Search Results (90)

The rhizosphere microbiome plays an important role in carbon- and nitrogen-cycling in soil and in the stress response of plants. It also affects the function of the ammonium transporter (AmtB) that senses nitrogen levels inside and outside the cells of the associative nitrogen-fixing bacterium GXGL-4A. However, the potential mechanism of the interaction between the AmtB deletion mutant of GXGL-4A (∆amtB) and microorganisms in the rhizosphere of plants under low-nitrogen stress is still unclear. As revealed by transcriptome analyses, mutation of the amtB gene in GXGL-4A resulted in a significant up-regulation of many functional genes associated with nitrogen fixation and transportation at transcription level. The application of ∆amtB changed the nitrogen level in the rhizosphere of cucumber seedlings and reshaped the microbial community structure in the rhizosphere, enriching the relative abundance of Actinobacteriota and Gemmatimonadota. Based on bacterial functional prediction analyses, the metabolic capacities of rhizobacteria were improved after inoculation of cucumber seedlings with the original strain GXGL-4A or the ∆amtB mutant, resulting in the enhancement of amino acids, lipids, and carbohydrates in the cucumber rhizosphere, which promoted the growth of cucumber plants under a low-nitrogen stress condition. The results contribute to understanding the biological function of gene amtB, revealing the regulatory role of the strain GXGL-4A on cucumber rhizosphere nitrogen metabolism and laying a theoretical foundation for the development of efficient nitrogen-fixing bacterial agents for sustainable agricultural production. Full article

Heavy metal pollution represents a pervasive environmental challenge that significantly exacerbates the ever-increasing crisis of antimicrobial resistance and the capacity of microorganisms to endure and proliferate despite antibiotic interventions. This review examines the intricate relationship between heavy metals and AMR, with an emphasis on the underlying molecular mechanisms and ecological ramifications. Common environmental metals, including arsenic, mercury, cadmium, and lead, exert substantial selective pressures on microbial communities. These induce oxidative stress and DNA damage, potentially leading to mutations that enhance antibiotic resistance. Key microbial responses include the overexpression of efflux pumps that expel both metals and antibiotics, production of detoxifying enzymes, and formation of protective biofilms, all of which contribute to the emergence of multidrug-resistant strains. In the soil environment, particularly the rhizosphere, heavy metals disrupt plant–microbe interactions by inhibiting beneficial organisms, such as rhizobacteria, mycorrhizal fungi, and actinomycetes, thereby impairing nutrient cycling and plant health. Nonetheless, certain microbial consortia can tolerate and detoxify heavy metals through sequestration and biotransformation, rendering them valuable for bioremediation. Advances in biotechnology, including gene editing and the development of engineered metal-resistant microbes, offer promising solutions for mitigating the spread of metal-driven AMR and restoring ecological balance. By understanding the interplay between metal pollution and microbial resistance, we can more effectively devise strategies for environmental protection and public health. Full article

This study demonstrated that application of the particular plant growth-promoting rhizobacteria (PGPR) strains Erwinia sp. and Serratia sp. (named C15 and C20, respectively) significantly enhanced tea plant resilience in Zn (zinc)-, Pb (lead)-, and Zn + Pb-contaminated soils by the improving survival rates (over 60%) and chlorophyll content of tea plants, and by reducing the accumulation of these metals in tea plants’ tissues (by 19–37%). The PGPRs elevated key soil nutrients organic carbon (OC), total nitrogen (TH), hydrolysable nitrogen (HN), and available potassium (APO) and phosphorus (APH) contents. Compared to non-PGPR controls, both strains consistently increased microbial α-diversity (Chao1 index: +28–42% in Zn/Pb soils; Shannon index: +19–33%) across all contamination regimes. PCoA/UniFrac analyses confirmed distinct clustering of PGPR-treated communities, with strain-specific enrichment of metal-adapted taxa, including Pseudomonas (LDA = 6) and Bacillus (LDA = 4) under Zn stress; Rhodanobacter (LDA = 4) under Pb stress; and Lysobacter (LDA = 5) in Zn + Pb co-contamination. Fungal restructuring featured elevated Mortierella (LDA = 6) in Zn soils and stress-tolerant Ascomycota dominance in co-contaminated soils. Multivariate correlations revealed that the PGPR-produced auxin was positively correlated with soil carbon dynamics and Mortierellomycota abundance (r = 0.729), while the chlorophyll content in leaves was closely associated with Cyanobacteria and reduced by Pb accumulation. These findings highlighted that PGPR could mediate and improve in tea plant physiology, soil fertility, and stress-adapted microbiome recruitment under heavy metal contaminated soil and stress. Full article

