Objective To screen the microbial strains producing volatile organic compounds (VOCs) with both broad-spectrum antagonistic activity and postharvest fruit preservation potential. Methods Endophytic bacterial strains were isolated and purified by the dilution plating method from the roots and branches of wild tea plants in Guangxi, China. Candidate strains were initially selected based on the number of functional traits via six types of functional media: cellulase, amylase, siderophore, organic phosphorus, inorganic phosphorus, and nitrogen-fixing media. The antagonistic activity of the strains against seven common plant pathogenic fungi was determined by the dual-culture assay, and thus the broad-spectrum antagonistic strains were screened out. Strains with superior overall performance were further selected to evaluate their antagonistic activity against the postharvest anthracnose pathogens—Colletotrichum fructicola and Colletotrichum musae—of mangoes and bananas. An in vitro banana preservation assay was conducted with the chemical preservative prochloraz as a positive control. Results Functional screening on selective media yielded 98 strains that simultaneously possessed four or more plant growth-promoting or stress-tolerance traits, including nitrogen fixation, phosphate solubilization, and siderophore production. In dual-culture assays against seven common plant pathogenic fungi, 18 broad-spectrum antagonistic strains significantly inhibiting at least five pathogens were screened out, among which four strains exhibited stable and strong antagonistic activity against all the seven pathogens. On this basis, two key indicators, number of functional traits and broad-spectrum inhibition rate, were comprehensively evaluated, and five strains with the best overall performance were finally selected for subsequent specific antagonism assays against the pathogens causing mango and banana anthracnose and for validation of their postharvest fruit preservation effects. In dual-culture assays, the inhibition rates of the tested strains against the two anthracnose pathogens ranged from 43.36% to 83.50%. In plate-on-plate assays, the VOCs produced by these strains exhibited inhibition rates of 56.80%-99.25% against C. fructicola and 54.50%-99.85% against C. musae, with several strains showing nearly 100.00% inhibitory activity against both pathogens. In vitro fruit preservation tests demonstrated that VOCs produced by the antagonistic strains delayed the postharvest decay of mangoes and bananas to varying degrees. Strain T-1-6 showed the most pronounced effect, extending the onset of visible banana decay to 21 days (the final decay grade was grade 0), and its preservation effect was comparable to that of the chemical preservative prochloraz, achieving approximately 50% control efficacy against surface molds on mangoes. Analysis of 16S rRNA gene and gyrB sequences revealed that all the five dominant antagonistic strains belonged to the genus Bacillus, including B. amyloliquefaciens, B. thuringiensis, B. cereus, and B. subtilis. Conclusion The VOCs-producing endophytic Bacillus strains from tea plants possess multiple functional traits and broad-spectrum antagonistic activity. This study provides promising candidate strains and a theoretical basis for the green disease control and biopreservation of postharvest tropical fruits such as mangoes and bananas.

Objective To obtain microbial communities capable of degrading polystyrene microplastics (PS) and polypropylene microplastics (PP) and analyze their degradation efficiency and synergistic mechanisms, thus providing resources and theoretical support for the in-situ bioremediation and enriching our understanding of the mechanisms underlying the synergistic degradation of complex pollutants by microbial communities. Methods The microbial communities capable of degrading PS and PP were enriched from plastic-contaminated activated sludge of enterprises. A 60-day degradation experiment was carried out to evaluate the degradation efficiency of the microbial communities on the two microplastics based on the weight loss rate. The surface structures, hydrophobicity, and molecular weight changes of microplastics were characterized by scanning electron microscopy (SEM), water contact angle (WCA), and gel permeation chromatography (GPC). Fourier transform infrared spectroscopy (FTIR) and GC-MS were employed to analyze the degradation products and metabolic pathways of microplastics. The dominant groups, core functional bacteria, and their encoded related enzymes in the microbial communities were clarified through metagenomic analysis, on the basis of which the synergistic degradation mechanisms of the microbial communities were explored. Results The enriched microbial communities were dominated by Bacillota and Pseudomonadota. Bacillus initiated the initial degradation and Achromobacter participated in the intermediate metabolism, forming an “initiation-metabolism” synergistic network. PS and PP could be degraded without pretreatment within 60 days, with weight loss rates of (13.4±2.3)% and (23.2±2.4)%, respectively. Characterization confirmed that the microplastics during degradation presented damaged surfaces, reduced hydrophobicity, and decreased molecular weights. FTIR and GC-MS revealed that PS generated phenols and aldehydes through benzene ring hydroxylation and other processes, and entered the tricarboxylic acid cycle through the aromatic degradation pathway; PP were metabolized through the fatty acid degradation pathway via the oxidation chain of hydroxylation→carbonylation→esterification. The functional annotation of metagenomic data revealed that the genes encoding primary degradative enzymes and metabolic enzymes from Bacillus and Achromobacter exhibited complementary functions, forming the molecular basis for efficient degradation. Conclusion The microbial communities identified in this study efficiently degrade PS and PP. It is hypothesized that their core functional bacteria, Bacillus and Achromobacter, achieve degradation of both microplastics through a synergistic “initiation-metabolism” network and functionally complementary enzyme systems. This provides insights for managing residual microplastics after source control and deepens our understanding of the mechanisms underlying microbial synergistic degradation of complex pollutants.

