[Objective] Microorganisms are key executors of the migration and transformation of geochemical elements in intertidal zones. Fungi play an important role in the cycling of carbon, nitrogen, and phosphorus and the degradation of organic pollutants. [Methods] In this study, soil samples were collected from the rhizosphere and non-rhizosphere of Phragmites australis, Tamarix chinensis, and Suaeda salsa (intertidal zone and saline inland), which were the typical intertidal plants in the Yellow River Delta. The fungal community structures in different soil samples were investigated by high-throughput sequencing. [Results] In the rhizosphere, the soil sample of S. salsa in saline inland showed higher fungal abundance, richness, and evenness than other soil samples, with a distinct fungal community structure. In the non-rhizosphere, the fungal abundance, richness, and evenness were the highest in the soil samples of P. australis, S. salsa in saline inland, and T. chinensis, respectively, and the fungal community structure of P. australis was similar with that of S. salsa in saline inland. Ascomycota and Basidiomycota were the dominant fungal phyla in both the rhizosphere and non-rhizosphere. However, the functional fungi were different among plants. Saprophytic fungi such as Alternaria and Aspergillus were the dominant functional fungi in the rhizosphere and non-rhizosphere of P. australis, T. chinensis, and S. salsa in saline inland, with the relative abundance of 13.60%, 6.33%, and 20.16% in the rhizosphere and 11.98%, 24.25%, and 8.52% in the non-rhizosphere, respectively. Saprophytic fungi were essential for the production of humus by decomposition of organic matter and the improvement of soil aeration and physicochemical properties. Aureobasidium (1.51%) were identified in the non-rhizosphere of T. chinensis, and they were haloduric fungi and could work synergistically with plants to prevent soil salinization. The dominant functional fungi in the rhizosphere of S. salsa in intertidal zone were mainly Talaromyces (15.90%) and Stachybotrys (0.53%), which were involved in sugar degradation. They were able to break down cellulose into glucose, produce humus, and form a stable soil aggregate structure to improve soil aeration. Trichoderma (0.13%) were identified in the rhizosphere of S. salsa in saline inland, and they could promote soil nitrogen and phosphorus conversion and prevent the soil pollution caused by excessive inorganic phosphorus. The relative abundance of functional fungi was less than 0.10% in the non-rhizosphere. In addition, Phanerochaete (0.15%) capable of degrading persistent organic pollutants and Penicillium (1.16%) capable of degrading quinones were identified in the non-rhizosphere, providing microbial resources for the remediation of organic pollution in soil. However, they were not identified in the plant rhizosphere. The fungal diversity and evenness in the rhizosphere were positively correlated with soil factors such as electrical conductance (EC), calcium concentration, and salinity. In the non-rhizosphere, the fungal richness and diversity were positively correlated with total nitrogen, while the fungal evenness was positively correlated with pH, salinity, and ammonia nitrogen. [Conclusion] This study established a framework for understanding the structures and functions of fungal communities in the intertidal zone of the Yellow River Delta. Additionally, it provides a theoretical foundation for the future application of different functional fungi in soil structure improvement, biodiversity maintenance, organic pollution treatment, ecological protection, and saline-alkali land restoration.

[Objective] To investigate the plant microbiome changes in response to wheat head blight and the correlation between the abundance of differential microorganisms and the pathogen Fusarium graminearum, and elucidate the intricate interplay between plant microbiome and disease occurrence. [Methods] We collected samples from both healthy and diseased plants in the field, combined with high-throughput sequencing to analyze the characteristics of plant microbiome changes, and the abundance of pathogen was determined by RT-qPCR to reveal the response of plant microbial community changes to wheat head blight. [Results] The alpha diversity of bacteria in wheat spikes and fungi in the rhizosphere significant increased under the disease stress, with enrichment of potentially beneficial bacteria in spikes of diseased wheat plants. Healthy plants displayed higher stability of microbial community and network than diseased plants. Plant microbial diversity can predict alterations in pathogen abundance. Notably, the microbial diversity and community stability explained the most (76.95%) variations in pathogen abundance. High fungal diversity and community stability were associated with reduced pathogen colonization. [Conclusion] Significant discrepancies of the plant microbiome were identified between healthy and diseased plants. The stable microbial community and network interactions in the spikes of healthy plants facilitate the resistance against F. graminearum infection. Additionally, the “call for help” phenomenon was observed as wheat plants recruited beneficial microflora in spikes, expanding the applicability of the “call for help” strategy. By examining the connection between plant microbiome and disease occurrence, this study presents crucial data and a theoretical framework for the targeted manipulation of plant microbiome to enhance disease prevention and control.

