[Objective] To unravel the mechanism underlying the high-yield performance of hybrid pepper (Capsicum annuum L.) progenies and dissect parent-progeny differences across four interconnected dimensions: plant nutrient accumulation, rhizosphere soil physicochemical properties, microbial community composition, and nutrient metabolism-related functional genes. [Methods] For both parental lines and their hybrid progenies, the yields and the content of nitrogen (N), phosphorus (P), and potassium (K) in roots, fruits, and rhizosphere soil were determined, alongside rhizosphere soil physicochemical properties. High-throughput sequencing was adopted to analyze the structures of root endophytic and rhizosphere microbial communities, while metagenomic sequencing was used to quantify the abundance differences of genes associated with rhizosphere nutrient metabolism. [Results] Hybrid progenies exhibited a significant yield increase, with the highest yield increase observed in the Z3 line. All hybrids showed elevated K content in fruits, and Z3 specifically achieved transgressive accumulation of N and P in roots. A distinct turnover of the root endophytic microbial community was detected between parents and progenies. In the hybrids, functional genera including Dyella, Burkholderia-Caballeronia-Paraburkholderia, and Trichoderma were enriched, which were significantly correlated with plant nutrient uptake. In terms of rhizosphere soil properties, all hybrids had higher available phosphorus content and lower rhizosphere pH than parental lines. Notably, Z3 possessed unique advantages of high total nitrogen reserve and increased organic matter content in the rhizosphere. Additionally, the abundance of genes related to P and K metabolism was higher in hybrids than in parents, which was particularly prominent in Z3. [Conclusion] The transgressive yields of pepper hybrids is driven by the synergy among the rhizosphere environment, microbial communities, and the host plant. Specifically, hybrid progenies constructed an efficient microecosystem by enriching functional microbes (e.g., Dyella) and enhanced nutrient metabolism efficiency through increased abundance of P and K metabolism-related genes. These improvements ultimately led to the formation of nutrient utilization advantages, characterized by efficient nutrient absorption in roots and effective nutrient translocation to fruits. This study provides a novel theoretical framework for deciphering the microbial-driven mechanisms underlying parent-progeny differences in nutrient use efficiency of crops and further enriches the theory of plant-microbe-soil interactions.

[Objective] We explored the nuclear translocation dynamics and pathways of the structural protein VP1 of Junonia coenia densovirus (JcDV) in the epidermal cell line HaEpi derived from the larvae of Helicoverpa armigera, aiming to provide theoretical support for clarifying the assembly and proliferation processes of JcDV. [Methods] The wild-type and mutant plasmids of VP1 protein fused with green fluorescent protein (GFP) were constructed and transfected into HaEpi cells. Subsequently, the subcellular localization dynamics of the VP1 protein were analyzed, and the nuclear localization signal (NLS) and key amino acid residues of the protein were identified. The importin genes expressed by HaEpi cells were cloned. Subsequently, the plasmids of importins fused with DsRed2 were constructed to analyze their subcellular localization. The co-localization and co-immunoprecipitation (Co-IP) assays were employed to analyze the interactions between VP1 protein and importins. [Results] The VP1 protein was located in the cytoplasm at 6 h post transfection, and then gradually translocated to the nucleus until 48 h. The NLS of VP1 protein was located at 325-EGTKRKADTPVEEGPSKKGAH-345, among which K328, R329, K341 were the key amino acid residues affecting the nuclear localization. The importins Haimpα1, Haimpα4, and Haimpα7 were located in the nucleus, while Haimpβ1 was mainly located around the nuclear membrane. The co-localization and Co-IP results indicated that the VP1 protein interacted with Haimpα1, Haimpα4, and Haimpβ1 but not with Haimpα7. [Conclusion] The structural protein VP1 of JcDV can be translocated into the nucleus through the dual pathways of importin α/β and importin β.

