Grassland soil microorganisms play a pivotal role in maintaining the health and stability of grassland ecosystems. However, systematic studies on the diversity, geographical distribution, isolation techniques, and functional potential of novel bacterial taxa in grassland soils remain limited. Here, we conducted a meta-analysis of 104 novel bacterial taxa described in 74 studies from grassland ecosystems across 19 countries between 2004 and 2025. We further predicted their functions via whole-genome data and compared them with background soil bacterial communities in grassland soils. Our results showed that novel bacterial taxa in grassland soils were mainly affiliated with the phyla Actinomycetota and Pseudomonadota, and their discovery frequency closely matched the abundance of background soil microorganisms. Their geographical distribution exhibited clear latitudinal zonality, with high-latitude regions being enriched with dormant taxa adaptive to harsh environments. Functional potential analysis suggested that these novel species not only provide the physiological verification of microbial dark matter, but may also play important roles in key ecosystem processes. Several representative taxa showed distinct ecological functional potential. Amnibacterium soli contributes to carbon and nitrogen cycling through efficient hydrolase systems; Chthonobacter albigriseus mediates methane oxidation to mitigate the greenhouse effect; Noviherbaspirillum agri possesses nitrogen-fixing, plant growth-promoting, and salt-alkali adaptation capabilities; and Streptomyces ziwulingensis can contribute to microbial defenses through secondary metabolite production. Together, these findings highlight the ecological and biotechnological potential of core grassland microbial taxa. Future studies integrating multidisciplinary approaches are needed to elucidate the functions and evolution of novel phyllosphere and rhizosphere taxa and bridge the gap between genomic sequences and ecological functions, thus providing microbiological support for improving the productivity and maintaining the ecosystem stability of grassland.

Acidic soil accounts for approximately 50% of the world’s available arable land. Its highly active aluminum ions and low pH environment not only directly inhibit plant growth but also significantly alter the microbial community structure in the rhizosphere, weaken the functions of beneficial microorganisms, and exacerbate soil-borne diseases. Brassinolide (BR), as a group of important plant signaling molecules, play a core role in enhancing the plant stress resistance in acidic soil by precisely regulating plant-microorganism interactions. BR promote the root secretion of organic acids such as malic acid and oxalic acid by activating BZR1/BES1 and transcription factors. These secretions act as carbon sources and chemotactic signals to specifically recruit beneficial microorganisms such as Paenibacillus azotofixans, Pseudomonas, and ectomycorrhizal fungi, reshaping the microbial community structure in the rhizosphere. The microbial community reassembly induced by BR significantly enhances aluminum ion chelation, nutrient activation, and pathogen inhibition. For instance, nitrogen-fixing bacteria enriched utilize malic acid for metabolic activities and secrete auxin and other substances to promote plant growth in acidic environments. Ectomycorrhizal fungi alleviate aluminum toxicity through oxalic acid secretion. Meanwhile, BR, in collaboration with plant hormones such as auxin and gibberellin, optimizes the root structure, expands the microbial colonization niche, and forms a complex synergistic network for enhancing stress resistance. Future research should focus on the specific regulatory mechanisms of BR on the rhizosphere microbiome, unveil the direct action pathways of BR as microbial signaling molecules, and develop efficient BR-microbial compound preparations in combination with microbial community engineering, providing innovative strategies and application solutions for the regulation of acidic soil microorganisms.

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.

Mangrove ecosystems, situated at the land-sea interface, serve as vital blue carbon sinks, playing a key role in the global carbon cycle and climate regulation with their efficient carbon sequestration capacity. Microorganisms are central drivers of carbon sequestration in mangrove sediments, capable of fixing carbon through diverse metabolic pathways. This review first summarizes the currently identified microbial carbon fixation pathways and carbon sequestration mechanisms in mangrove sediments, with a focus on three primary processes: the Calvin-Benson-Bassham cycle, the reductive tricarboxylic acid cycle, and the reductive acetyl-CoA (Wood-Ljungdahl) pathway. Furthermore, we discuss the influences of key environmental factors, such as vegetation type, sediment physicochemical properties, and nutrient inputs, on microbial carbon fixation and sequestration. Finally, we propose the future directions for studies on microbial carbon fixation and sequestration in mangrove sediments, including the couplings of nutrient cycling processes, microbiome engineering, and microorganism-plant interactions. This review proposes potential novel strategies for enhancing blue carbon capacity in mangrove ecosystems.

