[Objective] To study the influencing factors and mechanism of biogenic gas production in shale. [Methods] The shale in Yulin was chosen as the object of this study, and methanogens specifically enriched by our research team in the preliminary stage were used as functional microbiota. An orthogonal design was adopted to optimize the biogenic gas production conditions. The simulated biogenic gas production characteristics and changes in physical and chemical properties of the shale before and after gas production were comprehensively analyzed by gas chromatography (GC), X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FT-IR), Raman spectroscopy (Ram), and nuclear magnetic resonance spectroscopy (NMR). [Results] The optimal conditions for gas production from shale were as follows: 15% inoculum, a shale particle size of less than 0.125 mm, and an incubation temperature of 35 ℃, under which a cumulative methane yield of 81.22 μmol/g shale was achieved within 50 days. Industrial and elemental analyses conducted before and after gas production revealed that methanogens consumed the organic components of shale to produce methane. XRD results indicated that the inorganic mineral components in shale also contributed to the anaerobic degradation process associated with gas production. FT-IR and Ram results showed that the organic matter in shale was mostly long-chain aliphatic hydrocarbons. During gas production, the carbonyl and ether bonds in some compounds reacted to form intermediate metabolites containing carboxyl groups. After gas production, the D and G peaks in the shale samples were not obvious, indicating that the graphitization degree and maturity of kerogen in the shale increased. In addition, NMR results confirmed that fatty alcohols or fatty amines were utilized by microorganisms in gas production. [Conclusion] Microorganisms can utilize the organic components of the shale to produce gas, while also consuming the inorganic mineral components. This leads to chemical structure organic components, leading to formation of smaller compounds after gas production.

[Objective] To study the distribution characteristics and enzyme potential of halophilic bacteria in two distinct types of salt lakes located in Xinjiang, China. [Methods] Soil samples were collected from sulfate-type (Qijiaojing) and carbonate-type (Nanhu Alkaline Lake) salt lakes, and their physicochemical properties were analyzed. The diversity, dominant taxa, and enzyme activities of halophilic bacteria were compared between the two salt lakes by Illumina MiSeq and culture experiments. [Results] The physicochemical properties of soil differed significantly between the two salt lakes, and the soil salinity of Qijiaojing salt lake (227.15 mg/g) was higher than that of Nanhu Alkaline Lake (158.61 mg/g). Significant differences were also observed in pH, HCO₃^-, Cl^-, Mg²⁺, and K⁺ content. Spearman correlation analysis revealed positive correlations between Cl^- and Mg²⁺ content and the relative abundance of dominant bacterial genera such as Pontibacter and Bacteroides. Illumina MiSeq results of bacterial 16S rRNA genes indicated that the Simpson and Shannon indexes of Nanhu Alkaline Lake were significantly higher than those of Qijiaojing. Halophilic bacteria belonging to 590 genera of 37 phyla were identified, including Bacteroidota (33.41%), Bacillota (24.71%), Actinomycetota (14.64%), and Pseudomonadota (10.58%). The dominant phylum was Bacteroidota (35.05%) in Nanhu Alkaline Lake, while it was Bacillota (44.66%) in Qijiaojing. The richness of halophilic bacteria in Nanhu Alkaline Lake exceeded that in Qijiaojing, with Pontibacter identified as the dominant genus in both lakes. A total of 1 130 strains were obtained from two salt lakes, belonging to 9 genera, 7 families of 4 phyla, among which Bacillota, Actinomycetota, and Pseudomonadota accounted for 40.53%, 36.81%, and 21.15%, respectively. The results of culture experiments with seven different media indicated that the F6 medium exhibited the highest selectivity towards halophilic microorganisms. Culture experiments demonstrated similar dominant species in both lakes, primarily comprising low-abundant bacteria, such as Nocardiopsis and Bacillus. Enzyme activity screening results revealed that 46.81%, 44.07%, and 20.88% of halophilic bacteria produced esterase, cellulase, and amylase, respectively, with Bacillus exhibiting the highest overall enzyme production capability. [Conclusion] There are significant differences in the halophilic bacterial diversity between sulfate- and carbonate-type salt lakes in Xinjiang. The halophilic bacteria in the carbonate-type Nanhu Alkaline Lake salt lake have higher diversity and exhibit stronger enzyme activities. This investigation contributes valuable insights for the advancement and sustainable utilization of microbial resources and the ecological preservation in salt lakes.

