Daniel Frank Mcginnis

Linking crenarchaeal and bacterial nitrification to anammox in the Black Sea

Active expression of putative ammonia monooxygenase gene subunit A (amoA) of marine group I Crenarchaeota has been detected in the Black Sea water column. It reached its maximum, as quantified by reverse-transcription quantitative PCR, exactly at the nitrate maximum or the nitrification zone modeled in the lower oxic zone. Crenarchaeal amoA expression could explain 74.5% of the nitrite variations in the lower oxic zone. In comparison, amoA expression by γ-proteobacterial ammonia-oxidizing bacteria (AOB) showed two distinct maxima, one in the modeled nitrification zone and one in the suboxic zone. Neither the amoA expression by crenarchaea nor that by β-proteobacterial AOB was significantly elevated in this latter zone. Nitrification in the suboxic zone, most likely microaerobic in nature, was verified by 15NO2− and 15N15N production in 15NH4+ incubations with no measurable oxygen. It provided a direct local source of nitrite for anammox in the suboxic zone. Both ammonia-oxidizing crenarchaea and γ-proteobacterial AOB were important nitrifiers in the Black Sea and were likely coupled to anammox in indirect and direct manners respectively. Each process supplied about half of the nitrite required by anammox, based on 15N-incubation experiments and modeled calculations. Because anammox is a major nitrogen loss in marine suboxic waters, such nitrification–anammox coupling potentially occurring also in oceanic oxygen minimum zones would act as a short circuit connecting regenerated ammonium to direct nitrogen loss, thus reducing the presumed direct contribution from deep-sea nitrate.

Fate of rising methane bubbles in stratified waters: How much methane reaches the atmosphere?

There is growing concern about the transfer of methane originating from water bodies to the atmosphere. Methane from sediments can reach the atmosphere directly via bubbles or indirectly via vertical turbulent transport. This work quantifies methane gas bubble dissolution using a combination of bubble modeling and acoustic observations of rising bubbles to determine what fraction of the methane transported by bubbles will reach the atmosphere. The bubble model predicts the evolving bubble size, gas composition, and rise distance and is suitable for almost all aquatic environments. The model was validated using methane and argon bubble dissolution measurements obtained from the literature for deep, oxic, saline water with excellent results. Methane bubbles from within the hydrate stability zone (typically below ∼500 m water depth in the ocean) are believed to form an outer hydrate rim. To explain the subsequent slow dissolution, a model calibration was performed using bubble dissolution data from the literature measured within the hydrate stability zone. The calibrated model explains the impressively tall flares (>1300 m) observed in the hydrate stability zone of the Black Sea. This study suggests that only a small amount of methane reaches the surface at active seep sites in the Black Sea, and this only from very shallow water areas (<100 m). Clearly, the Black Sea and the ocean are rather effective barriers against the transfer of bubble methane to the atmosphere, although substantial amounts of methane may reach the surface in shallow lakes and reservoirs.

Extreme Methane Emissions from a Swiss Hydropower Reservoir: Contribution from Bubbling Sediments

Methane emission pathways and their importance were quantified during a yearlong survey of a temperate hydropower reservoir. Measurements using gas traps indicated very high ebullition rates, but due to the stochastic nature of ebullition a mass balance approach was crucial to deduce system-wide methane sources and losses. Methane diffusion from the sediment was generally low and seasonally stable and did not account for the high concentration of dissolved methane measured in the reservoir discharge. A strong positive correlation between water temperature and the observed dissolved methane concentration enabled us to quantify the dissolved methane addition from bubble dissolution using a system-wide mass balance. Finally, knowing the contribution due to bubble dissolution, we used a bubble model to estimate bubble emission directly to the atmosphere. Our results indicated that the total methane emission from Lake Wohlen was on average >150 mg CH(4) m(-2) d(-1), which is the highest ever documented for a midlatitude reservoir. The substantial temperature-dependent methane emissions discovered in this 90-year-old reservoir indicate that temperate water bodies can be an important but overlooked methane source.