[Objective] To analyze the application trends and distribution of artificial intelligence in synthetic biology from the patent perspective, providing practical insights and theoretical support for technological innovation, research and development (R&D) direction, and industrial layout of this field. [Methods] The paper presents a comprehensive overview of the research contents and methodologies of synthetic biology, and delves into the evolving landscape of artificial intelligence in synthetic biology by extensive patent network mining and literature analysis. [Results] Through thorough examination of pertinent patent data, this study unveils the application patterns and disclosure trends of artificial intelligence in synthetic biology alongside the major countries involved and key applicants. Furthermore, it analyzes the advancements in biosynthetic gene clusters, protein structure analysis, and transcription factor binding sites from the patent perspective. Additionally, this paper expounds the challenges confronting the integration of artificial intelligence into synthetic biology while offering recommendations to address them. [Conclusion] The findings presented herein offer valuable insights into understanding the technical developmental context surrounding artificial intelligence in synthetic biology while serving as a reference for relevant enterprises and research institutions when making R&D decisions. Moreover, this paper underscores the pivotal role played by artificial intelligence in advancing development of synthetic biology while emphasizing its significance. Simultaneously, it provides suggestions to further bolster research efforts on integrating artificial intelligence into synthetic biology with an aim to generate innovative ideas and technical support for constructing national science and technology information systems in global science and technology competition scenarios—particularly concerning advances in synthetic biology.

Phaseolus vulgaris L. is one of the key edible legumes in the world. Rhizosphere microorganisms have mutually beneficial interactions with plants, being important factors promoting crop growth and health. However, studies are limited regarding how to utilize the microbiomes of legumes to promote crop growth. [Objective] To investigate the structural and functional differences of microbial communities in the rhizosphere and root nodules between two varieties (‘Ziguan' and ‘Juguan') of P. vulgaris, screen rhizobial strains, and evaluate their nitrogen-fixing and growth-promoting properties. [Methods] We employed 16S rRNA gene sequencing to analyze the bacterial community structures in the rhizosphere and root nodules of the two varieties. The rhizobial strains were screened by the plate streaking method. Pot experiments with nitrogen-free vermiculite were carried out to evaluate the nitrogen-fixing performance of the 11 rhizobial strains screened out. [Results] The bacterial diversity in the rhizosphere soil of ‘Juguan' was significantly lower than that of ‘Ziguan', and the bacterial diversity in the rhizosphere soil samples of both varieties was significantly higher than that in the root nodule samples. In addition, the rhizosphere of P. vulgaris harbored beneficial bacterial genera such as Rhizobium, Sphingomonas, Burkholderia, among which Rhizobium was dominant in the root nodules of both varieties. Gephi network analysis showed that bacterial communities in the rhizosphere and root nodules had positive correlations, with the relative abundance of 75.52% and 86.67%, respectively. PICRUSt2 function prediction indicated that the bacteria in the rhizosphere mainly had the functions related to carbohydrate, amino acid, and lipid metabolism, with abundant genes involved in nitrogen metabolism. Pot experiments showed that Rhizobium lusitanum NZ5 and R. etli GLJ10 increased the underground dry weight of ‘Ziguan' by 43.21% and 48.15%, respectively. R. lusitanum NZ5, R. etli GLZ1, and R. changzhiense GLJ12 increased the underground dry weight of ‘Juguan' by 77.37%, 68.42%, and 67.37%, respectively. [Conclusion] P. vulgaris possesses ability to selectively enrich a variety of microorganisms in the soil, establishing a closely coordinated and highly functional microbial community in the rhizosphere. Moreover, different rhizobial strains exerted varied growth-promoting effects on P. vulgaris.

