Diversity and enrichment of nitrite-dependent anaerobic methane oxidizing bacteria from wastewater sludge

Recent findings in methanotrophs: genetics, molecular ecology, and biopotential

The potential consequences for mankind could be disastrous due to global warming, which arises from an increase in the average temperature on Earth. The elevation in temperature primarily stems from the escalation in the concentration of greenhouse gases (GHG) such as CO2, CH4, and N2O within the atmosphere. Among these gases, methane (CH4) is particularly significant in driving alterations to the worldwide climate. Methanotrophic bacteria possess the distinctive ability to employ methane as both as source of carbon and energy. These bacteria show great potential as exceptional biocatalysts in advancing C1 bioconversion technology. The present review describes recent findings in methanotrophs including aerobic and anaerobic methanotroph bacteria, phenotypic characteristics, biotechnological potential, their physiology, ecology, and native multi-carbon utilizing pathways, and their molecular biology. The existing understanding of methanogenesis and methanotrophy in soil, as well as anaerobic methane oxidation and methanotrophy in temperate and extreme environments, is also covered in this discussion. New types of methanogens and communities of methanotrophic bacteria have been identified from various ecosystems and thoroughly examined for a range of biotechnological uses. Grasping the processes of methanogenesis and methanotrophy holds significant importance in the development of innovative agricultural techniques and industrial procedures that contribute to a more favorable equilibrium of GHG. This current review centers on the diversity of emerging methanogen and methanotroph species and their effects on the environment. By amalgamating advanced genetic analysis with ecological insights, this study pioneers a holistic approach to unraveling the biopotential of methanotrophs, offering unprecedented avenues for biotechnological applications. KEY POINTS: • The physiology of methanotrophic bacteria is fundamentally determined. • Native multi-carbon utilizing pathways in methanotrophic bacteria are summarized. • The genes responsible for encoding methane monooxygenase are discussed.

Methane mitigation via the nitrite-DAMO process induced by nitrate dosing in sewers

Nitrate or nitrite-dependent anaerobic methane oxidation (n-DAMO) is a microbial process that links carbon and nitrogen cycles as a methane sink in many natural environments. This study demonstrates, for the first time, that the nitrite-dependent anaerobic methane oxidation (nitrite-DAMO) process can be stimulated in sewer systems under continuous nitrate dosing for sulfide control. In a laboratory sewer system, continuous nitrate dosing not only achieved complete sulfide removal, but also significantly decreased dissolved methane concentration by ∼50 %. Independent batch tests confirmed the coupling of methane oxidation with nitrate and nitrite reduction, revealing similar methane oxidation rates of 3.68 ± 0.5 mg CH4 L-1 h-1 (with nitrate as electron acceptor) and 3.57 ± 0.4 mg CH4 L-1 h-1 (with nitrite as electron acceptor). Comprehensive microbial analysis unveiled the presence of a subgroup of the NC10 phylum, namely Candidatus Methylomirabilis (n-DAMO bacteria that couples nitrite reduction with methane oxidation), growing in sewer biofilms and surface sediments with relative abundances of 1.9 % and 1.6 %, respectively. In contrast, n-DAMO archaea that couple methane oxidation solely to nitrate reduction were not detected. Together these results indicated the successful enrichment of n-DAMO bacteria in sewerage systems, contributing to approx. 64 % of nitrite reduction and around 50 % of dissolved methane removal through the nitrite-DAMO process, as estimated by mass balance analysis. The occurrence of the nitrite-DAMO process in sewer systems opens a new path to sewer methane emissions.

Regulation of nitrite-dependent anaerobic methane oxidation bacteria by available phosphorus and microbial communities in lake sediments of cold and arid regions

As global anthropogenic nitrogen inputs continue to rise, nitrite-dependent anaerobic methane oxidation (N-DAMO) plays an increasingly significant role in CH4 consumption in lake sediments. However, there is a dearth of knowledge regarding the effects of anthropogenic activities on N-DAMO bacteria in lakes in the cold and arid regions. Sediment samples were collected from five sampling areas in Lake Ulansuhai at varying depth ranges (0-20, 20-40, and 40-60 cm). The ecological characterization and niche differentiation of N-DAMO bacteria were investigated using bioinformatics and molecular biology techniques. Quantitative PCR confirmed the presence of N-DAMO bacteria in Lake Ulansuhai sediments, with 16S rRNA gene abundances ranging from 1.72 × 104 to 5.75 × 105 copies·g-1 dry sediment. The highest abundance was observed at the farmland drainage outlet with high available phosphorus (AP). Anthropogenic disturbances led to a significant increase in the abundance of N-DAMO bacteria, though their diversity remained unaffected. The heterogeneous community of N-DAMO bacteria was affected by interactions among various environmental characteristics, with AP and oxidation-reduction potential identified as the key drivers in this study. The Mantel test indicated that the N-DAMO bacterial abundance was more readily influenced by the presence of the denitrification genes (nirS and nirK). Network analysis revealed that the community structure of N-DAMO bacteria generated numerous links (especially positive links) with microbial taxa involved in carbon and nitrogen cycles, such as methanogens and nitrifying bacteria. In summary, N-DAMO bacteria exhibited sensitivity to both environmental and microbial factors under various human disturbances. This study provides valuable insights into the distribution patterns of N-DAMO bacteria and their roles in nitrogen and carbon cycling within lake ecosystems.

Nitrite-dependent anaerobic methane oxidation (N-DAMO) in global aquatic environments: A review

The vast majority of processes in the carbon and nitrogen cycles are driven by microorganisms. The nitrite-dependent anaerobic oxidation of methane (N-DAMO) process links carbon and nitrogen cycles, offering a novel approach for the simultaneous reduction of methane emissions and nitrite pollution. However, there is currently no comprehensive summary of the current status of the N-DAMO process in natural aquatic environments. Therefore, our study aims to fill this knowledge gap by conducting a comprehensive review of the global research trends in N-DAMO processes in various aquatic environments (excluding artificial bioreactors). Our review mainly focused on molecular identification, global study sites, and their interactions with other elemental cycling processes. Furthermore, we performed a data integration analysis to unveil the effects of key environmental factors on the abundance of N-DAMO bacteria and the rate of N-DAMO process. By combining the findings from the literature review and data integration analysis, we proposed future research perspectives on N-DAMO processes in global aquatic environments. Our overarching goal is to advance the understanding of the N-DAMO process and its role in synergistically reducing carbon emissions and removing nitrogen. By doing so, we aim to make a significant contribution to the timely achievement of China's carbon peak and carbon neutrality targets.

Methane-dependent complete denitrification by a single Methylomirabilis bacterium

Methane-dependent nitrate and nitrite removal in anoxic environments is thought to rely on syntrophy between ANME-2d archaea and bacteria in the genus 'Candidatus Methylomirabilis'. Here we enriched and purified a single Methylomirabilis from paddy soil fed with nitrate and methane, which is capable of coupling methane oxidation to nitrate reduction via nitrite to dinitrogen independently. Isotope labelling showed that this bacterium we name 'Ca. Methylomirabilis sinica' stoichiometrically performed methane-dependent complete nitrate reduction to dinitrogen gas. Multi-omics analyses collectively demonstrated that 'M. sinica' actively expressed a well-established pathway for this process, especially including nitrate reductase Nap. Furthermore, 'M. sinica' exhibited a higher nitrate affinity than most denitrifiers, implying its competitive fitness under oligotrophic nitrogen-limited conditions. Our findings revise the paradigm of methane-dependent denitrification performed by two organisms, and the widespread presence of 'M. sinica' in public databases suggests that the coupling of methane oxidation and complete denitrification in single cells substantially contributes to global methane and nitrogen budgets.

Prospect of denitrifying anaerobic methane oxidation (DAMO) application on wastewater treatment and biogas recycling utilization

Old-fashioned wastewater treatments for nitrogen depend on heterotrophic denitrification process. It would utilize extra organic carbon source as electron donors when the C/N of domestic wastewater was too low to ensure heterotrophic denitrification process. It would lead to non-compliance with carbon reduction targets and impose an economic burden on wastewater treatment. Denitrifying anaerobic methane oxidation (DAMO), which could utilize methane serving as electron donors to replace traditional organic carbon (methanol or sodium acetate), supplies a novel approach for wastewater treatment. As the primary component of biogas, methane is an inexpensive carbon source. With anaerobic digestion becoming increasingly popular for sludge reduction in wastewater treatment plants (WWTPs), efficient biogas utilization through DAMO can offer an environmentally friendly option for in-situ biogas recycling. Here, we reviewed the metabolic principle and relevant research for DAMO and biogas recycling utilization, outlining the prospect of employing DAMO for wastewater treatment and biogas recycling utilization in WWTPs. The application of DAMO provides a new focal point for enhancing efficiency and sustainability in WWTPs.

