Microbial Methane Consumption Research Articles

The diversification and potential function of microbiome in sediment-water interface of methane seeps in South China Sea.

The sediment-water interfaces of cold seeps play important roles in nutrient transportation between seafloor and deep-water column. Microorganisms are the key actors of biogeochemical processes in this interface. However, the knowledge of the microbiome in this interface are limited. Here we studied the microbial diversity and potential metabolic functions by 16S rRNA gene amplicon sequencing at sediment-water interface of two active cold seeps in the northern slope of South China Sea, Lingshui and Site F cold seeps. The microbial diversity and potential functions in the two cold seeps are obviously different. The microbial diversity of Lingshui interface areas, is found to be relatively low. Microbes associated with methane consumption are enriched, possibly due to the large and continuous eruptions of methane fluids. Methane consumption is mainly mediated by aerobic oxidation and denitrifying anaerobic methane oxidation (DAMO). The microbial diversity in Site F is higher than Lingshui. Fluids from seepage of Site F are mitigated by methanotrophic bacteria at the cyclical oxic-hypoxic fluctuating interface where intense redox cycling of carbon, sulfur, and nitrogen compounds occurs. The primary modes of microbial methane consumption are aerobic methane oxidation, along with DAMO, sulfate-dependent anaerobic methane oxidation (SAMO). To sum up, anaerobic oxidation of methane (AOM) may be underestimated in cold seep interface microenvironments. Our findings highlight the significance of AOM and interdependence between microorganisms and their environments in the interface microenvironments, providing insights into the biogeochemical processes that govern these unique ecological systems.

A New Dynamic Modeling Approach to Predict Microbial Methane Generation and Consumption in Marine Sediments

Methane, as a clean energy source and a potent greenhouse gas, is produced in marine sediments by microbes via complex biogeochemical processes associated with the mineralization of organic matter. Quantitative modeling of biogeochemical processes is a crucial way to advance the understanding of the global carbon cycle and the past, present, and future of climate change. Here, we present a new approach of dynamic transport-reaction model combined with sediment deposition. Compared to other studies, since the model does not need the methane concentration in the bottom of sediments and predicts that value, it provides us with a robust carbon budget estimation tool in the sediment. We applied the model to the Blake Ridge region (Ocean Drilling Program, Leg 164, site 997). Based on seafloor data as input, our model remarkably reproduces measured values of total organic carbon, dissolved inorganic carbon, sulfate, calcium, and magnesium concentration in pore waters and the in situ methane presented in three phases: dissolved in pore water, trapped in gas hydrate, and as free gas. Kinetically, we examined the coexistence of free gas and hydrate, and demonstrated how it might affect methane gas migration in marine sediment within the gas hydrate stability zone.

Carbon isotopic characterisation and oxidation of UK landfill methane emissions by atmospheric measurements.

Biological oxidation of methane in landfill cover material can be calculated from the carbon isotopic signature (δ13CCH4) of emitted CH4. Enhanced microbial consumption of methane in the aerobic portion of the landfill cover is indicated by a shift to heavier (less depleted) isotopic values in the residual methane emitted to air. This study was conducted at four landfill sites in southwest England. Measurement of CH4 using a mobile vehicle mounted instrument at the four sites was coupled with Flexfoil bag sampling of ambient air for high-precision isotope analysis. Gas well collection systems were sampled to estimate landfill oxidised proportion. Closed or active status, seasonal variation, cap stripping and site closure impact on landfill isotopic signature were also assessed. The δ13CCH4 values ranged from -60 to -54‰, with an average value of -57±2‰. Methane emissions from active cells are more depleted in 13C than closed sites. Methane oxidation, estimated from the isotope fractionation, ranged from 2.6 to 38.2%, with mean values of 9.5% for active and 16.2% for closed landfills, indicating that oxidised proportion is highly site specific.

