Search Results (311)

Understanding the interaction between plants and rhizosphere microorganisms is critical for the development of biofertilizers. Fluorescent labeling of rhizosphere microorganisms serves as a key strategy to track their behavior during plant–microbe coculture. However, most newly isolated strains are novel and lack available molecular tools for such studies. In this research, Planococcus dechangensis NEAU-ST10-9^T (P. dechangensis NEAU-ST10-9^T), a salt-tolerant strain, was obtained from the China General Microbiological Culture Collection Center (CGMCC). It significantly increased maize root length by approximately 1.56-fold. To investigate the underlying mechanism, a donor strain (Ec102) and a shuttle plasmid (pAS104) were engineered to mediate conjugation with P. dechangensis NEAU-ST10-9^T and drive GFP overexpression in the bacterium, generating the genetically labeled strain Pd103. The fluorescence intensity (expressed as GFP/OD₆₀₀, arbitrary units) of Pd103 increased with bacterial growth and was approximately tenfold higher than that of the wild-type strain after 16 h of culture. Following inoculation onto maize seeds, confocal microscopy analysis revealed that Pd103 colonized the epidermis and endodermis of maize roots. These results indicated that P. dechangensis NEAU-ST10-9^T could invade maize roots and promote maize seedling growth. In summary, we have successfully established a robust fluorescence labeling and tracking system tailored for P. dechangensis NEAU-ST10-9^T, which constitutes a valuable tool for elucidating the cellular and molecular mechanisms governing its plant–microbe interaction. Full article

Rhizosphere microbiome engineering is a promising approach that can enhance crop resilience and input use efficiency by redirecting plant–microbe–soil interactions toward predictable functions. Here, we review the mechanistic bases underlying rhizosphere assembly and stability, including root exudate-mediated selection, priority effects, keystone taxa, and metabolite-driven signaling, and connect these principles to proposed design rules for microbial inoculants. We present a generalizable Design–Build–Test–Learn (DBTL) framework for engineering synthetic microbial consortia, covering trait-to-module mapping (nutrient acquisition, phytohormone modulation, ACC deaminase activity, stress-protective metabolites, and biocontrol), compatibility screening, minimal yet robust community architectures, and iterative optimization driven by multi-omics and high-throughput phenotyping. Translation to field settings is framed as an engineering challenge defined by formulation and administration limitations, including carrier type, seed coating and encapsulation methods, shelf life, strain invasiveness, and permanence of colonization amid environmental diversity. We also summarize how integrative measurement pipelines (amplicon and shotgun sequencing, transcriptomics, metabolomics, and network or causal analyses) can advance microbiome studies from correlation to actionability. We describe how precision agriculture (sensors, remote sensing, and variable-rate inputs) and AI/ML (split-sample comparisons, transfer learning, and active learning) approaches can accelerate strain discovery, mixture optimization, and adaptive experimentation, driven by the need for stringent controls, metadata-rich reporting, and cross-site comparability. Use cases focus on stress conditions (drought, salinity, thermal extremes, and biotic stress) to demonstrate how microbial functions translate to agronomic outcomes and to highlight critical bottlenecks for reproducible, scalable microbiome products. Full article

Short-rotation sugar beet (Beta vulgaris L.) cultivation in the Western Forest-Steppe of Ukraine is often accompanied by increased phytopathogenic pressure and impaired rhizosphere functioning, creating a need for biological tools to stabilize the plant–soil system. This study evaluated the effects of arbuscular mycorrhiza and an antagonistic microbial consortium on pathogen pressure, rhizosphere activity, yield, and technological quality of sugar beet under different crop rotations. Field experiments were conducted in 2023–2025 using a three-factor design that included rotation, mycorrhizal inoculation, and microbial inoculation. The highest phytopathogenic pressure was recorded in the maize–soybean–sugar beet rotation, where the cumulative frequency of dominant pathogens reached 94.0% and the root rot severity index in the control was 28.6%. Arbuscular mycorrhiza reduced disease development by 14.6–16.4%, whereas the antagonistic consortium reduced it by 25.6–27.9% relative to the control. Their combined application was most effective, decreasing root rot severity to 9.6–17.1% and increasing root colonization, available phosphorus, and dehydrogenase activity in the rhizosphere. The highest yield (80.5 t/ha) and sugar content (18.5%) were obtained in the soybean–winter wheat–sugar beet rotation under combined inoculation. AMF can improve phosphorus acquisition and mycorrhiza-induced tolerance, whereas antagonistic fungi can directly suppress soil-borne pathogens through competition, antibiosis, and mycoparasitism, their combined use may provide complementary protection in disease-conducive rotations. Overall, integrating arbuscular mycorrhiza with antagonistic microorganisms is a promising approach for reducing pathogen pressure and improving sugar beet performance in short-rotation systems. Full article

