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River Avon catchment. (A) Overview of the River Avon catchment and tributaries relevant to this study (adapted from Jarvie et al. 2005a).
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We investigated the seasonal dynamics of in-stream metabolism at the reach scale (∼ 150 m) of headwaters across contrasting geological sub-catchments: clay, Greensand, and Chalk of the upper River Avon (UK). Benthic metabolic activity was quantified by aquatic eddy co-variance while water column activity was assessed by bottle incubations. Seasonal...
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... study was performed within the upper reaches of the 1650 km 2 catchment of the (Hampshire) River Avon in southern England (Fig. 1A). The catchment is mainly spring- fed which results in relatively stable flows throughout the year, with local hydrological differences being linked to par- ticular sub-catchment geologies ( Jarvie et al. 2005b). Geologi- cal data of the 1393.5 km 2 upper catchment 1 area showed that Chalk, Greensand, and clay represent the main catch- ...
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... 2014 win- ter as the result of an extreme flood (< 1 in 100 yr). Average u * values ranged from 0.2 cm s 21 to 2.5 cm s 21 and revealed a consistent cross-seasonal linear relationship to the average stream flow velocities. The bottom drag coefficient, C D , of the upper catchment amounted to 0.0033, on average, (R 2 5 0.89; Supporting Information Fig. 1) and the average sediment roughness parameter, z 0 , ranged from 1.0 6 0.6 mm at CL to 0.8 6 1.1 mm at CW, to 0.5 6 0.4 mm at GN. Daily PAR values, at the streambed, ranged from < 5 mol quanta m 22 d 21 in the winter to 28.6 mol quanta m 22 d 21 during the summer. Nitrate and phosphate concentrations in the water column at each site ...
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... in the water column, dark respiration, and NEM w rates were obtained at each site during each cam- paign except during the extreme 2014 winter flooding at the CL reach. Suspended sediment concentrations decreased across the reaches, from CL to GN to CW (Heppell and Bin- ley 2016a) leading to a clear gradient in water column tur- bidity ( Fig. 1). Within the respective reaches, however, O 2 rates for the surface, midstream and bottom bottle incuba- tions at each reach were not significantly different (e.g., Fig. 2). This indicated that depth attenuation in light was negli- gible at all the targeted reaches (Table 2). Therefore, the indi- vidual rates were averaged and presented ...
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... short-lived flashy flows lasting up to several days can tran- siently enhance turbidity and limit GPP (e.g., Leggieri et al. 2013). On annual time scales, stream turbidity is modulated by sub-catchment geologies, with reduced turbidity at the reaches fed by groundwater and higher turbidity at the reaches dominated by surface runoff (e.g., Fig. ...
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... vegetation was minimal at CL and scattered as isolated macrophytes patches at GN; benthic pri- mary production was mainly mediated by benthic microal- gae. In contrast, CW was characterized by the frequent occurrence of small (0.5 3 0.5 m) macrophyte patches, which were included and well-integrated in the footprint, and by sparse, larger patches (Fig. 1B). Those large patches exceeded h and were deliberately left outside the footprint area to avoid flow disturbances. Thus, part of the overall metabolic contribution from macrophytes might not have been fully integrated in the AEC approach as applied at CW. Contributions from lotic vegetation are usually poorly defined in assessments of ...
Citations
... Similar factors can also influence the riverbed physicochemistry at local scales. Our previous work in the Hampshire Avon catchment (UK) has shown BFI to be highly correlated with various physico-chemical variables including pore-water oxygen concentration, sediment particle size, dissolved organic C, and pH [8,17,18]. BFI therefore integrates up-stream catchment permeability and thus offers a potential path to upscale our understanding of the microbial communities driving fluvial biogeochemistry. ...
