Global ocean methane emissions dominated by shallow coastal waters

Distribution and sea-to-air fluxes of nitrous oxide and methane from a seasonally hypoxic coastal zone in the southeastern Arabian Sea

The seasonal variability, pathways, and sea-to-air fluxes of nitrous oxide (N2O) and methane (CH4) in the coastal environment, where coastal upwelling and mudbanks co-exist are presented based on the monthly time-series measurements from November 2021 to December 2022. Upwelling-driven hypoxic water's shoreward propagation and persistence were the major factors controlling the N2O concentrations, while the freshwater influx and sedimentary fluxes modulate CH4 concentrations. The N2O concentrations were high during the southwest monsoon (up to 35 nM; 19 ± 8 nM)), followed by spring inter-monsoon (up to 19 nM; 10 ± 5 nM), and lowest during the northeast monsoon (up to 13 nM; 8 ± 2 nM), whereas the CH4 levels were high during the spring inter-monsoon (8.4 to 65 nM), followed by southwest monsoon (6.8 to 53.1 nM) and relatively lower concentrations during the northeast monsoon (3.3 to 32.6 nM). The positive correlations of excess N2O with Apparent Oxygen Utilisation (AOU) and the sum of nitrate and nitrite (NOx) indicate that nitrification is the primary source of N2O in the mudbank regime. The negative correlation of CH4 concentrations with salinity indicates considerable input of CH4 through freshwater influx. CH4 exhibited a highly significant positive correlation with Chlorophyll-a throughout the study period. Furthermore, it displayed a statistically significant positive correlation with phosphate (PO43-) during the northeast monsoon while a strong negative correlation with PO43- during the spring inter-monsoon, pointing towards the role of aerobic CH4 production pathways in the mudbank regime. N2O and CH4 exhibited a contrasting seasonal pattern of sea-to-air fluxes, characterised by the highest N2O fluxes during the southwest monsoon (hypoxia) (13 ± 10 μM m-2 d-1), followed by spring inter-monsoon (12 ± 16 μM m-2 d-1), and the lowest during the northeast monsoon (0.6 ± 3 μM m-2 d-1). Conversely, the highest sea-to-air fluxes of CH4 were noticed during the spring inter-monsoon (74 ± 56 μM m-2 d-1), followed by the southwest monsoon (45 ± 35 μM m-2 d-1), and the lowest values during the northeast monsoon (19 ± 16 μM m-2d-1). Long-term time-series measurements will be invaluable in understanding the longer-term impacts of climate-driven variability on marine biogeochemical cycles in dynamic nearshore systems.

Marine aquaculture can deliver 40% lower carbon footprints than freshwater aquaculture based on feed, energy and biogeochemical cycles

Freshwater aquaculture is an increasingly important source of blue foods but produces substantial methane and nitrous oxide emissions. Marine aquaculture, also known as mariculture, is a smaller sector with a large growth potential, but its climate impacts are challenging to accurately quantify. Here we assess the greenhouse gas emissions from mariculture's aquatic environment in global potentially suitable areas at 10 km resolution on the basis of marine biogeochemical cycles, greenhouse gas measurements from research cruises and satellite-observed net primary productivity. Mariculture's aquatic emissions intensities are estimated to be 1-6 g CH4 kg-1 carcass weight and 0.05-0.2 g N2O kg-1 carcass weight, >98% and >80% lower than freshwater systems. Using a life-cycle assessment approach, we show that mariculture's carbon footprints are ~40% lower than those of freshwater aquaculture based on feed, energy use and the aquatic environment emissions. Adoption of mariculture alongside freshwater aquaculture production could offer considerable climate benefits to meet future dietary protein and nutritional needs.

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.

Correlation of methane production with physiological traits in Trichodesmium IMS 101 grown with methylphosphonate at different temperatures

The diazotrophic cyanobacterium Trichodesmium has been recognized as a potentially significant contributor to aerobic methane generation via several mechanisms including the utilization of methylphophonate (MPn) as a source of phosphorus. Currently, there is no information about how environmental factors regulate methane production by Trichodesmium. Here, we grew Trichodesmium IMS101 at five temperatures ranging from 16 to 31°C, and found that its methane production rates increased with rising temperatures to peak (1.028 ± 0.040 nmol CH4 μmol POC-1 day-1) at 27°C, and then declined. Its specific growth rate changed from 0.03 ± 0.01 d-1 to 0.34 ± 0.02 d-1, with the optimal growth temperature identified between 27 and 31°C. Within the tested temperature range the Q10 for the methane production rate was 4.6 ± 0.7, indicating a high sensitivity to thermal changes. In parallel, the methane production rates showed robust positive correlations with the assimilation rates of carbon, nitrogen, and phosphorus, resulting in the methane production quotients (molar ratio of carbon, nitrogen, or phosphorus assimilated to methane produced) of 227-494 for carbon, 40-128 for nitrogen, and 1.8-3.4 for phosphorus within the tested temperature range. Based on the experimental data, we estimated that the methane released from Trichodesmium can offset about 1% of its CO2 mitigation effects.

Nitrite-dependent anaerobic methane oxidation (N-DAMO) in global aquatic environments: A review

The vast majority of processes in the carbon and nitrogen cycles are driven by microorganisms. The nitrite-dependent anaerobic oxidation of methane (N-DAMO) process links carbon and nitrogen cycles, offering a novel approach for the simultaneous reduction of methane emissions and nitrite pollution. However, there is currently no comprehensive summary of the current status of the N-DAMO process in natural aquatic environments. Therefore, our study aims to fill this knowledge gap by conducting a comprehensive review of the global research trends in N-DAMO processes in various aquatic environments (excluding artificial bioreactors). Our review mainly focused on molecular identification, global study sites, and their interactions with other elemental cycling processes. Furthermore, we performed a data integration analysis to unveil the effects of key environmental factors on the abundance of N-DAMO bacteria and the rate of N-DAMO process. By combining the findings from the literature review and data integration analysis, we proposed future research perspectives on N-DAMO processes in global aquatic environments. Our overarching goal is to advance the understanding of the N-DAMO process and its role in synergistically reducing carbon emissions and removing nitrogen. By doing so, we aim to make a significant contribution to the timely achievement of China's carbon peak and carbon neutrality targets.

