Search Results (290)

Continuous cropping obstacles (CCOs) seriously constrain tomato yield and quality in facility agriculture, primarily due to rhizosphere microbial imbalance. Indigenous synthetic microbial communities (SynCom) offer superior colonization and stability compared to single strains. This study aimed at constructing a simplified SynCom from indigenous rhizobacteria in Northwest China to alleviate tomato CCOs. A total of 155 rhizobacterial strains (29 genera) were isolated. Sixteen strains with significant growth-promoting effects were selected through seedling assays. Based on the carbon source niche overlap index (NOI > 70%) with Ralstonia solanacearum QL-Rs1115, eight candidate strains were retained. Using the broken-stick model, 29 simplified SynComs were constructed. SynCom28, composed of six functionally complementary strains (Azospirillum brasilense, Massilia niabensis, Enterobacter hormaechei, Chryseobacterium sp., Priestia megaterium and Pseudomonas brassicacearum), showed the best performance. Pot experiments revealed that SynCom28 reduced the bacterial wilt disease index to 32.41, with a biocontrol efficacy of 41.72%. Greenhouse trials under continuous cropping demonstrated that SynCom28 significantly increased seedling Dickson quality index (DQI), stem diameter and biomass. Fruit yield increased by 12.98–15.30% across the 2nd to 4th cropping cycles (p < 0.05). Fruit quality parameters were also enhanced, with soluble sugar, lycopene, and vitamin C contents increasing by 47.22–65.07%, 33.07–81.71% and 80.56–166.67%, respectively. In conclusion, the indigenous simplified SynCom28 effectively alleviates tomato CCOs, enhancing growth, yield, and quality while suppressing bacterial wilt, providing a promising strategy for sustainable facility agriculture. Full article

Driven by increasingly severe drought stress associated with global warming, this study investigated a synthetic microbial community, SynCom-SASW01, with strong stress tolerance and plant growth-promoting potential, and systematically elucidated its mechanisms for enhancing drought resistance in wheat (Triticum aestivum L.). Dual-site field trials demonstrated that SynCom-SASW01 significantly alleviated drought-induced growth suppression, increasing grain yields by 10.42% and 8.52% at the Hohhot and Hulunbuir sites, respectively. This improvement was primarily associated with increased effective tiller number and enhanced root vigor. Physiologically, inoculation promoted root proline and glutathione accumulation and enhanced antioxidant enzyme activities, including superoxide dismutase, thereby reducing malondialdehyde levels. Environmental analyses showed that the consortium established rhizosphere “micro-reservoirs” through exopolysaccharide secretion, improving soil relative water content and the availability of alkali-hydrolyzable nitrogen and phosphorus. High-throughput sequencing revealed that SynCom-SASW01 reshaped the endosphere microbiome through early colonization priority effects, selectively enriching beneficial taxa such as Pseudomonas. Functional prediction indicated upregulated branched-chain amino acid biosynthesis, promoting osmotic adjustment and redox homeostasis. These findings provide a microbiome-based strategy for stabilizing wheat productivity in arid regions. Full article

Highlighting its pivotal role in modern pharmacology, the gut microbiome is emerging as a key determinant of drug efficacy, toxicity, and bioavailability. This review proposes the Gut Microbiome Dependency Continuum, a four-layer framework describing progressively deeper levels of microbiome involvement in drug discovery and therapeutic function. The first layer, intact functional microbiome-dependent therapeutics and includes interventions such as faecal microbiota transplantation and defined microbial consortia. The second layer, microbiome-modulated approved drugs include widely used therapeutics whose pharmacokinetics or pharmacodynamics are strongly influenced by microbial metabolism. Examples include metformin, irinotecan, levodopa, and digoxin, where gut microbial interactions influence efficacy, toxicity, and inter-individual variability in treatment outcomes. The third layer, microbiota-transformable natural products, encompasses dietary and plant-derived compounds such as polyphenols, ginsenosides, alkaloids, fibres, isoflavones, lignans, and glucosinolates. Their biological activity depends on microbial biotransformation into bioactive metabolites. The fourth layer, engineered microbiome therapeutics, includes synthetic biology approaches such as programmable microbial systems, engineered probiotics, CRISPR-based microbiome editing, and microbiome-responsive drug delivery systems. It also includes synthetic microbial consortia, enabling targeted sensing, therapeutic delivery, and ecological reprogramming of gut microbial communities. Altogether, these layers define a continuum in which the gut microbiome evolves from a passive modulator to an essential metabolic organ and ultimately a programmable therapeutic platform. The article provides an integrated framework for microbiome-informed drug discovery. It also supports the development of precision, ecology-aware, and engineered microbial therapeutics. Full article

