Microbiological and environmental significance of metal-dependent anaerobic oxidation of methane

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.

Maximizing pollutant removal and greenhouse gas emission reduction in vertical flow constructed wetlands: an orthogonal experimental approach

Owing to the impact of the effluent C/N from the secondary structures of urban domestic wastewater treatment plants, the denitrification efficiency in constructed wetlands (CWs) is not satisfactory, limiting their widespread application in the deep treatment of urban domestic wastewater. To address this issue, we constructed enhanced CWs and conducted orthogonal experiments to investigate the effects of different factors (C/N, fillers, and plants) on the removal of conventional pollutants and the reduction of greenhouse gas (GHG) emission. The experimental results indicated that a C/N of 8, manganese sand, and calamus achieved the best denitrification efficiencies with removal efficiencies of 85.7%, 95.9%, and 88.6% for TN, NH4+-N, and COD, respectively. In terms of GHG emission reduction, this combination resulted in the lowest global warming potential (176.8 mg/m2·day), with N2O and CH4 emissions of 0.53 and 1.25 mg/m2·day, respectively. Characterization of the fillers revealed the formation of small spherical clusters of phosphates on the surfaces of manganese sand and pyrite and iron oxide crystals on the surface of pyrite. Additionally, the surface Mn (II) content of the manganese sand increased by 8.8%, and the Fe (III)/Fe (II) and SO42-/S2- on pyrite increased by 2.05 and 0.26, respectively, compared to pre-experiment levels. High-throughput sequencing indicated the presence of abundant autotrophic denitrifying bacteria (Sulfuriferula, Sulfuritalea, and Thiobacillus) in the CWs, which explains denitrification performance of the enhanced CWs. This study aimed to explore the mechanism of efficient denitrification and GHG emission reduction in the enhanced CWs, providing theoretical guidance for the deep treatment of urban domestic wastewater.

Potential electron acceptors for ammonium oxidation in wastewater treatment system under anoxic condition: A review

Anaerobic ammonium oxidation has been considered as an environmental-friendly and energy-efficient biological nitrogen removal (BNR) technology. Recently, new reaction pathway for ammonium oxidation under anaerobic condition had been discovered. In addition to nitrite, iron trivalent, sulfate, manganese and electrons from electrode might be potential electron acceptors for ammonium oxidation, which can be coupled to traditional BNR process for wastewater treatment. In this paper, the pathway and mechanism for ammonium oxidation with various electron acceptors under anaerobic condition is studied comprehensively, and the research progress of potentially functional microbes is summarized. The potential application of various electron acceptors for ammonium oxidation in wastewater is addressed, and the N2O emission during nitrogen removal is also discussed, which was important greenhouse gas for global climate change. The problems remained unclear for ammonium oxidation by multi-electron acceptors and potential interactions are also discussed in this review.

Active anaerobic methane oxidation in the groundwater table fluctuation zone of rice paddies

Rice paddies are globally important sources of methane emissions and also active regions for methane consumption. However, the impact of fluctuating groundwater levels on methane cycling has received limited attention. In this study, we delved into the activity and microbial mechanisms underlying anaerobic oxidation of methane (AOM) in paddy fields. A comprehensive approach was employed, including 13C stable isotope assays, inhibition experiments, real-time quantitative reverse transcription PCR, metagenomic sequencing, and binning technology. Geochemical profiles revealed the abundant coexistence of both methane and electron acceptors in the groundwater table fluctuation (GTF) zone, at a depth of 40-60 cm. Notably, the GTF zone exhibited the highest rate of AOM, potentially linked to the reduction of iron oxides and nitrate. Within this zone, Candidatus Methanoperedens (belonging to the ANME-2d group) dominated the Archaea population, accounting for a remarkable 85.4 %. Furthermore, our results from inhibition experiments, RT-qPCR, and metagenome-assembled genome (MAG) analysis highlighted the active role of Ca. Methanoperedens GTF50 in the GTF zone. This microorganism could independently mediate AOM process through the intriguing "reverse methanogenesis" pathway. Considering the similarity in geochemical conditions across different paddy fields, it is likely that Ca. Methanoperedens-mediated AOM is prevalent in the GTF zones.

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.

Soil carbon and nitrogen cycles driven by iron redox: A review

Soil carbon and nitrogen cycles affect agricultural production, environmental quality, and global climate. Iron (Fe), regarded as the most abundant redox-active metal element in the Earth's crust, is involved in a biogeochemical cycle that includes Fe(III) reduction and Fe(II) oxidation. The redox reactions of Fe can be linked to the carbon and nitrogen cycles in soil in various ways. Investigating the transformation processes and mechanisms of soil carbon and nitrogen species driven by Fe redox can provide theoretical guidance for improving soil fertility, and addressing global environmental pollution as well as climate change. Although the widespread occurrence of these coupling processes in soils has been revealed, explorations of the effects of Fe redox on soil carbon and nitrogen cycles remain in the early stages, particularly when considering the broader context of global climate and environmental changes. The key functional microorganisms, mechanisms, and contributions of these coupling processes to soil carbon and nitrogen cycles have not been fully elucidated. Here, we present a systematic review of the research progress on soil carbon and nitrogen cycles mediated by Fe redox, including the underlying reaction processes, the key microorganisms involved, the influencing factors, and their environmental significance. Finally, some unresolved issues and future perspectives are addressed. This knowledge expands our understanding of the interconnected cycles of Fe, carbon and nitrogen in soils.

Floating plants reduced methane fluxes from wetlands by creating a habitat conducive to methane oxidation

Wetlands are one of the important natural sources of atmospheric methane (CH4), as an important part of wetlands, floating plants can be expected to affect methane release. However, the effects of floating plants on methane release are limited. In this study, methane fluxes, physiochemical properties of the overlying water, methane oxidation potential and rhizospheric bacterial community were investigated in simulated wetlands with floating plants Eichhornia crassipes, Hydrocharis dubia, and Trapa natans. We found that E. crassipes, H. dubia, and T. natans plants could inhibit 84.31% - 97.31%, 4.98% - 88.91% and 43.62% - 92.51% of methane fluxes at interface of water-atmosphere compared to Control, respectively. Methane fluxes were negatively related to nutrients concentration in water column but positively related to the aerenchyma proportions of roots, stems, and leaves. At the same biomass, root of E. crassipes (36.44%) had the highest methane oxidation potential, followed by H. dubia (12.99%) and T. natans (11.23%). Forty-five bacterial phyla in total were identified on roots of three plants and 7 bacterial genera (2.10% - 3.33%) were known methanotrophs. Type I methanotrophs accounted for 95.07% of total methanotrophs. The pmoA gene abundances ranged from 1.90 × 1016 to 2.30 × 1018 copies/g fresh weight of root biofilms. Abundances of pmoA gene was significantly positively correlated with environmental parameters. Methylotrophy (5.40%) and methanotrophy (3.75%) function were closely related to methane oxidation. This study highlights that floating plant restoration can purify water and promote carbon neutrality partially by reducing methane fluxes through methane oxidation in wetlands.

Active pathways of anaerobic methane oxidization in deep-sea cold seeps of the South China Sea

IMPORTANCE

Cold seeps occur in continental margins worldwide and are deep-sea oases. Anaerobic oxidation of methane is an important microbial process in the cold seeps and plays an important role in regulating methane content. This study elucidates the diversity and potential activities of major microbial groups in dependent anaerobic methane oxidation and sulfate-dependent anaerobic methane oxidation processes and provides direct evidence for the occurrence of nitrate-/nitrite-dependent anaerobic methane oxidation (Nr-/N-DAMO) as a previously overlooked microbial methane sink in the hydrate-bearing sediments of the South China Sea. This study provides direct evidence for occurrence of Nr-/N-DAMO as an important methane sink in the deep-sea cold seeps.

