In marine aquaculture, the accumulation of antibiotics such as sulfamethoxazole (SMX) has contributed to the spread of antibiotic-resistant bacteria and genes, posing a serious threat to ecological health. Biological treatment of antibiotic-contaminated wastewater is an essential approach to mitigate these environmental risks. [Objective] To isolate a salt-tolerant strain LS-1 with high SMX degradation efficiency from the sediment of an inshore aquaculture pond, examine the effects of environmental factors on the degradation capacity of this strain, optimize the SMX degradation conditions, elucidate the degradation pathway through product analysis, and evaluate the toxicity of the degradation products. [Methods] The isolated strain was identified by 16S rRNA gene sequencing and phylogenetic analysis. Single factor experiments and response surface methodology were employed to optimize the degradation conditions. GC-MS and the luminescent bacteria test for acute toxicity were adopted to analyze the degradation products and their toxicity. [Results] Strain LS-1 showed 99.79% sequence similarity with Alcaligenes aquatilis strain AS1. Tryptone was determined to be the optimal exogenous carbon source for both growth and SMX degradation. The strain exhibited robust growth across a temperature range of 20‒35 ℃, salinities of 15‰‒35‰, SMX concentrations from 10 to 100 mg/L, and pH 7.0‒9.0. Response surface analysis revealed that SMX concentration, initial pH, and temperature significantly influenced the SMX degradation rate, in descending order of importance. Under optimal conditions (SMX concentration of 33 mg/L, pH 7.4, and 30 ℃), the strain achieved a maximum degradation rate of 60.17% within 48 h. MS results indicated that LS-1 degraded SMX via acetylation and hydroxylation pathways. The results of the luminescent bacteria test for acute toxicity demonstrated a progressive reduction in biological toxicity during the SMX degradation process. [Conclusion] The SMX-degrading strain LS-1 can effectively adapt to marine environmental conditions, reducing SMX-induced toxicity in water. This study highlights the potential of LS-1 for controlling antibiotic pollution in marine aquaculture wastewater.

Ion-adsorbed rare earth ore is a strategically important resource of global concern, playing a vital role in developing multiple industries in China. However, large-scale mining activities have led to soil degradation, nutrient losses, and heavy metal pollution. [Objective] To analyze the microbial community structure in the vertical profile of an ion-adsorbed rare earth mine and its response to environmental factors, exploring the depth-dependent variation pattern of microbial communities and their relationship with environmental variables. The findings will provide a scientific basis for the ecological restoration of polluted mining areas. [Methods] The soil samples were collected from an ion-adsorbed rare earth mine within the depth range of 1–15 m, and the physicochemical properties of the soil were analyzed. High-throughput sequencing was employed to investigate the distribution patterns of soil microorganisms along the vertical profile of the mine and to establish the relationships between environmental factors and microbial community succession. [Results] As the mining depth increased, soil pH and total carbon (TC) gradually decreased. Ammonia nitrogen (NH₃-N) was the dominant N form in the mine soil, reaching up to 13.0 mg/kg in the intermediate soil layers. Iron (Fe), magnesium (Mg), and total rare earth elements (TREEs) were abundant, with higher accumulation levels in deeper soil layers. The microbial communities exhibited a distinct succession pattern along the vertical profile of the mine. Alpha diversity indexes (e.g., Chao1 for richness and Shannon for diversity) indicated a decline in soil microbial diversity with the increase in depth. In contrast, beta diversity analyses such as principal component analysis (PCA) and principal co-ordinates analysis (PCoA) revealed significant clustering differences among soil layers. Correlation analysis demonstrated that environmental factors regulated microbial community differentiation, and the soil nutrient cycling characteristics were distinct across different depth layers. The dominant bacterial phyla in the mine soil included Chloroflexota, Pseudomonadota, Actinomycetota, and Acidobacteriota, which likely played crucial roles in biogeochemical cycles. The microbial succession in the mine soil followed a depth-dependent pattern. Specifically, Chloroflexota, Acidobacteriota, and Actinomycetota predominated in the surface soil. In intermediate layers, the relative abundance of Chloroflexota declined, while Pseudomonadota became dominant with a relative abundance of 60%. In deep layers with extreme anaerobic environments, Pseudomonadota adapted metabolically to oligotrophic conditions, emerging as the dominant group with a relative abundance of 70%. These microorganisms play vital roles in the cycling of soil carbon (C) and nitrogen (N). For C cycling, surface microorganisms primarily relied on the Calvin cycle for C fixation. Microorganisms adopt a glycolysis strategy and the TCA cycle to meet metabolic demands in intermediate layers, where a microaerobic-anaerobic transition occurs. Deep-layer anaerobic conditions drove microorganisms to employ fermentation as the main metabolic pathway. As for N cycling, surface microorganisms mainly adopted dissimilatory nitrate reduction to ammonium (DNRA); microorganisms in intermediate layers were pivotal in denitrification; deep-layer anaerobic microorganisms employed a dual metabolic system of DNRA (primary) and denitrification (secondary), exhibiting significantly higher N transformation intensity than surface microorganisms. [Conclusion] The microbial communities in the vertical profile of the ion-adsorbed rare earth mine exhibit a distinct differentiation pattern and are closely correlated with multiple environmental factors, suggesting their potential role in the nutrient cycling of the mine soil. The findings provide a scientific basis for future regulation and remediation of pollution in rare earth mining areas.

