Iron oxides stimulate sulfate-driven anaerobic methane oxidation in seeps

Sulfide Toxicity as Key Control on Anaerobic Oxidation of Methane in Eutrophic Coastal Sediments

Coastal zones account for 75% of marine methane emissions, despite covering only 15% of the ocean surface area. In these ecosystems, the tight balance between methane production and oxidation in sediments prevents most methane from escaping into seawater. However, anthropogenic activities could disrupt this balance, leading to an increased methane escape from coastal sediments. To quantify and unravel potential mechanisms underlying this disruption, we used a suite of biogeochemical and microbiological analyses to investigate the impact of anthropogenically induced redox shifts on methane cycling in sediments from three sites with contrasting bottom water redox conditions (oxic-hypoxic-euxinic) in the eutrophic Stockholm Archipelago. Our results indicate that the methane production potential increased under hypoxia and euxinia, while anaerobic oxidation of methane was disrupted under euxinia. Experimental, genomic, and biogeochemical data suggest that the virtual disappearance of methane-oxidizing archaea at the euxinic site occurred due to sulfide toxicity. This could explain a near 7-fold increase in the extent of escape of benthic methane at the euxinic site relative to the hypoxic one. In conclusion, these insights reveal how the development of euxinia could disrupt the coastal methane biofilter, potentially leading to increased methane emissions from coastal zones.

Sulfur cycling likely obscures dynamic biologically-driven iron redox cycling in contemporary methane seep environments

Deep-sea methane seeps are amongst the most biologically productive environments on Earth and are often characterised by stable, low oxygen concentrations and microbial communities that couple the anaerobic oxidation of methane to sulfate reduction or iron reduction in the underlying sediment. At these sites, ferrous iron (Fe2+) can be produced by organoclastic iron reduction, methanotrophic-coupled iron reduction, or through the abiotic reduction by sulfide produced by the abundant sulfate-reducing bacteria at these sites. The prevalence of Fe2+in the anoxic sediments, as well as the availability of oxygen in the overlying water, suggests that seeps could also harbour communities of iron-oxidising microbes. However, it is unclear to what extent Fe2+ remains bioavailable and in solution given that the abiotic reaction between sulfide and ferrous iron is often assumed to scavenge all ferrous iron as insoluble iron sulfides and pyrite. Accordingly, we searched the sea floor at methane seeps along the Cascadia Margin for microaerobic, neutrophilic iron-oxidising bacteria, operating under the reasoning that if iron-oxidising bacteria could be isolated from these environments, it could indicate that porewater Fe2+ can persist is long enough for biology to outcompete pyritisation. We found that the presence of sulfate in our enrichment media muted any obvious microbially-driven iron oxidation with most iron being precipitated as iron sulfides. Transfer of enrichment cultures to sulfate-depleted media led to dynamic iron redox cycling relative to abiotic controls and sulfate-containing cultures, and demonstrated the capacity for biogenic iron (oxyhydr)oxides from a methane seep-derived community. 16S rRNA analyses revealed that removing sulfate drastically reduced the diversity of enrichment cultures and caused a general shift from a Gammaproteobacteria-domainated ecosystem to one dominated by Rhodobacteraceae (Alphaproteobacteria). Our data suggest that, in most cases, sulfur cycling may restrict the biological "ferrous wheel" in contemporary environments through a combination of the sulfur-adapted sediment-dwelling ecosystems and the abiotic reactions they influence.

Insights into biogeochemistry and hot spots distribution characteristics of redox-sensitive elements in the hyporheic zone: Transformation mechanisms and contributing factors

Biogeochemical hot spots play a crucial role in the cycling and transport of redox-sensitive elements (RSEs) in the hyporheic zone (HZ). However, the transformation mechanisms of RSEs and patterns of RSEs hot spots in the HZ remain poorly understood. In this study, hydrochemistry and multi-isotope (N/C/S/O) datasets were collected to investigate the transformation mechanisms of RSEs, and explore the distribution characteristics of RSEs transformation hot spots. The results showed that spatial variability in key drivers was evident, while temporal change in RSEs concentration was not significant, except for dissolved organic carbon. Bacterial sulfate reduction (BSR) was the primary biogeochemical process for sulfate and occurred throughout the area. Ammonium enrichment was mainly caused by the mineralization of nitrogenous organic matter and anthropogenic inputs, with adsorption serving as the primary attenuation mechanism. Carbon dynamics were influenced by various biogeochemical processes, with dissolved organic carbon mainly derived from C3 plants and dissolved inorganic carbon from weathering of carbonate rocks and decomposition of organic matter. The peak contribution of dissolved organic carbon decomposition to the DIC pool was 46.44 %. The concentration thresholds for the ammonium enrichment and BSR hot spots were identified as 1.5 mg/L and 8.84 mg/L, respectively. The distribution pattern of RSEs hot spots was closely related to the hydrogeological conditions. Our findings reveal the complex evolution mechanisms and hot spots distribution characteristics of RSEs in the HZ, providing a basis for the safe utilization and protection of groundwater resources.

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.

Aerobic methanotrophy increases the net iron reduction in methanogenic lake sediments

In methane (CH4) generating sediments, methane oxidation coupled with iron reduction was suggested to be catalyzed by archaea and bacterial methanotrophs of the order Methylococcales. However, the co-existence of these aerobic and anaerobic microbes, the link between the processes, and the oxygen requirement for the bacterial methanotrophs have remained unclear. Here, we show how stimulation of aerobic methane oxidation at an energetically low experimental environment influences net iron reduction, accompanied by distinct microbial community changes and lipid biomarker patterns. We performed incubation experiments (between 30 and 120 days long) with methane generating lake sediments amended with 13C-labeled methane, following the additions of hematite and different oxygen levels in nitrogen headspace, and monitored methane turnover by 13C-DIC measurements. Increasing oxygen exposure (up to 1%) promoted aerobic methanotrophy, considerable net iron reduction, and the increase of microbes, such as Methylomonas, Geobacter, and Desulfuromonas, with the latter two being likely candidates for iron recycling. Amendments of 13C-labeled methanol as a potential substrate for the methanotrophs under hypoxia instead of methane indicate that this substrate primarily fuels methylotrophic methanogenesis, identified by high methane concentrations, strongly positive δ13CDIC values, and archaeal lipid stable isotope data. In contrast, the inhibition of methanogenesis by 2-bromoethanesulfonate (BES) led to increased methanol turnover, as suggested by similar 13C enrichment in DIC and high amounts of newly produced bacterial fatty acids, probably derived from heterotrophic bacteria. Our experiments show a complex link between aerobic methanotrophy and iron reduction, which indicates iron recycling as a survival mechanism for microbes under hypoxia.

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.

