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.

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.

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] 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.

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.

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] 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.

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.

[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.

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.