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Small headwater streams are recognized for intense outgassing to the atmosphere of climate-relevant carbon dioxide (CO2) and methane (CH4). Though these headwaters are markedly oversaturated for both CO2 and CH4, the origins and controls over the fate of these two carbon-gases are still poorly constrained, especially for the stronger greenhouse gas CH4. Here, by measuring stream-based production of CO2 and CH4, concurrently with their rates of outgassing to the atmosphere, we identify distinct biophysical control mechanisms for each gas. We show that while CO2 is largely imported from the catchment in proportion to discharge, CO2 outgassing can be modulated by in-stream metabolism to offset outgassing by up to 30% in spring and summer. In contrast, CH4 shows a non-linear response to seasonal changes in discharge and is predominantly produced in the streambed in relation to sediment type. Further, once released from the streambed, outgassing of CH4 at the surface and flow-driven dilution occur far more rapidly than biological methane oxidation and CH4 leaves the water largely unaltered by biology. Incorporating the intense carbon cycling of headwater streams into the global carbon cycle will require distinct parameterizations for each carbon gas in Earth system models.

Small headwater streams are recognized for intense outgassing to the atmosphere of climate-relevant carbon dioxide (CO2) and methane (CH4). Though these headwaters are markedly oversaturated for both CO2 and CH4, the origins and controls over the fate of these two carbon-gases are still poorly constrained, especially for the stronger greenhouse gas CH4. Here, by measuring stream-based production of CO2 and CH4, concurrently with their rates of outgassing to the atmosphere, we identify distinct biophysical control mechanisms for each gas. We show that while CO2 is largely imported from the catchment in proportion to discharge, CO2 outgassing can be modulated by in-stream metabolism to offset outgassing by up to 30% in spring and summer. In contrast, CH4 shows a non-linear response to seasonal changes in discharge and is predominantly produced in the streambed in relation to sediment type. Further, once released from the streambed, outgassing of CH4 at the surface and flow-driven dilution occur far more rapidly than biological methane oxidation and CH4 leaves the water largely unaltered by biology. Incorporating the intense carbon cycling of headwater streams into the global carbon cycle will require distinct parameterizations for each carbon gas in Earth system models.

Cold-water coral (CWC) reefs are distributed globally and form complex three-dimensional structures on the deep seafloor, providing habitat for numerous species. Here, we measured the community O2 and dissolved inorganic nitrogen (DIN) flux of CWC reef habitats with different coral cover and bare sediment (acting as reference site) in the Logachev mound area (NE Atlantic). Two methodologies were applied: the non-invasive in situaquatic eddy co-variance (AEC) technique, and ex situ whole box core (BC) incubations. The AEC system was deployed twice per coral mound (69 h in total), providing an integral estimate of the O2 flux from a total reef area of up to 500 m2, with mean O2 consumption rates ranging from 11.6 ± 3.9 to 45.3 ± 11.7 mmol Om–2 d–1 (mean ± SE). CWC reef community Ofluxes obtained from the BC incubations ranged from 5.7 ± 0.3 to 28.4 ± 2.4 mmol Om–2 d–1 (mean ± SD) while the Oflux measured by BC incubations on the bare sediment reference site reported 1.9 ± 1.3 mmol Om–2 d–1 (mean ± SD). Overall, Ofluxes measured with AEC and BC showed reasonable agreement, except for one station with high habitat heterogeneity. Our results suggest Ofluxes of CWC reef communities in the North East Atlantic are around five times higher than of sediments from comparable depths and living CWCs are driving the increased metabolism. DIN flux measurements by the BC incubations also revealed around two times higher DIN fluxes at the CWC reef (1.17 ± 0.87 mmol DIN m–2 d–1), compared to the bare sediment reference site (0.49 ± 0.32 mmol DIN m–2 d–1), due to intensified benthic release of NH4+. Our data indicate that the amount of living corals and dead coral framework largely contributes to the observed variability in Ofluxes on CWC reefs. A conservative estimate, based on the

The benthic environment is a crucial component of marine systems in the provision of ecosystem services, sustaining biodiversity and in climate regulation, and therefore important to human society. With the contemporary increase in computational power, model resolution and technological improvements in quality and quantity of benthic data, it is necessary to ensure that benthic systems are appropriately represented in coupled benthic-pelagic biogeochemical and ecological modelling studies. In this paper we focus on five topical challenges related to various aspects of modelling benthic environments: organic matter reactivity, dynamics of benthic-pelagic boundary layer, microphytobenthos, biological transport and small-scale heterogeneity, and impacts of episodic events. We discuss current gaps in their understanding and indicate plausible ways ahead. Further, we propose a three-pronged approach for the advancement of benthic and benthic-pelagic modelling, essential for improved understanding, management and prediction of the marine environment. This includes: (A) development of a traceable and hierarchical framework for benthic-pelagic models, which will facilitate integration among models, reduce risk of bias, and clarify model limitations; (B) extended cross-disciplinary approach to promote effective collaboration between modelling and empirical scientists of various backgrounds and better involvement of stakeholders and end-users; (C) a common vocabulary for terminology used in benthic modelling, to promote model development and integration, and also to enhance mutual understanding.

