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

Vertical distribution of Candidatus Methylomirabilis and Methanoperedens in agricultural soils

Candidatus Methylomirabilis-related bacteria conduct anaerobic oxidation of methane (AOM) coupling with NO2- reduction, and Candidatus Methanoperedens-related archaea perform AOM coupling with reduction of diverse electron acceptors, including NO3-, Fe (III), Mn (IV) and SO42-. Application of nitrogen fertilization favors the growth of these methanotrophs in agricultural fields. Here, we explored the vertical variations in community structure and abundance of the two groups of methanotrophs in a nitrogen-rich vegetable field via using illumina MiSeq sequencing and quantitative PCR. The retrieved Methylomirabilis-related sequences had 91.12%-97.32% identity to the genomes of known Methylomirabilis species, and Methanoperedens-related sequences showed 85.49%-97.48% identity to the genomes of known Methanoperedens species which are capable of conducting AOM coupling with reduction of NO3- or Fe (III). The Methanoperedens-related archaeal diversity was significantly higher than Methylomirabilis-related bacteria, with totally 74 and 16 operational taxonomic units, respectively. In contrast, no significant difference in abundance between the bacteria (9.19 × 103-3.83 × 105 copies g-1 dry soil) and the archaea (1.55 × 104-3.24 × 105 copies g-1 dry soil) was observed. Furthermore, the abundance of both groups of methanotrophs exhibited a strong vertical variation, which peaked at 30-40 and 20-30 cm layers, respectively. Soil water content and pH were the key factors influencing Methylomirabilis-related bacterial diversity and abundance, respectively. For the Methanoperedens-related archaea, both soil pH and ammonium content contributed significantly to the changes of these archaeal diversity and abundance. Overall, we provide the first insights into the vertical distribution and regulation of Methylomirabilis-related bacteria and Methanoperedens-related archaea in vegetable soils. KEY POINTS: • The archaeal diversity was significantly higher than bacterial. • There was no significant difference in the abundance between bacteria and archaea. • The abundance of bacteria and archaea peaked at 30-40 and 20-30 cm, respectively.

Anaerobic oxidation of methane driven by different electron acceptors: A review

Methane, the most significant reduced form of carbon on Earth, acts as a crucial fuel and greenhouse gas. Globally, microbial methane sinks encompass both aerobic oxidation of methane (AeOM), conducted by oxygen-utilizing methanotrophs, and anaerobic oxidation of methane (AOM), performed by anaerobic methanotrophs employing various alternative electron acceptors. These electron acceptors involved in AOM include sulfate, nitrate/nitrite, humic substances, and diverse metal oxides. The known anaerobic methanotrophic pathways comprise the internal aerobic oxidation pathway found in NC10 bacteria and the reverse methanogenesis pathway utilized by anaerobic methanotrophic archaea (ANME). Diverse anaerobic methanotrophs can perform AOM independently or in cooperation with symbiotic partners through several extracellular electron transfer (EET) pathways. AOM has been documented in various environments, including seafloor methane seepages, coastal wetlands, freshwater lakes, soils, and even extreme environments like hydrothermal vents. The environmental activities of AOM processes, driven by different electron acceptors, primarily depend on the energy yields, availability of electron acceptors, and environmental adaptability of methanotrophs. It has been suggested that different electron acceptors driving AOM may occur across a wider range of habitats than previously recognized. Additionally, it is proposed that methanotrophs have evolved flexible metabolic strategies to adapt to complex environmental conditions. This review primarily focuses on AOM, driven by different electron acceptors, discussing the associated reaction mechanisms and the habitats where these processes are active. Furthermore, it emphasizes the pivotal role of AOM in mitigating methane emissions.

