Search Results (724)

Controlled environment agriculture (CEA) relies on hydroponic systems to achieve high yields, yet optimizing plant performance remains a challenge. Beneficial endophytic bacteria offer a sustainable solution by promoting growth and nutrient uptake. Here, we investigated the mechanistic basis of growth enhancement in lettuce (Lactuca sativa) inoculated with Pseudomonas psychrotolerans IALR632 in a nutrient film technique (NFT) system. Growth measurements showed significant increases in shoot and root biomass and leaf greenness. RNA-seq profiling at 4, 10, and 15 days after transplanting revealed dynamic transcriptional reprogramming, with 38, 796, and 7642 differentially expressed genes, respectively. MapMan and GO analyses indicated up-regulation of pathways related to cell wall remodeling, lipid metabolism, nitrogen assimilation, and stress adaptation, alongside modulation of ethylene signaling. Root bacterial microbiome through 16S metabarcoding sequencing demonstrated distinct community shifts, confirmed by analysis of similarity (ANOSIM) (R = 1, p = 0.028), with enrichment of genera linked to nutrient cycling and plant growth promotion. These findings provide integrated molecular and ecological evidence that IALR632 enhances lettuce growth by coordinating host gene expression and rhizobiome restructuring, offering a mechanistic framework for microbial inoculant strategies in hydroponic horticulture. Full article

Cymbidium goeringii, an important orchid species, holds significant aesthetic and commercial potential in horticulture. However, stem rot caused by Fusarium oxysporum has emerged as a major biological constraint hindering industry development. In this study, we isolated five endophytic fungal strains from C. goeringii roots—namely, DG3 (Bjerkandera), DG4 (Cylindrocarpon), CLG3 (Talaromyces), CLG6 (Clonostachys), and Z3 (Trichoderma)—and assessed their inhibitory efficacy against stem rot and their potential to promote growth in C. goeringii. In vitro assays indicated that all five fungal strains had the ability to fix nitrogen and produce indole-3-acetic acid, as well as the capability to produce protease and exert broad-spectrum antimicrobial effects. The five endophytic fungal strains exhibited stem rot-resistant effects, among which strain Z3 showed the best inhibitory effect against stem rot, with a control efficacy reaching 68.89%. Treatment of C. goeringii seedlings with these endophytic fungal fermentation broths for 100 d significantly promoted growth compared to the control. The fresh weight increased by 10.53% to 88.16%, and root activity was enhanced by 50% to 162.5%. Additionally, the plant height and the longest leaf length increased by up to 23.68% and 47.50%, respectively, compared to the control. Additionally, the total chlorophyll content was up to 25.34% higher than that of the control group, and the soluble protein content was up to 39.54% higher. The MDA content was reduced by up to 40.23% compared to the control group. These endophytes also regulated the activity of defense-related enzymes in C. goeringii, including delaying the decline in the activities of antioxidant enzymes such as superoxide dismutase, peroxidase, and catalase. These results highlight the potential of these five endophytic fungi as effective agents for managing stem rot in C. goeringii. Full article

Hypersaline waters contaminated with crude oil represent a major obstacle for phytoremediation, as few plant species tolerate both high salinity and hydrocarbon toxicity. In this study, the halophyte Halocnemum strobilaceum (Pallas) M. Bieb. was grown hydroponically in hypersaline solutions (50 and 80 g L⁻¹ NaCl) containing crude oil (600 mg L⁻¹). The plant was inoculated with endophytic bacteria isolated in a previous step from its root and selected for salt tolerance and hydrocarbon-degrading potential. The plant behaviour was assessed through growth and photosynthetic performance, while the degradation of hydrocarbons (C < 12 and C > 12) was monitored over time. At 50 g L⁻¹ NaCl, crude oil reduced the plant growth by 60%, but inoculation with endophytic bacteria mitigated this decline, demonstrating their positive influence under combined salt and hydrocarbon stress. At 80 g L⁻¹ NaCl, neither plant biomass nor chlorophyll fluorescence was significantly affected by crude oil, with or without bacterial inoculation, consistent with the strong intrinsic salt tolerance of H. strobilaceum, which likely buffered additional stress inputs. Metagenomic analyses revealed distinct root-associated microbial communities under different treatments, suggesting synergistic plant–microbe interactions that enhanced photosynthetic efficiency and metabolic stability. The presence of endophytes accelerated the degradation of aliphatic hydrocarbons (C10–C40) at both salinity levels. These findings highlight the potential of endophytic bacteria to enhance resilience in H. strobilaceum and its phytoremediation capacity, offering a promising nature-based approach for the sustainable treatment of highly saline, crude oil-contaminated industrial waters. Full article