Haloxylon ammodendron is a keystone shrub widely used for ecological restoration in arid regions of Northwest China. However, how rhizosphere bacterial communities reorganize across stand ages remains poorly understood. Rhizosphere soils were collected from one-, three-, and six-year-old stands using full-length 16S rRNA sequencing. Although alpha diversity remained relatively stable, beta diversity revealed pronounced community turnover. The dominant phyla were conserved across stands, whereas genus- and species-level composition shifted systematically along the age gradient. Younger stands were enriched in stress-tolerant and early colonizing taxa, intermediate stands showed increased representation of plant-associated and nitrogen-cycling bacteria, and older stands harbored taxa associated with complex carbon turnover and stress adaptation. Network analysis suggested modular co-occurrence patterns across stand ages and PICRUSt2-based functional inference indicated a conserved core metabolic repertoire accompanied by gradual ecological differentiation in pathways related to resource utilization and environmental response. Together, these findings suggest a stand age–associated pattern of rhizosphere bacterial succession and provide insight into microbial community differentiation in a desert shrub system. Full article

Native soils host diverse symbiotic microflora that contribute to sustainable agricultural practices and plant establishment. This study aims to investigate the benefits of rhizosphere soil microbiota associated with four Mediterranean native plants, Rhus pentaphylla (NS1), Drimia maritima (NS2), Pistacia lentiscus (NS3), and Withania frutescens (NS4), growing in proximity to the local Moroccan almond variety Prunus dulcis (Mill.) (NS5). Native soils were applied directly as living substrates to evaluate their effects on the germination and early development of almond, with particular emphasis on the potential of arbuscular mycorrhizal fungi (AMFs). Root analysis revealed high mycorrhizal colonization intensity (M% = 87.5–95%) and infectivity (F% = 100%). Under the tested soil conditions, three native soils (NS1, NS3, and NS5) achieved germination rates exceeding 70% after 28 days. Moreover, NS5 and NS1 soils showed the strongest effects on almond germination and seedling growth, respectively. Overall, the use of native soils enhanced almond germination and early development, highlighting the role of AMFs as natural biofertilizers. The associated native plant species may also function as nurse plants that facilitate almond establishment. These findings support the use of the rhizosphere microbiome as a bio-based strategy to promote sustainable almond cultivation in local and Mediterranean agroecosystems. Full article

Integrating biochar with plant growth-promoting rhizobacteria (PGPR) is a promising strategy for sustainable soil management; however, the synergistic mechanisms governing rhizosphere microbial assembly remain inadequately understood. In this study, we investigated the combined effects of maize biochar (YM) and Bacillus amyloliquefaciens (BA) on tomato performance, soil physicochemical properties, and bacterial community dynamics via a controlled pot experiment. The results demonstrated that the synergistic treatment (YMBA) significantly enhanced tomato yield by 18.3% compared to the control, outperforming individual applications. This promotion was coupled with a comprehensive improvement in soil fertility, characterized by significant increases in soil organic matter (SOM), available nutrients (N, P, and K), and the activities of urease and acid phosphatase. High-throughput sequencing revealed that YMBA treatment significantly restructured the rhizosphere bacterial community, significantly increasing microbial richness and diversity. Notably, the synergistic application promoted the recruitment of beneficial taxa, particularly within the phylum Pseudomonadota. Mantel test analysis further elucidated that SOM and available phosphorus (AP) were the primary environmental drivers shaping the bacterial community turnover. Our findings suggest that biochar acts as a functional niche that facilitates B. amyloliquefaciens colonization and modulates the indigenous microbiota, providing a theoretical framework for utilizing cross-trophic synergies to optimize crop productivity and soil health. Full article

