The rising level of atmospheric nitrous oxide (N₂O) has garnered the attention of researchers to microorganism-mediated N₂O synthesis in recent years. According to the recent studies, one of the main sources of N₂O in the world is the nitrification process carried out by aerobic aerobic ammonia oxidizing microorganisms (AOMs). We summarized the taxa of AOMs, the ecological distribution of AOMs, the environmental factors influencing the distribution, and the hotspots, pathways, and influencing factors of AOM-mediated N₂O production. Finally, we prospected the future research directions in this field. This review improves our understanding of AOMs and their mechanisms of N₂O production.

China has considerable demands for crude oil and natural gas. After oil recovery by conventional methods (such as water flooding, gas flooding, chemical flooding, and microbial enhanced oil recovery), more than 50% of the crude oil remains inaccessible in subsurface oil reservoirs, unable to be recovered by conventional flooding techniques. The residual crude oil could be converted into natural gas by anaerobic microorganisms, which makes it exploitable as biogas. This innovative approach shows promise as a microbial enhanced energy recovery technology for exploiting residual crude oil in depleted oil reservoirs. This review summaries the historical development and recent advancements in the methanogenic degradation of crude oil and makes an outlook on the future research directions to facilitate the industrial application of this approach.

The wastewater containing petroleum hydrocarbons is mainly produced in the process of petroleum exploitation and petroleum products processing. It encompasses the water polluted by leakage in oil exploitation, the wastewater produced in machining, and the wastewater produced using auxiliaries in leather printing and dyeing. The wastewater containing petroleum hydrocarbons has high organic matter content, high toxicity, and poor biodegradability. Biodegradation has become one of the main research hotspots of the treatment of wastewater containing petroleum hydrocarbons because of no secondary pollution. Based on the latest literature and our research results, this paper details the composition of wastewater containing petroleum hydrocarbon, microbial species for biodegradation, biodegradation mechanism, biochar immobilization and remediation technology, and degradation genes and enzymes. This paper can provide reference for the further study of microbial flora degradation of wastewater containing petroleum hydrocarbon.

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.

Coastal wetlands, among the most productive ecosystems on Earth, are situated at the interface between land and ocean, receiving substantial nitrogen inputs. These ecosystems exhibit active nitrogen cycling and play a crucial role in global nitrogen budgets and climate regulation. Archaea constitute a critical component of the microbial communities in coastal wetlands, yet their ecological significance was overlooked. The advancements in novel biological technologies have unveiled the diversity and ecological functions of archaea, highlighting their significant contributions to nitrogen cycling. This review summarizes the distribution and diversity of archaea in coastal wetland ecosystems, with a particular focus on their roles in key nitrogen cycling processes such as nitrogen fixation, nitrification, denitrification, and nitrate ammonification. In addition, for the application of archaea in global climate change mitigation, we explore the idea of using archaeal communities to reduce nitrous oxide emissions from coastal wetlands.

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.

Microbial communities in aquatic sediments are highly sensitive to environmental changes and serve as key indicators for assessing ecosystem health. As an emerging ecological remediation material, calcium peroxide (CaO₂) has showcased increasing application in the treatment of aquatic sediments, and its impact on microbial communities has become a frontier topic in ecological research. This review fucoses on the influencing mechanisms of CaO₂ on microbial communities in aquatic sediments from the perspective of microbial ecology. CaO₂ exerts multidimensional effects on the structures and functions of microbial communities by significantly altering the redox environment of the sediments. Regarding the community diversity, CaO₂ substantially enhances the alpha-diversity and species richness of microbial communities. In terms of the community composition, CaO₂ promotes the proliferation of functional genera such as Nitrosomonas and Thiobacillus, which possess ammonia-oxidizing and sulfur-oxidizing capabilities, respectively, while suppressing the growth of anaerobic fermenters (e.g., Clostridium) and sulfate reducers (e.g., Desulfovibrio). This function-oriented control mechanism indicates that CaO₂ selectively enriches microbial groups that facilitate nitrogen and sulfur cycling, while inhibiting the proliferation of anaerobic taxa that produce harmful metabolites, thereby optimizing the functions and structures of microbial communities in the sediments. This review further elucidates the ecological effects of CaO₂ on microbial communities, revealing its mechanistic role as an ecological remediation material in regulating microbial ecosystems within aquatic sediments. These findings provide significant theoretical references and scientific foundations for ecological restoration of waterbody sediments.