Lycium ruthenicum is a typical desert halophyte with strong stress resistance and high medicinal value in the Tarim Basin. Root endophytic microbes play critical roles in host adaptation, nutrient cycling, and secondary metabolite accumulation. To clarify the diversity patterns of root endophytic bacteria and fungi and their relationships with environmental factors and fruit quality, high-throughput sequencing was used to analyze microbial community characteristics of Lycium ruthenicum collected from different habitats in the Tarim Basin. The results showed that rarefaction curves of alpha diversity indices (Chao1, Shannon, Pielou_e) tended to be saturated, indicating sufficient sequencing depth. Principal coordinate analysis (PCoA) revealed significant habitat-driven differentiation in both bacterial and fungal community structures. Community composition analysis showed that the relative abundance of dominant taxa at the phylum and genus levels differed significantly among sampling sites. Co-occurrence network analysis indicated that bacterial and fungal networks exhibited high modularity and were dominated by positive synergistic interactions, with Pseudomonas, Bacillus, Sphingomonas, Alternaria, and Fusarium as key hub genera. Moreover, root endophytic communities were significantly correlated with climatic variables, soil physicochemical properties, and fruit quality traits, including anthocyanin (AC), proanthocyanidin (PA), total flavonoids (TF), and total polyphenols (TP). Several keystone microbial genera were closely associated with the accumulation of functional metabolites in fruits. This study reveals the biogeographic distribution and co-occurrence characteristics of root endophytes in Lycium ruthenicum and provides a theoretical basis for understanding microbe–host–environment interactions and the quality improvement of desert medicinal plants. Full article

Endophytes are a type of microorganism that lives in harmony with plants, playing a significant role in promoting the growth of the host and enhancing the host’s stress resistance. Understanding the ecological functions of root endophytic fungi and screening functional strains can effectively alleviate the stress conditions of crops. In this study, endophyte 1R13 was isolated from the roots of rice. Through morphological observation and five-gene combined phylogenetic analysis, it was identified as Bussabanomyces oryzae (B. oryzae), which was proposed as a new species, Bussabanomyces oryzae nov. The colonization pattern of B. oryzae was mainly through invasion of the rice roots, entering the epidermal cells and then the cortical cells, and finally reaching the vascular bundle cells. In the co-culture assays with rice, B. oryzae can promote the growth of rice, increasing its growth volume by approximately 23% and its fresh weight by 52%. Meanwhile, it could enhance the stress resistance of rice, mainly manifested as increasing the ability of rice leaves to resist rice blast and improving the survival rate of transplanted seedlings in the field. Full article

Brassicaceae plants are generally considered non-mycorrhizal; however, recent studies have challenged this non-host status, suggesting occasional colonization during reproductive stages or by overlooked fungi such as Mucoromycotina Fine Root Endophytes (MFRE). To re-evaluate the non-host status of Brassicaceae, we cultivated five Brassicaceae species, including rapid life cycle Brassica rapa (Fast plants) using field soil containing both Glomeromycotina Arbuscular Mycorrhizal Fungi (G-AMF) and MFRE. To ensure inoculum potential, a co-planting system with lettuce (Lactuca sativa) as a nurse plant was employed. While lettuce roots were rapidly colonized by both G-AMF and MFRE, no mycorrhizal colonization was observed in any Brassicaceae roots throughout their entire life cycle, from vegetative growth to flowering and seed maturation in Fast plants. Furthermore, co-planting with Brassicaceae did not significantly affect the mycorrhizal colonization or shoot phosphorus concentrations of the neighboring lettuce. These results demonstrate that Brassicaceae plants maintain a robust non-host status against both G-AMF and MFRE. Moreover, they function as “neutral non-hosts” that do not disrupt the symbiotic networks of neighboring plants. This characteristic reinforces the value of Brassicaceae in sustainable crop rotation systems. Full article