... BFI is not acting on microbial communities per se-BFI is a synthetic concept, and a microorganism cannot sense the BFI of its habitat afterall. However, BFI is strongly correlated with a number of smallscale variables that do act directly upon microbial communities such as redox profiles, pH, pore water oxygen saturation, and importantly geological sediment type [8,17,18,74]. Furthermore, BFI will not explain all of the variation in microbial community composition and functionality, as river biodiversity is likely structured by a hierarchy of variables acting at different spatial scales. ...
Sediment microbial communities drive the biogeochemical cycles that make rivers globally important sources and sinks of carbon (C) and nitrogen (N). The structure of these communities is strongly determined by the local physico-chemical environment. However, we currently lack an understanding of the factors that determine microbial community structures at the catchment scale. Here, we show that the contribution of groundwater to total river flow (quantified as base flow index; BFI) predicts the structure and diversity of the different microbial functional groups that cycle N and C across nine UK rivers, spanning a geological BFI gradient from 0.23 (clay sediment) to 0.95 (chalk gravel sediment). Furthermore, the GC-content (percentage of guanine-cytosine bases in a DNA sequence) and codon-usage bias of ammonia monooxygenase DNA sequences, and the hydrophobicity and net-charge of the corresponding amino acid sequences, were all strongly correlated with BFI, likely reflecting physiological adaptations to different riverbed sediment structure along the BFI gradient. Our results offer an opportunity to overcome the “paradox of scales” that has seen microbial ecologists focus on small- rather than large-scale environmental variables, enabling us to scale-up our understanding of microbial biogeochemistry to the catchment and beyond.
... Benthic O2 flux was calculated using custom-developed software written using MATLAB (MathWorks, v. 2018, Natick, MA, USA) and Python (v. 3.8, Python Software Foundation, Beaverton, OR, USA) following established protocols [36][37][38]. Before the derivation of O2 flux, the data were verified and corrected in three sequential steps. ...
... Benthic O 2 flux was calculated using custom-developed software written using MAT-LAB (MathWorks, v. 2018, Natick, MA, USA) and Python (v. 3.8, Python Software Foundation, Beaverton, OR, USA) following established protocols [36][37][38]. Before the derivation of O 2 flux, the data were verified and corrected in three sequential steps. ...
We measured oxygen (O2) fluxes in two major shallow subtidal benthic habitats (kelp bed (KB) and bare rock (BR) covered with crustose coralline algae) of Dokdo islet in the East Sea by applying noninvasive in-situ aquatic eddy covariance (AEC). The AEC device allows time series measurements (~24 h) of three-dimensional velocity (u, v, and w components) and high-resolution dissolved O2. This allows estimation of O2 exchange flux via benthic habitats. Local flow rates and irradiance levels were found to be major factors controlling O2 exchange flux in the rocky habitats. Gross primary production rates tended to be significantly higher in KB (163 mmol O2 m–2 d–1) than in BR (51 mmol O2 m–2 d–1). The net ecosystem metabolisms were assessed as opposite types, with 8 mmol O2 m–2 d–1 in KB (autotrophy) and –12 mmol O2 m–2 d–1 in BR (heterotrophy). Our results indicate that kelp beds are important for organic carbon cycling in rocky coastal waters and that AEC application to macroalgae habitats is a useful assessment approach.
... The aim of this study was to characterize how discharge and in-stream carbon metabolism together exert biophysical controls on the sources and final fates of CO 2 and CH 4 in temperate, low-gradient headwater streams (maximum catchment area of ∼60 km 2 ) in our case study catchment of the lowland Hampshire River Avon, UK. Within the catchment, we performed a seasonal study on six streams with distinct geologies (two each on the clay, Greensand and Chalk) and over a wide spectrum of hydrological characteristics, e.g., flashy to stable hydrograph, hydrological connectivity to the land and in-stream carbon metabolism (see Heppell et al., 2017;Rovelli et al., 2017Rovelli et al., , 2018. To quantify how much outgassing of CO 2 and CH 4 could be accounted for by either in-stream production or input from the catchment, we combined: (a) traditional measurements of benthic metabolism via isolated benthic chambers (Trimmer et al., 2009) with; (b) integrated estimates of whole stream metabolism using the state-of-the-art and non-invasive aquatic eddy covariance technique (Rovelli et al., 2017(Rovelli et al., , 2018; and (c) direct quantification of CO 2 and CH 4 outgassing from anchored floating chambers (Podgrajsek et al., 2014) (see Figure 1). ...