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] 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.

[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 effects of drainage on the soil properties and microbial community characteristics in coastal saline-alkali land. [Methods] Soil samples were collected before and after drainage for decreasing salt from the coastal saline-alkali land in Nantong, Jiangsu. The soil pH, nutrient elements (nitrogen, phosphorus, and potassium), enzyme activity, and microbial community structure were analyzed by soil physical and chemical property characterization and high-throughput sequencing. Bioinformatic analysis was conducted to study the correlations between microbial community structure characteristics and soil physical and chemical properties and the possible anaerobic metabolic process. [Results] Drainage for decreasing salt significantly reduced the soil pH and electrical conductivity (EC), while causing the losses of nutrients in the soil to a certain extent. After drainage, the activities of sucrase and peroxidase and the richness and diversity of fungi in the soil increased to a certain extent, while the richness and diversity of bacteria and archaea decreased. Principal component analysis showed that microbial community structure had significantly positive correlations with soil EC and potassium content, while it had significantly negative correlations with catalase and sucrase activities in the soil. Redundancy analysis and functional prediction showed that fungi and archaea were significantly correlated with EC, while archaea may change the community structure by adapting to salinity. [Conclusion] Drainage for decreasing salt reduced the salinity and pH in the soil, which affected the soil properties and microbial community structure.

[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 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.

Artemisia desertorum, a dominant xerophyte in the Tengger Desert, possesses exceptional drought resistance, salt tolerance, and sand-fixing capabilities. [Objective] To investigate the diversity of soil microbial communities in the rhizosphere and non-rhizosphere of A. desertorum in the Shapotou Nature Reserve located at the southeastern edge of the Tengger Desert, Ningxia, and the potential interactions between the dominant microbial genera and plants, thus laying a theoretical foundation for ecological restoration in deserts. [Methods] Soil samples were collected from the rhizosphere and non-rhizosphere of A. desertorum, in the plantation cultivated for 42 years of sand fixation, and the sand was collected as the control. Physicochemical properties of each soil sample were measured, and fungal and bacterial communities were analyzed via high-throughput sequencing. [Results] Total nitrogen (TN), available nitrogen (AN), and available potassium (AK) in the rhizosphere and non-rhizosphere soil samples were significantly higher than in shifting sands those in the control (P<0.05). Rhizosphere soil samples also had significantly higher levels of available rhizosphere soils also had significantly higher levels of available phosphorus (AP), AK, soil organic matter (OM), and electrical conductivity (EC) than non-rhizosphere soil samples (P<0.05). Rhizosphere soil samples had slightly higher TN, total phosphorus (TP), AN, and pH than non-rhizosphere soil samples, without significant differences. Bacterial diversity and abundance were higher in non-rhizosphere soil samples, while fungal diversity and abundance were greater in rhizosphere soil samples. Both rhizosphere and non-rhizosphere soil samples had more unique microbial operational taxonomic units (OTUs) than the control. Rhizosphere soil samples contained more fungal OTUs but fewer bacterial OTUs than non-rhizosphere soil samples. Dominant fungal phyla included Ascomycota, Basidiomycota, unclassified fungal phyla, and Rozellomycota, with major fungal genera comprising Candida, Paraphoma, Alternaria, unclassified fungal genera, and Penicillium. Dominant bacterial phyla included Actinobacteriota, Proteobacteria, Bacteroidota, Chloroflexi, and Acidobacteria, with key bacterial genera being Arthrobacter, Nocardioides, Streptomyces, Agromyces, and Sphingomonas. Linear discriminant analysis effect size (LEfSe) identified 212 bacterial taxa and 25 fungal taxa significantly distinguishing rhizosphere soil samples from non-rhizosphere soil samples, with Ascomycota and Proteobacteria being the key taxa. Redundancy analysis showed that OM was the main factor affecting the structure of soil microbial community, positively correlating with Basidiomycota, Acidobacteria, Chloroflexi, and unclassified fungal phyla, while negatively correlating with Ascomycota, Rozellomycota, Actinobacteriota, Proteobacteria, and Bacteroidota. [Conclusion] The cultivation of A. desertorum significantly increased the nutrient levels and fungal diversity and abundance in the rhizosphere soil at the southeastern edge of the Tengger Desert, contributing to soil ecosystem stability. This study offers theoretical insights into regional ecological restoration and provides a scientific basis for restoration scheme optimization and sustainable management of A. desertorum ecosystems.