Microplastics promote methane emission in estuarine and coastal wetlands

Increasing microplastic (MP) pollution poses significant threats to estuarine and coastal ecosystems. However, the effects of MPs on the emission of methane (CH4), a potent greenhouse gas, within these ecosystems and the underlying regulatory mechanisms have not been elucidated. Here, a combination of 13C stable isotope-based method and molecular techniques was applied to investigate how conventional petroleum-based MPs [polyethylene (PE) and polyvinyl chloride (PVC)] and biodegradable MPs [polylactic acid (PLA) and polyadipate/butylene terephthalate (PBAT)] regulate CH4 production and consumption and thus affect CH4 emission dynamics in estuarine and coastal wetlands. Results indicated that both conventional and biodegradable MPs enhanced the emission of CH4 (P < 0.05), with the promoting effect being more significant for biodegradable MPs. However, the mechanisms by which conventional and biodegradable MPs promote CH4 emissions were different. Specifically, conventional MPs stimulated the emission of CH4 by inhibiting the processes of CH4 consumption, but had no significant effect on CH4 production rate. Nevertheless, biodegradable MPs promoted CH4 emissions via accelerating the activities the methanogens while inhibiting the oxidation of CH4, thus resulting in a higher degree of promoting effect on CH4 emissions than conventional MPs. Consistently, quantitative PCR further revealed a significant increase in the abundance of methyl-coenzyme M reductase gene (mcrA) of methanogens under the exposure of biodegradable MPs (P < 0.05), but not conventional MPs. Furthermore, the relative abundance of most genes involved in CH4 oxidation exhibited varying degrees of reduction after exposure to all types of MPs, based on metagenomics data. This study reveals the effects of MPs on CH4 emissions in estuarine and coastal ecosystems and their underlying mechanisms, highlighting that the emerging biodegradable MPs exhibited a greater impact than conventional MPs on promoting CH4 emissions in these globally important ecosystems, thereby accelerating global climate change.

Simultaneous methane mitigation and nitrogen removal by denitrifying anaerobic methane oxidation in lake sediments

Methane (CH4) is a potent greenhouse gas, with lake ecosystems significantly contributing to its global emissions. Denitrifying anaerobic methane oxidation (DAMO) process, mediated by NC10 bacteria and ANME-2d archaea, links global carbon and nitrogen cycles. However, their potential roles in mitigating methane emissions and removing nitrogen from lake ecosystems remain unclear. This study explored the spatial variations in activities of nitrite- and nitrate-DAMO and their functional microbes in Changdanghu Lake sediments (Jiangsu Province, China). The results showed that although the average abundance of ANME-2d archaea (5.0 × 106 copies g-1) was significantly higher than that of NC10 bacteria (2.1 × 106 copies g-1), the average potential rates of nitrite-DAMO (4.59 nmol 13CO2 g-1 d-1) and nitrate-DAMO (5.01 nmol 13CO2 g-1 d-1) showed no significant difference across all sampling sites. It is estimated that nitrite- and nitrate-DAMO consumed approximately 6.46 and 7.05 mg CH4 m-2 d-1, respectively, which accordingly achieved 15.07-24.95 mg m-2 d-1 nitrogen removal from the studied lake sediments. Statistical analyses found that nitrite- and nitrate-DAMO activities were both significantly related to sediment nitrate contents and ANME-2d archaeal abundance. In addition, NC10 bacterial and ANME-2d archaeal community compositions showed significant correlations with sediment organic carbon content and water depth. Overall, this study underscores the dual roles of nitrite- and nitrate-DAMO processes in CH4 mitigation and nitrogen elimination and their key environmental impact factors (sediment organic carbon and inorganic nitrogen contents, and water depth) in shallow lake, enhancing the understanding of carbon and nitrogen cycles in freshwater aquatic ecosystems.

Seasonal and anthropogenic influences on bacterioplankton communities: ecological impacts in the coastal waters of Qinhuangdao, Northern China

Marine bacterioplankton play a crucial role in the cycling of carbon, nitrogen, and phosphorus in coastal waters. And the impact of environmental factors on bacterial community structure and ecological functions is a dynamic ongoing process. To systematically assess the relationship between environmental changes and bacterioplankton communities, this study delved into the spatiotemporal distribution and predicted metabolic characteristics of bacterioplankton communities at two estuarine beaches in Northern China. Coastal water samples were collected regularly in spring, summer, and autumn, and were analyzed in combination with environmental parameters and bacterioplankton community. Results indicated significant seasonal variations in bacterioplankton communities as Bacteroidetes and Actinobacteria were enriched in spring, Cyanobacteria proliferated in summer. While Pseudomonadota and microorganisms associated with organic matter decomposition prevailed in autumn, closely linked to seasonal variation of temperature, light and nutrients such as nitrogen and phosphorus. Particularly in summer, increased tourism activities and riverine inputs significantly raised nutrient levels, promoting the proliferation of specific photosynthetic microorganisms, potentially linked to the occurrence of phytoplankton blooms. Spearman correlation analysis further revealed significant correlations between bacterioplankton communities and environmental factors such as salinity, chlorophyll a, and total dissolved phosphorus (TDP). Additionally, the metabolic features of the spring bacterioplankton community were primarily characterized by enhanced activities in the prokaryotic carbon fixation pathways, reflecting rapid adaptation to increased light and temperature, as well as significant contributions to primary productivity. In summer, the bacterial communities were involved in enhanced glycolysis and biosynthetic pathways, reflecting high energy metabolism and responses to increased light and biomass. In autumn, microorganisms adapted to the accelerated decomposition of organic matter and the seasonal changes in environmental conditions through enhanced amino acid metabolism and material cycling pathways. These findings demonstrate that seasonal changes and human activities significantly influence the structure and function of bacterioplankton communities by altering nutrient dynamics and physical environmental conditions. This study provides important scientific insights into the marine biological responses under global change.