Revisiting the biological pathway for methanogenesis in landfill from metagenomic perspective-A case study of county-level sanitary landfill of domestic waste in North China plain

Landfill is the third highest contributor to anthropogenic methane (CH₄) emissions, produced primarily by the anaerobic decomposition of organic matter by microbes. However, how various microbial metabolic processes contribute to CH₄ production in domestic waste landfill remains elusive. We addressed this problem by investigating the methanogenic communities, methanogenic functional genes, KEGG modules and KEGG pathways in a county-level MSW sanitary landfill in North China Plain, China. Results showed that Methanomicrobiales, Methanobacteriales, Methanosarcinales, Micrococcales, Corynebacteriales and Bacillales were the dominant methanogens. M00357, M00346, M00567 and M00563 were the four major methane metabolic modules. The most abundant genes were ACSS, ackA and fwd with the relative abundance of 19.26-54.54%, 6.14-25.78% and 6.76-16.51%, respectively. The two essential genes of methanogenesis were detected with the relative abundance of 2.66-9.58% (mtr) and 1.63-9.14% (mcr). These findings indicated that acetotrophic and hydrogenotrophic methanogenesis were the major pathways. Methanomicrobiales, Methanosarcinales and Clostridiales were the key microbes to these pathways identified by co-occurrence network. Analysis of relative contribution of species to function further showed that Micrococcales, Corynebacteriales and Bacillales were special contributors to acetotrophic methanogenesis pathway. Redundancy analysis revealed that above functional genes and microbes were mainly controlled by NH₄⁺ and pH. Our results can help to provide develop the fine management strategies for methane utilization and emission reduction in landfill.

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.

Iron-based passivator mitigates the coupling process of anaerobic methane oxidation and arsenate reduction in paddy soils

Arsenic (As) is a toxic metalloid that is ubiquitous in paddy soils, where passivation is the most widely used method for remediating As contamination. Recently, anaerobic methane oxidation coupled with arsenate (As(V)) reduction (AOM-AsR) has been shown to act as a critical driver for As release in paddy fields. However, the effect and mechanism of the passivators on the AOM-AsR process remain unclear. In this study, we incubated arsenate-contaminated paddy soils under anaerobic conditions. Using isotopically labelled methane and different passivators, we found that an iron-based passivator containing calcium sulfate and iron oxide (9:1, m/m) named IBP showed a much better performance than the other passivators. Adding IBP decreased the arsenite (As(III)) concentration in the soil solution by 78% and increased the AOM rate by 55%. Furthermore, we employed high-throughput sequencing and real-time quantitative polymerase chain reaction (qPCR) to investigate the ability of IBP to control As release mediated by AOM-AsR in paddy fields, as well as its underlying mechanism. Our results showed that IBP addition significantly increased anaerobic methanotrophic (ANME) archaea (ANME-2a-c, ANME-2d, and ANME-3) by 91%, and increased the methane-oxidizing bacterium Methylobacter by 262%. Similarly, IBP addition significantly increased the Fe(III) concentration in soil solution by 39% and increased the absolute abundance of Fe(III)-reducing bacteria (Geobacteraceae) by 21 times in soil. Adding IBP may significantly promote AOM coupled with Fe(III) reduction, significantly reducing electron transfer from AOM to As(V) reduction. Hence, IBP may be used as an efficient passivator to remediate As-contaminated soil using an active AOM-AsR process. These results provide a novel insight into controlling soil As release by regulating an active and critical As mobilization pathway in the environment.

Hydrobiogechemical interactions in the hyporheic zone of a sulfate-impacted, freshwater stream and riparian wetland ecosystem

Coupled abiotic and biotic processes in the hyporheic zone, where surface water and groundwater mix, play a critical role in the biogeochemical cycling of carbon, nutrients, and trace elements in streams and wetlands. Dynamic hydrologic conditions and anthropogenic pollution can impact redox gradients and biogeochemical response, although few studies examine the resulting hydrobiogeochemical interactions generated within the hyporheic zone. This study examines the effect of hyporheic flux dynamics and anthropogenic sulfate loading on the biogeochemistry of a riparian wetland and stream system. The hydrologic gradient as well as sediment, surface water, and porewater geochemistry chemistry was characterized at multiple points throughout the 2017 spring-summer-fall season at a sulfate-impacted stream flanked by wetlands in northern Minnesota. Results show that organic-rich sediments largely buffer the geochemical responses to brief or low magnitude changes in hydrologic gradient, but sustained or higher magnitude fluxes may variably alter the redox regime and, ultimately, the environmental geochemistry. This has implications for a changing climate that is expected to dramatically alter the hydrological cycle. Further, increased sulfate loading and dissolved or adsorbed ferric iron complexes in the hyporheic zone may induce a cryptic sulfur cycle linked to iron and carbon cycling, as indicated by the abundance of intermediate valence sulfur compounds (e.g., polysulfide, elemental sulfur, thiosulfate) throughout the anoxic wetland and stream-channel sediment column. The observed deviation from a classical redox tower coupled with potential changes in hydraulic gradient in these organic-rich wetland and stream hyporheic zones has implications for nutrient, trace element, and greenhouse gas fluxes into surface water and groundwater, ultimately influencing water quality and global climate.

A Reduced F420-Dependent Nitrite Reductase in an Anaerobic Methanotrophic Archaeon

Anaerobic methanotrophic archaea (ANME), which oxidize methane in marine sediments through syntrophic associations with sulfate-reducing bacteria, carry homologs of coenzyme F₄₂₀-dependent sulfite reductase (Fsr) of Methanocaldococcus jannaschii, a hyperthermophilic methanogen from deep-sea hydrothermal vents. M. jannaschii Fsr (MjFsr) and ANME-Fsr belong to two phylogenetically distinct groups, FsrI and FsrII, respectively. MjFsrI reduces sulfite to sulfide with reduced F₄₂₀ (F₄₂₀H₂), protecting methyl coenzyme M reductase (Mcr), an essential enzyme for methanogens, from sulfite inhibition. However, the function of FsrIIs in ANME, which also rely on Mcr and live in sulfidic environments, is unknown. We have determined the catalytic properties of FsrII from a member of ANME-2c. Since ANME remain to be isolated, we expressed ANME2c-FsrII in a closely related methanogen, Methanosarcina acetivorans. Purified recombinant FsrII contained siroheme, indicating that the methanogen, which lacks a native sulfite reductase, produced this coenzyme. Unexpectedly, FsrII could not reduce sulfite or thiosulfate with F₄₂₀H₂. Instead, it acted as an F₄₂₀H₂-dependent nitrite reductase (FNiR) with physiologically relevant K_m values (nitrite, 5 μM; F₄₂₀H_2, 14 μM). From kinetic, thermodynamic, and structural analyses, we hypothesize that in FNiR, F₄₂₀H₂-derived electrons are delivered at the oxyanion reduction site at a redox potential that is suitable for reducing nitrite (E⁰' [standard potential], +440 mV) but not sulfite (E⁰', -116 mV). These findings and the known nitrite sensitivity of Mcr suggest that FNiR may protect nondenitrifying ANME from nitrite toxicity. Remarkably, by reorganizing the reductant processing system, Fsr transforms two analogous oxyanions in two distinct archaeal lineages with different physiologies and ecologies. IMPORTANCE Coenzyme F₄₂₀-dependent sulfite reductase (Fsr) protects methanogenic archaea inhabiting deep-sea hydrothermal vents from the inactivation of methyl coenzyme M reductase (Mcr), one of their essential energy production enzymes. Anaerobic methanotrophic archaea (ANME) that oxidize methane and rely on Mcr, carry Fsr homologs that form a distinct clade. We show that a member of this clade from ANME-2c functions as F₄₂₀-dependent nitrite reductase (FNiR) and lacks Fsr activity. This specialization arose from a distinct feature of the reductant processing system and not the substrate recognition element. We hypothesize FNiR may protect ANME Mcr from inactivation by nitrite. This is an example of functional specialization within a protein family that is induced by changes in electron transfer modules to fit an ecological need.