Global climate change and soil heavy metal pollution have raised higher requirements for the synergistic adaptability of conventional remediation technologies. Microbially induced carbonate precipitation (MICP) technology, with its unique biological metabolism and environmental interaction characteristics, provides a new pathway for the synergistic management of carbon sequestration and heavy metal stabilization. This technology induces calcium carbonate formation through two core enzyme-mediated pathways involving urease and carbonic anhydrase, enabling simultaneous CO₂ sequestration by mineralization and heavy metal immobilization. In carbon sequestration scenarios, MICP technology can enhance the geological stability of carbon sequestration sites through lithological improvement and strengthen carbon sequestration efficiency through high-efficiency mineralization reactions. In heavy metal remediation scenarios, it can achieve heavy metal stabilization through multiple mechanisms such as adsorption, co-precipitation, and surface complexation, and different calcium carbonate crystal forms can adapt to varied pollution scenarios. However, the large-scale application of MICP technology currently faces three major bottlenecks: insufficient tolerance of functional strains to extreme environments, compatibility conflicts between exogenous strains and native ecosystems, and coupling barriers between metabolic pathways for carbon sequestration and heavy metal immobilization. To address these issues, this paper proposes a three-stage synergistic process flow hypothesis for heavy metal immobilization, carbon sequestration by mineralization and long-term monitoring. Sequentially switching metabolic pathways theoretically resolves the pH requirement conflict between heavy metal immobilization and carbon sequestration by mineralization, providing new solutions for the engineering application of MICP technology. Future research should focus on the modification of functional strains for extreme habitats, regulation of interactions between exogenous and native microorganisms, and precise optimization of process parameters, to advance this synergistic model from theoretical design to on-site validation, providing technical support for achieving carbon neutrality and the safe utilization of polluted soils.

Perfluorooctanoic acid (PFOA), a representative per- and polyfluoroalkyl substance (PFAS), has emerged as a priority-controlled emerging contaminant of global concern due to its extreme environmental persistence, bioaccumulation potential, and toxicity. It poses a serious threat to ecosystem stability and human health. Microbial degradation has become one of the most promising technological approaches for PFOA remediation, owing to its core advantages of being environmentally friendly, cost-effective, and amenable to large-scale application. This paper systematically reviews the research progress in PFOA-degrading microorganisms in terms of the characteristics, degradation efficiency, and underlying mechanisms of isolated and identified functional strains (bacteria and fungi). Subsequently, this paper synthesizes the response patterns of microbial communities and strategies for resource exploration in various contaminated habitats harboring potential PFOA degraders. Finally, it highlights key scientific challenges currently facing the field and makes an outlook on future research directions. This review aims to provide a reference for the resource development, mechanism elucidation, and engineering application of PFOA-degrading microorganisms, offering theoretical support and forward-looking perspectives for advancing microbial remediation technologies targeting global PFOA contamination.

The deep sea encompasses a wide range of ecosystems, including cold seeps, hydrothermal vents, seamounts, and hadal trenches, whose extreme environmental conditions support diverse and unique microbial communities. Among them, viruses, as one of the most abundant biological entities on Earth, exhibit remarkable novelty in terms of genome composition, functional proteins, and evolutionary lineages and play crucial roles in regulating microbial community structure, driving biogeochemical cycles, and facilitating horizontal gene transfer. In recent years, with the rapid development of deep-sea sampling technologies, high-throughput sequencing, multi-omics approaches, and artificial intelligence-based analyses, a vast number of uncultivated deep-sea viral genomes have been identified, revealing a substantial reservoir of viral “dark matter” and significantly expanding our understanding of viral diversity, ecological functions, and adaptive strategies in deep-sea environments. Accumulating evidence indicates that deep-sea viruses participate in ecological processes through diverse infection strategies, including lytic, lysogenic, and chronic infections. During long-term adaptation to extreme environments and virus-host coevolution, deep-sea viruses have accumulated a rich repertoire of unique genetic resources, including virus-encoded functional genes and enzymes with significant potential for biotechnological applications. This review systematically summarizes recent advances in the abundance, distribution, diversity, ecological functions, and genetic resource exploration of deep-sea viruses. Furthermore, this paper discusses the main challenges and future perspectives in this field, with the aim of providing a theoretical framework for a deeper understanding of deep-sea microbial ecological processes and the sustainable utilization of deep-sea genetic resources.

