Rapid Sediment Accumulation Results in High Methane Effluxes from Coastal Sediments

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.

Eutrophication and Deoxygenation Drive High Methane Emissions from a Brackish Coastal System

Coastal environments are a major source of marine methane in the atmosphere. Eutrophication and deoxygenation have the potential to amplify the coastal methane emissions. Here, we investigate methane dynamics in the eutrophic Stockholm Archipelago. We cover a range of sites with contrasting water column redox conditions and rates of organic matter degradation, with the latter reflected by the depth of the sulfate-methane transition zone (SMTZ) in the sediment. We find the highest benthic release of methane (2.2-8.6 mmol m-2 d-1) at sites where the SMTZ is located close to the sediment-water interface (2-10 cm). A large proportion of methane is removed in the water column via aerobic or anaerobic microbial pathways. At many locations, water column methane is highly depleted in 13C, pointing toward substantial bubble dissolution. Calculated and measured rates of methane release to the atmosphere range from 0.03 to 0.4 mmol m-2 d-1 and from 0.1 to 1.7 mmol m-2 d-1, respectively, with the highest fluxes at locations with a shallow SMTZ and anoxic and sulfidic bottom waters. Taken together, our results show that sites suffering most from both eutrophication and deoxygenation are hotspots of coastal marine methane emissions.

Seasonal dynamics of the microbial methane filter in the water column of a eutrophic coastal basin

In coastal waters, methane-oxidizing bacteria (MOB) can form a methane biofilter and mitigate methane emissions. The metabolism of these MOBs is versatile, and the resilience to changing oxygen concentrations is potentially high. It is still unclear how seasonal changes in oxygen availability and water column chemistry affect the functioning of the methane biofilter and MOB community composition. Here, we determined water column methane and oxygen depth profiles, the methanotrophic community structure, methane oxidation potential, and water-air methane fluxes of a eutrophic marine basin during summer stratification and in the mixed water in spring and autumn. In spring, the MOB diversity and relative abundance were low. Yet, MOB formed a methane biofilter with up to 9% relative abundance and vertical niche partitioning during summer stratification. The vertical distribution and potential methane oxidation of MOB did not follow the upward shift of the oxycline during summer, and water-air fluxes remained below 0.6 mmol m-2 d-1. Together, this suggests active methane removal by MOB in the anoxic water. Surprisingly, with a weaker stratification, and therefore potentially increased oxygen supply, methane oxidation rates decreased, and water-air methane fluxes increased. Thus, despite the potential resilience of the MOB community, seasonal water column dynamics significantly influence methane removal.

Versatile methanotrophs form an active methane biofilter in the oxycline of a seasonally stratified coastal basin

The potential and drivers of microbial methane removal in the water column of seasonally stratified coastal ecosystems and the importance of the methanotrophic community composition for ecosystem functioning are not well explored. Here, we combined depth profiles of oxygen and methane with 16S rRNA gene amplicon sequencing, metagenomics and methane oxidation rates at discrete depths in a stratified coastal marine system (Lake Grevelingen, The Netherlands). Three amplicon sequence variants (ASVs) belonging to different genera of aerobic Methylomonadaceae and the corresponding three methanotrophic metagenome-assembled genomes (MOB-MAGs) were retrieved by 16S rRNA sequencing and metagenomic analysis, respectively. The abundances of the different methanotrophic ASVs and MOB-MAGs peaked at different depths along the methane oxygen counter-gradient and the MOB-MAGs show a quite diverse genomic potential regarding oxygen metabolism, partial denitrification and sulphur metabolism. Moreover, potential aerobic methane oxidation rates indicated high methanotrophic activity throughout the methane oxygen counter-gradient, even at depths with low in situ methane or oxygen concentration. This suggests that niche-partitioning with high genomic versatility of the present Methylomonadaceae might contribute to the functional resilience of the methanotrophic community and ultimately the efficiency of methane removal in the stratified water column of a marine basin.