Revisiting the Engineering Roadmap of Nitrate/Nitrite-Dependent Anaerobic Methane Oxidation

Nitrate/nitrite-dependent anaerobic oxidation of methane (n-DAMO) is a recently discovered process, which provides a sustainable perspective for simultaneous nitrogen removal and greenhouse gas emission (GHG) mitigation by using methane as an electron donor for denitrification. However, the engineering roadmap of the n-DAMO process is still unclear. This work constitutes a state-of-the-art review on the classical and most recently discovered metabolic mechanisms of the n-DAMO process. The versatile combinations of the n-DAMO process with nitrification, nitritation, and partial nitritation for nitrogen removal are also clearly presented and discussed. Additionally, the recent advances in bioreactor development are systematically reviewed and evaluated comprehensively in terms of methane supply, biomass retention, membrane requirement, startup time, reactor performance, and limitations. The key issues including enrichment and operation strategy for the scaling up of n-DAMO-based processes are also critically addressed. Moreover, the challenges inherent to implementing the n-DAMO process in practical applications, including application scenario recognition, GHG emission mitigation, and operation under realistic conditions, are highlighted. Finally, prospects as well as opportunities for future research are proposed. Overall, this review provides a roadmap for potential applications and further development of the n-DAMO process in the field of wastewater treatment.

Microbial Niche Differentiation during Nitrite-Dependent Anaerobic Methane Oxidation

Nitrite-dependent anaerobic methane oxidation (n-DAMO) has been demonstrated to play important roles in the global methane and nitrogen cycle. However, despite diverse n-DAMO bacteria widely detected in environments, little is known about their physiology for microbial niche differentiation. Here, we show the microbial niche differentiation of n-DAMO bacteria through long-term reactor operations combining genome-centered omics and kinetic analysis. With the same inoculum dominated by both species "Candidatus Methylomirabilis oxyfera" and "Candidatus Methylomirabilis sinica", n-DAMO bacterial population was shifted to "Ca. M. oxyfera" in a reactor fed with low-strength nitrite, but shifted to "Ca. M. sinica" with high-strength nitrite. Metatranscriptomic analysis showed that "Ca. M. oxyfera" harbored more complete function in cell chemotaxis, flagellar assembly, and two-component system for better uptake of nitrite, while "Ca. M. sinica" had a more active ion transport and stress response system, and more redundant function in nitrite reduction to mitigate nitrite inhibition. Importantly, the half-saturation constant of nitrite (0.057 mM vs 0.334 mM NO₂^-) and inhibition thresholds (0.932 mM vs 2.450 mM NO₂^-) for "Ca. M. oxyfera" vs "Ca. M. sinica", respectively, were highly consistent with genomic results. Integrating these findings demonstrated biochemical characteristics, especially the kinetics of nitrite affinity and inhibition determine niche differentiation of n-DAMO bacteria.

Effects of periodic drying-wetting on microbial dynamics and activity of nitrite/nitrate-dependent anaerobic methane oxidizers in intertidal wetland sediments

Nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) plays an important role in methane (CH₄) consumption in intertidal wetlands. However, little is known about the responses of n-DAMO in intertidal wetlands to periodic drying-wetting caused by tidal cycling. Here, comparative experiments (waterlogged, desiccated, reflooded) with the Yangtze estuarine intertidal sediments were performed to examine the effects of periodic tidal changes on n-DAMO microbial communities, abundances, and potential activities. Functional gene sequencing indicated the coexistence of n-DAMO bacteria and archaea in the tide-fluctuating environments and generally higher biodiversity under reflooded conditions than consecutive inundation or emersion. The n-DAMO microbial abundance and associated activity varied significantly during alternative exposure and inundation, with higher abundance and activity under the waterlogged than desiccated conditions. Reflooding of intertidal wetlands might intensify n-DAMO activities, indicating the resilience of n-DAMO microbial metabolisms to the wetting-drying events. Structural equation modeling and correlation analysis showed that n-DAMO activity was highly related to n-DAMO microbial abundance and substrate availability under inundation, whereas salt accumulation in sediment was the primary factor restraining n-DAMO activity under the desiccation. Overall, this study reveals tidal-induced shifts of n-DAMO activity and associated contribution to mitigating CH₄, which may help accurately project CH₄ emission from intertidal wetlands under different tidal scenarios.

Impact of Pipe Material and Temperature on Drinking Water Microbiome and Prevalence of Legionella, Mycobacterium, and Pseudomonas Species

In drinking water distribution systems (DWDSs), pipe material and water temperature are some of the critical factors affecting the microbial flora of water. Six model DWDSs consisting of three pipe materials (galvanized steel, copper, and PEX) were constructed. The temperature in three systems was maintained at 22 °C and the other 3 at 32 °C to study microbial and elemental contaminants in a 6-week survey using 16S rRNA next-generation sequencing (NGS) and inductively coupled plasma-optical emission spectrometry (ICP-OES). Pipe material and temperature were preferentially linked with the composition of trace elements and the microbiome of the DWDSs, respectively. Proteobacteria was the most dominant phylum across all water samples ranging from 60.9% to 91.1%. Species richness (alpha diversity) ranking was PEX < steel ≤ copper system and elevated temperature resulted in decreased alpha diversity. Legionellaceae were omni-prevalent, while Mycobacteriaceae were more prevalent at 32 °C (100% vs. 58.6%) and Pseudomonadaceae at 22 °C (53.3% vs. 62.9%). Heterogeneity between communities was disproportionately driven by the pipe material and water temperature. The elevated temperature resulted in well-defined microbial clusters (high pseudo-F index) in all systems, with the highest impact in PEX (10.928) followed by copper (9.696) and steel (5.448). Legionellaceae and Mycobacteriaceae are preferentially prevalent in warmer waters. The results suggest that the water temperature has a higher magnitude of impact on the microbiome than the pipe material.

Spatial variations of activity and community structure of nitrite-dependent anaerobic methanotrophs in river sediment

Rivers are an important site for methane emissions and reactive nitrogen removal. The process of nitrite-dependent anaerobic methane oxidation (n-damo) links the global carbon cycle and the nitrogen cycle, but its role in methane mitigation and nitrogen removal in rivers is poorly known. In the present study, we investigated the activity, abundance, and community composition of n-damo bacteria in sediment of the upper, middle, and lower reaches of Wuxijiang River (Zhejiang Province, China). The ¹³CH₄ stable isotope experiments showed that the methane oxidation activity of n-damo was 0.11-1.88 nmol CO₂ g^-1 (dry sediment) d^-1, and the activity measured from the middle reaches was significantly higher than that from the remaining regions. It was estimated that 3.27 g CH₄ m^-2 year^-1 and 8.72 g N m^-2 year^-1 could be consumed via n-damo. Quantitative PCR confirmed the presence of n-damo bacteria, and their 16S rRNA gene abundance varied between 5.45 × 10⁵ and 5.86 × 10⁶ copies g^-1 dry sediment. Similarly, the abundance of n-damo bacteria was significantly higher in the middle reaches. High-throughput sequencing showed a high n-damo bacterial diversity, with totally 152 operational taxonomic units being detected at 97 % sequence similarity cut-off. In addition, the n-damo bacterial community composition also varied spatially. The inorganic nitrogen (NH₄⁺, NO₂^-, NO₃^-) level was found to be the key environmental factor controlling the n-damo activity and bacterial community composition. Overall, our results showed the spatial variations and environmental regulation of the activity and community structure of n-damo bacteria in river sediment, which expanded our understanding of the quantitative importance of n-damo in both methane oxidation and reactive nitrogen removal in riverine systems.

Distribution pattern of N-damo bacteria along an anthropogenic nitrogen input gradient from the coastal mangrove wetland to the South China sea sediments

Microbial nitrite-dependent anaerobic methane oxidation (n-damo) process is important for mitigating methane emission and anthropogenic nitrogen inputs in the marine environment. However, the distribution pattern of n-damo bacteria along an anthropogenic N-input gradient from the coastal wetland to the pristine South China Sea is poorly understood. This study investigated the diversity and abundance of n-damo bacteria in samples collected along a N-input gradient from Mai Po (MP) mangrove wetland sediments of the Pearl River Estuary (PRE) to the deep ocean sediments of the South China Sea (SCS). Retrieved 16S rDNA sequences showed a shift of n-damo community composition of complex structures with both freshwater and marine n-damo lineages in MP intertidal sediments to marine dominated characteristic in SCS sediments. The observed variation of Shannon and Chao1 indexes of n-damo bacteria shared a similar trend of a decrease at first followed by an increase along the targeting gradient with previously investigated methanogens, anaerobic methanotrophic archaea, ammonia-oxidizing archaea and ammonia-oxidizing bacteria, but had a reverse pattern with anammox bacteria. The community structure of pmoA gene sequences contained freshwater lineages only in SCS continental shelf sediments closer to the PRE, and turned to group with other marine samples in deeper and pristine sediments. Results suggested that n-damo bacteria might be a major contributor to anaerobic denitrification in the SCS sediments because their abundances were much higher than previously studied anammox bacteria in the same sample set. The distribution pattern of n-damo bacterial diversity, richness and abundance along the anthropogenic N-input gradient implies that they could be used as a bio-indicator for monitoring the anthropogenic/terrestrial inputs in marine environments.