Sediment Trapping by Dams Creates Methane Emission Hot Spots

Inland waters transport and transform substantial amounts of carbon and account for ∼18% of global methane emissions. Large reservoirs with higher areal methane release rates than natural waters contribute significantly to freshwater emissions. However, there are millions of small dams worldwide that receive and trap high loads of organic carbon and can therefore potentially emit significant amounts of methane to the atmosphere. We evaluated the effect of damming on methane emissions in a central European impounded river. Direct comparison of riverine and reservoir reaches, where sedimentation in the latter is increased due to trapping by dams, revealed that the reservoir reaches are the major source of methane emissions (∼0.23 mmol CH4 m(-2) d(-1) vs ∼19.7 mmol CH4 m(-2) d(-1), respectively) and that areal emission rates far exceed previous estimates for temperate reservoirs or rivers. We show that sediment accumulation correlates with methane production and subsequent ebullitive release rates and may therefore be an excellent proxy for estimating methane emissions from small reservoirs. Our results suggest that sedimentation-driven methane emissions from dammed river hot spot sites can potentially increase global freshwater emissions by up to 7%.

Measurements of eddy correlation oxygen fluxes in shallow freshwaters: Towards routine applications and analysis

Benthic fluxes of dissolved oxygen are measured in a shallow reservoir using the eddy correlation technique. Flux variations depict the diurnal production-consumption cycle, with daytime oxygen release following the solar radiation trend. The average nighttime uptake of -40 +/- 11 mmol m(-2) d(-1) is in excellent agreement with the rate of -35 +/- 3 mmol m(-2) d(-1) derived from sediment oxygen mic-roprofiles. Separating large-scale advective and turbulent fluctuations is a crucial and uncertain component of the flux computation and the largest source of error. To compensate for the 2.25 s oxygen sensor response time, the oxygen flux calculations are corrected by only similar to 5% using a first-order spectral enhancement. This work demonstrates that only a slightly faster oxygen sensor would be needed to resolve the entire flux spectrum. The 18 hours of data are the first measurements obtained in a freshwater reservoir that capture the diurnal oxygen production-consumption cycle.

Atmospheric methane flux from bubbling seeps: spatially extrapolated quantification from a Black Sea shelf area

Bubble transport of methane from shallow seep sites in the Black Sea west of the Crimea Peninsula between 70 and 112 m water depth has been studied by extrapolation of results gained through different hydroacoustic methods and direct sampling. Ship-based hydroacoustic echo sounders can locate bubble releasing seep sites very precisely and facilitate their correlation with geological or other features at the seafloor. Here, the backscatter strength of a multibeam system was integrated with single-beam data to estimate the amount of seeps/m2 for different backscatter intensities, resulting in 2709 vents in total. Direct flux measurements by submersible revealed methane fluxes from individual vents of 0.32–0.85 l/min or 14.5–37.8 mmol/min at ambient pressure and temperature conditions. A conservative estimate of 30 mmol/min per site was used to estimate the flux into the water to be 1219–1355 mmol/s. The flux to the atmosphere was calculated by applying a bubble dissolution model taking release depth, temperature, gas composition, and bubble size spectra into account. The flux into the atmosphere (3930–4533 mol/d) or into the mixed layer (6186–6899 mol/d) from the 21.8 km2 large study area is three times higher than independently measured fluxes of dissolved methane for the same area using geochemical methods (1030–2495 mol/d). The amount of methane dissolving in the mixed layer is 2256–2366 mol/d. This close match shows that the hydroacoustic approach for extrapolating the number of seeps/m2 and the applied bubble dissolution model are suitable to extrapolate methane fluxes over larger areas.

Application of Oxygen Eddy Correlation in Aquatic Systems

Abstract The eddy correlation technique is rapidly becoming an established method for resolving dissolved oxygen fluxes in natural aquatic systems. This direct and noninvasive determination of oxygen fluxes close to the sediment by simultaneously measuring the velocity and the dissolved oxygen fluctuations has considerable advantages compared to traditional methods. This paper describes the measurement principle and analyzes the spatial and temporal scales of those fluctuations as a function of turbulence levels. The magnitudes and spectral structure of the expected fluctuations provide the required sensor specifications and define practical boundary conditions for the eddy correlation instrumentation and its deployment. In addition, data analysis and spectral corrections are proposed for the usual nonideal conditions, such as the time shift between the sensor pair and the limited frequency response of the oxygen sensor. The consistency of the eddy correlation measurements in a riverine reservoir has been...