Methanotrophic potential of Dutch canal wall biofilms is driven by Methylomonadaceae

Global urbanization of waterways over the past millennium has influenced microbial communities in these aquatic ecosystems. Increased nutrient inputs have turned most urban waters into net sources of the greenhouse gases carbon dioxide (CO2) and methane (CH4). Here, canal walls of five Dutch cities were studied for their biofilm CH4 oxidation potential, alongside field observations of water chemistry, and CO2 and CH4 emissions. Three cities showed canal wall biofilms with relatively high biological CH4 oxidation potential up to 0.48 mmol gDW-1 d-1, whereas the other two cities showed no oxidation potential. Salinity was identified as the main driver of biofilm bacterial community composition. Crenothrix and Methyloglobulus methanotrophs were observed in CH4-oxidizing biofilms. We show that microbial oxidation in canal biofilms is widespread and is likely driven by the same taxa found across cities with distinctly different canal water chemistry. The oxidation potential of the biofilms was not correlated with the amount of CH4 emitted but was related to the presence or absence of methanotrophs in the biofilms. This was controlled by whether there was enough CH4 present to sustain a methanotrophic community. These results demonstrate that canal wall biofilms can directly contribute to the mitigation of greenhouse gases from urban canals.

Gene-Based Modeling of Methane Oxidation in Coastal Sediments: Constraints on the Efficiency of the Microbial Methane Filter

Methane is a powerful greenhouse gas that is produced in large quantities in marine sediments. Microbially mediated oxidation of methane in sediments, when in balance with methane production, prevents the release of methane to the overlying water. Here, we present a gene-based reactive transport model that includes both microbial and geochemical dynamics and use it to investigate whether the rate of growth of methane oxidizers in sediments impacts the efficiency of the microbial methane filter. We focus on iron- and methane-rich coastal sediments and, with the model, show that at our site, up to 10% of all methane removed is oxidized by iron and manganese oxides, with the remainder accounted for by oxygen and sulfate. We demonstrate that the slow growth rate of anaerobic methane-oxidizing microbes limits their ability to respond to transient perturbations, resulting in periodic benthic release of methane. Eutrophication and deoxygenation decrease the efficiency of the microbial methane filter further, thereby enhancing the role of coastal environments as a source of methane to the atmosphere.

Methane supply drives prokaryotic community assembly and networks at cold seeps of the South China Sea

Marine cold seeps are unique chemosynthetic habitats fuelled by deeply sourced hydrocarbon-rich fluids discharged at the seafloor. Through oxidizing methane and other hydrocarbons, microorganisms inhabiting cold seeps supply subsurface-derived energy to higher trophic levels, sustaining highly productive oases of life in the deep sea. Despite the central role of microbiota in mediating biogeochemical cycles, the factors that govern the assembly and network of prokaryotic communities in cold seeps remain poorly understood. Here we analysed the geochemical and microbiological profiles of 11 different sediment cores from two spatially distant cold seeps of the South China Sea. We show that prokaryotic communities belonging to the same methane-supply regimes (high-methane-supply, low-methane-supply and non-seep control sediments) had a highly similar community structure, regardless of geographical location, seep-associated biota (mussel, clam, microbial mat) and sediment depth. Methane supply appeared to drive the niche partitioning of anaerobic methanotrophic archaea (ANME) at the regional scale, with ANME-1 accounting for >60% sequence abundance of ANME in the high-methane-supply sediments, while ANME-2 dominated (>90%) the low-methane-supply sediments. Increasing methane supply enhanced the contribution of environmental selection but lessened the contributions of dispersal limitation and drift to overall community assembly. High methane supply, moreover, promoted a more tightly connected, less stable prokaryotic network dominated by positive correlations. Together, these results provide a potentially new framework for understanding the niches and network interplay of prokaryotic communities across different methane seepage regimes in cold-seep sediments.

Vertical organization of microbial communities in Salineta hypersaline wetland, Spain

Microbial communities inhabiting hypersaline wetlands, well adapted to the environmental fluctuations due to flooding and desiccation events, play a key role in the biogeochemical cycles, ensuring ecosystem service. To better understand the ecosystem functioning, we studied soil microbial communities of Salineta wetland (NE Spain) in dry and wet seasons in three different landscape stations representing situations characteristic of ephemeral saline lakes: S1 soil usually submerged, S2 soil intermittently flooded, and S3 soil with halophytes. Microbial community composition was determined according to different redox layers by 16S rRNA gene barcoding. We observed reversed redox gradient, negative at the surface and positive in depth, which was identified by PERMANOVA as the main factor explaining microbial distribution. The Pseudomonadota, Gemmatimonadota, Bacteroidota, Desulfobacterota, and Halobacteriota phyla were dominant in all stations. Linear discriminant analysis effect size (LEfSe) revealed that the upper soil surface layer was characterized by the predominance of operational taxonomic units (OTUs) affiliated to strictly or facultative anaerobic halophilic bacteria and archaea while the subsurface soil layer was dominated by an OTU affiliated to Roseibaca, an aerobic alkali-tolerant bacterium. In addition, the potential functional capabilities, inferred by PICRUSt2 analysis, involved in carbon, nitrogen, and sulfur cycles were similar in all samples, irrespective of the redox stratification, suggesting functional redundancy. Our findings show microbial community changes according to water flooding conditions, which represent useful information for biomonitoring and management of these wetlands whose extreme aridity and salinity conditions are exposed to irreversible changes due to human activities.