Nitrate/nitrite-dependent anaerobic oxidation of methane (N-AOM) as a technology platform for greenhouse gas abatement in wastewater treatment plants: State-of-the-art and challenges

Nitrate/nitrite-dependent anaerobic oxidation of methane (N-AOM) is a metabolic process recently discovered and partially characterized in terms of the microorganisms and pathways involved. The N-AOM process can be a powerful tool for mitigating the impacts of greenhouse gas emissions from wastewater treatment plants by coupling the reduction of nitrate or nitrite with the oxidation of residual dissolved methane. Besides specific anaerobic methanotrophs such as bacteria members of the phylum NC10 and archaea belonging to the lineage ANME-2d, recent reports suggested that other methane-oxidizing bacteria in syntrophy with denitrifiers can also perform the N-AOM process, which facilitates the application of this metabolic process for the oxidation of residual methane under realistic scenarios. This work constitutes a state-of-art review that includes the fundamentals of the N-AOM process, new information on process microbiology, bioreactor configurations, and operating conditions for process implementation in WWTP. Potential advantages of the N-AOM process over aerobic methanotrophic biotechnologies are presented, including the potential interrelation of the N-AOM with other nitrogen removal processes within the WWTP, such as the anaerobic ammonium oxidation. This work also addressed the challenges of this biotechnology towards its application at full scale, identifying and discussing critical research niches.

Potential role of nitrite-dependent anaerobic methane oxidation in methane consumption and nitrogen removal in Chinese paddy fields

Nitrite-dependent anaerobic methane oxidation (n-damo), catalyzed by bacteria closely related to Candidatus Methylomirabilis oxyfera, links the global carbon and nitrogen cycles. Currently, the contribution of n-damo in controlling methane emissions and nitrogen removal, and the key regulatory factors of this process in Chinese paddy fields are poorly known. Here, soil samples from 20 paddy fields located in different climate zones across China were collected to examine the n-damo activity and bacterial communities. The n-damo activity and bacterial abundance varied from 1.05 to 5.97 nmol CH₄ g^-1 (dry soil) d^-1 and 2.59 × 10⁵ to 2.50 × 10⁷ copies g^-1 dry soil, respectively. Based on the n-damo activity, it was estimated that approximately 0.91 Tg CH₄ and 2.17 Tg N could be consumed annually via n-damo in Chinese paddy soils. The spatial variations in n-damo activity and community structure of n-damo bacteria were significantly (p < 0.05) affected by the soil ammonium content, labile organic carbon content and pH. Furthermore, significant differences in n-damo activity, bacterial abundance and community composition were observed among different climate zones. The n-damo activity was found to be positively correlated with the mean annual air temperature. Taken together, our results demonstrated the potential importance of n-damo in both methane consumption and nitrogen removal in Chinese paddy soils, and this process was regulated by local soil and climatic factors.

Denitrifying anaerobic methane oxidation and mechanisms influencing it in Yellow River Delta coastal wetland soil, China

Methane oxidation coupled to denitrification is mediated by Candidatus "Methylomirabilis oxyfera" (M. oxyfera), which belongs to the candidate phylum NC10, and plays a crucial role in the global carbon and nitrogen cycle. Using the Yellow River Delta coastal wetland as the study area, molecular biology technology and laboratory incubation were used to determine the abundance of NC10 bacteria and the denitrifying anaerobic methane oxidation (DAMO) rate in soils from different vegetation areas. The results of the electrophoresis detection show that M. oxyfera-like bacteria can be found in the four types of soils, according to the growth analysis by the system, OTU1 (SA) has been found the highest similarity to first-discovered Candidatus Methylomir-abilis oxyfera (FP565575) (over 98%); Vegetation cover significantly increased the abundance of M. oxyfera-like bacteria compared to beach areas, which abundance was significantly higher in deeper layers than in surface ones. Nitrate, nitrite, total nitrogen, and conductivity were identified as the main environmental factors affecting the DAMO rate. This study showed that both groups A and B of Candidatus M. oxyfera-like bacteria exist in the coastal wetland of the Yellow River Delta, which provides molecular biological evidence for the existence of the DAMO process therein. Moreover, it was revealed the influence mechanism of physical and chemical characteristics of each region on the DAMO rate. This is of significance for furthering our understanding of the coupled effect of the global carbon and nitrogen cycle.

The Polygonal Cell Shape and Surface Protein Layer of Anaerobic Methane-Oxidizing Methylomirabilis lanthanidiphila Bacteria

Methylomirabilis bacteria perform anaerobic methane oxidation coupled to nitrite reduction via an intra-aerobic pathway, producing carbon dioxide and dinitrogen gas. These diderm bacteria possess an unusual polygonal cell shape with sharp ridges that run along the cell body. Previously, a putative surface protein layer (S-layer) was observed as the outermost cell layer of these bacteria. We hypothesized that this S-layer is the determining factor for their polygonal cell shape. Therefore, we enriched the S-layer from M. lanthanidiphila cells and through LC-MS/MS identified a 31 kDa candidate S-layer protein, mela_00855, which had no homology to any other known protein. Antibodies were generated against a synthesized peptide derived from the mela_00855 protein sequence and used in immunogold localization to verify its identity and location. Both on thin sections of M. lanthanidiphila cells and in negative-stained enriched S-layer patches, the immunogold localization identified mela_00855 as the S-layer protein. Using electron cryo-tomography and sub-tomogram averaging of S-layer patches, we observed that the S-layer has a hexagonal symmetry. Cryo-tomography of whole cells showed that the S-layer and the outer membrane, but not the peptidoglycan layer and the cytoplasmic membrane, exhibited the polygonal shape. Moreover, the S-layer consisted of multiple rigid sheets that partially overlapped, most likely giving rise to the unique polygonal cell shape. These characteristics make the S-layer of M. lanthanidiphila a distinctive and intriguing case to study.

Novel biotechnologies for nitrogen removal and their coupling with gas emissions abatement in wastewater treatment facilities

Wastewaters contaminated with nitrogenous pollutants, derived from anthropogenic activities, have exacerbated our ecosystems sparking environmental problems, such as eutrophication and acidification of water reservoirs, emission of greenhouse gases, death of aquatic organisms, among others. Wastewater treatment facilities (WWTF) combining nitrification and denitrification, and lately partial nitrification coupled to anaerobic ammonium oxidation (anammox), have traditionally been applied for the removal of nitrogen from wastewaters. The present work provides a comprehensive review of the recent biotechnologies developed in which nitrogen-removing processes are relevant for the treatment of both wastewaters and gas emissions. These novel processes include the anammox process with alternative electron acceptors, such as sulfate (sulfammox), ferric iron (feammox), and anodes in microbial electrolysis cells (anodic anammox). New technologies that couple nitrate/nitrite reduction with the oxidation of methane, H₂S, volatile methyl siloxanes, and other volatile organic compounds are also described. The potential of these processes for (i) minimizing greenhouse gas emissions from WWTF, (ii) biogas purification, and (iii) air pollution control is critically discussed considering the factors that might trigger N₂O release during nitrate/nitrite reduction. Moreover, this review provides a discussion on the main challenges to tackle towards the consolidation of these novel biotechnologies.

Denitrifying anaerobic methane oxidation (DAMO) cultures: Factors affecting their enrichment, performance and integration with anammox bacteria

The recently discovered process, denitrifying anaerobic methane oxidation (DAMO), links the carbon and nitrogen biogeochemical cycles via coupling the anaerobic oxidation of methane to denitrification. The DAMO process, in this respect, has the potential to mitigate the greenhouse effect through the assimilation of dissolved methane. Denitrification via methane oxidation rather than organic matter, provides a new perspective to performing this once thought to be well established process. The two main species responsible for this process are "Candidatus Methylomirabilis oxyfera (M. oxyfera), and "Candidatus Methanoperedens nitroreducens" (M. nitroreducens). M. oxyfera is responsible of reducing nitrite while M. nitroreducens reduces nitrate to nitrite. These two microorganisms, despite their different pathways, were found to exist together in nature through a syntrophic relationship. Their co-existence with anaerobic ammonium oxidation (Anammox) bacteria was also revealed in the last decade. Anammox bacteria are chemolithoautotrophs, converting ammonium and nitrite to N₂ and nitrate. They are responsible for the release of more than 50% of oceanic N₂, hence play an important role in the global nitrogen cycle. Factors leading to the enrichment of DAMO cultures and their cultivation with Anammox cultures are of significance for improved nitrogen removal systems with decreased greenhouse effect, and even for further full-scale applications. This study, therefore, aims to present an updated review of the DAMO process, by focusing on the factors that might have a significant role in enrichment of DAMO microorganisms and their co-existence with Anammox bacteria. Factors such as temperature, pH, inoculum and feed type, trace metals and reactor configuration are among the ones discussed in detail. Factors, which have not been investigated, are also elucidated to provide a better understanding of the process and set research goals that will aid in the development of DAMO-centered wastewater treatment alternatives.

