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Stream ecosystems are supported by both green (i.e. based on grazing) and brown (i.e. detritus) food webs, whereas methane-derived carbon is not considered generally to be important; here, we add circumstantial evidence for this potential third way. Grazing cased-caddis (Trichoptera) larvae in the family Glossosomatidae can be very abundant in springs and headwaters and frequently have much lower stable carbon isotope ratios (i.e. they are depleted in the heavier C-13 stable isotope) than the biofilm (epilithon) on the upper surfaces of the stones on which they live, and which is their presumed diet. Evidence for similar isotopic depletion in other lotic invertebrates is currently limited, however; even for glossosomatids it has been observed so far only in some streams draining the southern English cretaceous chalk and in a few headwaters in northern California. If this phenomenon proves to be more widespread, among streams or taxa, it could imply a more general underpinning of stream food webs by isotopically light carbon derived from methane and accessed via consumers feeding on methanotrophic bacteria. Here, we sampled 58 stream sites to examine whether caddis larvae are also C-13-depleted in streams draining other geologies. We focused mainly on carboniferous limestone and sandstone, as well as on further chalk streams representative of most of the British chalk aquifer: together, these new sites covered an area of almost 90,000 km(2), around three times greater than that surveyed previously. At all 58 sites methane gas was supersaturated relative to the atmospheric equilibrium, and at 49 of them larvae were conspicuously C-13-depleted (from -17.5 parts per thousand to -3.6 parts per thousand) relative to the bulk epilithon (components of which we know can oxidise methane). Although still most pronounced on chalk, this phenomenon was geographically and geologically much more widespread than shown previously and suggests methane-derived carbon could indeed play a prominent role in stream food webs (i.e. the third way).

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 dynamics across reaches were specific for the three types of geologies. During the spring, all reaches were net autotrophic, with rates of up to 290 mmol C m-2 d-1 in the clay reach. During the remaining seasons, the clay and Greensand reaches were net heterotrophic, with peak oxygen consumption of 206 mmol m-2 d-1 during the autumn, while the Chalk reach was net heterotrophic only in winter. Overall, the water column alone still contributed to ∼ 25% of the annual respiration and primary production in all reaches. Net ecosystem metabolism (NEM) across seasons and reaches followed a general linear relationship with increasing stream light availability. Sub-catchment specific NEM proved to be linearly related to the local hydrological connectivity, quantified as the ratio between base flow and stream discharge, and expressed on a timescale of 9 d on average. This timescale apparently represents the average period of hydrological imprint for carbon turnover within the reaches. Combining a general light response and sub-catchment specific base flow ratio provided a robust functional relationship for predicting NEM at the reach scale. The novel approach proposed in this study can help facilitate spatial and temporal upscaling of riverine metabolism that may be applicable to a broader spectrum of catchments.

Anthropogenic nitrogen fixation and subsequent use of this nitrogen as fertilizer has greatly disturbed the global nitrogen cycle. Rivers are recognized hotspots of nitrogen removal in the landscape as interaction between surface water and sediments creates heterogeneous redox environments conducive for nitrogen transformations. Our understanding of riverbed nitrogen dynamics to date comes mainly from shallow sediments or hyporheic exchange flow pathways with comparatively little attention paid to groundwater-fed, gaining reaches. We have used 15N techniques to quantify in situ rates of nitrate removal to 1m depth within a groundwater-fed riverbed where subsurface hydrology ranged from strong upwelling to predominantly horizontal water fluxes. We combine these rates with detailed hydrologic measurements to investigate the interplay between biogeochemical activity and water transport in controlling nitrogen attenuation along upwelling flow pathways. Nitrate attenuation occurred via denitrification rather than dissimilatory nitrate reduction to ammonium or anammox (range = 12 to >17000 nmol 15N L-1 h-1). Overall, nitrate removal within the upwelling groundwater was controlled by water flux rather than reaction rate (i.e. Damkohler numbers 80% of nitrate removal occurs within sediments not exposed to hyporheic exchange flows under baseflow conditions, illustrating the importance of deep sediments as nitrate sinks in upwelling systems.

