Objective The rhizosphere microbial community plays a critical role in plant growth, development, and quality formation. Therefore, this study systematically isolated plant growth-promoting microbial resources from the rhizosphere of Bupleurum chinense and evaluated their application potential, aiming to provide excellent strains for the development of microbial fertilizers to reduce the use of chemical fertilizers and pesticides. Methods Plant growth-promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) were isolated and identified from the rhizosphere of B. chinense by the culture-dependent methods. Functional traits of PGPR strains were screened through in vitro assays, and the synergistic growth-promoting effects of PGPR and AMF were subsequently evaluated by a pot experiment. Results A total of 25 PGPR species and 2 AMF species (Funneliformis mosseae and Entrophospora etunicata) were isolated from the rhizosphere of B. chinense. Functional screening of PGPR revealed that Lysobacter antibioticus, Pseudomonas germanica, Rhodococcus corynebacterioides, and Methylobacterium marchantiae exhibited outstanding abilities in indole-3-acetic acid production, organic phosphorus solubilization, inorganic phosphorus solubilization, and nitrogen fixation, respectively. The pot experiment showed that co-inoculation with PGPR and AMF significantly enhanced the plant growth, biomass accumulation, and nutrient uptake of B. chinense, with plant growth-promoting effects markedly greater than single inoculation treatments. Conclusion This study isolated and identified some plant growth-promoting microorganisms from the rhizosphere of B. chinense and demonstrated the synergistic effects between PGPR and AMF, providing valuable microbial resources and theoretical bases for the sustainable cultivation of B. chinense.

Objective To isolate and characterize plant growth-promoting rhizobacteria (PGPR) from the roots of the rice variety YTZ and the backcross progeny H8 with tolerance to low nitrogen and low phosphorus, and evaluate the potential of PGPR in promoting the growth of rice seedlings. Methods Bacterial strains were isolated by plate streaking and taxonomically identified through 16S rRNA gene sequencing. Functional traits, including phosphate solubilization, nitrogen fixation, and indole-3-acetic acid (IAA) production, were assessed for strain selection. Whole-genome sequencing was performed to mine functional genes and elucidate potential molecular mechanisms of target strains. Pot experiments were conducted to evaluate strain effects on the physicochemical properties of soil and nutrient (nitrogen and phosphorus) uptake of seedlings, while 16S rRNA gene amplicon sequencing was employed to analyze rhizosphere microbial community dynamics. In addition, synthetic microbial consortia and carrier combinations were developed and assessed for application feasibility. Results Seven strains with phosphate-solubilizing and nitrogen-fixing capabilities were obtained, and their IAA production was quantitatively determined. Five representative strains were selected for pot experiments. Among them, B. altitudinis Hxx04 exhibited the strongest plant growth-promoting effect, increasing the fresh weight by 47.2% and plant height by 48.6%, while significantly enhancing nitrogen and phosphorus uptake efficiency of rice seedlings. Inoculation with Hxx04 led to marked reductions in soil total nitrogen, alkali-hydrolyzable nitrogen, total phosphorus, and available phosphorus, indicating improved nutrient uptake by rice plants. Rhizosphere community analysis revealed increased microbial abundance following inoculation, which supported the nitrogen supply for seedling growth. Furthermore, a synthetic microbial consortium centered on B. altitudinis Hxx04 performed optimally when being inoculated with the carrier combination of bentonite and straw. Conclusion B. altitudinis Hxx04 demonstrated high efficiency in nitrogen and phosphorus utilization and significantly promoted rice growth (evidenced by increased fresh weight and plant height), thereby reducing chemical fertilizer dependence. Its dual contribution to yield enhancement and environmental sustainability highlights its potential as a valuable microbial resource for green agriculture, supporting the goal of coordinating nutrient use efficiency with ecological conservation in rice production.

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.