Methanotrophic denitrification in wastewater treatment: microbial aspects and engineering strategies

Anaerobic technologies are consolidated for sewage treatment and are the core processes for mining marketable products from waste streams. However, anaerobic effluents are supersaturated with methane, which represents a liability regarding greenhouse gas emissions. Meanwhile, anaerobic technologies are not capable of nitrogen removal, which is required to ensure environmental protection. Methane oxidation and denitrification processes can be combined to address both issues concurrently. Aerobic methane oxidizers can release intermediate organic compounds that can be used by conventional denitrifiers as electron donors. Alternatively, anoxic methanotrophic species combine methane oxidation with either nitrate or nitrite reduction in the same metabolism. Engineered systems need to overcome the long doubling times and low NO_x consumption rates of anoxic methanotrophic microorganisms. Another commonly reported bottleneck of methanotrophic denitrification relates to gas-liquid mass transfer limitations. Although anaerobic effluents are supersaturated with methane, experimental setups usually rely on methane supply in a gaseous mode. Hence, possibilities for the application of methane-oxidation coupled to denitrification in full scale might be overlooked. Moreover, syntrophic relationships among methane oxidizers, denitrifiers, nitrifiers, and other microorganisms (such as anammox) are not well understood. Integrating mixed populations with various metabolic abilities could allow for more robust methane-driven wastewater denitrification systems. This review presents an overview of the metabolic capabilities of methane oxidation and denitrification and discusses technological aspects that allow for the application of methanotrophic denitrification at larger scales.

Methane in wastewater treatment plants: status, characteristics, and bioconversion feasibility by methane oxidizing bacteria for high value-added chemicals production and wastewater treatment

Methane is a type of renewable fuel that can generate many types of high value-added chemicals, however, besides heat and power production, there is little methane utilization in most of the wastewater treatment plants (WWTPs) all round the world currently. In this review, the status of methane production performance from WWTPs was firstly investigated. Subsequently, based on the identification and classification of methane oxidizing bacteria (MOB), the key enzymes and metabolic pathway of MOB were presented in depth. Then the production, extraction and purification process of high value-added chemicals, including methanol, ectoine, biofuel, bioplastic, methane protein and extracellular polysaccharides, were introduced in detail, which was conducive to understand the bioconversion process of methane. Finally, the use of methane in wastewater treatment process, including nitrogen removal, emerging contaminants removal as well as resource recovery was extensively explored. These findings could provide guidance in the development of sustainable economy and environment, and facilitate biological methane conversion by using MOB in further attempts.

Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications

Methane is the final product of the anaerobic decomposition of organic matter. The conversion of organic matter to methane (methanogenesis) as a mechanism for energy conservation is exclusively attributed to the archaeal domain. Methane is oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic methanotrophic bacteria belong to the phyla Proteobacteria and Verrucomicrobia, while anaerobic methane oxidation is also mediated by more recently discovered anaerobic methanotrophs with representatives in both the bacteria and the archaea domains. The anaerobic oxidation of methane is coupled to the reduction of nitrate, nitrite, iron, manganese, sulfate, and organic electron acceptors (e.g., humic substances) as terminal electron acceptors. This review highlights the relevance of methanotrophy in natural and anthropogenically influenced ecosystems, emphasizing the environmental conditions, distribution, function, co-existence, interactions, and the availability of electron acceptors that likely play a key role in regulating their function. A systematic overview of key aspects of ecology, physiology, metabolism, and genomics is crucial to understand the contribution of methanotrophs in the mitigation of methane efflux to the atmosphere. We give significance to the processes under microaerophilic and anaerobic conditions for both aerobic and anaerobic methane oxidizers. In the context of anthropogenically influenced ecosystems, we emphasize the current and potential future applications of methanotrophs from two different angles, namely methane mitigation in wastewater treatment through the application of anaerobic methanotrophs, and the biotechnological applications of aerobic methanotrophs in resource recovery from methane waste streams. Finally, we identify knowledge gaps that may lead to opportunities to harness further the biotechnological benefits of methanotrophs in methane mitigation and for the production of valuable bioproducts enabling a bio-based and circular economy.

Methanotrophic Community Detected by DNA-SIP at Bertioga's Mangrove Area, Southeast Brazil

Methanotrophic bacteria can use methane as sole carbon and energy source. Its importance in the environment is related to the mitigation of methane emissions from soil and water to the atmosphere. Brazilian mangroves are highly productive, have potential to methane production, and it is inferred that methanotrophic community is of great importance for this ecosystem. The scope of this study was to investigate the functional and taxonomic diversity of methanotrophic bacteria present in the anthropogenic impacted sediments from Bertioga´s mangrove (SP, Brazil). Sediment sample was cultivated with methane and the microbiota actively involved in methane oxidation was identified by DNA-based stable isotope probing (DNA-SIP) using methane as a labeled substrate. After 4 days (96 h) of incubation and consumption of 0.7 mmol of methane, the most active microorganisms were related to methanotrophs Methylomonas and Methylobacter as well as to methylotrophic Methylotenera, indicating a possible association of these bacterial groups within a methane-derived food chain in the Bertioga mangrove. The abundance of genera Methylomonas, able to couple methane oxidation to nitrate reduction, may indicate that under low dissolved oxygen tensions, some aerobic methanotrophs could shift to intraerobic methane oxidation to avoid oxygen starvation.

Enhancement of nitrite-dependent anaerobic methane oxidation via Geobacter sulfurreducens

Nitrite-dependent anaerobic methane-oxidation (n-damo) is a potential novel technology for nitrogen removal in anaerobic wastewater treatment. In this study, Geobacter sulfurreducens (G) was applied to stimulate n-damo activity. Conductive materials such as nano-magnetite (M) or aggregating agents such as hydroxylapatite (H) were co-added with G. sulfurreducens to further investigate the enhancement effect. Results showed that the nitrite reduction activity of the n-damo culture was promoted by G. sulfurreducens, with 1.71-2.38 times higher in treatment G, G + M, and G + H than that in the control, but was inhibited by the single addition of hydroxylapatite. N-damo bacterial abundances based on the qPCR of the n-damo-specific pmoA gene increased in treatments with G. sulfurreducens, compared with that of the control. High-throughput sequencing analysis revealed the enrichment of uncultured phylum WPS-2 in treatments with G. sulfurreducens. Fluorescence in situ hybridization verified the co-occurrence pattern of n-damo bacteria (NC10), G. sulfurreducens, and type-I aerobic methanotrophs (Methylomonas spp.). The above results corroborated the microbial interspecies electron transfer (MIET) potentiality of the n-damo enrichment. Our study provides a novel pathway for enhancing MIET to stimulate n-damo process.

Rapid formation of granules coupling n-DAMO and anammox microorganisms to remove nitrogen

Granular sludge exhibits unique features, including rapid settling velocity, high loading rate and relative insensitivity against inhibitors, thus being a favorable platform for the cultivation of slow-growing and vulnerable microorganisms, such as anaerobic ammonium oxidation (anammox) bacteria and nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) microorganisms. While anammox granules have been widely applied, little is known about how to speed up the granulation process of n-DAMO microorganisms, which grow even slower than anammox bacteria. In this study, we used mature anammox granules as biotic carriers to embed n-DAMO microorganisms, which obtained combined anammox + n-DAMO granules within 6 months. The results of whole-granule 16S rRNA gene amplicon sequencing showed the coexistence of anammox bacteria, n-DAMO bacteria and n-DAMO archaea. The microbial stratification along granule radius was further elucidated by cryosection-16S rRNA gene amplicon sequencing, showing the dominance of n-DAMO archaea and anammox bacteria at inner and outer layers, respectively. Moreover, the images of cryosection-fluorescence in situ hybridization (FISH) verified this stratification and also indicated a shift in microbial stratification. Specifically, n-DAMO bacteria and n-DAMO archaea attached to the anammox granule surface initially, which moved to the inner layer after 4-months operation. On the basis of combined anammox + n-DAMO granules, a practically useful nitrogen removal rate (1.0 kg N/m³/d) was obtained from sidestream wastewater, which provides new avenue to remove nitrogen from wastewater using methane as carbon source.