Diversity of Anaerobic Methane Oxidizers in the Cold Seep Sediments of the Okinawa Trough

Active cold seeps in the Okinawa Trough (OT) have been widely identified, but the sediment microbial communities associated with these sites are still poorly understood. Here, we investigated the distribution and biomass of the microbial communities, particularly those associated with the anaerobic oxidation of methane (AOM), in sediments from an active cold seep in the mid-Okinawa Trough. Methane-oxidizing archaea, including ANME-1a, ANME-1b, ANME-2a/b, ANME-2c, and ANME-3, were detected in the OT cold seep sediments. Vertical stratification of anaerobic methanotrophic archaea (ANME) communities was observed in the following order: ANME-3, ANME-1a, and ANME-1b. In addition, the abundance of methyl coenzyme M reductase A (mcrA) genes corresponded to high levels of dissolved iron, suggesting that methane-metabolizing archaea might participate in iron reduction coupled to methane oxidation (Fe-AOM) in the OT cold seep. Furthermore, the relative abundance of ANME-1a was strongly related to the concentration of dissolved iron, indicating that ANME-1a is a key microbial player for Fe-AOM in the OT cold seep sediments. Co-occurrence analysis revealed that methane-metabolizing microbial communities were mainly associated with heterotrophic microorganisms, such as JS1, Bathy-1, and Bathy-15.

A Genome-Scale Metabolic Model of Methanoperedens nitroreducens: Assessing Bioenergetics and Thermodynamic Feasibility

Methane is an abundant low-carbon fuel that provides a valuable energy resource, but it is also a potent greenhouse gas. Therefore, anaerobic oxidation of methane (AOM) is an essential process with central features in controlling the carbon cycle. Candidatus ‘Methanoperedens nitroreducens’ (M. nitroreducens) is a recently discovered methanotrophic archaeon capable of performing AOM via a reverse methanogenesis pathway utilizing nitrate as the terminal electron acceptor. Recently, reverse methanogenic pathways and energy metabolism among anaerobic methane-oxidizing archaea (ANME) have gained significant interest. However, the energetics and the mechanism for electron transport in nitrate-dependent AOM performed by M. nitroreducens is unclear. This paper presents a genome-scale metabolic model of M. nitroreducens, iMN22HE, which contains 813 reactions and 684 metabolites. The model describes its cellular metabolism and can quantitatively predict its growth phenotypes. The essentiality of the cytoplasmic heterodisulfide reductase HdrABC in the reverse methanogenesis pathway is examined by modeling the electron transfer direction and the specific energy-coupling mechanism. Furthermore, based on better understanding electron transport by modeling, a new energy transfer mechanism is suggested. The new mechanism involves reactions capable of driving the endergonic reactions in nitrate-dependent AOM, including the step reactions in reverse canonical methanogenesis and the novel electron-confurcating reaction HdrABC. The genome metabolic model not only provides an in silico tool for understanding the fundamental metabolism of ANME but also helps to better understand the reverse methanogenesis energetics and its thermodynamic feasibility.

Spatial distribution and biogeochemistry of redox active species in arctic sedimentary porewaters and seeps

Redox active species in Arctic lacustrine sediments play an important, regulatory role in the carbon cycle, yet there is little information on their spatial distribution, abundance, and oxidation states. Here, we use voltammetric microelectrodes to quantify the in situ concentrations of redox-active species at high vertical resolution (mm to cm) in the benthic porewaters of an oligotrophic Arctic lake (Toolik Lake, AK, USA). Mn(II), Fe(II), O₂, and Fe(III)-organic complexes were detected as the major redox-active species in these porewaters, indicating both Fe(II) oxidation and reductive dissolution of Fe(III) and Mn(IV) minerals. We observed significant spatial heterogeneity in their abundance and distribution as a function of both location within the lake and depth. Microbiological analyses and solid phase Fe(III) measurements were performed in one of the Toolik Lake cores to determine the relationship between biogeochemical redox gradients and microbial communities. Our data reveal iron cycling involving both oxidizing (FeOB) and reducing (FeRB) bacteria. Additionally, we profiled a large microbial iron mat in a tundra seep adjacent to an Arctic stream (Oksrukuyik Creek) where we observed Fe(II) and soluble Fe(III) in a highly reducing environment. The variable distribution of redox-active substances at all the sites yields insights into the nature and distribution of the important terminal electron acceptors in both lacustrine and tundra environments capable of exerting significant influences on the carbon cycle.

Insight into SO4(-II)- dependent anaerobic methane oxidation in landfill: Dual-substrates dynamics model, microbial community, function and metabolic pathway

In anaerobic landfill, SO42- could serve as electron receptor for methane oxidation. In theory, concentrations of both methane and SO42- should be related to methane oxidation rate. However, the dynamics process has yet to be discovered, and the understanding of metabolic pathways of the sulfate-dependent anaerobic methane oxidation (S-DAMO) process in landfill remains limited. In this study, S-DAMO dynamics was investigated by observing the CH4 oxidation rates under different CH4/ SO42-counter-gradients. The CH4-SO42- dual-substrate model based on MichaeliseMenten equation was got (maximum substrate degradation rate Vmax [22.9 ± 1.31] µmol/[kg·d], half-saturation constants [Formula: see text] , and [Formula: see text] ). High-throughput sequencing analysis indicated Methanobacterials, Methanosarcinales, and Soil Crenarchaeotic were the main functional microorganisms for S-DAMO in landfill. The metabolic pathway of S-DAMO was speculated as the reverse methanogenesis pathway through Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUST) analysis, while methanogenesis was the methyl nutrition way based on methanol. The enzymes related to the carbon and sulfur cycles and their relative abundances in the microcosms were analyzed to graph the methane metabolic pathway and the sulfur metabolic pathway. The findings provide important parameters for CH4 mitigation in landfills, and give a new insight for understanding S-DAMO metabolic pathway in landfill.