Photo-methanification of aquatic dissolved organic matters with different origins under aerobic conditions: Non-negligible role of hydroxyl radicals

Lingering inconsistencies in the global methane (CH4) budget and ambiguity in CH4 sources and sinks triggered efforts to identify new CH4 formation pathways in natural ecosystems. Herein, we reported a novel mechanism of light-induced generation of hydroxyl radicals (•OH) that drove the production of CH4 from aquatic dissolved organic matters (DOMs) under ambient conditions. A total of five DOM samples with different origins were applied to examine their potential in photo-methanification production under aerobic conditions, presenting a wide range of CH4 production rates from 3.57 × 10-3 to 5.90 × 10-2 nmol CH4 mg-C-1 h-1. Experiments of •OH generator and scavenger indicated that the contribution of •OH to photo-methanificaiton among different DOM samples reached about 4∼42 %. In addition, Fourier transform infrared spectroscopy and Fourier transform ion cyclotron resonance mass spectrometry showed that the carbohydrate- and lipid-like substances containing nitrogen-bonded methyl groups, methyl ester, acetyl groups, and ketones, were the potential precursors for light-induced CH4 production. Based on the experimental results and simulated calculations, the contribution of photo-methanification of aquatic DOMs to the diffusive CH4 flux across the water-air interface in a typical eutrophic shallow lake (e.g., Lake Chaohu) ranged from 0.1 % to 18.3 %. This study provides a new perspective on the pathways of CH4 formation in aquatic ecosystems and a deeper understanding on the sources and sinks of global CH4.

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.

Anaerobic oxidation of methane in landfill and adjacent groundwater environments: Occurrence, mechanisms, and potential applications

Landfills remain the predominant means of solid waste management worldwide. Widespread distribution and significant stockpiles of waste in landfills make them a significant source of methane emissions, exacerbating climate change. Anaerobic oxidation of methane (AOM) has been shown to play a critical role in mitigating methane emissions on a global scale. The rich methane and electron acceptor environment in landfills provide the necessary reaction conditions for AOM, making it a potentially low-cost and effective strategy for reducing methane emissions in landfills. However, compared to other anaerobic habitats, research on AOM in landfill environments is scarce, and there is a lack of analysis on the potential application of AOM in different zones of landfills. Therefore, this review summarizes the existing knowledge on AOM and its occurrence in landfills, analyzes the possibility of AOM occurrence in different zones of landfills, discusses its potential applications, and explores the challenges and future research directions for AOM in landfill management. The identification of research gaps and future directions outlined in this review encourages further investigation and advancement in the field of AOM, paving the way for more effective waste stabilization, greenhouse gas reduction, and pollutant mitigation strategies in landfills.

Different responses of marine microalgae Phaeodactylum tricornutum upon exposures to WAF and CEWAF of crude oil: A case study coupled with stable isotopic signatures

