Para-ethoxyaniline (ETH), a widely used industrial raw material and intermediate, persists in the environment, posing potential risks to ecosystems and human health. Objective To isolate an efficient ETH-degrading strain from activated sludge, optimize its degradation conditions, and elucidate the gene regulatory mechanisms and metabolic pathways under ETH stress by transcriptomic and mass spectrometric analyses. Methods A strain capable of utilizing ETH as the sole carbon source was isolated from activated sludge and identified through morphological observation, physiological and biochemical tests, and phylogenetic tree construction based on 16S rRNA gene sequences. The effects of temperature, pH, and initial ETH concentration on bacterial growth and degradation efficiency were examined. Transcriptome sequencing was employed to identify differentially expressed genes (DEGs), with selected up-regulated DEGs validated by real-time reverse transcription quantitative (RT-qPCR). Furthermore, mass spectrometry was employed to investigate the metabolic pathways. Results A highly efficient ETH-degrading strain, designated DQ78 and identified as Pseudomonas sp., was isolated. Under optimal conditions (28 ℃, pH 8.0, 4 mmol/L ETH, and 1% inoculum), it completely degraded ETH within 40 h. Three metabolic intermediates were identified, allowing the proposal of a preliminary degradation pathway. Transcriptomic analysis revealed 3 380 DEGs under ETH stress, including 1 609 up-regulated and 1 771 down-regulated genes. GO enrichment indicated up-regulated genes were primarily involved in 57 GO terms such as amino acid metabolism, cell motility, iron binding, and transport, which might activate the synthesis of ETF-degrading enzymes and enhance substrate uptake and transmembrane metabolism of intermediates. The down-regulated genes were enriched in 58 GO terms such as peptide metabolism and synthesis, ribosomal structure, and cellular components, suggesting a metabolic reallocation toward stress adaptation. KEGG analysis predicted 183 up-regulated pathways and 184 down-regulated pathways such as flagellar assembly, sulfur metabolism, and extracellular biosynthesis under ETH stress, indicating enhanced chemotaxis, enzyme secretion, and stress-resistant substance synthesis. Conclusion Strain DQ78 achieved complete degradation of ETH within 40 h, being a promising candidate for the bioremediation of ETH-contaminated environments. Transcriptomic analysis reveals the molecular regulatory mechanism of this strain in response to ETH, which lays a theoretical foundation for further exploring the genetic foundation of microbial degradation of organic pollutants.

Fusarium proliferatum is a critical pathogenic fungus causing soybean root rot. A halotolerant biocontrol strain Bacillus sp. YH7-4 was isolated from the Yuncheng Salt Lake. Objective To investigate strain YH7-4 in terms of the effect on soybean growth and the control efficacy against soybean root rot. Additionally, we sought to elucidate the antifungal mechanisms of this strain and identify antimicrobial genes through whole genome sequencing. Methods The plate dual-culture method was adopted to assess the antifungal activity of strain YH7-4. Pot experiments were conducted to evaluate the safety of the strain to soybean seedlings and the control efficacy against root rot. Illumina and PacBio platforms were used for whole genome sequencing of YH7-4. Subsequent analyses included metabolic system assessment, virulence factor prediction, transporter analysis, identification of genes related to biocontrol functions, comparative genomics, and biochemical assays. Results Strain YH7-4 demonstrated the inhibition rates exceeding 75.00% against several plant pathogens, including F. proliferatum, Phytophthora sojae, Colletotrichum truncatum, and Phomopsis longicolla. Pot experiments showed that at the OD₆₀₀ value of 0.8, YH7-4 suspension significantly increased the root length and dry weight of soybean seedlings, while excessively high concentrations abolished this effect. The control efficacy of YH7-4 against F. proliferatum-induced soybean root rot reached 56.02%. Whole genome sequencing revealed a genome of 3 945 352 bp with the G+C content of 46.51% and 3 756 predicted coding genes. These genes were annotated against databases including NR, Swiss-Prot, Pfam, COG, GO, and KEGG, with 3 753, 3 537, 3 358, 3 082, 1 756, and 2 845 sequences successfully annotated, respectively. Among the proteins encoded by these genes, 130 proteins belonged to the CAZy family. Twelve secondary metabolite biosynthetic gene clusters were identified, including eight known biosynthetic gene clusters for antibiotics (surfactin, macrolactin H, bacillaene, fengycin, difficidin, bacillibactin, bacilysin, and butirosin A/butirosin B) and four gene clusters with unknown functions. Additionally, two siderophore-related genes, one gene encoding 2,3-butanediol (associated with induced systemic resistance), and 15 genes involved in biofilm formation were identified. Comparative genomics analysis indicated that YH7-4 was a strain of Bacillus velezensis and shared 2 898 orthologous core gene clusters. Biochemical characterization showed that YH7-4 had the ability to produce amylase, protease, pectinase, and cellulase. Conclusion The halotolerant strain B. velezensis YH7-4 isolated from the Yuncheng Salt Lake shows excellent control efficacy against soybean root rot. Its genome harbors genes linked to biocontrol traits and antimicrobial substance production, which makes this strain a promising candidate for managing soybean root rot and other plant fungal diseases. This study applies salt lake-derived bacteria to plant roots, demonstrating their influence on soybean growth while providing a theoretical basis for further elucidating the antifungal mechanisms of B. velezensis YH7-4.