Methanogen Productivity and Microbial Community Composition Varies With Iron Oxide Mineralogy

Quantifying the flux of methane from terrestrial environments remains challenging, owing to considerable spatial and temporal variability in emissions. Amongst a myriad of factors, variation in the composition of electron acceptors, including metal (oxyhydr)oxides, may impart controls on methane emission. The purpose of this research is to understand how iron (oxyhydr)oxide minerals with varied physicochemical properties influence microbial methane production and subsequent microbial community development. Incubation experiments, using lake sediment as an inoculum and acetate as a carbon source, were used to understand the influence of one poorly crystalline iron oxide mineral, ferrihydrite, and two well-crystalline minerals, hematite and goethite, on methane production. Iron speciation, headspace methane, and 16S-rRNA sequencing microbial community data were measured over time. Substantial iron reduction only occurred in the presence of ferrihydrite while hematite and goethite had little effect on methane production throughout the incubations. In ferrihydrite experiments the time taken to reach the maximum methane production rate was slower than under other conditions, but methane production, eventually occurred in the presence of ferrihydrite. We suggest that this is due to ferrihydrite transformation into more stable minerals like magnetite and goethite or surface passivation by Fe(II). While all experimental conditions enriched for Methanosarcina, only the presence of ferrihydrite enriched for iron reducing bacteria Geobacter. Additionally, the presence of ferrihydrite continued to influence microbial community development after the onset of methanogenesis, with the dissimilarity between communities growing in ferrihydrite compared to no-Fe-added controls increasing over time. This work improves our understanding of how the presence of different iron oxides influences microbial community composition and methane production in soils and sediments.

Independent of direct interspecies electron transfer: Magnetite-mediated sulphur cycle for anaerobic degradation of benzoate under low-concentration sulphate conditions

The aim of this study was to investigate the primary mechanism of magnetite promoting anaerobic degradation of aromatic compounds under the low-concentration sulphate conditions. Under influent conditions of benzoate at 50 mM-chemical oxygen demand (COD) and sulphate at 15 mM, magnetite promoted benzoate degradation (77.1% vs 56.3%), while the effluent sulphate concentration was slightly higher than that without magnetite (1.6 mM vs 0.7 mM), inconsistent with functional gene prediction that both sulphate respiration and sulphur compound respiration were relatively more active in the presence of magnetite. Remarkably, X-ray diffraction showed that, signal related to Fe₃O₄ faded away and finally was replaced by FeSO₄ and FeS, indicating that magnetite participated in benzoate degradation coupled to sulphate reduction via dissimilatory Fe(III) reduction. Further X-ray photoelectron spectroscopy showed that, signal related to S⁰ was only detected with magnetite, suggesting the possibility of re-oxidation of sulphide to elemental sulphur coupled to Fe(III) reduction. This was further supported by the increase in abundance of Desulfuromonas acetexigens capable of growing on Fe(III). In addition, magnetite specially enriched the chemolithotrophic sulphur-disproportionating microbes, Desulfovibrio aminophilus, which might proceed the disproportionation of elemental sulphur to sulphate and sulphide to achieve a sulphur cycle for benzoate degradation.

Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site

During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (LFLS, Sydney, Australia). The microbial function and population dynamics in a waste trench during a rainfall event have been previously investigated revealing a broad abundance of candidate and potentially undescribed taxa in this iron-rich, radionuclide-contaminated environment. Applying genome-based metagenomic methods, we recovered 37 refined archaeal MAGs, mainly from undescribed DPANN Archaea lineages without standing in nomenclature and 'Candidatus Methanoperedenaceae' (ANME-2D). Within the undescribed DPANN, the newly proposed orders 'Ca. Gugararchaeales', 'Ca. Burarchaeales' and 'Ca. Anstonellales', constitute distinct lineages with a more comprehensive central metabolism and anabolic capabilities within the 'Ca. Micrarchaeota' phylum compared to most other DPANN. The analysis of new and extant 'Ca. Methanoperedens spp.' MAGs suggests metal ions as the ancestral electron acceptors during the anaerobic oxidation of methane while the respiration of nitrate/nitrite via molybdopterin oxidoreductases would have been a secondary acquisition. The presence of genes for the biosynthesis of polyhydroxyalkanoates in most 'Ca. Methanoperedens' also appears to be a widespread characteristic of the genus for carbon accumulation. This work expands our knowledge about the roles of the Archaea at the LFLS, especially, DPANN Archaea and 'Ca. Methanoperedens', while exploring their diversity, uniqueness, potential role in elemental cycling, and evolutionary history.

Nitrate-dependent anaerobic methane oxidation and chemolithotrophic denitrification in a temperate eutrophic lake

While the emissions of methane (CH4) by natural systems have been widely investigated, CH4 aquatic sinks are still poorly constrained. Here, we investigated the CH4 cycle and its interactions with nitrogen (N), iron (Fe) and manganese (Mn) cycles in the oxic-anoxic interface and deep anoxic waters of a small, meromictic and eutrophic lake, during two summertime sampling campaigns. Anaerobic CH4 oxidation (AOM) was measured from the temporal decrease of CH4 concentrations, with the addition of three potential electron acceptors (NO3-, iron oxides (Fe(OH)3) and manganese oxides (MnO2)). Experiments with the addition of either 15N-labeled nitrate (15N-NO3-) or 15N-NO3- combined with sulfide (H2S), to measure denitrification, chemolithotrophic denitrification and anaerobic ammonium oxidation (anammox) rates, were also performed. Measurements showed AOM rates up to 3.8 µmol CH4 L-1 d-1 that strongly increased with the addition of NO3- and moderately increased with the addition of Fe(OH)3. No stimulation was observed with MnO2 added. Potential denitrification and anammox rates up to 63 and 0.27 µmol N2 L-1 d-1, respectively, were measured when only 15N-NO3- was added. When H2S was added, both denitrification and anammox rates increased. Altogether, these results suggest that prokaryote communities in the redoxcline are able to efficiently use the most available substrates.

Exploring simultaneous nitrous oxide and methane sink in wetland sediments under anoxic conditions

Methane (CH₄) and nitrous oxide (N₂O) are the most powerful greenhouse gases globally; recent emissions exceed previous estimates. The potential link between N₂O reduction and CH₄ oxidation in anoxic wetland sediments would be a sink for both gases, which has attracted broad attention. To explore the simultaneous N₂O and CH₄ biotransformation, wetland sediments were used to inoculate an enrichment reactor, continuously fed with CH₄ and N₂O for 500 days. After enrichment, the CH₄ oxidation rate reached 2.8 μmol·g^-1_dw·d^-1, which was 800-fold higher than the rate of the wetland sediments used as inoculum. Moreover, stable isotopic tracing proved CH₄ oxidation was driven by N₂O consumption under anoxic conditions. Genomic sequencing showed that the microbial community was dominated by methanotrophs. Species of Methylocaldum genus, belonging to γ-Proteobacteria class, were significantly enriched, and became the predominant methanotrophs. Quantitative analysis indicated methane monooxygenase and nitrous oxide reductase increased by 38- and 8-fold compared to the inoculum. As to the potential mechanisms, we propose that N₂O-driven CH₄ oxidation was mediated by aerobic methanotrophs solely or along with denitrifying bacteria under hypoxia. Electrons and energy are generated and transferred in the oxidative phosphorylation pathway. Our findings expand the range of electron acceptors associated with CH₄ oxidation as well as elucidate the significant role of methanotrophs relative to both carbon and nitrogen cycles.

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.

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.