Persistent oxygen depletion of bottom waters caused by methane seepage: Evidence from the South China Sea

Seepage of methane and oil is widespread at active and passive continental margins worldwide. Large-scale methane release may have caused bottom water oxygen depletion and acidification in the geological past, but direct evidence of low-oxygen conditions caused by methane leakage in natural systems is scarce. Here we report on the geochemical composition of sediments of two deepwater seep sites (>1700 m) from the South China Sea. The δ34S values of chromium reducible sulfur (δ34SCRS), δ13C values of total inorganic carbon (δ13CTIC), total sulfur (TS) and total organic carbon (TOC) contents, as well as redox-sensitive elements (Fe, U, and Mn) are used to constrain the intensity of fluid seepage and its impact on bottom water redox conditions. Sediment horizons affected by methane seepage are characterized by relatively high TS/TOC ratios (>1.4), low δ13CTIC values (<−27‰), and positive δ34S values (>22‰). The identified horizons show elevated authigenic U contents, high U/Th, as well as low Mn/Al ratios, suggesting oxygen depletion during their deposition. It is shown that local oxygen concentration of bottom waters was related to methane flux, with periods of larger methane release initiating during the Last Glacial Maximum. Much oxygen was apparently consumed during times of intense methane seepage, resulting in low oxygen conditions of bottom waters – conditions that persisted for ten thousand years and more. Our observations suggest that the interplay of flow intensity and microbial processes at seeps can locally affect the oxygen concentration in the deep ocean. The impact of microbial methane consumption on the oxygen concentration in the deep ocean should consequently be considered when looking into potential effects of future warming of the ocean, as more gas hydrate is susceptible to destabilization during ocean warming.

Hydrologic Controls of Methane Dynamics in Karst Subterranean Estuaries

AbstractKarst subterranean estuaries (KSEs) extend into carbonate platforms along 12% of all coastlines. A recent study has shown that microbial methane (CH4) consumption is an important component of the carbon cycle and food web dynamics within flooded caves that permeate KSEs. In this study, we obtained high‐resolution (~2.5‐day) temporal records of dissolved methane concentrations and its stable isotopic content (δ13C) to evaluate how regional meteorology and hydrology control methane dynamics in KSEs. Our records show that less methane was present in the anoxic fresh water during the wet season (4,361 ± 89 nM) than during the dry season (5,949 ± 132 nM), suggesting that the wet season hydrologic regime enhances mixing of methane and other constituents into the underlying brackish water. The δ13C of the methane (−38.1 ± 1.7‰) in the brackish water was consistently more 13C‐enriched than fresh water methane (−65.4 ± 0.4‰), implying persistent methane oxidation in the cave. Using a hydrologically based mass balance model, we calculate that methane consumption in the KSE was 21–28 mg CH4·m−2·year−1 during the 6‐month dry period, which equates to ~1.4 t of methane consumed within the 102‐ to 138‐km2 catchment basin for the cave. Unless wet season methane consumption is much greater, the magnitude of methane oxidized within KSEs is not likely to affect the global methane budget. However, our estimates constrain the contribution of a critical resource for this widely distributed subterranean ecosystem.

Co-cultivation of the strictly anaerobic methanogen Methanosarcina barkeri with aerobic methanotrophs in an oxygen-limited membrane bioreactor

Wetlands contribute to 30% of global methane emissions due to an imbalance between microbial methane production and consumption. Methanogenesis and methanotrophy have mainly been studied separately, and little is known about their potential interactions in aquatic environments. To mimic the interaction between methane producers and oxidizers in the environment, we co-cultivated the methanogenic archaeon Methanosarcina barkeri with aerobic Methylocystaceae methanotrophs in an oxygen-limited bioreactor using acetate as methanogenic substrate. Methane, acetate, dissolved oxygen, available nitrogen, pH, temperature, and cell density were monitored to follow system stability and activity. Stable reactor operation was achieved for two consecutive periods of 2 months. Fluorescence in situ hybridization micrographs indicated close association between both groups of microorganisms. This association suggests that the methanotrophs profit from direct access to the methane that is produced from acetate, while methanogens are protected by the concomitant oxygen consumption of the methanotrophs. This proof of principle study can be used to set up systems to study their responses to environmental changes.

Monodeuterated Methane, an Isotopic Tool To Assess Biological Methane Metabolism Rates.