α-ketoglutarate is an important short-chain organic acid that is widely used in various fields such as food, medicine, cosmetics, and animal feed. However, the efficiency of producing α-ketoglutarate through biological fermentation remains to be improved, primarily due to the limitations in the synthetic capacity of microbial metabolic pathways. [Objective] To address the above issues, we developed an engineered Escherichia coli that can efficiently produce α-ketoglutarate, thereby providing theoretical support for the large-scale production of α-ketoglutarate in the future. [Methods] We employed an efficient approach combining rational and irrational modifications to overcome the constraints of endogenous metabolic pathways and enhance the biosynthesis efficiency of α-ketoglutarate. [Results] The oxidative TCA pathway was reconstructed to improve α-ketoglutarate production through expressing pyruvate carboxylase, citrate synthase, aconitase, and isocitrate dehydrogenase. The metabolic network for α-ketoglutarate biosynthesis was irrationally optimized and strengthened to enhance its biosynthesis capability by atmospheric pressure room temperature plasma mutagenesis. To improve the supply efficiency of the precursor for α-ketoglutarate biosynthesis, we reduced the dissipation of carbon flux in the pyruvate node by knocking out genes related to the accumulation of lactate, acetate, and formate. Furthermore, we knocked out the genes related to the degradation pathway of α-ketoglutarate to achieve the retention of carbon flux at α-ketoglutarate node and improve its production. Through the optimization of fermentation conditions, the fermentation in a 5 L fermenter with the engineered strain E. coli KA29 achieved the α-ketoglutarate titer, yield, and productivity of 28.7 g/L, 0.29 g/g, and 0.48 g/(L·h), respectively. [Conclusion] The research strategies mentioned above lay a foundation for the development and application of strains with high production of α-ketoglutarate and provide a reference for metabolic engineering to produce other organic acids.

[Objective] Aluminum (Al) toxicity in acidic soils severely inhibits plant growth by inducing oxidative stress. Ectomycorrhizal fungus (ECMF) can enhance host plant Al tolerance, but the underlying physiological mechanisms, particularly in fine roots, are not fully understood. This study investigates how ECMF colonization mitigates Al toxicity by modulating the antioxidant physiology of plants, with an aim in applying ECMF for the ecological restoration of Al-contaminated acidic soils. [Methods] Pinus massoniana seedlings were inoculated with Lactarius deliciosus 2 or Pisolithustinctorius 715, with non-ectomycorrhizal seedlings as the control. After a 6-month exposure to 0.0 mmol/L or 1.0 mmol/L Al³⁺, we assessed seedling biomass, fine root morphology, plasma membrane permeability, reactive oxygen species (ROS) levels, antioxidant enzyme activities, and osmoregulatory substance content. [Results] Under Al stress, inoculation with either L. deliciosus 2 or P. tinctorius 715 significantly promoted seedling growth and fine root development. The inoculated seedlings exhibited 1.26-1.33 folds greater biomass and 2.25-3.99 folds increases in the total root length, root surface area, root volume, and root tip number compared to the non-inoculated control. The ECMF inoculation also significantly reduced the accumulation of malondialdehyde (MDA), hydrogen peroxide (H₂O₂), proline, and soluble proteins in fine roots. Furthermore, inoculation with L. deliciosus 2 resulted in significantly higher root surface area and root volume, along with greater peroxidase (POD) and catalase (CAT) activities and a more pronounced reduction in proline content in fine roots, compared to inoculation with P. tinctorius 715. [Conclusion] Our findings demonstrate that ECMF inoculation alleviates Al stress in P. massoniana seedlings by promoting fine root development, bolstering the antioxidant system (notably through increased POD and CAT activities), reducing H₂O₂ accumulation, preserving plasma membrane integrity, and decreasing the synthesis of osmoregulatory substances. The superior performance of L. deliciosus 2 highlights its potential for its application in the ecological restoration of Al-contaminated acidic soils.

Probiotic microbiota in roots can enhance nutrient uptake and stress tolerance, thereby improving plant growth. [Objective] To identify elite microbial resources from alfalfa roots. [Methods] We used eight functional bacterial strains isolated from the roots of Medicago sativa var. ‘Caoyuan No. 3’ and eight synthetic microbial communities (synthetic microbial communities, SynComs) composed of different strains for seed soaking treatments under 0, 200, and 250 mmol/L NaCl stress conditions. The germination potential (rate), radicle (embryonic shoot) length, and seed fresh weight were measured, and the effectiveness of the bacterial strains and SynComs in improving stress tolerance and growth was comprehensively evaluated via the membership function method. The effects of strains isolated from roots on alfalfa seed germination were thus evaluated. [Results] Under non-saline conditions, seed soaking had no significant impact on alfalfa seed germination. However, under salt stress, seed soaking significantly enhanced seed germination. Under 200 mmol/L and 250 mmol/L NaCl stress, MS8 was the most effective strain in promoting seed germination. Compared with the control treated with sterile water, MS8 treatment improved the germination potential by 76.67%. Compared with the control, the seeds treated with SynCom 1 exhibited increases of 113.04% to 405.41% in germination rate, significant increases of 47.87% to 56.67% in radicle length, significant increases of 19.13% to 24.01% in embryonic shoot length, and significant rises of 157.64% to 1 300.00% in fresh seed weight. [Conclusion] Under 200 mmol/L and 250 mmol/L NaCl stress, SynCom 1 was the most effective synthetic microbial community in enhancing seed germination, outperforming strain MS8. This study provides a theoretical foundation and technical support for the subsequent development of efficient functional bacterial agents to enhance the salt tolerance of alfalfa.

