[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.

Crop diseases caused by phytopathogens result in great harm to global agriculture. Biocontrol has garnered increasing attention in plant disease prevention and control because of its effectiveness and environmental friendliness. [Objective] To identify, analyze the genome, and evaluate the disease-resistant and plant growth-promoting effects of the strains with antagonistic activities that were screened from the culture collection. [Methods] Antagonistic strains were screened by plate confrontation method. and identified by morphological observation, phylogenetic analysis based on the 16S rRNA gene and genome, comparative analysis of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values, and physiological and biochemical tests. The whole genome sequence of the target strain was analyzed for the mining of functional genes. The plant growth-promoting effect of the target strain was characterized in terms of the phosphorus-solubilizing, siderophore-producing, and proteinase- and cellulose-producing properties. The inhibition of volatile gas produced by the target strain on phytopathogenic fungi was examined in petri dishes with a septum. The effects of the target strain on tomato growth and diseases were studied by pot experiments. [Results] Strain MB1019 with obvious inhibitory effects on Ralstonia solanacearum and three phytopathogenic fungal strains was screened out and identified as Bacillus velezensis. The physiological and biochemical tests showed that strain MB1019 tolerated the temperature of 15-50 ℃, 10.0% NaCl, and pH 5.0-9.0. The genome of strain MB1019 was 3.8 Mb in length, with the G+C content of 46.4%. The prediction on antiSMASH suggested that the MB1019 genome had 17 synthetic gene clusters for secondary metabolites. The prediction on dbCAN2 suggested that MB1019 carried 108 genes belonging to 52 types of the CAZy family, among which glycoside hydrolases (GHs) were the richest and most abundant. The volatile gas produced by MB1019 significantly inhibited the growth of phytopathogenic fungi. The results of pot experiments showed that MB1019 promoted the growth and inhibited the diseases of tomato seedlings. [Conclusion] B. velezensis MB1019 capable of antagonizing R. solanacearum and phytopathogenic fungi has tolerance to high temperatures and saline-alkali and demonstrates plant growth-promoting effects. Its genome contains a large number of functional genes, and the volatile gas produced by this strain can inhibit the growth of pathogenic fungi. The fermentation broth of MB1019 has the effects of promoting the growth and preventing the diseases of tomato seedlings. In summary, B. velezensis MB1019 can be used as an elite strain in the research and development of microbial fertilizers and pesticides, demonstrating promising development and application prospects.

Oudemansiella raphanipes is a rare edible and medicinal mushroom, while it is highly susceptible to cobweb disease caused by Cladobotryum varium. [Objective] To obtain bacteria capable of controlling cobweb disease and promoting the mycelial growth of O. raphanipes from casing soil. [Methods] Bacteria were isolated from the casing soil of O. raphanipes, and their antagonistic activity against the mycelial growth of both O. raphanipes and C. varium was evaluated. The strains with disease-preventing and growth-promoting properties were screened out, and their functioning mechanisms were studied based on genome data. [Results] A total of 90 bacterial strains were isolated from the casing soil, of which 38 strains showed significant inhibitory activity against the mycelial growth of C. varium and no inhibitory activity against that of O. raphanipes. The supernatants of two strains significantly inhibited the mycelial growth of C. varium and promoted that of O. raphanipes. Based on the genome data, the above two strains were identified as Peribacillus simplex and Ochrobactrum rhizosphaerae, respectively, and they carried multiple functional genes and biosynthetic gene clusters of secondary metabolites. [Conclusion] Two bacterial strains capable of controlling the disease and promoting the growth of edible fungi were obtained, providing valuable microbial resources for the future biocontrol of cobweb disease.

[Objective] To investigate the regulatory effect of transforming growth factor-beta 1 (TGF-β1)/Smad3 on orosomucoid (ORM) expression during infection with influenza A/WSN/33 virus (hereinafter referred to as WSN). [Methods] A549 cells were either infected with WSN or treated with TGF-β1, followed by treatment with Smad3 inhibitors. The mRNA levels of ORMs were assessed by RT-PCR. Subsequently, cell lines with signal transducer and activator of transcription 3 (STAT3) overexpression and knockdown were established, and RT-PCR and Western blotting were employed to evaluate the impact of STAT3 on ORM expression induced by the influenza virus. Furthermore, A549 cells underwent treatment with TGF-β1, after which the phosphorylation status of STAT3 was analyzed via Western blotting. Finally, the phosphorylation level of STAT3 was detected after inhibiting the activity of Smad3 or knocking down the expression of Smad3 in A549 cells infected with WSN or treated with TGF-β1. [Results] TGF-β1 regulated the expression of ORM1 and ORM2 through the activation of Smad3, a key mediator in the TGF-β signaling pathway. Concurrently, STAT3 was implicated in modulating ORM1 and ORM2 expression during WSN infection. Additionally, TGF-β1 was shown to induce STAT3 phosphorylation. Notably, inhibiting Smad3 activation or knocking down Smad3 expression suppressed STAT3 phosphorylation. [Conclusion] The regulation of ORM1 and ORM2 expression by WSN relied on STAT3 phosphorylation mediated by TGF-β1/Smad3.