Baltic Sea coastal sediment-bound eukaryotes have increased year-round activities under predicted climate change related warming

Climate change related warming is a serious environmental problem attributed to anthropogenic activities, causing ocean water temperatures to rise in the coastal marine ecosystem since the last century. This particularly affects benthic microbial communities, which are crucial for biogeochemical cycles. While bacterial communities have received considerable scientific attention, the benthic eukaryotic community response to climate change remains relatively overlooked. In this study, sediments were sampled from a heated (average 5°C increase over the whole year for over 50 years) and a control (contemporary conditions) Baltic Sea bay during four different seasons across a year. RNA transcript counts were then used to investigate eukaryotic community changes under long-term warming. The composition of active species in the heated and control bay sediment eukaryotic communities differed, which was mainly attributed to salinity and temperature. The family level RNA transcript alpha diversity in the heated bay was higher during May but lower in November, compared with the control bay, suggesting altered seasonal activity patterns and dynamics. In addition, structures of the active eukaryotic communities varied between the two bays during the same season. Hence, this study revealed that long-term warming can change seasonality in eukaryotic diversity patterns. Relative abundances and transcript expression comparisons between bays suggested that some taxa that now have lower mRNA transcripts numbers could be favored by future warming. Furthermore, long-term warming can lead to a more active metabolism in these communities throughout the year, such as higher transcript numbers associated with diatom energy production and protein synthesis in the heated bay during winter. In all, these data can help predict how future global warming will affect the ecology and metabolism of eukaryotic community in coastal sediments.

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.

Biotic interactions between benthic infauna and aerobic methanotrophs mediate methane fluxes from coastal sediments

Coastal ecosystems dominate oceanic methane (CH4) emissions. However, there is limited knowledge about how biotic interactions between infauna and aerobic methanotrophs (i.e. CH4 oxidizing bacteria) drive the spatial-temporal dynamics of these emissions. Here, we investigated the role of meio- and macrofauna in mediating CH4 sediment-water fluxes and aerobic methanotrophic activity that can oxidize significant portions of CH4. We show that macrofauna increases CH4 fluxes by enhancing vertical solute transport through bioturbation, but this effect is somewhat offset by high meiofauna abundance. The increase in CH4 flux reduces CH4 pore-water availability, resulting in lower abundance and activity of aerobic methanotrophs, an effect that counterbalances the potential stimulation of these bacteria by higher oxygen flux to the sediment via bioturbation. These findings indicate that a larger than previously thought portion of CH4 emissions from coastal ecosystems is due to faunal activity and multiple complex interactions with methanotrophs.

Hydrogen-independent CO2 reduction dominates methanogenesis in five temperate lakes that differ in trophic states

Emissions of microbially produced methane (CH4) from lake sediments are a major source of this potent greenhouse gas to the atmosphere. The rates of CH4 production and emission are believed to be influenced by electron acceptor distributions and organic carbon contents, which in turn are affected by anthropogenic inputs of nutrients leading to eutrophication. Here, we investigate how eutrophication influences the abundance and community structure of CH4 producing Archaea and methanogenesis pathways across time-resolved sedimentary records of five Swiss lakes with well-characterized trophic histories. Despite higher CH4 concentrations which suggest higher methanogenic activity in sediments of eutrophic lakes, abundances of methanogens were highest in oligotrophic lake sediments. Moreover, while the methanogenic community composition differed significantly at the lowest taxonomic levels (OTU), depending on whether sediment layers had been deposited under oligotrophic or eutrophic conditions, it showed no clear trend in relation to in situ distributions of electron acceptors. Remarkably, even though methanogenesis from CO2-reduction was the dominant pathway in all sediments based on carbon isotope fractionation values, taxonomic identities, and genomes of resident methanogens, CO2-reduction with hydrogen (H2) was thermodynamically unfavorable based on measured reactant and product concentrations. Instead, strong correlations between genomic abundances of CO2-reducing methanogens and anaerobic bacteria with potential for extracellular electron transfer suggest that methanogenic CO2-reduction in lake sediments is largely powered by direct electron transfer from syntrophic bacteria without involvement of H2 as an electron shuttle.

Untapped talents: insight into the ecological significance of methanotrophs and its prospects

The deep ocean is a rich reservoir of unique organisms with great potential for bioprospecting, ecosystem services, and the discovery of novel materials. These organisms thrive in harsh environments characterized by high hydrostatic pressure, low temperature, and limited nutrients. Hydrothermal vents and cold seeps, prominent features of the deep ocean, provide a habitat for microorganisms involved in the production and filtration of methane, a potent greenhouse gas. Methanotrophs, comprising archaea and bacteria, play a crucial role in these processes. This review examines the intricate relationship between the roles, responses, and niche specialization of methanotrophs in the deep ocean ecosystem. Our findings reveal that different types of methanotrophs dominate specific zones depending on prevailing conditions. Type I methanotrophs thrive in oxygen-rich zones, while Type II methanotrophs display adaptability to diverse conditions. Verrumicrobiota and NC10 flourish in hypoxic and extreme environments. In addition to their essential role in methane regulation, methanotrophs contribute to various ecosystem functions. They participate in the degradation of foreign compounds and play a crucial role in cycling biogeochemical elements like metals, sulfur, and nitrogen. Methanotrophs also serve as a significant energy source for the oceanic food chain and drive chemosynthesis in the deep ocean. Moreover, their presence offers promising prospects for biotechnological applications, including the production of valuable compounds such as polyhydroxyalkanoates, methanobactin, exopolysaccharides, ecotines, methanol, putrescine, and biofuels. In conclusion, this review highlights the multifaceted roles of methanotrophs in the deep ocean ecosystem, underscoring their ecological significance and their potential for advancements in biotechnology. A comprehensive understanding of their niche specialization and responses will contribute to harnessing their full potential in various domains.