Pyrogenic Carbon Promotes Anaerobic Oxidation of Methane Coupled with Iron Reduction via the Redox-Cycling Mechanism

Pyrogenic carbon (PC) can mediate electron transfer and thus catalyze biogeochemical processes to impact greenhouse gas (GHG) emissions. Here, we demonstrate that PC can contribute to mitigating GHG emissions by promoting the Fe(III)-dependent anaerobic oxidation of methane (AOM). It was found that the amendment PCs in microcosms dominated by Methanoperedenaceae performing Fe(III)-dependent AOM simultaneously promoted the rate of AOM and Fe(III) reduction with a consistent ratio close to the theoretical stoichiometry of 1:8. Further correlation analysis showed that the AOM rate was linearly correlated with the electron exchange capacity, but not the conductivity, of added PC materials, indicating the redox-cycling electron transfer mechanism to promote the Fe(III)-dependent AOM. The mass content of the C═O moiety from differentially treated PCs was well correlated with the AOM rate, suggesting that surface redox-active quinone groups on PCs contribute to facilitating Fe(III)-dependent AOM. Further microbial analyses indicate that PC likely shuttles direct electron transfer from Methanoperedenaceae to Fe(III) reduction. This study provides new insight into the climate-cooling impact of PCs, and our evaluation indicates that the PC-facilitated Fe(III)-dependent AOM could have a significant contribution to suppressing methane emissions from the world's reservoirs.

Retracted: The bidirectional extracellular electron transfer process aids iron cycling by Geoalkalibacter halelectricus in a highly saline-alkaline condition

Bidirectional extracellular electron transfer (EET) is crucial to upholding microbial metabolism with insoluble electron acceptors or donors in anoxic environments. Investigating bidirectional EET-capable microorganisms is desired to understand the cell-cell and microbe-mineral interactions and their role in mineral cycling besides leveraging their energy generation and conversion, biosensing, and bio-battery applications. Here, we report on iron cycling by haloalkaliphilic Geoalkalibacter halelectricus via bidirectional EET under haloalkaline conditions. It efficiently reduces Fe3+ oxide (Fe2O3) to Fe0 at a 0.75 ± 0.08 mM/mgprotein/d rate linked to acetate oxidation via outward EET and oxidizes Fe0 to Fe3+ at a 0.24 ± 0.03 mM/mgprotein/d rate via inward EET to reduce fumarate. Bioelectrochemical cultivation confirmed its outward and inward EET capabilities. It produced 895 ± 23 µA/cm2 current by linking acetate oxidation to anode reduction via outward EET and reduced fumarate by drawing electrons from the cathode (‒2.5 ± 0.3 µA/cm2) via inward EET. The cyclic voltammograms of G. halelectricus biofilms revealed redox moieties with different formal potentials, suggesting the involvement of different membrane components in bidirectional EET. The cyclic voltammetry and GC-MS analysis of the cell-free spent medium revealed the lack of soluble redox mediators, suggesting direct electron transfer by G. halelecctricus in achieving bidirectional EET. By reporting on the first haloalkaliphilic bacterium capable of oxidizing and reducing insoluble Fe0 and Fe3+ oxide, respectively, this study advances the limited understanding of the metabolic capabilities of extremophiles to respire on insoluble electron acceptors or donors via bidirectional EET and invokes the possible role of G. halelectricus in iron cycling in barely studied haloalkaline environments. IMPORTANCE Bidirectional extracellular electron transfer (EET) appears to be a key microbial metabolic process in anoxic environments that are depleted in soluble electron donor and acceptor molecules. Though it is an ecologically important and applied microbial phenomenon, it has been reported with a few microorganisms, mostly from nonextreme environments. Moreover, direct electron transfer-based bidirectional EET is studied for very few microorganisms with electrodes in engineered systems and barely with the natural insoluble electron acceptor and donor molecules in anoxic conditions. This study advances the understanding of extremophilic microbial taxa capable of bidirectional EET and its role in barely investigated Fe cycling in highly saline-alkaline environments. It also offers research opportunities for understanding the membrane components involved in the bidirectional EET of G. halelectricus. The high rate of Fe3+ oxide reduction activity by G. halelectricus suggests its possible use as a biocatalyst in the anaerobic iron bioleaching process under neutral-alkaline pH conditions.

Enhanced anaerobic oxidation of methane with the coexistence of iron oxides and sulfate fertilizer in paddy soil

Iron oxides and sulfate are usually abundant in paddy soil, but their role in reducing methane emissions is little known. In this work, paddy soil was anaerobically cultivated with ferrihydrite and sulfate for 380 days. An activity assay, inhibition experiment, and microbial analysis were conducted to evaluate the microbial activity, possible pathways, and community structure, respectively. The results showed that anaerobic oxidation of methane (AOM) was active in the paddy soil. The AOM activity was much higher with ferrihydrite than sulfate, and an extra 10% of AOM activity was stimulated when ferrihydrite and sulfate coexisted. The microbial community was highly similar to the duplicates but totally different with different electron acceptors. The microbial abundance and diversity decreased due to the oligotrophic condition, but mcrA-carrying archaea increased 2-3 times after 380 days. Both the microbial community and the inhibition experiment implied that there was an intersection between iron and sulfur cycles. A "cryptic sulfur cycle" might link the two cycles, in which sulfate was quickly regenerated by iron oxides, and it might contribute 33% of AOM in the tested paddy soil. Complex links between methane, iron, and sulfur geochemical cycles occur in paddy soil, which may be significant in reducing methane emissions from rice fields.

Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems

Around 50% of humankind relies on groundwater as a source of drinking water. Here we investigate the age, geochemistry, and microbiology of 138 groundwater samples from 95 monitoring wells (<250 m depth) located in 14 aquifers in Canada. The geochemistry and microbiology show consistent trends suggesting large-scale aerobic and anaerobic hydrogen, methane, nitrogen, and sulfur cycling carried out by diverse microbial communities. Older groundwaters, especially in aquifers with organic carbon-rich strata, contain on average more cells (up to 1.4 × 10⁷ mL^-1) than younger groundwaters, challenging current estimates of subsurface cell abundances. We observe substantial concentrations of dissolved oxygen (0.52 ± 0.12 mg L^-1 [mean ± SE]; n = 57) in older groundwaters that seem to support aerobic metabolisms in subsurface ecosystems at an unprecedented scale. Metagenomics, oxygen isotope analyses and mixing models indicate that dark oxygen is produced in situ via microbial dismutation. We show that ancient groundwaters sustain productive communities and highlight an overlooked oxygen source in present and past subsurface ecosystems of Earth.

Tracing the Century-Long Evolution of Microplastics Deposition in a Cold Seep

Microplastic (MP) pollution is one of the greatest threats to marine ecosystems. Cold seeps are characterized by methane-rich fluid seepage fueling one of the richest ecosystems on the seafloor, and there are approximately more than 900 cold seeps globally. While the long-term evolution of MPs in cold seeps remains unclear. Here, how MPs have been deposited in the Haima cold seep since the invention of plastics is demonstrated. It is found that the burial rates of MPs in the non-seepage areas significantly increased since the massive global use of plastics in the 1930s, nevertheless, the burial rates and abundance of MPs in the methane seepage areas are much lower than the non-seepage area of the cold seep, suggesting the degradation potential of MPs in cold seeps. More MP-degrading microorganism populations and functional genes are discovered in methane seepage areas to support this discovery. It is further investigated that the upwelling fluid seepage facilitated the fragmentation and degradation behaviors of MPs. Risk assessment indicated that long-term transport and transformation of MPs in the deeper sediments can reduce the potential environmental and ecological risks. The findings illuminated the need to determine fundamental strategies for sustainable marine plastic pollution mitigation in the natural deep-sea environments.