Nowadays, approximately 50% of chemical surfactants come from petrochemical sources and pose environmental risks due to poor biodegradability, affecting microbial communities, aquatic organisms, and terrestrial ecosystems. Biosurfactants are eco-friendly alternatives, thanks to their strong surface tension-reducing activity, stability, low toxicity, and biodegradability, but their large-scale production is still limited by high costs and low yields. In this study, rice husk was evaluated as a renewable substrate from the agro-industrial field for lipopeptide production by the endophytic Bacillus subtilis AC7. Medium optimization through Plackett–Burman designs identified nitrogen sources and pH 6.5 as key factors enhancing biosurfactant production. Under optimized conditions, surfactin production increased from 4.2 mg/L in untreated rice husk to 266–276 mg/L with NaNO₃ and NH₄NO₃ supplementation, respectively. Combined laccase–amylolytic pretreatment further improved substrate utilization, enhancing sugar availability and supporting higher biomass and metabolic activity. In bench-scale fermentation, this condition yielded the highest surfactin concentration (237.5 mg/L). LC-MS/MS analysis confirmed surfactin as the main product, with C15 as the dominant homologue, in both shake-flask and bench-scale fermentations. These findings highlight a novel, sustainable process for surfactin production, offering a renewable alternative to synthetic surfactants while addressing both environmental and economic concerns. Full article

Global salinization affects approximately one billion hectares of land in more than 100 countries, posing a severe threat to food security and ecosystem sustainability. Microbial remediation using plant growth-promoting microorganisms offers an eco-friendly alternative to physicochemical methods. However, bridging the gap between laboratory cultivation of single strains and field-scale application of synthetic microbial communities (SynComs) remains difficult, owing to inconsistent efficacy and a lack of unified design frameworks. This review examines the evolution from single strains to rationally designed SynComs for saline soil remediation. A ‘structure–function–mechanism’ framework is proposed, integrating five core microbial modules, namely ion regulation and osmotic stabilization, ethylene and phytohormone modulation, antioxidant activation, nutrient cycle activation, and systemic resistance induction. The review elucidates key determinants of synthetic community success, including functional complementarity, strain compatibility, and host–environment matching, while revealing a marked quantitative gap between controlled experiments and field performance. Key bottlenecks are identified, including the lack of high-throughput compatibility screening, poorly quantified long-term ecological risks, and the absence of standardized application guidelines across agro-ecological zones. Finally, emerging avenues are discussed, such as microbial–microalgal symbiosis and AI-assisted design, outlining a roadmap for next-generation smart microbial products integrated into climate-resilient farming systems. Full article