Increasing use of chemical dispersants for oil spills highlights the need to understand their adverse effects on marine microalgae and nutrient assimilation because the toxic components of crude oil can be more bioavailable. We employed the crude oil water-accommodated fraction (WAF) and chemically enhanced WAF (CEWAF) to compare different responses in marine microalgae (Phaeodactylum tricornutum) coupled with stable isotopic signatures. The concentration and proportion of high-molecular-weight polycyclic aromatic hydrocarbons (HMW PAHs), which are key toxic components in crude oil, increased after dispersant addition. CEWAF exposure caused higher percent growth inhibition and a lower chlorophyll-a level of microalgae than those after WAF exposure. Compared with WAF exposure, CEWAF led to an enhancement in the self-defense mechanism of P. tricornutum, accompanied by an increased content of extracellular polymeric substances. 13C-depletion and carbon assimilation were altered in P. tricornutum, suggesting more HMW PAHs could be utilized as carbon sources by microalgae under CEWAF. CEWAF had no significant effects on the isotopic fractionation or assimilation of nitrogen in P. tricornutum. Our study unveiled the impact on the growth, physiological response, and nutrient assimilation of microalgae upon WAF and CEWAF exposures. Our data provide new insights into the ecological effects of dispersant applications for coastal oil spills.

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.

Spatial heterogeneity of sedimentary organic matter sources in the Yangtze River estuary: Implications from fatty acid biomarkers

This study investigated the sources of sedimentary organic matter (OM) in the Yangtze River estuary (YRE), using multiple biomarkers. The results of stable carbon isotope (δ13C) and total organic carbon to nitrogen ratio (TOC/TN) suggests the contribution of marine-derived OM significantly increased seawards, while fatty acid (FA) composition provides more specific information on OM sources. In total, 30 components of FAs were identified at the studied 17 sites, which mainly composed of phytoplankton FA, followed by ubiquitous FA and bacterial FA, while terrestrial FA contributed less to the total FAs. Under the strong impacts of the large physicochemical gradients in the YRE, TOC, TN and FA components showed higher concentrations in the estuary mixing zone (especially within the turbidity maximum zone), attributing to their strong binding with OM-enriched fine particles. The spatial heterogeneity of sedimentary OM sources was highly impacted by salinity and Chl-a, as well as bacteria-mediated OM degradation.

Role of n-DAMO in Mitigating Methane Emissions from Intertidal Wetlands Is Regulated by Saltmarsh Vegetations

Coastal wetlands are hotspots for methane (CH4) production, reducing their potential for global warming mitigation. Nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) plays a crucial role in bridging carbon and nitrogen cycles, contributing significantly to CH4 consumption. However, the role of n-DAMO in reducing CH4 emissions in coastal wetlands is poorly understood. Here, the ecological functions of the n-DAMO process in different saltmarsh vegetation habitats as well as bare mudflats were quantified, and the underlying microbial mechanisms were explored. Results showed that n-DAMO rates were significantly higher in vegetated habitats (Scirpus mariqueter and Spartina alterniflora) than those in bare mudflats (P < 0.05), leading to an enhanced contribution to CH4 consumption. Compared with other habitats, the contribution of n-DAMO to the total anaerobic CH4 oxidation was significantly lower in the Phragmites australis wetland (15.0%), where the anaerobic CH4 oxidation was primarily driven by ferric iron (Fe3+). Genetic and statistical analyses suggested that the different roles of n-DAMO in various saltmarsh wetlands may be related to divergent n-DAMO microbial communities as well as environmental parameters such as sediment pH and total organic carbon. This study provides an important scientific basis for a more accurate estimation of the role of coastal wetlands in mitigating climate change.

Anaerobic oxidation of methane in terrestrial wetlands: The rate, identity and metabolism

The recent discovery of anaerobic oxidation of methane (AOM) in freshwater ecosystems has caused a great interest in "cryptic methane cycle" in terrestrial ecosystems. Anaerobic methanotrophs appears widespread in wetland ecosystems, yet, the scope and mechanism of AOM in natural wetlands remain poorly understood. In this paper, we review the recent progress regarding the potential of AOM, the diversity and distribution, and the metabolism of anaerobic methanotrophs in wetland ecosystems. The potential of AOM determined through laboratory incubation or in situ isotopic labeling ranges from 1.4 to 704.0 nmol CH4·g-1 dry soil·d-1. It appears that the availability of electron acceptors is critical in driving different AOM in wetland soils. The environmental temperature and salinity exert a significant influence on AOM activity. Reversal methanogenesis and extracellular electron transfer are likely involved in the AOM process. In addition to anaerobic methanotrophic archaea, the direct involvement of methanogens in AOM is also probable. This review presented an overview of the rate, identity, and metabolisms to unravel the biogeochemical puzzle of AOM in wetland soils.

