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.

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 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 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.

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.

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 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 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.

Objective Although the coupling of carbon (C), nitrogen (N), and sulfur (S) cycles is crucial in mangrove ecosystems, direct experimental evidence from pure microbial cultures demonstrating this coupling remains scarce. This work aims to elucidate the coupling process of C, N, and S cycles in mangrove-derived Vibrio ziniensis ZWAL4003. Methods An integrated approach combining genomic analysis, phylogenetic analysis, 16S rRNA gene abundance quantification, and physiological-biochemical characterization was employed to explore the potential coupling process of element metabolism in ZWAL4003. Results The genome of ZWAL4003 carried genes associated with complete metabolic pathways including tricarboxylic acid cycle, oxidative phosphorylation, dissimilatory nitrate reduction to ammonium, and assimilatory sulfur reduction. Glucose, sucrose, starch, and glycerol as C sources significantly enhanced the nitrate reduction activity of ZWAL4003. NaNO₃ as the N source inhibited the sulfate reduction activity of ZWAL4003. Na₂S₂O₃, Na₂SO₄, and Na₂SO₃ as the S sources inhibited the nitrate reduction activity. Furthermore, V. ziniensis strains were widely distributed in the mangrove sediments along the southeast coast of China, with the relative abundance of 0.004 19%-0.073 04%, showing an increasing trend from north to south. Conclusion This study demonstrates that C source utilization promotes nitrate and sulfate reductions, while mutual inhibition exists between nitrate and sulfate reductions, forming the coupling process of C, N, and S metabolisms in ZWAL4003. The wide distribution of V. ziniensis strains in the mangrove ecosystems of China suggests the potential important role of V. ziniensis as an executor in coupling element cycles. These findings enrich our understanding of the integrity of microbe-driven geochemical processes in mangrove ecosystems.

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.