Genomic Insights into Niche Partitioning across Sediment Depth among Anaerobic Methane-Oxidizing Archaea in Global Methane Seeps

Marine sediments are important methane reservoirs. Methane efflux from the seabed is significantly restricted by anaerobic methanotrophic (ANME) archaea through a process known as anaerobic oxidation of methane (AOM). Different clades of ANME archaea occupy distinct niches in methane seeps, but their underlying molecular mechanisms still need to be fully understood. To provide genetic explanations for the niche partitioning of ANME archaea, we applied comparative genomic analysis to ANME archaeal genomes retrieved from global methane seeps. Our results showed that ANME-2 archaea are more prevalent than ANME-1 archaea in shallow sediments because they carry genes that encode a significantly higher number of outer membrane multiheme c-type cytochromes and flagellar proteins. These features make ANME-2 archaea perform direct interspecies electron transfer better and benefit more from electron acceptors in AOM. Besides, ANME-2 archaea carry genes that encode extra peroxidase compared to ANME-1 archaea, which may lead to ANME-2 archaea better tolerating oxygen toxicity. In contrast, ANME-1 archaea are more competitive in deep layers than ANME-2 archaea because they carry extra genes (mtb and mtt) for methylotrophic methanogenesis and a significantly higher number of frh and mvh genes for hydrogenotrophic methanogenesis. Additionally, ANME-1 archaea carry exclusive genes (sqr, TST, and mddA) involved in sulfide detoxification compared to ANME-2 archaea, leading to stronger sulfide tolerance. Overall, this study reveals the genomic mechanisms shaping the niche partitioning among ANME archaea in global methane seeps. IMPORTANCE Anaerobic methanotrophic (ANME) archaea are important methanotrophs in marine sediment, controlling the flux of biologically generated methane, which plays an essential role in the marine carbon cycle and climate change. So far, no strain of this lineage has been isolated in pure culture, which makes metagenomics one of the fundamental approaches to reveal their metabolic potential. Although the niche partitioning of ANME archaea was frequently reported in different studies, whether this pattern was consistent in global methane seeps had yet to be verified, and little was known about the genetic mechanisms underlying it. Here, we reviewed and analyzed the community structure of ANME archaea in global methane seeps and indicated that the niche partitioning of ANME archaea was statistically supported. Our comparative genomic analysis indicated that the capabilities of interspecies electron transfer, methanogenesis, and the resistance of oxygen and hydrogen sulfide could be critical in defining the distribution of ANME archaea in methane seep sediment.

Long-term effects of soluble and insoluble ferric irons on anaerobic oxidation of methane in paddy soil

Iron-dependent anaerobic oxidation of methane (Fe-AOM) is an important process to reduce methane emissions into the atmosphere. It is well known that iron bioavailability largely influences microbial iron reduction, but the long-term effects of different ferric irons on soil Fe-AOM remain unknown. In this work, paddy soil in the ferruginous zone was collected and inoculated with insoluble ferrihydrite and soluble EDTA-Fe(III) for 420 days. Stable isotope experiments, activity inhibition tests, and molecular biological techniques were performed to reveal the activity, microbial community, and possible mechanism of paddy soil Fe-AOM. The results showed that ferrihydrite was a better electron acceptor for long-term Fe-AOM cultivation. Although EDTA-Fe(III) is highly bioavailable and could stimulate Fe-AOM activity for a short time, it restricted the activity increase in the long term. The abundances of archaea, iron-reducing bacteria (IRB), and gene mcrA largely increased after cultivation, indicating the important roles of mcrA-carrying archaea and IRB. Remarkably, archaeal communities were similar, but bacteria were totally different with different ferric irons. The results of the microbial community and activity inhibition suggested that Fe-AOM was performed likely by the cooperation between archaea (Methanomassiliicoccaceae or pGrfC26) and IRB in the cultures.

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.

Coupling and environmental implications of in situ formed biogenic Fe-Mn minerals induced by indigenous bacteria and oxygen perturbations for As(III) immobilization in groundwater

Iron (Fe)-manganese (Mn) minerals formed in situ can be used for the natural remediation of the primary poor-quality groundwater with coexistence of arsenite [As(III)], Mn(II), and Fe(II) (PGAMF). However, the underlying mechanisms of immobilization and coupling of As, Mn, and Fe during in-situ formation of Fe-Mn minerals in PGAMF remains unclear. The simultaneous immobilization and coupling of arsenic (As), Mn, and Fe in PGAMF during in-situ formation of biogenic Fe-Mn minerals induced by O₂ perturbations and indigenous bacteria (Comamonas sp. RM6) were investigated at the different molar ratios of Fe(II):Mn(II) (1:1, 2:1, and 3:1). Compared with systems without Fe(II) in the presence of Mn(II), the coexisted Fe(II) significantly enhanced Mn(II) bio-oxidation and mineral precipitation, resulting in As immobilization increased by 5, 7, and 7 times at initial Fe(II) concentration of 0.3, 0.6, and 0.9 mM, respectively. Moreover, the As(III) immobilization efficiencies in Mn(II) and Fe(II) mixed system at initial Fe(II) concentration of 0.3, 0.6, and 0.9 mM were 73%, 91%, and 92%, respectively, that were significantly higher than those of single Fe(II) system (30%, 59%, and 74%) and those of single Mn(II) system (12%), indicating that Fe(II) and Mn(II) oxidation synergically enhanced As(III) immobilization. This was mainly attributed to the formation and As adsorption capacity of biogenic Fe-Mn minerals (BFMM). The formed BFMM significantly facilitated simultaneous immobilization of Fe, Mn, and As in PGAMF by oxidation, adsorption, and precipitation/coprecipitation, a coupling of biological, physical, and chemical processes. Fe component was mainly responsible for As fixation, and Mn component dominated As(III) oxidation. Based on the results from this work, biostimulation and bioaugmentation techniques can be developed for in-situ purification and remediation of PGAMF. This work provides insights into the simultaneous immobilization of pollutants in PGAMF, as well as promising strategies for in-situ purification and remediation of PGAMF.

Seasonal variations of geofluids from mud volcano systems in the Southern Junggar Basin, NW China

Variations in the chemical composition of geofluids and of gas fluxes are significant parameters for understanding mud volcanism and correctly estimate their emissions in carbon species, particularly greenhouse gas, methane. In this study, muddy water and gas samples were collected from the Anjihai, Dushanzi, Aiqigou, and Baiyanggou mud volcanoes in the southern Junggar Basin during the four seasons, around a year. This region hosts the most active mud volcanism throughout China. Gas and water were analyzed for major molecular compositions, carbon and hydrogen isotopes of the gas phase, as well as cations and anions, hydrogen and oxygen isotopes of water. The emitted gases are dominated by CH₄ with some C₂H₆, CO₂, and N₂. The seasonal changes in the chemical composition and carbon isotopes of emitted gases are not significant, whereas clear variations in the amounts of cations and anions dissolved in the water are reported. These are higher in spring and summer than autumn and winter. The CH₄, CO₂, and C₂H₆ fluxes are 157.3-1108 kg/a, 1.8-390.1 kg/a, and 10.2-118.7 kg/a, respectively, and a clear seasonal trend of the gas seepage flux has been observed. In January, the macro-seepage flux of open vents is ≥65 % higher than in April, whereas the micro-seepage flux significantly decreased, probably due to the frozen shallow ground and blockage of soil fractures around the vents by heavy snow and ice during January. This probably causes an extra gas pressure transferred to the major vents, resulting in higher flux of the macro-seepage in the cold season. However, the total flux of the whole mud volcano system is generally consistent around a year.

Geoalkalibacter halelectricus SAP-1 sp. nov. possessing extracellular electron transfer and mineral-reducing capabilities from a haloalkaline environment

The extracellular electron transfer (EET)-capable electroactive microorganisms (EAMs) play crucial roles in mineral cycling and interspecies electron transfer in different environments and are used as biocatalysts in microbial electrochemical technologies. Studying EAMs from extreme environments is desired to advance the electromicrobiology discipline, understanding their unique metabolic traits with implications to extreme microbiology, and develop specific bioelectrochemical applications. Here, we present a novel haloalkaliphilic bacterium named Geoalkalibacter halelectricus SAP-1, isolated from a microbial electroactive biofilm enriched from the haloalkaline lake sediments. It is a rod-shaped Gram-negative heterotrophic anaerobe that uses various carbon and energy sources and respires on soluble and insoluble terminal electron acceptors. Besides 16S-rRNA and whole-genome-based phylogeny, the GGDC values of 21.7 %, ANI of 78.5, and 2.77 % genomic DNA GC content difference with the closest validly named species Geoalkalibacter ferrihydriticus (DSM 17813^T ) confirmed its novelty. When grown with the solid-state electrode as the only electron acceptor, it produced 460±23 μA/cm² bioelectrocatalytic current, thereby confirming its electroactivity. Further electrochemical analysis revealed the presence of membrane redox components with high formal potentials, putatively involved in the direct mode of EET. These are distinct from EET components reported for any known electroactive microorganisms, including well-studied Geobacter spp., Shewanella spp. and Desulfuromonas acetexigens. Further the capabilities of G. halelectricus SAP-1 to respire soluble as well insoluble electron acceptors including fumarate, SO₄ ^2- , Fe³⁺ , and Mn⁴⁺ suggests its role in cycling these elements in haloalkaline environments. This article is protected by copyright. All rights reserved.

