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.