Objective To characterize the cultivable bacterial diversity patterns and extracellular enzyme-producing capacity in mangrove sediments from the Zhangjiang Estuary, with a particular focus on the distribution of dominant Bacillus sensu lato and the environmental factors shaping their assemblages. Methods Bacterial isolates were obtained by dilution plating. Taxonomic identification was performed by 16S rRNA gene sequencing. Plate-based assays were used to evaluate the activities of eight extracellular enzymes. Results In total, 1 392 isolates were obtained, representing 97 genera of 4 phyla. Bacillus sensu lato constituted the dominant assemblage (57.8%). Preliminary screening suggested 263 isolates (18.9%) as putative novel taxa, largely concentrated in Bacillus and allied genera such as Halobacillus. The Shannon diversity of cultivable bacteria was higher in the core mangrove zone and at the estuarine outlet than at the inlet (P<0.05), and the community composition differed among sites (P<0.05), being mainly associated with salinity and metal ions. By contrast, the community structure of Bacillus sensu lato was comparatively stable across space and was primarily associated with pH and carbon-nitrogen nutrient variables. Enzyme screening showed the highest positive rates for proteases (64.2%) and lipases (52.6%). Isolates affiliated with Bacillus sensu lato displayed higher positive rates than the overall community across multiple enzymes, indicating broad metabolic potential. Conclusion Mangrove sediments from the Zhangjiang Estuary harbor abundant cultivable bacterial resources. In addition to the dominant Bacillus-related taxa, Pseudomonadota and Bacteroidota appear to be key components underpinning overall community diversity. The high ecological stability and multi-substrate degradation capacity of Bacillus sensu lato, together with other bacterial groups, contribute to element cycling in mangrove sediments.

The application of natural microbiomes is limited by their complex composition and uncontrollable functions, which makes synthetic microbiomes a core direction in microbiome engineering. Early binary synthetic microbiomes can achieve functional synergy under controlled conditions, whereas they exhibit poor stability and limited functional persistence in real complex environments due to their simple metabolic pathways and insufficient ecological redundancy. In recent years, the research on synthetic microbiomes has shifted from an empirically driven approach to rational design, achieving significant progress in strain resource acquisition, construction strategies (top-down, bottom-up, and their hybrid paradigms), and computational tools (e.g., genome-scale metabolic models). However, current design frameworks still focus primarily on functional realization, with insufficient attention paid to the long-term stability, system robustness, and multi-level ecological interactions of communities in complex environments. This paper systematically sorts out the evolutionary trajectory of synthetic microbiome construction paradigms and reviews the key elements for enhancing community stability. By establishing a multi-level metabolic network, this paradigm significantly improves the functional persistence and ecological robustness of synthetic microbiomes in complex and fluctuating environments. The future research on synthetic microbiomes needs to further integrate multidisciplinary technologies to improve the predictability and long-term stability of engineered microbiomes, providing a systematic theoretical framework and research directions for constructing highly robust synthetic microbiomes.