Plants require a large amount of phosphorus for metabolic processes. However, the available phosphorus in the soil is typically less than 0.1% of total phosphorus, which is difficult to meet the growth and development of plants. The symbiosis system of ectomycorrhizal fungi and mycorrhizal helper bacteria can significantly improve the availability of soil phosphorus and promote the efficient uptake of phosphorus by plants. In this review, we discussed the solubilization and mineralization of chelated inorganic phosphorus, soluble organic phosphorus, and chelated organic phosphorus by ectomycorrhizal fungi and mycorrhizal helper bacteria. Ectomycorrhizal fungi mainly promote the solubilization of chelated inorganic phosphorus by regulating the organic acid and proton metabolism of mycorrhizal helper bacteria. They accelerate the mineralization of soluble organic phosphorus by enhancing the activities of related phosphatases in themselves and in mycorrhizal helper bacteria. Ectomycorrhizal fungi may first stimulate the mycorrhizal helper bacteria to secrete organic acids for solubilizing chelated organic phosphorus into soluble phosphorus before mineralization. Moreover, we explored the molecular mechanisms of metabolite signal exchange and secretion in the symbiosis system and outlined the prospects for studying the interactions between ectomycorrhizal fungi and mycorrhizal helper bacteria in promoting plant phosphorus uptake.

[Objective] To investigate the invitro inhibitory activity of Gan Dan oral liquid (GD) against Vibrioparahaemolyticus and decipher the inhibition mechanism at the transcriptome level. [Methods] The invitro inhibitory activity of GD against V. parahaemolyticus was evaluated based on the minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and growth curve. Scanning electron microscopy and transmission electron microscopy were employed to analyze the effect of GD on the cellular structure of V. parahaemolyticus. Transcriptome sequencing coupled with bioinformatics methods were employed to investigate the effect of GD at 1/4MIC on the transcriptome of V. parahaemolyticus, and the obtained results were examined by real-time quantitative reverse transcription PCR (RT-qPCR). [Results] GD exhibited high invitro inhibitory activity against V. parahaemolyticus, with the MIC and MBC of 7.6 mg/mL and 15.2 mg/mL, respectively. The GD treatment at a concentration of 1/4MIC disrupted the cell wall integrity and increased cell membrane permeability of the pathogen, and leading to the leakage of intracellular macromolecules. The results of transcriptome sequencing showed that GD treatment significantly altered the transcriptome profile of V. parahaemolyticus, resulting in significant upregulation of 1 074 genes and significant downregulation of 1 179 genes. The downregulated genes were mainly enriched in pathways related to the synthesis of inosinate and ribonucleoside, whereas the upregulated genes were primarily categorized into pathways associated with transcription factor activity and cell wall synthesis. [Conclusion] GD may inhibit V. parahaemolyticus by disrupting cell structure and inhibiting cellular energy metabolism and biosynthesis.

[Objective] To explore the role of VraSR in regulating the biological functions of Staphylococcus epidermidisvia the CidA-LrgAB system. [Methods] The recombinant plasmid pKOR1-ΔlrgAB was constructed and then electroporated into SE1457 ∆vraSR to delete lrgAB from the genome of ∆vraSR by homologous recombination. The suspected mutant ∆vraSR-lrgAB was verified by PCR, RT-PCR, and sequencing. The growth, drug susceptibility, autolysis, and biofilm formation of ∆vraSR-lrgAB were determined. [Results] The S. epidermidis mutant ∆vraSR-lrgAB was successfully constructed. Compared with SE1457, ∆vraSR, and ∆lrgAB, ∆vraSR-lrgAB exhibited retarded growth, especially at 25 ℃ and 40 ℃ (P<0.001), increased drug susceptibility (P<0.01), enhanced autolysis (P<0.001), and reduced biofilm formation (P<0.01). [Conclusion] VraSR may regulate the growth, drug susceptibility, autolysis, and biofilm formation of S. epidermidis partly via the LrgAB system.