Soil nutrient deficiency is a major limiting factor affecting crop yields. Excessive use of chemical fertilizers can lead to soil compaction, environmental pollution, and decreased crop yields and quality. Microalgae-based fertilizer, functioning as a novel green bio-fertilizer, not only effectively promotes crop growth but also enhances soil fertility under various adverse soil conditions. Objectives This study investigated the effects of different fertilizer treatments on the growth of foxtail millet (Setaria italica L.) and the physicochemical properties, enzymes activities, and microbial communities of infertile soil, aiming to provide theoretical support for the application of microalgae-based fertilizer in chemical fertilizer reduction and green sustainable agricultural production. Methods The foxtail millet cultivar ‘Jingu 21’ was cultivated in this study under five fertilizer treatments: full chemical fertilizer (T1), chemical-microalgae integrated fertilizer (T2: 80% chemical fertilizer+20% microalgae-based fertilizer; T3: 60% chemical fertilizer+40% microalgae-based fertilizer; T4: 40% chemical fertilizer+60% microalgae-based fertilizer), and full microalgae-based fertilizer (T5). The growth indexes, biomass, and pigment content of foxtail millet in each treatment were determined, and the physicochemical properties, enzyme activities, and bacterial community characteristics of the infertile soil were measured, after 90 days of cultivation. Results Among the five fertilizer treatments, T4 had the most significant effect of promoting the seedling growth of foxtail millet in the infertile soil. Compared with T1, T4 increased the seedling height, the aboveground dry weight, and the content of chlorophyll a, chlorophyll b, and carotenoids by 26.41%, 126.47%, 17.1%, 24.5%, and 28.0%, respectively. In addition, T5, T2, T3, and T4 increased the content of total nitrogen, available phosphorus, and organic matter and the activities of sucrase, nitrate reductase, peroxidase, and phosphatase in the soil, compared with T1, and T4 had the most significant soil improvement effect. The 16S rRNA gene amplicon sequencing results showed that compared with T1 and T5, T4 increased the diversity of soil microorganisms, in which the relative abundance of Acidobacteriota and Chloroflexi was significantly increased. The correlation analysis showed that the composition of soil microbial diversity was significantly and positively correlated with urease, and the soil microbial community composition had significantly positive correlations with available phosphorus, sucrase, peroxidase, and urease. Redundancy analysis showed that urease and available phosphorus were the main environmental factors affecting the soil bacterial community structure. The relative abundance of Chloroflexi had significantly positive correlations with the urease activity and the available phosphorus content. Conclusion The combined application of microalgae-based fertilizer with reduced chemical fertilizer not only effectively improves the nutrient content and enzyme activities but also enhances the microbial diversity and community structure in the soil, thereby promoting the growth of foxtail millet seedlings in infertile soil.

Quorum sensing (QS) is a communication mechanism through which microorganisms secrete and sense signal molecules to regulate mircobial population behaviors. QS plays important roles in biofilm formation and gut colonization of probiotics. In recent years, interfering with the QS of probiotics has become a trending research field of synthetic biology. In this review, we summarize the distribution of QS systems in probiotics and highlights interfering strategies designed to regulate probiotic functions. We summary currently identified QS systems in probiotics and their detection methods, such as photoelectrochemical assays and chromatography-mass spectrometry techniques. Meanwhile, this review outlines the QS interfering approaches for probiotics, including the use of QS agonists and the optimization of related metabolic pathways. Finally, the probiotic intervention strategy targeting QS is proposed in this paper, providing a novel approach for regulating the efficacy of engineered probiotics, which is of great significance for the development and improvement of probiotic functional foods.