Methane emissions offset atmospheric carbon dioxide uptake in coastal macroalgae, mixed vegetation and sediment ecosystems

Coastal ecosystems can efficiently remove carbon dioxide (CO₂) from the atmosphere and are thus promoted for nature-based climate change mitigation. Natural methane (CH₄) emissions from these ecosystems may counterbalance atmospheric CO₂ uptake. Still, knowledge of mechanisms sustaining such CH₄ emissions and their contribution to net radiative forcing remains scarce for globally prevalent macroalgae, mixed vegetation, and surrounding depositional sediment habitats. Here we show that these habitats emit CH₄ in the range of 0.1 - 2.9 mg CH₄ m^-2 d^-1 to the atmosphere, revealing in situ CH₄ emissions from macroalgae that were sustained by divergent methanogenic archaea in anoxic microsites. Over an annual cycle, CO₂-equivalent CH₄ emissions offset 28 and 35% of the carbon sink capacity attributed to atmospheric CO₂ uptake in the macroalgae and mixed vegetation habitats, respectively, and augment net CO₂ release of unvegetated sediments by 57%. Accounting for CH₄ alongside CO₂ sea-air fluxes and identifying the mechanisms controlling these emissions is crucial to constrain the potential of coastal ecosystems as net atmospheric carbon sinks and develop informed climate mitigation strategies.

Sulfate concentrations affect sulfate reduction pathways and methane consumption in coastal wetlands

Coastal wetlands are an important source of methane emissions, and understanding the mechanisms that control methane emissions from coastal wetlands is of great significance to global warming. Anaerobic oxidation of methane driven by sulfate is an important process to prevent methane emissions from coastal wetlands. The effects of environmental changes on this process and the function of the sulfate-methane transition zone (SMTZ) are poorly understood. In this study, spatiotemporal variations in pore-water geochemistry (concentrations of SO₄^2-, CH₄ and DIC as well as δ¹³C-DIC and δ¹³C-CH₄) in the Beidagang wetland, Tianjin, China, were investigated to unravel factors controlling the role of anaerobic oxidation of methane in coastal wetlands. Results show that the geochemical profile of pore-water is characterized by significant spatial and temporal variability, which may be related to changes in sulfate concentration, temperature and dissolved oxygen. The carbon isotope fractionation factors (ε_C) during methane oxidation range from 8.9‰ to 12.5‰, indicating that the sulfate-driven anaerobic oxidation of methane (S-AOM) dominates the methane oxidation in the Beidagang coastal wetland in both winter and summer, in both high and low salinity wetlands, and in both open water and littoral areas. However, sulfate concentration has a strong influence on the sulfate reduction pathways and methane consumption. The consumption of methane and sulfate by S-AOM is more significant in coastal wetlands with high sulfate concentrations, with S-AOM consuming nearly all of the upward-diffusing methane (96%) and downward-diffusing sulfate (96%). In addition, the dissolved inorganic carbon (DIC) produced in the pore-water mainly comes from methanogenesis, accounting for more than 80% of the total DIC pool, but in the areas with high sulfate concentrations in water column, the contribution of S-AOM to the DIC pool is greater, although only a small fraction of the total DIC pool (9%). The depth and width of the SMTZ show a clear spatial and temporal pattern, with active methanogenesis activity and upward high methane flux shoaling the SMTZ and increasing the risk of high methane emissions from coastal wetlands with low sulfate concentrations. Our findings highlight the importance of sulfate-driven anaerobic oxidation of methane in coastal wetlands and the effect of sulfate concentration on it. It contributes to our understanding of the mechanism of methane production and emissions from the coastal wetland system, particularly in light of the increased demand for coastal wetland restoration under global warming.