Effects of microplastics on denitrification and associated N2O emission in estuarine and coastal sediments: insights from interactions between sulfate reducers and denitrifiers

Global estuarine and coastal zones are facing severe microplastics (MPs) pollution. Sulfate reducers (SRB) and denitrifiers (DNB) are two key functional microorganisms in these zones, exhibiting intricate interactions. However, whether and how MPs modulate the interactions between SRB and DNB, with implications for denitrification and associated N2O emissions, remains poorly understood. Here, we simultaneously investigated the spatial response patterns of SRB-DNB interactions and denitrification and associated N2O emissions to different MPs exposure along an estuarine gradient in the Yangtze Estuary. Spatial responses of denitrification to polyvinyl chloride (PVC) and polyadipate/butylene terephthalate (PBAT) MPs exposure were heterogeneous, while those of N2O emissions were not. Gradient-boosted regression tree and multiple regression model analyses showed that sulfide, followed by nitrate (NO3-), controlled the response patterns of denitrification to MPs exposure. Further mechanistic investigation revealed that exposure to MPs resulted in a competitive and toxic (sulfide accumulation) inhibition of SRB on DNB, ultimately inhibiting denitrification at upstream zones with high sulfide but low NO3- levels. Conversely, MPs exposure induced a competitive inhibition of DNB on SRB, generally promoting denitrification at downstream zones with low sulfide but high NO3- levels. These findings advance the current understanding of the impacts of MPs on nitrogen cycle in estuarine and coastal zones, and provide a novel insight for future studies exploring the response of biogeochemical cycles to MPs in various ecosystems.

Effects of salinity on methane emissions and methanogenic archaeal communities in different habitat of saline-alkali wetlands

The increase in temperature caused by global climate change has promoted the salinization of wetlands. Inland saline-alkaline wetlands have an environment of over-humidity and shallow water and are hot spots for CH4 emissions. However, there are few reports on the effect of salinity on CH4 emissions in inland saline-alkaline wetlands. This study conducted simulation experiments of increased salinity to investigate the impact of salinity, habitat, and their interactions on CH4 emissions, as well as to examine the response of methanogenic archaea to salinity. Overall, salinity inhibited CH4 emissions. But there were different responses in the three habitat soils. Salinity decreased the relative abundance of methanogenic archaea and changed the community structure. In addition, salinity changed soil pH and dissolved organic carbon (DOC) and ammonium (NH4+) concentrations, which were significantly correlated with methanogenic archaea. Our study showed that salinity changed the soil physicochemical properties and characteristics of the methanogenic archaeal community, affecting CH4 emissions.

Mediative Mechanism of Freezing/Thawing on Greenhouse Gas Emissions in an Inland Saline-Alkaline Wetland: a Metagenomic Analysis

Inland saline-alkaline wetlands distributed in the mid-high latitude have repeatedly experienced freezing and thawing. However, the response of greenhouse gas (GHG) emission and microbially-mediated carbon and nitrogen cycle to freezing and thawing remains unclear. We monitored the GHG flux in an inland saline-alkaline wetland and found that, compared with the growth period, the average CO2 flux decreased from 171.99 to 76.61-80.71 mg/(m2‧h), the average CH4 flux decreased from 10.72 to 1.96-3.94 mg/(m2‧h), and the average N2O flux decreased from 56.17 to - 27.14 to - 20.70 μg/(m2‧h). Freezing and thawing significantly decreased the relative abundance of functional genes involved in carbon and nitrogen cycles. The aceticlastic methanogenic pathway was the main methanogenic pathway, whereas the Candidatus Methylomirabilis oxyfera was the most abundant methane oxidizer in the wetland. Ammonia-oxidizing archaea and denitrifier belonging to proteobacteria was the major microbial N2O source, while bacteria within clade II nosZ was the major microbial N2O sink. Freezing and thawing reduced the relative abundance of these genes, leading to a decrease in GHG flux.

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.

