Microbiome analysis further implied that, compared with the CK, DK treatment could significantly improve the α-diversity of fungi in the rhizosphere soil (the Shannon index increased by 14.27%) and increased the amount of unique bacterial genera in the rhizosphere soil of plants, totaling fourteen genera. Meanwhile, this aggregated the most biomarkers and beneficial microorganisms and strengthened the interactions among beneficial microorganisms. After DK treatment, twenty of the positively accumulated differential metabolites (DMs) in the plant rhizosphere were highly positively associated with six plant traits such as shoot length and root length, as well as beneficial microorganisms (e.g., Apodus and Pseudogymnoascus), but two DMs were highly negatively related to plant pathogenic fungi (including Cistella and Alternaria). Specifically, DK mainly inhibited the growth of pathogenic fungi through regulating the accumulation of D-(+)-Malic acid and Gamma-Aminobutyric acid (Cistella and Alternaria decreased by 84.20% and 58.53%, respectively). In contrast, the F18-3 strain mainly exerted its antibacterial effect by enriching Acidovorax genus microorganisms. This study verified the core role of local fungi in the restoration of mining areas in the Qinghai–Tibet Plateau and provided a new direction for the development of microbial agents for ecological restoration in the Qinghai–Tibet Plateau. Full article

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

Plant-essential phosphorus (P) is a sparingly available mineral in soils. Phosphorus fertilizers—produced by the transformation of insoluble to soluble phosphates—are thus applied to agroecosystems. With advancements in commercial agriculture, crops have been increasingly adapted to grow in fertile environments. Wild crop relatives, however, are adapted to grow in unfertilized soils. In response to these two conditions of P bioavailability (fertilized agroecosystems and unfertilized natural soils), domesticated crops and wild species employ different strategies to grow and develop. It is essential to understand strategies related to P acquisition that may have been lost to domestication, and here we present, for the first time, that across species, modern cultivars engage in physical (i.e., root morphological) mechanisms while their wild relatives promote ecological (i.e., root-microbial) mechanisms. Domesticated crops showcase shallower root system architecture and engage in topsoil foraging to acquire P from the nutrient-stratified environments common to fertilized agroecosystems. Wild species associate with P-cycling bacteria and AM fungi. This divergence in P recovery strategies is a novel delineation of current research that has implications for enhancing agricultural sustainability. By identifying the traits related to P recovery that have been lost to domestication, we can strengthen the P recovery responses by modern crops and reduce P fertilization. Full article

Although many plant families are predominantly mycorrhizal, few symbiotic relationships between plants and arbuscular mycorrhizal fungi (AMF) have been thoroughly studied. Mycorrhized plants tend to exhibit greater tolerance to soil-borne pathogens and enhanced plant defence. Legumes, including common bean (Phaseolus vulgaris L.), are essential sources of protein globally. To improve common bean productivity, identifying efficient native microsymbionts is crucial. This study aimed to identify native AMF associated with common bean roots that could act as biostimulants and protect against soil diseases under varying environmental conditions. Agronomic trials were conducted at MBG-CSIC (Pontevedra, Spain) in 2021 and 2022, testing combinations of nitrogen fertilization, Burkholderia alba, Trichoderma harzianum, and a control. Traits such as nodulation, biomass, plant vigor, disease severity, nutrient content, and yield were evaluated. Four AMF species across three genera were identified. No consistent pattern was observed in AMF influence on agronomic traits. However, reduced mycorrhization in 2022 was associated with decreased nodulation, likely due to higher temperatures. Surprisingly, yields were higher in 2022 despite lower colonization. These findings suggest that intelligent use of AMF could reduce pesticide use, enhance sustainability, and promote healthier food systems. Continued research and conservation efforts are essential to optimize their benefits in legume production. Full article

Potato early dying disease complex (PED) leads to premature senescence and rapid decline in potato plants. Unlike potato wilt caused solely by Verticillium species, PED symptoms are more severe due to the synergistic effects of multiple pathogens, including root-lesion nematodes, fungi such as Colletotrichum and Fusarium, and soft-rot bacteria. To investigate the microbiome responsible for PED, soil and stem samples from healthy-looking and symptomatic plants were analyzed using amplicon-targeted next-generation sequencing (Illumina MiSeq and PacBio technologies). Samples were collected from four locations in New Brunswick, Canada from fields previously rotated with barley or oat. Comparative analysis of the bacterial, fungal, and eukaryotic diversity in soil samples showed minimal differences, with only bacterial alpha diversity influenced by the plant health status. Verticillium dahliae was abundant in all soil samples, and its abundance was significantly higher in the stems of diseased plants. Additional fungal species implicated in PED, including Plectosphaerella cucumerina, Colletotrichum coccodes, Botrytis sp., and Alternaria alternata, were also identified in the stems. This study highlights the complex, plant-associated microbial interactions underlying PED and provides a foundation for microbiome-informed disease management strategies. Full article