Aerobic and anaerobic methane oxidation in a seasonally anoxic basin

Shallow coastal waters are dynamic environments that dominate global marine methane emissions. Particularly high methane concentrations are found in seasonally anoxic waters, which are spreading in eutrophic coastal systems, potentially leading to increased methane emissions to the atmosphere. Here we explore how the seasonal development of anoxia influenced methane concentrations, rates of methane oxidation, and the community composition of methanotrophs in the shallow eutrophic water column of Mariager Fjord, Denmark. Our results show the development of steep concentration gradients toward the oxic-anoxic interface as methane accumulated to 1.4 μM in anoxic bottom waters. Yet, the fjord possessed an efficient microbial methane filter near the oxic-anoxic interface that responded to the increasing methane flux. In experimental incubations, methane oxidation near the oxic-anoxic interface proceeded both aerobically and anaerobically with nearly equal efficiency reaching turnover rates as high as 0.6 and 0.8 d^-1, respectively, and was seemingly mediated by members of the Methylococcales belonging to the Deep Sea-1 clade. Throughout the period, both aerobic and anaerobic methane oxidation rates were high enough to consume the estimated methane flux. Thus, our results indicate that seasonal anoxia did not increase methane emissions.

Influence of seasonal and environmental variables on the emission of methane from the mangrove sediments of Goa

Mangrove sediments are known sources for methane emission that has a very high global warming potential. The spatio-temporal emission of methane in the mangrove sediments was quantified in the present study using the static closed chamber technique. Besides, the effects of environmental parameters on methane emission were estimated at Betim (mouth), Chorão (midstream), and Volvoi (upstream) stations along the tropical Mandovi estuary. On an average, the methane emission at the upstream estuarine station at Volvoi was maximum (1268.68 ± 176 nM cm^-2 h^-1) compared to the other two stations. Annually, the methane emission was significantly influenced by physicochemical parameters like salinity at Betim and Volvoi and, the redox potential at the midstream station at Chorão. The variation of methane emission between the 3 stations (P < 0.001) is attributed to the variation in methanotrophy (P < 0.05) and methanogenesis (P < 0.05) influenced by differences in the concentration of nutrients (P < 0.05) and organic carbon (P < 0.05). Seasonally, the highest methane emission at Chorão was during the post-monsoon, at Betim was during the monsoon season (1305.34 ± 108.58 nM cm^-2 h^-1), and at the upstream station at Volvoi, the emission of methane was highest during the pre-monsoon season (1514.68 ± 130.94 nM cm^-2 h^-1). The influence of environmental parameters was more prominent on methane emission at the 3 stations during the monsoon season. Spearman's correlation analysis indicated that seasonal changes in methane emission are not only attributed to the influence of seasonal rainfall that leads to the fresh water input, but also to the variation in biogeochemical parameters.

Effect of degradation of a black mangrove forest on seasonal greenhouse gas emissions

Mangroves play an essential role in the global carbon cycle. However, they are highly vulnerable to degradation with little-known effects on greenhouse gas (GHG) emissions. This study compared seasonal soil carbon dioxide (CO₂), methane (CH₄), and nitrous oxide (N₂O) fluxes from a black mangrove (Avicennia germinans) forest in the Tampamachoco coastal lagoon, Veracruz, Mexico, in areas subjected to different degrees of environmental degradation (full canopy, transitional and dead mangrove), caused by hydrological perturbation. Furthermore, we aimed at determining the environmental factors driving seasonal fluxes. There was a combined effect of seasonality and degradation on CH₄ fluxes, highest during the rainy season in the dead mangrove (0.93 ± 0.18 mg CH₄ m^-2 h^-1). CO₂ fluxes were highest during the dry season (220 ± 23 mg CO₂ m^-2 h^-1), with no significant differences among degradation levels. N₂O fluxes did not vary among seasons or degradation levels (- 3.8 to 2.9 mg N₂O m^-2 h^-1). The overall CO₂-eq emission rate was 15.3 ± 2.7 Mg CO₂-eq ha^-1 year^-1, with CO₂ as the main gas contributing to total emissions. The main factors controlling CH₄ fluxes were seasonal porewater salinity and the availability of NO₂^-, NO₃^-, and SO₄^-2 in the soil, favored by high water level and temperature in the absence of pneumatophores. The main determining factors controlling CO₂ fluxes were water level, porewater redox potential, and soil Cl^- and SO₄^-2 concentration. Finally, N₂O fluxes were related to NO₂^-, NO₃^-, and SO₄^-2 soil concentrations. This study contributes to improving the knowledge of soil GHG fluxes dynamics in mangroves and the effect of degradation of these ecosystems on the coastal biogeochemical cycles, which may bring important insights for assessing accurate ways to mitigate climate change protecting and restoring these ecosystems.