[Objective] Rummeliibacillus, a genus encompassing three known species, R. stabekisii, R. pycnus, and R. suwonensis, has a wide range of potential applications in biodegradation, probiotics, animal feed, and production of arginine, caproic acid, and other compounds. This study aims to explore the genetic diversity of this genus at the genomic level. [Methods] A comparative pangenome analysis of 12 strains isolated from different sources was conducted. In addition, the phylogenetic analysis, functional annotation, genomic metabolic pathway analysis, and prediction of mobile genetic elements were carried out. [Results] A total of 8 024 gene clusters were identified. The core genome, accessory genome, and strain-specific genes comprised 1 550, 3 941, and 2 533 gene clusters, respectively. In the core genome, the arginine cycle of six strains was complete. Seven strains had the ability to completely biosynthesize acetoin. However, only R. pycnus and R. suwonensis 3B-1 were able to completely biosynthesize caproic acid. The phylogenetic tree, DNA-DNA hybridization, and average nucleotide identity showed that Rummeliibacillus sp. G93 and Rummeliibacillus sp. TYF-LIM-RU47 were strains of R. stabekisii. Rummeliibacillus sp. POC4 and Rummeliibacillus sp. TYF005 may belong to a new species of this genus. In addition, genomic islands were identified in all the 12 strains, with the number ranging from four (R. stabekisii DSM 25578 and R. stabekisii NBRC 104870) to 14 (Rummeliibacillus sp. SL167 and Rummeliibacillus sp. TYF005), and prophage sequences were found in five of the 12 strains. [Conclusion] This study provides a genomic framework for Rummeliibacillus that could assist the further exploration of this genus.

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] 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 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.

The fermentation, morphological observation, and metabolite purification of mycelial pellets and the application of mycelial pellets in sewage treatment and energy recovery have gained widespread attention from researchers in the fields of environment and biology. To get a full picture of the research hotspots and trends of mycelial pellets. We screened 1 337 scientific articles related to the application of mycelial pellets that were published in the past 20 years from the Web of Science. The clustering and temporal trends of keywords and the co-occurrence of countries, authors or institutions were visually analyzed. The annual number of published articles was on the rise, involving a total of 97 topics, and interdisciplinary articles were abundant and tended to have higher cited frequency. China's achievements in this field kept a leading position and China maintained close cooperation with other countries. The hot keywords remained stable (growth, morphology, fermentation, removal, degradation, mycelial pellets, biological control, fungi, culture, optimization, biodegradation, and biosorption), and the uptrending and emerging keywords changed in recent years. The application of mycelial pellets in water treatment had been increasingly studied, with the related keywords (waste water, performance) becoming increasingly frequent. Emerging keywords related to wastewater treatment with mycelial pellets as carriers (biomass, bacteria), synthesis by mycelial pellets (biosynthesis), and water treatment with both mycelial pellets and algae (Chlorella vulgaris, microalgae) remained hot. This result indicates that research on the application of mycelial pellets in water treatment has gradually evolved into more systematic research directions, which will become future research hotspots and opportunities.

Type 2 diabetes mellitus (T2DM) is a prevalent metabolic disease, yet its pathogenesis remains inconclusive. Recent studies have revealed a close relationship between the gut microbiota and T2DM, and specific gut microbiota structures and metabolic characteristics are associated with the onset and progression of T2DM. Exercise is an effective intervention for the prevention and management of T2DM, capable of reversing the dysbiosis induced by T2DM and regulating gut metabolites. However, the effects of exercise on the gut microbiota in T2DM patients still present many unresolved issues. Furthermore, the regulation of gut microbiota by exercise in T2DM patients is closely linked to multiple organs and can exert alleviation effects on T2DM via various gut-organ axis pathways. This paper reviews the characteristics of gut microbiota in T2DM and the effects of exercise on the gut microbiota in T2DM, with a particular focus on the mechanisms by which exercise regulates the gut microbiota to ameliorate T2DM via the gut-organ axis. This review aims to provide a reference for elucidating the relationship between exercise, gut microbiota, and T2DM.