Methane-based denitrification kinetics and syntrophy in a membrane biofilm reactor at low methane pressure

Using RNA-Stable isotope probing to investigate methane oxidation metabolites and active microbial communities in methane oxidation coupled to denitrification

The active denitrifying communities performing methane oxidation coupled to denitrification (MOD) were investigated using samples from an aerobic reactor (∼20% O2 and 2% CH4) and a microaerobic reactor (2% O2, 2% CH4) undertaking denitrification. The methane oxidation metabolites excreted in the reactors were acetate, methanol, formate and acetaldehyde. Using anaerobic batch experiments supplemented with exogenously supplied 13C-labelled metabolites, the active denitrifying bacteria were identified using 16S rRNA amplicon sequencing and RNA-stable isotope probing (RNA-SIP). With the aerobic reactor (AR) samples, the maximum NO3- removal rates were 0.43 mmol g-1 d-1, 0.40 mmol g-1 d-1, 0.33 mmol g-1 d-1 and 0.10 mmol g-1 d-1 for exogenously supplied acetate, formate, acetaldehyde and methanol batch treatments respectively, while with the microaerobic reactor (MR) samples, the maximum NO3- removal rates were 0.41 mmol g-1 d-1, 0.33 mmol g-1 d-1, 0.38 mmol g-1 d-1 and 0.14 mmol g-1 d-1 for exogenously supplied acetate, formate, acetaldehyde and methanol batch treatments respectively. The RNA-SIP experiments with 13C-labelled acetate, formate, and methanol identified Methyloversatilis, and Hyphomicrobium as the active methane-driven denitrifying bacteria in the AR samples, while Pseudoxanthomonas, Hydrogenophaga and Hyphomicrobium were the active MOD bacteria in the MR samples. Collectively, all the data indicate that formate is a key cross-feeding metabolite excreted by methanotrophs and consumed by denitrifiers performing MOD.

Management of biofilm by an innovative layer-structured membrane for membrane biofilm reactor (MBfR) to efficient methane oxidation coupled to denitrification (AME-D)

Aerobic methane oxidation coupled with denitrification (AME-D) has garnered significant attention as a promising technology for nitrogen removal from water. Effective biofilm management on the membrane surface is essential to enhance the efficiency of nitrate removal in AME-D systems. In this study, we introduce a novel and scalable layer-structured membrane (LSM) developed using a meticulously designed polyurethane sponge. The application of the LSM in advanced biofilm management for AME-D resulted in a substantial enhancement of denitrification performance. Our experimental results demonstrated remarkable improvements in nitrate-removal flux (92.8 mmol-N m-2 d-1) and methane-oxidation rate (325.6 mmol m-2 d-1) when using an LSM in a membrane biofilm reactor (L-MBfR) compared with a conventional membrane reactor (C-MBfR). The l-MBfR exhibited 12.4-, 6.8- and 3.4-fold increases in nitrate-removal rate, biomass-retention capacity, and methane-oxidation rate, respectively, relative to the control C-MBfR. Notably, the l-MBfR demonstrated a 3.5-fold higher abundance of denitrifying bacteria, including Xanthomonadaceae, Rhodocyclaceae, and Methylophilaceae. In addition, the denitrification-related enzyme activity was twice as high in the l-MBfR than in the C-MBfR. These findings underscore the LSM's ability to create anoxic/anaerobic microenvironments conducive to biofilm formation and denitrification. Furthermore, the LSM exhibited a unique advantage in shaping microbial community structures and facilitating cross-feeding interactions between denitrifying bacteria and aerobic methanotrophs. The results of this study hold great promise for advancing the application of MBfRs in achieving efficient and reliable nitrate removal through the AME-D pathway, facilitated by effective biofilm management.

