Objective Coastal wetlands are important natural sources of nitrous oxide (N₂O), and the distribution of denitrification genes nirS and nirK directly influences their N₂O emission potential. Vegetation types can significantly regulate the abundance of these genes by altering soil physicochemical properties and carbon-nitrogen availability, while the underlying mechanisms remain unclear. Methods Soils were collected from five representative habitats—Kandelia obovata (mangrove), Spartina alterniflora, Cyperus malaccensis, Phragmites australis, and unvegetated mudflat—in the Minjiang River estuary wetland at depths of 0-10, 10-20, and 20-30 cm. The abundance of nirS and nirK was quantified by real-time quantitative PCR, and their environmental drivers were analyzed through random forest modeling and correlation analysis. Results The abundance of nirS and nirK in all the vegetated soils was significantly higher than that in the unvegetated mudflat, with the highest values observed in the surface soil (0-10 cm) under P. australis. Both genes showed significantly decreased abundance as the soil depth increased, presenting a distinct surface enrichment effect. The nirS/nirK ratio was greater than 5 across all soil samples, indicating the dominance of nirS-type denitrifiers. The mangrove surface soil exhibited the highest nirS/nirK ratio, likely due to low dissolved organic carbon (DOC) levels limiting nirK-type denitrifiers. Random forest analysis identified soil electrical conductivity as the primary driver of nirS and nirK abundance, while available phosphorus (AP) was the dominant factor influencing the nirS/nirK ratio. High salinity promoted the enrichment of both genes, whereas high AP concentrations increased the nirS/nirK ratio. Conclusion Vegetation type and soil depth jointly shape the distribution patterns of nitrite reductase genes in the Minjiang River estuary wetland by regulating soil salinity, DOC, and nutrient availability. The results provide insights for nitrogen cycle management in coastal wetlands.

Objective To investigate the changes in microbial community structure and function in degraded mangrove sediment, and to explore their potential relationships with environmental factors and mangrove degradation. Methods Sedimental samples were collected from degraded mangroves in Guangxi Beihai Coastal National Wetland Park, marked as healthy (ZC), early-stage/deteriorating (BY), and necrotic (SW) groups. The physicochemical factors, including total nitrogen (TN), total phosphorus (TP), total organic carbon (TOC), oils, and various heavy metals, were analyzed using standard methods. High-throughput sequencing of 16S rRNA gene and ITS region was performed. Subsequent analyses, including diversity indices, Venn plot, LEfSe analysis, Z_i-P_i analysis, and FAPROTAX/FUNGuild functional prediction, were employed to compare the composition and functional differences of bacterial and fungal communities and to identify their driving environmental factors. Results The richness and diversity of the bacterial community followed the order of SW>ZC≈BY. The dominant phyla were Pseudomonadota and Chloroflexi. In contrast, fungal richness and diversity were lowest in SW, where Ascomycota was the dominant phylum. LEfSe analysis indicated that the bacterial community in ZC was characterized by Actinomycetota and several Desulfobacterota; BY was enriched in Gemmatimonadota; SW was dominated by Bacillota, Campylobacterota, and Spirochaetota. Z_i-P_i analysis revealed that keystone fungal taxa in BY were mainly from Ascomycota, while those in SW contained both Ascomycota and Basidiomycota. Functional prediction suggested that bacterial communities were predominantly chemoheterotrophic, with fermentation as a major pathway. Fungal communities were primarily saprotrophic and notably pathogenic. Correlation analysis further demonstrated that TN, TP, oils, and heavy metals (e.g., As, Cu) significantly influenced microbial community structure. Conclusion By investigating microbial community structure and function, this study elucidates the dynamic response of microbial communities to environmental shifts in degrading mangrove ecosystems, thus providing a crucial microbiological reference for future ecosystem health assessment and restoration efforts.