Spatio-temporal variations of activity of nitrate-driven anaerobic oxidation of methane and community structure of Candidatus Methanoperedens-like archaea in sediment of Wuxijiang river

Nitrate-driven anaerobic oxidation of methane (AOM), catalyzing by Candidatus Methanoperedens-like archaea, is a new addition in the global CH₄ cycle. This AOM process acts as a novel pathway for CH₄ emission reduction in freshwater aquatic ecosystems; however, its quantitative importance and regulatory factors in riverine ecosystems are nearly unknown. Here, we examined the spatio-temporal changes of the communities of Methanoperedens-like archaea and nitrate-driven AOM activity in sediment of Wuxijiang River, a mountainous river in China. These archaeal community composition varied significantly among reaches (upper, middle, and lower reaches) and between seasons (winter and summer), but their mcrA gene diversity showed no significant spatial or temporal variations. The copy numbers of Methanoperedens-like archaeal mcrA genes were 1.32 × 10⁵-2.47 × 10⁷ copies g^-1 (dry weight), and the activity of nitrate-driven AOM was 0.25-1.73 nmol CH₄ g^-1 (dry weight) d^-1, which could potentially reduce 10.3% of CH₄ emissions from rivers. Significant spatio-temporal variations of mcrA gene abundance and nitrate-driven AOM activity were found. Both the gene abundance and activity increased significantly from upper to lower reaches in both seasons, and were significantly higher in sediment collected in summer than in winter. In addition, the variations of Methanoperedens-like archaeal communities and nitrate-driven AOM activity were largely impacted by the sediment temperature, NH₄⁺ and organic carbon contents. Taken together, both time and space scales need to be considered for better evaluating the quantitative importance of nitrate-driven AOM in reducing CH₄ emissions from riverine ecosystems.

Role and regulation of anaerobic methane oxidation catalyzed by NC10 bacteria and ANME-2d archaea in various ecosystems

Freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands are recognized as important sources of atmospheric methane (CH₄). Currently, increasing evidence shows the potential importance of the anaerobic oxidation of methane (AOM) mediated by NC10 bacteria and a novel cluster of anaerobic methanotrophic archaea (ANME)-ANME-2d in mitigating CH₄ emissions from different ecosystems. To better understand the role of NC10 bacteria and ANME-2d archaea in CH₄ emission reduction, the current review systematically summarizes different AOM processes and the functional microorganisms involved in freshwater wetlands, paddy fields, inland aquatic ecosystems and coastal wetlands. NC10 bacteria are widely present in these ecosystems, and the nitrite-dependent AOM is identified as an important CH₄ sink and induces nitrogen loss. Nitrite- and nitrate-dependent AOM co-occur in the environment, and they are mainly affected by soil/sediment inorganic nitrogen and organic carbon contents. Furthermore, salinity is another key factor regulating the two AOM processes in coastal wetlands. In addition, ANME-2d archaea have the great potential to couple AOM to the reduction of iron (III), manganese (IV), sulfate, and even humics in different ecosystems. However, the study on the environmental distribution of ANME-2d archaea and their role in CH₄ mitigation in environments is insufficient. In this study, we propose several directions for future research on the different AOM processes and respective functional microorganisms.

Detection and Quantification of Candidatus Methanoperedens-Like Archaea in Freshwater Wetland Soils

Candidatus Methanoperedens-like archaea, which can use multiple electron acceptors (nitrate, iron, manganese, and sulfate) for anaerobic methane oxidation, could play an important role in reducing methane emissions from freshwater wetlands. Currently, very little is known about the distribution and community composition of Methanoperedens-like archaea in freshwater wetlands, particularly based on their alpha subunit of methyl-coenzyme M reductase (mcrA) genes. Here, the community composition, diversity, and abundance of Methanoperedens-like archaea were investigated in a freshwater wetland through high-throughput sequencing and quantitative PCR on their mcrA genes. A large number of Methanoperedens-like mcrA gene sequences (119,250) were recovered, and a total of 31 operational taxonomic units (OTUs) were generated based on 95% sequence similarity cut-off. The majority of Methanoperedens-like sequences can be grouped into three distinct clusters that were closely associated with the known Methanoperedens species which can couple anaerobic methane oxidation to nitrate or iron reduction. The community composition of Methanoperedens-like archaea differed significantly among different sampling sites, and their mcrA gene abundance was 1.49 × 10⁶ ~ 4.62 × 10⁶ copies g^-1 dry soil in the examined wetland. In addition, the community composition of Methanoperedens-like archaea was significantly affected by the soil water content, and the archaeal abundance was significantly positively correlated with the water content. Our results suggest that the mcrA gene is a good biomarker for detection and quantification of Methanoperedens-like archaea, and provide new insights into the distribution and environmental regulation of these archaea in freshwater wetlands.