Anoxic mineralization of organic matter releases dissolved inorganic carbon and produces reduced mineralization products. The reoxidation of these reduced compounds is essential for biogeochemical cycling in sediments and is mainly performed by chemoautotrophic microbes, which synthesize new organic carbon by dark CO2 fixation. At present however, the biogeochemical importance of chemoautotrophy in high-latitude sediments is largely unknown. Here, we determine the seasonal variation in sedimentary chemoautotrophic production in Kobbefjord (SW Greenland). Intact sediment cores from the fjord were incubated, and dark CO2 fixation was quantified by combining bacterial phospholipid-derived fatty acid analysis with 13C stable isotope probing (PLFA-SIP). Our results reveal a distinct seasonal cycle in chemoautotrophic activity, which increases after the spring bloom and shows lowest activity in the late winter when the fjord is covered by sea ice. The depth distribution of chemoautotrophic activity also varied seasonally, likely due to seasonal variation in the bioturbation activity of sediment infauna. Although chemoautotrophy rates (0.4 ± 0.2 mmol C m-2d-1) were in the low range for coastal sediments, they are comparable to those from intertidal sandflats and brackish tropical lagoons, and scale with the sulfide production through sulfate reduction in the fjord. Chemoautotrophic production in these fjord sediments thus appears to be mainly driven by sulfide oxidation and can re-fix 4% of the CO2 produced by mineralization

Headwater streams are important in the carbon cycle and there is a need to better parametrize and quantify exchange of carbon-relevant gases. Thus, we characterized variability in the re-aeration coefficient (k2) and dissolved oxygen (O2) gas transfer velocity (k) in two lowland headwaters of the River Avon (UK). The traditional one-station open-water method was complemented by in situ quantification of riverine sources and sinks of O2 (i.e., groundwater inflow, photosynthesis and respiration in both the water column and benthic compartments - sediments) enabling direct hourly estimates of k2 at the reach–scale (~150 m) without relying on the nighttime regression method. Obtained k2 values ranged from 0.001 – 0.600 h-1. Average daytime k2 were a factor two higher than values at night, likely due to diel changes in water temperature and wind. Temperature contributed up to 46% of the variability in k on an hourly scale, but clustering temperature incrementally strengthened the statistical relationship. Our analysis suggested that k variability is aligned with dominant temperature trends rather than with short-term changes. Similarly, wind correlation with k increased when clustering wind speeds in increments correspondent with dominant variations (1 m s-1). Time scale is thus an important consideration when resolving physical drivers of re-aeration. Mean estimates of k from recent parametrizations proposed for upscaling, when applied to the settings of this study, were found to be in agreement with our independent O2 budget assessment (within <15%), adding further support to the validity of upscaling efforts aiming at quantifying large-scale riverine gas emissions.

Hadal trenches are considered to act as depo-centers for organic material at the trench axis and host unique and elevated biomasses of living organisms as compared to adjacent abyssal plains. To explore the diagenetic activity in hadal trench environments we quantified in situ benthic O2 consumption rates and sediment characteristics from the trench axis of two contrasting trench systems in the Pacific Ocean; the Izu-Bonin Trench underlying mesotrophic waters and the Tonga Trench underlying oligotrophic waters. In situ oxygen consumption at the Izu-Bonin Trench axis site (9200 m; 746±103 µmol m−2 d−1; n=27) was 3-times higher than at the Tonga Trench axis site (10800 m; 225±50 µmol m−2 d−1; n=7) presumably reflecting the higher surface water productivity in the Northern Pacific. Comparing benthic O2 consumption rates measured in the central hadal Tonga Trench to that of nearby (60 km distance) abyssal settings (6250 m; 92±44 µmol m−2 d−1; n=16) revealed a 2.5 higher activity at the trench bottom. Onboard investigations on recovered sediment furthermore revealed that the prokaryotic abundance and concentrations of phytopigments followed this overall trend (i.e minimum values at the abyssal site followed by higher values from the Tonga and Izu-Bonin Trenches axis, respectively). Excess 210Pb profiles suggested that mass-wasting events contributed to the deposition of material enhancing the concentration of organic matter in the central trench as compared to the abyssal settings. Our results complement recent findings from the Challenger deep in the Mariana Trench area, which also revealed elevated diagenetic activity in the central trench underpinning the importance of hadal ecosystems for the deep sea carbon cycling.