[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.

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.

[Objective] To compare the bacterial diversity and community composition between the rhizosphere and non-rhizosphere soil of Gynostemma longipes in different planting regions and reveal the key environmental factors by correlating the bacterial community composition with soil physicochemical properties. The findings are expected to provide a reference for the cultivation and introduction of this plant and lay a basis for exploring the relationship between rhizosphere microorganisms and the chemical component content of G. longipes in different planting regions. [Methods] High-throughput sequencing and soil physicochemical property measurement were employed to compare the bacterial diversity and community composition of G. longipes in different planting regions and reveal the key environmental factors influencing the bacterial community. [Results] A total of 97 085 bacterial amplicon sequence variants (ASVs) were obtained. The bacterial community composition in G. longipes soil showed significant differences among different planting regions (R=0.562, P=0.001) but no significant differences between rhizosphere and non-rhizosphere soil. Proteobacteria (27.40%‒36.67%) and Acidobacteriota (15.60%‒22.19%) were the dominant bacterial phyla. Soil pH, available phosphorus, available potassium, soil organic matter, and alkali-hydrolyzable nitrogen were identified as key environmental factors influencing the bacterial community composition in G. longipes soil. [Conclusion] Based on the sample analysis in this study, the bacterial community diversity and composition of G. longipes varied significantly aross different locations and were closely associated with soil physicochemical properties. This study provides a reference for the cultivation and introduction of G. longipes and gives insights into the relationship between soil microorganisms and secondary metabolite accumulation of G. longipes.

[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.