... Within the catchment, we performed a seasonal study on six streams with distinct geologies (two each on the clay, Greensand and Chalk) and over a wide spectrum of hydrological characteristics, e.g., flashy to stable hydrograph, hydrological connectivity to the land and in-stream carbon metabolism (see Heppell et al., 2017;Rovelli et al., 2017Rovelli et al., , 2018. To quantify how much outgassing of CO 2 and CH 4 could be accounted for by either in-stream production or input from the catchment, we combined: (a) traditional measurements of benthic metabolism via isolated benthic chambers (Trimmer et al., 2009) with; (b) integrated estimates of whole stream metabolism using the state-of-the-art and non-invasive aquatic eddy covariance technique (Rovelli et al., 2017(Rovelli et al., , 2018; and (c) direct quantification of CO 2 and CH 4 outgassing from anchored floating chambers (Podgrajsek et al., 2014) (see Figure 1). The seasonal study was complemented by measurements of CO 2 and CH 4 concentrations in riparian soils and streambeds and laboratory-based assessments of the potential for methane oxidation in the water column. ...
... Parallel studies at these reaches have also directly linked hydrological regime and baseflow index (BFI) to the dynamics of key stream sediment processes such as nitrogen gas (N 2 ) production (Lansdown et al., 2016), and . Integrated baseflow, as a proportion of total flow over a single day, has also been identified as a robust predictor of seasonal differences in stream metabolism dynamics across the different reaches (Rovelli et al., 2017). The water column of these lowland headwaters has been shown to contribute to about a quarter of their annual whole-stream respiration and primary production, with water column respiration in the turbid waters, for example River Sem on the clay, contributing, on average, 71.3% of the spring and summer whole-stream respiration (Rovelli et al., 2017(Rovelli et al., , 2018. ...
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.
... Aquatic eddy-covariance (AEC) devices deployed just above the benthos simultaneously record fluxes in O 2 via microelectrode, and vertical water velocity via acoustic Doppler velocimeter, to produce information of benthic metabolism or production at fine temporal scales without disturbing the benthic surface. Because the sensors do not interfere with natural benthic processes, AEC devices have potential application to studies involving GW-SW exchange and by extension periphyton processes (Rovelli et al. 2017). Berg et al. (2003) note that other devices aside from O 2 microelectrodes, such as sensors Table 1. ...
... measuring carbon dioxide and methane, could easily be substituted to understand other flux dynamics at the benthic interface (Berg et al. 2003;Berg and Huettel 2008;Rovelli et al. 2017). ...
Groundwater–surface water (GW–SW) interactions represent an important, but less visible, linkage in lake ecosystems. Periphyton is most abundant at the GW–SW interface and can rapidly assimilate nutrients from the water column. Despite the importance of periphyton in regulating whole‐lake metabolism, they are less well studied or monitored in comparison with planktonic taxa and pelagic systems. This is in stark contrast to studies of flowing waters and wetlands, where variability in GW–SW connectivity and periphyton productivity is more often incorporated into study designs. To bridge the gap between groundwater's influence on lake benthic communities, this synthesis aims to prime researchers with information necessary to incorporate groundwater and periphyton sampling into lake studies and equip investigators with tools that will facilitate cross‐disciplinary collaboration. Specifically, we (1) propose how to overcome barriers associated with studying littoral ecological‐hydrological dynamics; (2) summarize field, laboratory, and modeling techniques for assessing spatiotemporal periphyton patterns and benthic hydrological fluxes; and (3) identify paths for hydrological techniques to be incorporated into ecological studies, deepening our understanding of whole‐lake ecosystem function. We argue that coupling hydrological and periphyton measurements can yield dualistic insights into lake ecosystem functioning: how benthic periphyton modulate constituents within groundwater, and conversely, the extent to which constituents in groundwater modulate the productivity of periphyton assemblages. We assert that priming ecologists and hydrologists alike with a shared understanding of how each discipline studies the nearshore zone presents a tangible path forward for both integrating these disciplines and further contextualizing lake processes within the limnological landscape.