Methyl-compounds driven benthic carbon cycling in the sulfate-reducing sediments of South China Sea

Methane is a potent greenhouse gas; methane production and consumption within seafloor sediments has generated intense interest. Anaerobic oxidation of methane (AOM) and methanogenesis (MOG) primarily occur at the depth of the sulfate-methane transition zone or underlying sediment respectively. Methanogenesis can also occur in the sulfate-reducing sediments through the utilization of non-competitive methylated compounds; however, the occurrence and importance of this process are not fully understood. Here, we combined a variety of data, including geochemical measurements, rate measurements and molecular analyses to demonstrate the presence of a cryptic methane cycle in sulfate-reducing sediments from the continental shelf of the northern South China Sea. The abundance of methanogenic substrates as well as the high MOG rates from methylated compounds indicated that methylotrophic methanogenesis was the dominant methanogenic pathway; this conclusion was further supported by the presence of the methylotrophic genus Methanococcoides. High potential rates of AOM were observed in the sediments, indicating that methane produced in situ could be oxidized simultaneously by AOM, presumably by ANME-2a/b as indicated by 16S rRNA gene analysis. A significant correlation between the relative abundance of methanogens and methanotrophs was observed over sediment depth, indicating that methylotrophic methanogenesis could potentially fuel AOM in this environment. In addition, higher potential rates of AOM than sulfate reduction rates at in situ methane conditions were observed, making alternative electron acceptors important to support AOM in sulfate-reducing sediment. AOM rates were stimulated by the addition of Fe/Mn oxides, suggesting AOM could be partially coupled to metal oxide reduction. These results suggest that methyl-compounds driven methane production drives a cryptic methane cycling and fuels AOM coupled to the reduction of sulfate and other electron acceptors.

A Review of Landfill Microbiology and Ecology: A Call for Modernization With 'Next Generation' Technology

Engineered and monitored sanitary landfills have been widespread in the United States since the passage of the Clean Water Act (1972) with additional controls under RCRA Subtitle D (1991) and the Clean Air Act Amendments (1996). Concurrently, many common perceptions regarding landfill biogeochemical and microbiological processes and estimated rates of gas production also date from 2 to 4 decades ago. Herein, we summarize the recent application of modern microbiological tools as well as recent metadata analysis using California, USEPA and international data to outline an evolving view of landfill biogeochemical/microbiological processes and rates. We focus on United States landfills because these are uniformly subject to stringent national and state requirements for design, operations, monitoring, and reporting. From a microbiological perspective, because anoxic conditions and methanogenesis are rapidly established after daily burial of waste and application of cover soil, the >1000 United States landfills with thicknesses up to >100 m form a large ubiquitous group of dispersed 'dark' ecosystems dominated by anaerobic microbial decomposition pathways for food, garden waste, and paper substrates. We review past findings of landfill ecosystem processes, and reflect on the potential impact that application of modern sequencing technologies (e.g., high throughput platforms) could have on this area of research. Moreover, due to the ever evolving composition of landfilled waste reflecting transient societal practices, we also consider unusual microbial processes known or suspected to occur in landfill settings, and posit areas of research that will be needed in coming decades. With growing concerns about greenhouse gas emissions and controls, the increase of chemicals of emerging concern in the waste stream, and the potential resource that waste streams represent, application of modernized molecular and microbiological methods to landfill ecosystem research is of paramount importance.

High-Throughput Sequencing Reveals a Potentially Novel Sulfurovum Species Dominating the Microbial Communities of the Seawater-Sediment Interface of a Deep-Sea Cold Seep in South China Sea

In the Formosa cold seep of the South China Sea (SCS), large amounts of methane and sulfide hydrogen are released from the subseafloor. In this study, we systematically investigated the microbial communities in the seawater–sediment interface of Formosa cold seep using high-throughput sequencing techniques including amplicon sequencing based on next-generation sequencing and Pacbio amplicon sequencing platforms, and metagenomics. We found that Sulfurovum dominated the microbial communities in the sediment–seawater interface, including the seawater close to the seepage, the surface sediments, and the gills of the dominant animal inhabitant (Shinkaia crosnieri). A nearly complete 16S rRNA gene sequence of the dominant operational taxonomic units (OTUs) was obtained from the Pacbio sequencing platforms and classified as OTU-L1, which belonged to Sulfurovum. This OTU was potentially novel as it shared relatively low similarity percentages (<97%) of the gene sequence with its close phylogenetic species. Further, a draft genome of Sulfurovum was assembled using the binning technique based on metagenomic data. Genome analysis suggested that Sulfurovum sp. in this region may fix carbon by the reductive tricarboxylic acid (rTCA) pathway, obtain energy by oxidizing reduced sulfur through sulfur oxidizing (Sox) pathway, and utilize nitrate as electron acceptors. These results demonstrated that Sulfurovum probably plays an important role in the carbon, sulfur, and nitrogen cycles of the Formosa cold seep of the SCS. This study improves our understanding of the diversity, distribution, and function of sulfur-oxidizing bacteria in deep-sea cold seep.

Enhancing anaerobic oxidation of methane in municipal solid waste landfill cover soil

Landfills are the third largest anthropogenic source of the greenhouse gas methane worldwide. In the upper portions of landfill covers, methane is oxidized aerobically by microorganisms to form the less-potent greenhouse gas carbon dioxide; however, because of the low permeability of oxygen, no aerobic oxidation occurs in deeper portions of the cover. Therefore, the goal of this study was to enhance anaerobic oxidation of methane (AOM) in the deeper parts of landfill covers, to increase overall methane removal, via addition of electron acceptors besides oxygen. In batch tests, landfill cover soil was amended using five alternate electron acceptors: iron(III), nitrate, nitrite, sulfate, and manganese. AOM was then measured via column tests, which included realistic conditions of gas flow, cover thickness, and compaction. In the batch tests, soils amended with nitrate, sulfate, and the combination of sulfate + hematite removed more methane compared to control soil. Methane generation inhibitor had no impact on net methane removal. Adding nutrients to the soil significantly enhanced methane removal only for the case of soil without electron acceptors. Greater methane removal was observed for reactors with higher initial methane concentration. Results of the column tests showed that soil amended with sulfate + iron had the highest (around 10%) removal of methane in the anoxic zone, followed by soil amended with sulfate. Hydrogen sulfide (H₂S) gas was measured in the headspace of these two columns, which indicated that sulfate-reducing bacteria were likely responsible for methane removal.

Formation of large carbonate concretions in black cherts in the Gufeng Formation (Guadalupian) at Enshi, South China

The formation of carbonate concretions is a cementation process which passively infills the pore spaces within sediments. They record the original environments of deposition and diagenetic conditions of the host rocks. Little is known about the precise mechanisms responsible for the precipitation of carbonate concretions. The most common host rocks are mudstones/shales, sandstones, and limestones. This study presents an example of large carbonate concretions from an unusual host rock, the black bedded cherts of the Gufeng Formation (Guadalupian) at Enshi on the northern Yangtze Platform, South China. Petrographic observations (X-ray diffraction, optical microscopy, scanning electron microscopy) and multiple geochemical analyses (pyrite- and carbonate-associated-sulfate (CAS)-sulfur isotopes, carbon isotopes) indicate that (a) the studied carbonate concretion are mainly composed of micritic calcite with subordinate dolomite; (b) the concretions may have been mainly formed in the bacterial sulfate reduction (BSR) zone during very early diagenesis near the sediment-water surface; (c) the paleo-bottom water overlying the sediments during formation of the concretions was mainly euxinic; and (d) the growth of the studied concretions proceeded via a pervasive model, where later cementation phase initiated in the lower part of the concretions and progressed upward.