Biodegradable mulch films (BDMs), distinguished by their extensive application potential and ecological friendliness, are progressively supplanting traditional mulch film and considered as a highly promising approach to address “white pollution”. China has witnessed notable advancements in the production technology of BDMs in recent years, establishing a strong foundation for their large-scale manufacturing and widespread application. Despite the great prospects of BDMs, the complexity and controllability of their degradation process, alongside their potential impacts on the eco-environment, remain highly concerned. This paper comprehensively analyzes five promising polyester and polycarbonate-based BDMs and delves into the primary degrading microorganisms and their degradation mechanisms. Furthermore, this paper summarizes the current research regarding the impacts of BDMs on the soil environment. This review aims to lay a theoretical foundation for discovering efficient microbial degraders, pinpointing key rate-limiting steps in degradation, and enhancing long-term ecological effect studies, thus providing new perspectives and solutions for the large-scale and safe utilization of BDMs.

Microplastics are novel pollutants that are widespread in the oceans, soil, and atmosphere, affecting the process of pollutant transport and transformation through physical, chemical or biological interactions. The heavy metal pollution caused by mining activities in the soil and water environment around antimony mining regions is increasing year by year. However, the effect of microplastics on the biogeochemical transformation of heavy metal contaminants in the mining regions has been rarely reported. [Objective] To understand the effects of microplastic type, size and concentration on microbially mediated antimony release from stibnite. [Methods] We took Pseudomonas sp. J-1 with strong antimony tolerance and promoting antimony release and widely used polypropylene, polyvinyl chloride, and polystyrene as the objects of the study. The changes in pH, redox potential (ORP), microbial biomass, and antimony concentration were analyzed. Furthermore, microplastic adsorption of antimony under different pH values was studied, and confocal laser scanning microscopy (CLSM) and scanning electron microscope-energy dispersive X-ray spectroscopy (SEM-EDS) were employed to reveal the mechanism by which microplastics affected the biogeochemical cycle of antimony. [Results] Polypropylene with a particle size of 13 μm and a high concentration had the strongest inhibitory effect on stibnite dissolution with the participation of Pseudomonas sp. J-1. Microplastics inhibited the growth of the bacterial colony, which led to weakened promoting effect on the release of antimony, and the growth of Pseudomonas sp. J-1 was even completely inhibited by the high concentration of microplastics. Microplastics were able to adsorb antimony, while the adsorption capacity was independent of solution pH. [Conclusion] The type, particle size, and concentration of microplastics are the key factors affecting the stibnite dissolution mediated by Pseudomonas sp. J-1 and they indirectly affect stibnite dissolution mainly by influencing microbial growth.

Viruses, non-cellular biological entities composed of a protein shell and genetic materials, must parasitize living cells to proliferate and are the most numerous biological entities on Earth. Soil is an important reservoir of viruses, predominantly bacteriophages that infect prokaryotes. Soil viruses play crucial ecological roles in regulating host community structure, driving microbial evolution, and mediating biogeochemical cycles. Delving into these functions and their mechanisms not only elucidates the indispensable role of viruses in soil ecosystems but also underpins sustainable soil management. In this paper, we summarized current knowledge on the ecological functions of soil bacteriophages, including (1) host community modulation: selective survival strategies (e.g., lytic-lysogenic switches) that reshape microbial composition and diversity, while altering host virulence and fitness; (2) evolutionary drivers: horizontal gene transfer mediated by viral vectors and host-pathogen coevolution dynamics; (3) biogeochemical catalysts: the viral shunt mechanism, alongside auxiliary metabolic genes enhancing nutrient cycling; (4) cross-kingdom impacts: direct interactions with plant rhizospheres and indirect effects on human health via zoonotic gene dissemination. According to the research progress, we make an outlook on the future research directions regarding the ecological functions of soil viruses.

Organic matter degradation in shallow lake sediments is a key process in regulating the carbon cycle and greenhouse gas emissions, while the mechanism by which submerged plant residue degradation regulates the long-term succession of microbial communities has not yet been clarified. [Objective] To investigate the mechanisms of microbial community succession driven by submerged plant residue degradation on long time scales. [Methods] We investigated the degradation dynamics of Potamogeton wrightii residues in Taihu Lake sediments through a 4-year microcosmic simulation experiment and analyzed in detail the dynamic impacts of organic matter fraction evolution and extracellular enzyme activities on microbial community succession. [Results] The rapid consumption of labile organic matter pool was accompanied by a surge in β- glucosidase activity, while the accumulation of recalcitrant organic matter pool was coupled with a lagged response of phenol oxidase activity. Microbial communities showed significant functional differentiation, with Bacillota and Basidiomycota dominating the degradation of recalcitrant organic matter pool in bacterial and fungal communities, respectively, revealing the metabolic division of labor in the degradation of lignin-like polymers. Variance decomposition showed that both labile and recalcitrant organic matter pools independently explained microbial community variations, highlighting the role of chemical complexity of organic matter in screening functional taxa. [Conclusion] Degradation of submerged plant residues significantly drove microbial community structure succession in the microcosmic culture system, and microbial community composition and organic matter fractions showed synergistic changes. In addition, the degradation promoted the growth of microorganisms with different growth strategies. This study elucidates the dynamic interactions between microbial functional differences and organic matter pool complexity in the degradation of submerged plant residues, providing a theoretical basis for carbon stability assessment and ecological restoration of shallow lakes.

