An oilfield has entered the stage of high water-cut development, and the conventional water flooding effect is declining. It is urgent to develop microbial enhanced oil recovery (MEOR) technology to tap the remaining oil. Objective To analyze the indigenous bacterial community characteristics of different oil reservoirs and identify the indigenous oil-displacing bacteria, thus providing a scientific basis for the activation-type MEOR involving indigenous bacteria. Methods Produced fluid samples were collected from three high water-cut reservoirs (K₁h₂, J₂x, and J₂t). The 16S rRNA gene high-throughput sequencing combined with alpha diversity analysis, beta diversity analysis, linear discriminant analysis effect size (LEfSe)-based differential species identification, and canonical correlation analysis (CCA) of environmental factor correlations was employed to systematically reveal the bacterial community structure and analyze its driving mechanism. Additionally, the oil-displacement potential of the indigenous strain was assessed by core flooding test. Results A total of 174 OTUs were shared among the three groups, while the community composition was significantly different. Temperature, salinity, and water content were the main environmental influencing factors. The K₁h₂ group demonstrated prominent diversity, mainly consisting of bacteria with the potential to produce biosurfactants, such as Pseudomonas and unclassified_f_Rhodobacteraceae. The J₂x group enriched salt-tolerant hydrocarbon-degrading Marinobacter and significantly enriched sulfate-reducing groups. The J₂t group was dominated by thermophilic hydrocarbon-degrading bacteria such as Tepidiphilus and Burkholderiales. Core flooding test indicated that P. aeruginosa LD8 isolated from the K₁h₂ reservoir increased the oil recovery by 9.61% in the simulated reservoir environment. Conclusion The differences in physicochemical and microbial environments among different reservoirs emphasize the necessity of developing particular MEOR strategies. This study provides a research basis for the targeted activation of dominant oil-displacing bacteria, the avoidance of corrosion risks, and the optimization of on-site implementation plans.

Objective To compare the compositional differences, assembly characteristics, and ecological roles of generalist and specialist microeukaryotes between the dry and rainy seasons in the lower reaches of the Yarlung Zangbo River and to clarify how spatial heterogeneity and seasonal hydrological fluctuations influence microeukaryotic diversity. Methods Water samples were collected from 34 paired sampling sites in May 2022 (dry season) and July 2023 (rainy season). Environmental factor measurements, 18S rRNA gene high-throughput sequencing, and multivariate statistical analyses were conducted to examine the assembly processes, environmental responses, species associations, and state-transition characteristics of the generalist and specialist subcommunities. Results A total of 14 828 high-quality amplicon sequence variants (ASVs) were obtained, with 10 240 and 8 737 detected in the dry and rainy seasons, respectively. In the dry season, 146 generalists and 933 specialists were identified, whereas 526 generalists and 1 420 specialists were identified in the rainy season. The relative abundance of generalists and specialists was 6.29% and 73.18% in the dry season and 4.45% and 77.49% in the rainy season, respectively. The composition of generalists and specialists differed significantly in both seasons, and beta diversity was mainly driven by species turnover. Stochastic processes generally dominated community assembly, although the relative contributions of ecological processes differed between the two ecological strategy groups. In the rainy season, dispersal limitation weakened in specialists, whereas the contribution of deterministic processes increased in generalists, mainly due to increased homogeneous selection. Binary-state speciation and extinction (BiSSE) parameters indicated that specialists had higher state-transition rates, suggesting faster state turnover under contrasting seasonal conditions. Spatial and water physicochemical factors jointly drove community differentiation and niche divergence, with latitude, turbidity, and chemical oxygen demand as the main explanatory variables. Co-occurrence network analysis showed that both groups contributed to maintaining network complexity and stability, while network simplification was more pronounced after specialists were removed. Conclusion Generalist and specialist microeukaryotes in the lower reaches of the Yarlung Zangbo River showed marked differences in community assembly across seasonal transitions. Their distribution was jointly shaped by spatial heterogeneity, hydrological connectivity, and environmental filtering. Specialists contributed more strongly to network connectivity and may play a more important role in maintaining community resilience than generalists.