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.

Methylphosphonate-driven methane formation and its link to primary production in the oligotrophic North Atlantic

Methylphosphonate is an organic phosphorus compound used by microorganisms when phosphate, a key nutrient limiting growth in most marine surface waters, becomes unavailable. Microbial methylphosphonate use can result in the formation of methane, a potent greenhouse gas, in oxic waters where methane production is traditionally unexpected. The extent and controlling factors of such aerobic methane formation remain underexplored. Here, we show high potential net rates of methylphosphonate-driven methane formation (median 0.4 nmol methane L-1 d-1) in the upper water column of the western tropical North Atlantic. The rates are repressed but still quantifiable in the presence of in-situ or added phosphate, suggesting that some methylphosphonate-driven methane formation persists in phosphate-replete waters. The genetic potential for methylphosphonate utilisation is present in and transcribed by key photo- and heterotrophic microbial taxa, such as Pelagibacterales, SAR116, and Trichodesmium. While the large cyanobacterial nitrogen-fixers dominate in the surface layer, phosphonate utilisation by Alphaproteobacteria appears to become more important in deeper depths. We estimate that at our study site, a substantial part (median 11%) of the measured surface carbon fixation can be sustained by phosphorus liberated from phosphonate utilisation, highlighting the ecological importance of phosphonates in the carbon cycle of the oligotrophic ocean.

Biogenic methane in coastal unconsolidated sediment systems: A review

Marine sediments are the world's largest known reservoir of methane. In many coastal regions, methane is trapped in sediments buried at depths ranging from centimeters to hundreds of meters below the seafloor, in the forms of gas pockets, dispersed gas bubbles and dissolved gas, also known as shallow gas (methane-dominated gas mixture). The existence of shallow gas affects the engineering geological environment and threatens the safety of artificial facilities. The escape of shallow gas from sediments into the atmosphere can even threaten ecosystem security and affect global climate change. However, until now, shallow gas has remained a mystery to the scientific community. For example, how it is generated, how it distributes and migrates in sediments, and what are the factors that influence these processes that are still unclear. In the context of increasingly intense offshore development and global warming, there is a huge gap between existing scientific understanding of shallow gas and the need to develop scientific solutions for related problems. Based on this, this paper systematically collects the information on all aspects of shallow gas mentioned above, comprehensively summarizes the current scientific understanding, and analyzes the existing shortcomings, which will provide systematic references for the research on environmental disaster prevention, engineering technology, climate change, and other fields.

V, Vijayan NT, Subramanian M, Gauns MU. Applications of Machine Learning in Chemical and Biological Oceanography

Machine learning (ML) refers to computer algorithms that predict a meaningful output or categorize complex systems based on a large amount of data. ML is applied in various areas including natural science, engineering, space exploration, and even gaming development. This review focuses on the use of machine learning in the field of chemical and biological oceanography. In the prediction of global fixed nitrogen levels, partial carbon dioxide pressure, and other chemical properties, the application of ML is a promising tool. Machine learning is also utilized in the field of biological oceanography to detect planktonic forms from various images (i.e., microscopy, FlowCAM, and video recorders), spectrometers, and other signal processing techniques. Moreover, ML successfully classified the mammals using their acoustics, detecting endangered mammalian and fish species in a specific environment. Most importantly, using environmental data, the ML proved to be an effective method for predicting hypoxic conditions and harmful algal bloom events, an essential measurement in terms of environmental monitoring. Furthermore, machine learning was used to construct a number of databases for various species that will be useful to other researchers, and the creation of new algorithms will help the marine research community better comprehend the chemistry and biology of the ocean.

Microbial Niche Differentiation during Nitrite-Dependent Anaerobic Methane Oxidation

Nitrite-dependent anaerobic methane oxidation (n-DAMO) has been demonstrated to play important roles in the global methane and nitrogen cycle. However, despite diverse n-DAMO bacteria widely detected in environments, little is known about their physiology for microbial niche differentiation. Here, we show the microbial niche differentiation of n-DAMO bacteria through long-term reactor operations combining genome-centered omics and kinetic analysis. With the same inoculum dominated by both species "Candidatus Methylomirabilis oxyfera" and "Candidatus Methylomirabilis sinica", n-DAMO bacterial population was shifted to "Ca. M. oxyfera" in a reactor fed with low-strength nitrite, but shifted to "Ca. M. sinica" with high-strength nitrite. Metatranscriptomic analysis showed that "Ca. M. oxyfera" harbored more complete function in cell chemotaxis, flagellar assembly, and two-component system for better uptake of nitrite, while "Ca. M. sinica" had a more active ion transport and stress response system, and more redundant function in nitrite reduction to mitigate nitrite inhibition. Importantly, the half-saturation constant of nitrite (0.057 mM vs 0.334 mM NO₂^-) and inhibition thresholds (0.932 mM vs 2.450 mM NO₂^-) for "Ca. M. oxyfera" vs "Ca. M. sinica", respectively, were highly consistent with genomic results. Integrating these findings demonstrated biochemical characteristics, especially the kinetics of nitrite affinity and inhibition determine niche differentiation of n-DAMO bacteria.

Super-Aerophilic Biomimetic Cactus for Underwater Dispersed Microbubble Capture, Self-Transport, Coalescence, and Energy Harvesting

Human ocean activities are inseparable from the supply of energy. The energy contained in the gas-phase components dispersed in seawater is a potential universal energy source for eupelagic or deep-sea equipment. However, the low energy density of bubbles dispersed in water introduces severe challenges to the potential energy harvesting of gas-phase components. Here, a super-aerophilic biomimetic cactus is developed for underwater dispersive microbubble capture and energy harvesting. The bubbles captured by the super-aerophilic biomimetic cactus spines, driven by the surface tension and liquid pressure, undergo automatic transport, coalescence, accumulation, and concentrated release. The formerly unavailable low-density dispersive surface free energy of the bubbles is converted into high-density concentrated gas buoyancy potential energy, thereby providing an energy source for underwater in situ electricity generation. Experiments show a continuous process of microbubble capture by the biomimetic cactus and demonstrate a 22.76-times increase in output power and a 3.56-times enhancement in electrical energy production compared with a conventional bubble energy harvesting device. The output energy density is 3.64 times that of the existing bubble energy generator. This work provides a novel approach for dispersive gas-phase potential energy harvesting in seawater, opening up promising prospects for wide-area in situ energy supply in underwater environments.