In situ characterization of benthic fluxes and denitrification efficiency in a newly re-established mussel farm

Mussel farming has been proposed as a mechanism to mitigate eutrophication in coastal waters. However, localizing the intensive filtration of organic matter by mussels can cause a concomitant enrichment of organic matter in sediments below farms, which may influence biogeochemical processes and fates of nutrients in the system. In the context of mitigating eutrophication, it is important to quantify sedimentary changes induced at early life stages of mussel farms. Accordingly, this study investigated how a newly re-established mussel farm affected sedimentation rates, sediment characteristics, sediment-water solute fluxes and nitrate (NO₃^-) reduction rates (measured in situ) during the first year of production. Sedimentation rates were enhanced at the farm relative to a reference station, and both organic and inorganic carbon accumulated in the sediment with time. Increased organic matter input likely drove the slightly elevated sedimentary effluxes of ammonium (NH₄⁺) and dissolved inorganic phosphorus (DIP) in the farm. Denitrification was the main NO₃^- reduction process, however, there was a relative increase in the remobilization of bioavailable nitrogen underneath the farm as dissimilatory nitrate reduction to ammonium (DNRA) rates were enhanced by >200% and the denitrification efficiency was 49% lower compared to the reference station. The sedimentary methane (CH₄) release tended to be higher at the farm, but fluxes were not significantly different from reference conditions. Low sedimentary pigment concentrations indicated a reduced presence of benthic microalgae at the farm, which likely influenced sediment-water solute fluxes. Over the production cycle, the release of dissolved inorganic nitrogen (DIN) and DIP underneath the farm were respectively 426% and 510% relative to reference conditions. Impacts of the mussel farm were thus measurable already during the first year of establishment. These immediate changes to the sediment biogeochemistry, as well as long-term effects, should be considered when estimating the environmental impact of mussel aquaculture.

Electron Acceptor Availability Shapes Anaerobically Methane Oxidizing Archaea (ANME) Communities in South Georgia Sediments

Anaerobic methane oxidizing archaea (ANME) mediate anaerobic oxidation of methane (AOM) in marine sediments and are therefore important for controlling atmospheric methane concentrations in the water column and ultimately the atmosphere. Numerous previous studies have revealed that AOM is coupled to the reduction of different electron acceptors such as sulfate, nitrate/nitrite or Fe(III)/Mn(IV). However, the influence of electron acceptor availability on the in situ ANME community composition in sediments remains largely unknown. Here, we investigated the electron acceptor availability and compared the microbial in situ communities of three methane-rich locations offshore the sub-Antarctic island South Georgia, by Illumina sequencing and qPCR of mcrA genes. The methanic zone (MZ) sediments of Royal Trough and Church Trough comprised high sulfide concentrations of up to 4 and 19 mM, respectively. In contrast, those of the Cumberland Bay fjord accounted for relatively high concentrations of dissolved iron (up to 186 μM). Whereas the ANME community in the sulfidic sites Church Trough and Royal Trough mainly comprised members of the ANME-1 clade, the order-level clade “ANME-1-related” (Lever and Teske, 2015) was most abundant in the iron-rich site in Cumberland Bay fjord, indicating that the availability of electron acceptors has a strong selective effect on the ANME community. This study shows that potential electron acceptors for methane oxidation may serve as environmental filters to select for the ANME community composition and adds to a better understanding of the global importance of AOM.

Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments

Large amounts of methane, a potent greenhouse gas, are produced in anoxic sediments by methanogenic archaea. Nonetheless, over 90% of the produced methane is oxidized via sulfate-dependent anaerobic oxidation of methane (S-AOM) in the sulfate-methane transition zone (SMTZ) by consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). Coastal systems account for the majority of total marine methane emissions and typically have lower sulfate concentrations, hence S-AOM is less significant. However, alternative electron acceptors such as metal oxides or nitrate could be used for AOM instead of sulfate. The availability of electron acceptors is determined by the redox zonation in the sediment, which may vary due to changes in oxygen availability and the type and rate of organic matter inputs. Additionally, eutrophication and climate change can affect the microbiome, biogeochemical zonation, and methane cycling in coastal sediments. This review summarizes the current knowledge on the processes and microorganisms involved in methane cycling in coastal sediments and the factors influencing methane emissions from these systems. In eutrophic coastal areas, organic matter inputs are a key driver of bottom water hypoxia. Global warming can reduce the solubility of oxygen in surface waters, enhancing water column stratification, increasing primary production, and favoring methanogenesis. ANME are notoriously slow growers and may not be able to effectively oxidize methane upon rapid sedimentation and shoaling of the SMTZ. In such settings, ANME-2d (Methanoperedenaceae) and ANME-2a may couple iron- and/or manganese reduction to AOM, while ANME-2d and NC10 bacteria (Methylomirabilota) could couple AOM to nitrate or nitrite reduction. Ultimately, methane may be oxidized by aerobic methanotrophs in the upper millimeters of the sediment or in the water column. The role of these processes in mitigating methane emissions from eutrophic coastal sediments, including the exact pathways and microorganisms involved, are still underexplored, and factors controlling these processes are unclear. Further studies are needed in order to understand the factors driving methane-cycling pathways and to identify the responsible microorganisms. Integration of the knowledge on microbial pathways and geochemical processes is expected to lead to more accurate predictions of methane emissions from coastal zones in the future.