Microbial chromate reduction coupled with anaerobic oxidation of methane in a membrane biofilm reactor

It has been reported that microbial reduction of sulfate, nitrite/nitrate and iron/manganese could be coupled with anaerobic oxidation of methane (AOM), which plays a significant role in controlling methane emission from anoxic niches. However, little is known about microbial chromate (Cr(VI)) reduction coupling with AOM. In this study, a microbial consortium was enriched via switching nitrate dosing to chromate feeding as the sole electron acceptor under anaerobic condition in a membrane biofilm reactor (MBfR), in which methane was continuously provided as the electron donor through bubble-less hollow fiber membranes. According to long-term reactor operation and chromium speciation analysis, soluble chromate could be reduced into Cr(III) compounds by using methane as electron donor. Fluorescence in situ hybridization and high-throughput 16S rRNA gene amplicon profiling further indicated that after feeding chromate Candidatus 'Methanoperedens' (a known nitrate-dependent anaerobic methane oxidation archaeon) became sole anaerobic methanotroph in the biofilm, potentially responsible for the chromate bio-reduction driven by methane. Two potential pathways of the microbial AOM-coupled chromate reduction were proposed: (i) Candidatus 'Methanoperedens' independently utilizes chromate as electron acceptor to form Cr(III) compounds, or (ii) Candidatus 'Methanoperedens' oxidizes methane to generate intermediates or electrons, which will be utilized to reduce chromate to Cr(III) compounds by unknown chromate reducers synergistically. Our findings suggest a possible link between the biogeochemical chromium and methane cycles.

Metal-dependent anaerobic methane oxidation in marine sediment: Insights from marine settings and other systems

Anaerobic oxidation of methane (AOM) plays a crucial role in controlling global methane emission. This is a microbial process that relies on the reduction of external electron acceptors such as sulfate, nitrate/nitrite, and transient metal ions. In marine settings, the dominant electron acceptor for AOM is sulfate, while other known electron acceptors are transient metal ions such as iron and manganese oxides. Despite the AOM process coupled with sulfate reduction being relatively well characterized, researches on metal-dependent AOM process are few, and no microorganism has to date been identified as being responsible for this reaction in natural marine environments. In this review, geochemical evidences of metal-dependent AOM from sediment cores in various marine environments are summarized. Studies have showed that iron and manganese are reduced in accordance with methane oxidation in seeps or diffusive profiles below the methanogenesis zone. The potential biochemical basis and mechanisms for metal-dependent AOM processes are here presented and discussed. Future research will shed light on the microbes involved in this process and also on the molecular basis of the electron transfer between these microbes and metals in natural marine environments.

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

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

A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction

Microbially mediated anaerobic oxidation of methane (AOM) is a key process in the regulation of methane emissions to the atmosphere. Iron can serve as an electron acceptor for AOM, and it has been suggested that Fe(III)-dependent AOM potentially comprises a major global methane sink. Although it has been proposed that anaerobic methanotrophic (ANME) archaea can facilitate this process, their active metabolic pathways have not been confirmed. Here we report the enrichment and characterisation of a novel archaeon in a laboratory-scale bioreactor fed with Fe(III) oxide (ferrihydrite) and methane. Long-term performance data, in conjunction with the ¹³C- and ⁵⁷Fe-labelling batch experiments, demonstrated that AOM was coupled to Fe(III) reduction to Fe(II) in this bioreactor. Metagenomic analysis showed that this archaeon belongs to a novel genus within family Candidatus Methanoperedenaceae, and possesses genes encoding the "reverse methanogenesis" pathway, as well as multi-heme c-type cytochromes which are hypothesised to facilitate dissimilatory Fe(III) reduction. Metatranscriptomic analysis revealed upregulation of these genes, supporting that this archaeon can independently mediate AOM using Fe(III) as the terminal electron acceptor. We propose the name Candidatus "Methanoperedens ferrireducens" for this microorganism. The potential role of "M. ferrireducens" in linking the carbon and iron cycles in environments rich in methane and iron should be investigated in future research.

A Critical Look at the Combined Use of Sulfur and Oxygen Isotopes to Study Microbial Metabolisms in Methane-Rich Environments

Separating the contributions of anaerobic oxidation of methane and organoclastic sulfate reduction in the overall sedimentary sulfur cycle of marine sediments has benefited from advances in isotope biogeochemistry. Particularly, the coupling of sulfur and oxygen isotopes measured in the residual sulfate pool (δ¹⁸O_SO4 vs. δ³⁴S_SO4). Yet, some important questions remain. Recent works have observed patterns that are inconsistent with previous interpretations. We differentiate the contributions of oxygen and sulfur isotopes to separating the anaerobic oxidation of methane and organoclastic sulfate reduction into three phases; first evidence from conventional high methane vs. low methane sites suggests a clear relationship between oxygen and sulfur isotopes in porewater and the metabolic process taking place. Second, evidence from pure cultures and organic matter rich sites with low levels of methane suggest the signatures of both processes overlap and cannot be differentiated. Third, we take a critical look at the use of oxygen and sulfur isotopes to differentiate metabolic processes (anaerobic oxidation of methane vs. organoclastic sulfate reduction). We identify that it is essential to develop a better understanding of the oxygen kinetic isotope effect, the degree of isotope exchange with sulfur intermediates as well as establishing their relationships with the cell-specific metabolic rates if we are to develop this proxy into a reliable tool to study the sulfur cycle in marine sediments and the geological record.

Low biodegradability of dissolved organic matter and trace metals from subarctic waters

The heterotrophic mineralization of dissolved organic matter (DOM) controls the CO₂ flux from the inland waters to the atmosphere, especially in the boreal waters, although the mechanisms of this process and the fate of trace metals associated with DOM remain poorly understood. We studied the interaction of culturable aquatic (Pseudomonas saponiphila) and soil (Pseudomonas aureofaciens) Gammaproteobacteria with seven different organic substrates collected in subarctic settings. These included peat leachate, pine crown throughfall, fen, humic lake, stream, river, and oligotrophic lake with variable dissolved organic carbon (DOC) concentrations (from 4 to 60mgL^-1). The highest removal of DOC over 4days of reaction was observed in the presence of P. aureofaciens (33±5%, 43±3% and 53±7% of the initial amount in fen water, humic lake and stream, respectively). P. saponiphila degraded only 5% of DOC in fen water but did not affect all other substrates. Trace elements (TE) were essentially controlled by short-term (0-1h) adsorption on the surface of cells. Regardless of the nature of organic substrate and the identity of bacteria, the degree of adsorption ranged from 20 to 60% for iron (Fe³⁺), 15 to 55% for aluminum (Al), 10 to 60% for manganese (Mn), 10 to 70% for nickel (Ni), 20 to 70% for copper (Cu), 10 to 60% for yttrium (Y), 30 to 80% for rare earth elements (REE), and 15 to 50% for uranium (U^VI). Rapid adsorption of organic and organo-mineral colloids on bacterial cell surfaces is novel and potentially important process, which deserves special investigation. The long-term removal of dissolved Fe and Al was generally consistent with solution supersaturation degree with respect to Fe and Al hydroxides, calculated by visual Minteq model. Overall, the biomass-normalized biodegradability of various allochthonous substrates by culturable bacteria is much lower than that of boreal DOM by natural microbial consortia.