Litchi (Litchi chinensis Sonn.) is one of the important tropical and subtropical fruits in China. However, litchi downy blight caused by the infection of Peronophythora litchii (Peronophythora litchii Chen ex Ko et al.) a severe disease damaging litchi during production, storage, and transportation, seriously threatening the healthy development of China’s litchi industry. Objective We screened effective antagonistic bacteria against P. litchii and evaluated their plant growth-promoting potential, aiming to enrich the resources of antagonistic bacteria against P. litchii. Methods Soil samples from the litchi rhizosphere were collected, and the bacteria in the samples were isolated through a high-throughput isolation and culture method. The strains were identified by means of 16S rRNA gene sequence analysis. The antagonistic strains against P. litchii were screened via the plate confrontation method, and the plant growth-promoting functions [phosphorus solubilization, potassium solubilization, nitrogen fixation, siderophore secretion, and indole-3-acetic acid (IAA) production] of the antagonistic strains were further evaluated through functional plates. Results A total of 327 bacterial strains were isolated in this study, among which 92 (28.13%) strains were identified as antagonists (with mycelial growth inhibition rates>40%) against P. litchii. These antagonistic strains belonged to 4 phyla, 6 classes, 12 orders, 20 families, and 42 genera, with Bacillota and Pseudomonadota being the dominant phyla, and Bacillus and Paenibacillus as the dominant genera. Functional evaluation of the 92 antagonistic strains revealed that 55 (59.8%) strains exhibited more than one plant growth-promoting function, while 30 (32.6%) strains possessed three or more such functions. Through comprehensive evaluation of antagonistic activity and plant growth-promoting functions, one Brevibacillus strain T101, four Paenibacillus strains (T431, T270, T327, and T234a), and one Paraburkholderia strain R116b were identified as the most promising strains for biocontrol applications. Conclusion Multiple antagonistic strains against P. litchi,with functions of phosphorus solubilization, potassium solubilization, nitrogen fixation, siderophore secretion, and IAA production, are screened out, which provides efficient strain resources for the green control of litchi downy blight.

Objective To explore microbial resources suitable for the ecological restoration of saline-alkaline soils and elucidate their stress tolerance and plant growth-promoting traits, thereby providing a theoretical basis for biotechnology-driven sustainable agricultural development. Methods Plant growth-promoting rhizobacteria (PGPR) were isolated and screened from the rhizosphere soils of three representative halophytes—Tamarix ramosissima, Lycium ruthenicum, and Kalidium foliatum—growing in the Minqin Oasis, Gansu Province, northwestern China. Selected strains were taxonomically identified by 16S rRNA gene sequence analysis. Their functional traits were systematically evaluated, including nitrogen fixation, phosphate solubilization, and production of indole-3-acetic acid (IAA), exopolysaccharides (EPS), and siderophores. In addition, stress tolerance under salinity, drought, pH, and temperature gradients, as well as antagonistic activity against six common phytopathogenic fungi, was assessed. Results A total of 62 bacterial isolates were obtained, among which seven multifunctional PGPR strains (HL3, HL6, HL12, HG3, HG8, HG12, and HG24) were selected and identified as Priestia filamentosa, Bacillus atrophaeus, Pantoea endophytica, Peribacillus frigoritolerans, Bacillus aryabhattai, Bacillus subtilis subsp. stercoris,and Paenibacillus peoriae, respectively. All the selected strains exhibited at least two plant growth-promoting traits. Notably, strains HL6 and HG24 simultaneously possessed nitrogen-fixing ability, phosphate-solubilizing capacity, and the ability to produce IAA, EPS and siderophores, showcasing pronounced multifunctionality. Stress tolerance assays showed that strains HL3 and HL6 tolerated up to 12% NaCl, while HL3 and HG8 withstood osmotic stress equivalent to -20 bar. Most strains remained active under alkaline conditions (pH 9.0) and within a temperature range of 28-45 ℃. Antagonistic assays revealed that HL6 inhibited all six tested phytopathogenic fungi, and HG24 exhibited broad-spectrum antagonistic activity against five pathogens, with the strongest inhibition observed against Alternaria solani. Conclusion This study demonstrates that PGPR isolated from the rhizosphere of halophytes in arid regions possess diverse plant growth-promoting functions and strong stress tolerance. These multifunctional and resilient strains represent valuable microbial resources for saline-alkaline soil remediation and the development of locally adapted biofertilizers, contributing to sustainable agriculture and ecological restoration in arid environments.