Objective To elucidate the community structures and environmental adaptation mechanisms of bacteria and archaea in the sodium sulfate-type Yuncheng Salt Lake in Shanxi Province, China and explore the assembly patterns of microbial interaction networks under extreme hypersaline conditions. The findings are expected to provide a theoretical basis for assessing the ecosystem functions of salt lakes and developing halophilic microbial resources. Methods Water samples were collected from 10 sampling sites with salinity gradients of 6.0%-34.2% in Yuncheng Salt Lake. The physicochemical analysis of water quality, high-throughput 16S rRNA gene sequencing, molecular ecological network analysis, and multivariate statistical methods were employed to systematically investigate the microbial community structure and its interactions with environmental factors. Results The dominant taxa included Euryarchaeota, Pseudomonadota, and Bacteroidota. Archaea were primarily represented by Halarchaeum and Halorubrum, while the dominant bacterial genera were Roseovarius and Spiribacter. A microbial network consisting of 53 nodes and 73 edges was constructed, with negative correlations accounting for 63%. Key taxa included Halolamina, Geitlerinema, and Halorubrum. Salinity, nitrogen, and sulfide emerged as the three core drivers with high connectivity in the network, exhibiting significant correlations with multiple microbial groups. Conclusion Microbial community assembly in Yuncheng Salt Lake is dominated by negative correlations (e.g., potential competition, niche differentiation, or environmental stress), and this highly competitive network structure enhances the system resistance to environmental disturbances. The study reveals unique microbial adaptation strategies in sodium sulfate-type salt lakes and provides new insights for the exploitation of extremophilic microbial resources.

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.

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.

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.

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 To explore the regulatory effect of the synergistic and efficient remediation of petroleum-contaminated soil by Rhodococcus sp. OS62 and Pseudomonas sp. P35. Methods High-throughput sequencing was employed to determine the bacterial community structure and diversity during the remediation of petroleum-contaminated soil. Redundancy analysis, non-metric multidimensional scale analysis, Mantel test, and molecular ecological network analysis were performed to evaluate the changes of the soil microbial community structure and the correlations of petroleum degradation efficiency with soil physicochemical factors, soil enzyme activities, and bacterial community structure during the remediation process. Results The addition of the bacterial consortium significantly increased the activities of soil dehydrogenase, lipase, polyphenol oxidase, and catalase and the remediation efficiency, and its remediation effect was better than that of strain OS62 with excellent petroleum degradation ability or strain P35 with weak petroleum degradation ability. Correlation analysis showed that soil petroleum residue was positively correlated with soil total nitrogen and nitrate nitrogen content and negatively correlated with soil enzyme activities and nitrite nitrogen content. The addition of Rhodococcus sp. OS62 or Pseudomonas sp. P35 had mild influences on soil microbial alpha diversity and molecular ecological network. Both strains had great contributions to the differences of bacterial community structure. Under different treatments, Nocardioides occupied a dominant position and were hub nodes in the molecular ecological network, while Mantel test showed that Nocardioides had a weak correlation with soil petroleum residue. Conclusion This study clarified that Pseudomonas sp. P35 with weak petroleum degradation ability could cooperate with Rhodococcus sp. OS62 with high petroleum degradation ability to enhance soil enzyme activities and improve the remediation efficiency of petroleum-contaminated soil. It provides a theoretical basis and practical reference for optimizing the application of bacteria consortium in bioremediation of petroleum-contaminated soil.

Objective To investigate the effects of the carbon-to-nitrogen ratio (C/N) on dissimilatory nitrate reduction pathways in paddy soil and clarify the competition between microbially mediated denitrification (DEN) and dissimilatory nitrate reduction to ammonium (DNRA), thus providing a theoretical basis for managing nitrogen fate through C/N regulation. Methods An anaerobic incubation experiment was conducted with paddy soil. Soil C/N was adjusted by applying different ratios of potassium nitrate (KNO₃) and trisodium citrate (C₆H₅Na₃O₇). Two treatments C/N=5:1 and C/N=20:1 were established. The effects of C/N on nitrate reduction pathways were evaluated by measuring nitrous oxide (N₂O) emissions and ammonium nitrogen (NH₄⁺-N) accumulation. The 16S rRNA gene sequencing and bioinformatic analysis were employed to analyze the bacterial community structure under different C/N, thereby revealing the underlying microbial regulatory mechanisms. Results The high C/N treatment (C/N=20:1) showed significantly lower cumulative N₂O release than the low C/N treatment (C/N=5:1), with the cumulative release being reduced by 32.87%. Furthermore, high C/N promoted NH₄⁺-N accumulation, resulting in an increase of 276.61 mg/kg in NH₄⁺-N accumulation compared with low C/N. Microbial analysis indicated that the C/N significantly influenced bacterial community structure, with higher C/N enhancing bacterial richness and diversity. In addition, high C/N increased the diversity of DNRA-associated bacteria (e.g., Anaeromyxobacter, Nitrospira, and Myxococcus), while suppressing the abundance of DEN-associated bacteria (e.g., Achromobacter and Pseudomonas). Network analysis further revealed that high C/N weakened the interspecific interactions among DEN-related bacteria, reducing the complexity and stability of their co-occurrence network, while promoting tighter and more stable interactions among DNRA-related bacteria. Conclusion The soil C/N was a key environmental factor governing the competition between DEN and DNRA in paddy soil. High C/N significantly reduced N₂O emissions, promoted NH₄⁺-N accumulation, reshaped the composition and interactions of functional bacteria (reducing the abundance of DEN-related bacteria and increasing the diversity of DNRA-related bacteria). This study provides theoretical support for understanding the microbially driven nitrogen retention mechanisms in soil and lays a foundation for developing novel fertilization strategies through C/N regulation.

