Search Results (463)

The root system of rice (Oryza sativa L.) is a central determinant of stress resilience and yield, functioning in resource acquisition, anchorage, and environmental sensing. This review synthesizes recent advances in understanding how the gaseous hormone ethylene acts as a master regulator to sculpt root system architecture by spatiotemporally integrating developmental cues and stress signals. We detail the core molecular machinery of ethylene in rice, encompassing its biosynthesis, perception, and signal transduction pathways. Ethylene modulates root development through intricate crosstalk with auxin, abscisic acid, and jasmonic acid, inhibiting primary root elongation while promoting lateral root initiation, adventitious rooting, root hair development, and aerenchyma formation. The review further dissects the context-dependent role of ethylene signaling in mediating adaptive responses to key abiotic stresses, including drought, hypoxia, salinity, and heavy metal stress. It also examines how ethylene influences root-microbe interactions, shaping the rhizosphere microbiome. Finally, we discuss root trait optimization strategies that leverage the ethylene signaling network, providing a mechanistic foundation for breeding next-generation rice varieties with enhanced stress tolerance and resource-use efficiency. Full article

This study aims to reveal the rhizosphere bacteriome patterns, biomarkers, and metabolic functions of dominant plants in the water-level fluctuation zone (WLFZ) of the Three Gorges Reservoir through comparative analyses with the non-rhizosphere bacteriome. The present study showed that a total of 4546–5011 amplicon sequence variants (ASVs) were identified in both rhizosphere and non-rhizosphere soils of Artemisia annua L. and Persicaria lapathifolia (L.) Delarbre. Pseudomonadota and Acidobacteriota were the most abundant bacterial phyla in both rhizosphere and non-rhizosphere bacteriomes. The α-diversity indices of microbial communities in the non-rhizosphere soils were lower than those in the rhizosphere soils associated with the two dominant plant species. Distinctive key biomarkers were successfully identified for both rhizosphere and non-rhizosphere bacterial assemblages, and these biomarkers exhibited a strong plant-specific pattern. Functional annotation revealed that metabolic processes, genetic information processing, and two core functional traits (chemoheterotrophy and aerobic chemoheterotrophy) accounted for the highest relative abundance within the bacteriomes. However, notable discrepancies were observed in the subdominant functional traits between the rhizosphere and non-rhizosphere bacteriomes. Overall, the present study brings novel insight into the plant-microbe interactions in the WLFZ of large reservoirs under the extreme environmental conditions. Full article

Nanofertilizers have attracted increasing attention as an approach to improve the low nutrient use efficiency of conventional fertilizers, in which only a limited fraction of applied nitrogen, phosphorus, and potassium is ultimately taken up by crops. Beyond their capacity to minimize nutrient losses, nanofertilizers have attracted increasing attention for their possible role in addressing environmental issues, including soil eutrophication and the contamination of groundwater systems. Owing to their nanoscale characteristics, including large specific surface area and enhanced adsorption capacity, these materials enable more precise nutrient delivery to the rhizosphere and sustained release over extended periods, while also influencing soil–plant–microbe interactions. In this review, nanofertilizers are classified into six major categories—macronutrient-based, micronutrient-based, organic, controlled-release, composite, and nano-enhanced formulations—and representative examples and preparation routes are summarized, including green synthesis approaches and conventional chemical methods. The agronomic mechanisms associated with nanofertilizer application are discussed, with emphasis on enhanced nutrient uptake, modification of soil physicochemical properties, and shifts in microbial community composition. Reported studies indicate that nanofertilizers can increase crop yield across different crop species and formulations, while also contributing to improved nutrient cycling. Despite these advantages, several limitations continue to restrict their broader adoption. These include uncertainties regarding long-term environmental behavior, relatively high production costs compared with conventional fertilizers, and the absence of well-defined regulatory and safety assessment frameworks in many regions. Overall, this review highlights both the opportunities and challenges associated with nanofertilizer application and points to the need for further development of cost-effective formulations and standardized evaluation systems that account for their distinct environmental interactions. Full article