[Objective] Roseobacter play a significant ecological role in the material cycling and energy flow of marine ecosystems. However, their environmental responses on long time scales and community assembly mechanisms remain unclear. We collected samples over 60 consecutive weeks from the coastal waters near Qingdao to investigate the annual dynamics, environmental responses, and community assembly mechanisms of free-living and particle-associated Roseobacter. [Methods] The 16S rRNA gene amplicon sequencing was performed for the surface seawater samples to reveal the seasonal diversity variations of Roseobacter groups with different lifestyles. Furthermore, the correlations of Roseobacter with various environmental factors and the community assembly mechanisms were explored. [Results] In the surface seawater of the coastal zone, the relative abundance of Roseobacter in total bacteria and archaea exhibited significant seasonal fluctuations (2.64%-34.10%), with being markedly higher in winter and spring than in summer and autumn. Based on the temporal distribution patterns, Roseobacter groups can be classified into summer-autumn, winter-spring, and outbreak growth types. The free-living Roseobacter groups showed more pronounced seasonal patterns, while the particle-associated groups showed higher diversity. Temperature, inorganic nitrogen, and inorganic phosphorus were the main environmental factors influencing Roseobacter diversity, with their explanatory power on particle-associated groups (16.82%) being higher than that on free-living groups (9.06%). In terms of community assembly, deterministic processes had a greater impact on particle-associated Roseobacter groups, indicating that environmental changes had more significant effects on these groups. [Conclusion] This study, by examining the dynamic changes and environmental driving mechanisms of Roseobacter at a fine time scale, reveals their seasonal distribution patterns and provides scientific insights for understanding the spatiotemporal dynamics and ecological functions of this crucial marine bacterial group.

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.

[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] To study changes of the bacterial community structure in the Second Drainage Ditch in Ningxia after ecological engineering. [Methods] We employed high-throughput sequencing to study the bacterial community structures in water samples. We explored the factors affecting the bacterial community structure by non-metric multidimensional scaling (NMDS) and redundancy analysis (RDA). [Results] From August 2021 to August 2022, the ammonium nitrogen, total nitrogen (TN), permanganate index, dichromate oxidizability (COD_Cr), and fluoride in the water decreased substantially after the ecological engineering. The dominant bacterial phyla in the water were Proteobacteria, Actinobacteria, Bacteroidetes, and Chloroflexi and the dominant genera included hgcI_clade, SAR11_cladeIII, Limnohabitans, Rhodoferax, and Flavobacterium. The bacterial community structures showed significant differences across different sampling locations. The NMDS results revealed significant variations in the bacterial community structure across different sampling months. The RDA results indicated that total phosphorus (TP), COD_Cr, and pH were the key factors influencing the bacterial community structure. Notably, TP, COD_Cr, and TN together explained the largest variance (8.81%) in the bacterial community structure, followed by TP combined with COD_Cr (-8.05%). [Conclusion] After ecological engineering, the water quality of the Second Drainage Ditch improved, and the bacterial community structure became more diverse. The physicochemical properties of the water strongly influence the distribution and diversity of bacterial communities in the Second Drainage Ditch in Ningxia, which provide a scientific basis for managing the regional water environment.