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.

Objective The ecosystem of alpine lakes in northwestern Yunnan Province is well-preserved, while the microbial communities and functional characteristics in the sediments remain unclear. This study aims to elucidate the vertical distribution patterns of microbial communities in alpine lake sediments within this region and their functional differentiation in carbon, nitrogen, and sulfur cycling. Methods Three adjacent alpine lakes (Taiji Lake, Tiancai Lake, and Rencai Lake) in Laojunshan National Park, Lijiang City, Yunnan Province were selected. Samples were collected from four depths (0-1, 10-11, 20-21, 30-31 cm) of sediment cores and subjected to metagenomic sequencing. Medium and high-quality metagenome-assembled genomes (MAGs) were recovered through binning analysis, with taxonomic annotation conducted against the GTDB database. Meanwhile, functional gene annotation was performed against the CAZymes and KEGG databases to characterize the vertical stratification of community structure and biogeochemical cycling functions. Results A total of 478 MAGs (belonging to 27 bacterial phyla and 9 archaeal phyla) were obtained. Approximately 95.0% of these MAGs could not be identified at the species level, indicating that there were a large number of uncultured microbial groups in the sediments. The bacterial communities exhibited distinct succession with depth. The surface layer was dominated by Cyanobacteriota and Bacteroidota, while the middle and lower layers were mainly occupied by Pseudomonadota and Chloroflexota. The archaeal community was mainly composed of Nanobdellota, Thermoproteota, and Halobacteriota, and exhibited increasing stability with sediment depth. Carbohydrate-active enzymes (CAZymes) in the surface layer were mainly enzymes (e.g., glycosyl transferases GT51 and glycoside hydrolases GH59) targeting readily degradable carbon sources, while those in deeper layers were mainly enzymes (e.g., carbohydrate-binding modules CBM38 and auxiliary activity family AA6) acting on recalcitrant carbon sources. Nitrogen and sulfur cycling functions also exhibited a distinct vertical hierarchical structure. The bacteria primarily participated in nitrogen and sulfur cycling processes in surface sediments, whereas archaea predominated in deeper sediment layers. Conclusion The microbial communities in the sediments of alpine lakes in northwestern Yunnan Province exhibited distinct vertical distribution patterns related to carbon, nitrogen, and sulfur cycling, reflecting the influences of the sediment redox gradient and the organic matter composition on microorganisms. This study provides a new perspective for understanding the microbial ecology and biogeochemical cycling process in alpine lakes.