Hydrous ferric oxides (HFO's) precipitated from contaminated waters at several abandoned Sb deposits - Interdisciplinary assessment

The presented paper represents a comprehensive analysis of ochre sediments precipitated from Fe rich drainage waters contaminated by arsenic and antimony. Ochre samples from three abandoned Sb deposits were collected in three different seasons and were characterized from the mineralogical, geochemical, and microbiological point of view. They were formed mainly by poorly crystallized 2-line ferrihydrite, with the content of arsenic in samples ranging from 7 g·kg^-1 to 130 g·kg^-1 and content of antimony ranging from 0.25 g·kg^-1 up to 12 g·kg^-1. Next-generation sequencing approach with 16S RNA, 18S RNA and ITS markers was used to characterize bacterial, fungal, algal, metazoal and protozoal communities occurring in the HFOs. In the 16S RNA, the analysis dominated bacteria (96.2%) were mainly Proteobacteria (68.8%) and Bacteroidetes (10.2%) and to less extent also Acidobacteria, Actinobacteria, Cyanobacteria, Firmicutes, Nitrosprae and Chloroflexi. Alpha and beta diversity analysis revealed that the bacterial communities of individual sites do not differ significantly, and only subtle seasonal changes were observed. In this As and Sb rich, circumneutral microenvironment, rich in iron, sulfates and carbonates, methylotrophic bacteria (Methylobacter, Methylotenera), metal/reducing bacteria (Geobacter, Rhodoferax), metal-oxidizing and denitrifying bacteria (Gallionella, Azospira, Sphingopyxis, Leptothrix and Dechloromonas), sulfur-oxidizing bacteria (Sulfuricurvum, Desulphobulbaceae) and nitrifying bacteria (Nitrospira, Nitrosospira) accounted for the most dominant ecological groups and their impact over Fe, As, Sb, sulfur and nitrogen geocycles is discussed. This study provides evidence of diverse microbial communities that exist in drainage waters and are highly important in the process of mobilization or immobilization of the potentially toxic elements.

Overview of Diverse Methyl/Alkyl-Coenzyme M Reductases and Considerations for Their Potential Heterologous Expression

Methyl-coenzyme M reductase (MCR) is an archaeal enzyme that catalyzes the final step of methanogenesis and the first step in the anaerobic oxidation of methane, the energy metabolisms of methanogens and anaerobic methanotrophs (ANME), respectively. Variants of MCR, known as alkyl-coenzyme M reductases, are involved in the anaerobic oxidation of short-chain alkanes including ethane, propane, and butane as well as the catabolism of long-chain alkanes from oil reservoirs. MCR is a dimer of heterotrimers (encoded by mcrABG) and requires the nickel-containing tetrapyrrole prosthetic group known as coenzyme F₄₃₀. MCR houses a series of unusual post-translational modifications within its active site whose identities vary depending on the organism and whose functions remain unclear. Methanogenic MCRs are encoded in a highly conserved mcrBDCGA gene cluster, which encodes two accessory proteins, McrD and McrC, that are believed to be involved in the assembly and activation of MCR, respectively. The requirement of a unique and complex coenzyme, various unusual post-translational modifications, and many remaining questions surrounding assembly and activation of MCR largely limit in vitro experiments to native enzymes with recombinant methods only recently appearing. Production of MCRs in a heterologous host is an important step toward developing optimized biocatalytic systems for methane production as well as for bioconversion of methane and other alkanes into value-added compounds. This review will first summarize MCR catalysis and structure, followed by a discussion of advances and challenges related to the production of diverse MCRs in a heterologous host.

Microbial methane emissions from the non-methanogenesis processes: A critical review

Methane, a potent greenhouse gas of global importance, has traditionally been considered as an end product of microbial methanogenesis of organic matter. Paradoxically, growing evidence has shown that some microbes, such as cyanobacteria, algae, fungi, purple non-sulfur bacteria, and cryptogamic covers, produce methane in oxygen-saturated aquatic and terrestrial ecosystems. The non-methanogenesis process could be an important potential contributor to methane emissions. This systematic review summarizes the knowledge of microorganisms involved in the non-methanogenesis process and the possible mechanisms of methane formation. Cyanobacteria-derived methane production may be attributed to either demethylation of methyl phosphonates or linked to light-driven primary productivity, while algae produce methane by utilizing methylated sulfur compounds as possible carbon precursors. In addition, fungi produce methane by utilizing methionine as a possible carbon precursor, and purple non-sulfur bacteria reduce carbon dioxide to methane by nitrogenase. The microbial methane distribution from the non-methanogenesis processes in aquatic and terrestrial environments and its environmental significance to global methane emissions, possible mechanisms of methane production in each open water, water-to-air methane fluxes, and the impact of climate change on microorganisms are also discussed. Finally, future perspectives are highlighted, such as establishing more in-situ experiments, quantifying methane flux through optimizing empirical models, distinguishing individual methane sources, and investigating nitrogenase-like enzyme systems to improve our understanding of microbial methane emission from the non-methanogenesis process.

Anaerobic methane oxidation linked to Fe(III) reduction in a Candidatus Methanoperedens-enriched consortium from the cold Zoige wetland at Tibetan Plateau

Anaerobic oxidation of methane (AOM) is a microbial process degrading ample methane in anoxic environments, and Ca. Methanoperedens mediated nitrate- or metal-reduction linked AOM is believed important in freshwater systems. This work, via 16S rRNA gene diversity survey and 16S rRNA quantification, found abundant Ca. Methanoperedens along with iron in the cold Zoige wetland at Tibetan Plateau. The wetland soil microcosm performed Fe(III) reduction, rather than nitrate- nor sulphate-reduction, coupled methane oxidation (3.87 μmol d^-1 ) with 32.33 μmol Fe(II) accumulation per day at 18°C, but not at 30°C. A metagenome-assembled genome (MAG) recovered from the microcosm exhibits ~74% average nucleotide identity with the reported Ca. Methanoperedens spp. that perform Fe(III) reduction linked AOM, thus a novel species Ca. Methanoperedens psychrophilus was proposed. Ca. M. psychrophilus contains the whole suite of CO₂ reductive methanogenic genes presumably involving in AOM via a reverse direction, and comparative genome analysis revealed its unique gene categories: the multi-heme clusters (MHCs) cytochromes, the S-layer proteins highly homologous to those recovered from lower temperature environments and type IV pili, those could confer Ca. M. psychrophilus of cold adaptability. Therefore, this work reports the first methanotroph implementing AOM in an alpine wetland.

Anaerobic oxidation of methane mediated by microbial extracellular respiration

Anaerobic oxidation of methane (AOM) can be microbially mediated by the reduction of different terminal electron acceptors. AOM coupled to reduction of sulfate, manganese/iron oxides, humic substances, selenate, arsenic and other artificial extracellular electron acceptors are recognized as processes associated with microbial extracellular respiration. In these processes, methane-oxidizing archaea transfer electrons to external electron acceptors or to interdependent microbial species, which are mechanistically dependent on versatile extracellular electron transfer (EET) pathways. This review compiles recent progress in the research of electromicrobiology of AOM based on the catalogue of different electron acceptors. Naturally distributed and artificially constructed EET-mediated AOM is summarized, with the discussion of their environmental importance and application potentials. The diversity of responsible microorganisms involved in EET-mediated AOM is discussed with both methane-oxidizing archaea and their putative bacterial partners. More importantly, the review highlights progress and deficiencies in our understanding of EET pathways in EET-mediated AOM, raising open research questions for future research.