Fundamentals and potential environmental significance of denitrifying anaerobic methane oxidizing archaea

Many properties of denitrifying anaerobic methane oxidation (DAMO) bacteria have been explored since their first discovery, while DAMO archaea have attracted less attention. Since nitrate is more abundant than nitrite not only in wastewater but also in the natural environment, in depth investigations of the nitrate-DAMO process should be conducted to determine its environmental significance in the global carbon and nitrogen cycles. This review summarizes the status of research on DAMO archaea and the catalyzed nitrate-dependent anaerobic methane oxidation, including such aspects as laboratory enrichment, environmental distribution, and metabolic mechanism. It is shown that appropriate inocula and enrichment parameters are important for the culture enrichment and thus the subsequent DAMO activity, but there are still relatively few studies on the environmental distribution and physiological metabolism of DAMO archaea. Finally, some hypotheses and directions for future research on DAMO archaea, anaerobic methanotrophic archaea, and even anaerobically metabolizing archaea are also discussed.

Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments

Large amounts of methane, a potent greenhouse gas, are produced in anoxic sediments by methanogenic archaea. Nonetheless, over 90% of the produced methane is oxidized via sulfate-dependent anaerobic oxidation of methane (S-AOM) in the sulfate-methane transition zone (SMTZ) by consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Coastal systems account for the majority of total marine methane emissions and typically have lower sulfate concentrations, hence S-AOM is less significant. However, alternative electron acceptors such as metal oxides or nitrate could be used for AOM instead of sulfate. The availability of electron acceptors is determined by the redox zonation in the sediment, which may vary due to changes in oxygen availability and the type and rate of organic matter inputs. Additionally, eutrophication and climate change can affect the microbiome, biogeochemical zonation, and methane cycling in coastal sediments. This review summarizes the current knowledge on the processes and microorganisms involved in methane cycling in coastal sediments and the factors influencing methane emissions from these systems. In eutrophic coastal areas, organic matter inputs are a key driver of bottom water hypoxia. Global warming can reduce the solubility of oxygen in surface waters, enhancing water column stratification, increasing primary production, and favoring methanogenesis. ANME are notoriously slow growers and may not be able to effectively oxidize methane upon rapid sedimentation and shoaling of the SMTZ. In such settings, ANME-2d (Methanoperedenaceae) and ANME-2a may couple iron- and/or manganese reduction to AOM, while ANME-2d and NC10 bacteria (Methylomirabilota) could couple AOM to nitrate or nitrite reduction. Ultimately, methane may be oxidized by aerobic methanotrophs in the upper millimeters of the sediment or in the water column. The role of these processes in mitigating methane emissions from eutrophic coastal sediments, including the exact pathways and microorganisms involved, are still underexplored, and factors controlling these processes are unclear. Further studies are needed in order to understand the factors driving methane-cycling pathways and to identify the responsible microorganisms. Integration of the knowledge on microbial pathways and geochemical processes is expected to lead to more accurate predictions of methane emissions from coastal zones in the future.

Microbial abundance and activity of nitrite/nitrate-dependent anaerobic methane oxidizers in estuarine and intertidal wetlands: Heterogeneity and driving factors

Nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) is a crucial link between carbon and nitrogen cycles in estuarine and coastal ecosystems. However, the factors that affect the heterogeneous variability in n-DAMO microbial abundance and activity across estuarine and intertidal wetlands remain unclear. This study examined the spatiotemporal variations in n-DAMO microbial abundance and associated activity in different estuarine and intertidal habitats via quantitative PCR and ¹³C stable isotope experiments. The results showed that Candidatus 'Methylomirabilis oxyfera' (M. oxyfera)-like DAMO bacteria and Candidatus 'Methanoperedens nitroreducens' (M. nitroreducens)-like DAMO archaea cooccurred in estuarine and intertidal wetlands, with a relatively higher abundance of the M. oxyfera-like bacterial pmoA gene (4.0 × 10⁶-7.6 × 10⁷ copies g^-1 dry sediment) than the M. nitroreducens-like archaeal mcrA gene (4.5 × 10⁵-9.4 × 10⁷ copies g^-1 dry sediment). The abundance of the M. oxyfera-like bacterial pmoA gene was closely associated with sediment pH and ammonium (P<0.05), while no significant relationship was detected between M. nitroreducens-like archaeal mcrA gene abundance and the measured environmental parameters (P>0.05). High n-DAMO microbial activity was observed, which varied between 0.2 and 84.3 nmol ¹³CO₂ g^-1 dry sediment day^-1 for nitrite-DAMO bacteria and between 0.4 and 32.6 nmol ¹³CO₂ g^-1 dry sediment day^-1 for nitrate-DAMO archaea. The total n-DAMO potential tended to be higher in the warm season and in the upstream freshwater and low-salinity estuarine habitats and was significantly related to sediment pH, total organic carbon, Fe(II), and Fe(III) contents (P<0.05). In addition to acting as an important methane (CH₄) sink, n-DAMO microbes had the potential to consume a substantial amount of reactive N in estuarine and intertidal environments, with estimated nitrogen elimination rates of 0.5-224.7 nmol N g^-1 dry sediment day^-1. Overall, our investigation reveals the distribution pattern and controlling factors of n-DAMO bioprocesses in estuarine and intertidal marshes and gains a better understanding of the coupling mechanisms between carbon and nitrogen cycles.

Primer evaluation and development of a droplet digital PCR protocol targeting amoA genes for the quantification of Comammox in lakes

To date, little is known about the ecological significance of Comammox (COMplete AMMonia OXidizers) Nitrospira in the water column of freshwater lakes. Water samples collected along depth profiles were used to investigate the distribution of Comammox in 13 lakes characterized by a wide range of physicochemical properties. Several published primers, which target the α-subunit of the ammonia monooxygenase, generated non-specific PCR products or did not amplify target genes from lake water and other habitats. Therefore, a new primer set has been designed for specific detection of Comammox in lakes. The high specificity of the PCR assay was confirmed by sequencing analysis. Quantification of Comammox amoA genes in lake water samples based on droplet digital PCR (ddPCR) revealed very low abundances (not exceeding 85 amoA copies ml^-1), which suggest that Comammox is of minor importance for the nitrification process in the water column of the study sites. Surprisingly, samples taken from the sediment/water-interface along an oxygen gradient in dimictic Piburger See showed Comammox abundances three to four magnitudes higher than in the pelagic realm of the lake, which indicates a preference of Comammox to a particle-attached lifestyle.

Evaluation of nitrogen removal and the microbial community in a submerged aerated biological filter (SABF), secondary decanters (SD), and horizontal subsurface flow constructed wetlands (HSSF-CW) for the treatment of kennel effluent

To ensure microbial activity and a reaction equilibrium with efficiency and energy saving, it is important to know the factors that influence microbiological nitrogen removal in wastewater. Thus, it was investigated the microorganisms and their products involved in the treatment of kennel effluents operated with different aeration times, phase 1 (7 h of continuous daily aeration), phase 2 (5 h of continuous daily aeration), and phase 3 (intermittent aeration every 2 h), monitoring chemical and physical parameters weekly, monthly microbiological, and qualitative and quantitative microbiological analyzes at the end of each applied aeration phase. The results showed a higher mean growth of nitrifying bacteria (NB) (10⁶) and denitrifying bacteria (DB) (10²²) in phase with intermittent aeration, in which better total nitrogen (TN) removal performance, with 33%, was achieved, against 21% in phase 1 and 17% in phase 2, due to the longer aeration time and lower carbon/nitrogen ratio (15.7), compared with the other phases. The presence of ammonia-oxidizing bacteria (AOB), the genus Nitrobacter nitrite-oxidizing bacteria (NOB), and DB were detected by PCR with specific primers at all phases. The analysis performed by 16S-rRNA DGGE revealed the genres Thauera at all phases; Betaproteobacteria and Acidovorax in phase 3; Azoarcus in phases 2 and 3; Clostridium, Bacillus, Lactobacillus, Turicibacter, Rhodopseudomonas, and Saccharibacteria in phase 1, which are related to the nitrogen removal, most of them by denitrifying. It is concluded that, with the characterization of the microbial community and the analysis of nitrogen compounds, it was determined, consistently, that the studied treatment system has microbiological capacity to remove TN, with the phase 3 aeration strategy, by simultaneous nitrification and denitrification (SND). Due to the high density of DB, most of the nitrification occurred by heterotrophic nitrification-aerobic. And denitrification occurred by heterotrophic and autotrophic forms, since the higher rate of oxygen application did not harm the DB. Therefore, the aeration and carbon conditions in phase 3 favored the activity of the microorganisms involved in these different routes. It is considered that, in order to increase autotrophic nitrification-aerobic, it is necessary to exhaust the volume of sludge in the secondary settlers (SD), further reducing the carbon/nitrogen ratio, through more frequent cleaning, whose periodicity should be the object of further studies. Graphical abstract.