Objective To screen the microbial strains capable of efficiently activating soil cadmium, addressing the technical bottleneck of low efficiency in cadmium-contaminated soil remediation by hyperaccumulators. Methods Farmland soils with potential Cd contamination were collected from various locations in Hunan Province. Acid-producing bacteria were initially screened via the bromocresol purple discoloration method. The pH of the fermentation broth, cadmium chloride tolerance, and cadmium carbonate activation capacity were compared among strains to identify dominant strains, which were then subjected to species identification. On this basis, bacterial strains with application potential were further screened. The desorption effect of the selected strain on soil cadmium under different carbon and nitrogen sources was investigated through shake flask experiments. Pot experiments were carried out to analyze the activation effect on soil cadmium under different nutrient conditions. Results A total of 372 acid-producing bacterial strains were isolated via the bromocresol purple discoloration method. Through comprehensive screening based on the ratio of the discoloration zone diameter (D) to the colony diameter (d) on solid plates, fermentation broth pH, cadmium chloride tolerance, and cadmium carbonate activation assays, four elite strains, designated HT-B1, HTQ-B1, QBS-B2, and MY-B1, were selected. They were identified as Staphylococcus epidermidis, Staphylococcus hominis, Priestia megaterium, and Acinetobacter sp., respectively, based on molecular evidence. In accordance with microbial fertilizer safety standards, strain QBS-B2 was prioritized for further study. This strain exhibited a minimum fermentation broth pH of 3.65 and achieved a cadmium carbonate activation rate of 92.27%. Culture with glucose as the carbon source and ammonium chloride as the nitrogen source were found to be optimal for enhancing cadmium desorption from soil by strain QBS-B2. Under these conditions, the soluble cadmium concentration reached 170.77 μg/L, which was 66.5 times higher than that of the control group, corresponding to a soil cadmium desorption rate of 46.21%. Furthermore, strain QBS-B2 significantly increased the content of available cadmium and available phosphorus in the soil. The application of compound fertilizer enhanced the cadmium activation of QBS-B2, resulting in a soil cadmium activation rate of 17.37%. The application of organic fertilizer significantly promoted the colonization and growth of the strain in the soil and increased the available phosphorus content by 5.9 times compared with the control. Conclusion This study provides elite microbial resources for the development of cadmium-activating microbial inoculants and bio-organic fertilizers based on P. megaterium QBS-B2. Furthermore, it establishes a theoretical foundation and demonstrates application potential for bio-augmented phytoextraction in the remediation of cadmium-contaminated soils.

Objective The microbial communities preserved within vertebrate bone remains serve as crucial biological archives recording their burial processes and environmental histories. However, how bone microbial communities respond to environmental changes across different geographical and chronological scales, as well as their specific indicative potential in paleoenvironmental reconstruction, remains unclear. This study aims to reveal the spatio-temporal variation patterns of vertebrate bone microbial communities in northern China and evaluate their feasibility as paleoenvironmental biomarkers. Methods Ancient DNA extraction and shotgun metagenomic sequencing techniques were employed to analyze the microbial community composition of 43 animal bone fossil or subfossil samples collected from different geographical regions (Northeast and Northwest China) and geological periods (Late-Pleistocene and Holocene) in northern China. Diversity statistics and differential species identification were combined to systematically compare the spatio-temporal variation characteristics of community structures. Results Microbial communities exhibited significant differences across both geographical regions and geological periods. Samples from Northeast China showed higher microbial diversity, being dominated by soil-derived taxa such as Acidobacteria sp. GGB63485, while samples from Northwest China were dominated by freshwater and chemoautotrophic taxa including Curvibacter and Sulfuricaulis. Cold-tolerant and oligotrophic taxa were enriched in Late-Pleistocene samples, while taxa associated with aquatic environments and plant degradation were more prominent in Holocene samples. Conclusion The compositional differences of microbial communities in bone remains are jointly driven by local environmental factors and temporal climate change. The structural characteristics can effectively reflect paleoenvironmental conditions including soil type, hydrological status, redox potential, and temperature changes. This study provides empirical evidence and methodological approaches for paleoenvironmental reconstruction with skeletal microbiomes, expands the boundaries of traditional paleoenvironmental indicator systems, and offers new perspectives for understanding the assembly mechanisms and ecological responses of microbial communities during long-term burial.

Objective Efficient carbon-fixing microorganisms are a critical functional resource for achieving the “dual carbon” goals. However, the unstable carbon fixation performance makes natural strains difficult to directly meet industrial application needs. The molecular mechanisms underlying the enhancement of carbon fixation performance by atmospheric and room temperature plasma (ARTP) mutagenesis remain unclear. Methods Five carbon-fixing bacterial strains preserved in our laboratory were used as the starting strains. Through ARTP mutagenesis combined with directed screening and carbon-fixing enzyme activity tracking, a genetically stable and efficient carbon-fixing mutant B4-5 was constructed. Whole-genome sequencing, combined analysis of single nucleotide polymorphism (SNP) and insertion/deletion (InDel), and metabolic characterization were employed to systematically elucidate the carbon fixation enhancement mechanism. Results The mutant B4-5 showed increases of 33.16%, 72.54%, and 72.61% in key carbon-fixing enzyme activity, carbon assimilation amount, and carbon assimilation rate, respectively, with the Calvin cycle serving as the core carbon fixation pathway. Whole-genome comparison revealed that the genome of the mutant was highly collinear with that of the parent strain (similarity>98.50%), indicating that there were no large-scale chromosomal structural variations in the genome of the mutant. The combined analysis of SNP and InDel identified four key mutation sites (spoⅡE, nprR, glnQ, and murB) related to carbon fixation performance, and these sites optimized carbon source allocation, coordinated carbon-nitrogen metabolism balance, and reprogrammed carbon flux. Finally, a cascade mechanism of genomic micro-variation-metabolic regulation-phenotype enhancement was established. Conclusion This study clarifies the regulatory mechanism underlying the enhancement of carbon fixation metabolism by ARTP mutagenesis, providing a theoretical basis and engineered strain resources for the development of microbial carbon neutralization technologies.