Climate change is expected to have a pronounced effect on biogeochemical cycling in Arctic fjords, but current insight on the biogeochemical functioning of these systems is limited. Here, we present seasonal data on primary production, export of particulate organic carbon (POC), and the coupling to benthic biogeochemistry in Kobbefjord (SW Greenland). Primary production and associated POC export from the photic zone showed marked seasonality, with annual integrated values of 7.2 and 19.9 mol C m-2 yr-1, respectively. This discrepancy, the isotopic signature, and C:N ratio of the sedimentating material suggested substantial import of marine POC from outside the fjord. At least 52% of the POC export reached the sediment, but the seasonality in pelagic productivity was not reflected in the sediment biogeochemistry, showing only moderate variation. Benthic mineralization and burial of organic carbon amounted to 3.2 and 5.3 mol C m-2 yr-1, respectively. Sulfate reduction was the most prominent mineralization pathway, accounting for 69% of the benthic mineralization, while denitrification accounted for 2%. Overall, the carbon mineralization and burial in Kobbefjord were significantly higher than previously observed in other more northerly Arctic fjords. Data compilation from Arctic fjords suggests proportional increases in surface production, POC export, benthic mineralization and burial of organic material with increasing duration of the ice-free period. Thus, the projected decline in ice coverage in higher Arctic Greenlandic fjords will, as a first approximation, entail proportional increases in productivity, mineralization, and burial of organic carbon in the fjords, which will thus become similar to present-day southerly systems.

The quantification of benthic fluxes with the aquatic eddy correlation (EC) technique is based on simultaneous measurement of the current velocity and a targeted bottom water parameter (e. g., O-2, temperature). High-frequency measurements (64Hz) are performed at a single point above the seafloor using an acoustic Doppler velocimeter (ADV) and a fast-responding sensor. The advantages of aquatic EC technique are that 1) it is noninvasive, 2) it integrates fluxes over a large area, and 3) it accounts for in situ hydrodynamics. The aquatic EC has gained acceptance as a powerful technique; however, an accurate assessment of the errors introduced by the spatial alignment of velocity and water constituent measurements and by their different response times is still needed. Here, this paper discusses uncertainties and biases in the data treatment based on oxygen EC flux measurements in a large-scale flume facility with well-constrained hydrodynamics. These observations are used to review data processing procedures and to recommend improved deployment methods, thus improving the precision, reliability, and confidence of EC measurements. Specifically, this study demonstrates that 1) the alignment of the time series based on maximum cross correlation improved the precision of EC flux estimations; 2) an oxygen sensor with a response time of <0.4 s facilitates accurate EC fluxes estimates in turbulence regimes corresponding to horizontal velocities <11 cm s(-1); and 3) the smallest possible distance (<1 cm) between the oxygen sensor and the ADV's sampling volume is important for accurate EC flux estimates, especially when the flow direction is perpendicular to the sensor's orientation.

In the last decade, the aquatic eddy correlation (EC) technique has proven to be a powerful approach for non-invasive measurements of oxygen fluxes across the sediment water interface. Fundamental to the EC approach is the correlation of turbulent velocity and oxygen concentration fluctuations measured with high frequencies in the same sampling volume. Oxygen concentrations are commonly measured with fast responding electrochemical microsensors. However, due to their own oxygen consumption, electrochemical microsensors are sensitive to changes of the diffusive boundary layer surrounding the probe and thus to changes in the ambient flow velocity. The so-called stirring sensitivity of microsensors constitutes an inherent correlation of flow velocity and oxygen sensing and thus an artificial flux which can confound the benthic flux determination. To assess the artificial flux we measured the correlation between the turbulent flow velocity and the signal of oxygen microsensors in a sealed annular flume without any oxygen sinks and sources. Experiments revealed significant correlations, even for sensors designed to have low stirring sensitivities of ~0.7%. The artificial fluxes depended on ambient flow conditions and, counter intuitively, increased at higher velocities because of the nonlinear contribution of turbulent velocity fluctuations. The measured artificial fluxes ranged from 2 - 70 mmol m-2 d-1 for weak and very strong turbulent flow, respectively. Further, the stirring sensitivity depended on the sensor orientation towards the flow. For a sensor orientation typically used in field studies, the artificial flux could be predicted using a simplified mathematical model. Optical microsensors (optodes) that should not exhibit a stirring sensitivity were tested in parallel and did not show any significant correlation between O2 signals and turbulent flow. In conclusion, EC data obtained with electrochemical sensors can be affected by artificial flux and we recommend u