Objective Microbial-Fenton process driven by dissimilatory iron reduction is increasingly recognized as a major source of hydroxyl radicals (•OH) in redox-fluctuating environments (e.g., tidal sediments), thereby playing an important role in biogeochemical element cycling. However, extracellular polymeric substances (EPS), which are ubiquitous and closely associated with the cell-mineral interface, remain poorly understood in terms of their regulatory roles in this process. This study aims to elucidate the mechanisms by which EPS derived from Shewanella decolorationis influence •OH generation under oxic-anoxic conditions. Methods S. decolorationis S12, its extracellular electron transfer-deficient mutants (S12ΔBA and S12ΔccmA), extracted EPS, and ferrihydrite were employed as model components. By simulating oxic-anoxic alternating conditions, we employed a combination of chemical and spectroscopic approaches to characterize the physicochemical properties of EPS and to investigate their effects on iron reduction and •OH generation. Results Although EPS exhibited intrinsic redox activity and could mediate electron transfer in S. decolorationis, they exerted inhibitory effects on iron reduction efficiency and •OH generation under oxic-anoxic conditions, decreasing the Fe(Ⅱ) accumulation and •OH production by up to (56.63±4.67)% and (26.86±5.30)%, respectively. This inhibition was primarily attributed to the strong affinity between EPS and iron minerals, which led to the formation of EPS-Fe(Ⅲ) complexes that hindered electron transfer efficiency. In addition, EPS promoted the transformation of ferrihydrite into secondary iron mineral phases with lower bioavailability, thereby decreasing the reducibility of Fe(Ⅲ) and further suppressing •OH generation. Conclusion EPS act as a critical interfacial chemical mediator in the microbe-iron mineral system, regulating dissimilatory iron reduction and consequently influencing •OH production. These findings provide new insights into the biogeochemical processes in tidal soil and water environments such as intertidal sediments.

Tropical rainforests are the most biodiverse regions on Earth, in which plant root endophytic fungi play an important role in the ecosystem structure, function, and stability. Different mycorrhizal types of forest trees can affect the physical and chemical properties of rhizosphere soil by regulating root traits, thereby changing the structural characteristics of endophytic fungal communities in roots. However, there is no systematic dataset that demonstrates the mechanisms by which different mycorrhizal types of tropical trees regulate the endophytic fungal communities in their roots. To reveal the intrinsic relationship between mycorrhizal types in tropical forests and endophytic fungal communities in roots, as well as the ecological driving mechanisms underlying this relationship, this study established a database by systematically integrating data on endophytic fungal communities in roots of trees at different successional stages in tropical forests, based on the two most common mycorrhizal types, arbuscular mycorrhiza (AM) and ectomycorrhiza (ECM). This database provides fundamental data support for analyzing the ecological functions of different mycorrhizal types in tropical forests, belowground symbiotic interaction networks, and the maintenance mechanisms of ecosystem functions. Drawing on published literature and the dataset of Hogan et al. on root endophytic fungi in tropical trees, we systematically integrated and standardized data to establish a fungal community database associated with different mycorrhizal types of tropical trees. All functional trait data of roots were processed through the arithmetic mean method, while soil environmental data were weighted by the relative abundance of tree species. Other data were aggregated by tree species identity and finally classified according to mycorrhizal type. The entire data processing workflow was subjected to rigorous quality control, including verification of mycorrhizal types, standardization of data formats, and handling of outliers. This database contains a total of 5 969 standardized records, encompassing the Latin names of 66 woody plant species, mycorrhizal types (AM and ECM), 24 indicators related to root morphological traits (such as root length, root tissue density, and root volume), 13 indicators related to root tissue nutrients (such as root carbon content, nitrogen content, and phosphorus content), 7 indicators related to soil physical and chemical properties (such as soil organic matter, total nitrogen, and total phosphorus), and operational taxonomic units (OTUs) of endophytic fungi in roots, along with corresponding classification information. The establishment of this database provides a reliable data foundation for analyzing the belowground ecological interaction mechanisms of tropical forests, comparing the functions of mycorrhizal symbiosis, and informing the development of regional forest conservation and restoration strategies.

Porcine enteric coronaviruses (PECs) include porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), and porcine deltacoronavirus (PDCoV). Infections with PECs can cause severe diarrhea in pigs, particularly newborn piglets, resulting in high mortality rates and posing a serious threat and economic loss to the global swine industry. Such infections induce oxidative stress to activate various transcription factors and alter their transcriptional pathways, thereby affecting cellular metabolism and the viral life cycle. This leads to cellular dysfunction and further promotes viral replication, forming a vicious cycle. The oxidative stress associated with PECs is considered one of the potential common pathogenic mechanisms. This review summarizes the information about the oxidative stress induced by infections with PECs and emphasizes that antioxidant strategies represent one of the effective approaches to counteract such infections.

Colorectal cancer (CRC), one of the most common malignancies of the digestive system, is characterized by complex pathogenic mechanisms and an overall poor prognosis. The gut microbiota and its metabolites play a dual role in CRC by modulating various forms of programmed cell death (PCD), either promoting or inhibiting tumorigenesis and influencing the tumor responses to chemotherapy and immunotherapy. This review systematically summarizes recent advances in understanding how the gut microbiota regulates CRC initiation, progression, and responses to therapies through the modulation of apoptosis, autophagy, ferroptosis, and pyroptosis. Furthermore, it discusses the potential clinical-translational implications of these findings, aiming to provide a theoretical foundation for elucidating CRC pathogenesis and developing novel therapeutic strategies targeting the gut microbiota.