Structure and distribution of nitrite-dependent anaerobic methane oxidation bacteria vary with water tables in Zoige peatlands

The recently discovered nitrite-dependent anaerobic methane oxidation (n-damo) is an important methane sink in natural ecosystems performed by NC10 phylum bacteria. However, the effect of water table (WT) gradient due to global change on n-damo bacterial communities is not well studied in peatlands. Here, we analysed the vertical distribution (0-100 cm) of n-damo bacterial communities at three sites with different WTs of the Zoige peatlands in the Qinghai-Tibetan Plateau. Using an n-damo bacterial specific 16S rRNA gene clone library, we obtained 25 operational taxonomic units (OTUs) that could be divided into Groups A, B, C, D and E (dominated by A and B). The dominant group was Group B at the high (OTU14 and OTU20) and intermediate (OTU7 and OTU8) WT sites and Group A was dominant at the low WT site (OTU6 and OTU5). Using high-throughput sequencing, we observed that n-damo bacteria mainly distributed in subsurface soils (50-60 and 20-30 cm), and their relative abundances were higher at the low WT site than at the other two sites. In addition, we found that pH and nitrate were positively correlated with Group A, while total organic carbon, total nitrogen and ammonia were positively associated with Group B. Our study provides new insights into our understanding of the response of n-damo bacteria to WT gradient in peatlands, with important implications for global change.

Strategy for denitrifying anaerobic methane-oxidizing bacteria growing under the oxygen-present condition

Denitrifying anaerobic methane oxidizing (DAMO) bacteria are newly discovered microorganisms that use methane as the electron donor to reduce nitrite into dinitrogen. They have potential value on nitrogen removal from wastewater. However, the oxygen exposure in engineering is considered one of the bottlenecks for DAMO engineering application. In this work, we cultured DAMO bacteria under oxic and anoxic conditions in a gas-lift sequencing batch reactor (GLSBR) to explore DAMO bacterial response to oxygen stress. Under oxic conditions (7.5-8 mg O₂/L), the extension of hydraulic retention time (HRT) from 2 days to 4 days increased DAMO bacterial abundance by 3.8 times. Under anoxic conditions (0.2-0.5 mg O₂/L), DAMO bacterial abundance increased by 30.1 times and were kept over 2.0 × 10¹¹ copies g^-1 wet sludge. During the enrichment, microbial aggregates were formed and DAMO bacteria tended to be distributed inside the aggregates. Notably, aerobic methanotrophs existed in the whole process, capable of consuming oxygen and providing a suitable environment for DAMO bacterial growth. Finally, DAMO bacteria were enriched and the relative abundance was 16.16%. This work provides new insights into DAMO bacterial enrichment and their application in wastewater treatment.

Diversity, enrichment, and genomic potential of anaerobic methane- and ammonium-oxidizing microorganisms from a brewery wastewater treatment plant

Anaerobic wastewater treatment offers several advantages; however, the effluent of anaerobic digesters still contains high levels of ammonium and dissolved methane that need to be removed before these effluents can be discharged to surface waters. The simultaneous anaerobic removal of methane and ammonium by denitrifying (N-damo) methanotrophs in combination with anaerobic ammonium-oxidizing (anammox) bacteria could be a potential solution to this challenge. After a molecular survey of a wastewater plant treating brewery effluent, indicating the presence of both N-damo and anammox bacteria, we started an anaerobic bioreactor with a continuous supply of methane, ammonium, and nitrite to enrich these anaerobic microorganisms. After 14 months of operation, a stable enrichment culture containing two types of 'Candidatus Methylomirabilis oxyfera' bacteria and two strains of 'Ca. Brocadia'-like anammox bacteria was achieved. In this community, anammox bacteria converted 80% of the nitrite with ammonium, while 'Ca. Methylomirabilis' contributed to 20% of the nitrite consumption. The analysis of metagenomic 16S rRNA reads and fluorescence in situ hybridization (FISH) correlated well and showed that, after 14 months, 'Ca. Methylomirabilis' and anammox bacteria constituted approximately 30 and 20% of the total microbial community. In addition, a substantial part (10%) of the community consisted of Phycisphaera-related planctomycetes. Assembly and binning of the metagenomic sequences resulted in high-quality draft genome of two 'Ca. Methylomirabilis' species containing the marker genes pmoCAB, xoxF, and nirS and putative NO dismutase genes. The anammox draft genomes most closely related to 'Ca. Brocadia fulgida' included the marker genes hzsABC, hao, and hdh. Whole-reactor and batch anaerobic activity measurements with methane, ammonium, nitrite, and nitrate revealed an average anaerobic methane oxidation rate of 0.12 mmol h^-1 L^-1 and ammonium oxidation rate of 0.5 mmol h^-1 L^-1. Together, this study describes the enrichment and draft genomes of anaerobic methanotrophs from a brewery wastewater treatment plant, where these organisms together with anammox bacteria can contribute significantly to the removal of methane and ammonium in a more sustainable way. KEY POINTS: • An enrichment culture containing both N-damo and anammox bacteria was obtained. • Simultaneous consumption of ammonia, nitrite, and methane under anoxic conditions. • In-depth metagenomic biodiversity analysis of inoculum and enrichment culture.

Depth-specific distribution and significance of nitrite-dependent anaerobic methane oxidation process in tidal flow constructed wetlands used for treating river water

Tidal flow constructed wetlands (TF CWs) have been considered an effective approach to treat contaminated river water, as well as a significant role in global matter cycles, especially for carbon and nitrogen. Notably, it has been thought that methane oxidation was completely catalyzed by the aerobic process, ignoring the anaerobic methane oxidation, such as the nitrite-dependent anaerobic methane oxidation (n-damo) process. In our current work, therefore, we used molecular and stable isotopes to investigate the biodiversity, quantity and potential rate of n-damo bacteria in the TF CWs located in the Xisha Wetland Park in the Yangtze River estuary, China. The results revealed that n-damo process was active in the collected soil cores, with a decreasing trend along water depths and rates ranging from 8.48 to 23.45 nmol CO₂ g^-1 dry soil d^-1. The n-damo bacterial contributions to CH₄ oxidation and N₂ production in TF CWs reached 9.49-26.26% and 20.73-47.11%, respectively, suggesting that n-damo bacteria was an important nitrogen and methane sink in the TF CWs, but had been previously overlooked. The copy numbers of total bacterial 16S rRNA and pmoA genes were 1.84-11.21 × 10⁹ and 0.59-2.72 × 10⁶ copies g^-1 ds, respectively, as the higher abundance was found in the soil at lower water levels during tidal submergence. Diverse n-damo bacterial 16S rRNA gene sequences belonged to group B, C and D were measured, and it was found that group B and C were the most frequently measured n-damo clusters in the TF CWs. In addition, nitrite was the key factor regulating the n-damo bacterial distribution in the TF CWs. This study would broaden our horizons and help us better understand the nitrogen and methane cycles in tidal ecosystems.

Long-term performance of denitrifying anaerobic methane oxidation under stepwise cooling and ambient temperature conditions

Nitrate-dependent anaerobic methane oxidation (N-DAMO), a bioprocess that couples the oxidation of green gas and the removal of nitrogen oxides in a microbial group, has gained much attention as a potential economical method of biological removal of nitrates and methane from wastewater. Low-temperature (20 °C) operation of N-DAMO would be beneficial to utilize the methane dissolved in the effluent and thus decrease the cost of maintaining the bioreactor temperature in wastewater treatment. Here, the long-term (>350 days) operational activities of N-DAMO were evaluated to assess the performance of N-DAMO from stepwise cooling (30-20 °C) to ambient temperatures (13-38 °C). Under stepwise cooling conditions, the activity of the N-DAMO community was first inhibited and then rapidly adjusted. Notably, a similar N-DAMO activity was observed at 30 °C and 20 °C. Under ambient temperature conditions, the highest nitrate removal rate observed at the beginning of the test was 7.14 mg-N/L/d, which was 5.3 times higher than that recorded at the end of the test. This indicates that the long-term temperature fluctuation irreversibly inhibited N-DAMO activity. 16S rRNA gene sequencing analyses found that the functional archaea were ANME-2D, which has been deemed as the dominant culture in the N-DAMO process. The abundance of ANME-2D on the last day at stepwise cooling temperature conditions was much higher than on day 0, but disappeared after a long period of operation at ambient temperature. It was assumed that N-DAMO would stabilize at stepwise cooling temperature conditions, but not at ambient temperature. Our findings could offer a promising technology for anaerobic wastewater treatment plants (WWTPs) in temperate and warm climate zones.