[Objective] To investigate the interactions between coral-associated Symbiodiniaceae and bacteria in mediating heat stress adaptation of corals. [Methods] Using Pocillopora damicornis harbouring distinct Symbiodiniaceae clades, we performed a laboratory-controlled heat stress simulation experiment to examine the dynamics of symbiotic bacterial community shifts via 16S rRNA gene amplicon sequencing. [Results] Bacterial alpha diversity exhibited a transient increase during the initial stress, followed by a significant decrease under prolonged stress, in P. damicornis harbouring clade C (Cladocopium spp.) or clade D (Durusdinium spp.) algal symbionts (i.e., PdC versus PdD holobionts). Compared with PdD, PdC demonstrated enhanced bacterial community shifts, alongside progressively diminished network stability and complexity with prolonged heat stress. Analysis of bacterial abundance at the class level revealed divergent trajectories of the two holobionts, with the abundance of Alphaproteobacteria increasing in both PdC and PdD, whereas that of Cyanobacteriota increasing in PdC but decreasing in PdD over the course of the experiment. During the later stage of heat stress, Cladocopium spp. in PdC showed increased sensitivity, coinciding with the enrichment of potentially opportunistic pathogens, whereas Durusdinium spp. in PdD were thermotolerant, coinciding with elevated abundance of bacteria possibly involved in photosynthesis, quorum sensing, calcification, and ABC transport. [Conclusion] These findings suggest that different clades of Symbiodiniaceae might interact with bacteria to differentially regulate the P. damicornis response to heat stress. Thermal sensitive Cladocopium spp., combined with the proliferation of potential opportunistic pathogens, may exacerbate the risk of thermal bleaching in PdC, whereas resilience could be strengthened in PdD via thermotolerant Durusdinium spp. coordinating with beneficial bacteria with supportive metabolic potential (e.g., photosynthesis, calcification, and quorum sensing). This algal-bacterial interaction mode provides critical insights into the microbially-mediated thermal bleaching mechanisms and an important reference for the practice of reef restoration in the context of global climate change.

[Objective] Birds, with unique life history characteristics, are ideal models for studying gut microorganisms. The niche overlap between wild birds and poultry increased the risk of interactive transmission of pathogens. This study focused on the community characteristics of gut fungi and pathogens in wild birds (crested myna, tundra swan, and common coot) and sympatric poultry (domestic duck and domestic chicken) in Chaohu Lake. [Methods] High-throughput sequencing (Illumina MiSeq) was employed to analyze the fungal communities in guts of wild birds and sympatric poultry in Chaohu Lake of China, and the characteristics of gut pathogens of each species were particularly studied. [Results] The gut fungal diversity of domestic duck and common coot was significantly higher than that of domestic chicken, crested myna, and tundra swan. There were significant differences in gut fungal community composition among different species. Due to grain-based diets, the guts of poultry were significantly enriched with the fungal taxa related to grain degradation, such as Ascomycota, Mortierellomycota, and Kazachstania. Tundra swan is herbivorous waterfowl. The genus Cladosporium, efficient plant-degrading fungi, dominated in the gut of tundra swan. The gut of tundra swan maintained higher relative abundance of plant saprotroph. The fungal community assembly in guts of wild birds was dominated by deterministic processes, which indicated that wild birds had a stronger gut filtering capacity. In addition, wild birds had lower diversity and relative abundance of pathogens. [Conclusion] The characteristics of gut fungal communities in wild birds and domestic poultry showed significant host specificity. Due to grain-based diets, the guts of poultry were significantly enriched with fungal groups related to grain degradation. The guts of wild birds had a stronger filtering capacity, which reduced the diversity and relative abundance of pathogens.