Gravity complexes as a focus of seafloor fluid seepage: the Rio Grande Cone, SE Brazil

Seafloor methane emissions can affect Earth's climate and ocean chemistry. Vast quantities of methane formed by microbial decomposition of organic matter are locked within gas hydrate and free gas on continental slopes, particularly in large areas with high sediment accumulations such as deep-sea fans. The release of methane in slope environments has frequently been associated with dissociation of gas hydrates near the edge of the gas hydrate stability zone on the upper slope, with discharges in greater water depths less understood. Here we show, using data from the Rio Grande Cone (western South Atlantic), that the intrinsic, gravity-induced downslope collapse of thick slope sediment accumulations creates structures that serve as pathways for gas migration, unlocking methane and causing seafloor emissions via giant gas flares in the water column. The observed emissions in the study region (up to 310 Mg year^-1) are three times greater than estimates for the entire US North Atlantic margin and reveal the importance of collapsing sediment accumulations for ocean carbon cycling. Similar outgassing systems on the Amazon and Niger fans suggest that gravity tectonics on passive margins is a common yet overlooked mechanism driving massive seafloor methane emissions in sediment-laden continental slopes.

Spatial and temporal variation of methane emissions in the coastal Balearic Sea, Western Mediterranean

Methane (CH₄) gas is the most important GHG after carbon dioxide, with open ocean areas acting as discreet CH₄ sources and coastal regions as intense but variable CH₄ sources to the atmosphere. Here, we report CH₄ concentrations and air-sea fluxes in the coastal area of the Balearic Islands Archipelago (Western Mediterranean Basin). CH₄ levels and related biogeochemical variables were measured in three coastal sampling sites between 2018 and 2021, with two located close to the densely populated island of Mallorca and one in a pristine area in the Cabrera Archipelago National Park. CH₄ concentrations in seawater during the study period ranged from 2.7 to 10.9 nM, without significant differences between the sampling sites. Averaged estimated CH₄ fluxes during the sampling period for the three stations oscillated between 0.2 and 9.7 μmol m^-2 d^-1 according to a seasonal pattern and in general all sites behaved as weak CH₄ sources throughout the sampling period.

Passive Automatic Switch Relying on Laplace Pressure for Efficient Underwater Low-Gas-Flux Bubble Energy Harvesting

The buoyancy potential energy contained in bubbles released by subsea geological and biological activities represents a possible in situ energy source for underwater sensing and detection equipment. However, the low gas flux of the bubble seepages that exist widely on the seabed introduces severe challenges. Herein, a passive automatic switch relying on Laplace pressure is proposed for efficient energy harvesting from low-gas-flux bubbles. This switch has no moving mechanical parts; it uses the Laplace-pressure difference across a curved gas-liquid interface in a biconical channel as an invisible "microvalve". If there is mechanical equilibrium between the Laplace-pressure difference and the liquid-pressure difference, the microvalve will remain closed and prevent the release of bubbles as they continue to accumulate. After the accumulated gas reaches a threshold value, the microvalve will open automatically, and the gas will be released rapidly, relying on the positive feedback of interface mechanics. Using this device, the gas buoyancy potential energy entering the energy harvesting system per unit time can be increased by a factor of more than 30. Compared with a traditional bubble energy harvesting system without a switch, this system achieves a 19.55-fold increase in output power and a 5.16-fold enhancement in electrical energy production. The potential energy of ultralow flow rate bubbles (as low as 3.97 mL/min) is effectively collected. This work provides a new design philosophy for passive automatic-switching control of gas-liquid two-phase fluids, presenting an effective approach for harvesting of buoyancy potential energy from low-gas-flux bubble seepages. This opens a promising avenue for in situ energy supply for subsea scientific observation networks.

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.

Aerobic oxidation of methane significantly reduces global diffusive methane emissions from shallow marine waters

Methane is supersaturated in surface seawater and shallow coastal waters dominate global ocean methane emissions to the atmosphere. Aerobic methane oxidation (MOx) can reduce atmospheric evasion, but the magnitude and control of MOx remain poorly understood. Here we investigate methane sources and fates in the East China Sea and map global MOx rates in shallow waters by training machine-learning models. We show methane is produced during methylphosphonate decomposition under phosphate-limiting conditions and sedimentary release is also source of methane. High MOx rates observed in these productive coastal waters are correlated with methanotrophic activity and biomass. By merging the measured MOx rates with methane concentrations and other variables from a global database, we predict MOx rates and estimate that half of methane, amounting to 1.8 ± 2.7 Tg, is consumed annually in near-shore waters (<50 m), suggesting that aerobic methanotrophy is an important sink that significantly constrains global methane emissions.

High spatiotemporal variability of methane concentrations challenges estimates of emissions across vegetated coastal ecosystems

Coastal methane (CH₄ ) emissions dominate the global ocean CH₄ budget and can offset the "blue carbon" storage capacity of vegetated coastal ecosystems. However, current estimates lack systematic, high-resolution, and long-term data from these intrinsically heterogeneous environments, making coastal budgets sensitive to statistical assumptions and uncertainties. Using continuous CH₄ concentrations, δ¹³ C-CH₄  values, and CH₄  sea-air fluxes across four seasons in three globally pervasive coastal habitats, we show that the CH₄ distribution is spatially patchy over meter-scales and highly variable in time. Areas with mixed vegetation, macroalgae, and their surrounding sediments exhibited a spatiotemporal variability of surface water CH₄ concentrations ranging two orders of magnitude (i.e., 6-460 nM CH₄ ) with habitat-specific seasonal and diurnal patterns. We observed (1) δ¹³ C-CH₄  signatures that revealed habitat-specific CH₄ production and consumption pathways, (2) daily peak concentration events that could change >100% within hours across all habitats, and (3) a high thermal sensitivity of the CH₄ distribution signified by apparent activation energies of ~1 eV that drove seasonal changes. Bootstrapping simulations show that scaling the CH₄ distribution from few samples involves large errors, and that ~50 concentration samples per day are needed to resolve the scale and drivers of the natural variability and improve the certainty of flux calculations by up to 70%. Finally, we identify northern temperate coastal habitats with mixed vegetation and macroalgae as understudied but seasonally relevant atmospheric CH₄  sources (i.e., releasing ≥ 100 μmol CH₄  m^-2  day^-1 in summer). Due to the large spatial and temporal heterogeneity of coastal environments, high-resolution measurements will improve the reliability of CH₄ estimates and confine the habitat-specific contribution to regional and global CH₄ budgets.