Size Does Matter: Importance of Large Bubbles and Small-Scale Hot Spots for Methane Transport

Ebullition (bubbling) is an important mechanism for the transfer of methane (CH4) from shallow waters to the atmosphere. Because of their stochastic nature, however, ebullition fluxes are difficult to accurately resolve. Hydroacoustic surveys have the potential to significantly improve the spatiotemporal observation of emission fluxes, but knowledge of bubble size distribution is also necessary to accurately assess local, regional, and global water body CH4 emission estimates. Therefore, we explore the importance of bubble size and small-scale flux variability on CH4 transport in and emissions from a reservoir with a bubble-size-calibrated echosounder that can efficiently and economically survey greater areas while still resolving individual bubbles. Using a postprocessing method that resolves bubble density, we found that the largest 10% of the >6700 observed bubbles were responsible for more than 65% of the total CH4 transport. Furthermore, the asymmetry of CH4 ebullition flux distribution and the high spatial heterogeneity of those fluxes suggests that inadvertently omitting emission hot spots (i.e., areas of high flux) could lead to significant underestimations of CH4 emissions from localized areas and potentially from entire water bodies. While the bubble sizes resolved by the hydroacoustic method may provide insight into the factors controlling ebullition (e.g., sediment type, carbon sedimentation), the better resolution of small-scale CH4 emission hot spots afforded by hydroacoustics will bring us closer to the true CH4 emission estimates from all shallow waters, be them lakes, reservoirs, or coastal oceans and seas.

Discovery of a natural CO2 seep in the German North Sea: Implications for shallow dissolved gas and seep detection

A natural carbon dioxide (CO2) seep was discovered during an expedition to the southern German North Sea (October 2008). Elevated CO2 levels of ∼10–20 times above background were detected in seawater above a natural salt dome ∼30 km north of the East-Frisian Island Juist. A single elevated value 53 times higher than background was measured, indicating a possible CO2 point source from the seafloor. Measured pH values of around 6.8 support modeled pH values for the observed high CO2 concentration. These results are presented in the context of CO2 seepage detection, in light of proposed subsurface CO2 sequestering and growing concern of ocean acidification. We explore the boundary conditions of CO2 bubble and plume seepage and potential flux paths to the atmosphere. Shallow bubble release experiments conducted in a lake combined with discrete-bubble modeling suggest that shallow CO2 outgassing will be difficult to detect as bubbles dissolve very rapidly (within meters). Bubble-plume modeling further shows that a CO2 plume will lose buoyancy quickly because of rapid bubble dissolution while the newly CO2-enriched water tends to sink toward the seabed. Results suggest that released CO2 will tend to stay near the bottom in shallow systems (<200 m) and will vent to the atmosphere only during deep water convection (water column turnover). While isotope signatures point to a biogenic source, the exact origin is inconclusive because of dilution. This site could serve as a natural laboratory to further study the effects of carbon sequestration below the seafloor.

Methanotrophic microbial communities associated with bubble plumes above gas seeps in the Black Sea

Bubbles evolving from active gas seeps can be traced by hydroacoustic imaging up to 1000 m high in the Black Sea water column. Although methane concentrations are not distinguishable between the water column above the deep seep and reference sites, atmospheric noble gas measurements clearly show the constant input of gases (mainly methane) via seepage into the Black Sea. Archaea (ANME-1, ANME-2) and methanotrophic bacteria detected with specific 16S rRNA-targeted oligonucleotide probes are related to active gas seeps in the oxic and anoxic water column. It is suggested that methane seeps have a much greater influence on the Black Sea methane budget than previously acknowledged and that ANME-1 and ANME-2 are injected via gas bubbles from the sediment into the anoxic water column mediating methane oxidation. Our results show further that only minor amounts of methane evolving from Black Sea gas seeps reach the atmosphere due to the very effective microbial barrier. Hence only major thermodynamically and/or tectonically triggered gas hydrate dissociation has the potential to induce rapid climate changes as suggested by the “clathrate gun hypothesis.”