Subterranean termites, particularly Odontotermes obesus, cause severe damage to forest nurseries and plantations in arid and semi-arid ecosystems. This study demonstrates the dual functional role of endophytic entomopathogenic fungi, Metarhizium anisopliae and Beauveria bassiana, in termite suppression and induction of plant defense responses. Laboratory bioassays revealed significantly higher virulence of M. anisopliae, with a lower LT₅₀ (lethal time required to cause 50% mortality) of 33.1 h compared to B. bassiana (46.7 h), a steeper probit slope (5.4 ± 0.3), and strong model fit (R² = 0.95), indicating rapid and synchronized mortality. Endophytic colonization varied across host species and application methods, with soil incorporation consistently outperforming foliar inoculation. Maximum colonization (82.5%) was recorded in Tecomella undulata and exceeded 80% in Azadirachta indica under M. anisopliae. Biochemical analyses revealed significant increases in protein (up to 3.5 mg g⁻¹), phenols (3.7 mg g⁻¹), and tannins (2.7 mg g⁻¹). Activity of defense enzymes was significantly enhanced, with catalase reaching 263.5 U mL⁻¹, while Phenylalanine ammonia-lyase and Tyrosine ammonia-lyase exceeded 170 and 198 U mL⁻¹, respectively, indicating activation of antioxidant and phenylpropanoid pathways. Molecular docking analysis further revealed strong interactions between fungal metabolites and termite cellulase, with Bassianin (−8.4 kcal mol⁻¹) and Tenellin (−8.1 kcal mol⁻¹) showing the highest binding affinities. These findings highlight the combined biochemical and molecular mechanisms underlying fungal-mediated termite suppression and plant defense induction, and future research should prioritize transcriptomic validation, rhizosphere microbiome interactions, formulation optimization, and long-term multi-location field evaluation to support sustainable termite management strategies. Full article

Microbial communities associated with the rhizosphere and phyllosphere are recognized as fundamental components influencing essential plant processes, including nutrient acquisition, growth promotion, and tolerance to stress. Biological control agents (BCAs), such as Trichoderma spp. and Bacillus spp., are widely applied in citrus crops. However, while BCAs effectiveness against plant pathogens is widely established, their resulting impact on indigenous, non-target bacterial and fungal communities remains poorly understood. The aim of this study was to evaluate the non-target effects of two commercial microbial formulations—one containing Trichoderma asperellum ICC 012 and T. gamsii ICC 080, and the other Bacillus amyloliquefaciens QST 713—on the resident microbiomes of Citrus volkameriana seedlings by using the amplicon-based metagenomic analysis, targeting the 16S rRNA and ITS1 regions. The application of the Trichoderma formulation as a soil drench in the rhizosphere resulted in minimal changes to the overall composition and diversity (α- and β-diversity) of the bacterial communities. This stability is considered a desirable trait for overall soil health. However, specific taxonomic changes were observed, such as a notable decrease in the genus Rhodococcus (0.4% vs. 1.5% in controls) among bacteria. In the fungal communities, the treatment led to a significant shift in phylum relative abundance, characterized by an increase in Basidiomycota (38% vs. 28% in controls) and a corresponding decrease in Ascomycota (51% vs. 56% in controls). Successful colonization was confirmed by a substantially higher relative abundance of the inoculated Trichoderma genus compared to control plants (1.4% vs. 0.1% in controls). Conversely, the foliar application of the Bacillus product induced a substantial restructuring of the phyllosphere bacterial community. This treatment caused a statistically significant reduction in bacterial α-diversity and a clear differentiation in community composition (β-diversity) relative to untreated controls. The successful colonization by the BCA resulted in the dominance of the Bacillus genus in the treated samples (27% vs. 2% in controls). Importantly, this ecological shift was accompanied by the enrichment of other beneficial bacterial taxa, including Sphingomonas (15% vs. 4% in controls) and the Burkholderia-Caballeronia-Paraburkholderia group (4% vs. 2% in controls). While fungal phyla abundances remained generally stable in the phyllosphere, specific genera such as Cladosporium (15% vs. 23% in controls) and Symmetrospora (21% vs. 13% in controls) prevailed post-treatment. In conclusion, these findings highlight the importance of considering non-target microbiome shift when implementing microbial biocontrol strategies in citrus production systems, since in this study was demonstrated that commercial BCAs exert a markedly differential influence based on the compartment of application: Trichoderma promoted ecological stability in the rhizosphere, whereas Bacillus induced a directional community shift in the phyllosphere. Full article