[Objective] Fusarium oxysporum is a fungal pathogen that causes plant wilt, severely affecting plant growth. Therefore, it is necessary to use appropriate and environmentally friendly biological methods for control of this pathogen. [Methods] We employed the point inoculation method to isolate a marine Bacillus strain antagonistic to Fusarium oxysporum from mangrove soil. The Bacillus strain was identified based on physiological and biochemical characteristics and 16S rRNA gene sequence. The antifungal substance was extracted from the fermentation supernatant, and the inhibitory activity and mechanism of the substance against Fusarium oxysporum were evaluated in vitro. [Results] A Bacillus strain with strong antagonistic activity against Fusarium oxysporum was isolated from mangrove soil and identified as Bacillus velezensis. The antifungal substance secreted by strain K3 exhibited broad-spectrum antimicrobial properties, being effective against both bacteria and fungi. This substance was likely a protein or peptide and had good thermal stability. It showed the minimum inhibitory concentration (MIC) of 1 mg/mL against Fusarium oxysporum, significantly inhibiting spore germination and causing leakage of electrolytes, nucleic acids, and proteins. The treatment with 3×MIC of the antifungal substance for 10 h showed the inhibition rate of 49.85% on the germination of Fusarium oxysporum spores. Moreover, the treated Fusarium oxysporum hyphal cells showed compromised cell integrity, disrupted membrane homeostasis, increased malondialdehyde content, and enhanced activities of superoxide dismutase, peroxidase, and catalase in the membrane. [Conclusion] The antifungal substance produced by B. velezensis K3 isolated from mangrove soil of marine origin exhibits a broad antimicrobial spectrum and strong inhibitory activity against Fusarium oxysporum, with potential commercial application value.

[Objective] Iron reduction-dependent anaerobic oxidation of methane (Fe-AOM) is an important pathway for methane emission reduction in anaerobic environments. However, it remains unclear how methane-oxidizing microbes perform Fe-AOM under nitrogen-limiting conditions. [Methods] Focusing on a methane-oxidizing consortium and ferrihydrite, this study employed nitrogen isotope tracing, three-dimensional fluorescence spectroscopy, electrochemical analysis, and high-throughput sequencing to investigate the Fe-AOM efficiency and the possibility of coupling Fe-AOM with biological nitrogen fixation under nitrogen-limiting conditions. [Results] The methane-oxidizing consortium was able to catalyze Fe-AOM under nitrogen-limiting conditions, reducing ferrihydrite to minerals such as siderite. The nitrogenase activity and ¹⁵N assimilation of the methane-oxidizing consortium in the presence of methane were significantly higher than those in the absence of methane, which demonstrated that the consortium could couple Fe-AOM with biological nitrogen fixation. Three-dimensional fluorescence spectroscopy and electrochemical analysis revealed that Fe-AOM promoted the production of dissolved protein-like substances, enhanced the redox activity of the methane-oxidizing consortium, and reduced ferrihydrite via direct electron transfer. Microbial community structure analysis showed significant enrichment of Methanobacterium (19.32%), iron-reducing bacteria such as Geobacter (6.14%) and Desulfovibrio (17.52%), as well as nitrogen-fixing bacteria like Azoarcus (1.69%) and Azospirillum (0.43%) during the Fe-AOM process. DNA-SIP analysis found that Azoarcus was significantly enriched in the heavy fraction of the labeled isotope group, confirming that it fixed isotope nitrogen. [Conclusion] It is thus hypothesized that the coupling of Fe-AOM with biological nitrogen fixation was primarily carried out by Methanobacterium which oxidized methane, Geobacter and Desulfovibrio responsible for the reduction of ferrihydrite, and Azoarcus catalyzing biological nitrogen fixation. Additionally, the positive correlations of the methane-oxidizing bacterium Methylocystis with iron-reducing bacteria and nitrogen-fixing bacteria suggested a certain contribution of Methylocystis to this process. These results provide new insights into understanding iron-dependent methane oxidation and nitrogen fixation in anaerobic environments.