Objective To develop a fluorescence method for Vibrio parahaemolyticus detection by the combination of CRISPR system and the hybridization chain reaction (HCR), thus achieving rapid, sensitive, and accurate detection of the pathogen. Methods Cascade probe (RP/I) and HCR hairpin structures were first designed according to a specific conserved sequences screened from V. parahaemolyticus. Subsequently, the feasibility, specificity, and sensitivity of the method were evaluated after the optimization of reaction conditions. Furthermore, V. parahaemolyticus-contaminated aquatic products were used to validate the interference resistance of the method. Results The cleavage of CRISPR/Cas13a was activated upon binding to the target RNA (T-RNA), leading to the trans-cleavage of the RP/I cascade probe and the release of I strand. Then, the released I strand subsequently triggered HCR, generating a significant fluorescence signal for target detection. The established method successfully distinguished target sequences with single-base, double-base, and triple-base mismatches and enabled the specific identification of V. parahaemolyticus against other non-target bacteria, including V. alginolyticus, V. vulnificus, V. harveyi, V. cholerae, and Escherichia coli, demonstrating excellent specificity. The assay showed a good linear correlation over a T-RNA concentration range of 25 pmol/L to 10 nmol/L. The corresponding linear regression equation was y=7 236.75×lg C_T-RNA-8 590.11 (R²=0.99, C represents the T-RNA concentration and y represents the fluorescence intensity), with the LOD of 1.01 pmol/L. The proposed method enabled rapid detection of RNA extracted from V. parahaemolyticus in various aquatic products, yielding results consistent with those obtained by RT-qPCR. Conclusion The fluorescence method based on CRISPR/Cas13a-HCR established in this study realizes rapid detection of V. parahaemolyticus, demonstrating good sensitivity, specificity, and accuracy.

The dark matter of microbes, encompassing uncultivated microbial taxa and unknown biological features, has been widely accepted by microbiologists. With the advancement of microbial investigation methods, a series of dark matter concepts related to microbes have been successively proposed, and numerous research advances in this field have been well-documented. However, these concepts exhibit complex and overlapping connotations, and their inherent connections and distinctions have not yet been clearly clarified. This review work systematically summarizes the current conceptual frameworks of different dark matter types of microbes and analyzes the relevant investigation methodologies and their development trends. This article will help researchers in the microbial resource field gain a clearer understanding of the conceptual connotation and current research status of microbe-associated dark matter and promote the in-depth development of dark matter resource mining.

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.

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.

Objective To address problems such as the poor structure and fertility degradation in strongly acidic soils, we isolated acid-tolerant exopolysaccharide (EPS)-producing microorganisms, constructed a composite microbial inoculant, and evaluated its improvement effects on the structure and comprehensive fertility of acidic soils. Methods Target strains were obtained through primary and secondary screening from strongly acidic soils (pH<4.5) in Nanchuan, Chongqing and Qujing, Yunnan. After their antagonistic activity and plant growth-promoting traits were assessed, a composite microbial inoculant was constructed. A laboratory soil culture experiment was conducted to investigate changes in nutrient contents and aggregate composition in strongly acidic soils treated with different inoculants, comprehensively evaluate the fertility-improving effects of the inoculants, and clarify the correlation between aggregate formation and EPS content. Results Three strains—Paraburkholderia fungorum C3, Burkholderia cepacia A13, and Cystobasidium minutum B14—with acid tolerance and high EPS-producing capabilities were successfully isolated and screened out. All the strains exhibited the capabilities of secreting indole-3-acetic acid (IAA), synthesizing siderophores, and solubilizing phosphorus. When these strains were applied individually or as a composite inoculant to soils, the composite inoculant showed the best effect of improving soil nutrients, increasing the content of soil organic matter, alkaline-hydrolyzable nitrogen, available phosphorus, and available potassium by 4.51%, 13.92%, 4.92%, and 3.71%, respectively. Application of all the inoculants effectively promoted the formation of soil macro-aggregates, among which the single-strain inoculant C3 had the most significant effect in promoting aggregate formation, increasing the soil mean weight diameter (MWD) by 19.39%. The integrated fertility index of the soil treated with the composite inoculant reached 0.61, indicating the optimal comprehensive improvement effect. The single-strain inoculant C3 and the composite inoculant significantly increased the soil EPS content by 53.17% and 35.79%, respectively. Correlation analysis results showed that soil EPS had significantly positive correlations with macro-aggregate content and MWD, significantly promoting the formation and enhancing the stability of soil macro-aggregates. Conclusion The composite inoculant composed of the three acid-tolerant EPS-producing strains screened in this study effectively improved the soil structure and enhanced the integrated soil fertility. These findings lay a theoretical foundation for the development of biological agents for acidic soil remediation.