As global eco-environmental issues have aroused increasing concern, ecological restoration has become a key research topic. As an emerging technology for ecological restoration, aggregate spray-seeding offers significant advantages in vegetation restoration. [Objective] To reveal the relationship between plant community assembly and soil microbial communities during the aggregate spray-seeding restoration process. [Methods] A comprehensive investigation was conducted at plots of various seeding batches on the slopes of Changqin Island in Zhuhai City, focusing on the internal relationships of the structures of pioneer plant communities with soil nutrient content and characteristics of soil fungal and bacterial communities. [Results] The soil fungal community in the aggregate spray-seeding restoration area of Changqin Island was mainly composed of 9 phyla, among which Ascomycota and Basidiomycota were dominant. The soil bacterial community was dominated by Pseudomonadota, Acidobacteriota, and Bacteroidota. The soil fungi of plant pathogens, wood saprotrophs, and endophytes exhibited high abundance, while a large proportion of bacteria were involved in nitrogen cycling. Using the support vector machine method, we identified 24 soil microbial and nutrient indicators related to differences across aggregate spray-seeding batches. The cluster analysis classified the main restoration plants into two groups and the 24 soil-microbial and nutrient indicators into four categories. The inter-group correlation analysis showed significant associations of plant combinations with soil microbial and nutrient indicators. [Conclusion] Substantial differences in community structure and diversity are observed among different aggregate spray-seeding batches. Plant community assembly significantly influences the structures and functions of soil microbial communities. The findings of this study provide essential theoretical support for ecological restoration practices, contributing to the optimization of restoration strategies and enhancing ecosystem stability and sustainability.

[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.

[Objective] To screen CO₂-fixing microbial strains in grassland soil, clarify their physiological and biochemical characteristics, and determine their optimal CO₂ fixation conditions, providing a theoretical basis for understanding the mechanisms of soil CO₂ fixation and enhancing grassland soil carbon sink. [Methods] The carbon-free solid medium and the dilution plating method were employed to isolate CO₂-fixing microbial strains from grassland soil in the Loess Plateau. The strains were identified via 16S rRNA gene sequencing. Physiological and biochemical characteristics of the strains were determined by Gram staining and starch hydrolysis, indole production, methyl red, and lactic acid fermentation tests. Culture experiments with carbon-free liquid medium and sterilized soil were carried out to assess the CO₂ fixation efficiency under varying temperatures (20-40 ℃), soil moisture levels (3.00%-27.00%), and the presence of electron donors (NaNO₂ and Na₂S). [Results] Nine bacterial strains with effective CO₂ fixation were isolated, belonging to Bacillus, Streptomyces, Sinorhizobium, Agrobacterium, Enterobacter, Brevundimonas, and Prolinoborus. Among them, strains A4 (Agrobacterium) and A7 (Brevundimonas) exhibited the highest CO₂ fixation efficiency (P<0.05), both being Gram-positive. Optimal conditions for CO₂ fixation of the nine strains were 25-30 ℃ and soil moisture of 3.00%, 15.00%, or 27.00% (P<0.05). Electron donor supplementation enhanced CO₂ fixation efficiency, and the enhancement effect followed the order: single addition of NaNO₂>single addition of Na₂S>co-addition of NaNO₂+Na₂S (P<0.05). [Conclusion] This study identified the dominant CO₂-fixing microbial strains and the conditions suitable for CO₂ fixation, providing a theoretical basis and technical support for enhancing the carbon sink of the terrestrial ecosystem on the Loess Plateau and mitigating the greenhouse effect.

[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.