Objective In view of the issues of reservoir acidification and pipeline corrosion caused by sulfate-reducing bacteria (SRB) during oil and gas field development, this study focused on the green synthesis of silver nanoparticles with bamboo leaf extract and systematically evaluated their effectiveness and mechanism in inhibiting SRB. Methods Under alkaline conditions (pH 11.0) and at 80 ℃, silver nanoparticles with a particle size of 20-50 nm and good monodispersity were successfully prepared through ultrasonically assisted ethanol extraction of active substances from bamboo leaves. Results Real-time quantitative PCR results showed that 50 μg/mL of silver nanoparticles reduced the total bacterial count from 5.21×10⁹ copies/mL to 2.01×10⁷ copies/mL. Meanwhile, the abundance of sulfate-reducing functional genes dsrB and aprA decreased from 1.76×10⁹ copies/mL and 2.03×10⁹ copies/mL to undetectable levels. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) reduction assay indicated that silver nanoparticles reduced SRB activity in a dose-dependent manner, with the SRB activity in the 50 μg/mL silver nanoparticles group decreasing to 40% of that in the control group. The lactate dehydrogenase (LDH) release assay confirmed that the cytotoxic effect of the synthesized silver nanoparticles ranged from 32.8% to 42.1%. Under SEM/TEM, silver nanoparticles were observed to adsorb onto the cell membrane surface, forming a nanoscale coating that altered membrane permeability and disrupted the cell wall structure. At a concentration of 50 μg/mL, silver nanoparticles completely inhibited biofilm formation. Core simulation experiments further validated the effective inhibition of SRB by the nanoparticles in reservoir environments, with hydrogen sulfide production decreasing from 83.16 mg/L to below the limit of detection. Conclusion This study demonstrates that bamboo leaf-mediated synthesized silver nanoparticles exhibit high efficiency in inhibiting SRB, environmental friendliness, and resistance to microbial drug resistance. It provides a green prevention and control strategy for microbial corrosion in oil and gas development processes.

Soil degradation represents a major constraint to sustainable agricultural production. Arbuscular mycorrhizal fungi (AMF), as pivotal rhizosphere symbionts, play a crucial role in promoting host plant growth and remodeling microbial communities. Objective This study elucidated the regulatory impacts of AMF inoculation on tobacco growth, as well as the structure, interaction network, and metabolic functions of the endophytic bacterial community in the roots of tobacco cultivated in barren soil. The aim is to provide theoretical support for leveraging AMF to optimize plant-microbe interactions and enhance crop adaptation to nutrient-poor environments. Methods A pot experiment was conducted in combination with Illumina MiSeq high-throughput sequencing. The root endophytic bacterial community was systematically investigated via microbial co-occurrence network analysis, functional prediction, and structural equation modeling (SEM). Results AMF inoculation significantly enhanced tobacco growth, increasing the shoot fresh weight, root fresh weight, plant height, and root length by 118.4%, 157.6%, 78.6%, and 73.4%, respectively. Although AMF inoculation significantly reduced the species richness and diversity of the endophytic bacterial community, it markedly reshaped the community composition by enriching specific taxa (e.g., Gammaproteobacteria). This restructuring resulted in a more compact, positive interaction-dominated co-occurrence network, in which ASV149 (belonging to the genus Steroidobacter) was identified as a keystone taxon. Functionally, AMF inoculation significantly upregulated key metabolic pathways, including cell growth and death, xenobiotic biodegradation and metabolism, amino acid metabolism, and lipid metabolism. SEM further confirmed that bacterial richness and diversity were the major drivers shaping the network structure. Conclusion In barren soil, AMF not only directly promotes tobacco growth but also enhances the stability of the root microecosystem and the tobacco adaptability to barren soil by restructuring the root endophytic bacterial community. From the perspective of the “plant-AMF-endophytic bacteria” tripartite interaction, this study deepens the insight into the intrinsic mechanisms underlying microbial synergism in enhancing plant environmental adaptability.

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.

