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.

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 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.

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.

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.

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 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 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 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.

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.