Biological methane oxidation is a globally relevant process that mediates the flux of an important greenhouse gas through both aerobic and anaerobic metabolic pathways. However, measuring these metabolic rates presents many obstacles, from logistical barriers to regulatory hurdles and poor precision. Here we present a new approach for investigating microbial methane metabolism based on hydrogen atom dynamics, which is complementary to carbon-focused assessments of methanotrophy. The method uses monodeuterated methane (CH3D) as a metabolic substrate, quantifying the aqueous D/H ratio over time using off-axis integrated cavity output spectroscopy. This approach represents a nontoxic, comparatively rapid, and straightforward approach that supplements existing radiotopic and stable carbon isotopic methods; by probing hydrogen atoms, it offers an additional dimension for examining rates and pathways of methane metabolism. We provide direct comparisons between the CH3D procedure and the well-established 14CH4 radiotracer method for several methanotrophic systems, including type I and II aerobic methanotroph cultures and methane-seep sediment slurries and carbonate rocks under anoxic and oxic incubation conditions. In all applications tested, methane consumption values calculated via the CH3D method were directly and consistently proportional to 14C radiolabel-derived methane oxidation rates. We also employed this method in a nontraditional experimental setup, using flexible, gas-impermeable bags to investigate the role of pressure on seep sediment methane oxidation rates. Results revealed an 80% increase over atmospheric pressure in methanotrophic rates the equivalent of ~900-m water depth, highlighting the importance of this parameter on methane metabolism and exhibiting the flexibility of the newly described method. IMPORTANCE Microbial methane consumption is a critical component of the global carbon cycle, with wide-ranging implications for climate regulation and hydrocarbon exploitation. Nonetheless, quantifying methane metabolism typically involves logistically challenging methods and/or specialized equipment; these impediments have limited our understanding of methane fluxes and reservoirs in natural systems, making effective management difficult. Here, we offer an easily implementable, precise method using monodeuterated methane (CH3D) that advances three specific aims. First, it allows users to directly compare methane consumption rates between different experimental treatments of the same inoculum. Second, by empirically linking the CH3D procedure with the well-established 14C radiocarbon approach, we determine absolute scaling factors that facilitate rate measurements for several aerobic and anaerobic systems of interest. Third, CH3D represents a helpful tool in evaluating the relationship between methane activation and full oxidation in methanotrophic metabolisms. The procedural advantages, consistency, and novel research questions enabled by the CH3D method should prove useful in a wide range of culture-based and environmental microbial systems to further elucidate methane metabolism dynamics.

Bioconversion of methane to lactate by an obligate methanotrophic bacterium.

Methane is the second most abundant greenhouse gas (GHG), with nearly 60% of emissions derived from anthropogenic sources. Microbial conversion of methane to fuels and value-added chemicals offers a means to reduce GHG emissions, while also valorizing this otherwise squandered high-volume, high-energy gas. However, to date, advances in methane biocatalysis have been constrained by the low-productivity and limited genetic tractability of natural methane-consuming microbes. Here, leveraging recent identification of a novel, tractable methanotrophic bacterium, Methylomicrobium buryatense, we demonstrate microbial biocatalysis of methane to lactate, an industrial platform chemical. Heterologous overexpression of a Lactobacillus helveticus L-lactate dehydrogenase in M. buryatense resulted in an initial titer of 0.06 g lactate/L from methane. Cultivation in a 5 L continuously stirred tank bioreactor enabled production of 0.8 g lactate/L, representing a 13-fold improvement compared to the initial titer. The yields (0.05 g lactate/g methane) and productivity (0.008 g lactate/L/h) indicate the need and opportunity for future strain improvement. Additionally, real-time analysis of methane utilization implicated gas-to-liquid transfer and/or microbial methane consumption as process limitations. This work opens the door to develop an array of methanotrophic bacterial strain-engineering strategies currently employed for biocatalytic sugar upgrading to “green” chemicals and fuels.