Dynamic modeling of anaerobic methane oxidation coupled to sulfate reduction: role of elemental sulfur as intermediate

The process dynamics of anaerobic oxidation of methane (AOM) coupled to sulfate reduction (SR), and the potential role of elemental sulfur as intermediate are presented in this paper. Thermodynamic screening and experimental evidence from the literature conclude that a prominent model to describe AOM-SR is based on the concept that anaerobic methane oxidation proceeds through the production of the intermediate elemental sulfur. Two microbial groups are involved in the process: (a) anaerobic methanotrophs (ANME-2) and (b) Desulfosarcina/Desulfococcus sulfur reducers cluster (DSS). In this work, a dynamic model was developed to explore the interactions between biotic and abiotic processes to simulate the microbial activity, the chemical composition and speciation of the liquid phase, and the gas phase composition in the reactor headspace. The model includes the microbial kinetics for the symbiotic growth of ANME-2 and DSS, mass transfer phenomena between the gas and liquid phase for methane, hydrogen sulfide, and carbon dioxide and acid-base reactions for bicarbonate, sulfide, and ammonium. A data set from batch experiments, running for 250 days in artificial seawater inoculated with sediment from Marine Lake Grevelingen (The Netherlands) was used to calibrate the model. The inherent characteristics of AOM-SR make the identification of the kinetic parameters difficult due to the high correlation between them. However, by meaningfully selecting a set of kinetic parameters, the model simulates successfully the experimental data for sulfate reduction and sulfide production. The model can be considered as the basic structure for simulating continuous flow three-phase engineered systems based on AOM-SR.

Shifts in methanogenic archaea communities and methane dynamics along a subtropical estuarine land use gradient

In coastal aquatic ecosystems, prokaryotic communities play an important role in regulating the cycling of nutrients and greenhouse gases. In the coastal zone, estuaries are complex and delicately balanced systems containing a multitude of specific ecological niches for resident microbes. Anthropogenic influences (i.e. urban, industrial and agricultural land uses) along the estuarine continuum can invoke physical and biochemical changes that impact these niches. In this study, we investigate the relative abundance of methanogenic archaea and other prokaryotic communities, distributed along a land use gradient in the subtropical Burnett River Estuary, situated within the Great Barrier Reef catchment, Australia. Microbiological assemblages were compared to physicochemical, nutrient and greenhouse gas distributions in both pore and surface water. Pore water samples from within the most urbanised site showed a high relative abundance of methanogenic Euryarchaeota (7.8% of all detected prokaryotes), which coincided with elevated methane concentrations in the water column, ranging from 0.51 to 0.68 μM at the urban and sewage treatment plant (STP) sites, respectively. These sites also featured elevated dissolved organic carbon (DOC) concentrations (0.66 to 1.16 mM), potentially fuelling methanogenesis. At the upstream freshwater site, both methane and DOC concentrations were considerably higher (2.68 μM and 1.8 mM respectively) than at the estuarine sites (0.02 to 0.66 μM and 0.39 to 1.16 mM respectively) and corresponded to the highest relative abundance of methanotrophic bacteria. The proportion of sulfate reducing bacteria in the prokaryotic community was elevated within the urban and STP sites (relative abundances of 8.0%– 10.5%), consistent with electron acceptors with higher redox potentials (e.g. O₂, NO₃^-) being scarce. Overall, this study showed that ecological niches in anthropogenically altered environments appear to give an advantage to specialized prokaryotes invoking a potential change in the thermodynamic landscape of the ecosystem and in turn facilitating the generation of methane–a potent greenhouse gas.

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.