Objective To compare the regulatory effects and underlying physiological mechanisms of Pseudomonas huaxiensis M11 and Bacillus megaterium M28 on the photosynthetic characteristics of maize subjected to low soil fertility stress. Methods A pot experiment was implemented with four treatments: normal soil control (CK), low nutrient treatment (LNT), and bacterial inoculation under LNT conditions (M11+LNT, M28+LNT). At the tasseling stage, measurements were taken for soil nutrients, plant growth indices, gas exchange parameters, chlorophyll fluorescence characteristics, and the fast chlorophyll a fluorescence induction kinetics (O-J-I-P chlorophyll a fluorescence transient, OJIP curve). Yield components were assessed at physiological maturity. Results Inoculation with M11 significantly increased the content of available phosphorus, available potassium, and organic matter, while reducing the electrical conductivity in soil. M28 significantly enhanced the total nitrogen content. Both bacterial treatments significantly promoted maize growth, increasing the plant height, leaf area, SPAD value, and biomass. Moreover, they highly significantly enhanced the net photosynthetic rate (P_n), stomatal conductance (G_s), transpiration rate (T_r), and water use efficiency (WUE), while reducing the intercellular CO₂ concentration (C_i). Chlorophyll fluorescence analysis revealed a decrease in minimal fluorescence (F_o) and increases in the maximum photochemical efficiency (F_v/F_m), actual photochemical quantum yield of PSII (Φ_PSII), apparent photosynthetic electron transport rate (ETR), photochemical quenching (qP), and the fraction of open PSII centers based on excitation energy (qL), with no significant change in non-photochemical quenching (NPQ). The OJIP curves indicated the absence of a K-step in inoculated plants, a decrease in fluorescence at the J-step, and increases at the I-step and P-step. The differential kinetic curves of relative variable fluorescence (ΔV_t analysis) confirmed that both strains synchronized the optimization of electron transport on both the donor and acceptor sides of photosystem II (PSII). The increased amplitude of the I-P phase suggested enhanced photosystem I (PSI) activity. Junction-intermediate-peak test (JIP-test) parameters demonstrated that inoculation significantly enhanced the performance index based on absorbed light energy (PI_ABS), the performance index on a cross-section basis (PI_CS), the probability that a trapped exciton moves an electron into the electron transport chain beyond Q_A (Ψ_o), the quantum yield for electron transport (φ_Eo), and the electron transport flux per reaction center (ET_o/RC). Conversely, dissipated energy flux per cross-sectional area (DI_o/RC) and quantum ratio for dissipated energy (φ_Do) decreased. Consequently, compared with the LNT group, the M11 and M28 treatments resulted in significant increases of 30.61% and 22.64% in maize fresh weight and 26.68% and 23.41% in dry weight, respectively. Conclusion P. huaxiensis M11 primarily enhances photosynthetic performance by increasing soil available phosphorus and potassium content, directly optimizing energy metabolism and stomatal movement, whereas B. megaterium M28 mainly acts by elevating soil total nitrogen content, focusing on stabilizing the structure of the photosynthetic apparatus. Together, they protect the integrity of photosynthetic apparatus and optimize the electron transport efficiency of photosystems, significantly improving the photosynthetic performance and yield of maize under low fertility stress. These findings provide a theoretical basis for the targeted application of microbial inoculants in sustainable agricultural production.

Objective To investigate the mechanism by which the microbial fermentation product of the traditional Chinese medicine YA3D3 (YA3D3-MHF) improves cognitive function in the APP/PS1 transgenic mouse model of Alzheimer’s disease (AD) via the microbiota-gut-brain axis. Methods APP/PS1 mice were administered either the water extract of YA3D3 (YA3D3-HF) or YA3D3-MHF for 90 days. The gut microbiota structure was analyzed by 16S rRNA gene sequencing, and the fecal levels of short-chain fatty acids (SCFAs) were assessed by GC-MS. The neurotransmitter content in the brain tissue was measured via ELISA, and cognitive function was assessed via the Morris water maze. Network pharmacology and mass spectrometry were employed to identify active components and changes in chemical composition. Results Compared with the model group and the YA3D3-HF group, YA3D3-MHF significantly ameliorated cognitive impairment in mice. The Morris water maze test showed that the high-dose YA3D3-MHF (MH) group had the shortest escape latency and the highest number of platform crossings, approaching the performance of the normal control group. ELISA confirmed that the MH group had the highest levels of 5-hydroxytryptamine (5-HT), γ-aminobutyric acid (GABA), and glutamate (GLU) in the brain. The results of 16S rRNA gene sequencing revealed that the MH group exhibited the highest alpha diversity (Shannon index≈3.2) of gut microbiota and the highest abundance of beneficial bacteria, along with the lowest abundance of pro-inflammatory bacteria. GC-MS analysis indicated that the MH group had the highest levels of total SCFAs, acetate, and butyrate. MS demonstrated that YA3D3-MHF components exhibited reduced polarity and the emergence of new high-activity peaks. Conclusion YA3D3-MHF improves cognitive function in AD mice by modulating the gut microbiota-SCFAs-neurotransmitter axis, outperforming YA3D3-HF. This study provides experimental evidence for AD intervention targeting the gut-brain axis.