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

Anaerobic oxidation of methane (AOM) can be coupled to the reduction of sulfate, nitrate and nitrite, which effectively reduces methane emission into the atmosphere. Recently, metal-dependent AOM (metal-AOM, AOM coupled to metal reduction) was demonstrated to occur in both environmental samples and enrichment cultures. Anaerobic methanotrophs are capable of respiration using Fe(III) or Mn(IV), whether they are in the form of soluble metal species or insoluble minerals. Given the wide distribution of Fe(III)/Mn(IV)-bearing minerals in aquatic methane-rich environments, metal-AOM is considered to be globally important, although it has generally been overlooked in previous studies. In this article, we discuss the discovery of this process, the microorganisms and mechanisms involved, environmental significance and factors influencing metal-AOM. Since metal-AOM is poorly studied to date, some discussion is included on the present understanding of sulfate- and nitrate-AOM and traditional metal reduction processes using organic substrates or hydrogen as electron donors. Metal-AOM is a relatively new research field, and therefore more studies are needed to fully characterize the process. This review summarizes current studies and discusses the many unanswered questions, which should be useful for future research in this field.

Iron-Coupled Anaerobic Oxidation of Methane Performed by a Mixed Bacterial-Archaeal Community Based on Poorly Reactive Minerals

Anaerobic oxidation of methane (AOM) was shown to reduce methane emissions by over 50% in freshwater systems, its main natural contributor to the atmosphere. In these environments iron oxides can become main agents for AOM, but the underlying mechanism for this process has remained enigmatic. By conducting anoxic slurry incubations with lake sediments amended with ¹³C-labeled methane and naturally abundant iron oxides the process was evidenced by significant ¹³C-enrichment of the dissolved inorganic carbon pool and most pronounced when poorly reactive iron minerals such as magnetite and hematite were applied. Methane incorporation into biomass was apparent by strong uptake of ¹³C into fatty acids indicative of methanotrophic bacteria, associated with increasing copy numbers of the functional methane monooxygenase pmoA gene. Archaea were not directly involved in full methane oxidation, but their crucial participation, likely being mediators in electron transfer, was indicated by specific inhibition of their activity that fully stopped iron-coupled AOM. By contrast, inhibition of sulfur cycling increased ¹³C-methane turnover, pointing to sulfur species involvement in a competing process. Our findings suggest that the mechanism of iron-coupled AOM is accomplished by a complex microbe-mineral reaction network, being likely representative of many similar but hidden interactions sustaining life under highly reducing low energy conditions.

Shifting microbial communities sustain multiyear iron reduction and methanogenesis in ferruginous sediment incubations

Reactive Fe(III) minerals can influence methane (CH4 ) emissions by inhibiting microbial methanogenesis or by stimulating anaerobic CH4 oxidation. The balance between Fe(III) reduction, methanogenesis, and CH4 oxidation in ferruginous Archean and Paleoproterozoic oceans would have controlled CH4 fluxes to the atmosphere, thereby regulating the capacity for CH4 to warm the early Earth under the Faint Young Sun. We studied CH4 and Fe cycling in anoxic incubations of ferruginous sediment from the ancient ocean analogue Lake Matano, Indonesia, over three successive transfers (500 days in total). Iron reduction, methanogenesis, CH4 oxidation, and microbial taxonomy were monitored in treatments amended with ferrihydrite or goethite. After three dilutions, Fe(III) reduction persisted only in bottles with ferrihydrite. Enhanced CH4 production was observed in the presence of goethite, highlighting the potential for reactive Fe(III) oxides to inhibit methanogenesis. Supplementing the media with hydrogen, nickel and selenium did not stimulate methanogenesis. There was limited evidence for Fe(III)-dependent CH4 oxidation, although some incubations displayed CH4 -stimulated Fe(III) reduction. 16S rRNA profiles continuously changed over the course of enrichment, with ultimate dominance of unclassified members of the order Desulfuromonadales in all treatments. Microbial diversity decreased markedly over the course of incubation, with subtle differences between ferrihydrite and goethite amendments. These results suggest that Fe(III) oxide mineralogy and availability of electron donors could have led to spatial separation of Fe(III)-reducing and methanogenic microbial communities in ferruginous marine sediments, potentially explaining the persistence of CH4 as a greenhouse gas throughout the first half of Earth history.

Is denitrifying anaerobic methane oxidation-centered technologies a solution for the sustainable operation of wastewater treatment Plants?

With the world's increasing energy crisis, society is growingly considered that the operation of wastewater treatment plants (WWTPs) should be shifted in sustainable paradigms with low energy input, or energy-neutral, or even energy output. There is a lack of critical thinking on whether and how new paradigms can be implemented in WWTPs based on the conventional process. The denitrifying anaerobic methane oxidation (DAMO) process, which uses methane and nitrate (or nitrite) as electron donor and acceptor, respectively, has recently been discovered. Based on critical analyses of this process, DAMO-centered technologies can be considered as a solution for sustainable operation of WWTPs. In this review, a possible strategy with DAMO-centered technologies was outlined and illustrated how this applies for the existing WWTPs energy-saving and newly designed WWTPs energy-neutral (or even energy-producing) towards sustainable operations.

Co-existence of Methanogenesis and Sulfate Reduction with Common Substrates in Sulfate-Rich Estuarine Sediments

The competition between sulfate reducing bacteria and methanogens over common substrates has been proposed as a critical control for methane production. In this study, we examined the co-existence of methanogenesis and sulfate reduction with shared substrates over a large range of sulfate concentrations and rates of sulfate reduction in estuarine systems, where these processes are the key terminal sink for organic carbon. Incubation experiments were carried out with sediment samples from the sulfate-methane transition zone of the Yarqon (Israel) estuary with different substrates and inhibitors along a sulfate concentrations gradient from 1 to 10 mM. The results show that methanogenesis and sulfate reduction can co-exist while the microbes share substrates over the tested range of sulfate concentrations and at sulfate reduction rates up to 680 μmol L-1 day-1. Rates of methanogenesis were two orders of magnitude lower than rates of sulfate reduction in incubations with acetate and lactate, suggesting a higher affinity of sulfate reducing bacteria for the available substrates. The co-existence of both processes was also confirmed by the isotopic signatures of δ34S in the residual sulfate and that of δ13C of methane and dissolved inorganic carbon. Copy numbers of dsrA and mcrA genes supported the dominance of sulfate reduction over methanogenesis, while showing also the ability of methanogens to grow under high sulfate concentration and in the presence of active sulfate reduction.