Methanotrophy controls groundwater methane export from a barrier island

Methane concentrations can be high in coastal groundwater, resulting in methane export driven by submarine groundwater discharge. However, the magnitude of this methane flux depends significantly on the rate of methanotrophy, the often overlooked process of microbial methane consumption that occurs within coastal aquifer sediments. Here we describe a zone of methanogenesis within the freshwater lens of a barrier island aquifer and investigate the methane source/sink behavior of the barrier island system as a whole. The median concentration of methane dissolved in fresh groundwater beneath the center of the island was 0.6mM, supported by high rates of potential methanogenesis (22mmolm−2day−1). However, rates of microbial methane consumption were also elevated in surrounding sediments (18mmolm−2day−1). Groundwater flowing from the zone of methanogenesis to the point of discharge into the ocean had a long residence time within methanotrophic sediments (∼195days) such that the majority of the methane produced within the barrier island aquifer was likely consumed there.

Methods for Detecting Microbial Methane Production and Consumption by Gas Chromatography.

Methane is an energy-dense fuel but is also a greenhouse gas 25 times more detrimental to the environment than CO2. Methane can be produced abiotically by serpentinization, chemically by Sabatier or Fisher-Tropsh chemistry, or biotically by microbes (Berndt et al., 1996; Horita and Berndt, 1999; Dry, 2002; Wolfe, 1982; Thauer, 1998; Metcalf et al., 2002). Methanogens are anaerobic archaea that grow by producing methane gas as a metabolic byproduct (Wolfe, 1982; Thauer, 1998). Our lab has developed and optimized three different gas chromatograph-utilizing assays to characterize methanogen metabolism (Catlett et al., 2015). Here we describe the end point and kinetic assays that can be used to measure methane production by methanogens or methane consumption by methanotrophic microbes. The protocols can be used for measuring methane production or consumption by microbial pure cultures or by enrichment cultures.

Mathematical modeling of diffuse flow in seafloor hydrothermal systems: The potential extent of the subsurface biosphere at mid-ocean ridges

We describe a variety of one- and two-dimensional mathematical modeling approaches to characterizing diffuse flow circulation at mid-ocean ridge hydrothermal systems. The goal is to estimate the potential extent of the sub-seafloor microbial biosphere based on subsurface contours of the 120 °C isotherm as determined from the various models. The models suggest that the sub-seafloor depth for microbial life may range from less than 1 m in some places to the thickness of crustal layer 2A of ∼500 m in others. This depth depends primarily on how diffuse flow is driven. The 120 °C isotherm tends to be much deeper if diffuse flow is induced as boundary layer flow near high-temperature plumes, than if it results from conductive cooling or mixing near the seafloor. Because the heat flow alone may not allow identification of the flow regime in the subsurface, we highlight the use of chemical tracers as an additional constraint that sheds light into the flow and reaction patterns associated with vents. We use thermodynamic modeling, which connects the temperature of the diffuse fluid to its chemical composition. As the temperature-composition relationships differ for mixing versus conductive heating and cooling, the fluid geochemistry can shed light on subsurface transport. Using methane as an example, the geochemical models indicate subsurface microbial methane production and consumption in different regions of the vent field near EPR 9°50′N.

The rise and fall of methanotrophy following a deepwater oil-well blowout

The blowout of the Macondo oil well in the Gulf of Mexico in April 2010 injected up to 500,000 tonnes of natural gas, mainly methane, into the deep sea. Spatially extensive measurements of methane dynamics in the months following the spill reveal a rapid rise and fall in the microbial consumption of methane. The blowout of the Macondo oil well in the Gulf of Mexico in April 2010 injected up to 500,000 tonnes of natural gas, mainly methane, into the deep sea1. Most of the methane released was thought to have been consumed by marine microbes between July and August 20102,3. Here, we report spatially extensive measurements of methane concentrations and oxidation rates in the nine months following the spill. We show that although gas-rich deepwater plumes were a short-lived feature, water column concentrations of methane remained above background levels throughout the rest of the year. Rates of microbial methane oxidation peaked in the deepwater plumes in May and early June, coincident with a rapid rise in the abundance of known and new methane-oxidizing microbes. At this time, rates of methane oxidation reached up to 5,900 nmol l−1 d−1—the highest rates documented in the global pelagic ocean before the blowout4. Rates of methane oxidation fell to less than 50 nmol l−1 d−1 in late June, and continued to decline throughout the remainder of the year. We suggest the precipitous drop in methane consumption in late June, despite the persistence of methane in the water column, underscores the important role that physiological and environmental factors play in constraining the activity of methane-oxidizing bacteria in the Gulf of Mexico.