Objective To screen potential probiotics with antagonistic effects against Nocardia seriolae from the intestine of healthy largemouth bass (Micropterus salmoides). Methods Intestinal samples were collected from healthy largemouth bass, and strains were isolated and purified via serial dilution and spreading on TSA plates. The hole-punch method was adopted to select strains with antagonistic effects against N. seriolae as test strains for subsequent experiments. The species of the test strains were identified through morphological characterization, physiological and biochemical tests, 16S rRNA gene sequence alignment, and phylogenetic analysis. Additionally, the growth characteristics, adhesion ability, antibacterial activity of cell-free fermentation supernatants, and biosafety of the test strains were determined and analyzed. Results Among the 40 bacterial strains isolated from the intestinal samples of healthy largemouth bass, two strains (XXLC06 and XXLC08) with stable and significant antagonistic effects against N. seriolae were selected. XXLC06 was identified as Lysinibacillus macroides and XXLC08 as Lysinibacillus fusiformis. Both strains grew well at 25-37 ℃, salinities of 5‰-30‰, and pH 5.5-9.0, with survival rates higher than 53% at 0.3% and 0.5% bile salt concentrations. Auto-aggregation assays showed that the auto-aggregation rates of XXLC06 and XXLC08 after 8 h were 68.09% and 63.16%, respectively. In the three organic solvents, both XXLC06 and XXLC08 exhibited hydrophobicity rates exceeding 50%. After co-incubation with N. seriolae for 8 h, the co-aggregation rates of the two strains reached 54.62% and 52.44%, respectively. The diameters of the inhibition zones of cell-free fermentation supernatants of XXLC06 and XXLC08 against N. seriolae were (28.15±0.44) mm and (22.63±0.52) mm, respectively. Neither strain showed hemolytic activity, and both were sensitive to 23 tested antibacterial agents. Acute toxicity tests confirmed that they were non-pathogenic to largemouth bass. Conclusion Strains XXLC06 and XXLC08 exhibited favorable growth adaptability, adhesion capability, biosafety, and stable antagonistic activity in vitro . This study provides potential probiotic resources and experimental evidence for the control of N. seriolae.

Objective To analyze the expression strategy, DNA-binding characteristics, and the role in heavy metal responses and transcriptional regulation of the UrcA-like membrane protein Chr1_2170 from Sphingobium xenophagum C1. Methods Chr1_2170 was expressed in Escherichia coli BL21(DE3) by codon optimization, dual-signal peptide guidance, and co-expression with homologous molecular chaperones. The interacting genes of Chr1_2170 were screened by constructing a functional promoter library of protein-bound genomic DNA fragments. The heavy metal response characteristics of Chr1_2170 were analyzed via the Chr1_2170-Luc reporter system. Results Chr1_2170 was successfully expressed in E. coli BL21(DE3). Six promoter regions specifically bound by Chr1_2170 were screened out and identified, with the conserved motif of 5′-AATXGCGXGTA-3′. Gene function annotation predicted that Chr1_2170 regulated multiple genes, including those encoding β-N-acetylglucosaminidase, two-component system ATP-binding protein, DNA topoisomerase IV subunit B, and serine hydrolase. Chr1_2170 showed dose-dependent responses to Cu²⁺ (1-80 μmol/L), Zn²⁺ (1-80 μmol/L), and Ba²⁺ (1-150 μmol/L). Conclusion Chr1_2170 functions not only as a heavy metal sensing element but also as a multifunctional transcriptional regulator. It regulates the expression of related genes by recognizing specific DNA sequences, playing a key role in environmental adaptation and stress responses of bacteria.