... Eddy Covariance measurements thus allow for taking into account the bioturbation activities and the respiration of large mobile benthic fauna and overall to integrate the strong spatial heterogeneity of complex coastal benthic systems. To date, this new alternative technique was used to assess benthic metabolisms of various aquatic soft-bottom habitats, i.e. from lakes McGinnis et al., 2008;Lorrai et al., 2010), sandy-bottom river and sea sediments (Berg et al., 2003;Chipman et al., 2012;Berg et al., 2013;Koopmans and Berg, 2015;Rovelli et al., 2017;Attard et al., 2019), vegetated and muddy lagoon sediments (Berg et al., 2003;Hume et al., 2011;Rheuban et al., 2014), vegetated and shallow sandy sea sediments (Attard et al., 2019), sandy intertidal bays (Kuwae et al., 2006;Berg et al., 2013), continental shelf (Reimers et al., 2012) to deeper oceanic realms (Berg et al., 2009;Donis et al., 2016;Attard et al., 2019). The use of the EC technique is particularly suitable over hardbottom substrates such as coral reefs Rovelli et al., 2015), Maerl beds , macroalgal and mussel reefs (Attard et al., 2019) and rocky embayments (Glud et al., 2010). ...
To the best of our knowledge, the understanding of benthic metabolism of coastal sedimentary areas is still limited due to the complexity of determining their true in situ dynamics over large spatial and temporal scales. Multidisciplinary methodological approaches are then necessary to increase our comprehension of factors controlling benthic processes and fluxes. An aquatic Eddy Covariance (EC) system and Benthic Chambers (BC) were simultaneously deployed during the winter of 2013 in the Bay of Brest within a Maerl bed and a bare mudflat to quantify and compare O2 exchange at the sediment-water interface. Environmental abiotic parameters (i.e., light, temperature, salinity, current velocity and water depth) were additionally monitored to better understand the mechanisms driving benthic O2 exchange. At both sites, EC measurements showed short-term variations (i.e. 15 min) in benthic O2 fluxes according to environmental conditions. At the Maerl station, EC fluxes ranged from -21.0 mmol m⁻² d⁻¹ to 71.3 mmol m⁻² d⁻¹ and averaged 22.0 ± 32.7 mmol m⁻² d⁻¹ (mean ± SD), whilst at the bare muddy station, EC fluxes ranged from -43.1 mmol m⁻² d⁻¹ to 12.1 mmol m⁻² d⁻¹ and averaged -15.9 ± 14.0 mmol m⁻² d⁻¹ (mean ± SD) during the total deployment. Eddy Covariance and Benthic Chambers measurements showed similar patterns of temporal O2 flux changes at both sites. However, at the Maerl station, BC may have underestimated community respiration. This may be due to the relative large size of the EC footprint (compared to BC), which takes into account the mesoscale spatial heterogeneity (e.g. may have included contributions from bare sediment patches). Also, we hypothesize that the influence of bioturbation induced by large-sized mobile benthic fauna on sediment oxygen consumption was not fully captured by BC compared to EC. Overall, the results of the present study highlight the importance of taking into account specific methodology limitations with respect to sediment spatial macro-heterogeneity and short-term variations of environmental parameters to accurately assess benthic O2 exchange in the various benthic ecosystems of the coastal zone.