Comparative studies of pelagic microbial methane oxidation within the redox zones of the Gotland Deep and Landsort Deep (central Baltic Sea)

Abstract. Pelagic methane oxidation was investigated in dependence on differing hydrographic conditions within the redox zone of the Gotland Deep (GD) and Landsort Deep (LD), central Baltic Sea. The redox zone of both deeps, which indicates the transition between oxic and anoxic conditions, was characterized by a pronounced methane concentration gradient between the deep water (GD: 1233 nM, 223 m; LD: 2935 nM, 422 m) and the surface water (GD and LD &lt; 10 nM). This gradient together with a 13C CH4 enrichment (δ13C CH4 deep water: GD −84‰, LD −71‰; redox zone: GD −60‰, LD −20‰; surface water: GD −47‰, LD −50‰; δ13C CH4 vs. Vienna Pee Dee Belemnite standard), clearly indicating microbial methane consumption within the redox zone. Expression analysis of the methane monooxygenase identified one active type I methanotrophic bacterium in both redox zones. In contrast, the turnover of methane within the redox zones showed strong differences between the two basins (GD: max. 0.12 nM d−1, LD: max. 0.61 nM d−1), with a nearly four-times-lower turnover time of methane in the LD (GD: 455 d, LD: 127 d). Vertical mixing rates for both deeps were calculated on the base of the methane concentration profile and the consumption of methane in the redox zone (GD: 2.5 × 10–6 m2 s−1, LD: 1.6 × 10–5 m2 s−1). Our study identified vertical transport of methane from the deep-water body towards the redox zone as well as differing hydrographic conditions (lateral intrusions and vertical mixing) within the redox zone of these deeps as major factors that determine the pelagic methane oxidation.

Seafloor oxygen consumption fuelled by methane from cold seeps

The leakage of cold, methane-rich fluids from subsurface reservoirs to the sea floor sustains some of the richest ecosystems on the sea bed. These cold-seep communities consume around two orders of magnitude more oxygen than the surrounding sea floor as a result of the microbial consumption of seep methane.

Response of the Black Sea methane budget to massive short-term submarine inputs of methane

Abstract. A steady state box model was developed to estimate the methane input into the Black Sea water column at various water depths. Our model results reveal a total input of methane of 4.7 Tg yr−1. The model predicts that the input of methane is largest at water depths between 600 and 700 m (7% of the total input), suggesting that the dissociation of methane gas hydrates at water depths equivalent to their upper stability limit may represent an important source of methane into the water column. In addition we discuss the effects of massive short-term methane inputs (e.g. through eruptions of deep-water mud volcanoes or submarine landslides at intermediate water depths) on the water column methane distribution and the resulting methane emission to the atmosphere. Our non-steady state simulations predict that these inputs will be effectively buffered by intense microbial methane consumption and that the upward flux of methane is strongly hampered by the pronounced density stratification of the Black Sea water column. For instance, an assumed input of methane of 179 Tg CH4 d−1 (equivalent to the amount of methane released by 1000 mud volcano eruptions) at a water depth of 700 m will only marginally influence the sea/air methane flux increasing it by only 3%.

Methane oxidation in permeable sediments at hydrocarbon seeps in the Santa Barbara Channel, California

Abstract. A shallow-water area in the Santa Barbara Channel, California, known collectively as the Coal Oil Point seep field, is one of the largest natural submarine hydrocarbon emission areas in the world. Both gas and oil are seeping constantly through a predominantly sandy seabed into the ocean. This study focused on the methanotrophic activity within the surface sediments (0–15 cm) of the permeable seabed in the so-called Brian Seep area at a water depth of ∼10 m. Detailed investigations of the sediment biogeochemistry of active gas vents indicated that it is driven by fast advective transport of water through the sands, resulting in a deep penetration of oxidants (oxygen, sulfate). Maxima of microbial methane consumption were found at the sediment-water interface and in deeper layers of the sediment, representing either aerobic or anaerobic oxidation of methane, respectively. Methane consumption was relatively low (0.6–8.7 mmol m−2 d-1) in comparison to gas hydrate-bearing fine-grained sediments on the continental shelf. The low rates and the observation of free gas migrating through permeable coastal sediments indicate that a substantial proportion of methane can escape the microbial methane filter in coastal sediments.