Coupling methanotrophic denitrification to anammox in a moving bed biofilm reactor for nitrogen removal under hypoxic conditions

Simultaneous removal of ammonium and nitrate was achieved in a methane-fed moving bed biofilm reactor (MBBR). In the reactor, methanotrophic microorganisms oxidized methane under hypoxic conditions likely to methanol, hence providing an electron donor to denitrifiers to reduce nitrate to nitrite that then allowed anaerobic ammonium oxidizing bacteria (Anammox) to remove excess ammonium as N₂. The ammonium and nitrate removal rates reached 72.09 ± 5.81 mgNH₄⁺-N/L/d and 62.61 ± 4.17 mgNO₃^--N/L/d when the MBBR was operated in continuous mode. Nitrate removal by the methane-fed mixed consortia was confirmed in a batch test revealing a CH₄/NO₃^- molar removal ratio of 1.15. The functional populations were unveiled by FISH analysis and 16S rRNA gene sequencing, which showed that the biofilm was dominated by Anammox bacteria (Candidatus Kuenenia) and diverse taxa associated with the capacity for denitrification: aerobic methanotrophs (Methylobacter, Methylomonas, and unclassified Methylococcaceae), methylotrophic denitrifiers (Opitutaceae and Methylophilaceae), and other heterotrophic denitrifiers (Ignavibacteriaceae, Anaerolineaceae, Comamonadaceae, Rhodocyclaceae and Thauera). Neither DAMO archaea nor DAMO bacteria were found in the sequencing analysis, indicating that more unknown community members possess the metabolic capacity of methanotrophic denitrification.

Heterotrophic denitrification: An overlooked factor that contributes to nitrogen removal in n-DAMO mixed culture

Nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) has been recognized as a sustainable process for simultaneous removal of nitrogen and methane. The metabolisms of denitrifying anaerobic methanotrophs, including Candidatus Methanoperedens and Candidatus Methylomirabilis, have been well studied. However, potential roles of heterotrophs co-existing with these anaerobic methanotrophs are generally overlooked. In this study, we pulse-fed methane and nitrate into an anaerobic laboratory sequencing batch bioreactor and enriched a mixed culture with stable nitrate removal rate (NRR) of ∼28 mg NO₃^--N L^-1 d^-1. Microbial community analysis indicates abundant heterotrophs, e.g., Arenimonas (5.3%-18.9%) and Fimbriimonadales ATM1 (6.4%), were enriched together with denitrifying anaerobic methanotrophs Ca. Methanoperedens (10.8%-13.2%) and Ca. Methylomirabilis (27.4%-34.3%). The results of metagenomics and batch tests suggested that the denitrifying anaerobic methanotrophs were capable of generating methane-derived intermediates (i.e., formate and acetate), which were employed by non-methanotrophic heterotrophs for denitrification and biomass growth. These findings offer new insights into the roles of heterotrophs in n-DAMO mixed culture, which may help to optimize n-DAMO process for nitrogen removal from wastewater.

Biofilm stratification in counter-diffused membrane biofilm bioreactors (MBfRs) for aerobic methane oxidation coupled to aerobic/anoxic denitrification: Effect of oxygen pressure

Aerobic methane oxidation coupled with denitrification (AME-D) executed in membrane biofilm bioreactors (MBfRs) provides a high promise for simultaneously mitigating methane (CH₄) emissions and removing nitrate in wastewater. However, systematically experimental investigation on how oxygen partial pressure affects the development and characteristics of counter-diffusional biofilm, as well as its spatial stratification profiles, and the cooperative interaction of the biofilm microbes, is still absent. In this study, we combined Optical Coherence Tomography (OCT) with Confocal Laser Scanning Microscopy (CLSM) to in-situ characterize the development of counter-diffusion biofilm in the MBfR for the first time. It was revealed that oxygen partial pressure onto the MBfR was capable of manipulating biofilm thickness and spatial stratification, and then managing the distribution of functional microbes. With the optimized oxygen partial pressure of 5.5 psig (25% oxygen content), the manipulated counter-diffusional biofilm in the AME-D process obtained the highest denitrification efficiency, due mainly to that this biofilm had the proper dynamic balance between the aerobic-layer and anoxic-layer where suitable O₂ gradient and sufficient aerobic methanotrophs were achieved in aerobic-layer to favor methane oxidation, and complete O₂ depletion and accessible organic sources were kept to avoid constraining denitrification activity in anoxic-layer. By using metagenome analysis and Fluorescence in situ hybridization (FISH) staining, the spatial distribution of the functional microbes within counter-diffused biofilm was successfully evidenced, and Rhodocyclaceae, one typical aerobic denitrifier, was found to survive and gradually enriched in the aerobic layer and played a key role in denitrification aerobically. This in-situ biofilm visualization and characterization evidenced directly for the first time the cooperative path of denitrification for AME-D in the counter-diffused biofilm, which involved aerobic methanotrophs, heterotrophic aerobic denitrifiers, and heterotrophic anoxic denitrifiers.