Tea cultivar genotype plays a critical role in shaping rhizosphere microbiome assembly, yet the underlying mechanisms remain poorly understood. This study employed a controlled pot experiment with five widely cultivated Chinese tea cultivars (Camellia sinensis) to investigate how cultivar-specific variation influences rhizosphere microbial communities and their assembly processes. Rhizosphere soil microbiomes (bacterial and fungal communities) and metabolomes were characterized using 16S rRNA and ITS2 amplicon sequencing combined with untargeted metabolomics. Significant differences in rhizosphere metabolite composition, primarily organic acids, fatty acids, and carbohydrates, were observed among cultivars, which corresponded to distinct bacterial and fungal community structures. Redundancy analysis (RDA) revealed that rhizosphere metabolites explained 19.87% of bacterial and 21.63% of fungal community compositional variation, second only to soil physicochemical properties. Neutral community model and modified stochasticity ratio analyses indicated that microbial assembly across cultivars was predominantly deterministic, and rhizosphere metabolite profiles were strongly correlated with microbial community structure. Notably, arbuscular mycorrhizal fungi made up about 11% of the fungal communities in minimally fertilized pot systems, contrasting sharply with their near-absence in conventionally managed systems plantations. These findings demonstrate that tea cultivar genotype significantly shapes rhizosphere microbiome assembly through metabolic differentiation, providing a theoretical foundation for integrating microbiome considerations into tea breeding programs and developing cultivar-specific management strategies. Full article

Soybean (Glycine max) is a globally important crop, as it has high protein and lipid content and plays a central role in sustainable agriculture. Recent advances in rhizosphere biology have highlighted the critical role of soybean root exudates, particularly isoflavones and other secondary metabolites, in shaping microbial community structure and function. These exudates mediate complex, bidirectional signalling with rhizosphere microorganisms, influencing nutrient acquisition, stress resilience, and disease suppression. This review describes current knowledge on soybean–microbe interactions, with a focus on the emerging concept of the rhizosphere as a dynamic communication network. Particular attention is given to Bacillus velezensis S141, a plant growth-promoting rhizobacterium (PGPR) with distinctive traits, including β-glucosidase-mediated isoflavone hydrolysis, phytohormone production, and drought resilience. Coinoculation studies with Bradyrhizobium spp. demonstrate enhanced nodulation, nitrogen fixation, and yield, supported by transcriptomic and ultrastructural evidence. Comparative genomic analyses further underscore host-adaptive features of S141, distinguishing it from other Bacillus strains. Despite promising findings, mechanistic gaps remain regarding metabolite-mediated signalling and environmental robustness. Future research integrating metabolomics, synthetic ecology, and microbial consortia design will be essential to harness rhizosphere signalling for climate-resilient, low-input soybean cultivation. Full article

The integration of oil-degrading microorganisms with phytoremediation has the potential to generate a synergistic effect in the removal of petroleum pollutants. This study analyzed the influence of two aquatic plant species (Eichhornia crassipes and Pistia stratiotes) and hydrocarbon-oxidizing bacterial strains (Rhodococcus erythropolis and Pseudomonas brenneri), as well as a microbial preparation, on the formation of bacterial consortia under oil-polluted conditions. The study assessed the losses of petroleum alkanes, the rheological properties of water, and the structure of emerging rhizospheric microbial communities by high-throughput sequencing. E. crassipes demonstrated a higher potential for stimulating the development of an oil-oxidizing microbial community. However, the introduced bacterial strains did not establish themselves within the formed microbial community, indicating the complexity of selecting compatible plant–microbe combinations for efficient bioremediation. Nevertheless, this approach remains a promising direction for enhancing the efficiency of hydrocarbon degradation in aquatic ecosystems. Full article