Saline–alkali stress is a severe abiotic factor that limits plant growth and development. Endophytic bacteria can improve plant tolerance to such stress through various mechanism, including osmoregulatory substance accumulation and antioxidant enzyme activity. In this study, four saline–alkali-tolerant endophytic strains, designated SYM-2, SYM-4, SYM-9, and SYM-15, were isolated from the roots of alfalfa grown in saline–alkali soil. Though 16S rDNA sequencing, morphological observations, and physiological–biochemical characterization, the strains were identified as closely related to Bacillus cereus, B. thuringiensis, B. halotolerans, and Pantoea agglomerans, respectively. These strains demonstrated the ability to produce 1-aminocyclopropane-1-carboxylate (ACC) deaminase, siderophores, and indole-3-acetic acid (IAA), as well as solubilizing phosphorus. Under saline–alkali conditions, inoculation with these strains significantly increased alfalfa growth parameters. Plant height increased by 4.07–33.90% and root length by 7.49–27.94%, and fresh and dry weight (both above and below ground) increased compared with the control. Strain SYM-15 showed the highest promoting effects, increasing plant height by 33.90%, root length by 27.94% and shoot dry weight by 59.26%. Additionally, root activity increased by 11.23–40%, proline content by 19.09–129–87%, and soluble protein by 7.71–42.49%, and the activities of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) were significantly elevated across treatments. At the same time, inoculation reduced the levels of hydrogen peroxide (H₂O₂), superoxide anion (O₂⁻), and malondialdehyde (MDA). Compared with the control and other treatments, including SYM-9, the peroxidase activity and superoxide dismutase activity of alfalfa significantly increased after the SYM-15 treatment, while hydrogen peroxide content, phosphorus content, and neutral detergent fiber and acid detergent fiber contents decreased (p < 0.05). Therefore, SYM-15 plays an important role in promoting growth and represents a promising, high-quality strain resource for the large-scale development of microbials aimed at improving alfalfa tolerance under saline–alkali conditions. Full article

This study demonstrates that the ericoid mycorrhizal (ERM) fungus RM2 can colonize the non-ericaceous host Malus robusta as a functional endophyte, enhancing drought resilience through an active avoidance strategy. Under drought, inoculation was associated with qualitative changes in root growth patterns, and inoculated seedlings showed a more extensive and branched root appearance compared with non-inoculated controls. This morphological tendency was accompanied by a distinctive physiological state of oxidative priming, characterized by elevated H₂O₂ as a signaling molecule, reduced antioxidant enzyme activity, and a marked shift toward proline-mediated osmotic adjustment. Transcriptomic analysis suggested a molecular basis for these responses: endophytic colonization reprogrammed auxin and brassinosteroid signaling, including the repression of auxin inactivation (GH3) and activation of genes involved in auxin transport (AUX1) and cell wall loosening (TCH4), which is consistent with sustained root growth under drought. Our findings indicate that ERM fungi can transcend traditional host barriers and improve drought performance via integrated oxidative signaling and hormonal regulation, highlighting their potential as cultivable biostimulants for sustainable horticulture. Full article

Armillaria solidipes, the causal agent of Armillaria root rot, poses a severe and persistent threat to poplar forest plantations. This study evaluated the biocontrol efficacy of the endophytic bacterium Bacillus velezensis BY6 against this pathogen and elucidated its multimodal mechanisms of action. BY6 application significantly reduced disease severity by 37.19% at 30 days post-treatment. 16S rRNA (V3–V4) microbiome analysis revealed that BY6 reshaped both the rhizosphere and phyllosphere bacterial communities, consistently enriching beneficial taxa, including Pantoea ananatis and members of Acidobacteria, while suppressing opportunistic groups. Concurrently, BY6 activated systemic defenses in poplar, evidenced by enhanced activities of key enzymes PAL and POD, and the upregulated expression of SA/JA pathway marker genes (PR1, JAZ, and COI1), coupled with the downregulation of the auxin transporter gene AUX1. These data indicate that the biocontrol efficacy of B. velezensis BY6 was mediated by a dual mechanism: the modulation of both rhizospheric and phyllospheric bacterial communities, direct elicitation of systemic defense pathways in poplar, which synergistically enhanced resistance against A. solidipes. Full article