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.

Soil nitrogen substances and denitrifying communities regulate the anaerobic oxidation of methane in wetlands of Yellow River Delta, China

Anaerobic oxidation of methane (AOM) in wetland soils is widely recognized as a key sink for the greenhouse gas methane (CH₄). The occurrence of this reaction is influenced by several factors, but the exact process and related mechanism of this reaction remain unclear, due to the complex interactions between multiple influencing factors in nature. Therefore, we investigated how environmental and microbial factors affect AOM in wetlands using laboratory incubation methods combined with molecular biology techniques. The results showed that wetland AOM was associated with a variety of environmental factors and microbial factors. The environmental factors include such as vegetation, depth, hydrogen ion concentration (pH), oxidation-reduction potential (ORP), electrical conductivity (EC), total nitrogen (TN), nitrate (NO₃^-), sulfate (SO₄^2-), and nitrous oxide (N₂O) flux, among them, soil N substances (TN, NO₃^-, N₂O) have essential regulatory roles in the AOM process, while NO₃^- and N₂O may be the key electron acceptors driving the AOM process under the coexistence of multiple electron acceptors. Moreover, denitrification communities (narG, nirS, nirK, nosZI, nosZII) and anaerobic methanotrophic (ANME-2d) were identified as important functional microorganisms affecting the AOM process, which is largely regulated by the former. In the environmental context of growing global anthropogenic N inputs to wetlands, these findings imply that N cycle-mediated AOM processes are a more important CH₄ sink for controlling global climate change. This studying contributes to the knowledge and prediction of wetland CH₄ biogeochemical cycling and provides a microbial ecology viewpoint on the AOM response to global environmental change.

Nitrate-dependent anaerobic methane oxidation (N-DAMO) as a bioremediation strategy for waters affected by agricultural runoff

Agricultural drainage ditches are subjected to high anthropogenic nitrogen input, leading to eutrophication and greenhouse gas emissions. Nitrate-dependent anaerobic methane oxidation (N-DAMO) could be a promising remediation strategy to remove methane (CH4) and nitrate (NO3-) simultaneously. Therefore, we aimed to evaluate the potential of N-DAMO to remove excess NO3- and decrease CH4 release from agricultural drainage ditches. Microcosm experiments were conducted using sediment and surface water collected from three different sites: a sandy-clay ditch (SCD), a freshwater-fed peatland ditch (FPD), and a brackish peatland ditch (BPD). The microcosms were inoculated with an N-DAMO enrichment culture dominated by Candidatus Methanoperedens and Candidatus Methylomirabilis and supplemented with 13CH4 and 15NO3-. A significant decrease in CH4 and NO3- concentration was only observed in the BPD sediment. In freshwater sediments (FPD and SCD), the effect of N-DAMO inoculation on CH4 and NO3- removal was negligible, likely because N-DAMO microorganisms were outcompeted by heterotrophic denitrifiers consuming NO3- much faster. Overall, our results suggest that bioaugmentation with N-DAMO might be a potential strategy for decreasing NO3- concentrations and CH4 emission in brackish ecosystems with increasing agricultural activities where the native microbial community is incapable of efficient denitrification.

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.

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.

Quinolone antibiotics enhance denitrifying anaerobic methane oxidation in Wetland sediments: Counterintuitive results

Denitrifying anaerobic methane oxidation (DAMO) plays an important role in the element cycle of wetlands. In recent years, the content of antibiotics in wetlands has gradually increased due to human activities. However, the impact of antibiotics on the ecological function of DAMO remains unclear. Here we studied the influence of three high-content quinolone antibiotics (QNs) on DAMO in the sediments of the Baiyangdian Wetland. The results show that QNs can significantly promote the potential DAMO rates. Moreover, the enhancement of potential DAMO rates is positively correlated with the dosage of QNs. This promotion effect of QNs on nitrate-DAMO can be attributed to the hormesis phenomenon or their inhibition of substrate competitors. As antibacterial agents, QNs inhibit nitrite-DAMO conducted by bacteria, but greatly promote nitrate-DAMO conducted by archaea. These results suggest that the short-term effect of QNs on DAMO in wetlands is promotion rather than inhibition.