Salmonella as common zoonotic pathogens can cause a variety of foodborne diseases. Salmonella Typhimurium (STM) is one of the key serotypes, and the research, prevention, and control of STM are of great significance to public health. [Objective] To investigate the effects of greA and greB on the biological characteristics and pathogenicity of STM. [Methods] Red homologous recombination was employed to construct the greA- and greB-deleted STM strains well as the complemented strains. The strains were then characterized in terms of growth characteristics, biofilm formation, and adhesion and invasion in Caco-2 cells. Mouse models were used to evaluate the effects of greA and greB deletion on STM pathogenicity. [Results] The mutant strains STM LT2ΔgreA and STM LT2ΔgreB were successfully constructed. Compared with the wild-type strain, the deletion of greA and greB did not affect the cell growth rate, while inhibiting the biofilm formation, adhesion, and invasion of STM. In addition, the deletion of greA and greB decreased the colonization of STM in the liver and spleen of mice, increasing the LD₅₀ of STM by 39.81 times and 2.5 times, respectively. [Conclusion] The deletion of greA and greB could reduce the pathogenicity of STM. This finding provides a theoretical basis for further revealing the pathogenicity of Salmonella.

Acheta domesticus densovirus (AdDV) was first isolated from infected crickets in Switzerland, 1977 and caused several outbreaks in Europe and the United States. Cricket iridovirus (CrIV), first identified in the Netherlands in 1996, caused a high mortality rate, reduced the fertility, and shortened the life span of infected crickets. The house cricket (Acheta domesticus), was originated from south west Asia and introduced into China as food for reptile pets in recent decades. AdDV and CrIV are common pathogenic viruses that infect house crickets. Unveiling the virus epidemics of house crickets becomes increasingly important with the development of the house cricket industry. [Objective] To understand the epidemic status of AdDV and CrIV in China, so as to lay a theoretical basis for controlling AdDV and CrIV infections in the house cricket industry and developing effective prevention and control measures. [Methods] Virus-specific PCR was performed to detect pathogens of the crickets reared in farms spanning different regions of China. The pathogens of the infected crickets were further proved by Sanger sequencing. Transmission electron microscopy was employed to observe the virions in different tissue samples (e.g., gut and fat body) of the infected crickets. [Results] AdDV virions were icosahedral-shaped particles, nearly spherical, without envelope, with a diameter around 20 nm. It formed dense chromatin regions in the nucleus of the host cell, showing typical features of densovirus. CrIV virions were nonenveloped icosahedral-shaped particles with a diameter of 120-140 nm. A large number of CrIV virions formed a lattice-like arrangement in the cytoplasm, which is a typical feature of iridovirus. The virus-specific PCR detected AdDV in crickets collected from all the on-line shops distributed in different regions of China. CrIV was also detected in crickets collected from most (91%) of the on-line shops. The majority (91%) of detected crickets were infected with both AdDV and CrIV. [Conclusion] For the first time AdDV and CrIV were found to have been widely spread in China.

[Objective] To understand the microbial community structure and its relationship with soil quality in the rhizosphere of the dominant plant Xanthium sibiricum in the water-level-fluctuation zone (WLFZ) of the Three Gorges Reservoir. [Methods] We collected the rhizosphere soil samples of X. sibiricum exposed to different flooding stress conditions in a typical WLFZ in Yunyang County, the heart of the Three Gorges Reservoir area. High-throughput sequencing was carried out to analyze the microbial diversity and community structure, and the redundancy analysis was then conducted. [Results] Proteobacteria was the dominant bacterial phylum in the rhizosphere bacteria of X. sibiricum under strong flooding stress (XaRLL) and weak flooding stress (XaRHL), while Ascomycota and Basidiomycota were the dominant fungal phyla in the two types of soil, respectively. Regardless of bacteria or fungi, the linear discriminant analysis effect size (LEfSe) showed that XaRLL always had more key biomarkers than XaRHL. Functional prediction revealed that PWY-3781 associated with aerobic respiration was a dominant metabolic pathway enriched by microorganisms from both XaRLL and XaRHL. Overall, the bacteria and fungi in the rhizosphere of X. sibiricum had strong responses to changes in soil physicochemical properties and enzyme activity. [Conclusion] The results provide a theoretical basis for understanding the relationship between plants and their rhizosphere microorganisms in the WLFZ, as well as their adaptability to strong flooding stress.