Periodontal disease is a chronic inflammatory condition driven by polymicrobial biofilms whose interaction with the host immune response drives the destruction of tooth-supporting tissues. Within these communities, bacterial cell–cell communication—particularly quorum sensing (QS)—coordinates virulence factor expression, biofilm maturation, and interspecies behaviour, allowing pathogens to mount population-dependent attacks on the host. Disrupting these signals has therefore drawn growing attention as an anti-virulence strategy for biofilm-associated oral infection. Quorum quenching (QQ)—the inhibition or disruption of QS pathways—prevents bacteria from coordinating these virulence-related activities. The candidate inhibitors investigated to date fall into three broad classes: conventional antibiotics used at sub-inhibitory concentrations, plant-derived natural compounds, and synthetic molecules designed to interfere with signal synthesis, signal reception, or signal transduction. In experimental work on periodontal pathogens, agents from each class reduce biofilm formation, suppress virulence factor production, and disrupt microbial communication within polymicrobial biofilms. Clinical translation, however, lags behind the laboratory evidence. Most data still come from in vitro systems and animal models, and the ecological complexity of the oral biofilm makes therapeutic targeting difficult: signals that drive virulence in pathogens also support cooperation among commensals. Toxicity profiles, pharmacokinetics, and well-powered clinical trials are needed before quorum-quenching agents can be considered for routine periodontal care. Even with these caveats, targeting bacterial communication offers a different therapeutic logic from conventional antimicrobials: attenuating virulence rather than killing cells, and so exerting weaker selective pressure for resistance. Further dissection of QS networks in oral biofilms—and the rational design of quenching agents that act on pathogenic rather than commensal signalling—may yield useful adjuncts to current periodontal therapy. Full article

Green roofs offer significant potential for urban stormwater management, yet their capacity to improve runoff water quality is constrained by the limited pollutant retention of conventional substrates and inherent nutrient leaching risks. This critical review synthesizes recent advances in substrate engineering and phytoremediation to establish an integrated framework for transforming green roofs into active bio-filtration systems. Our analysis reveals that amending conventional substrates with waste-derived biosorbents substantially enhances heavy metal and nutrient retention through complementary mechanisms of surface complexation, ion exchange, and microprecipitation. When strategically coupled with hyperaccumulator plant species and rhizospheric microbial communities, these amended substrates significantly reduce contaminant loads in urban runoff while maintaining hydraulic functionality. We critically evaluate standard growing media versus substrates amended with targeted biosorbents: biochar, which enhances heavy metal retention and hydraulic conductivity via surface complexation; seaweed biomass, which provides superior water retention and cation exchange while reducing synthetic fertilizer dependence; and chitin-rich crab shell waste, which promotes microprecipitation of metals and phosphates while valorizing marine waste. The novelty resides not in the materials themselves, but in their synergistic combination and the systematic comparative analysis of their retention mechanisms under green roof hydrological conditions. This review further identifies critical engineering trade-offs, including biosorbent-induced hydraulic conductivity reductions and long-term adsorption site saturation, and provides actionable design thresholds for amendment dosing, substrate depth, and species selection. Ultimately, this work establishes a mechanistic and practical roadmap for next-generation green roofs that simultaneously optimize stormwater retention, runoff quality, and circular economy valorization, highlighting priority research directions for long-term field validation and climate-adaptive standardization. Full article

In this study, the methane yield, substance conversion rate and microbial community structure of individual components of lignocellulose, synthetic mixtures, and corn straw subjected to different pretreatments (thermal hydrolysis, chemical, biological, and combined pretreatment) during anaerobic digestion were comparatively investigated. The synthetic mixture of cellulose and hemicellulose (MCXY) exerted a positive promoting effect on biomethane production, with a synergistic effect index of 101.51%. The methane yield per volatile solids (VS) of microcrystalline cellulose (MC), xylan (XY), and MCXY reached 320.81 ± 1.85 mL/g VS, 352.70 ± 6.58 mL/g VS, and 340.60 ± 10.94 mL/g VS, respectively. Lignin did not produce biogas in anaerobic digestion (AD) system, and its presence had an inhibitory effect on the methanogenesis of cellulose and hemicellulose, especially that of hemicellulose. Notably, pretreatment significantly improved the methane production potential of corn stover. Deep eutectic solvent-pretreated corn stover (DES_CS) achieved the highest methane yield of 356.57 ± 8.50 mL/g VS, which was 55.46% higher than that of the untreated group. DES pretreatment deconstructed lignocellulosic matrix and distinctly increased DOM molecular diversity, thus providing superior substrate conditions for improving anaerobic digestion performance. Microbial community analysis revealed that DES pretreatment significantly reshaped the bacterial structure, enriching syntrophic taxa over the carbohydrate-degrading Bacteroides found in raw corn stover, thereby fostering a more robust metabolic network for methane production. While acetoclastic Methanothrix dominated the pretreated groups, its synergistic coexistence with hydrogenotrophic Methanobacterium across all digesters facilitated stable dual-pathway methanogenesis. This work can provide a theoretical basis and technical reference for the optimization and application of pretreatment strategies for efficient anaerobic digestion of corn stover. Full article