Impact of interannual and multidecadal trends on methane-climate feedbacks and sensitivity

We estimate the causal contributions of spatiotemporal changes in temperature (T) and precipitation (Pr) to changes in Earth’s atmospheric methane concentration (C_CH4) and its isotope ratio δ¹³CH₄ over the last four decades. We identify oscillations between positive and negative feedbacks, showing that both contribute to increasing C_CH4. Interannually, increased emissions via positive feedbacks (e.g. wetland emissions and wildfires) with higher land surface air temperature (LSAT) are often followed by increasing C_CH4 due to weakened methane sink via atmospheric ^•OH, via negative feedbacks with lowered sea surface temperatures (SST), especially in the tropics. Over decadal time scales, we find alternating rate-limiting factors for methane oxidation: when C_CH4 is limiting, positive methane-climate feedback via direct oceanic emissions dominates; when ^•OH is limiting, negative feedback is favoured. Incorporating the interannually increasing C_CH4 via negative feedbacks gives historical methane-climate feedback sensitivity ≈ 0.08 W m⁻² °C⁻¹, much higher than the IPCC AR6 estimate.

Record-breaking rates of increasing atmospheric methane concentrations in 2020 and 2021 are alarming, but puzzling, in view of declining methane emissions from fossil fuel in 2020. The authors show that interannual variation of both positive and negative feedbacks contribute positively to the rising methane concentration.

Spatial and seasonal dynamics of the methane cycle in a tropical coastal lagoon and its tributary river

Coastal aquatic ecosystems such as estuaries and coastal lagoons are important atmospheric methane sources that must be better constrained. This work presents a detailed characterization of the methane cycle in a tropical coastal lagoon (La Mancha, Veracruz, Mexico) and its tributary river over three distinct seasons, along a transect from the river to the sea connection. In addition to several physicochemical parameters, the dissolved methane, carbon dioxide, and oxygen concentrations were measured with high resolution in the sediments and the water column, combined with production/uptake rates. Methane and carbon dioxide cycles were further constrained by determining atmospheric flux over the entire river and lagoon sections. The results indicate that La Mancha is a highly contrasted ecosystem. The river section is characterized by a strong pycnocline, relatively high methane concentration, and active methanogenesis and methanotrophy, discharging into a relatively homogeneous lagoon section where the methane and carbon cycles are less active. Overall, both the river and the lagoon were a net source of methane and carbon dioxide, with an annual emission of 2.9 metric tons of methane and 2757 metric tons of carbon dioxide. The spatial structure of the main components of the methane, carbon dioxide, and oxygen cycles was established, and it was observed that depthwise heterogeneities predominated in the river section. In contrast, lengthwise heterogeneities dominated in the lagoon section.

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.

Anaerobic methane oxidation in a coastal oxygen minimum zone: spatial and temporal dynamics

Coastal waters are a major source of marine methane to the atmosphere. Particularly high concentrations of this potent greenhouse gas are found in anoxic waters, but it remains unclear if and to what extent anaerobic methanotrophs mitigate the methane flux. Here we investigate the long-term dynamics in methanotrophic activity and the methanotroph community in the coastal oxygen minimum zone (OMZ) of Golfo Dulce, Costa Rica, combining biogeochemical analyses, experimental incubations, and 16S rRNA gene sequencing over three consecutive years. Our results demonstrate a stable redox zonation across the years with high concentrations of methane (up to 1.7 μmol L^-1 ) in anoxic bottom waters. However, we also measured high activities of anaerobic methane oxidation in the OMZ core (rate constant, k, averaging 30 yr^-1 in 2018 and 8 yr^-1 in 2019-2020). The OPU3 and Deep Sea-1 clades of the Methylococcales were implicated as conveyors of the activity, peaking in relative abundance 5-25 m below the oxic-anoxic interface and in the deep anoxic water, respectively. Although their genetic capacity for anaerobic methane oxidation remains unexplored, their sustained high relative abundance indicates an adaptation of these clades to the anoxic, methane-rich OMZ environment, allowing them to play major roles in mitigating methane fluxes. This article is protected by copyright. All rights reserved.

Nitrous oxide and methane in a changing Arctic Ocean

Human activities are changing the Arctic environment at an unprecedented rate resulting in rapid warming, freshening, sea ice retreat and ocean acidification of the Arctic Ocean. Trace gases such as nitrous oxide (N₂O) and methane (CH₄) play important roles in both the atmospheric reactivity and radiative budget of the Arctic and thus have a high potential to influence the region's climate. However, little is known about how these rapid physical and chemical changes will impact the emissions of major climate-relevant trace gases from the Arctic Ocean. The combined consequences of these stressors present a complex combination of environmental changes which might impact on trace gas production and their subsequent release to the Arctic atmosphere. Here we present our current understanding of nitrous oxide and methane cycling in the Arctic Ocean and its relevance for regional and global atmosphere and climate and offer our thoughts on how this might change over coming decades.