Background: The adaptability of leguminous plant–rhizobia symbionts enables enhanced plant stress tolerance in environmentally stressed areas. However, how rock desertification (RD) severity affects the endophytic and nitrogen-fixing bacterial communities in Pisum sativum root nodules remains unclear. Methods: We systematically surveyed the microbial communities of P. sativum nodules across a gradient of four RD areas. We sequenced 16S rRNA and nifH amplicons, determined soil physicochemical properties, and performed bioinformatic analyses to relate nodule microbiome diversity to soil variables. Results: The dominant endophytic genera across all sites were Allorhizobium–Neorhizobium–Pararhizobium–Rhizobium and Pseudomonas, with Rhizobium identified as the primary nitrogen-fixing taxon. Soil pH and total phosphorus (TP) showed significant correlations with the overall endophytic bacterial community, whereas total nitrogen (TN), TP, and soil water content (SWC) were associated with nitrogen-fixing taxa. Notably, P. sativum nodules from areas of slight rocky desertification (SRD) harbored higher endophytic bacterial diversity and enhanced carbohydrate metabolism compared to those from moderately rocky desertified (MRD) sites. Conclusions: This study sheds light on how bacterial communities within legume root nodules respond to RD stress, deepening our understanding of plant–microbe co-adaptation and informing microbial-assisted restoration strategies in karst desertification areas. Full article

The plant holobiont comprises the host plant and its associated microbial communities functioning together as a single ecological and evolutionary unit that influences plant health, productivity, and environmental adaptability. Endophytes, formerly classified primarily as plant growth-promoting agents, are currently gaining traction as integral components of plant-associated microbiomes such as the rhizobiome and phytobiome. They can alter host-mediated root exudation patterns, microbial community structure, and nutrient dynamics within the rhizosphere. Endophytes play an important role in modulating host signaling pathways, thus influencing plant growth. Various mechanisms by which endophytes contribute to improved plant performance include soil microbiome dynamics, carbon sequestration, and strengthening the host’s ability to tolerate abiotic stressors. Multi-omics, single-cell, and systems-level approaches integrated with CRISPR, metabolic engineering, and AI, together with systems biology, guided by in vitro and field studies, support predictive modeling and provide evidence for the evolution of system-driven strategies for developing effective bioinoculants. This review highlights the potential of endophytes to serve as a scalable and sustainable component of climate-resilient and regenerative agricultural systems, while acknowledging ecological variability and field-level constraints. Full article

Disparities in root fungal endophyte (RFE) communities are well documented among plant species, yet differences among plant functional groups (PFGs) remain unclear. Given that RFE community structure is influenced by host plant abundance and species-specific root functional traits, and that PFGs exhibit divergent relative abundances and root traits, we hypothesize that PFGs harbor unique RFE communities, potentially aligned with their functional traits. We investigated RFE communities in 45 alpine meadow species representing four PFGs (grasses, legumes, dicot forbs, and monocot forbs), using high-throughput sequencing. Ascomycota dominated all groups (>50%) except monocot forbs (38.9%). Distinct differences in the RFE community species composition were found among PFGs. In particular, the differences were significant between dicot forbs and monocot forbs, and between monocot forbs and grasses, which contradicted with conventional PFG classification that combined monocot and dicot forbs as a single PFG. Moreover, marker operational taxonomic units (OTUs) with symbiotic lifestyles were more abundant in legumes, and their functional composition differed significantly from grasses. Roots’ nitrogen concentration was the strongest predictor of RFE variation, followed by root length, biomass, and species abundance. These results emphasize the importance of integrating microbial partners into understanding plants’ functional diversity and ecosystem resilience in alpine environments. Full article