Neodymium as Metal Cofactor for Biological Methanol Oxidation: Structure and Kinetics of an XoxF1-Type Methanol Dehydrogenase

The methane-oxidizing bacterium Methylacidimicrobium thermophilum AP8 thrives in acidic geothermal ecosystems that are characterized by high degassing of methane (CH₄), H₂, H₂S, and by relatively high lanthanide concentrations. Lanthanides (atomic numbers 57 to 71) are essential in a variety of high-tech devices, including mobile phones. Remarkably, the same elements are actively taken up by methanotrophs/methylotrophs in a range of environments, since their XoxF-type methanol dehydrogenases require lanthanides as a metal cofactor. Lanthanide-dependent enzymes seem to prefer the lighter lanthanides (lanthanum, cerium, praseodymium, and neodymium), as slower methanotrophic/methylotrophic growth is observed in medium supplemented with only heavier lanthanides. Here, we purified XoxF1 from the thermoacidophilic methanotroph Methylacidimicrobium thermophilum AP8, which was grown in medium supplemented with neodymium as the sole lanthanide. The neodymium occupancy of the enzyme is 94.5% ± 2.0%, and through X-ray crystallography, we reveal that the structure of the active site shows interesting differences from the active sites of other methanol dehydrogenases, such as an additional aspartate residue in close proximity to the lanthanide. Nd-XoxF1 oxidizes methanol at a maximum rate of metabolism (V_max) of 0.15 ± 0.01 μmol · min^-1 · mg protein^-1 and an affinity constant (K_m) of 1.4 ± 0.6 μM. The structural analysis of this neodymium-containing XoxF1-type methanol dehydrogenase will expand our knowledge in the exciting new field of lanthanide biochemistry. IMPORTANCE Lanthanides comprise a group of 15 elements with atomic numbers 57 to 71 that are essential in a variety of high-tech devices, such as mobile phones, but were considered biologically inert for a long time. The biological relevance of lanthanides became evident when the acidophilic methanotroph Methylacidiphilum fumariolicum SolV, isolated from a volcanic mud pot, could only grow when lanthanides were supplied to the growth medium. We expanded knowledge in the exciting and rapidly developing field of lanthanide biochemistry by the purification and characterization of a neodymium-containing methanol dehydrogenase from a thermoacidophilic methanotroph.

Distribution of Dissolved Nitrogen Compounds in the Water Column of a Meromictic Subarctic Lake

In order to better understand the biogeochemical cycle of nitrogen in meromictic lakes, which can serve as a model for past aquatic environments, we measured dissolved concentrations of nitrate, nitrite, ammonium, and organic nitrogen in the deep (39 m maximal depth) subarctic Lake Svetloe (NW Russia). The lake is a rare type of freshwater meromictic water body with high concentrations of methane, ferrous iron, and manganese and low concentrations of sulfates and sulfides in the monimolimnion. In the oligotrophic mixolimnion, the concentration of mineral forms of nitrogen decreased in summer compared to winter, likely due to a phytoplankton bloom. The decomposition of the bulk of the organic matter occurs under microaerophilic/anaerobic conditions of the chemocline and is accompanied by the accumulation of nitrogen in the form of N-NH4 in the monimolimnion. We revealed a strong relationship between methane and nitrogen cycles in the chemocline and monimolimnion horizons. The nitrate concentrations in Lake Svetloe varied from 9 to 13 μM throughout the water column. This fact is rare for meromictic lakes, where nitrate concentrations up to 13 µM are found in the monimolimnion zone down to the bottom layers. We hypothesize, in accord with available data for other stratified lakes that under conditions of high concentrations of manganese and ammonium at the boundary of redox conditions and below, anaerobic nitrification with the formation of nitrate occurs. Overall, most of the organic matter in Lake Svetloe undergoes biodegradation essentially under microaerophilic/anaerobic conditions of the chemocline and the monimolimnion. Consequently, the manifestation of the biogeochemical nitrogen cycle is expressed in these horizons in the most vivid and complex relationship with other cycles of elements.

The role and related microbial processes of Mn-dependent anaerobic methane oxidation in reducing methane emissions from constructed wetland-microbial fuel cell

Anaerobic oxidation of methane (AOM) plays an important role in global carbon cycle and greenhouse gas emission reduction. In this study, an effective green technology to reduce methane emissions was proposed by introducing Mn-dependent anaerobic oxidation of methane (Mn-AOM) and microbial fuel cell (MFC) technology into constructed wetland (CW). The results indicate that the combination of biological methods and bioelectrochemical methods can more effectively control the methane emission from CW than the reported methods. The role of dissimilated metal reduction in methane control in CW and the biochemical process associated with Mn-AOM were also investigated. The results demonstrated that using Mn ore as the matrix and operating MFC effectively reduced methane emissions from CW, and higher COD removal rate was obtained in CW-MFC (Mn) during the 200 days of operation. Methane emission from CW-MFC (Mn) (53.76 mg/m²/h) was 55.61% lower than that of CW (121.12 mg/m²/h). The highest COD removal rate (99.85%) in CW-MFC (Mn) was obtained. As the dissimilative metal-reducing microorganisms, Geobacter (5.10%) was found enriched in CW-MFC (Mn). The results also showed that the presence of Mn ore was beneficial to the biodiversity of CW-MFCs and the growth of electrochemically active bacteria (EAB) including Proteobacteria (35.32%), Actinobacteria (2.38%) and Acidobacteria (2.06%), while the growth of hydrogenotrophic methanogens Methanobacterium was effectively inhibited. This study proposed an effective way to reduce methane from CW. It also provided reference for low carbon technology of wastewater treatment.

Comprehensive evaluation of manganese oxides and iron oxides as metal substrate materials for constructed wetlands from the perspective of water quality and greenhouse effect

Manganese oxides and iron oxides have been widely introduced in constructed wetlands (CWs) for sewage treatment due to their extensiveness in nature and their ability to participate in various reactions, but their effects on greenhouse gas (GHG) emissions remain unclear. Here, a set of vertical subsurface-flow CWs (Control, Fe-VSSCWs, and Mn-VSSCWs) was established to comprehensively evaluate which are the better metal substrate materials for CWs, iron oxides or manganese oxides, through water quality and the global warming potential (GWP) of nitrous oxide (N₂O), methane (CH₄), and carbon dioxide (CO₂). The results revealed that the removal efficiencies of chemical oxygen demand (COD), total nitrogen (TN), and total phosphorus (TP) in Mn-VSSCWs were all higher than that in Fe-VSSCWs, and manganese oxides could almost completely suppress the CH₄ production and reduce GWP (from 8.15 CO₂-eq/m²/h to 7.17 mg CO₂-eq/m²/h), however, iron oxides promoted GWP (from 8.15 CO₂-eq/m²/h to 10.84 mg CO₂-eq/m²/h), so manganese oxides are the better CW substrate materials to achieve effective sewage treatment while reducing the greenhouse gas effect.

Spatial methane pattern in a deep freshwater lake: Relation to water depth and topography

Freshwater lakes are regarded as important methane (CH₄) sources, accounting for ~20% of natural emission. To improve the assessment of the global greenhouse effect, it is necessary to consider spatial variability within lakes. Here, CH₄ concentrations in the water column and sediment layers, as well as the sediment CH₄ production potentials and diffusive fluxes, were studied in the littoral, intermediate, and profundal zones of the medium-sized (425 ha), deep (maximum depth 69.5 m) Lake Stechlin (Germany). Sediment CH₄ concentrations, production potentials and sediment-water interface diffusive fluxes showed significant spatial heterogeneity and were highest in the profundal zone. CH₄ concentrations in the surface water did not differ among the studied locations, indicating a decoupling from the production sites in the sediment. The high amount of CH₄ in profundal sediments that might potentially be released to the atmosphere is either trapped or oxidized within the water column, while the surface water dissolved CH₄ is more related to the dynamics in the epilimnion. The divergence in sediment physical (water content, grain size) and chemical (organic matter quantity or quality, sulfate) properties across the lake leads to variations in CH₄ dynamics which are restricted to deeper habitats in this type of lake.

Mineralosphere Microbiome Leading to Changed Geochemical Properties of Sedimentary Rocks from Aiqigou Mud Volcano, Northwest China

The properties of rocks can be greatly affected by seepage hydrocarbons in petroleum-related mud volcanoes. Among them, the color of sedimentary rocks can reflect the changes of sedimentary environment and weathering history. However, little is known about the microbial communities and their biogeochemical significance in these environments. In this study, contrasting rock samples were collected from the Aiqigou mud volcano on the southern margin of the Junggar Basin in Northwest China as guided by rock colors indicative of redox conditions. The physicochemical properties and mineral composition are similar under the same redox conditions. For example, the content of chlorite, muscovite, quartz, and total carbon were higher, and the total iron was lower under reduced conditions compared with oxidized environments. High-throughput sequencing of 16S rRNA gene amplicons revealed that different functional microorganisms may exist under different redox conditions; microbes in oxidized conditions have higher diversity. Statistical analysis and incubation experiments indicated that the microbial community structure is closely related to the content of iron which may be an important factor for color stratification of continental sedimentary rocks in the Aiqigou mud volcano. The interactions between organics and iron-bearing minerals mediated by microorganisms have also been hypothesized.

