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.