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.

Yuncheng Salt Lake located in the southwest of Shanxi Province is one of the three major sodium sulfate inland salt lakes in the world, harboring rich microbial resources, while there is still a lack of systematic research on the archaeal diversity in this salt lake. Objective To explore the diversity of archaea in soil sediments of Yuncheng Salt Lake and analyze the influences of environmental factors on the diversity. Methods Soil physical and chemical analysis was carried out on 54 samples from 18 sampling sites in Yuncheng Salt Lake, and the effects of environmental factors on the archaeal diversity were analyzed by amplicon high-throughput sequencing. Results Amplicon analysis showed that Halobacteriota, Thermoproteota, Nanobdellota, Thermoplasmatota, and Asgardarchaeota were the main taxa. Among them, Halobacteriota and Thermoproteota were the dominant groups of archaea in the soil sediments of Yuncheng Salt Lake. The analysis of diversity and community composition showed that there were obvious differences in archaeal communities among different sampling sites. Redundancy analysis showed that total nitrogen, total carbon, ammonium nitrogen, and SO₄^2- had the greatest effect on the archaeal diversity in soil sediments, followed by nitrate nitrogen, Cl^-, Mg²⁺, and Na⁺, while Ca²⁺, total phosphorus, and total potassium had mild effects. Conclusion The archaeal community in soil sediments of Yuncheng Salt Lake has high diversity and is closely related to environmental factors. This study enriches the biological information of archaeal resources in soil sediments of Yuncheng Salt Lake and provides a theoretical basis for the mining and research of archaeal resources in salt lakes.

Objective The survival mechanisms of aerobic methylotrophs in oxygen-deficient environments represent a focal topic in current microbial ecology. This study aims to investigate the extracellular electron transfer (EET) mechanism by which the aerobic methylotroph Methylophilus sp. 14 utilizes insoluble iron minerals (ferrihydrite) under oxygen-deficient conditions and to elucidate the synergistic role of exogenous and endogenous electron shuttles in this process. Methods Anaerobic culture (initial O₂ level: 2%) of Methylophilus sp. 14 isolated from sediments of Fuxian Lake was conducted with methanol as the carbon source and ferrihydrite as the sole terminal electron acceptor. Iron reduction kinetics were measured along with electrochemical analyses (differential pulse voltammetry and cyclic voltammetry) and microscopic characterization (scanning/transmission electron microscopy) to systematically evaluate the iron-reducing capacity of the strain and explore the roles of exogenous shuttles (humic substances, HS; anthraquinone-2,6-disulfonate, AQDS) and endogenous flavins in electron transfer. Results Methylophilus sp. 14 coupled methanol oxidation with ferrihydrite reduction, increasing the Fe(II) concentration from 0.49 μmol/L to 8.29 μmol/L within 20 days and promoting the partial transformation of ferrihydrite into magnetite. Exogenous addition of HS and AQDS further enhanced Fe(II) production to 10.73 μmol/L and 11.22 μmol/L, respectively, improving the cumulative electron transfer efficiency by approximately 1.5 folds. Electrochemical analyses indicated that the redox potential of the bacterial cells was lower than that of ferrihydrite, thermodynamically favoring spontaneous electron transfer. Soluble AQDS formed a conductive microenvironment that accelerated electron flux. Notably, this study first revealed that Methylophilus sp. 14 synthesized and secreted flavins, whose extracellular concentration showed a strong positive correlation with the EET rate (r=0.94, P<0.001). Furthermore, exogenous shuttles stimulated increases of 30%‒50% in total flavin secretion. Flavins functioned as a critical electron bridge, mediating electron transfer from intracellular metabolism to exogenous shuttles and thereby establishing a cooperative electron transport chain. Conclusion This work reveals a novel EET strategy employed by aerobic methylotrophs to adapt to oxygen-deficient conditions. That is, exogenous electron shuttles not only construct an extracellular conductive microenvironment but also stimulate the secretion of endogenous flavins, resulting in a synergistic electron transfer mechanism that efficiently drives the reduction of solid-phase iron minerals. These findings deepen our understanding of the metabolic flexibility of aerobic microorganisms and their ecological role at aerobic-anerobic interfaces.

