New molecular method to detect denitrifying anaerobic methane oxidation bacteria from different environmental niches

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.

Towards an integrated view on microbial CH4, N2O and N2 cycles in brackish coastal marsh soils: A comparative analysis of two sites

Coastal ecosystems, facing threats from global change and human activities like excessive nutrients, undergo alterations impacting their function and appearance. This study explores the intertwined microbial cycles of carbon (C) and nitrogen (N), encompassing methane (CH4), nitrous oxide (N2O), and nitrogen gas (N2) fluxes, to determine nutrient transformation processes between the soil-plant-atmosphere continuum in the coastal ecosystems with brackish water. Water salinity negatively impacted denitrification, bacterial nitrification, N fixation, and n-DAMO processes, but did not significantly affect archaeal nitrification, COMAMMOX, DNRA, and ANAMMOX processes in the N cycle. Plant species age and biomass influenced CH4 and N2O emissions. The highest CH4 emissions were from old Spartina and mixed Spartina and Scirpus sites, while Phragmites sites emitted the most N2O. Nitrification and incomplete denitrification mainly governed N2O emissions depending on the environmental conditions and plants. The higher genetic potential of ANAMMOX reduced excessive N by converting it to N2 in the sites with higher average temperatures. The presence of plants led to a decrease in the N fixers' abundance. Plant biomass negatively affected methanogenetic mcrA genes. Microbes involved in n-DAMO processes helped mitigate CH4 emissions. Over 93 % of the total climate forcing came from CH4 emissions, except for the Chinese bare site where the climate forcing was negative, and for Phragmites sites, where almost 60 % of the climate forcing came from N2O emissions. Our findings indicate that nutrient cycles, CH4, and N2O fluxes in soils are context-dependent and influenced by environmental factors and vegetation. This underscores the need for empirical analysis of both C and N cycles at various levels (soil-plant-atmosphere) to understand how habitats or plants affect nutrient cycles and greenhouse gas emissions.

How methanotrophs respond to pH: A review of ecophysiology

Varying pH globally affects terrestrial microbial communities and biochemical cycles. Methanotrophs effectively mitigate methane fluxes in terrestrial habitats. Many methanotrophs grow optimally at neutral pH. However, recent discoveries show that methanotrophs grow in strongly acidic and alkaline environments. Here, we summarize the existing knowledge on the ecophysiology of methanotrophs under different pH conditions. The distribution pattern of diverse subgroups is described with respect to their relationship with pH. In addition, their responses to pH stress, consisting of structure-function traits and substrate affinity traits, are reviewed. Furthermore, we propose a putative energy trade-off model aiming at shedding light on the adaptation mechanisms of methanotrophs from a novel perspective. Finally, we take an outlook on methanotrophs' ecophysiology affected by pH, which would offer new insights into the methane cycle and global climate change.

Denitrifying anaerobic methane-oxidizing bacteria in river networks of the Taihu Basin: Community dynamics and assembly process

Denitrifying anaerobic methane-oxidizing bacteria (DAMO bacteria) plays an important role in reducing methane emissions from river ecosystems. However, the assembly process of their communities underlying different hydrologic seasons remains unclarified. In this study, the dynamics of DAMO bacterial communities in river networks of the Taihu Basin were investigated by amplicon sequencing across wet, normal, and dry seasons followed by multiple statistical analyses. Phylogenetic analysis showed that Group B was the major subgroup of DAMO bacteria and significant dynamics for their communities were observed across different seasons (constrained principal coordinate analysis, p = 0.001). Furthermore, the neutral community model and normalized stochasticity ratio model were applied to reveal the underlying assembly process. Stochastic process and deterministic process dominated the assembly process in wet season and normal season, respectively and similar contributions of deterministic and stochastic processes were observed in dry season. Meanwhile, abundant (relative abundance >0.1%) and rare (relative abundance <0.01%) DAMO bacterial communities were found to be shaped via distinct assembly processes. Deterministic and stochastic processes played a considerable role in shaping abundant DAMO bacterial communities, while deterministic process mainly shaped rare DAMO bacterial communities. Results of this study revealed the dynamics of DAMO bacterial communities in river networks and provided a theoretical basis for further understanding of the assembly process.

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.

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.