Soil salinity adversely affects crop growth and development, leading to reduced soil fertility and agricultural productivity. The indigenous salt-tolerant plant growth-promoting rhizobacteria (PGPR), as a sustainable microbial resource, do not only promote growth and alleviate salt stress, but also improve the soil microecology of crops. The strain H5 isolated from saline-alkali soil in Bachu of Xinjiang was studied through whole-genome analysis, functional annotation, and plant growth-promoting, salt-tolerant trait gene analysis. Phylogenetic tree analysis and 16S rDNA sequencing confirmed its classification within the genus Halomonas. Functional annotation revealed that the H5 genome harbored multiple functional gene clusters associated with plant growth promotion and salt tolerance, which were critically involved in key biological processes such as bacterial survival, nutrient acquisition, environmental adaptation, and plant growth promotion. The pot experiment under moderate salt stress demonstrated that seed inoculation with Halomonas sp. H5 not only significantly improved the agronomic traits of tomato seedlings, but also increased plant antioxidant enzyme activities under salt stress. Additionally, soil analysis revealed H5 treatment significantly decreased the total salt (9.33%) and electrical conductivity (8.09%), while significantly improving organic matter content (11.19%) and total nitrogen content (10.81%), respectively (p < 0.05). Inoculation of strain H5 induced taxonomic and functional shifts in the rhizosphere microbial community, increasing the relative abundance of microorganisms associated with plant growth-promoting and carbon and nitrogen cycles, and reduced the relative abundance of the genera Alternaria (15.14%) and Fusarium (9.76%), which are closely related to tomato diseases (p < 0.05). Overall, this strain exhibits significant potential in alleviating abiotic stress, enhancing growth, improving disease resistance, and optimizing soil microecological conditions in tomato plants. These results provide a valuable microbial resource for saline soil remediation and utilization. Full article

Cadmium (Cd) is a highly toxic heavy metal that can greatly affect crops and pose a threat to food security. Plant growth-promoting rhizobacteria (PGPR) are capable of alleviating the harm of Cd to crops. In this research, a Cd-tolerant PGPR strain was isolated and screened from the root nodules of semi-wild soybeans. The strain was identified as Pseudomonas sp. strain KM25 by 16S rRNA. Strain KM25 has strong Cd tolerance and can produce indole-3-acetic acid (IAA) and siderophores, dissolve organic and inorganic phosphorus, and has 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. Under Cd stress, all growth indicators of soybean seedlings were significantly inhibited. After inoculation with strain KM25, the heavy metal stress of soybeans was effectively alleviated. Compared with the non-inoculated group, its shoot height, shoot and root dry weight, fresh weight, and chlorophyll content were significantly increased. Strain KM25 increased the superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities of soybean seedlings, reduced the malondialdehyde (MDA) content, increased the Cd content in the roots of soybeans, and decreased the Cd content in the shoot parts. In addition, inoculation treatment can affect the community structure of endophytic bacteria in the roots of soybeans under Cd stress, increasing the relative abundance of Proteobacteria, Bacteroidetes, Sphingomonas, Rhizobium, and Pseudomonas. This study demonstrates that strain KM25 is capable of significantly reducing the adverse effects of Cd on soybean plants while enhancing their growth. Full article

Sweet cherry (Prunus avium L.), as a high-economic-value fruit with both nutritional and health functions, faces severely constrained plant growth due to underdeveloped root systems and suboptimal orchard site conditions. Plant growth-promoting rhizobacteria (PGPR) demonstrate application potential in regulating plant development and improving soil structure through the release of volatile organic compounds (VOCs). This study systematically evaluated the effects of VOCs from three PGPR strains—Pantoea ananatis D1-28, Burkholderia sp. D4-24, and Burkholderia territorii D4-36—on cherry root development and rhizosphere microbial communities. The results indicate that when D1-28 and D4-24 strains were at 10³ cfu·mL⁻¹ and D4-36 was at 10⁵ CFU·mL⁻¹, their VOCs exhibited optimal growth-promoting effects. Compared with the control group, significant improvements were observed in cherry seedling parameters, including plant height, total biomass, root length, root surface area, and root volume. The VOCs from these strains synergistically promoted plant growth by regulating auxin synthesis pathways in cherry roots while enhancing the relative abundance of beneficial rhizosphere microorganisms. This study establishes the strain-concentration–effect relationship, providing a theoretical foundation to optimize soil microbial environments and promote cherry root development using PGPR. Full article