In this study we show for the first time the microscale (mm) 2- and 3-dimensional spatial distribution and abundance of prokaryotes, viruses, and oxygen in a tidal sediment. Prokaryotes and viruses were highly heterogeneously distributed with patches of elevated abundances surrounded by areas of ca. 3-fold lower abundance within distances of <2 mm. Abundances of prokaryotes and viruses ranged from 1.3 x 10(9) to 4.2 x 10(9) cells cm(-3) and 4.1 x 10(9) to 13.1 x 10(9) viruses cm-3, respectively. The results showed oxygen concentration and uptake rates to be heterogeneously distributed at the same spatial scale, with the oxygen penetration depth varying from 1.5 to 5.8 mm and with an average (+/- SD) diffusive oxygen uptake of 18.9 +/- 6.4 mmol m(-2) d(-1). Locally, prokaryotes, viruses, and oxygen were found to be positively, negatively, or not correlated, but overall no significant relationship was detected. The lack of consistent spatial correlation between viruses and prokaryotes was explained by a temporal experiment using organic carbon-enriched homogenized sediment samples. Enhancement in metabolic activity and the proliferation of prokaryotes and viruses were not completely phased. These results suggest that local nourishment is likely to be an important driver of a high small-scale heterogeneity in abundance and dynamics of benthic viruses and prokaryotes. This is expected to influence the rates and regulation of benthic virus-host inter actions and thus microbial biogeochemical cycling.

The effect of salinity, pH, and dissolved inorganic carbon (TCO(2)) on growth and survival of three Arctic sea ice algal species, two diatoms (Fragilariopsis nana and Fragilariopsis sp.), and one species of chlorophyte (Chlamydomonas sp.) was assessed in controlled laboratory experiments. Our results suggest that the chlorophyte and the two diatoms have different tolerance to fluctuations in salinity and pH. The two species of diatoms exhibited maximum growth rates at a salinity of 33, and growth rates at a salinity of 100 were reduced by 50% compared to at a salinity of 33. Growth ceased at a salinity of 150. The chlorophyte species was more sensitive to high salinities than the two diatom species. Growth rate of the chlorophyte was greatly reduced already at a salinity of 50 and it could not grow at salinities above 100. At salinity 33 and constant TCO(2) concentration, all species exhibited maximal growth rate at pH 8.0 and/or 8.5. The two diatom species stopped growing at pH > 9.5, while the chlorophyte species still was able to grow at a rate which was 1/3 of its maximum growth rate at pH 10. Thus, Chlamydomonas sp. was able to grow at high pH levels in the succession experiment and therefore outcompeted the two diatom species. Complementary experiments indicated that growth was mainly limited by pH, while inorganic carbon limitation only played an important role at very high pH levels and low TCO(2) concentrations

Using a two-dimensional simulation analysis, we investigated the effects of sediment flushing on denitrification and the implications for two methods commonly used to measure denitrification in intact sediment cores: the N2:Ar-ratio method and isotope pairing technique (IPT). Our simulations of experimental chamber incubations showed that advective flushing of the sediment can significantly increase sediment denitrification driven by NO3– from the water column (up to a factor of 5), but that nitrification and coupled nitrification-denitrification is reduced under conditions of sediment flushing (up to a factor of 6). N2 fluxes across SWI may differ significantly from actual rates of denitrification for periods lasting from 1 up to more than 5 d after changes in parameters such as sediment flushing rate and water column NO3– concentrations. Simulations of the isotope pairing technique, showed that the rate of labeled N2 production, after the addition of 15NO3– may take up to ~24 h to reach steady state, depending on NO3– concentrations in the water column and sediment flushing rate. Measurements of denitrification in sand using IPT confirmed that short term incubations (11 h) underestimated the actual denitrification. Furthermore, model simulations were able to give a good estimate of measured N2 fluxes across SWI at different flushing rates under non–steady state conditions, confirming the ability of the model to realistically simulate experimental situations., Using a two-dimensional simulation analysis, we investigated the effects of sediment flushing on denitrification and the implications for two methods commonly used to measure denitrification in intact sediment cores: the N2:Ar-ratio method and isotope pairing technique (IPT). Our simulations of experimental chamber incubations showed that advective flushing of the sediment can significantly increase sediment denitrification driven by NO3– from the water column (up to a factor of 5), but that nitrification and coupled nitrification-denitrification is reduced under conditions of sediment flushing (up to a factor of 6). N2 fluxes across SWI may differ significantly from actual rates of denitrification for periods lasting from 1 up to more than 5 d after changes in parameters such as sediment flushing rate and water column NO3– concentrations. Simulations of the isotope pairing technique, showed that the rate of labeled N2 production, after the addition of 15NO3– may take up to ~24 h to reach steady state, depending on NO3– concentrations in the water column and sediment flushing rate. Measurements of denitrification in sand using IPT confirmed that short term incubations (11 h) underestimated the actual denitrification. Furthermore, model simulations were able to give a good estimate of measured N2 fluxes across SWI at different flushing rates under non–steady state conditions, confirming the ability of the model to realistically simulate experimental situations.