Nitrite reduction using a membrane biofilm reactor (MBfR) in a hypoxic environment with dilute methane under low pressures

Methane-based membrane biofilm reactors (MBfRs) can be an effective solution for nitrogen control in wastewater, but there is limited information on nitrite reduction for dilute wastewater (e.g., municipal wastewater) in hypoxic MBfRs. This study assessed the impacts of dilute (20 %), low-pressure methane (0.35-2.41 kPa) applied to MBfRs at hydraulic retention times (HRTs) of 2-12 h on nitrite removals, dissolved methane concentrations, and the resulting changes in the microbial community. High nitrite flux along with rapid and virtually complete (>99 %) nitrite removals were observed at methane pressures of 1.03-2.41 kPa at HRTs above 4 h, despite the use of diluted methane gas for the MBfR. The lowest methane pressure (0.35 kPa) was also able to achieve up to 98 % nitrite removals but required HRTs of up to 12 h. All scenarios had low dissolved methane concentrations (<10 mg/L), indicating that dilute methane at low supply pressures can effectively remove nitrite while meeting dissolved methane guidelines in treated effluent. Methylococcus genus was the key bacterium in MBfR biofilm grown at different HRTs and methane pressures, along with Methylocystis and other heterotrophic denitrifiers (Terrimonas and Hyphomicrobium). This study indicates that methane-based denitrification MBfRs can be a valuable tool to meet nitrogen limits for dilute wastewater coupled to partial nitrification, while limiting the release of methane to the environment.

Application of external carbon source in heterotrophic denitrification of domestic sewage: A review

The carbon source is essential as an electron donor in the heterotrophic denitrification process. When there is a lack of organic carbon sources in the system, an external carbon source is needed to improve denitrification efficiency. This review compiles the effects of liquid, solid and gaseous carbon sources on denitrification. Sodium acetate has better denitrification efficiency and is usually the first choice for external carbon sources. Fermentation by-products have been demonstrated to have the same denitrification efficiency as sodium acetate. Compared with cellulose-rich materials, biodegradable polymers have better and more stable denitrification performance in solid-phase nitrification, but their price is higher than the former. Methane as a gaseous carbon source is studied mainly by aerobic methane oxidation coupled with denitrification, which is feasible using methane as a carbon source. Liquid carbon sources are better controlled and utilized than solid carbon sources and gaseous carbon sources. In addition, high carbon to nitrogen ratio and hydraulic retention time can promote denitrification, while high dissolved oxygen (DO>2.0 mg L^-1) will inhibit the denitrification process. At the same time, high temperature is conducive to the decomposition of carbon sources by microorganisms. This review also considers the advantages and disadvantages of different carbon sources and cost analysis to provide a reference for looking for more economical and effective external carbon sources in the future.

RNA stable isotope probing and high-throughput sequencing to identify active microbial community members in a methane-driven denitrifying biofilm

AIMS

Aerobic methane oxidation coupled to denitrification (AME-D) is a promising process for removing nitrate from groundwater and yet its microbial mechanism and ecological implications are not fully understood. This study used RNA stable isotope probing (RNA-SIP) and high-throughput sequencing to identify the micro-organisms that are actively involved in aerobic methane oxidation within a denitrifying biofilm.

METHODS AND RESULTS

Two RNA-SIP experiments were conducted to investigate labelling of RNA and methane monooxygenase (pmoA) transcripts when exposed to ¹³ C-labelled methane over a 96-hour time period and to determine active bacteria involved in methane oxidation in a denitrifying biofilm. A third experiment was performed to ascertain the extent of ¹³ C labelling of RNA using isotope ratio mass spectrometry (IRMS). All experiments used biofilm from an established packed bed reactor. IRMS confirmed ¹³ C enrichment of the RNA. The RNA-SIP experiments confirmed selective enrichment by the shift of pmoA transcripts into heavier fractions over time. Finally, high-throughput sequencing identified the active micro-organisms enriched with ¹³ C.