The quality and flavor of probiotic fermented milk are highly dependent on the strain composition of the starter culture and their metabolic interactions. Although constructing a multi-strain system is an effective strategy for enhancing product quality, traditional formulation methods rely heavily on empirical approaches and lack mechanistic guidance. Herein, this study utilized genome-scale metabolic models (GEMs) to rationally design a multi-strain co-fermentation system. The results demonstrated that the GEM-predicted optimal system, comprising Lacticaseibacillus paracasei subsp. paracasei 63 (L. paracasei subsp. paracasei 63) and Lactococcus cremoris 290 (Lc. cremoris 290), significantly reduced the curd time by approximately 44.0% and 71.0% compared to the L. paracasei subsp. paracasei 63 and Lc. cremoris 290 monocultures, respectively. Furthermore, the co-fermented milk exhibited a 4.3-fold increase in apparent viscosity relative to the 290 single-strain group and achieved a significantly higher diacetyl concentration (1.98 ± 0.09 mg/L), representing a 2.8-fold enhancement. Volatile flavor profiling and untargeted metabolomics provided suggestive evidence supporting the GEM-predicted cross-feeding mechanisms, particularly within the arginine and pyruvate metabolic pathways. This study offers a solid theoretical foundation and practical guidance for the rational design of synthetic microbial communities to develop high-quality fermented dairy products with optimized flavor and functional properties. Full article

In intensive animal production, the overuse of antibiotics has exacerbated bacterial antimicrobial resistance and environmental pollution. Together with gut microbiota dysbiosis and recurrent disease outbreaks, these challenges severely constrain the sector’s high-quality development. Quorum sensing (QS), a cell-density-dependent bacterial communication mechanism, can be modulated through agents that specifically inhibit or activate QS circuitry to regulate microbial community functions. Such QS modulators possess notable advantages, such as environmental benignity and high target specificity, and thus offer innovative strategies to decrease antibiotic reliance, enhance production efficiency, and reduce environmental emissions. This review examines QS modulators sourced from plants, microorganisms, animals, and synthetic processes, while highlighting key challenges such as environmental interference, resistance development, high costs, and the lack of standardized biosafety evaluations. Future research should focus on enhancing specificity, stability, affordability, and safety, with an emphasis on rational design, synergistic systems, improved manufacturing processes, and multi-target modulators. This review may provide a theoretical basis for translating QS-regulation technologies into farm-level applications, thereby advancing sustainable animal production and antibiotic-free husbandry. 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

Trans-cinnamaldehyde (CIN), the main component of cinnamon essential oil, is a promising sustainable alternative to synthetic pesticides. Despite its use, ecotoxicological data on non-target species remain fragmented. This study systematically evaluates CIN’s acute toxicity across multiple trophic levels to characterize the biological sensitivity and environmental response of key organisms. Aquatic assays measured bioluminescence inhibition in Aliivibrio fischeri and immobilization in Daphnia magna. Terrestrial evaluations included lethality tests on Eisenia fetida and root elongation in Allium cepa. Additionally, the impact on soil and river microbial communities was analyzed via Biolog EcoPlates™. Significant dose–response relationships were observed across all bioindicators (p < 0.0001). A. fischeri was the most sensitive species (EC₅₀ = 1.428 mg·L⁻¹), followed by D. magna (EC₅₀ = 4.533 mg·L⁻¹). In terrestrial models, A. cepa (EC₅₀ = 11.644 mg·L⁻¹) exhibited higher sensitivity than E. fetida (LC₅₀ = 412.519 mg·kg⁻¹). Microbial metabolic activity showed dose-dependent inhibition, particularly affecting carbohydrate and polymer degradation at high concentrations. These findings define the first ecotoxicological benchmarks for CIN, establishing EC₁₀ and EC₅₀ values under standardized conditions. These data provide the necessary toxicological constraints to ensure environmental safety in future field-scale applications of this natural compound. Full article