Heavy metal reduction coupled to methane oxidation：Mechanisms, recent advances and future perspectives

Methane emission has contributed greatly to the global warming and climate change, and the pollution of heavy metals is an important concern due to their toxicity and environmental persistence. Recently, multiple heavy metals have been demonstrated to be electron acceptors for methane oxidation, which offers a potential for simultaneous methane emission mitigation and heavy metal detoxification. This review provides a comprehensive discussion of heavy metals reduction coupled to methane oxidation, and identifies knowledge gaps and opportunities for future research. The functional microorganisms and possible mechanisms are detailed in groups under aerobic, hypoxic and anaerobic conditions. The potential application and major environmental significances for global methane mitigation, the elements cycle and heavy metals detoxification are also discussed. The future research opportunities are also discussed to provide insights for further research and efficient practical application.

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.

Chemotrophic profiling of prokaryotic communities thriving on organic and mineral nutrients in a submerged coastal cave

The geothermal system of the Salento peninsula (Italy) is characterized by the presence of many hydrogen sulfide-rich underground waters and thermal springs. We focused our attention on the submerged section of Zinzulùsa (Castro, Italy), a cave of both naturalistic and archaeological interest. In pioneer studies, some hypotheses about the origin of the sulfurous waters of this area were proposed. The most accredited one is that sulfate-enriched waters of marine origin infiltrate deep along bands with greater permeability, and warm-up going upwards, due to the geothermal gradient. During their route, marine waters interact with organic deposits and generate hydrogen sulfide as a result of sulfate reduction. To date, no studies have been conducted to elucidate the hydrogen sulfide origin in this site. The nature of reducing power and energy sources supporting microbial life in this submerged habitat is currently unknown. Here we present a multidisciplinary experimental approach aimed at defining geochemical features and microbiological diversity of the submerged habitat of Zinzulùsa cave. Our integrated data provide strong evidence that the sulfate content of the marine water and the activity of sulfate-reducing bacteria may account for the hydrogen sulfide content of the thermal springs. Anaerobic, sulfate-reducing, thermophilic Thermodesulfovibrio and hyperthermophilic Fervidobacterium genera show a high percentage contribution in 16S rRNA gene metabarcoding analyses, despite the mesophilic conditions of the sampling site. Besides, supported by PICRUSt functional analysis, we propose a chemotrophic model in which hydrocarbon deposits, entrapped in the stratifications of the seafloor, may be exploited by anaerobic oil-degrading bacteria as carbon and energy sources to sustain efficient hydrogen, sulfur, and nitrogen biogeochemical cycles. The Zinzulùsa hydrothermal site represents an ecosystem useful to obtain new insights into prokaryotic mutual interactions in oligotrophic and aphotic conditions, which constitute the largest environment of the biosphere.

Methane-fueled microbial fuel cells with the formate-acclimating electroactive culture

Methane gas is widespread in natural environments and anaerobic wastewater treatment sites, bringing the risk of the greenhouse effect and energy loss if left unmanaged. A methane-fueled microbial fuel cell (MFC) can convert methane to electricity under mild condition, but faced difficulties in startup. In this study, the new startup strategy and operation performance for methane-fueled MFCs were investigated. After the pre-cultivation of formate-acclimating electroactive culture, the methane-fueled MFC was successfully started up in a short time of 53 d. Increasing concentrations of molybdenum and tungsten in medium facilitated both methane consumption and electricity generation. Under the optimal condition (batch duration of 11 h, 30 °C, pH 7 buffered by phosphate buffer solution), the methane-fueled MFC achieved the maximum power density of 166 mW/m³, a coulomb production of 6.58 ± 0.07C/batch, a CE of 27.4 ± 0.4% and a methane consumption of 31.2 ± 0.3 μmol/batch. This work explored a suitable inoculum (formate-acclimating electroactive culture) for methane-fueled MFCs.

Active Anaerobic Archaeal Methanotrophs in Recently Emerged Cold Seeps of Northern South China Sea

Cold seep ecosystems are developed from methane-rich fluids in organic rich continental slopes, which are the source of various dense microbial and faunal populations. Extensive studies have been conducted on microbial populations in this unique environment; most of them were based on DNA, which could not resolve the activity of extant organisms. In this study, RNA and DNA analyses were performed to evaluate the active archaeal and bacterial communities and their network correlations, particularly those participating in the methane cycle at three sites of newly developed cold seeps in the northern South China Sea (nSCS). The results showed that both archaeal and bacterial communities were significantly different at the RNA and DNA levels, revealing a higher abundance of methane-metabolizing archaea and sulfate-reducing bacteria in RNA sequencing libraries. Site ROV07-01, which exhibited extensive accumulation of deceased Calyptogena clam shells, was highly developed, and showed diverse and active anaerobic archaeal methanotrophs (ANME)-2a/b and sulfate-reducing bacteria from RNA libraries. Site ROV07-02, located near carbonate crusts with few clam shell debris, appeared to be poorly developed, less anaerobic and less active. Site ROV05-02, colonized by living Calyptogena clams, could likely be intermediary between ROV07-01 and ROV07-02, showing abundant ANME-2dI and sulfate-reducing bacteria in RNA libraries. The high-proportions of ANME-2dI, with respect to ANME-2dII in the site ROV07-01 was the first report from nSCS, which could be associated with recently developed cold seeps. Both ANME-2dI and ANME-2a/b showed close networked relationships with sulfate-reducing bacteria; however, they were not associated with the same microbial operational taxonomic units (OTUs). Based on the geochemical gradients and the megafaunal settlements as well as the niche specificities and syntrophic relationships, ANMEs appeared to change in community structure with the evolution of cold seeps, which may be associated with the heterogeneity of their geochemical processes. This study enriched our understanding of more active sulfate-dependent anaerobic oxidation of methane (AOM) in poorly developed and active cold seep sediments by contrasting DNA- and RNA-derived community structure and activity indicators.

A new insight on the effects of iron oxides and dissimilated metal-reducing bacteria on CH4 emissions in constructed wetland matrix systems

Iron oxides and dissimilated metal-reducing bacteria (DMRB) have been reported to result in a reduction in methane (CH₄) emissions in constructed wetlands (CWs), but their mechanisms on CH₄ production and oxidation remains unclear. Here, a set of CW matrix systems (Control, Fe-CWs, and FeB-CWs) was established to analyze the CH₄ emission reduction from various angles, including the valencies of iron, microbial community structure and enzyme activity. The results revealed that the addition of iron oxides promoted the electron transfer between methanogens and Geobacter to promote CH₄ production, but it was interesting that iron oxides also reduced the enzymes involved in the carbon dioxide (CO₂) reduction pathway and promoted the enzymes that participated in anaerobic oxidation of methane (AOM) thereby leading to the overall reduction in CH₄ emissions. Moreover, DMRB could promote iron reduction thereby further reducing CH₄ emissions by promoting AOM and competing with methanogens for organic substrates.

The role of humic substances in mitigating greenhouse gases emissions: Current knowledge and research gaps

Humic substances (HS) constitute a highly transformed fraction of natural organic matter (NOM) with a heterogeneous structure, which is rich in electron-transferring functional moieties. Because of this feature, HS display a versatile reactivity with a diversity of environmentally relevant organic and inorganic compounds either by abiotic or microbial processes. Consequently, extensive research has been conducted related to the potential of HS to drive relevant processes in bio-engineered systems, as well as in the biogeochemical cycling of key elements in natural environments. Nevertheless, the increase in the number of reports examining the relationship between HS and the microorganisms related to the production and consumption of greenhouse gases (GHG), the main drivers of global warming, has just emerged in the last years. In this paper, we discuss the importance of HS, and their analogous redox-active organic molecules (RAOM), on controlling the emission of three of the most relevant GHG due to their tight relationship with microbial activity, their abundance on the Earth's atmosphere, and their important global warming potentials: carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O). The current knowledge gaps concerning the microbial component, on-site occurrence, and environmental constraints affecting these HS-mediated processes are provided. Furthermore, strategies involving the metabolic traits that GHG-consuming/HS-reducing and -oxidizing microbes display for the development of environmental engineered processes are also discussed.