Objective To investigate the sedimentary characteristics of dolomite, the bacterial community structure, and their relationships with environmental factors in the sediments of Jibuhulangtu Salt Lake, Inner Mongolia. Methods Sediments were collected from four sites along an offshore-to-nearshore transect in Jibuhulangtu Salt Lake. Bacterial community composition, mineralogical characteristics, and physicochemical parameters of sediments were analyzed by 16S rRNA gene sequencing, X-ray diffraction with Rietveld refinement, and scanning electron microscopy with energy-dispersive spectroscopy, and ion chromatography. Results After removal of soluble salts, the dolomite content in the sediments ranged from 48.75% to 75.28%. The dolomite particles primarily exhibited a nano-spherical shape and transformed from regular spheres to spherical aggregates with the increase in depth. The Mg/Ca molar ratios of the dolomite ranged from 0.87 to 1.46, approaching the stoichiometric value (1.00) of ideal dolomite. At the phylum level, the five most abundant bacterial groups were Actinomycetota, Pseudomonadota, Gemmatimonadota, Chloroflexota, and Acidobacteriota. The sulfate-reducing phylum Desulfobacterota was also abundant (4.23%). Alpha diversity analysis revealed significant differences in bacterial community diversity among sampling sites (P<0.05), with site J4 exhibiting the highest species richness but the lowest evenness. Redundancy analysis indicated that the concentrations of SO₄^2-, Mg²⁺, K⁺, Ca²⁺, Cl^-, and F^- were the key environmental factors significantly shaping the bacterial community structure. Conclusion Dolomite is abundant in the sediments of Jibuhulangtu Salt Lake. Its formation is likely attributable to the extremely high sulfate concentrations and high Mg/Ca ratio of the lake water, as well as the metabolic activities of key functional groups such as sulfate-reducing bacteria.

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.

Objective To isolate and identify secondary metabolites from the deep-sea-derived fungus Talaromyces muroii SCSIO 40439 and evaluate their biological activities. Methods The strain SCSIO 40439 was fermented on a rice medium. The resulting extract was subjected to silica gel column, Sephadex LH-20 column, and semipreparative high performance liquid chromatography (HPLC) to obtain compounds. Structure elucidation was performed via high-resolution electrospray ionization mass spectrum (HRESIMS), nuclear magnetic resonance (NMR), and X-ray crystal diffraction and comparison with literature data. Antimicrobial activity was assessed through the filter paper disk diffusion method, while tyrosinase inhibitory activity was measured based on the rate of dopamine oxidation. Results Four compounds were isolated from the fermentation extract of T. muroii SCSIO 40439, including a new orsellinic acid-cysteine dimer dioscysmycine A (1) and three known polyketides: alternariol (2), altenusin (3), and 3′-hydroxyalternariol 5-O-methyl ether (4). Compound 1 exhibited tyrosinase inhibitory activity with an inhibition rate of 58% (the positive control, kojic acid, showed an inhibition rate of 90%). Compound 2 inhibited the growth of Staphylococcus aureus ATCC 29213 and methicillin-resistant S. aureus ATCC 43300. Conclusion This study expands the known structural diversity of secondary metabolites of Talaromyces and identified a candidate inhibitor for tyrosinase. Furthermore, the findings provide a new biosynthetic gene cluster of alternariol.

Objective To investigate the differences in the structure and function of rhizosphere soil microbial communities between two dominant halophytes—Suaeda salsa and Phragmites australis—in Yuncheng Salt Lake Wetland and to reveal their associations with soil environmental factors, thereby providing a theoretical basis for the ecological restoration of saline-alkali wetlands. Methods Rhizosphere soil samples of S. salsa and P. australis, as well as bare beach soil sample without plant cover, were collected as research objects. Metagenomic sequencing was employed to analyze the microbial community structure and functional genes, and key soil physicochemical properties were determined. Results The total dissolved solids (TDS), pH, and Cl^- concentration in the rhizosphere soils of S. salsa and the bare beach were higher than those in the rhizosphere of P. australis (P<0.05). The microbial diversity and abundance in the rhizosphere soils of both plant species were significantly higher than those in the bare beach soil. The bare beach soil was significantly enriched with the viral phylum Cressdnaviricota, while the rhizosphere soil of S. salsa was significantly enriched with the psychrophilic genus Algoriphagus. Both the rhizosphere soil of S. salsa and the bare beach soil showed co-enrichment of the genera Halomonas and Salegentibacter. TDS was the key factor driving the structures and functional distribution of soil microbial communities, with a contribution rate of 64.40%. Compared with the bare beach, the plant rhizospheres significantly increased the abundance of functional genes related to carbon (e.g., acdB and acs), nitrogen (e.g., gdh_K15371 and nasA), and sulfur (e.g., sudA and dmdB) cycling. Conclusion S. salsa and P. australis shape distinct rhizosphere microenvironments through different survival strategies, which enhance microbial diversity and the abundance of functional genes associated with element cycling, thereby improving the stability and functioning of the saline-alkali wetland ecosystem. This study provides a theoretical foundation for utilizing plant-microbe interactions in the bioremediation and sustainable agricultural use of saline-alkali land.