Effects of extreme meteorological conditions in 2018 on European methane emissions estimated using atmospheric inversions

The effect of the 2018 extreme meteorological conditions in Europe on methane (CH4) emissions is examined using estimates from four atmospheric inversions calculated for the period 2005-2018. For most of Europe, we find no anomaly in 2018 compared to the 2005-2018 mean. However, we find a positive anomaly for the Netherlands in April, which coincided with positive temperature and soil moisture anomalies suggesting an increase in biogenic sources. We also find a negative anomaly for the Netherlands for September-October, which coincided with a negative anomaly in soil moisture, suggesting a decrease in soil sources. In addition, we find a positive anomaly for Serbia in spring, summer and autumn, which coincided with increases in temperature and soil moisture, again suggestive of changes in biogenic sources, and the annual emission for 2018 was 33 ± 38% higher than the 2005-2017 mean. These results indicate that CH4 emissions from areas where the natural source is thought to be relatively small can still vary due to meteorological conditions. At the European scale though, the degree of variability over 2005-2018 was small, and there was negligible impact on the annual CH4 emissions in 2018 despite the extreme meteorological conditions. This article is part of a discussion meeting issue 'Rising methane: is warming feeding warming? (part 2)'.

Metabolic flexibility of aerobic methanotrophs under anoxic conditions in Arctic lake sediments

Methane (CH₄) emissions from Arctic lakes are a large and growing source of greenhouse gas to the atmosphere with critical implications for global climate. Because Arctic lakes are ice covered for much of the year, understanding the metabolic flexibility of methanotrophs under anoxic conditions would aid in characterizing the mechanisms responsible for limiting CH₄ emissions from high-latitude regions. Using sediments from an active CH₄ seep in Lake Qalluuraq, Alaska, we conducted DNA-based stable isotope probing (SIP) in anoxic mesocosms and found that aerobic Gammaproteobacterial methanotrophs dominated in assimilating CH₄. Aerobic methanotrophs were also detected down to 70 cm deep in sediments at the seep site, where anoxic conditions persist. Metagenomic analyses of the heavy DNA from ¹³CH₄-SIP incubations showed that these aerobic methanotrophs had the capacity to generate intermediates such as methanol, formaldehyde, and formate from CH₄ oxidation and to oxidize formaldehyde in the tetrahydromethanopterin (H₄MPT)-dependent pathway under anoxic conditions. The high levels of Fe present in sediments, combined with Fe and CH₄ profiles in the persistent CH₄ seep site, suggested that oxidation of CH₄, or, more specifically, its intermediates such as methanol and formaldehyde might be coupled to iron reduction. Aerobic methanotrophs also possessed genes associated with nitrogen and hydrogen metabolism, which might provide potentially alternative energy conservation options under anoxic conditions. These results expand the known metabolic spectrum of aerobic methanotrophs under anoxic conditions and necessitate the re-assessment of the mechanisms underlying CH₄ oxidation in the Arctic, especially under lakes that experience extended O₂ limitations during ice cover.

Atmospheric methane and nitrous oxide: challenges alongthe path to Net Zero

The causes of methane's renewed rise since 2007, accelerated growth from 2014 and record rise in 2020, concurrent with an isotopic shift to values more depleted in ¹³C, remain poorly understood. This rise is the dominant departure from greenhouse gas scenarios that limit global heating to less than 2°C. Thus a comprehensive understanding of methane sources and sinks, their trends and inter-annual variations are becoming more urgent. Efforts to quantify both sources and sinks and understand latitudinal and seasonal variations will improve our understanding of the methane cycle and its anthropogenic component. Nationally declared emissions inventories under the UN Framework Convention on Climate Change (UNFCCC) and promised contributions to emissions reductions under the UNFCCC Paris Agreement need to be verified independently by top-down observation. Furthermore, indirect effects on natural emissions, such as changes in aquatic ecosystems, also need to be quantified. Nitrous oxide is even more poorly understood. Despite this, options for mitigating methane and nitrous oxide emissions are improving rapidly, both in cutting emissions from gas, oil and coal extraction and use, and also from agricultural and waste sources. Reductions in methane and nitrous oxide emission are arguably among the most attractive immediate options for climate action. This article is part of a discussion meeting issue 'Rising methane: is warming feeding warming? (part 1)'.

Estimation of total flux of polycyclic aromatic hydrocarbons facilitated by methane ebullition into water column from global lake sediments

Methane ebullition and contamination are two typical characteristics from lakes, however, these two are generally studied independently. In fact, the exchange of matter and energy between methane bubbles and their surrounding environment can be very active to enhance the contaminant transport. There is limited research on understanding the characteristics and trends of gas ebullition facilitated contaminant emissions in large areas considering water and air as receptors. We herein estimate the transport capacity of methane ebullition for polycyclic aromatic hydrocarbons (PAHs) out of the sediment from global lakes, which may reach an average of 71 (up to 159) t yr^-1. Methane bubbles could transfer one third of the total PAH flux from sediments, or equivalent of 1.3-3.0 ng L^-1 of additional PAHs, into the water column with the rest going into air, offsetting from 52 to 118% of dry PAH deposition flux into global lakes sediment per year. Given the PAH concentration in lake water is often in the range of 0.1-100 ng L^-1, ebullition facilitated PAH flux may increase PAH concentration by a factor of 1.4 to 2.4 until 2,100, being a significant contributor for the PAH increment in lake waters.

Marine Gas Hydrate Geohazard Assessment on the European Continental Margins. The Impact of Critical Knowledge Gaps

This paper presents a geohazard assessment along the European continental margins and adjacent areas. This assessment is understood in the framework of the seafloor’s susceptibility to (i.e., likelihood of) being affected by the presence of hydrate deposits and the subsequent hazardous dissociation processes (liquefaction, explosion, collapse, crater-like depressions or submarine landslides). Geological and geophysical evidence and indicators of marine gas hydrates in the theoretical gas hydrate stability zone (GHSZ) were taken into account as the main factors controlling the susceptibility calculation. Svalbald, the Barents Sea, the mid-Norwegian margin-northwest British Islands, the Gulf of Cádiz, the eastern Mediterranean and the Black Sea have the highest susceptibility. Seafloor areas outside the theoretical GHSZ were excluded from this geohazard assessment. The uncertainty analysis of the susceptibility inference shows extensive seafloor areas with no data and a very low density of data that are defined as critical knowledge gaps.