Blueberry growth is closely tied to its rhizosphere’s microbial communities. Recent advancements in high-throughput sequencing and multi-omics technologies have enhanced the investigation of variations in rhizosphere microbial communities and their functional roles across different plant cultivars. In this study, high-throughput sequencing was utilized to assess the rhizosphere microbial diversity in highbush and rabbiteye blueberry groups, encompassing a total of eight cultivars. Notable variations were observed in both bacterial and fungal community diversity. Ten bacterial phyla, each with a relative abundance greater than 1%, constituted 92.32–97.08% of the total abundance across the eight cultivars, with Acidobacteriota, Actinobacteriota, and Pseudomonadota being predominant. Similarly, five major fungal phyla, each exceeding 1% in relative abundance, accounted for 88.18–97.20% of the total abundance, with Ascomycota and Basidiomycota being the most dominant. The results showed that the rhizospheres of blueberries host a variety of plant growth-promoting rhizobacteria (PGPR), including genera such as Burkholderia, Enterobacter, Streptomyces, Arthrobacter, and Pseudomonas. Rabbiteye blueberry cultivars exhibit a greater propensity for accumulating beneficial symbiotic microorganisms compared to highbush cultivars. Notably, the relative abundance of ericoid mycorrhizal fungi, specifically Oidiodendron, is significantly elevated in the cultivars Emerald, Premier, O’Neal, and Brightwell, with the most pronounced increase observed in Emerald. Furthermore, rabbiteye blueberries support a more diverse and abundant array of cultivar-specific fungal communities than their highbush counterparts. Understanding the interaction networks between blueberries and their associated microbes can provide a theoretical foundation for the targeted regulation of rhizosphere microbiomes and offer valuable insights for the management of rhizospheres in other acidophilic crops. Full article

The co-fertilization of nitrogen (N) and zinc (Zn) offers significant advantages in improving the growth and development of tea plants (Camellia sinensis L). However, the corresponding responses of rhizosphere microecology remain unclear. In this study, a pot experiment was performed to investigate the effects of N-Zn co-fertilization on rhizosphere soil’s N availability, the rhizobacterial community and the metabolism of tea plants. N-Zn co-fertilization significantly increased the soil total of N, NH₄⁺-N and NO₃⁻-N contents. 16S rRNA sequencing found that N-Zn co-fertilization recruited rhizobacteria associated with N cycling and Zn activation, including Proteobacteria, Acidobacteriota and Gemmatimonadota, resulting in complex rhizobacterial networks. Metabolomics analysis indicated obvious interferences in the metabolisms of lipids, amino acids and cofactors and vitamins after fertilization. PLS-PM analysis suggested that fertilization had both direct and indirect influences on the rhizobacterial community and differential metabolites. RDA models identified pH (R² = 0.734, p < 0.01; R² = 0.808, p < 0.01) and total N (R² = 0.633, p < 0.05; R² = 0.608, p < 0.01) as dominant factors influencing both the rhizobacterial community and differential metabolites. Finally, network analysis found significant associations between rhizobacteria related to N cycling and Zn mobilization and metabolic processes involved in N metabolism and responses to Zn stress. These findings underscored that appropriate N-Zn co-fertilization is crucial for the rhizosphere soil’s N availability and the microenvironment of tea plants. Full article

Rice sustains a large global population, making its sustainable production vital for food security. Alternate wetting-and-drying (AWD) irrigation offers a promising approach to reducing water use in rice paddies but can impact grain yields. Plant growth-promoting rhizobacteria (PGPR) can enhance rice productivity under AWD cultivation conditions. This review explores integrating PGPR into AWD systems, focusing on their mechanisms for promoting growth and water stress resilience. It examines diverse microbial communities, particularly bacteria, and their contributions to nutrient acquisition, root development, and other beneficial processes in rice under fluctuating moisture, as well as the influence of AWD on rice’s structural and physiological development. The challenges and opportunities of AWD are also addressed, along with the importance of bacterial selection and interactions with the native soil microbiome. This synthesizes current research to provide an overview of PGPR’s potential to improve sustainable and productive rice cultivation under AWD. Future studies can leverage powerful tools such as e-DNA and NGS for a deeper understanding of these complex interactions. 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