Methane cycle in the Barents Sea

Biogeochemical cycle of methane in the Barents Sea was studied using isotope geochemistry to determine the rates of microbial methane oxidation. It was established that microbiological processes (glucose consumption, 14CO2 assimilation, sulfate reduction, and slow methane oxidation) in oxidized surface and weakly reduced sediments are marked by only insignificant change in SO42− concentration and absence of notable growth of total alkalinity and N/NH4 downward the sediment core. Microbial methane productivity was 0.111 × 106 mol day−1. Taking into account the volume of water column, microbial methane consumption therein can be as much as 1.8 × 106 mol day−1.

Stable isotopic evidence in support of active microbial methane cycling in low-temperature diffuse flow vents at 9°50′N East Pacific Rise

A unique dataset from paired low- and high-temperature vents at 9°50′N East Pacific Rise provides insight into the microbiological activity in low-temperature diffuse fluids. The stable carbon isotopic composition of CH 4 and CO 2 in 9°50′N hydrothermal fluids indicates microbial methane production, perhaps coupled with microbial methane consumption. Diffuse fluids are depleted in 13C by ∼10‰ in values of δ 13C of CH 4, and by ∼0.55‰ in values of δ 13C of CO 2, relative to the values of the high-temperature source fluid (δ 13C of CH 4 =−20.1 ± 1.2‰, δ 13C of CO 2 =−4.08 ± 0.15‰). Mixing of seawater or thermogenic sources cannot account for the depletions in 13C of both CH 4 and CO 2 at diffuse vents relative to adjacent high-temperature vents. The substrate utilization and 13C fractionation associated with the microbiological processes of methanogenesis and methane oxidation can explain observed steady-state CH 4 and CO 2 concentrations and carbon isotopic compositions. A mass-isotope numerical box model of these paired vent systems is consistent with the hypothesis that microbial methane cycling is active at diffuse vents at 9°50′N. The detectable 13C modification of fluid geochemistry by microbial metabolisms may provide a useful tool for detecting active methanogenesis.

Aerobic methanotrophy in the oxic–anoxic transition zone of the Black Sea water column

Large amounts of dissolved methane (> 98%) are effectively oxidised by anaerobic and aerobic microorganisms in the Black Sea water column. In the oxic–anoxic transition zone methane concentrations rapidly decrease and an enrichment in 13CH 4 – most likely a result of microbial methane consumption – is observed. Using high performance liquid chromatography–mass spectrometry (HPLC–MS), we show that intact bacteriohopanoids, characteristic for aerobic methanotrophic bacteria, clearly increase in the sub-oxic part of the chemocline compared to water above and below this depth interval. Moreover, the co-occurrence of aminopentol (17 β(H),21 β(H)-35-aminobacteriohopane-30,31,32,33,34-pentol) with aminotetrol (17 β(H),21 β(H)-35-aminobacteriohopane-31,32,33,34-tetrol) argues for members of the type I and/or type X cluster as the dominating bacterial methanotrophs. Our data indicate that aerobic rather than anaerobic methanotrophs are responsible for the strong 13C enrichment in CH 4 occurring in sub-oxic waters within the oxic–anoxic transition zone of the Black Sea water column.

In situ quantification of methane oxidation in soils using Gas Push–Pull Tests

The Gas Push–Pull Test (GPPT) is a tool for measuring in situ soil processes including methane oxidation. To quantify methane oxidation, methane and non-reactive gases selected based on transport behaviour similar to methane, were injected into soil above a petroleum hydrocarbon contaminated aquifer and gas samples were extracted over time. The rate of loss of methane was compared to the loss of tracer gases and differences in the concentrations were attributed to microbial activity. To further support the evidence for microbial methane consumption, tests were also performed under conditions of inhibited microbial activity.