CONCLUSIONS

Methanotrophs (Methylovulum spp. and Methylocystis spp.), methylotrophs (Methylotenera spp.) and denitrifiers (Hyphomicrobium spp.) were actively involved in AME-D.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study to use RNA-SIP and high-throughput sequencing to determine the bacteria active within an AME-D community.

State-of-the-art management technologies of dissolved methane in anaerobically-treated low-strength wastewaters: A review

The recent advancement in low temperature anaerobic processes shows a great promise for realizing low-energy-cost, sustainable mainstream wastewater treatment. However, the considerable loss of the dissolved methane from anaerobically-treated low-strength wastewater significantly compromises the energy potential of the anaerobic processes and poses an environmental risk. In this review, the promises and challenges of existing and emerging technologies for dissolved methane management are examined: its removal, recovery, and on-site reuse. It begins by describing the working principles of gas-stripping and biological oxidation for methane removal, membrane contactors and vacuum degassers for methane recovery, and on-site biological conversion of dissolved methane into electricity or value-added biochemicals as direct energy sources or energy-compensating substances. A comparative assessment of these technologies in the three categories is presented based on methane treating efficiency, energy-production potential, applicability, and scalability. Finally, current research needs and future perspectives are highlighted to advance the future development of an economically and technically sustainable methane-management technology.

Anaerobic membrane bioreactors for wastewater treatment: Challenges and opportunities

Anaerobic membrane bioreactors (AnMBRs) have become a new mature technology and entered into the wastewater market, but there are several challenges to be addressed for wide applications. In this review, we discuss challenges and potentials of AnMBRs focusing on wastewater treatment. Nitrogen and dissolved methane control, membrane fouling and its control, and membrane associated cost including energy consumption are main bottlenecks to facilitating AnMBR application in wastewater treatment. Accumulation of dissolved methane in AnMBR permeate decreases the benefit of methane energy and contributes to methane gas emissions to atmosphere. Separate control units for nitrogen and dissolved methane add system complexity and increase capital and operating and maintenance (O & M) costs in AnMBR-centered wastewater treatment. Alternatively, methane-based denitrification can be an ideal nitrogen control process due to simultaneous removal of nitrogen and dissolved methane. Membrane fouling and energy associated with membrane fouling control are major limitations, in addition to membrane cost. More efforts are required to decrease capital and O & M costs associated with the control of dissolved methane nitrogen and membrane fouling to facilitate AnMBRs for wastewater treatment. PRACTITIONER POINTS: AnMBRs can accelerate anaerobic wastewater treatment including dilute wastewater. Nitrogen and dissolved methane control is detrimental for AnMBR application to wastewater treatment. Membrane biofilm reactors using gas-permeable membranes are suitable for simultaneous nitrogen and dissolved methane control. High capital and O & M costs from membranes are a major bottleneck to wide application of AnMBRs. Dynamic membranes could be an option to reduce capital and O & M costs for AnMBRs.

Simultaneous enhancement of nitrate removal flux and methane utilization efficiency in MBfR for aerobic methane oxidation coupled to denitrification by using an innovative scalable double-layer membrane