Different responses of nitrite- and nitrate-dependent anaerobic methanotrophs to increasing nitrogen loading in a freshwater reservoir

Nitrite (NO₂^-)- and nitrate (NO₃^-)-dependent anaerobic oxidation of methane (AOM) are two new additions in microbial methane cycle, which potentially act as important methane sinks in freshwater aquatic systems. Here, we investigated spatial variations of community composition, abundance and potential activity of NO₂^-- and NO₃^--dependent anaerobic methanotrophs in the sediment of Jiulonghu Reservoir (Zhejiang Province, China), a freshwater reservoir having a gradient of increasing nitrogen loading from upstream to downstream regions. High-throughput sequencing of total bacterial and archaeal 16S rRNA genes showed the cooccurrence of Candidatus Methylomirabilis oxyfera (M. oxyfera)-like and Candidatus Methanoperedens nitroreducens (M. nitroreducens)-like anaerobic methanotrophs in the examined reservoir sediments. The community structures of these methanotrophs differed substantially between the sediments of upstream and downstream regions. Quantitative PCR suggested higher M. oxyfera-like bacterial abundance in the downstream (8.6 × 10⁷ to 2.8 × 10⁸ copies g^-1 dry sediment) than upstream sediments (2.4 × 10⁷ to 3.5 × 10⁷ copies g^-1 dry sediment), but there was no obvious difference in M. nitroreducens-like archaeal abundance between these sediments (3.7 × 10⁵ to 4.8 × 10⁵ copies g^-1 dry sediment). The ¹³CH₄ tracer experiments suggested the occurrence of NO₂^-- and NO₃^--dependent AOM activities, and their rates were 4.7-14.1 and 0.8-2.6 nmol CO₂ g^-1 (dry sediment) d^-1, respectively. Further, the rates of NO₂^--dependent AOM in downstream sediment were significantly higher than those in upstream sediment. The NO₃^- concentration was the key factor affecting the spatial variations of abundance and activity of NO₂^--dependent anaerobic methanotrophs. Overall, our results showed different responses of NO₂^-- and NO₃^--dependent anaerobic methanotrophs to increasing nitrogen loading in a freshwater reservoir.

Methanosarcina acetivorans: A Model for Mechanistic Understanding of Aceticlastic and Reverse Methanogenesis

Acetate-utilizing methanogens are responsible for approximately two-thirds of the one billion metric tons of methane produced annually in Earth's anaerobic environments. Methanosarcina acetivorans has emerged as a model organism for the mechanistic understanding of aceticlastic methanogenesis and reverse methanogenesis applicable to understanding the methane and carbon cycles in nature. It has the largest genome in the Archaea, supporting a metabolic complexity that enables a remarkable ability for adapting to environmental opportunities and challenges. Biochemical investigations have revealed an aceticlastic pathway capable of fermentative and respiratory energy conservation that explains how Ms. acetivorans is able to grow and compete in the environment. The mechanism of respiratory energy conservation also plays a role in overcoming endothermic reactions that are key to reversing methanogenesis.

Niche Differentiation of Sulfate- and Iron-Dependent Anaerobic Methane Oxidation and Methylotrophic Methanogenesis in Deep Sea Methane Seeps

Methane seeps are widespread seafloor ecosystems shaped by complex physicochemical-biological interactions over geological timescales, and seep microbiomes play a vital role in global biogeochemical cycling of key elements on Earth. However, the mechanisms underlying the coexistence of methane-cycling microbial communities remain largely elusive. Here, high-resolution sediment incubation experiments revealed a cryptic methane cycle in the South China Sea (SCS) methane seep ecosystem, showing the coexistence of sulfate (SO4 2-)- or iron (Fe)-dependent anaerobic oxidation of methane (AOM) and methylotrophic methanogenesis. This previously unrecognized methane cycling is not discernible from geochemical profiles due to high net methane consumption. High-throughput sequencing and Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH) results suggested that anaerobic methane-oxidizing archaea (ANME)-2 and -3 coupled to sulfate-reducing bacteria (SRB) carried out SO4 2--AOM, and alternative ANME-2 and -3 solely or coupled to iron-reducing bacteria (IRB) might participate in Fe-AOM in sulfate-depleted environments. This finding suggested that ANME could alter AOM metabolic pathways according to geochemical changes. Furthermore, the majority of methylotrophic methanogens belonged to Methanimicrococcus, and hydrogenotrophic and acetoclastic methanogens were likely inhibited by sulfate or iron respiration. Fe-AOM and methylotrophic methanogenesis are overlooked potential sources and sinks of methane in methane seep ecosystems, thus influencing methane budgets and even the global carbon budget in the ocean.

Abundance and community succession of nitrogen-fixing bacteria in ferrihydrite enriched cultures of paddy soils is closely related to Fe(III)-reduction

In flooded paddy soils, some metal reducers are also capable of nitrogen (N) fixation, which is essential in ensuring a reliable N-supply for rice growth. Microbial iron [Fe(III)] reduction is an important biogeochemical process that can be stimulated by ferrihydrite amendment to paddy soil. Therefore, this study aimed to investigate the abundance and succession of the N₂-fixing bacterial community in ferrihydrite enriched paddy soils collected from Hunan (HN) and Sichuan (SC) provinces, China. The relationship between the N₂-fixing bacterial community and Fe(III) reduction was also assessed. When compared with the control treatment, ferrihydrite enrichment significantly enhanced nitrogenase (nifH) gene abundance by 8.05 × 10⁵ to 4.45 × 10⁶ copies g^-1 soil during the 40-day flooding of HN soil, while nifH gene abundance in SC soil was remarkably increased by 5.90 × 10⁷ to 9.56 × 10⁷ copies g^-1 soil during day 1 to 5 in response to ferrihydrite amendment. The relative abundance of N₂-fixing bacteria peaked on day 5 (21.5% in HN soil and 5.4% in SC soil) and gradually decreased to a stable abundance after day 20. Remarkable increases in relative abundance of N₂-fixing bacteria during the first 10 days of flooding were detected in both soils with ferrihydrite enrichment, whereas little difference was found after day 10 of flooding. During the early stage of flooding, the Shannon and Simpson indexes of N₂-fixing bacteria with ferrihydrite enrichment were significantly decreased, and the community structure changed greatly. Most N₂-fixing bacteria in ferrihydrite enriched paddy soils were phylogenetically related to the order Clostridiales, with some of those potentially capable of Fe(III) reduction. The community succession of N₂-fixing bacteria closely correlated with Fe(III) reduction. Thus, improving N₂-fixation via stimulation of Fe(III) reduction might aid in the reduction of N-fertilizer application to paddy field.

Humic Substances Mediate Anaerobic Methane Oxidation Linked to Nitrous Oxide Reduction in Wetland Sediments

Humic substances are redox-active organic molecules, which play pivotal roles in several biogeochemical cycles due to their electron-transferring capacity involving multiple abiotic and microbial transformations. Based on the redox properties of humic substances, and the metabolic capabilities of microorganisms to reduce and oxidize them, we hypothesized that they could mediate the anaerobic oxidation of methane (AOM) coupled to the reduction of nitrous oxide (N₂O) in wetland sediments. This study provides several lines of evidence indicating the coupling between AOM and the reduction of N₂O through an extracellular electron transfer mechanism mediated by the redox active functional groups in humic substances (e.g., quinones). We found that the microbiota of a sediment collected from the Sisal wetland (Yucatán Peninsula, southeastern Mexico) was able to reduce N₂O (4.6 ± 0.5 μmol N₂O g _sed.^–1 day^–1) when reduced humic substances were provided as electron donor in a close stoichiometric relationship. Furthermore, a microbial enrichment derived from the wetland sediment achieved simultaneous ¹³CH₄ oxidation (1.3 ± 0.1 μmol ¹³CO₂ g _sed.^–1 day^–1) and N₂O reduction (25.2 ± 0.5 μmol N₂O g _sed.^–1 day^–1), which was significantly dependent on the presence of humic substances as an extracellular electron shuttle. Taxonomic characterization based on 16S rRNA gene sequencing revealed Acinetobacter (a ɣ-proteobacterium), the Rice Cluster I from the Methanocellaceae and an uncultured archaeon from the Methanomicrobiaceae family as the microbes potentially involved in AOM linked to N₂O reduction mediated by humic substances. The findings reported here suggest that humic substances might play an important role to prevent the emission of greenhouse gases (CH₄ and N₂O) from wetland sediments. Further efforts to evaluate the feasibility of this novel mechanism under the natural conditions prevailing in ecosystems must be considered in future studies.