Dynamic and history of methane seepage in the SW Barents Sea: new insights from Leirdjupet Fault Complex

Methane emissions from Arctic continental margins are increasing due to the negative effect of global warming on ice sheet and permafrost stability, but dynamics and timescales of seafloor seepage still remain poorly constrained. Here, we examine sediment cores collected from an active seepage area located between 295 and 353 m water depth in the SW Barents Sea, at Leirdjupet Fault Complex. The geochemical composition of hydrocarbon gas in the sediment indicates a mixture of microbial and thermogenic gas, the latter being sourced from underlying Mesozoic formations. Sediment and carbonate geochemistry reveal a long history of methane emissions that started during Late Weichselian deglaciation after 14.5 cal ka BP. Methane-derived authigenic carbonates precipitated due to local gas hydrate destabilization, in turn triggered by an increasing influx of warm Atlantic water and isostatic rebound linked to the retreat of the Barents Sea Ice Sheet. This study has implications for a better understanding of the dynamic and future evolution of methane seeps in modern analogue systems in Western Antarctica, where the retreat of marine-based ice sheet induced by global warming may cause the release of large amounts of methane from hydrocarbon reservoirs and gas hydrates.

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.

Machine Learning Based Predictions of Dissolved Oxygen in a Small Coastal Embayment

Coastal dissolved oxygen (DO) concentrations have a profound impact on nearshore ecosystems and, in recent years, there has been an increased prevalance of low DO hypoxic events that negatively impact nearshore organisms. Even with advanced numerical models, accurate prediction of coastal DO variability is challenging and computationally expensive. Here, we apply machine learning techniques in order to reconstruct and predict nearshore DO concentrations in a small coastal embayment while using a comprehensive set of nearshore and offshore measurements and easily measured input (training) parameters. We show that both random forest regression (RFR) and support vector regression (SVR) models accurately reproduce both the offshore DO and nearshore DO with extremely high accuracy. In general, RFR consistently peformed slightly better than SVR, the latter of which was more difficult to tune and took longer to train. Although each of the nearshore datasets were able to accurately predict DO values using training data from the same site, the model only had moderate success when using training data from one site to predict DO at another site, which was likely due to the the complexities in the underlying dynamics across the sites. We also show that high accuracy can be achieved with relatively little training data, highlighting a potential application for correcting time series with missing DO data due to quality control or sensor issues. This work establishes the ability of machine learning models to accurately reproduce DO concentrations in both offshore and nearshore coastal waters, with important implications for the ability to detect and indirectly measure coastal hypoxic events in near real-time. Future work should explore the ability of machine learning models in order to accurately forecast hypoxic events.

Genomic and enzymatic evidence of acetogenesis by anaerobic methanotrophic archaea

Anaerobic oxidation of methane (AOM) mediated by anaerobic methanotrophic archaea (ANME) is the primary process that provides energy to cold seep ecosystems by converting methane into inorganic carbon. Notably, cold seep ecosystems are dominated by highly divergent heterotrophic microorganisms. The role of the AOM process in supporting heterotrophic population remains unknown. We investigate the acetogenic capacity of ANME-2a in a simulated cold seep ecosystem using high-pressure biotechnology, where both AOM activity and acetate production are detected. The production of acetate from methane is confirmed by isotope-labeling experiments. A complete archaeal acetogenesis pathway is identified in the ANME-2a genome, and apparent acetogenic activity of the key enzymes ADP-forming acetate-CoA ligase and acetyl-CoA synthetase is demonstrated. Here, we propose a modified model of carbon cycling in cold seeps: during AOM process, methane can be converted into organic carbon, such as acetate, which further fuels the heterotrophic community in the ecosystem.

Ocean cold seeps are poorly understood relative to related systems like hydrothermal vents. Here the authors use high pressure bioreactors and microbial communities from a cold seep mud volcano and find a previously missing step of methane conversion to acetate that likely fuels heterotrophic communities.

Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane Concentrations

Coastal zones are transitional areas between land and sea where large amounts of organic and inorganic carbon compounds are recycled by microbes. Especially shallow zones near land have been shown to be the main source for oceanic methane (CH4) emissions. Water depth has been predicted as the best explanatory variable, which is related to CH4 ebullition, but exactly how sediment methanotrophs mediates these emissions along water depth is unknown. Here, we investigated the relative abundance and RNA transcripts attributed to methane oxidation proteins of aerobic methanotrophs in the sediment of shallow coastal zones with high CH4 concentrations within a depth gradient from 10-45 m. Field sampling consisted of collecting sediment (top 0-2 cm layer) from eight stations along this depth gradient in the coastal Baltic Sea. The relative abundance and RNA transcripts attributed to the CH4 oxidizing protein (pMMO; particulate methane monooxygenase) of the dominant methanotroph Methylococcales was significantly higher in deeper costal offshore areas (36-45 m water depth) compared to adjacent shallow zones (10-28 m). This was in accordance with the shallow zones having higher CH4 concentrations in the surface water, as well as more CH4 seeps from the sediment. Furthermore, our findings indicate that the low prevalence of Methylococcales and RNA transcripts attributed to pMMO was restrained to the euphotic zone (indicated by Photosynthetically active radiation (PAR) data, photosynthesis proteins, and 18S rRNA data of benthic diatoms). This was also indicated by a positive relationship between water depth and the relative abundance of Methylococcales and pMMO. How these processes are affected by light availability requires further studies. CH4 ebullition potentially bypasses aerobic methanotrophs in shallow coastal areas, reducing CH4 availability and limiting their growth. Such mechanism could help explain their reduced relative abundance and related RNA transcripts for pMMO. These findings can partly explain the difference in CH4 concentrations between shallow and deep coastal areas, and the relationship between CH4 concentrations and water depth.

