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

Physiological Stress Response to Sulfide Exposure of Freshwater Anaerobic Methanotrophic Archaea

Freshwater wetlands and coastal sediments are becoming hotspots for the emission of the greenhouse gas methane. Eutrophication-induced deposition of organic matter leads to elevated methanogenesis and sulfate reduction, thereby increasing the concentrations of methane and toxic sulfide, respectively. However, the effects of sulfide stress on the anaerobic methanotrophic biofilter have not been well explored. Here, we show how an enrichment culture dominated by the freshwater anaerobic methane-oxidizing archaeon "Candidatus (Ca.) Methanoperedens" responds to short-term and long-term exposure to sulfide in a bioreactor. The methane-oxidizing activity decreased to 45% and 20% but partially recovered to 70% and 30% within 5 days after short- and long-term sulfide exposure, respectively. Metagenomics indicated that "Ca. Methanoperedens" remained dominant in the enrichment throughout the entire experiment. The first short-term sulfide pulse led to increased expression of genes encoding for sulfide detoxification by low abundant community members, whereas long-term exposure resulted in upregulation of "Ca. Methanoperedens" genes encoding sulfite reductases of group III (Dsr-LP). "Ca. Methanoperedens" consumed polyhydroxyalkanoates during long-term sulfide exposure, possibly to aid in stress adaptation. Together, these results provide a valuable baseline for understanding fundamental ecophysiological adaptations to methane cycling in sulfate- and nitrate-rich aquatic ecosystems.

Benthic methane fluxes and oxidation over the Western Indian Shelf: No evidence of pelagic methanotrophic denitrification

Despite its pelagic supersaturation and wide occurrence of gas-charged pockets in the sediments, methane occurs at unusually low concentrations in the shelf waters off Western Indian coast, even during euxinic events, compared to other anoxic coastal systems of the world. To understand the reason and benthic biogeochemistry of CH4, we measured benthic CH4 flux rates through whole-core incubations, and carried out CH4-spiked 15N-labeled incubations of the suboxic/anoxic shelf waters during 2011-2013. We observed very low rates of benthic CH4 influx or efflux (-0.23 to 0.37 μmol m-2 d-1) during normoxia, and low to moderate rates of benthic CH4 efflux (2.45-74.89 μmol m-2 d-1) during seasonal anoxia. However, high rates of the potential benthic CH4 efflux (23.82-154.25 μmol m-2 d-1) implied massive benthic CH4 oxidation. The diffusing CH4 was oxidized within the sediments up to 99-100% during normoxia and up to 51-89% during anoxia. The benthic-released CH4 was further oxidized in the water column aerobically at the rate of 0.84 μmol m-2 d-1 during normoxia, and anaerobically at the rate of 0.16 μmol m-2 d-1 during anoxia. However, we did not find any evidence for NOx- (NO3- and/or NO2-)-dependent anaerobic CH4 oxidation (N-DAMO) i.e. methanotrophic denitrification in the shelf waters during anoxia, which suggested the potential role of Fe3+ and Mn4+ and/or SO42- as the alternative oxidants in the anaerobic CH4 oxidation necessitating further research. The total annual benthic CH4- flux rate and oxidation rate from the entire innershelf were estimated to be 9.45 Gg y-1 and 30.71 Gg y-1, respectively. Our study revealed that benthic- and pelagic anaerobic CH4 oxidation combined together reduce the water column CH4 concentration by 78-98%. Therefore the shelf sediments act as an effective CH4 filter by substantially reducing the benthic CH4 flux and ultimately the sea-air CH4 emission.

Sediment properties control riverine methane emissions: A case study of the Liao river in northern China

River and stream sediments act as biogeochemical reactors for greenhouse gases, particularly methane. However, understanding how riverbed sediment properties influence river carbon emissions remains relatively unclear. The Liao River in northern China is a typical watershed with heterogeneous water and sediment sources, characterized by varying sediment properties. In this study, we surveyed CH4 and CO2 emissions from its mainstem and tributaries during flood and dry seasons. We found consistent seasonal patterns in CH4 and CO2 emissions, with peaks occurring during the flood season. The average CH4 and CO2 fluxes were 1.64 ± 1.80 mmol m-2 d-1 and 59.66 ± 44.60 mmol m-2 d-1, respectively. Notably, the percentage of sediment silt was significantly correlated with CH4 concentration and flux (R2 = 0.12-0.30, p < 0.05). Fine particles dominated the availability of sediment organic matter and redox conditions, which were related to riverine CH4 production and emissions. Structural equation modeling revealed that both grain size and the percentage of TOC (total organic carbon) directly influenced riverine CH4 and CO2 emissions. The organic content and redox conditions of the riverbed sediment collectively explained 65% of riverine CH4 emissions, while grain size composition indirectly controlled CH4 emissions by altering sediment substrate quality and redox conditions. In contrast, river CO2 emissions were only weakly dependent on anaerobic metabolism in riverbed sediments. These findings enhance our understanding of the sources and metabolic mechanisms of riverine CH4 and CO2 emissions and offer potential improvements for estimating carbon fluxes in regional or global riverine networks by considering riverbed sediment properties.

Autochthonous organic matter input in reservoirs: Limited methane oxidation in sediments fails to suppress methane emission

The interception of rivers leads to the accumulation of substantial organic matter in reservoirs, exerting a significant influence on greenhouse gas emissions. The diverse imported organic matter, coupled with sedimentary heterogeneity and intricate microbial processes, gives rise to seasonal variations in methane emissions from reservoirs. In this study, sediment cores were supplemented with terrestrial or autochthonous carbon to emulate reservoir carbon input across different seasons, thereby investigating methane emission potential and associated microbial mechanisms within the sediment cores. Results demonstrated that autochthonous organic matter enhanced sediment organic content, thereby providing more substrates for the methanogenic process and fostering the proliferation of methanogens (with a relative abundance of 47.17 % to 60.66 %). Notably, the dominant genera of Methanosaeta, Methanosarcina, and Candidatus Methanomethylicus were boost on the surface layer of sediment. Concurrently, the introduction of autochthonous organic carbon spurred an increase in methane-oxidizing microbe, reaching up to 5.59 %, with Methylobacter and Candidatus Methanoperedens as the predominant species, which led to a downward migration of the functional microbial group in the sediment. Under the priming impact of autochthonous carbon, however, the methane oxidation probably doesn't consume the substantial methane produced in sediment. Consequently, the sediment functions as a hotspot for methane release into the overlying water, highlighting the necessity to include summer as critical periods for integrated assessments, particularly during algae bloom.

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.