Open-air piling of coal gangue severely disrupts the soil structure and regional ecosystem health. Inoculation with sulfate-reducing bacteria (SRB) is an effective strategy to control acid pollution derived from coal gangue, as SRB can reduce sulfate and immobilize heavy metals. However, the remediation performance of SRB in coal gangue piles and the associated ecological response patterns along the depth gradient remain unclear. Objective To elucidate the overall ameliorating effect of SRB remediation on coal gangue piles, and to characterize the differentiation patterns and driving mechanisms of soil physicochemical properties, microbial community structure, and microbial functions along the vertical profile during remediation. Methods A typical coal gangue pile in an open-pit coal mine in Yulin City, Shaanxi Province, China was selected as the study site. Coal gangue piles with SRB remediation (treatment group) and without remediation (control group) were established. In the control dump, 0-20 cm mixed soil samples were collected to represent the background condition. In the SRB-remediated pile, soil samples were collected from the 0-5 cm shallow layer (SL), 5-10 cm middle layer (ML), and 10-20 cm deep layer (DL). Soil physicochemical properties were determined, and 16S rRNA gene high-throughput sequencing was performed. PICRUSt2 was used to predict microbial functions. Differences between groups and between vertical gradients within the treatment group were compared. Results Compared with the control, SRB remediation significantly increased the overall soil pH, electrical conductivity (EC), and soil organic matter (SOM) content of the coal gangue pile, and markedly enhanced the alpha diversity and altered the structure of the bacterial community. With the increase in depth of the remediated pile, pH, EC, and SOM increased progressively, while available potassium first increased and then decreased. The relative abundance of dominant bacterial phyla changed significantly along the depth gradient, and the complexity of the co-occurrence network (number of nodes, number of edges, and average degree) also increased. Soil pH and EC were identified as key environmental drivers of community structural variations. Functional prediction indicated that the abundance of genes related to carbon fixation, nitrogen cycling, and sulfur cycling in the deep layer was significantly higher than that in shallow and middle layers. Conclusion SRB bioremediation not only improved the overall soil environment and microbial community of the coal gangue pile but also shaped a depth-dependent differentiation pattern of environmental conditions and microbial functions within the pile. These findings provide an important theoretical basis for the long-term stable remediation of coal gangue piles and the regulation of microbially mediated processes.

Objective Revealing the succession patterns of soil microbial communities and their carbon cycle functions in the 0-20 cm topsoil following the conversion of natural forests to other land use types is critical for elucidating microbial carbon sequestration mechanisms and maintaining soil health. Methods The investigation selected natural forests in the southern Dongting Lake region and their converted plantations, paddy fields, and grasslands as research subjects. Metagenomic techniques were employed to systematically analyze changes in microbial community composition and carbon cycling genes in the 0-20 cm topsoil, as well as to identify key driving factors. Results Conversion of natural forests to plantations, paddy fields, and grasslands reduced soil bacterial diversity by 12%-24%. Fungal diversity in plantations and paddy fields was 65% and 76% lower than that in natural forests, respectively. Conversion of natural forests altered soil bacterial and fungal community composition. Soil available phosphorus content and pH value were identified as primary factors influencing bacterial diversity, whereas fungal diversity and community composition were mainly affected by soil available iron content. Following land use conversion, the relative abundance of carbon fixation genes ACAT/atoB and tktA/tktB decreased by 10%-45%. However, the relative abundance of ACO/acnA, korA/oorA/oforA, and mcmA1 was 25%-32% higher in grassland soil, and that of ppdK and korA/oorA/oforA was 13%-40% higher in paddy soil than in natural forest soil. Compared with natural forests, paddy fields and grasslands showed decreases of 39%-43% in the relative abundance of carbon decomposition genes bglX and amyA, while converted land use types showed increases of 77%-293% in the relative abundance of abfA and nplT. Conclusion Soil pH value and nitrate nitrogen content are identified as key environmental factors regulating the relative abundance of carbon fixation and decomposition genes. Therefore, scientific management of soil acidity or alkalinity and nitrogen levels can be considered as an effective strategy to enhance the carbon sequestration potential of soil microorganisms.

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.