Methanogenic archaea are pivotal drivers of carbon cycling in anoxic environments. Growing evidence shows that they also participate in the biogeochemical cycling of metal(loid)s, yet the underlying transformation mechanisms have not been systematically summarized. This review integrates the latest findings to dissect how methanogenic archaea oxidize, reduce, methylate, and demethylate representative metal(loid)s, including iron (Fe), mercury (Hg), vanadium (V), chromium (Cr), cadmium (Cd), arsenic (As), and selenium (Se). The research findings are summarized as follows: (1) Fe(Ⅲ) reduction exerts bidirectional control over methanogenesis. When extracellular Fe(Ⅲ) reduction is not coupled to energy metabolism, it markedly suppresses the growth and methane production of methanogenic archaea (e.g., Methanosarcina barkeri). Conversely, when extracellular Fe(Ⅲ) reduction is coupled to energy metabolism, it stimulates the physiological and metabolic activities of methanogenic archaea (e.g., Methanosarcina acetivorans). (2) For mercury methylation, methanogenic archaea convert Hg(Ⅱ) to methylmercury (MeHg) via a methyltransferase encoded by the hgcAB gene cluster. In some species (e.g., Methanomassiliicoccus luminyensis), the observed methylation activity is associated with enzymes released from lysed cells. (3) Arsenic transformation runs with diverse mechanisms. Methanosarcina acetivorans methylates As(Ⅲ) via the arsenic methyltransferase (ArsM) and concurrently reduces As(V) to As(Ⅲ) through arsenate reductase (ArsC), whereas archaeal communities in paddy soils are capable of demethylating organic arsine. (4) Selenium biotransformation exhibits dual effects: low concentrations of selenium nanoparticles (SeNPs) enhance methanogenic activity and induce organoselenium synthesis, whereas high concentrations trigger oxidative stress. Environmentally, metal (loid)s markedly affect the metabolic activity and community structure of methanogenic archaea by altering redox potential, competing for electron acceptors, or imposing toxic stress. This review highlights the multifunctionality of methanogenic archaea in metal (loid) cycling and proposes that future work should combine meta-omics and metabolomics approaches to elucidate enzyme-level mechanisms, while exploring methanogenic archaea-based strategies for the bioremediation of metal (loid) contamination.

[Objective] Soil salinization is a serious threat to land health, and microbial remediation of saline-alkali soil is an eco-friendly and practical approach. Endophytic fungi can enhance host resistance to both biotic and abiotic stresses. Consequently, there is a need for further research on the biological characteristics of endophytic fungi. Such research can expand the existing endophytic fungal database and provide elite strains and effective strategies for the green remediation of saline-alkali soil and soil restoration. [Methods] The characteristics of the fungal strain were analyzed by plate culture under stress, scanning electron microscopy (SEM), and multi-gene phylogenetic analysis. The colonization of the strain in rice roots was examined by GFP fluorescence labeling, trypan blue staining, SEM, and colonization curve plotting. Pot experiments under stress and non-stress conditions, the peroxidase activity assay, transcriptome analysis, and gene expression analysis were carried out to decipher the mechanism by which the strain enhanced the salt tolerance of rice plants. [Results] An endophytic fungal strain, LW2, capable of enhancing the salt tolerance of host rice plants, was obtained. The phylogenetic tree showed that LW2 clustered with Ophioceras leptosporum CBS 894.70 in the same minimal clade, and thus the strain was identified as O. leptosporum LW2. LW2 successfully colonized rice roots and promoted the growth of potted rice. The rice plants co-cultured with LW2 showed significant increases in the fresh weight, plant height, and stem width. The pot experiments under salt stress showed that LW2 improved the salt tolerance of rice by increasing the plant height and stem width under stress conditions while alleviating stress-induced wilting and yellowing. LW2 mitigated salt-induced damage of rice by increasing the peroxidase activity and promoting reactive oxygen species (ROS) scavenging. In addition, LW2 regulated the expression of EIL1 and HKTs in the ethylene signaling pathway which affected ion transport, thereby enhancing rice salt tolerance. [Conclusion] This study identified an endophytic fungal strain, O. leptosporum LW2, capable of enhancing the salt tolerance of host rice. We preliminarily investigate the salt tolerance mechanism of this strain, providing scientific evidence and an elite strain for microbial remediation of saline-alkaline soil and the development of green agriculture.