Respiratory viral infections pose a severe threat to global public health security, and exploring effective strategies to prevent them is of clinical significance. The gut microbiota plays a crucial role in regulating anti-infective immunity by remodeling the immune microenvironment, maintaining the immune homeostasis and boosting antiviral defenses of the host. Conversely, dysbiosis of the gut microbiota can disrupt immune homeostasis, resulting in impaired innate immune responses and abnormal activation of adaptive immunity, thereby raising the risk of respiratory viral infections in the host. This study elaborates on the essential role of the gut microbiota in the antiviral immune response of the host across multiple aspects. (1) It thoroughly explains how the gut microbiota contributes to forming an immune defense barrier by performing physiological functions such as secreting antimicrobial peptides, metabolizing nutrients, preserving mucosal barrier integrity, and modulating immune homeostasis of the host. (2) It analyzes the antiviral immune regulatory network that involves the regulation of type I interferon responses and immune cell differentiation, all within the context of gut microbiota balance and dysbiosis. (3) It explores how probiotics exert antiviral effects through mechanisms such as inhibiting viral proliferation, improving the host’s immune response, reducing secondary infections, and restoring gut microbiota balance. Although breakthroughs have been made in understanding the ternary interaction network of the microbiota, the immune system, and viral infection, the molecular mechanisms behind its dynamic balance and precise regulation still urgently need detailed investigation. Specifically, the mechanisms of interactions between gut microbiota metabolites and host epigenetic regulation, along with the long-term protective strategies of microbiota-induced immune homeostasis against viral infection, remain to be systematically revealed through multi-omics technologies.

As a crucial group of probiotics, lactic acid bacteria (LAB) play a vital role in the gut microbial ecosystem of insects. This article comprehensively reviewed the species composition, ecological functions, and practical values of LAB in the guts of major insect orders, including Hymenoptera, Diptera, Coleoptera, Hemiptera, Lepidoptera, Blattodea, and Orthoptera. To date, multiple LAB genera including Lactobacillus, Lactococcus, Leuconostoc, Pediococcus, Enterococcus, Bifidobacterium, and Weissella were successfully identified from insect guts. The community composition of these bacteria was shaped by factors such as host phylogeny, dietary traits, developmental stages, gut microenvironment, and external ecological conditions. The LAB in insect guts not only assist the hosts in degrading recalcitrant complexes by secreting extracellular enzymes but also inhibit pathogens through the synthesis of antimicrobial substances such as bacteriocins. Additionally, they modulate host immune responses, promote growth and development, regulate host behavior, and participate in the metabolic detoxification of xenobiotics, thereby enhancing host survival and adaptability. Furthermore, insect-derived LAB held great potential in the production of resource insects, pest management, agricultural waste utilization, and green manufacturing. In summary, insect guts represent an important reservoir for the discovery and isolation of novel LAB.

The general stress response (GSR) is a global regulatory strategy developed by bacteria to adapt to diverse environmental stresses by coordinating a suite of physiological and metabolic changes, thereby enabling survival in fluctuating conditions. The alternative sigma factor RpoS (σ^S) serves as a central GSR regulator in bacteria and is crucial for bacterial responses to various stress conditions. Such regulators in bacteria are conserved, while polymorphic variations in rpoS are prevalent across numerous natural isolates and acclimated strains. This polymorphism reflects the adaptive trade-off mechanism formed by bacteria during the evolutionary process, positioning RpoS as a key model for investigating fitness trade-offs in bacteria. This review summarizes the functions and polymorphisms of RpoS and explores the potential environmental drivers underlying its polymorphism.

γ-Aminobutyric acid (GABA), a key inhibitory neurotransmitter in the central nervous system, plays a vital role in physiological functions such as promoting sleep, relieving tremors, and regulating blood pressure. Currently, a variety of microorganisms capable of synthesizing GABA have been identified, offering diverse strategic options for the biosynthesis of GABA through different metabolic pathways. This review provides a detailed summary of the major pathways—the GABA shunt pathway and the putrescine pathway—for GABA synthesis in various microorganisms. It systematically outlines the key synthases and metabolites involved in the two pathways, while comparing their synthesis efficiency and respective advantages. Furthermore, this study delves into the regulatory mechanisms underlying GABA biosynthesis in different microorganisms, along with key regulatory targets for enhancing synthesis efficiency. The work aims to establish a theoretical framework for the regulatory mechanisms of microbial-derived GABA synthesis and to provide a scientific basis for improving the efficiency of GABA biosynthesis.