Spent mushroom substrate (SMS) is the residual biomass generated after harvesting the fruitbodies of edible fungi. It is produced in large quantities and contains abundant nutrients. Plant growth-promoting rhizobacteria (PGPR) are a group of plant-associated microorganisms known for their ability to enhance plant growth, improve disease resistance, and boost soil quality. In this study, three PGPR strains with the highest plant growth-promoting potential were selected based on their ability to grow effectively in SMS extract. The SMS substrates were mixed with PGPR solutions and sterile water to establish a batch culture system. The mixture was initially incubated at 28 °C for 3 days, followed by continuous aerobic decomposition in a ventilated environment for 180 days. Based on the quality analysis of the PGPR-treated SMS, the 54-day treatment for transplanting blueberry seedlings was selected. The PGPR-treated substrates showed significantly higher TN, HN, and AP than controls (p < 0.05), suggesting a potential role of PGPR in enhancing nutrient availability. Alpha diversity index analysis revealed significant differences in microbial diversity between the PGPR-treated substrates and the control. Furthermore, the PGPR-treated substrates significantly influenced plant growth characteristics, soil nutrient content, and rhizosphere microbial diversity. Enhanced plant growth characteristics were strongly correlated with increased soil nutrient levels, suggesting a potential link between rhizospheric microbial communities and plant growth performance. This study provides a novel approach and experimental framework for the utilization of SMS and the development of PGPR-based biofertilizers, offering valuable insights into sustainable agricultural practices. Full article

Previous research on soil bacteria focused on refining the nitrogen (N) rates during the wheat (Triticum aestivum L.) growth cycle. Studies concerning how additional and split N topdressing applications can affect wheat rhizobacteria are limited. To address this, a two-year field experiment took the cultivar ‘Gaoyou 2018’ of winter wheat as the experimental material from October 2020 to June 2022. Six nitrogen application regimes were established, including no nitrogen application (T1), single topdressing applications of 120 kg ha⁻¹ (T2) and 80 kg ha⁻¹ (T3) at the jointing stage, and split topdressing applications combining 80 kg ha⁻¹ at jointing with 40 kg ha⁻¹ at the booting stage (T4), the flowering stage (T5), and 10th day post-anthesis (T6). The delayed impacts of the split topdressing time on the rhizobacteria diversity were observed in the second year, with T4 exhibiting a 10.5% higher Chao1 index and 2% greater Shannon diversity than T6. Results from both years indicated that the dominant bacterial phylum compositions in the winter wheat rhizosphere were similar across the nitrogen treatments. The additional N treatments fostered 22.9–27.9% Bacteroidita abundance but diminished 24.0–35.9% Planctomycetota, compared to the thenon-fertilized control (T1). T6 increased the α-Proteobacteria abundance by 15.7–22.0% versus T4, while the N topdressing redistribution to the booting stage increased the MND1 genus abundance in Proteobacteria by 31.3–62.5% compared to T2. Redundancy analysis identified that the rhizosphere pH and soil moisture content were the predominant environmental drivers shaping the winter wheat rhizobacteria. Preliminary findings revealed that split nitrogen application during the jointing and booting stages of winter wheat improved the edaphic micro-environment and modulated the proliferation of beneficial rhizobacteria. However, this change was not transmitted to the yield variation. These results suggest that short-term N management strategies may enhance ecological benefits by intensifying soil–plant–microbe interactions, yet they lack direct agronomic yield advantages. Long-term trials are required to establish causality between rhizosphere microbial community dynamics and crop productivity under split N management regimes. Full article