Arbuscular mycorrhizal fungi (AMF) exhibit diverse strategies for colonization and survival, yet the extent to which different propagule types—roots, extraradical hyphae, and spores—contribute to these processes remains unclear. In a pot experiment using Allium tuberosum and soils from three field sites, we characterized AMF communities in root, hyphal, and spore fractions through 18S rRNA gene sequencing. A total of 427 OTUs were identified, with Glomus and Paraglomus dominating. Root fractions contained significantly more OTUs than hyphal fractions, suggesting strong specialization for intraradical colonization. Only a small subset of taxa occurred across all propagule types. Indicator species analysis revealed 21 OTUs with significant associations, mainly in root and hyphal fractions, while spore-specific taxa were rare. PERMANOVA revealed that both propagule type and soil type shaped the community structure, with propagule identity being the stronger factor. These results highlight propagule-type specialization as a key ecological trait in AMF and underscore the importance of examining multiple fungal compartments to fully capture AMF diversity and function. Full article

Understanding species-specific mechanisms governing symbiotic fungal responses to plant traits and soil factors is critical for optimizing urban tree “plant-soil-fungus” systems under pollution stress. To address this gap, we combined δ¹³C/δ¹⁵N isotope analysis and ITS sequencing for three common street trees in Beijing: Sophora japonica, Ginkgo biloba, and Populus tomentosa. In S. japonica, symbiotic fungal abundance was positively associated with leaf δ¹⁵N, indicating root exudate-mediated “plant-microbe” interactions during atmospheric NO_x assimilation. G. biloba, with weak NO_x assimilation, exhibited a negative correlation between fungal abundance and soil available N/P, suggesting mycorrhizal nutrient compensation under low fertility. P. tomentosa showed decreased fungal abundance with increasing soil N/P ratios and specific leaf area, reflecting carbon allocation trade-offs that limit mycorrhizal investment. These results demonstrate that symbiotic fungi respond to atmospheric and edaphic drivers in a tree species-dependent manner. Urban greening strategies should prioritize S. japonica for its NO_x mitigation potential and optimize fertilization for G. biloba (nutrient-sensitive fungi) and P. tomentosa (nutrient balance sensitivity). Strategic mixed planting of P. tomentosa with S. japonica could synergistically enhance ecosystem services through complementary resource acquisition patterns. This study provides mechanism-based strategies for optimizing urban tree management under atmospheric pollution stress. Full article

Modern wheat breeding has largely emphasized aboveground traits, often at the expense of belowground characteristics such as root biomass, architecture, and beneficial microbial associations. This has narrowed genetic diversity, impacting traits essential for stress resilience and efficient nutrient and water acquisition—factors expected to become increasingly critical under climate change. In this study, we evaluated 36 primary synthetic (PS) hexaploid wheat lines developed by crossing Aegilops tauschii with the durum wheat cultivar Langdon (LNG) and compared them with LNG and the hexaploid variety Norin 61 (N61). We observed significant variation in root length, biomass, and associations with fungal endophytes, including beneficial Arbuscular Mycorrhizal Fungi (AMF) and Serendipita indica, and pathogenic Alternaria sp. Clustering analysis based on these traits identified three distinct PS groups: (1) lines with greater root length and biomass, high AMF and S. indica colonization, and low Alternaria infection; (2) lines with intermediate traits; and (3) lines with reduced root traits and high Alternaria susceptibility. Notably, these phenotypic patterns corresponded closely with the soil classification of the Ae. tauschii progenitors’ origin, such as Cambisols (supportive of root growth), and Gleysols and Calcisols (restrictive of root growth). This highlights the soil microenvironment as a key determinant of belowground trait expression. By comparing PS lines with domesticated tetraploid and hexaploid wheat, we identified and selected PS lines derived from diverse Ae. tauschii with enhanced root traits. Our study emphasizes the potential of wild D-genome diversity to restore critical root traits for breeding resilient wheat. Full article