In recent decades, the extensive and inappropriate use of antibiotics has led to the emergence of antibiotic-resistant bacteria, posing a serious threat to human health. Phage therapy has emerged as a promising approach for preventing and treating infections caused by drug-resistant bacteria, garnering considerable research interest. However, the rapid development of phage-resistant bacterial strains complicates the effectiveness of phage therapy. The phage steering strategy holds promise for addressing this challenge. Objective To isolate virulent phages specific to Salmonella that are suitable for phage steering therapy. Methods Specific virulent phages for Salmonella S503 were isolated and purified from wastewater samples collected from a wet market via the double agar overlay method. Their fundamental biological characteristics, antibacterial efficacy, genomic information, and in vitro biological safety were analyzed. Phage-resistant strains were generated through co-culturing Salmonella S503 with the phages. Subsequently, growth curve analysis, bacterial virulence testing, and antibiotic sensitivity assays were employed to systematically compare the characteristics of the wild-type strain and its phage-resistant counterpart. Results The isolated Salmonella phage was designated HK-1. This phage exhibited strong antibacterial properties, high stability, and confirmed biological safety in vitro. Compared with the wild-type strain Salmonella S503, the phage-resistant strain Salmonella S503-R displayed slow growth, significantly reduced virulence, and increased susceptibility to 11 different antibiotics. Furthermore, phage HK-1 demonstrated synergistic bactericidal effects when being combined with rifampicin, ampicillin, fosfomycin, and gentamicin. Notably, the combinations of HK-1 with ampicillin, fosfomycin, and gentamicin effectively inhibited the growth of Salmonella S503 within 24 h. Conclusion We successfully isolated a virulent phage from wastewater samples. This phage is suitable for phage steering therapy and offers potential for the prevention and treatment of antibiotic-resistant Salmonella.

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 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.

China’s national food security faces rigid constraints due to land scarcity, a large population, and heavy reliance on imported feed proteins. In this context, the initiative to seek calories and proteins from microbes has become a strategic priority for building a diversified food supply system. Microbial alternative proteins represent a quintessential new quality productive force in agriculture. They offer distinct advantages, most notably high industrial efficiency and the ability to decouple protein production from food crops and arable land. This paper reviews China’s progress in this sector based on global biomanufacturing trends. The discussion focuses on synthetic biology-driven strain engineering, gas fermentation, and industrial-scale production. Furthermore, the article critically analyzes current bottlenecks, including intellectual property barriers for elite strains, high production costs, and lagging safety evaluation standards. Finally, we propose targeted recommendations to address these challenges. These include strengthening organized basic research, establishing an intelligent manufacturing system that integrates education, technology, and talents, and reforming regulatory frameworks. These insights aim to provide a strategic reference for China to secure a commanding position in the global bio-agriculture landscape.

Heavy ion radiation (HIR) is effective for generating new germplasm in plants and microorganisms due to its high mutation induction rate, broad mutagenesis spectrum, and excellent stability of mutants. However, the random mutagenesis induced by radiation limits the efficiency and quality of HIR-based mutation breeding, which has become a key problem to be tackled. According to the process of heavy ion radiation-based mutation breeding, this review proposes a set of tandem strategies to enable efficient and high-quality HIR-based mutation breeding practices. These strategies include adjusting the radiation parameters from multiple dimensions, regulating cellular sensitivity to radiation damage and damage repair capacity, combining heavy ion radiation with adaptive laboratory evolution, integrating heavy ion radiation with other mutagenic agents, adopting progressive radiation, formulating high-throughput screening schemes for mutants, and efficiently identifying, verifying, and integrating positive mutations. These strategies aim to improve the mutagenesis rate, screening efficiency, and utilization of positive mutations. Meanwhile, we envision a mutation breeding workstation that integrates a series of strategies to form a complete cycle for heavy-ion radiation-based mutation breeding. This study is expected to provide valuable insights for creating high-quality microbial resources through heavy-ion radiation.

Objective Chondroitinases are crucial enzymes for the preparation of low-molecular-weight chondroitin sulfate (CS), yet the existing enzymes are insufficient to meet the demands of diverse applications, highlighting the need to discover novel chondroitinases with enhanced properties. Methods A novel chondroitinase belonging to the polysaccharide lyase family 8 (PL8), designated SlChase, was discovered and identified from the model strain Streptomyces lividans TK24. Following heterologous expression in Escherichia coli and the subsequent purification, a soluble and highly active recombinant SlChase was successfully obtained. Results This enzyme exhibited substantial activity within the temperature range of 30-40 ℃ and pH range of 5.5-6.5, and demonstrated excellent long-term stability during storage at 4 ℃. Mg²⁺ and dithiothreitol (DTT) moderately enhanced its catalytic activity, whereas metal ions including Zn²⁺ and Fe³⁺ exerted inhibitory effects on its activity. Notably, SlChase displayed prominent activity towards unsulfated chondroitin (CS-0S), whereas its catalytic activity towards chondroitin sulfate A/C was drastically decreased. Conclusion The discovered SlChase not only expands the diversity of PL8 family enzymes but also affords a novel enzymatic tool for the specific degradation of unsulfated chondroitin, with promising applications in glycoscience research and related biocatalytic processes. Furthermore, this study provides a paradigm for the exploration and utilization of enzymatic resources derived from Streptomyces spp.