Arbuscular mycorrhizal fungi (AMF) are widely applied as bioinoculants to enhance crop performance, yet their broader ecological effects on rhizosphere microbial assembly under field conditions remain insufficiently understood. Here, we evaluated the impact of a commercial AMF inoculant and its carrier material on lettuce performance and rhizosphere microbial communities in an open-field experiment. We hypothesized that both viable AMF propagules and formulation components contribute to shifts in rhizosphere processes. Active AMF inoculation significantly increased root colonization and fresh biomass at harvest, confirming successful establishment and enhanced plant performance under field conditions. Colonization levels in the heat-inactivated carrier treatment were comparable to the non-inoculated control, indicating that the carrier did not inhibit indigenous AMF activity or induce nutrient-mediated suppression of symbiosis. Plant physiological responses were stage-dependent, supporting the context-dependent nature of AMF effects in dynamic field environments. High-throughput sequencing revealed no significant treatment effects on bacterial or fungal alpha diversity. However, beta-diversity analyses demonstrated significant compositional restructuring of rhizosphere communities, particularly within the bacterial domain. A stable core microbiome persisted across treatments, yet relative abundances and community evenness were altered by both active inoculation and carrier application. These results suggest that AMF inoculation reorganizes microbial community structure predominantly via shifts in ecological niche occupation. Collectively, our results show that AMF inoculation functions not only as a symbiotic nutrient-acquisition strategy but also as a driver of rhizosphere microbial reorganization under field conditions. Integrating plant performance with microbiome dynamics provides a more comprehensive framework for understanding and optimizing microbial inoculants in sustainable agricultural systems. Full article

To enhance the benefits and ecological safety of tomato residue retention, this study evaluated the regulatory effects of conventional ambient temperature retention (CR) and solar high-temperature retention (TR) on the initial soil environment and rhizosphere microecology of subsequent crops (continuous tomato and rotational cucumber). The results showed that CR promoted the accumulation of humic acid and increased the contents of phenolic acids and small-molecule organic acids in the soil. TR also increased small-molecule organic acids but primarily enriched fulvic acid, accompanied by higher concentrations of phenolic acids. Regarding microecological responses, CR enriched potential plant-growth-promoting bacteria (Pseudomonas, Sphingomonas, Lysobacter) in the rhizosphere, but it also increased the relative abundance of the potential pathogen Fusarium. In contrast, TR promoted the colonization of heat-tolerant beneficial biocontrol microbes (Bacillus, Chaetomium, Mycothermus), with no Fusarium enrichment observed. Redundancy analysis and Mantel tests revealed that the changes in soil nutrients and organic acid fractions induced by residue retention were correlated with the succession of the rhizosphere microbial community and the reconstruction of the metabolic profile. This study demonstrates that TR can effectively mitigate the risk of pathogen enrichment associated with ambient temperature retention, constructing a potentially disease-suppressive initial microecological environment for subsequent crops. Full article

Invasion by Spartina alterniflora has detrimental effects on existing ecosystems. Studies have shown that microorganisms can control plant growth and development. However, the root-associated community structures of bacteria, archaea, and fungi of S. alterniflora have rarely been investigated. Here, we applied metagenomics to reveal the bacterial, archaeal, and fungal communities across four root compartments, including the bulk soil, rhizosphere, rhizoplane, and endosphere. Our findings revealed the variation in different community structures. The bacterial and fungal communities exhibited greater potential environmental flexibility than the archaeal community. The endosphere environment had the simplest microbial networks and highest stability. Additionally, we identified root-exuded metabolites from S. alterniflora, which may influence microbial community assembly. Our results indicate that the rhizoplane plays a crucial role in controlling microbial entry into the root, selectively recruiting beneficial microbes for plant growth and colonization, thereby impacting nutrient cycling and plant health. This study provides insights into microbial diversity and function within the S. alterniflora root zone and suggests potential microbial-based strategies for managing this invasive species. Full article