Objective To isolate the Streptomyces hebeiensis strain JL9001 with significant biocontrol potential against tomato Fusarium wilt from Pseudostellaria heterophylla roots, elucidate the complete genome sequence and functional annotation of the strain, and extract genetic data pertaining to its secondary metabolites, thus offering a valuable microbial resource and a theoretical foundation for the biological management of tomato Fusarium wilt. Methods The colony morphology on various media was examined via the plate streaking technique. The antagonistic properties of strain JL9001 against Fusarium oxysporum were evaluated through the plate confrontation assay. The activities of metabolites (crude fermentation extract) against F. oxysporum were assessed via the microdilution method. The effectiveness of strain JL9001 in managing tomato Fusarium wilt was evaluated through root drenching with the fermentation broth. Whole genome sequencing of strain JL9001 was conducted, and the sequencing data were analyzed by appropriate software for species identification, gene prediction, functional annotation, and prediction of secondary metabolite biosynthesis gene clusters. Results Strain JL9001 demonstrated optimal spore production on the SIM medium. Antagonistic assays indicated that it inhibited the mycelial growth of F. oxysporum by 40.18%. Furthermore, the crude fermentation extract at a concentration of 1 000 μg/mL completely inhibited F. oxysporum. Pot trials revealed that irrigation with the fermentation broth of JL9001 resulted in a 51.61% reduction in tomato Fusarium wilt on day 13. The genome of strain JL9001 comprised 7 700 822 base pairs with the G+C content of 71.46%, encompassing 6 589 genes. Analysis predicted the presence of 27 biosynthetic gene clusters for secondary metabolites including terpenoids, polyketides, and siderophores, which may possess antimicrobial properties. Conclusion This study elucidates, through antagonistic and pot experiments, that strain JL9001 effectively mitigates the incidence of tomato Fusarium wilt. The analysis of the genomic composition and functional gene information of strain JL9001 provides a basis for exploring the antimicrobial mechanisms of natural products, examining secondary metabolite biosynthetic gene clusters, and assessing the potential of Streptomyces-derived secondary metabolites.

Objective To determine the efficacy of Cucurbita pepo cv Dayangua (CPD) in alleviating hypoxia and explore the potential mechanisms involving the modulation of the gut microbiota and its metabolites. Methods Male Kunming mice were randomly assigned into two groups: a control group (normoxia ddH₂O, ND) and a CPD intervention group (normoxia CPD, CPD). The CPD group received a dose of 800 mg/(kg·d) of CPD, while the ND group received an equal volume of ddH₂O for 15 consecutive days. One hour after the final administration, mice from each group were placed in wide-mouth bottles, and the survival time was observed and recorded. Fecal samples collected prior to the last administration were subjected to 16S rRNA gene amplicon sequencing and targeted metabolomics analysis. Correlation analysis between gut microbiota and metabolites was subsequently performed. Results CPD intervention significantly prolonged the survival time of mice under hypoxic conditions compared to the ND group. CPD altered the structural composition of the gut microbiota in mice. Linear discriminant analysis effect size (LEfSe) revealed significantly different bacterial taxa between the ND group and the CPD group, with higher relative abundance of Bacillota, Lactobacillus, and Alistipes in the CPD group. Microbial genera, including Paraprevotella and Lactobacillus, showed a positive correlation with survival time. Targeted metabolomics identified 9 upregulated and 31 downregulated metabolites in the CPD group. Notably, metabolites such as palmitoleic acid, glyoxylic acid, hendecanoic acid, l-aspartic acid, O-succinylhomoserine, and allantoic acid were significantly enriched and positively correlated with the survival time of mice after CPD intervention. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis of differential metabolites showed the highest enrichment in the tryptophan metabolism and glycine, serine, and threonine metabolism pathways. Conclusion CPD intervention significantly prolonged the survival time of hypoxic mice. CPD intervention enriched beneficial microorganisms, including Lactobacillus, and elevated the levels of beneficial metabolites such as choline and allantoic acid. These findings suggest that modulating the “gut microbiota-metabolite” axis may be one mechanism through which CPD enhances host hypoxia tolerance, providing a theoretical basis and potential targets for developing microecological intervention strategies against hypoxia-related diseases.