Microbial dark carbon fixation (DCF) is a key biogeochemical process in which chemoautotrophic or heterotrophic microbes convert inorganic carbon to organic carbon in the absence of light. Recent studies have shown that the contribution of this process to the global carbon cycle has long been underestimated, particularly in deep waters, sediments, soils, hot springs, and other extreme environments where it holds significant ecological importance. This review comprehensively summarizes the recent research advances in microbial DCF, with a focus on major carbon fixation pathways, functional microbial groups, and carbon fixation rates across different ecosystems. The published data demonstrate significant variations in microbial DCF rates across different ecosystems. The deep ocean exhibits the highest DCF rate, reaching approximately 2.14×10⁴ µmol C/(m²·d), followed by boreal lakes, where the maximum DCF rate reaches 1.33×10⁴ µmol C/(m²·d). Additionally, in the deep-water layer of stratified boreal lakes, the contribution of DCF to total primary productivity can be as high as 81.4%. In high-temperature hot spring environments, DCF can account for 80%-100% of the total carbon fixation. From the perspective of carbon fixation pathways, the Calvin cycle is the primary pathway for microbial DCF across various habitats, widely existing in ecosystems including lakes, oceans, soils, and hot springs. Meanwhile, different habitats adapt to their specific environmental conditions by incorporating additional metabolic pathways such as the Wood-Ljungdahl pathway and the reductive tricarboxylic acid cycle (rTCA) pathway to achieve efficient carbon fixation. Temperature, pH, salinity, oxygen concentration, nutrient conditions, and depth are key environmental factors regulating microbial DCF rates. These factors collectively determine the efficiency and contribution ratios of DCF processes in different ecosystems by influencing the community structure of DCF-related microorganisms, the selection of metabolic pathways, and enzyme activities. Finally, the review discusses current limitations in this field, including uncertainties in quantification methods and insufficient understanding of environmental response mechanisms, and highlights key directions for future research. These advances are expected to provide critical scientific evidence for improving the carbon cycle theory, assessing the impacts of climate change, and developing microbe-based carbon sequestration technologies.

Objective The uranium pollution risk and resource value associated with stone coal waste rock stockpiles constitute a core contradiction in mine environmental management and resource recovery. Microbial leaching is a key technology for recovering low-grade uranium resources, yet the potential of mixotrophic bacteria, which combine the advantages of both autotrophic and heterotrophic metabolism, remains unclear in this field. This study investigated the uranium leaching effect and mechanism of the indigenous mixotrophic bacterium Alicyclobacillus ferrooxydans S1-24WXX from stone coal waste rock, aiming to achieve the synergy between pollution control and resource utilization. Methods The indigenous acidophilic mixotrophic strain A. ferrooxydans S1-24WXX was isolated from a stone coal mine in Shangrao, Jiangxi. Leaching experiments were conducted with three groups of organic matter addition (T_OM), no organic matter addition (T_NOM), and a sterile control (CK) to systematically evaluate the uranium leaching efficiency of this strain from uranium-rich stone coal waste rock. X-ray diffraction was used for mineral characterization of the raw ore and leaching residues. Dynamic monitoring was performed on changes in pH, redox potential (Eh), iron ion concentration, and uranium leaching rate during the process. Results Inoculation with S1-24WXX significantly enhanced the acidity (pH<2.0), Eh (≈600 mV), and Fe³⁺ concentration (≈1 000 mg/L) of the leaching system, all of which far exceeded those of the chemical leaching control group. Under T_OM and T_NOM conditions, the maximum uranium leaching rates reached 46.9% and 44.2%, respectively, which were 4.07 and 3.84 times that of the control group. Mineral analysis indicated that the strain catalyzed pyrite oxidation, leading to the formation of a strongly acidic, highly oxidizing, and Fe³⁺-rich leaching environment, which was the dominant mechanism of promoting uranium release. Conclusion This study reveals the significant potential of the mixotrophic bacterium A. ferrooxydans in uranium bioleaching. The bacterium drives uranium dissolution through inorganic acidification rather than organic acid complexation, providing a new pathway for the green recovery of low-grade uranium resources. This holds important academic value for mine environmental management and sustainable resource utilization.