... Sources of variability within EC O 2 fluxes can be broadly grouped into two categories, namely (1) sources that bias the measured EC flux away from the "true" benthic flux (i.e. when EC O 2 flux = benthic O 2 flux) and (2) "true" temporal variability in the benthic O 2 exchange rate (i.e. when EC O 2 flux = benthic O 2 flux) ( Table 1). Despite there being numerous sources of variability, high-quality EC fluxes often show a tight coupling to sunlight (photosynthetic active radiation, PAR) availability on the hourly timescale, indicating a dominant primary production signal in many aquatic systems Chipman et al., 2016;Attard et al., 2014Attard et al., , 2015Rheuban et al., 2014;Long et al., 2013Long et al., , 2015Koopmans et al., 2020;Rovelli et al., 2017). Under ideal conditions, the measured EC fluxes represent the balance between habitat GPP and R. Hourly and daily GPP may therefore be computed from the EC fluxes as the sum of dark and light fluxes, that is GPP= FLUX day + |FLUX night |. ...
... It is well known that this approach provides conservative estimates of GPP, since R typically is higher during daytime in the presence of photosynthesis (Fenchel and Glud, 2000;Hotchkiss and Hall, 2014). Indeed, several EC studies have documented lower O 2 effluxes in the evening than in the morning under similar light intensities (a so-called "hysteresis") and high R rates at the onset of darkness (Rovelli et al., 2017;Rheuban et al., 2014;Koopmans et al., 2020). It is generally understood that R is stimulated by GPP; it increases progressively throughout the day as labile photosynthates accumulate (Epping and Jørgensen, 1996;de Winder et al., 1999), and the magnitude of the hysteresis is related to the lag in the ecosystem's response (in terms of O 2 production through GPP) to changing light levels (Adams et al., 2016). ...
... Reflected PAR was typically 8 %-10 % of incident PAR, indicating that ∼ 90 % of incident PAR was absorbed by the benthos. mented a much larger hysteresis than what we observe at the mussel bed (Rheuban et al., 2014;Rovelli et al., 2017). ...
Light-use efficiency defines the ability of primary producers to convert sunlight energy to primary production and is computed as the ratio between the gross primary production and the intercepted photosynthetic active radiation. While this measure has been applied broadly within terrestrial ecology to investigate habitat resource-use efficiency, it remains underused within the aquatic realm. This report provides a conceptual framework to compute hourly and daily light-use efficiency using underwater O2 eddy covariance, a recent technological development that produces habitat-scale rates of primary production under unaltered in situ conditions. The analysis, tested on two benthic flux datasets, documents that hourly light-use efficiency may approach the theoretical limit of 0.125 O2 per photon under low-light conditions, but it decreases rapidly towards the middle of the day and is typically 10-fold lower on a 24 h basis. Overall, light-use efficiency provides a useful measure of habitat functioning and facilitates site comparison in time and space.
... Direct measurements of benthic respiration flux are invaluable but suffer from the shortcoming of only providing point measurements of the riverbed where spatial variability is likely to be high. They are however routinely undertaken, employing a spectrum of established techniques to quantify oxygen removal such as in-situ chambers (Jahnke and Christaiansen, 1989;Jones et al., 1995) and aquatic eddy correlation (Berg et al., 2003;Rovelli et al., 2017). Alongside these, indirect estimates gained from metabolic data analysis and mathematical modelling of river channel environments (as described above) are commonplace given the increasing proliferation of river water quality data at basin-scale. ...