Core microbes and succession of the microbial community greatly influence soy sauce fermentation process. This study identified seven functionally important core microbes, including Weissella paramesenteroides, Lactiplantibacillus plantarum, Tetragenococcus halophilus, Pediococcus pentosaceus, Zygosaccharomyces rouxii, Candida orthopsilosis, and Aspergillus oryzae for soy sauce fermentation, based on dominant taxa, co-occurrence relationships, and volatile-associated taxa analysis. Four distinct fermentation phases were identified for soy sauce fermentation based on metagenomics and metabolomics data correlation analyses. Acceptable fermentation performance and comparable soy sauce flavor compounds were achieved using a temporal synthetic microbial community for fermentation. The synthetic microbial community was assembled with inoculation of dominant lactic acid bacteria (LAB) in the immediate early phase, other LAB in early and middle phases, and yeasts in the late phase. Glutamate and 4-ethylguaiacol were identified as soy sauce fermentation indicators for early to middle and late fermentation phases, respectively. These results may provide a possible solution for achieving precise control over the brewing process and improving the flavor and quality of soy sauce. Full article

Tomato (Solanum lycopersicum) is a globally important high-value cash crop. However, long-term continuous cropping causes frequent soil-borne diseases and soil microecological imbalance, while overreliance on chemical pesticides leads to pesticide residues and water eutrophication. Plant growth-promoting rhizobacteria (PGPR) are key resources for addressing tomato cultivation challenges, with their functions partly depending on the rhizosphere microenvironment inherently shaped by seedling tray materials. Using rhizosphere soil and substrates of tomato at different growth stages under biomass (BM) and plastic (PM) seedling tray treatments, this study combined culture-independent and culture-dependent techniques to analyze microbial community characteristics and screen high-efficiency PGPR. Results showed that pH and available nitrogen drove microbial community assembly. BM significantly enriched beneficial taxa (e.g., Trichoderma and Bacillus) and enhanced culturable microbial abundance and genetic diversity, while PM enriched potential pathogens (e.g., Fusarium and Pyrenochaeta). The multifunctional strain S25095 from BM, with phosphate-solubilizing, potassium-solubilizing, and indole-3-acetic acid (IAA)-producing abilities, significantly promoted tomato shoot and root growth, outperforming single-functional strains and synthetic consortia. This study reveals the effects of growth stages and seedling tray treatments on tomato rhizosphere microorganisms, providing valuable PGPR resources for tomato cultivation. Full article

The relationship between microorganisms and human health is inseparable. In today’s increasingly urbanized world, the relationship between indoor microbial communities and human health is particularly close. Studies have shown that the composition of indoor microbial communities is influenced by various factors, including temperature, humidity, and nutrient conditions. However, research on how to alter indoor microbial community structures by adjusting nutrient components to improve human health is still limited. In this work, we constructed artificial microbial communities composed of common indoor microorganisms, and analyzed the species composition, metabolic capabilities, antibiotic resistance, and virulence of the microbial communities before and after cultivation using metagenomic sequencing technologies and metatranscriptomic sequencing technologies. We then assessed their community characteristics and evolutionary direction under different nutrient conditions. Overall, when the nutrient conditions were altered and reduced, the evolutionary direction of indoor microbial communities changed significantly. Specifically, this evolutionary direction was manifested in a taxonomic succession of community composition, with marked shifts in the relative abundances of constituent species, as well as in a significant alteration of the community-level metabolic functions. In-depth research in this field can help improve the composition of indoor microbial communities, thereby benefiting human health and public health construction in urbanized environments. Full article