Granular Sludge Coupling Nitrate/Nitrite Dependent Anaerobic Methane Oxidation with Anammox: from Proof-of-Concept to High Rate Nitrogen Removal

This work developed a novel Membrane Granular Sludge Reactor (MGSR) equipped with a gas permeable membrane module for efficient methane delivery to cultivate nitrate/nitrite dependent anaerobic methane oxidation (n-DAMO) microorganisms in granular sludge. As proof of concept, the MGSR was fed with synthetic wastewater containing nitrate and ammonium to facilitate the growth of n-DAMO microorganisms. The granular sludge of n-DAMO and Anammox was gradually developed and achieved a nitrogen removal rate of 1.08 g NO₃^--N L^-1 d^-1 and 0.81 g NH₄⁺-N L^-1 d^-1. Finally, enriched granular sludge was successfully applied for nitrogen removal from the synthetic partial nitritation effluent. The combined dominance of n-DAMO archaea, Anammox bacteria, and n-DAMO bacteria in the microbial community was confirmed by 16S rRNA amplicon sequencing. Fluorescence in situ hybridization revealed that a layered structure was formed in the granular sludge with Anammox bacteria in the outer layer and n-DAMO microorganisms in the inner layer when granules were fed with nitrite and ammonium. The high performance of nitrogen removal (16.53 kg N m^-3 d^-1) with satisfactory effluent quality (∼8 mg N L^-1) and excellent biomass retention capacity (43 g VSS L^-1) make the MGSR promising for the practical application of n-DAMO and Anammox in wastewater treatment.

Denitrifying anaerobic methane oxidation in marsh sediments of Chongming eastern intertidal flat

Denitrifying anaerobic methane oxidation (DAMO) and associated microbial diversity and abundance in the marsh sediments of Chongming eastern intertidal flat, the Yangtze Estuary, were investigated using carbon-isotope tracing and molecular techniques. Co-existence of nitrate-DAMO archaea and nitrite-DAMO bacteria was evidenced, with higher biodiversity of DAMO archaea than DAMO bacteria. Abundance of DAMO archaeal mcrA gene and DAMO bacterial pmoA gene ranged from 4.2 × 10³ to 3.9 × 10¹⁰ copies g^-1 and from 4.5 × 10⁵ to 6.4 × 10⁶ copies g^-1, respectively. High DAMO potential was detected, ranging from 0.6 to 46.7 nmol ¹³CO₂ g^-1 day^-1 for nitrate-DAMO and from 1.3 to 39.9 nmol ¹³CO₂ g^-1 day^-1 for nitrite-DAMO. In addition to playing an important role as a CH₄ sink, DAMO bacteria also removed a substantial amount of reactive nitrogen (29.4 nmol N g^-1 day^-1) from the intertidal sediments. Overall, these results indicate the importance of DAMO bioprocess as methane and nitrate sinks in intertidal marshes.

Biological Treatment Technology for Landfill Leachate

Biological process for environmental preservation and treatment is not a new technology. It was used a decade ago until now. The most important tools in biological processes are the microorganism and upstream instruments (bioreactor, pond and others) to run the process. Furthermore, the efficiency of the process depends on many factors such as temperature, pH, type of microorganism, conditions, and other nutrients. To understand the factors that will affect the process, mechanisms of microorganisms to treat or protect the environment must be considered. For leachate treatment, biological process is one of the most widely used techniques for low cost and environmentally friendly.

Moving bed biofilm reactor technology in municipal wastewater treatment: A review

The review encompasses the development of municipal wastewater treatment process using MBBR from early stages, established application, and recent advancements. An overview of main drivers leading to the MBBR technology development over its early stage is discussed. Biocarriers types and features together with biofilm development and role of extracellular polymeric substances (EPS) are presented, ultimately, addressing the challenge in decreasing startup time required for full operation. Furthermore, the review investigates the state of the art of MBBR technology for nutrient removal (i.e., COD and BOD, nitrogen and phosphorus) through process functionality and configuration of established (e.g., IFAS) and under development (e.g. PN/A) applications. Reactor operational characteristics such as filling fractions, mixing properties, dissolved oxygen requirements, and loading rates are presented and related to full scale examples. Current literature discussing the most recent studies on MBBR capability in reduction and removal of chemicals of emerging concern (CEC) released is presented. Ultimately, high rate carbon and nitrogen removal through A/B stage process are examined in its main operational parameters and its application towards energy neutrality suggesting novel MBBR application to further reduce energy requirements and plant footprint.

Achieving high nitrogen removal efficiency by optimizing nitrite-dependent anaerobic methane oxidation process with growth factors

Nitrite-dependent anaerobic methane oxidation (N-DAMO) is a newly discovered bioprocess which uses methane as electron donor to reduce nitrite into dinitrogen. It is a promising clean bioprocess for denitrification in wastewater treatment. However, the low reaction rate and slow growth rate of N-DAMO bacteria within NC10 phylum limit the application of the process. In this study, we chose vitamin, heme, nucleobase and betaine to investigate their short- and long-term effects on N-DAMO bacteria. The concentrations of the growth factors of medium were improved according to the short-term experiments. The results were subsequently verified via long-term inoculations and were applied in a magnetically stirred gas lift reactor (MSGLR). The results indicated that nucleobase and betaine (5.0 and 200 μg L^-1, respectively) significantly stimulated the N-DAMO activity, whereas vitamin and heme had no significant effects in the tested concentration ranges. During the long-term incubation, N-DAMO bacteria continuously increased and finally achieved a relative abundance of 14.4% on day 300. Notably, larger aggregates of N-DAMO bacteria were observed at the end of the long-term incubation. And the nitrogen removal rate of the MSGLR increased to 70 mg N L^-1 day^-1, with the total nitrogen removal efficiency over 99.0%. However, the addition of betaine introduced methyl into the reactors and this made methylotrophs account a considerable part of the bacterial community, which limited the enrichment degree of N-DAMO bacteria. This work will contribute to the engineering application and enrichment of N-DAMO bacteria.

Nitric Oxide Dismutase (nod) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers

Oxygenic denitrification represents a new route in reductive nitrogen turnover which differs from canonical denitrification in how nitric oxide (NO) is transformed into dinitrogen gas. Instead of NO reduction via N₂O to N₂, NO is proposed to be directly disproportionated into N₂ and O₂ in oxygenic denitrification, catalyzed by the putative NO dismutase (Nod). Although a high diversity of nod genes has been recovered from various environments, still little is known about the niche partitioning and ecophysiology of oxygenic denitrifiers. One constraint is that nod as a functional marker for oxygenic denitrifiers is not well established. To address this issue, we compared the diversity and phylogeny of nod, 16S rRNA and pmoA gene sequences of four NC10 enrichments that are capable of methane-driven oxygenic denitrification and one environmental sample. The phylogenies of nod, 16S rRNA and pmoA genes of these cultures were generally congruent. The diversity of NC10 bacteria inferred from different genes was also similar in each sample. A new set of NC10-specific nod primers was developed and used in qPCR. The abundance of NC10 bacteria inferred from nod genes was constantly lower than via 16S rRNA genes, but the difference was within one order of magnitude. These results suggest that nod is a suitable molecular marker for studying the diversity and phylogeny of methane-driven oxygenic denitrifiers, the further investigation of which may be of value to develop enhanced strategies for sustainable nitrogen or methane removal.

Interactions between anaerobic ammonium- and methane-oxidizing microorganisms in a laboratory-scale sequencing batch reactor

The reject water of anaerobic digestors still contains high levels of methane and ammonium that need to be treated before these effluents can be discharged to surface waters. Simultaneous anaerobic methane and ammonium oxidation performed by nitrate/nitrite-dependent anaerobic methane-oxidizing(N-damo) microorganisms and anaerobic ammonium-oxidizing(anammox) bacteria is considered a potential solution to this challenge. Here, a stable coculture of N-damo archaea, N-damo bacteria, and anammox bacteria was obtained in a sequencing batch reactor fed with methane, ammonium, and nitrite. Nitrite and ammonium removal rates of up to 455 mg N-NO₂^- L^-1 day^-1 and 228 mg N-NH₄⁺ L^-1 were reached. All nitrate produced by anammox bacteria (57 mg N-NO₃^- L^-1 day^-1) was consumed, leading to a nitrogen removal efficiency of 97.5%. In the nitrite and ammonium limited state, N-damo and anammox bacteria each constituted about 30-40% of the culture and were separated as granules and flocs in later stages of the reactor operation. The N-damo archaea increased up to 20% and mainly resided in the granular biomass with their N-damo bacterial counterparts. About 70% of the nitrite in the reactor was removed via the anammox process, and batch assays confirmed that anammox activity in the reactor was close to its maximal potential activity. In contrast, activity of N-damo bacteria was much higher in batch, indicating that these bacteria were performing suboptimally in the sequencing batch reactor, and would probably be outcompeted by anammox bacteria if ammonium was supplied in excess. Together these results indicate that the combination of N-damo and anammox can be implemented for the removal of methane at the expense of nitrite and nitrate in future wastewater treatment systems.