Water scarcity can negatively affect crop yield, posing a significant threat to global food security, such as drought. Plant growth-promoting rhizobacteria (PGPR), either as single strains or synthetic communities (SynComs), has shown promise in alleviating drought stress in various plant species. In this study, we examined the effects of water limitation on Salvia officinalis and the potential of a SynCom composed of five phosphate-solubilizing, auxin-producing, and/or nitrogen-fixing Gram-negative bacteria to enhance plant growth and drought tolerance. Plant growth, morphology, physiology, and leaf metabolomic profiles were assessed using a combination of physiological measurements and LC-MS untargeted metabolomics. Mild water stress induced a conservative water-use strategy in S. officinalis, characterized by increased root-to-shoot ratio and altered leaf morphology, without compromising photosynthetic performance. SynCom inoculation under well-watered conditions elicited drought-like responses, including transient reductions in stomatal conductance. Leaf metabolomic analysis revealed that inoculation influenced the abundance of several metabolites, including biogenic amines and dipeptides, under both irrigation regimes. Notably, drought stress and SynCom inoculation increased histamine and α-ketoglutaric acid levels, highlighting potential impacts on food quality. Under reduced irrigation, inoculation further modulated leaf morphology and biomass allocation, promoting thicker leaves and increased root biomass allocation. These results demonstrate the ability of the SynCom to modulate plant physiology and metabolism in response to both optimal and reduced irrigation, potentially enhancing drought resilience without directly improving growth. The study also highlights the complex interactions among microbial inoculation, plant stress responses, and leaf metabolite profiles, emphasizing the importance of considering the effects on the production of bioactive compounds when developing microbial inoculants for edible plants. Full article

The study of the metagenomes of bacterial communities in saline areas is relevant in connection with the global salinization of agricultural lands. The aim of this study was to investigate the biodiversity and structure of rhizobacterial communities associated with the halophyte S. marina from low and moderate sulfate–chloride salinity habitats. The bacterial community of bulk and rhizosphere soil was analyzed using high-throughput sequencing of the V1–V9 region of 16S rRNA by Oxford Nanopore Technologies. Alpha and beta diversity indices were calculated. A total of 55 phyla and 309 genera of bacteria were identified, among which Proteobacteria and Bacteroidetes dominated. The occurrence of Planctomycetes, Verrucomicrobia, and Acidobacteria in the rhizosphere was higher than in the bulk soil. Bacterial alpha diversity in the bulk soil decreased with increasing salinity, while it increased in the rhizosphere. The proportion of the halotolerant bacteria of Flavobacterium and Alteromonas genera significantly grew with increasing salinity both in the bulk and rhizosphere soil. In addition, in the rhizosphere, the percentage of Comamonas, Methylibium, Lysobacter, Planctomyces, Sphingomonas, Stenotrophomonas, and Lewinella genera increased. Among them, several genera included plant growth promoting rhizobacteria (PGPR). In the more saline bulk soil, the proportion of halotolerant genera Bacillus, Salinimicrobium, Marinobacter, Clostridium, Euzebya, KSA1, Marinobacter, Clostridium, Salinimicrobium, and Halorhodospira was also higher compared to the low saline site. Thus, increasing the salinity changed the taxonomic structure of the bacterial communities of both bulk soil and rhizosphere. Full article

Climate change has reshaped global weather patterns and intensified extreme events, with drought and soil salinity negatively impacting the yield and quality of crop production. To mitigate the detrimental effects of drought stress, the introduction of beneficial plant growth-promoting rhizobacteria (PGPR) has proven to be a promising approach. In this study, we evaluated a synthetic microbial community (SynCom) comprising bacterial strains belonging to the species Bacillus velezensis, Pseudomonas simiae, P. salmasensis, Glutamicibacter halophytocola, and Leclercia sp., which have been demonstrated to promote tomato growth both individually and collectively. The SynCom and most of its individual bacterial strains were shown to mitigate the detrimental effects of polyethylene glycol (PEG)-induced drought stress in vitro in Arabidopsis thaliana seedlings, either by reducing alterations in xylem elements or promoting the formation of new xylem strands. In a greenhouse trial, soil drenching with the SynCom and two individual strains, B. velezensis PSE31B and P. salmasensis POE54, improved the water stress response in soilless-grown tomato plants under a 40% reduced irrigation regime. Additionally, bacterial treatments positively influenced the diversity of rhizosphere bacterial communities, with distinct changes in bacterial composition, which suggest a treatment-specific interplay between the introduced strains and the native microbiome. These findings highlight the potential of microbial consortia and individual PGPR strains as sustainable tools to improve plant resilience to abiotic stresses. Full article