Festulolium hybrids are cool-season forage grasses that form symbiotic relationships with the fungus Epichloë uncinata, which produces loline alkaloids that protect the host from herbivores. This study evaluated the nematotoxicity of shoot and root extracts of Festulolium loliaceum against the stubby root nematode Trichodorus primitivus. Methanolic root and shoot extracts from plants aged 8, 12, 16, and 20 weeks were tested in vitro at five concentrations (312.5–5000 µg mL⁻¹) over 24, 48, and 72 h. Nematode immobility, mortality, and phytochemical profiles, including flavonoids, loline alkaloids, and phenols, were quantified. Extracts from shoots caused significant concentration and time-dependent immobility of T. primitivus (p = 0.001), reaching ≥90% at 5000 µg mL⁻¹ after 72 h in 8–12-week-old plants. Endophyte presence enhanced nematotoxicity, where LD₅₀ values for E+ roots were two-fold lower at 12 weeks and fifty-fold lower at 20 weeks compared with E− root extracts. Shoot extracts of E+ grass had the highest nematicidal activity at 8 weeks, with a significantly lower LD₅₀ value than E− (p < 0.05). Loline alkaloid concentrations increased with plant age, while flavonoids and phenols declined. Nematotoxicity of F. loliaceum extracts was strongly influenced by plant age and endophyte presence. Younger E+ shoots produced the most potent shoot extracts, whereas older plants produced the most potent root extracts. Flavonoid content was negatively correlated with shoot biomass (R = −0.94, p < 0.001). Similarly, phenol content was negatively correlated to both root biomass (R = −0.79, p < 0.001) and shoot biomass (R = −0.67, p < 0.005). Full article

Climate change-induced drought threatens the persistence of Araucaria araucana, an endangered and endemic conifer of the Southern Andes. Beneficial plant–microbe interactions may contribute to drought resilience. Here, we evaluated the effects of a root-endophytic bacterium with the capacity to produce N-acyl homoserine lactones (AHLs) on the growth and drought tolerance of A. araucana. For this, a root endophytic bacterium was isolated from A. araucana and identified as Erwinia billingiae. It was characterized for plant growth-promoting traits, and inoculated into A. araucana seedlings under drought conditions). The bacteria produced N-butyryl-L-homoserine lactone (C4-HSL) under control conditions and C4-HSL and N-hexanoyl-L-homoserine lactone (C6-HSL) under drought stress. The strain also produces indoleacetic acid, ammonia, siderophores and solubilizes phosphate. Under drought stress, non-inoculated seedlings showed marked reductions in shoot and root biomass, chlorophyll content, relative water content (RWC), and soluble sugars. In contrast, inoculated seedlings under drought displayed significantly higher shoot and root biomass, reaching levels comparable to those of well-watered controls. Chlorophyll content increased from 5.42 to 9.35 mg L⁻¹, and RWC increased from 62% to 71% in inoculated plants under drought conditions. Soluble sugar content increased from 25.74 to 36.34 mg g⁻¹ fresh weight following inoculation. Drought-induced oxidative stress was significantly alleviated in inoculated seedlings, with lower malondialdehyde and proline accumulation compared to non-inoculated drought-stressed plants. Antioxidant responses were modulated, indicating improved redox balance under water limitation. These results demonstrate that a root-endophytic bacterium with AHL production can enhance drought tolerance in A. araucana seedlings. This study provides novel evidence supporting the role of beneficial endophytes in microbiome-based strategies for conserving native forest species under climate change. Full article

Drought stress is one of the most severe abiotic constraints limiting crop productivity worldwide, a challenge that is intensifying under ongoing climate change. In recent years, beneficial microorganisms have emerged as sustainable, nature-based tools to enhance plant drought tolerance and stabilize agricultural production under water-limited conditions. This review synthesizes current knowledge on the major groups of beneficial bacteria involved in drought stress mitigation, including plant growth-promoting rhizobacteria (PGPR), a functional subgroup of rhizosphere-associated microbes, endophytic bacteria, rhizosphere-associated microbes, and cyanobacteria, highlighting their primary physiological, biochemical, and soil-mediated mechanisms. These microorganisms enhance drought resilience through multiple complementary pathways, such as modulation of abscisic acid (ABA) and auxin (IAA) signaling, ACC deaminase activity, osmotic adjustment, antioxidant defense, improved nutrient acquisition, and enhancement of soil structure and water retention. The review further discusses practical application strategies, including seed inoculation, soil and root application, foliar spraying, the use of single strains versus microbial consortia, and advances in bioformulations and carrier materials that improve microbial survival and field efficacy. Emphasis is placed on recent experimental and field studies demonstrating the effectiveness of microbial inoculants under drought conditions. Collectively, the evidence highlights the potential of beneficial bacteria as key components of climate-resilient agriculture and underscores the need for integrated, formulation-driven approaches to translate laboratory success into consistent field performance. Full article