The supply of readily-degradable organic matter to river systems can cause stress to dissolved oxygen (DO) in slow-flowing waterbodies. To explore this threat, a multi-disciplinary study of the River Thames (UK) was undertaken over a six-year period (2009-14). Using a combination of observations at various time resolutions (monthly to hourly), physics-based river network water quality modelling (QUESTOR) and an analytical tool to estimate metabolic regime (Delta method), a decrease in 10th percentile DO concentration (10-DO, indicative of summer low levels) was identified during the study period. The assessment tools suggested this decrease in 10-DO was due to an increase in benthic heterotrophic respiration. Hydrological and dissolved organic carbon (DOC) data showed that the shift in 10-DO could be attributed to summer flooding in 2012 and consequent connection of pathways flushing degradable organic matter into the river. Comparing 2009-10 and 2013-14 periods, 10-DO decreased by 7.0% at the basin outlet (Windsor) whilst median DOC concentrations in a survey of upstream waterbodies increased by 5.5-48.1%. In this context, an anomalous opposing trend in 10-DO at one site on the river was also identified and discussed. Currently, a lack of process understanding of spatio-temporal variability in benthic respiration rates is hampering model predictions of river DO. The results presented here show how climatic-driven variation and urbanisation induce persistent medium-term changes in the vulnerability of water quality to multiple stressors across complex catchment systems.
... Process rates in these short residence time systems may be under-estimated by studies of larger downstream systems, because the reactivity of DOM declines with increasing water residence time (Catalán et al. 2016;Evans et al. 2017). Although biological activities in the benthic zone are usually considered a major driver of ecosystem processes in headwaters (Gardner and Doyle 2018), water column processes can contribute to a significant part of annual respiration and primary production, up to 25% according to Rovelli et al. (2017). ...
Dissolved organic matter (DOM) in freshwaters is recognised as a significant and active component of the global carbon budget. DOM exported from terrestrial ecosystems may be compositionally and functionally altered by chemical and biological reactions as it is transported downstream. The processes affecting DOM in headwater streams remain uncertain but are potentially highly variable depending on DOM composition and nutrient availability as a function of soils, land-use, and human pressures. To investigate variability of DOM reactivity we took water samples from two contrasting headwater catchments, considered functional ‘end-members’ for DOM export: one rich in aromatic DOM and low in inorganic nutrients (peatland), and another (nearby) catchment characterized by less aromatic DOM and high nutrient loadings (agricultural grassland). Under controlled laboratory conditions, we evaluated the effects of light, presence/absence of aquatic biota and nutrient enrichment on short-term changes in DOM quantity and quality in these samples. For the peat stream, exposure to sunlight (with UV) resulted in net abiotic DOM removal, whereas in the agricultural stream it led to net biological DOM production. Nutrient addition accelerated DOM production in both streams. We conclude that in-stream changes in DOM quantity and quality represent the net effect of multiple consumption and production processes whose relative importance is strongly influenced by source-dependent DOM composition and environmental factors such as inorganic nutrient content and sunlight exposure. Our findings suggest that headwater streams may be more active processors of carbon and nutrients than presumed hitherto.
... The collected ADV datasets were processed following established protocols (e.g., Attard et al. 2014;Rovelli et al. 2017). In brief, time series were averaged from 64 to 8 Hz to reduce instrument noise levels and reduce data size for more efficient data analyses. ...
Rocky benthic communities are common in Antarctic coastal habitats; yet little is known about their carbon turnover rates. Here, we performed a broad survey of shallow ( < 65 m depth) rocky ice-scoured habitats of South Bay (Doumer Island, Western Antarctic Peninsula), combining (i) biodiversity assessments from benthic imaging, and (ii) in situ benthic dissolved oxygen (O2) exchange rates quantified by the aquatic eddy covariance technique. The 18 study sites revealed a gradual transition from macroalgae and coralline-dominated communities at ice-impacted depths (15–25 m; zone I) to large suspension feeders (e.g., sponges, bivalves) at depth zone II (25–40 m) and extensive suspension feeders at the deepest study location (zone III; 40–65 m). Gross primary production (GPP) in zone I was up to 70 mmol O2 m⁻² d⁻¹ and dark ecosystem respiration (ER) ranged from 15 to 90 mmol m⁻² d⁻¹. Zone II exhibited reduced GPP (average 1.1 mmol m⁻² d⁻¹) and ER rates from 6 to 36 mmol m⁻² d⁻¹, whereas aphotic zone III exhibited ER between 1 and 6 mmol m⁻² d⁻¹. Benthic ER exceeded GPP at all study sites, with daily net ecosystem metabolism (NEM) ranging from − 22 mmol m⁻² d⁻¹ at the shallow sites to − 4 mmol m⁻² d⁻¹ at 60 m. Similar NEM dynamics have been observed for hard-substrate Arctic habitats at comparable depths. Despite relatively high GPP during summer, coastal rocky habitats appear net heterotrophic. This is likely due to active drawdown of organic material by suspension-feeding communities that are key for biogeochemical and ecological functioning of high-latitude coastal ecosystems.