Drought stress is a major abiotic factor limiting global crop productivity by disrupting cellular homeostasis, impairing photosynthesis, and restricting metabolic activity. Plant-associated microorganisms, including rhizobacteria, endophytes, and arbuscular mycorrhizal fungi, play key roles in enhancing drought resilience through molecular, biochemical, and physiological mechanisms. These beneficial microbes modulate phytohormone biosynthesis, enhance osmolyte accumulation, increase organic acid exudation, and activate ROS-scavenging antioxidant pathways. Microbe-mediated regulation of aquaporins, heat shock proteins, and root system architecture further improves water-use efficiency, hydraulic conductance, and stress acclimation. Advances in microbial genomics and systems biology have revealed the molecular drivers of plant–microbe synergism, enabling the development of tailored microbial consortia and next-generation bioinoculants. Complementarily, genetic and genome-guided modulation of drought-responsive regulatory hubs including transcription factors (e.g., DREBs, NACs, MYBs, and bZIPs), signal transducers (e.g., MAPKs and CDPKs), and protective proteins enhances adaptive plasticity under water deficit conditions. This review integrates current molecular insights into drought-induced perturbations in plants and highlights the convergence of microbial interventions and genome-guided strategies in reinforcing drought tolerance. Emphasizing mechanistic frameworks, scalable microbial technologies, and molecular breeding approaches, this work underscores their potential to improve crop resilience in increasingly water-limited environments. Full article

Drip irrigation burial depth is a critical management factor for saline-alkali agriculture, yet its mechanisms of influencing crop productivity through soil–microbe–plant interactions remain poorly understood. To explore the regulatory effects of drip irrigation burial depth on the growth and rhizosphere microenvironment of dryland wheat in saline-alkali soil, three treatments (no irrigation control, CK; 5 cm shallow-buried drip irrigation, T5; 25 cm deep-buried drip irrigation, T25) were set up, with soil physicochemical properties, microbial community characteristics, and crop yield analyzed. The results showed that drip irrigation significantly improved soil environment and yield, and T25 exhibited superior comprehensive benefits: soil electrical conductivity was reduced by 63%, organic matter content increased by 44%, and water-salt status was significantly optimized; meanwhile, microbial community structure was altered and root nutrient uptake capacity was enhanced, ultimately achieving a yield of 5347.1 kg ha⁻¹, 55.0% higher than CK. In conclusion, 25 cm deep-buried drip irrigation may provide advantages for wheat cultivation primarily through improved water distribution, desalination, and soil structure enhancement. Full article

Plant biostimulatory effects of the green alga Chlorella sp. MACC-360, the Kocuria rhizophila FSP120 bacterial strain, and the combined inter-kingdom co-culture of the alga and bacterium were investigated using Solanum lycopersicum as a model plant grown under controlled greenhouse conditions. The application of algal–bacterial co-cultures using the soil drench method significantly improved plant growth parameters, vegetative biomass yield, fruit yield, and photosynthetic performance of the tomato plants. The combined treatment resulted in a 43.7% increase in mean fruit yield, while individual applications of K. rhizophila FSP120 and Chlorella sp. MACC-360 enhanced yields by 30.85% and 19.44%, respectively. Although total yield increases did not reach statistical significance due to high intra-group variability, the treatment’s efficacy was statistically confirmed through key yield parameters including significantly higher fruit weight and fruit diameter (p < 0.05). The enhanced specific biostimulatory effects of the combined treatment could be at least partly attributed to the increased level of algal extracellular polymeric substances (EPS), which was a specific effect of algal co-cultivation with a Kocuria rhizophila bacterium. Detailed analysis of plant phenotypic alterations, biomass yield, fruit and flowering parameters, as well as microbial community analysis of the rhizosphere, were conducted and compared among the various treatments. Our results indicate that an appropriately chosen combination and application of biostimulatory microbes can significantly enhance crop production, which might contribute to more sustainable agriculture. Full article

Root exudates are key mediators of plant–soil–microbe interactions, shaping rhizosphere dynamics and influencing agroecosystem resilience. Comprising diverse primary and secondary metabolites, these compounds are actively secreted through specific transport pathways and are modulated by intrinsic plant traits and environmental conditions. Root exudates serve as chemical signals that recruit and structure microbial communities, facilitating nutrient mobilization, microbial feedbacks, and the regulation of plant growth and stress responses. By modulating soil chemical, physical, and biological properties, exudates contribute to carbon cycling, soil health, and the maintenance of ecosystem services. Moreover, they play multifunctional roles in enhancing plant tolerance to abiotic and biotic stresses, while also mediating interactions with neighboring plants. This review provides a holistic perspective on root exudation, encompassing their mechanisms and drivers, roles in rhizosphere ecology and plant stress adaptation, and methodological advances, while highlighting opportunities to harness these processes for resilient, productive, and sustainable agroecosystems. Full article