Rates and Microbial Players of Iron-Driven Anaerobic Oxidation of Methane in Methanic Marine Sediments

The flux of methane, a potent greenhouse gas, from the seabed is largely controlled by anaerobic oxidation of methane (AOM) coupled to sulfate reduction (S-AOM) in the sulfate methane transition (SMT). S-AOM is estimated to oxidize 90% of the methane produced in marine sediments and is mediated by a consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria. An additional methane sink, i.e., iron oxide coupled AOM (Fe-AOM), has been suggested to be active in the methanic zone of marine sediments. Geochemical signatures below the SMT such as high dissolved iron, low to undetectable sulfate and high methane concentrations, together with the presence of iron oxides are taken as prerequisites for this process. So far, Fe-AOM has neither been proven in marine sediments nor have the governing key microorganisms been identified. Here, using a multidisciplinary approach, we show that Fe-AOM occurs in iron oxide-rich methanic sediments of the Helgoland Mud Area (North Sea). When sulfate reduction was inhibited, different iron oxides facilitated AOM in long-term sediment slurry incubations but manganese oxide did not. Especially magnetite triggered substantial Fe-AOM activity and caused an enrichment of ANME-2a archaea. Methane oxidation rates of 0.095 ± 0.03 nmol cm-3 d-1 attributable to Fe-AOM were obtained in short-term radiotracer experiments. The decoupling of AOM from sulfate reduction in the methanic zone further corroborated that AOM was iron oxide-driven below the SMT. Thus, our findings prove that Fe-AOM occurs in methanic marine sediments containing mineral-bound ferric iron and is a previously overlooked but likely important component in the global methane budget. This process has the potential to sustain microbial life in the deep biosphere.

Diagenesis of sulfur, iron and phosphorus in sediments of an urban bay impacted by multiple anthropogenic perturbations

Solid-phase speciation and porewater chemistry measured by the diffusive gradients in thin films (DGT) technique were used to understand the diagenesis of sulfur (S), iron (Fe), and phosphorus (P) in sediments of Jiaozhou Bay (China), which has been impacted by multiple anthropogenic perturbations. Despite water eutrophication, sediments of the bay are low in organic carbon and sulfide, but high in unsulfidized Fe(II). Dissimilatory iron reduction (DIR) prevails in sediments of the bay, and there is no evidence for responses of S and Fe diagenesis to the water eutrophication, which is largely attributable to unique depositional and diagenetic regimes in association with multiple anthropogenic perturbations. Good coupling of porewater Fe²⁺ and P in the porewaters suggests that P mobilization is driven mainly by DIR. Low Fe²⁺/P ratios in porewaters imply that oxidative regeneration of Fe oxides within the upper sediments is incapable of efficiently scavenging upward diffusing P.

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.

Abundance and Biogeochemical Impact of Cable Bacteria in Baltic Sea Sediments

Oxygen depletion in coastal waters may lead to release of toxic sulfide from sediments. Cable bacteria can limit sulfide release by promoting iron oxide formation in sediments. Currently, it is unknown how widespread this phenomenon is. Here, we assess the abundance, activity, and biogeochemical impact of cable bacteria at 12 Baltic Sea sites. Cable bacteria were mostly absent in sediments overlain by anoxic and sulfidic bottom waters, emphasizing their dependence on oxygen or nitrate as electron acceptors. At sites that were temporarily reoxygenated, cable bacterial densities were low. At seasonally hypoxic sites, cable bacterial densities correlated linearly with the supply of sulfide. The highest densities were observed at Gulf of Finland sites with high rates of sulfate reduction. Microelectrode profiles of sulfide, oxygen, and pH indicated low or no in situ cable bacteria activity at all sites. Reactivation occurred within 5 days upon incubation of an intact sediment core from the Gulf of Finland with aerated overlying water. We found no relationship between cable bacterial densities and macrofaunal abundances, salinity, or sediment organic carbon. Our geochemical data suggest that cable bacteria promote conversion of iron monosulfides to iron oxides in the Gulf of Finland in spring, possibly explaining why bottom waters in this highly eutrophic region rarely contain sulfide in summer.

Wetland Sediments Host Diverse Microbial Taxa Capable of Cycling Alcohols

Understanding patterns of organic matter degradation in wetlands is essential for identifying the substrates and mechanisms supporting greenhouse gas production and emissions from wetlands, the main natural source of methane in the atmosphere. Alcohols are common fermentation products but are poorly studied as key intermediates in organic matter degradation in wetlands. By investigating genes, pathways, and microorganisms potentially accounting for the high concentrations of ethanol and isopropanol measured in Prairie Pothole wetland sediments, this work advanced our understanding of alcohol fermentations in wetlands linked to extremely high greenhouse gas emissions. Moreover, the novel alcohol dehydrogenases and microbial taxa potentially involved in alcohol metabolism may serve biotechnological efforts in bioengineering commercially valuable alcohol production and in the discovery of novel isopropanol producers or isopropanol fermentation pathways.