Rapid Sediment Accumulation Results in High Methane Effluxes from Coastal Sediments

Globally, the methane (CH4) efflux from the ocean to the atmosphere is small, despite high rates of CH4 production in continental shelf and slope environments. This low efflux results from the biological removal of CH4 through anaerobic oxidation with sulfate in marine sediments. In some settings, however, pore water CH4 is found throughout the sulfate-bearing zone, indicating an apparently inefficient oxidation barrier for CH4. Here we demonstrate that rapid sediment accumulation can explain this limited capacity for CH4 removal in coastal sediments. In a saline coastal reservoir (Lake Grevelingen, The Netherlands), we observed high diffusive CH4 effluxes from the sediment into the overlying water column (0.2-0.8 mol m-2 yr-1) during multiple years. Linear pore water CH4 profiles and the absence of an isotopic enrichment commonly associated with CH4 oxidation in a zone with high rates of sulfate reduction (50-170 nmol cm-3 d-1) both suggest that CH4 is bypassing the zone of sulfate reduction. We propose that the rapid sediment accumulation at this site (~ 13 cm yr-1) reduces the residence time of the CH4 oxidizing microorganisms in the sulfate/methane transition zone (< 5 years), thus making it difficult for these slow growing methanotrophic communities to build-up sufficient biomass to efficiently remove pore water CH4. In addition, our results indicate that the high input of organic matter (~ 91 mol C m-2 yr-1) allows for the co-occurrence of different dissimilatory respiration processes, such as (acetotrophic) methanogenesis and sulfate reduction in the surface sediments by providing abundant substrate. We conclude that anthropogenic eutrophication and rapid sediment accumulation likely increase the release of CH4 from coastal sediments.

Improved PCR primers to amplify 16S rRNA genes from NC10 bacteria

Anaerobic oxidation of methane (AOM) coupled to nitrite reduction (AOM-NIR) is ecologically significant for mitigating the methane-induced greenhouse effect. The microbes responsible for this reaction, NC10 bacteria, have been widely detected in diverse ecosystems. However, some defects were discovered in the commonly used NC10-specific primers, 202F and qP1F. In the present work, the primers were redesigned and improved to overcome the defects found in the previous primers. A new nested PCR method was developed using the improved primers to amplify 16S ribosomal RNA (rRNA) genes from NC10 bacteria. In the new nested PCR method, the qP1mF/1492R and 1051F/qP2R primer sets were used in the first and second rounds, respectively. The PCR products were sequenced, and more operational taxonomic units (OTUs) of the NC10 phylum were obtained using the new primers compared to the previous primers. The sensitivity of the new nested PCR was tested by the serial dilution method, and the limit of detection was approximately 10(3) copies g(-1) dry sed. for the environmental samples compared to approximately 10(5) copies g(-1) dry sed. by the previous method. Finally, the improved primer, qP1mF, was used in quantitative PCR (qPCR) to determine the abundance of NC10 bacteria, and the results agreed well with the activity of AOM-NIR measured by isotope tracer experiments. The improved primers are able to amplify NC10 16S rRNA genes more efficiently than the previous primers and useful to explore the microbial community of the NC10 phylum in different systems.

Methanogens rapidly transition from methane production to iron reduction

Methanogenesis, the microbial methane (CH4 ) production, is traditionally thought to anchor the mineralization of organic matter as the ultimate respiratory process in deep sediments, despite the presence of oxidized mineral phases, such as iron oxides. This process is carried out by archaea that have also been shown to be capable of reducing iron in high levels of electron donors such as hydrogen. The current pure culture study demonstrates that methanogenic archaea (Methanosarcina barkeri) rapidly switch from methanogenesis to iron-oxide reduction close to natural conditions, with nitrogen atmosphere, even when faced with substrate limitations. Intensive, biotic iron reduction was observed following the addition of poorly crystalline ferrihydrite and complex organic matter and was accompanied by inhibition of methane production. The reaction rate of this process was of the first order and was dependent only on the initial iron concentrations. Ferrous iron production did not accelerate significantly with the addition of 9,10-anthraquinone-2,6-disulfonate (AQDS) but increased by 11-28% with the addition of phenazine-1-carboxylate (PCA), suggesting the possible role of methanophenazines in the electron transport. The coupling between ferrous iron and methane production has important global implications. The rapid transition from methanogenesis to reduction of iron-oxides close to the natural conditions in sediments may help to explain the globally-distributed phenomena of increasing ferrous concentrations below the traditional iron reduction zone in the deep 'methanogenic' sediment horizon, with implications for metabolic networking in these subsurface ecosystems and in past geological settings.

Iron reduction in the DAMO/Shewanella oneidensis MR-1 coculture system and the fate of Fe(II)

Dissimilatory iron reduction and anaerobic methane oxidation processes play important roles in the global iron and carbon cycle, respectively. This study explored the ferrihydrite reduction process with methane as a carbon source in a coculture system of denitrifying anaerobic methane oxidation (DAMO) microbes enriched in laboratory and Shewanella oneidensis MR-1, and then characterized the reduced products. Ferrihydrite reduction was also studied in the DAMO and Shewanella systems alone. The ferrihydrite was reduced slightly (<13.3%) in the separate systems, but greatly (42.0-88.3%) in the coculture system. Isotope experiment of (13)CH4 addition revealed that DAMO microbes coupled to S. oneidensis MR-1 in a ferric iron reduction process with (13)CH4 consumption and (13)CO2 production. Compared with ferrihydrite, the reduced products showed increased crystallinity (from amorphous state to crystallinity 77.1%) and magnetism (from paramagnetic to ferromagnetic). The produced ferrous iron was formed into minerals primarily composed of siderite with a small amount vivianite and magnetite. A portion of products covered the cell surface and hindered further reactions. The results presented herein widen the current understanding of iron metabolism and mineralization in the ocean, and show that the coculture systems of DAMO microbes and Shewanella have the potential to be globally important to iron reduction and methane oxidation.

Redox processes in pore water of anoxic sediments with shallow gas

The Ría de Vigo (NW Spain) has a high organic matter content and high rates of sedimentation. The microbial degradation of this organic matter has led to shallow gas accumulations of methane, currently distributed all along the ría. These peculiar characteristics favor the development of anoxic conditions that can determine the dynamics of iron and manganese. In order to study the role played by iron and manganese in the processes that take place in anoxic sediments with shallow gas, four gravity cores were retrieved in anoxic sediments of the Ría de Vigo in November 2012. Methane was present in two of them, below 90cm in the inner zone and below 200cm, in the outer zone. Pore water was collected and analyzed for vertical profiles of pH, sulfide, sulfate, iron and manganese concentrations. Sulfate concentrations decreased with depth but never reached the minimum detection limit. High sulfide concentrations were measured in all cores. The highest sulfide concentrations were found in the inner zone with methane and the lowest were in the outer zone without methane. Concentrations of iron and manganese reached maximum values in the upper layers of the sediment, decreasing with depth, except in the outer zone without gas, where iron and manganese concentration increased strongly toward the bottom of the sediment. In areas with shallow gas iron reduction, sulfate reduction and methane production processes coexist, showing that the traditional redox cascade is highly simplified and suggesting that iron may be involved in a cryptic sulfur cycle and in the oxidation of methane.

A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes

Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.