Evidence from an increasing number of studies indicates that plant endophytic microorganisms play a significant role during biotic and abiotic stress resistance. To date, however, only a handful of studies on endophytes in response to the presence of phytoplasmas have been conducted. The production of jujube (Ziziphus jujuba) is threatened by jujube witches’ broom (JWB) disease, which is associated with the presence of the JWB phytoplasma ‘Candidatus Phytoplasma ziziphi’. To investigate the impact of jujube witches’ broom phytoplasma on the endophyte populations in jujube, high-throughput sequencing was performed in healthy and JWB-infected orchard jujube trees and in vitro jujube shoots. The results showed that the presence of JWB phytoplasma in jujube altered the abundance, diversity, and community structure of endophytic bacteria and fungi. In the branches and the roots, the presence of JWB phytoplasma was associated with an increase in the richness of the endophytic communities and a decrease in their diversity, with the phyla Proteobacteria, Firmicutes, and Bacteroidota and the genus ‘Ca. Phytoplasma’ becoming the most abundant. The presence of phytoplasmas was also associated with the remodeling of the endophytic microorganisms’ interaction network, shifting to a simpler biodiversity state. These results demonstrate the response of the jujube endophytic community to the presence of JWB phytoplasmas and shed light on the possible antagonistic agents that could be further evaluated for JWB disease biocontrol. Full article

In Montenegro, coniferous forests play a key ecological role in maintaining ecosystem stability. Root-associated mycorrhizal fungi and saprotrophic fungi inhabiting forest soils are well known for their roles in nutrient cycling, organic matter decomposition, and supporting host tree health. In contrast, the fungal communities residing within conifer needles, despite potentially important ecological functions, remain largely underexplored, particularly in natural and marginal forest ecosystems such as those in the Balkans. This study aimed to investigate the diversity and community composition of needle-associated fungi in three native conifers: Picea abies and Abies alba (at the edge of their native range), and the endemic Pinus heldreichii, from different mountainous regions in Montenegro. High-throughput sequencing was conducted to assess fungal diversity and community composition. Dothideomycetes dominated fungal communities in all three tree species, followed by Leotiomycetes and Tremellomycetes. Multivariate analysis revealed distinct fungal communities in P. heldreichii, whereas fungal communities in A. alba and P. abies were partially overlapping. Functional classification showed a dominance of saprotrophic, pathogenic, and endophytic fungi, with P. heldreichii exhibiting the highest proportion of saprotrophs, while A. alba and P. abies showed a considerable proportion of pathogens. The findings highlight strong host specificity, biogeographical influences, and the ecological importance of fungal communities in coniferous forests. This study provides new insights into the diversity and functional roles of needle-associated fungi, emphasizing the need for conservation efforts to maintain microbial biodiversity in native forests of Montenegro. Full article

Plants and the microorganisms living on their surfaces are an inseparable community that interacts with plant functional traits and influences plant growth, but the differences in microorganisms between plant organs and their relationship with plant functional traits have not been deeply explored. In this study, we used high-throughput sequencing to investigate the variation of microorganisms across different plant organs (leaves, twigs, trunks, and roots) of three species (Acer pictum subsp. mono, Acer tegmentosum, and Acer ukurunduense) in the Xiaoxing’an Mountains in Northeastern China and explored the relationship between microorganisms and plant functional traits. The results indicate that rhizosphere microorganisms have a high diversity. Plant organs explained 52.1% and 32.3% of the variations in bacterial and fungal community structures, respectively. The core microbiome consists of the phyla Proteobacteria and Actinobacteria in bacteria and the phyla Ascomycota and Basidiomycota in fungi. Plant functional traits such as specific leaf area and non-structural carbohydrates, as well as soil total carbon and total phosphorus content, were significantly correlated with microbial community composition. The results highlight that host plant organ characteristics are key drivers of variation in plant-associated microbial communities. By elucidating the regulatory role of host traits in microbiome assembly, our findings provide new mechanistic insights into plant–microbe interactions and ecological coexistence strategies. Full article

Rhizosphere microorganisms play pivotal roles in mitigating the challenges associated with continuous cropping in melon cultivation. While grafting and plant growth-promoting rhizobacteria (PGPR) independently influence rhizosphere microbial communities, their combined effects remain largely unexplored. This study investigates the synergistic regulation of Paenibacillus polymyxa NBmelon-1 inoculation and grafting on rhizosphere microbiome assembly, plant performance, and disease resistance in melon self-rootstocks. Field experiments demonstrated that NBmelon-1 inoculation significantly enhanced rootstock stem diameter (95.3% increase in spring) and root development, achieving a graft survival rate exceeding 95%. The combined treatment (NB+GJ) increased scion fruit yield by 29.8% in autumn and 36.5% in spring, as well as the single-fruit weight by 22.5% in autumn and 37.3% in spring, while maintaining fruit morphology. Integrated 16S rRNA and ITS sequencing revealed that the NB+GJ treatment selectively enriched antagonistic bacterial phyla (e.g., Firmicutes and Actinobacteriota) and suppressed pathogenic fungi (e.g., Fusarium and Melanconiella). Seasonal shifts in microbial diversity and functional gene profiles underscored the dynamic interplay between treatments and environmental factors. These findings establish a novel strategy for optimizing melon self-rootstock grafting systems and sustainably managing soil-borne diseases. Full article