Response of potential activity, abundance and community composition of nitrite-dependent anaerobic methanotrophs to long-term fertilization in paddy soils

The process of nitrite-dependent anaerobic methane oxidation (n-damo) catalysed by Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria is a novel pathway in regulating methane (CH₄ ) emissions from paddy fields. Nitrogen fertilization is essential to improve rice yields and soil fertility; however, its effect on the n-damo process is largely unknown. Here, the potential n-damo activity, abundance and community composition of M. oxyfera-like bacteria were investigated in paddy fields under three long-term (32 years) fertilization treatments, i.e. unfertilized control (CK), chemical fertilization (NPK) and straw incorporation with chemical fertilization (SNPK). Relative to the CK, both NPK and SNPK treatments significantly (p < 0.05) increased the potential n-damo activity (88%-110%) and the abundance (52%-105%) of M. oxyfera-like bacteria. The variation of soil organic carbon (OrgC) content and inorganic nitrogen content caused by the input of chemical fertilizers and straw returning were identified as the key factors affecting the potential n-damo activity and the abundance of M. oxyfera-like bacteria. However, the community composition and diversity of M. oxyfera-like bacteria did not change significantly by the input of fertilizers. Overall, our results provide the first evidence that long-term fertilization greatly stimulates the n-damo process, indicating its active role in controlling CH₄ emissions from paddy fields.

Response of nitrite-dependent anaerobic methanotrophs to elevated atmospheric CO2 concentration in paddy fields

Nitrite-dependent anaerobic methane oxidation (n-damo) catalyzed by Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria is a new pathway for the regulation of methane emissions from paddy fields. Elevated atmospheric CO₂ concentrations (e[CO₂]) can indirectly affect the structure and function of microbial communities. However, the response of M. oxyfera-like bacteria to e[CO₂] is currently unknown. Here, we investigated the effect of e[CO₂] (ambient CO₂ + 200 ppm) on community composition, abundance, and activity of M. oxyfera-like bacteria at different depths (0-5, 5-10, and 10-20 cm) in paddy fields across multiple rice growth stages (tillering, jointing, and flowering). High-throughput sequencing showed that e[CO₂] had no significant effect on the community composition of M. oxyfera-like bacteria. However, quantitative PCR suggested that the 16S rRNA gene abundance of M. oxyfera-like bacteria increased significantly in soil under e[CO₂], particularly at the tillering stage. Furthermore, ¹³CH₄ tracer experiments showed potential n-damo activity of 0.31-8.91 nmol CO₂ g^-1 (dry soil) d^-1. E[CO₂] significantly stimulated n-damo activity, especially at the jointing and flowering stages. The n-damo activity and abundance of M. oxyfera-like bacteria increased by an average of 90.9% and 50.0%, respectively, under e[CO₂]. Correlation analysis showed that the increase in soil dissolved organic carbon content caused by e[CO₂] had significant effects on the activity and abundance of M. oxyfera-like bacteria. Overall, this study provides the first evidence for a positive response of M. oxyfera-like bacteria to e[CO₂], which may help reduce methane emissions from paddy fields under future climate change conditions.

Mitigation of Eutrophication in a Shallow Lake: The Influences of Submerged Macrophytes on Phosphorus and Bacterial Community Structure in Sediments

Remediating water eutrophication is critical for maintaining healthy and sustainable development of lakes. The aim of this study was to explore the seasonal variation in phosphorus (P) speciation and bacterial community structure in sediments of Qin Lake (Taizhou, Jiangsu Province, China) associated with the growth of submerged macrophyte Vallisneria natans. The differences in sediment bacterial diversity and community structure between V. natans growing and control areas were analyzed over a period of one year. The results showed that V. natans growth reduced the total P and organic matter contents of the sediments and increased the bioavailable iron (Fe) and Fe-bound P contents. The α-diversity of sediment bacteria was significantly higher in the presence of V. natans than in the controls during the vigorous plant growth stage. In the presence of V. natans, there was a higher relative abundance of Proteobacteria and lower relative abundances of Chloroflexi and Acidobacteria. The Fe(II) content in the sediment had a larger influence on the spatial distribution of bacterial communities than sediment Fe-bound P, organic matter, and Fe(II) contents. V. natans growth could reshape sediment bacterial community structure in the shallow lake, which, in turn, enhanced P immobilization in the sediments and thereby improved the water quality.