(1) Background: Improving nitrogen use efficiency in peanuts is essential for achieving a high yield with reduced nitrogen fertilizer input. This study investigates the role of the fungal endophyte Phomopsis liquidambaris in regulating nitrogen utilization throughout the entire growth cycle of peanuts. (2) Methods: Field pot experiments and a two-year plot trial were conducted. The effects of Ph. liquidambaris colonization on the rhizosphere microbial community, soil nitrogen forms, and peanut physiology were analyzed. (3) Results: Colonization by Ph. liquidambaris significantly suppressed the abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the rhizosphere at the seedling stage. This led to a transient decrease in nitrate and an increase in ammonium availability, which enhanced nodulation-related physiological responses. Concurrently, the peanut-specific rhizobium Bradyrhizobium sp. was enriched in the rhizosphere, and the root exudates induced by the fungus further stimulated nodulation activity. These early-stage effects promoted the establishment of peanut–Bradyrhizobium symbiosis. During the mid-to-late growth stages, the fungus positively reshaped the composition of key functional microbial groups (including diazotrophs, AOA, and AOB), thereby increasing rhizosphere nitrogen availability. (4) Conclusions: Under low nitrogen fertilization, inoculation with Ph. liquidambaris maintained yield stability in long-term monocropped peanuts by enhancing early nodulation and late-stage rhizosphere nitrogen availability. This study provides a promising microbe-based strategy to support sustainable legume production with reduced nitrogen fertilizer application. Full article

To elucidate the potential of integrated multi-omics approaches for studying systemic mechanisms of mycorrhizal fungi in mediating plant-microbe interactions, this study employed the Tuber-inoculated Corylus system as a model to demonstrate how high-throughput profiling can investigate how fungal inoculation reshapes the rhizosphere microbial community and correlates with host metabolism. A pot experiment was conducted comparing inoculated (CTG) and non-inoculated (CK) plants, followed by integrated multi-omics analysis involving high-throughput sequencing (16S/ITS), functional prediction (PICRUSt2/FUNGuild), and metabolomics (UPLC-MS/MS). The results demonstrated that inoculation significantly restructured the fungal community, establishing Tuber as a dominant symbiotic guild and effectively suppressing pathogenic fungi. Although bacterial alpha diversity remained stable, the functional profile shifted markedly toward symbiotic support, including antibiotic biosynthesis and environmental adaptation. Concurrently, root metabolic reprogramming occurred, characterized by upregulation of strigolactones and downregulation of gibberellin A5, suggesting a potential “symbiosis-priority” strategy wherein carbon allocation shifted from structural growth to energy storage, and plant defense transitioned from broad-spectrum resistance to targeted regulation. Multi-omics correlation analysis further revealed notable associations between microbial communities and root metabolites, proposing a model in which Tuber acts as a core regulator that collaborates with the host to assemble a complementary micro-ecosystem. In summary, the integrated approach successfully captured multi-level changes, suggesting that Tuber-Corylus symbiosis constitutes a fungus-driven process that transforms the rhizosphere from a competitive state into a mutualistic state, thereby illustrating the role of mycorrhizal fungi as “ecosystem engineers” and providing a methodological framework for green agriculture research. Full article