[Objective] To obtain the enriched groups of target microorganisms from the natural environment of the study area and establish the pure culture, improve the key link of the basic research on bio-geochemistry in methane leakage areas, and provide ideas and references for the enrichment and culture of other unknown microorganisms. [Methods] Microorganisms in marine sediments from methane leakage areas were isolated and cultured, and a sound experimental methodology for marine microorganisms was refined, including on-site treatment of microbial samples, preparation and sterilization of anaerobic culture media, and enrichment, culture, and isolation of microorganisms. High-throughput sequencing of microorganisms was conducted for gene sequencing and microbial identification, and different experimental conditions and experimental cycles were designed for in vivo microbial culture experiments. The short-term experiment (1.5 d) was conducted with the single factor method to study the effects of environmental factors (light, medium concentration, temperature, and pH) on microorganisms. The medium-term experiment (22 d) verified the results of the short-term experiment and determined the more suitable culture conditions. The long-term experiment (more than 250 d) was carried out to further study the growth status and activity of enriched microbial groups under specific conditions by real-time quantitative tracking of microorganisms. [Results] In the short-term culture, the activity of anaerobic sludge microbial suspension significantly increased under natural light (reached the peak at the time point of 17 h, with the iron concentration of 16.7 mg/L, four times the initial value), while the buffer period was prolonged in the dark environment (0-15 h). The activity of marine sediment microbial suspension was better in the dark environment (with high values at time points of 14 h/35 h), and the activity in the acid/base environment (pH 5.0/9.0) was higher than that in the neutral environment (iron concentrations of 4.3 mg/L vs. 11.1 mg/L, respectively). In the medium-term culture, the activity of anaerobic sludge microbial suspension was stable under 4 ℃ and acid conditions (with the decrease of only 20% in iron concentration), while the marine sediment microbial suspension preferred higher temperature and alkaline environment (with the activity increased after adaptation to pH 9.0). The global analysis showed that the first 15 days were the temperature adaptation period, and then temperature became the key regulatory factor. In the long-term culture, the activity of anaerobic sludge microbial suspension fluctuated periodically (first decreasing and then increasing after change of the culture medium every 50 days), while it declined irreversibly after 150 d. The marine sediment microbial suspension showed strong adaptability (with the activity peaked on days 117-145 under high pressure and the estimated doubling cycle of about 130 d) and maintained serrated stable activity under room pressure (iron concentration of 3.0-10.4 mg/L). [Conclusion] Anaerobic sludge microorganisms are sensitive to light and medium concentration. Their activity is improved by short-term light but inhibited by long-term light. Dark environment and 100% concentration medium are more suitable for growth of anaerobic sludge microorganisms (4 ℃, acidic environment, doubling cycle of 15 d). However, marine sediment microorganisms under the dark+100% medium and high temperature+alkaline environment conditions demonstrate stronger adaptability. Although their short-term activity is less affected by light, it takes about 130 days to double, and the adaptability to the high pressure environment significantly affects the growth process.

[Objective] To further investigate the role of arsL and arsM genes in the synthesis of arsinothricin (AST) and the effects of AST on the community structure of soil bacteria. [Methods] Using Burkholderia oklahomensis NCTC 13388 as the research object, we obtained its BoarsL and BoarsM genes via PCR amplification, constructed recombinant plasmids pET21b-BoarsL and pET28a-BoarsM, and transformed them into the competent cells of Escherichia coli expression strain Rosetta(DE3). In addition, we employed high-throughput sequencing technology to analyze the effects of different concentrations of AST treatment on the composition and diversity of soil bacterial communities. [Results] Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) detected target proteins with relative molecular weights of 47.79 kDa and 41.50 kDa in recombinant strains, indicating successful expression of BoArsL and BoArsM. Cells expressing only the BoarsL gene produced AST-OH and a small amount of AST, while cells expressing only the BoarsM gene produced only a small amount of dimethylarsinic acid. Additionally, statistical analysis indicated that AST treatment at different concentrations had a significant impact on the alpha diversity of soil bacterial communities (P<0.05), as evidenced by significant differences in both the Chao1 and Shannon indices. The low-concentration treatment group had higher soil bacteria diversity and richness than the control group, whereas the high-concentration treatment caused statistically significant declines in both diversity and species richness. Further analysis revealed that bacterial community composition at the genus level also exhibited significant differences among the AST treatment groups of different concentrations (P<0.05), and high concentrations of AST significantly enriched bacteria of the genus Burkholderia-Caballeronia-Paraburkholderia but significantly inhibited bacteria of the genera Clostridium_sensu_stricto and Sedimentibacter. [Conclusion] The BoarsL gene of B. oklahomensis NCTC 13388 is essential for the biosynthesis of AST. High concentrations of AST significantly affect the structure of soil bacterial communities.

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.

[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.