Citrus reticulata cv. Gonggan in Deqing is a national geographical indication product of China, and its quality formation is intricately linked to microbial ecology. In-depth exploration of the microbial resources associated with Gonggan is of great significance for enhancing the quality and increasing the yield of this fruit. [Objective] To isolate and culture bacteria from the rhizosphere soil and phyllosphere surface of Gonggan in Deqing and systematically evaluate their plant growth-promoting functions, thus providing applicable bacterial resources for the eco-friendly cultivation of Gonggan in Deqing. [Methods] Samples of rhizosphere soil and leaves of Gonggan in Deqing were collected. Bacteria within the samples were isolated via the dilution plating method. Bacterial strains were identified based on the homology of their 16S rRNA gene sequences. The functional media for phosphate solubilization, potassium release, nitrogen fixation, and siderophore production were used to evaluate the plant growth-promoting ability of bacterial strains, and the strains with strong plant growth-promoting functions were screened out. Ultimately, pot experiments were conducted to validate the plant growth-promoting functions of the selected strains. [Results] A total of 240 bacterial isolates were obtained, including 96 strains from the rhizosphere soil and 144 strains from the phyllosphere. These strains belonged to 51 genera, 29 families of 4 phyla, where Pseudomonadota was the dominant phylum and Bacillaceae was the dominant family. Functional characterization revealed that 230 (95.83%) strains exhibited at least one plant growth-promoting function, while 123 strains (51.25%) possessed three or more such functions. Given the extended growth cycle of Gonggan in Deqing, we utilized tomato as a model plant to evaluate the plant growth-promoting functions of eight bacterial strains possessing at least two functions through pot experiments. The results demonstrated that the tested strains significantly increased both plant height and fresh weight of tomato plants. [Conclusion] The rhizosphere soil and phyllosphere of Gonggan in Deqing harbor abundant functional microbial resources. This study successfully screened multiple strains of plant growth-promoting bacteria, and pot experiments demonstrated their significant ability to promote tomato growth. These findings provide a solid theoretical foundation for exploiting microbial resources of Gonggan in Deqing and advancing eco-friendly cultivation practices.

[Objective] Human parainfluenza virus type 3 (HPIV-3) is a key factor in global acquired respiratory infections, and there is no specific therapy available. Due to the complexity and variability of the pathogen antigen, the development of vaccines against HPIV-3 is lagging behind. It is crucial to design a novel broad-spectrum vaccine for comprehensive protection against continuously mutated wild-type strains. [Methods] To overcome the antigenic variation of the virus, we downloaded different HPIV-3 antigen proteins (F, M, N, and HN proteins) from NCBI and generated consensus sequences through sequence alignment. Furthermore, a broad-spectrum T cell epitope vaccine targeting HPIV-3 was predicted and designed via methods of reverse vaccinology. [Results] The multi-epitope vaccine (MEV) incorporated 11 cytotoxic T lymphocyte (CTL) epitopes (9-mer) and 11 helper T lymphocyte (HTL) epitopes (15-mer) from the F, M, N and HN proteins, being composed of 355 amino acid residues without adjuvant. The predicted T cell epitopes had solubility, no allergenicity, high antigenicity, and immunogenicity. The designed vaccine can effectively bind to Toll-like receptors in natural immunity, with good stability, hydrophilicity, and high population coverage. [Conclusion] The designed vaccine could be a candidate vaccine against HPIV-3 infection. We provide a novel immunoinformatics approach for vaccine design and development.

Viruses are known as the most abundant and diverse biological entities on Earth and regarded as key ecological drivers in ecosystems. The discovery of giant viruses has challenged the conventional understanding of virology and the definition of life with their microscale-virions, megabase-genome sizes, and remarkably numerous eukaryote-specific genes, which were once considered to be hallmark genes of cellular life but barely seen in viruses. Therefore, these biological characteristics of giant viruses blur the boundary between viruses and cellular life. Metagenomics studies have revealed that giant viruses are globally distributed in marine, freshwater, and soil ecosystems, and their geographical distribution is influenced by environmental factors such as temperature, latitude, and host range. Giant virus genomes include core metabolic genes, which enhance environmental adaptability by regulating host metabolism. In addition, giant viruses may even be involved in the horizontal transfer of antibiotic resistance genes. We review the research progress in giant viruses in terms of their diversity, biogeographic distribution, ecological relationships with hosts and intracellular parasites, reprogramming of host cell metabolic systems, driving forces in biogeochemical cycles, and potential impacts on human health to explore the ecological roles of giant viruses from multiple dimensions. This review aims to revolutionize our knowledge of viruses by revealing the ecological significance of giant viruses and their roles in global biogeochemical cycles.