Bacterial communities in the rhizosphere and endorhizosphere of plants show distinct composition, function, and ecological roles during adaptation to diverse habitats. This study examines how rhizosphere and endophytic microbes associated with Aeluropus sinensis—a salt-excreting halophyte—contribute to its salt tolerance across saline-alkali environments. Microbial diversity and composition were analyzed via 16S rRNA gene amplicon sequencing. Soil physicochemical properties were measured to evaluate environmental effects. Linear regression assessed microbial–environment relationships, and co-occurrence networks identified key taxa and their adaptive strategies along environmental gradients. Soil salinity significantly affected rhizosphere bacterial diversity, with moderate levels increasing richness. Proteobacteria dominated both root and rhizosphere microbiomes across habitats. The endorhizosphere community strongly correlated with soil nutrients such as available phosphorus (AP) and total nitrogen (TN). Co-occurrence analysis reveals that chemoheterotrophic microbes in the A. sinensis rhizosphere employ distinct adaptive strategies across gradients, and ammonia-oxidizing bacteria (AOB) may support nitrogen cycling in the Yellow River Delta saline–alkaline ecosystem. This study underscores microbial adaptability in salt-tolerant grasses, demonstrating that comparing rhizosphere and endorhizosphere microbiomes in Poaceae under stress improves understanding of microbial functions in harsh environments. Full article

Domestication reduced the genetic diversity in modern crops, often resulting in reduced resilience to biotic and abiotic stress. Evidence is now accumulating that domestication also altered the structure and function of root-associated microbiomes, creating new opportunities to harness beneficial microbes for breeding and crop improvement. Using multi-region 16S rRNA sequencing, we compared the rhizosphere and endosphere bacterial communities of cultivated tomato (Solanum lycopersicum cv. Moneymaker) with six wild relatives (S. pimpinellifolium, S. huaylasense, S. peruvianum, S. chilense, S. habrochaites, and S. pennellii) spanning the main wild lineages within Solanum sect. Lycopersicon. Bacterial community structure in the rhizosphere was broadly conserved across all seven hosts, and diversity remained comparable among genotypes. Despite this overall stability, the rhizosphere microbiomes were ordered along a gradient consistent with host phylogeny, with Moneymaker clustering near S. pimpinellifolium, the four green-fruited Eriopersicon species forming a cohesive block, and S. pennellii occupying the most distinct position. Within this hierarchy, individual hosts showed specific recruitment preferences, including enrichment of Streptomycetaceae in S. pimpinellifolium, Bacillaceae in S. chilense, and contrasting patterns of nitrifiers among Eriopersicon species and S. pennellii. Differential abundance testing in the endosphere revealed consistent reductions in several bacterial families in wild accessions, alongside the enrichment of Streptomycetaceae and Rhodobiaceae in multiple wild species. Overall, our study suggests that domestication exerted a modest effect on tomato root microbiomes, while wild relatives retained microbial association traits that could be harnessed in microbiome-informed breeding to improve resilience in cultivated tomato. Full article

Biostimulants boost plant growth, productivity, and nutrient retention, and can be produced from agri-food waste via microbial fermentation. In this study, undersized and unsold kiwifruits were fermented with Lactiplantibacillus plantarum to produce a fermented kiwifruit-based biostimulant (FKB). FKB was applied to soilless tomato plants (cv. Solarino) at two concentrations (50 and 100 mL L⁻¹) at the root level, every two weeks throughout the crop cycle. Fruits were analyzed for technological and chemical parameters, including color, texture, total soluble solids, titratable acidity, sugar/acid ratio, pH, electrical conductivity, total polyphenol content, antioxidant activity, and lycopene concentration. Additionally, metataxonomic analysis characterized the substrate microbial community at the beginning and the end of cultivation. Overall, the results indicate a dose-dependent effect of FKB on fruit quality parameters, with the highest concentration showing the most pronounced effects, specifically for the fruit firmness (8.02 N for FKB at 100 mL L⁻¹ vs. 7.25 N for the Control). Moreover, both tested concentrations were associated with increased antioxidant activity (on average +28%), and lycopene content (on average +57%) compared with the Control fruits. While overall microbial diversity remained largely unchanged, the relative abundance of bacterial taxa associated with nutrient cycling and plant–microbe interactions was modulated by the biostimulant, indicating subtle but potentially functionally relevant shifts in the rhizosphere microbiota. These findings suggest that fermented kiwifruit biomass can serve as an effective biostimulant, improving both fruit quality and the functional structure of the rhizosphere microbial community in soilless tomato cultivation. Full article