Objective To determine the composition, diversity, functional metabolic characteristics, and their association with environmental factors of the microbial community in Xiaochaidan Salt Lake, and to evaluate its ecological functions and potential risk as a reservoir for antibiotic resistance genes (ARGs). Methods Metagenomic sequencing was applied to water-sediment mixed samples from the lake. Databases including non-redundant protein database (NR), clusters of orthologous groups of proteins (COG), Kyoto encyclopedia of genes and genomes (KEGG), carbohydrate-active enzymes database (CAZy), and comprehensive antibiotic resistance database (CARD) were used to annotate microbial taxonomy, functional genes, metabolic pathways, and ARGs. Additionally, Hellinger transformation-based principal component analysis (tb-PCA) was conducted to link microbial community structures with environmental factors. Results The salt lake exhibited high microbial diversity (Shannon index: 5.620-6.112), with a total of 16 850 identified species. Bacteria dominated the microbial community (relative abundance of 91.89%), mainly represented by Pseudomonadota (57.22%) and Bacteroidota (14.64%). Archaea (3.77%) were absolutely dominated by Euryarchaeota (92.64%). Siphoviridae and saprotrophic Oomycetes were the most dominant taxa in the viral and eukaryotic communities, respectively. Association analysis with environmental factors demonstrated that bacterial distribution was primarily driven by Cl^-, whereas archaeal community distribution was co-driven by Na⁺, Cl^-, and SO₄^2-. Metabolic functions related to amino acid and carbohydrate metabolism were highly active, as reflected by the enrichment of glycosyltransferase and glycoside hydrolase genes. Notably, diverse ARGs were detected, which were primarily conferred by efflux pump systems (e.g., novA). Conclusion Xiaochaidan Salt Lake harbors a complex and functionally synergistic microbial ecosystem. Local differences in ionic concentrations represent the primary driver of niche differentiation between bacteria and archaea. To adapt to this extreme habitat, indigenous microbes have evolved a strategy that integrates conservative osmoregulation and flexible carbon metabolism. The high abundance of efflux pump-associated ARGs implies that this hypersaline lake serves as a natural reservoir for ARGs, underscoring the potential risk of their ecological dissemination.

Objectives To screen copper-resistant and copper-reducing bacteria from deep-sea hydrothermal sediments and systematically analyze Cu(II) bioreduction process mediated by the bacteria, and mineralization product characteristics, thus filling the knowledge gap regarding microbial participation in copper cycling in deep-sea hydrothermal environments. Methods A strain, Shewanella sp. FeAMO, was obtained through anaerobic enrichment culture. With sodium lactate as the electron donor and Cu(II) as the terminal electron acceptor, inductively coupled plasma mass spectrometry, scanning electron microscopy-energy dispersive spectroscopy, X-ray diffraction, and X-ray photoelectron spectroscopy were employed to analyze bacterial growth, copper reduction kinetics, and physicochemical properties of the products. Results Strain FeAMO exhibited high tolerance to 400 μmol/L Cu(II), achieving a Cu(II) removal rate of 96.8% within 72 h. The mineralization products were spherical microspheres with diameters ranging from 5 to 10 µm. The bulk phase was predominant crystalline cuprous sulfide (Cu₂S), while the surface was stably enriched with metallic copper (Cu⁰) nanoparticles, forming a core-shell heterostructure. Conclusion Shewanella sp. FeAMO can tolerate Cu(II) with copper transporters and generate Cu₂S-Cu⁰ composite minerals by coupling copper reduction and sulfur reduction pathways. This study not only elucidates the mechanism of microbial-driven copper and sulfur cycling in hydrothermal environments but also provides a potential strategy for heavy metal immobilization and resource recovery.

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.