The majority of terrestrial plant species establish below-ground interconnections via arbuscular mycorrhizal (AM) mycelium, thereby forming extensive common mycorrhizal networks (CMNs). CMNs serve as critical infrastructure for nutrient acquisition, mediating soil nutrient capture and distribution. In nitrogen-fixing plants, phosphorus (P) transport is particularly dependent on functional CMNs. The rapid expansion in graphene oxide (GO) production and its broad application have raised significant ecological concerns, particularly regarding its potential impacts on terrestrial ecosystems. Despite these concerns, the impact of GO on P transport dynamics within legume–arbuscular mycorrhizal fungi (AMF) symbioses remains critically scarce. This study established a symbiotic system using the model nitrogen-fixing legume Medicago sativa L. and AMF. This experimental system enabled a comprehensive assessment of GO effects on rhizosphere P mobilization, plant P acquisition, CMNs architecture, fungal community composition, and expression of key P transporter genes. Our results demonstrated that high GO concentrations significantly altered rhizosphere properties, increasing pH while reducing organic acid content and alkaline phosphatase activity. Furthermore, GO exposure significantly inhibited root growth, mycorrhizal colonization rates, and plant P acquisition efficiency. Additionally, GO exposure altered AMF community composition, reduced rhizosphere microbial diversity, and suppressed P metabolism gene expression. Specifically, 0.6% GO induced significant downregulation of MsCS and GigmPT by 83.5% and 62.3%, respectively. This indicates that GO impairs plant P uptake by disrupting the core pathway involving GigmPT and MsCS, triggering P stress in M. sativa. Collectively, these findings provide compelling evidence that GO exposure disrupts legume–AMF symbiotic integrity, ultimately impairing P transport efficiency. Full article

The rhizosphere is a critical interface linking plants and soil; however, the mechanisms by which parasitic plants affect host growth through rhizosphere microecological changes remain unclear. This study systematically elucidates how Monochasma savatieri, a hemiparasitic plant, promotes blueberry growth by reshaping rhizosphere microecology. Pot experiments showed that parasitism significantly enhanced urease, sucrase, and soil nitrate reductase activities, improving organic matter decomposition and nutrient transformation efficiency. Concurrently, soil total nitrogen (TN), total phosphorus (TP), and total potassium (TK), along with alkali-hydrolyzable nitrogen (AN) and available potassium (AK), decreased, suggesting enhanced nutrient absorption by roots. At the microbial level, parasitism altered community composition and diversity, enriching functional taxa such as Nitrosomonas, OLB5, and Serendipita. Functionally, pathways related to stress resistance (necroptosis and glutamatergic synapses) were activated, whereas those linked to pathogen colonization (Pseudomonas aeruginosa biofilm formation and tryptophan metabolism) were suppressed. These modifications reduced harmful microbial competition, optimized nutrient cycling and signaling networks, and established a favorable rhizosphere microenvironment for root health. By integrating soil enzyme activity, nutrient dynamics, and microbial functions, M. savatieri systemically improves the rhizosphere microenvironment, ultimately enhancing blueberry growth. This study provides theoretical support for intercropping and management of parasitic plants with blueberries. Full article

The dynamic interaction between plants and their root-associated microbiota represents a sophisticated and profound biological communication that regulates plant development and the formation of adaptation to the surrounding environment. These interactions function as critical regulators of multiple physiological processes, finally influencing soil fertility and agricultural productivity. Plants have evolved epigenetic networks that regulate beneficial plant–microbe interactions through regulating immune responses, gene regulation, and metabolite production to enhance stress tolerance and soil adaptation. These regulations collectively govern microbial colonization patterns while establishing reciprocal feedback loops through root exudate–microbe interactions. This review systematically updates contemporary advances in understanding how epigenetic modifications shape rhizosphere microbiome composition and function, and discusses their potential applications in enhancing the yield and quality of horticultural crops, as well as in mitigating continuous cropping obstacles. Full article

Tripartite interaction among arbuscular mycorrhizal fungi (AMF), small grain cereals—including wheat, barley, oats, and rye—and pathogenic organisms constitute a highly complex ecological system with major implications for plant health, productivity and resilience. AMF colonization increases nutrient acquisition, particularly phosphorus and nitrogen, while concurrently priming host defense mechanisms that increase resistance to a broad spectrum of pathogens. These benefits, however, are strongly context-dependent and modulated by AMF species composition, host genotype, soil characteristics, and environmental conditions. AMF activate resistance pathways and modulate the rhizosphere microbiome, underscoring their central role in shaping plant–pathogen dynamics. Importantly, the relevance of these interactions extend beyond crop protection and yield stability to encompass food security and sustainability goals aligned with the One Health framework, which recognizes the interconnectedness of plant, environmental, and human health. Field implementation of AMF-based strategies has the potential to reduce reliance on chemical fertilizers and pesticides, thereby promoting sustainable cereal production, restoring soil biodiversity, and enhancing ecosystem services, with downstream benefits for human nutrition and environmental safety. This review integrates current knowledge on AMF–cereal–pathogen interactions, synthesizing mechanistic advances and applied perspectives while identifying critical knowledge gaps that must be addressed to effectively deploy AMF in resilient and sustainable agroecosystems within a One Health context. Full article