Alcohols are commonly derived from the degradation of organic matter and yet are rarely measured in environmental samples. Wetlands in the Prairie Pothole Region (PPR) support extremely high methane emissions and the highest sulfate reduction rates reported to date, likely contributing to a significant proportion of organic matter mineralization in this system. While ethanol and isopropanol concentrations up to 4 to 5 mM in PPR wetland pore fluids have been implicated in sustaining these high rates of microbial activity, the mechanisms that support alcohol cycling in this ecosystem are poorly understood. We leveraged metagenomic and transcriptomic tools to identify genes, pathways, and microorganisms potentially accounting for alcohol cycling in PPR wetlands. Phylogenetic analyses revealed diverse alcohol dehydrogenases and putative substrates. Alcohol dehydrogenase and aldehyde dehydrogenase genes were included in 62 metagenome-assembled genomes (MAGs) affiliated with 16 phyla. The most frequently encoded pathway (in 30 MAGs) potentially accounting for alcohol production was a Pyrococcus furiosus-like fermentation which can involve pyruvate:ferredoxin oxidoreductase (PFOR). Transcripts for 93 of 137 PFOR genes in these MAGs were detected, as well as for 158 of 243 alcohol dehydrogenase genes retrieved from these same MAGs. Mixed acid fermentation and heterofermentative lactate fermentation were also frequently encoded. Finally, we identified 19 novel putative isopropanol dehydrogenases in 15 MAGs affiliated with Proteobacteria, Acidobacteria, Chloroflexi, Planctomycetes, Ignavibacteriae, Thaumarchaeota, and the candidate divisions KSB1 and Rokubacteria. We conclude that diverse microorganisms may use uncommon and potentially novel pathways to produce ethanol and isopropanol in PPR wetland sediments.

IMPORTANCE Understanding patterns of organic matter degradation in wetlands is essential for identifying the substrates and mechanisms supporting greenhouse gas production and emissions from wetlands, the main natural source of methane in the atmosphere. Alcohols are common fermentation products but are poorly studied as key intermediates in organic matter degradation in wetlands. By investigating genes, pathways, and microorganisms potentially accounting for the high concentrations of ethanol and isopropanol measured in Prairie Pothole wetland sediments, this work advanced our understanding of alcohol fermentations in wetlands linked to extremely high greenhouse gas emissions. Moreover, the novel alcohol dehydrogenases and microbial taxa potentially involved in alcohol metabolism may serve biotechnological efforts in bioengineering commercially valuable alcohol production and in the discovery of novel isopropanol producers or isopropanol fermentation pathways.

Anaerobic Methane-Oxidizing Microbial Community in a Coastal Marine Sediment: Anaerobic Methanotrophy Dominated by ANME-3

The microbial community inhabiting the shallow sulfate-methane transition zone in coastal sediments from marine Lake Grevelingen (The Netherlands) was characterized, and the ability of the microorganisms to carry out anaerobic oxidation of methane coupled to sulfate reduction was assessed in activity tests. In vitro activity tests of the sediment with methane and sulfate demonstrated sulfide production coupled to the simultaneous consumption of sulfate and methane at approximately equimolar ratios over a period of 150 days. The maximum sulfate reduction rate was 5 μmol sulfate per gram dry weight per day during the incubation period. Diverse archaeal and bacterial clades were retrieved from the sediment with the majority of them clustered with Euryarchaeota, Thaumarcheota, Bacteroidetes, and Proteobacteria. The 16S rRNA gene sequence analysis showed that the sediment from marine Lake Grevelingen contained anaerobic methanotrophic Archaea (ANME) and methanogens as archaeal clades with a role in the methane cycling. ANME at the studied site mainly belong to the ANME-3 clade. This study provides one of the few reports for the presence of ANME-3 in a shallow coastal sediment. Sulfate-reducing bacteria from Desulfobulbus clades were found among the sulfate reducers, however, with very low relative abundance. Desulfobulbus has previously been commonly found associated with ANME, whereas in our study, ANME-3 and Desulfobulbus were not observed simultaneously in clusters, suggesting the possibility of independent AOM by ANME-3.

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.