Improving protein solubility and activity by introducing small peptide tags designed with machine learning models

Improving catalytic ability of enzymes is critical to the success of many metabolic engineering projects, but the search space of possible protein mutants is too large to explore exhaustively through experiments. To some extent, highly soluble enzymes tend to exhibit high activity due to their better folding quality. Here, we demonstrate that an optimization algorithm based on a regression model can effectively design short peptide tags to improve solubility of a few model enzymes. Based on the protein sequence information, a support vector regression model we recently developed was used to evaluate protein solubility after small peptide tags were introduced to a target protein. The optimization algorithm guided the sequences of the tags to evolve towards variants that had higher solubility. The optimization results were validated successfully by measuring solubility and activity of the model enzyme with and without the identified tags. The solubility of one protein (tyrosine ammonia lyase) was more than doubled and its activity was improved by 250%. This strategy successfully increased solubility of another two enzymes (aldehyde dehydrogenase and 1-deoxy-D-xylulose-5-phosphate synthase) we tested. The presented optimization methodology thus provides a valuable tool for improving enzyme performance for metabolic engineering and other biotechnology projects.

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Short tags were added to proteins to improve their protein solubility.

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Machine learning model was used to optimize amino acid composition of the tags.

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Multiple proteins’ solubility was substantially improved.

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Catalytic activity of one enzyme was increased when its solubility was enhanced.

Global reconstruction reduces the uncertainty of oceanic nitrous oxide emissions and reveals a vigorous seasonal cycle

Assessment of the global budget of the greenhouse gas nitrous oxide ([Formula: see text]O) is limited by poor knowledge of the oceanic [Formula: see text]O flux to the atmosphere, of which the magnitude, spatial distribution, and temporal variability remain highly uncertain. Here, we reconstruct climatological [Formula: see text]O emissions from the ocean by training a supervised learning algorithm with over 158,000 [Formula: see text]O measurements from the surface ocean-the largest synthesis to date. The reconstruction captures observed latitudinal gradients and coastal hot spots of [Formula: see text]O flux and reveals a vigorous global seasonal cycle. We estimate an annual mean [Formula: see text]O flux of 4.2 ± 1.0 Tg N[Formula: see text], 64% of which occurs in the tropics, and 20% in coastal upwelling systems that occupy less than 3% of the ocean area. This [Formula: see text]O flux ranges from a low of 3.3 ± 1.3 Tg N[Formula: see text] in the boreal spring to a high of 5.5 ± 2.0 Tg N[Formula: see text] in the boreal summer. Much of the seasonal variations in global [Formula: see text]O emissions can be traced to seasonal upwelling in the tropical ocean and winter mixing in the Southern Ocean. The dominant contribution to seasonality by productive, low-oxygen tropical upwelling systems (>75%) suggests a sensitivity of the global [Formula: see text]O flux to El Niño-Southern Oscillation and anthropogenic stratification of the low latitude ocean. This ocean flux estimate is consistent with the range adopted by the Intergovernmental Panel on Climate Change, but reduces its uncertainty by more than fivefold, enabling more precise determination of other terms in the atmospheric [Formula: see text]O budget.

A synthesis of methane emissions from shallow vegetated coastal ecosystems

Vegetated coastal ecosystems (VCEs; i.e., mangroves, salt marshes, and seagrasses) play a critical role in global carbon (C) cycling, storing 10× more C than temperate forests. Methane (CH₄ ), a potent greenhouse gas, can form in the sediments of these ecosystems. Currently, CH₄ emissions are a missing component of VCE C budgets. This review summarizes 97 studies describing CH₄ fluxes from mangrove, salt marsh, and seagrass ecosystems and discusses factors controlling CH₄ flux in these systems. CH₄ fluxes from these ecosystems were highly variable yet they all act as net methane sources (median, range; mangrove: 279.17, -67.33 to 72,867.83; salt marsh: 224.44, -92.60 to 94,129.68; seagrass: 64.80, 1.25-401.50 µmol CH₄ m^-2 day^-1 ). Together CH₄ emissions from mangrove, salt marsh, and seagrass ecosystems are about 0.33-0.39 Tmol CH₄ -C/year-an addition that increases the current global marine CH₄ budget by more than 60%. The majority (~45%) of this increase is driven by mangrove CH₄ fluxes. While organic matter content and quality were commonly reported in individual studies as the most important environmental factors driving CH₄ flux, they were not significant predictors of CH₄ flux when data were combined across studies. Salinity was negatively correlated with CH₄ emissions from salt marshes, but not seagrasses and mangroves. Thus the available data suggest that other environmental drivers are important for predicting CH₄ emissions in vegetated coastal systems. Finally, we examine stressor effects on CH₄ emissions from VCEs and we hypothesize that future changes in temperature and other anthropogenic activites (e.g., nitrogen loading) will likely increase CH₄ emissions from these ecosystems. Overall, this review highlights the current and growing importance of VCEs in the global marine CH₄ budget.

Discovery and quantification of a widespread methane ebullition event in a coastal inlet (Baltic Sea) using a novel sonar strategy

How much of the greenhouse gas methane is transported from the seafloor to the atmosphere is unclear. Here, we present data describing an extensive ebullition event that occurred in Eckernförde Bay, a shallow gas-hosting coastal inlet in the Baltic Sea, in the fall of 2014. A weak storm induced hydrostatic pressure fluctuations that in turn stimulated gas ebullition from the seabed. In a finely tuned sonar survey of the bay, we obtained a hydroacoustic dataset with exceptionally high sensitivity for bubble detection. This allowed us to identify 2849 bubble seeps rising within 28 h from the seafloor across the 90 km² study site. Based on our calculations, the estimated bubble-driven episodic methane flux from the seafloor across the bay is 1,900 μMol m⁻² d⁻¹. Our study demonstrates that storm-associated fluctuations of hydrostatic pressure induce bulk gas-driven ebullitions. Given the extensive occurrence of shallow gas-hosting sediments in coastal seas, similar ebullition events probably take place in many parts of the Western Baltic Sea. However, these are likely to be missed during field investigations, due to the lack of high-quality data acquisition during storms, such that atmospheric inputs of marine-derived methane will be highly underestimated.