Rates and pathways of CH4 oxidation in ferruginous Lake Matano, Indonesia

This study evaluates rates and pathways of methane (CH₄ ) oxidation and uptake using ¹⁴ C-based tracer experiments throughout the oxic and anoxic waters of ferruginous Lake Matano. Methane oxidation rates in Lake Matano are moderate (0.36 nmol L^-1  day^-1 to 117 μmol L^-1  day^-1 ) compared to other lakes, but are sufficiently high to preclude strong CH₄ fluxes to the atmosphere. In addition to aerobic CH₄ oxidation, which takes place in Lake Matano's oxic mixolimnion, we also detected CH₄ oxidation in Lake Matano's anoxic ferruginous waters. Here, CH₄ oxidation proceeds in the apparent absence of oxygen (O₂ ) and instead appears to be coupled to some as yet uncertain combination of nitrate ( NO 3 - ), nitrite ( NO 2 - ), iron (Fe) or manganese (Mn), or sulfate ( SO 4 2 - ) reduction. Throughout the lake, the fraction of CH₄ carbon that is assimilated vs. oxidized to carbon dioxide (CO₂ ) is high (up to 93%), indicating extensive CH₄ conversion to biomass and underscoring the importance of CH₄ as a carbon and energy source in Lake Matano and potentially other ferruginous or low productivity environments.

Key Physiology of a Nitrite-Dependent Methane-Oxidizing Enrichment Culture

Nitrite-dependent methane-oxidizing bacteria couple the reduction of nitrite to the oxidation of methane via a unique oxygen-producing pathway. This process is carried out by members of the genus Methylomirabilis that belong to the NC10 phylum. Contrary to other known anaerobic methane oxidizers, they do not employ the reverse methanogenesis pathway for methane activation but instead a canonical particulate methane monooxygenase similar to those used by aerobic methanotrophs. Methylomirabilis-like bacteria are detected in many natural and manmade ecosystems, but their physiology is not well understood. Here, using continuous cultivation techniques, batch activity assays, and state-of-the-art membrane-inlet mass spectrometry, we determined growth rate, doubling time, and methane and nitrite affinities of the nitrite-dependent methane-oxidizing bacterium "Candidatus Methylomirabilis lanthanidiphila." Our results provide insight into understanding the interactions of these microorganisms with methanotrophs and other nitrite-reducing microorganisms, such as anaerobic ammonium-oxidizing bacteria. Furthermore, our data can be used in modeling studies as well as wastewater treatment plant design.IMPORTANCE Methane is an important greenhouse gas with a radiative forcing 28 times that of carbon dioxide over a 100-year time scale. The emission of methane to the atmosphere is controlled by aerobic and anaerobic methanotrophs, which are microorganisms that are able to oxidize methane to conserve energy. While aerobic methanotrophs have been studied for over a century, knowledge on the physiological characteristics of anaerobic methanotrophs is scarce. Here, we describe kinetic properties of "Candidatus Methylomirabilis lanthanidiphila," a nitrite-dependent methane-oxidizing microorganism, which is ecologically important and can be applied in wastewater treatment.

Microbial communities controlling methane and nutrient cycling in leach field soils

Septic systems inherently rely on microbial communities in the septic tank and leach field to attenuate pollution from household sewage. Operating conditions of septic leach field systems, especially the degree of water saturation, are likely to impact microbial biogeochemical cycling, including carbon (C), nitrogen (N), and phosphorus (P), as well as greenhouse gas (GHG) emissions to the atmosphere. To study the impact of flooding on microbial methane (CH₄) and nutrient cycling, two leach field soil columns were constructed. One system was operated as designed and the other was operated in both flooded and well-maintained conditions. CH₄ emissions were significantly higher in flooded soils (with means between 0.047 and 0.33 g CH₄ m^-2 d^-1) as compared to well-drained soils (means between -0.0025 and 0.004 g CH₄ m^-2 d^-1). Subsurface CH₄ profiles were also elevated under flooded conditions and peaked near the wastewater inlet. Gene abundances of mcrA, a biomarker for methanogens, were also greatest near the wastewater inlet. In contrast, gene abundances of pmoA, a biomarker for methanotrophs, were greatest in surface soils at the interface of CH₄ produced subsurface and atmospheric oxygen. 16S rRNA, mcrA, and pmoA amplicon library sequencing revealed microbial community structure in the soil columns differed from that of the original soils and was driven largely by CH₄ fluxes and soil VWC. Additionally, active microbial populations differed from those present at the gene level. Flooding did not appear to affect N or P removals in the soil columns (between 75 and 99% removal). COD removal was variable throughout the experiment, and was negatively impacted by flooding. Our study shows septic system leach field soils are dynamic environments where CH₄ and nutrients are actively cycled by microbial populations. Our results suggest proper siting, installation, and routine maintenance of leach field systems is key to reducing the overall impact of these systems on water and air quality.

Optimization of a nitrite-dependent anaerobic methane oxidation (n-damo) process by enhancing methane availability

The nitrite-dependent anaerobic methane oxidation (n-damo) process is believed to have good application prospects, but its development is limited by the low growth rate and low specific activity of n-damo bacteria. In this study, immobilized biologically activated carbon (IC) and high static pressure (HP) were investigated to improve the performance of the n-damo process by enhancing methane availability. Both IC and HP improved the activity of n-damo bacteria, and the highest n-damo specific activity was obtained in the HP-IC system, which reached 47.65 ± 0.21 µmol N L^-1 g^-1 h^-1. The larger specific surface area of biomass in the HP system was conducive to the transfer of methane, whereas IC increased the methane absorption capacity by approximately 10-fold and facilitated the methane supply to n-damo bacteria. Furthermore, q-PCR analysis revealed that both HP and IC improved the growth rate of n-damo bacteria, while HP could also enrich the diversity of n-damo bacteria.

Response of the Anaerobic Methanotroph "Candidatus Methanoperedens nitroreducens" to Oxygen Stress

"Candidatus Methanoperedens nitroreducens" is an archaeon that couples the anaerobic oxidation of methane to nitrate reduction. In natural and man-made ecosystems, this archaeon is often found at oxic-anoxic interfaces where nitrate, the product of aerobic nitrification, cooccurs with methane produced by methanogens. As such, populations of "Ca Methanoperedens nitroreducens" could be prone to regular oxygen exposure. Here, we investigated the effect of 5% (vol/vol) oxygen exposure in batch activity assays on a "Ca Methanoperedens nitroreducens" culture, enriched from an Italian paddy field. Metagenome sequencing of the DNA extracted from the enrichment culture revealed that 83% of 16S rRNA gene reads were assigned to a novel strain, "Candidatus Methanoperedens nitroreducens Verserenetto." RNA was extracted, and metatranscriptome sequencing upon oxygen exposure revealed that the active community changed, most notably in the appearance of aerobic methanotrophs. The gene expression of "Ca Methanoperedens nitroreducens" revealed that the key genes encoding enzymes of the methane oxidation and nitrate reduction pathways were downregulated. In contrast to this, we identified upregulation of glutaredoxin, thioredoxin family/like proteins, rubrerythrins, peroxiredoxins, peroxidase, alkyl hydroperoxidase, type A flavoproteins, FeS cluster assembly protein, and cysteine desulfurases, indicating the genomic potential of "Ca Methanoperedens nitroreducens Verserenetto" to counteract the oxidative damage and adapt in environments where they might be exposed to regular oxygen intrusion.IMPORTANCE "Candidatus Methanoperedens nitroreducens" is an anaerobic archaeon which couples the reduction of nitrate to the oxidation of methane. This microorganism is present in a wide range of aquatic environments and man-made ecosystems, such as paddy fields and wastewater treatment systems. In such environments, these archaea may experience regular oxygen exposure. However, "Ca Methanoperedens nitroreducens" is able to thrive under such conditions and could be applied for the simultaneous removal of dissolved methane and nitrogenous pollutants in oxygen-limited systems. To understand what machinery "Ca Methanoperedens nitroreducens" possesses to counteract the oxidative stress and survive, we characterized the response to oxygen exposure using a multi-omics approach.

Optimization of methane-dependent oxygenic denitrification in sequencing batch reactors by insights into the microbial interactions

Methane-dependent oxygenic denitrification (O2DN) is a promising technology used for reducing greenhouse gas emissions of nitrous oxide (N₂O) during wastewater treatment. Heterotrophic bacteria are associated with methane-dependent O2DN bacteria, and it has been proposed that metabolic cross-feeding occurs between the two populations above. In this study, a mathematical model was developed to describe the microbial processes and interactions between methane-dependent O2DN bacteria and associated heterotrophic bacteria in a sequencing batch reactor (SBR). A growth factor-dependent decoupling of metabolism and growth of methane-dependent O2DN bacteria was introduced into the model. Effects of influent substrates, operating parameters, and initial biomass on microbial community and reactor performance were then investigated, and the above parameters were optimized using the model. Results surprisingly show that organic matter in the influent greatly stimulated the growth of methane-dependent O2DN bacteria but slightly limited the increase of heterotrophic bacteria. This effect could be explained by the increased excretion of growth factors by heterotrophic bacteria and the intensified competition for nitrite when methane-dependent O2DN bacteria increased. These results will assist in providing a new understanding of microbial interactions in methane-dependent O2DN systems and offer a new and efficient strategy for operating methane-dependent O2DN reactors.