... Mean removal requires first calculating an appropriate timescale that separates the higher-frequency fluxtransporting turbulent eddies from larger-scale advective motions (McGinnis et al. 2008, Lorrai et al. 2010. Common approaches in clude progressively increasing the averaging window size until the covariance of w' and C' (i.e. the turbulent flux) and/ or shear velocity converges (Attard et al. 2014, Rovelli et al. 2017), or selecting a timescale from inspection of the power spectra of vertical velocity fluctuations or co-spectra of w' and C' (Lorke et al. 2013). The fluctuations w' and C' are then calculated using either simple (block) averaging or linear detrending to remove means within each window, or by subtracting a running average (Holt appels et al. 2013. ...
... Berg et al. 2003), transport through benthic and pelagic oxyclines (Kreling et al. 2014), and for studying ecosystem metabolism (e.g. Attard et al. 2015, Koopmans & Berg 2015, Long et al. 2015, Rovelli et al. 2017. Benthic oxygen fluxes obtained from EC can show good agreement to other techniques such as sediment micro-profiling or benthic chambers, particularly over muddy sediments where little pore water flushing is expected (Berg et al. 2003, Attard et al. 2015, Donis et al. 2016. ...
... This can result in significant changes in storage of oxygen in the water column between the bed and the sensor. Corrections for this storage have been used elsewhere (Rheuban et al. 2014, Rovelli et al. 2017. The correction for storage assumes that rates of change in oxygen concentration are due solely to differences between the vertical flux of oxygen from the sediment surface and past the sensor (and hence storage in the water column between sensor and bed) and requires that oxygen concentrations are horizontally homogeneous. ...
Benthic oxygen fluxes were measured in situ using the eddy covariance method at 2 Chinook salmon farms located in the New Zealand Marlborough Sounds in 29-35 m depth and compared to sediment nutrient (C, N and P) and sulphide concentrations. Observations from 3 sites at a high-flow location (near-bed RMS velocities of 0.11 to 0.17 m s-1) showed oxygen fluxes increasing with sediment enrichment. Mean ± SE oxygen fluxes of -102 ± 4 mmol O2 m-2 d-1 were observed immediately adjacent the farm. Higher fluxes were observed at 120 m from the farm (-53 mmol O2 m-2 d-1) than at 50 m (-48 mmol O2 m-2 d-1), consistent with higher sediment nutrient concentrations at the more distant site, and reflecting the effect of currents on deposition patterns. Ratios of C, N and P in sediments indicated a reduction of N mineralisation rates as sediment enrichment increased. The low-flow site (near-bed RMS velocities of 0.033 m s-1) had similar oxygen fluxes (-108 ± 9 mmol O2 m-2 d-1) to the high-flow site closest to the farm, but sediments were more highly enriched with high sulphide concentrations. Oxygen fluxes at the low-flow site were close to the estimated maximum potential flux that could be achieved under the ambient hydrodynamic conditions. Less than 0.2% of surface PAR reached the sediments, and no evidence of benthic primary production was observed at any of the sites. By incorporating ambient hydrodynamic conditions, eddy covariance has the potential to obtain true in situ benthic oxygen fluxes, giving greater insight into aquaculture-environmental interactions.