Anaerobic Oxidation of Methane in Freshwater Sediments of Rzeszów Reservoir

The anaerobic oxidation of methane (AOM) is an important sink of methane that plays a significant role in global warming. However, evidence for the AOM in freshwater habitats is rare, especially in dam and weir (small-scale dam) reservoirs. Here, the AOM process was examined in freshwater sediments of a small-scale dam reservoir located in Rzeszów, SE Poland. The AOM rate was determined in the main experiment with the addition of the 13CH4 isotope marker (He+13CH4). Sediments were collected three times: in spring (in May, 15 °C), in summer (in July, 20 °C) and in autumn (in September, 10 °C). Further analysis considers the impact on AOM rate of potential electron acceptors present in pore-water (NO2−, NO3−, SO42−, and Fe3+ ions). The work suggests that an AOM process does take place in the studied reservoir sediments, with this evidenced by the presence in the headspace of an increased 13CO2 concentration deemed to derive from 13CH4 oxidation. Rates of AOM noted were of 0.36–1.42 nmol·g−1·h−1, with the most intensive oxidation in each sediment layer occurring at 20 °C. While none of the potential electron acceptors considered individually were found to have had a statistically significant influence on the AOM rate, their significance to the dynamics of the AOM process was not precluded.

Microbial vanadate and nitrate reductions coupled with anaerobic methane oxidation in groundwater

Vanadate contaminant in groundwater receives increasing attentions, but little is known on its biogeochemical transformation with gaseous electron donors. This study investigated bio-reduction of vanadate coupled with anaerobic methane oxidation and its relationship with nitrate reduction. Results showed 95.8 ± 3.1% of 1 mM vanadate was removed within 7 days using methane as the sole electron donor. Tetravalent vanadium compounds were the main reduction products, which precipitated naturally in groundwater environment. The introduction of nitrate inhibited vanadate reduction, though both were reduced in parallel. Accumulations of volatile fatty acids (VFAs) were observed from methane oxidation. Preliminary microbial community structure and metabolite analyses indicated that vanadate was likely reduced via Methylomonas coupled with methane oxidation or through synergistic relationships between methane oxidizing bacteria and heterotrophic vanadate reducers with VFAs served as the intermediates.

Methane emissions from aqueous sediments are influenced by complex interactions among microbes and environmental factors: A modeling study

Methane fluxes from aqueous sediments strongly influence global atmospheric methane. However, many questions still puzzle researchers; for example, why are some unstable sediments atmospheric methane sinks? In this study, a biofilm model originally developed for wastewater treatment was modified to simulate the microbial kinetics and substance conversions in aqueous surface sediments. The model was validated by the experimental data and could predict chemical profiles and microbial distributions in sediments. The model revealed complicated interactions between different microbial communities and environmental factors, including competition between aerobic methane-oxidizing bacteria, nitrite-dependent anaerobic methane-oxidizing bacteria, and anaerobic ammonia-oxidizing bacteria. The results of model simulations showed that the effects of environmental factors, especially dissolved oxygen and ammonia in overlying water, on methane fluxes are very complicated. Rapid environmental changes (which can be caused by tide, day-night alternation, or zoobenthic and human activity) and intensive competition between microbes greatly affected methane fluxes and resulted in alternation between atmospheric methane source and sink in unstable sediments. This study extends the application of a wastewater treatment model to ecological studies of microbial interactions in natural sediments and explains some problems that might be difficult to resolve by using experimental methods.

Geochemical Evidence of Metal-Driven Anaerobic Oxidation of Methane in the Shenhu Area, the South China Sea

Anaerobic oxidation of methane (AOM) is a common biochemical process in the ocean and it plays an important role in global climate change, elemental circulation, and atmospheric evolution over geological time. In this paper, we analyzed of δ³⁴S, Fe, Mn, Ca/Ti, and Sr/Ti ratios, and the date of carbon and sulfur from the site SH3 of Shenhu area. Result showed that (1) 0-6 mbsf (meter blow the sea floor) was mainly affected by OSR (anaerobic oxidation of organic matters) and 7-15 mbsf was a paleo-SMTZ (sulfate-methane transition zone) position. The modern SMTZ was mainly distributed at 19-25 mbsf. The barium sulfate precipitation above the modern SMTZ indicating that the current methane leakage was stable and lasted longer during geological history. (2) By studying the change of magnetic and the different carbonate minerals, results showed that there were two AOM stages. During the early stage, Fe²⁺ were mainly produced by sulfide abiotic reductive dissolution. During the later stage, Fe²⁺ were mainly produced by the metal-AOM. (3) Study of the mineral characteristics of the paleo-SMTZ and the modern SMTZ showed that the modern SMTZ carbonate minerals were mainly low-Mg calcite and aragonite, while the paleo-SMTZ carbon minerals were mainly high Mg minerals. The reason for this difference is that the modern SMTZ layer was only experienced the first stage of anaerobic oxidation of methane. In the paleo-SMTZ layer, it has experienced two stage of anaerobic oxidation of methane. During the last stage of metal-AOM, the low Mg carbonate minerals were converted into high Mg carbonate minerals. This research confirms the presence of metal-driven methane anaerobic oxidation at the bottom of sulfate-driven methane anaerobic oxidation and during the metal-driven methane anaerobic oxidation, methane and metal oxides or hydroxides would couple to convert the in situ metal oxides or hydroxides into metal ions, meanwhile the phosphorus adsorbed on the surface of the metal oxides is released into adjacent pore water, and convert to new P-bearing minerals under suitable conditions.

Physiology and Distribution of Archaeal Methanotrophs That Couple Anaerobic Oxidation of Methane with Sulfate Reduction

In marine anaerobic environments, methane is oxidized where sulfate-rich seawater meets biogenic or thermogenic methane. In those niches, a few phylogenetically distinct microbial types, i.e., anaerobic methanotrophs (ANME), are able to grow through anaerobic oxidation of methane (AOM). Due to the relevance of methane in the global carbon cycle, ANME have drawn the attention of a broad scientific community for 4 decades. This review presents and discusses the microbiology and physiology of ANME up to the recent discoveries, revealing novel physiological types of anaerobic methane oxidizers which challenge the view of obligate syntrophy for AOM. An overview of the drivers shaping the distribution of ANME in different marine habitats, from cold seep sediments to hydrothermal vents, is given. Multivariate analyses of the abundance of ANME in various habitats identify a distribution of distinct ANME types driven by the mode of methane transport. Intriguingly, ANME have not yet been cultivated in pure culture, despite intense attempts. Further advances in understanding this microbial process are hampered by insufficient amounts of enriched cultures. This review discusses the advantages, limitations, and potential improvements for ANME laboratory-based cultivation systems.

Thermophilic methanotrophs: in hot pursuit

Methane is a potent greenhouse gas responsible for 20–30% of global climate change effects. The global methane budget is ∼500–600 Tg y−1, with the majority of methane produced via microbial processes, including anthropogenic-mediated sources such as ruminant animals, rice fields, sewage treatment facilities and landfills. It is estimated that microbially mediated methane oxidation (methanotrophy) consumes >50% of global methane flux each year. Methanotrophy research has primarily focused on mesophilic methanotrophic representatives and cooler environments such as freshwater, wetlands or marine habitats from which they are sourced. Nevertheless, geothermal emissions of geological methane, produced from magma and lithosphere degassing micro-seepages, mud volcanoes and other geological sources, contribute an estimated 33–75 Tg y−1 to the global methane budget. The aim of this review is to summarise current literature pertaining to the activity of thermophilic and thermotolerant methanotrophs, both proteobacterial (Methylocaldum, Methylococcus, Methylothermus) and verrucomicrobial (Methylacidiphilum). We assert, on the basis of recently reported molecular and geochemical data, that geothermal ecosystems host hitherto unidentified species capable of methane oxidation at higher temperatures.