[Objective] To study the mechanisms of mutual promotion between chemolithoauto-trophic sulfur-oxidizing bacteria and chemoheterotrophic bacteria under co-culture based on carbon metabolism. [Methods] Ion chromatography was employed to determine the concentrations of S₂O₃^2‒ (thiosulfate) and SO₄^2‒ (sulfate). Bacterial growth dynamics were monitored by the dilution plate method. Extracellular carbon characteristics were analyzed via total organic carbon analyzer measurement and LC-MS. Cellular morphology was observed by scanning electron microscopy. The relative mRNA levels of related genes were quantified by RT-qPCR. [Results] During the growth process, sulfur-oxidizing bacteria continuously fixed inorganic carbon and secreted organics, providing a stable carbon source for the growth of heterotrophic bacterium. In return, heterotrophic bacteria significantly enhanced the sulfur-oxidizing and carbon-fixing capabilities of sulfur-oxidizing bacteria. This was evidenced by the significantly up-regulated expression of the enzyme gene soxB involved in sulfur oxidation and the RubisCO gene cbbL involved in carbon fixation. Additionally, the production of extracellular polymeric substances was induced, which enhanced the biofilm formation. [Conclusion] This study elucidated the interaction mechanisms between sulfur-oxidizing bacteria and heterotrophic bacteria, particularly the significant enhancement of the carbon-fixing capability of sulfur-oxidizing bacteria. The findings provide a new perspective for the enrichment culture of chemolithoautotrophic bacteria and for understanding the carbon fixation mechanisms of autotrophic sulfur-oxidizing bacteria in microbial communities. Additionally, this study offers theoretical support for the low-carbon and efficient treatment of wastewater.

[Objective] To investigate the bio-weathering effects and mechanisms of Acidithiobacillus ferrooxidans on granite under acidic conditions (pH 2.0). [Methods] A 36-day immersion experiment was conducted, comparing the microbial group, acid solution group (pH 2.0, H₂SO₄), and pure culture medium (control) group. Physicochemical parameters [pH, redox potential (Eh), and electrical conductivity (EC)] of the soultion, surface chromaticity (CIE-Lab) of granite, and mineral dissolution characteristics were analyzed. [Results] The microbial group significantly accelerated granite weathering, forming a distinct weathered layer on the surface after 9 days. During the initial phase (0‒3 days), plagioclase dissolution caused a pH increase followed by stabilization. Fe³⁺ accumulation-dominated Eh and EC were regulated by both the initial ion background and weathering products. After bio-weathering, the granite exhibited a decrease of 11.6 in L* (reduced brightness), an increase of 6.8 in a* value (enhanced reddish-brown tone), and an increase of 9.6 in b* value (increased bluish tone). Surface reddish-brown areas were directly correlated with jarosite deposition. [Conclusion] Under acidic conditions, A. ferrooxidans accelerate granite weathering via Fe³⁺-mediated redox reactions. The chromaticity parameters (ΔL*, Δa*, and Δb*) and morphological characteristics serve as indicators for rapidly assessing weathering intensity. These findings provide a novel basis for evaluating weathering risks caused by acid mine wastewater in surrounding rocks and guiding ecological remediation.

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.

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.

[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.

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] This study systematically reviews the research trends in microbially induced calcium carbonate precipitation (MICP) over the past 25 years. Through bibliometric analysis, we aim to elucidate the developmental trajectory, research hotspots, and academic impact distribution of MICP, offering data-driven insights for researchers and proposing strategic priorities for future studies. [Methods] A comprehensive dataset of 1 947 publications was extracted from the Web of Science Core Collection (1999-2024). Bibliometric analysis and CiteSpace visualization tools were employed to quantify publication volume, authorship patterns, country/institutional contributions, and keywords dynamics. Time-series analysis and network mapping were integrated to decode the evolutionary pathways and interdisciplinary frontiers of the field. [Results] Annual MICP publications exhibit sustained growth, with China emerging as the dominant contributor, accounting for 47.71% of global output. Leading institutions such as Nanyang Technological University, Chinese Academy of Sciences, Southeast University, and Chongqing University demonstrate strong academic influence through high publication output and citation frequency. The research hotspots are primarily concentrated in soil improvement, self-healing concrete, and bioremediation. Keywords clustering analysis reveals emerging interdisciplinary frontiers at the intersection of environmental geotechnics and biomaterials applications. [Conclusion] MICP research has entered a phase of rapid multidisciplinary integration, with China leading global advancements. Future efforts should prioritize fundamental studies on bio-mineral interaction mechanisms, accelerate MICP applications in environmental remediation and smart materials, and develop green, sustainable processes to enhance its role in carbon neutrality and ecological engineering.