Endevours on the enhancement of nitrate removal efficiency during methane oxidation coupled with denitrification (AME-D) has always overlooked the role of membrane employed. It would be highly beneficial to enrich the biomass content and to manage biofilm on the membrane, in the utilization of methane and denitrification. In this study, an innovative and scalable double-layer membrane (DLM) was designed and prepared for a membrane biofilm reactor (MBfR), to simultaneously enhance nitrate removal flux and methane utilization efficiency during aerobic methane oxidation coupled with the denitrification (AME-D) process. The DLM allowed quick bacterial attachment and biomass accumulation for biofilm growth, which would be then self-regulated for well distribution of functional microbes on/within the DLM. Upon a high biofilm density of over 70 g-VSS m^-2 achieved on the DLM, the methane utilization efficiency of the MBfR was enhanced significantly to over 1.3 times than the control MBfR with conventional polypropylene membrane. The MBfR employed DLM also demonstrated the maximum nitrate removal flux of 740 mg-NO₃^--N m^-2 d^-1 that was approximately 1.64 times of that in control MBfR at continuous-mode operation. This DLM indeed favored the enrichment of Type II aerobic methanotrophs of Methylocystaceae, and methanol-utilization denitrifiers of Rhodocyclaceae that preferentially utilize methanol as the cross-feeding intermediates to promote the methane utilization efficiency, and thus to enhance the nitrate removal flux. These results raised from new designed DLM confirmed the importance of membrane surface properties on the effectiveness of MBfR, and offered great potential to address challenging problems of MBfRs during engineering application.

Biotransformation of Methane and Carbon Dioxide Into High-Value Products by Methanotrophs: Current State of Art and Future Prospects

Conventional chemical methods to transform methane and carbon dioxide into useful chemicals are plagued by the requirement for extreme operating conditions and expensive catalysts. Exploitation of microorganisms as biocatalysts is an attractive alternative to sequester these C1 compounds and convert them into value-added chemicals through their inherent metabolic pathways. Microbial biocatalysts are advantageous over chemical processes as they require mild-operating conditions and do not release any toxic by-products. Methanotrophs are potential cell-factories for synthesizing a wide range of high-value products via utilizing methane as the sole source of carbon and energy, and hence, serve as excellent candidate for methane sequestration. Besides, methanotrophs are capable of capturing carbon dioxide and enzymatically hydrogenating it into methanol, and hence qualify to be suitable candidates for carbon dioxide sequestration. However, large-scale production of value-added products from methanotrophs still presents an overwhelming challenge, due to gas-liquid mass transfer limitations, low solubility of gases in liquid medium and low titer of products. This requires design and engineering of efficient reactors for scale-up of the process. The present review offers an overview of the metabolic architecture of methanotrophs and the range of product portfolio they can offer. Special emphasis is given on methanol biosynthesis as a potential biofuel molecule, through utilization of methane and alternate pathway of carbon dioxide sequestration. In view of the gas-liquid mass transfer and low solubility of gases, the key rate-limiting step in gas fermentation, emphasis is given toward reactor design consideration essential to achieve better process performance.

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.

Effects of oxygen tension on the microbial community and functional gene expression of aerobic methane oxidation coupled to denitrification systems

Aerobic CH₄ oxidation coupled to denitrification (AME-D) can not only mitigate the emission of greenhouse gas (e.g., CH₄) to the atmosphere, but also reduce NO₃^- and/or NO₂^- and alleviate nitrogen pollution. The effects of O₂ tension on the community and functional gene expression of methanotrophs and denitrifiers were investigated in this study. Although higher CH₄ oxidation occurred in the AME-D system with an initial O₂ concentration of 21% (i.e., the O₂-sufficient condition), more NO₃^--N was removed at the initial O₂ concentration of 10% (i.e., the O₂-limited environment). Type I methanotrophs, including Methylocaldum, Methylobacter, Methylococcus, Methylomonas, and Methylomicrobium, and type II methanotrophs, including Methylocystis and Methylosinus, dominated in the AME-D systems. Compared with type II methanotrophs, type I methanotrophs were more abundant in the AME-D systems. Proteobacteria and Actinobacteria were the main denitrifiers in the AME-D systems, and their compositions varied with the O₂ tension. Quantitative PCR of the pmoA, nirS, and 16S rRNA genes showed that methanotrophs and denitrifiers were the main microorganisms in the AME-D systems, accounting for 46.4% and 24.1% in the O₂-limited environment, respectively. However, the relative transcripts of the functional genes including pmoA, mmoX, nirK, nirS, and norZ were all less than 1%, especially the functional genes involved in denitrification under the O₂-sufficient condition, likely due to the majority of the denitrifiers being dormant or even nonviable. These findings indicated that an optimal O₂ concentration should be used to optimize the activity and functional gene expression of aerobic methanotrophs and denitrifiers in AME-D systems.