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.

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.

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 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.

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

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

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.

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.

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.