A fraction of organic carbon produced in the oceans by phytoplankton sinks storing 5‐15 gigatonnes of carbon annually in the ocean interior. The accepted paradigm is that rapid aggregation of phytoplankton cells occurs forming large, fresh particles which sink quickly; this concept is incorporated into ecosystem models used to predict the future climate. Here we demonstrate a slower, less efficient export pathway in the Eastern Tropical North Pacific. Lipid biomarkers suggest the large, fast‐sinking particles found beneath the mixed layer are compositionally distinct from those found in the mixed layer and thus not directly and efficiently formed from phytoplankton cells. We postulate they are formed from the in situ aggregation of smaller, slow‐sinking particles over time in the mixed layer itself. This export pathway is likely widespread where smaller phytoplankton species dominate. Its lack of representation in biogeochemical models suggests they may be currently over‐estimating the ability of the oceans to store carbon if large, fast‐sinking, labile particles dominate simulated particle export. Plain Language Summary The oceans are one of the largest sinks of atmospheric carbon dioxide on our planet. One method by which this occurs is through the production of organic material (phytoplankton ‐ plant‐like cells) in the surface ocean, which capture atmospheric carbon dioxide during photosynthesis. Eventually, the phytoplankton die and sink out of the surface ocean, transporting huge amounts of carbon to the deep ocean where it is stored for centuries or even millennia. Our current understanding is that generally, most organic material sinks quickly as large, fast‐sinking (100s of metres per day) particles (clumps of dead phytoplankton cells). However in our study in the Equatorial Pacific Ocean we were able to show that a different and much slower process occurs where phytoplankton first aggregate to smaller, slower sinking detrital particles and eventually form, very degraded larger particles that sink to the deep. This has consequences for estimating ocean carbon storage as smaller particles are respired much quicker than larger particles. Thus where they are an important part of this carbon sink, such as in the Equatorial Pacific, the proportion phytoplankton‐captured atmospheric carbon dioxide being stored in the deep ocean is likely reduced.

SUMMARY 1. Many rivers are oversaturated in methane (CH4) and carbon dioxide (CO2) relative to the atmosphere, but we know little about the biological controls on the balance between these two important greenhouse gases and how they might respond to warming. 2. We characterise the potential response to temperature in the biological production of CO2 and CH4 and the subsequent microbial oxidation of that CH4, that is the sink and source components of the CH4 cycle, in contrasting river bed sediments: fine sediments, which are largely anoxic, and oxic, coarse gravels. 3. In the fine sediments, anaerobic production of both CH4 and CO2 increased with temperature, with apparent activation energies for each being 0.51 eV and 0.24 eV, respectively. The difference between the two resulted in a 4% increase in the ratio of CH4:CO2 production for a 1 °C increase in temperature. 4. In the coarse gravels, microbial CH4 oxidation showed no response to temperature at CH4 concentrations characteristic of these gravel beds (30–200 nmol CH4 L 1 ), due to strong substrate limitation. In contrast, at higher (although still rate limiting) CH4 concentrations, more characteristic of the fine sediment patches (2–4 lmol CH4 L 1 ), CH4 oxidation exhibited an increasingly strong response to temperature, eventually exceeding that for CH4 production. 5. In the fine sediment, the surface layers had a CH4 oxidation capacity over 100 times greater than the gravels and the kinetic response to differing pore water CH4 concentrations meant CH4 was oxidised some 2000 times faster in the fine sediment patches compared with the coarse gravels. 6. The calculated kinetic and temperature responses showed that with warming, methanogenesis is unlikely to outstrip methanotrophy and the ratio of CO2 to CH4 emitted could be conserved. Consequently, any changes in the efflux ratio of CH4 to CO2 are unlikely to be due to the incapacity of methanotrophy to respond to CH4 production, but rather to a physical bypassing of the methanotrophic community (e.g. through ebullition or transport via plant stems) or contraction of the oxic layer.

River restoration and management practice promotes the (re)introduction of large woody debris (LWD) to support ecosystem services in lowland streams, such as the buffering of thermal extremes or enhanced nutrient attenuation. However, influences of LWD on spatial patterns and temporal dynamics of groundwater–surface water exchange fluxes, sediment transport and deposition, biogeochemical cycling, thermal patterns, and ecohydrological process dynamics are not yet fully understood. This study reviews research on the implications of interacting hydrodynamic and hydrostatic forcings on different types of LWD structures and their consequences for streambed residence time distributions, thermal conditions, and biogeochemical cycling. It analyzes the implications of LWD on structural heterogeneity in physical and chemical properties of lowland river streambed and provides an outlook of how enhanced nutrient loading of agricultural lowland rivers can be ameliorated by LWD-induced increase of biogeochemical turnover. Based on the analysis of the potential implications of different LWD structures, this study highlights how imminent research gaps can be overcome by integrating novel experimental and modeling technologies across traditional subject boundaries in order to provide robust scientific evidence of the efficiency of LWD in river restoration and management. Conflict of interest: The authors have declared no conflicts of interest for this article.

The ocean’s biological carbon pump plays a central role in regulating atmospheric CO2 levels. In particular, the depth at which sinking organic carbon is broken down and respired in the mesopelagic zone is critical, with deeper remineralisation resulting in greater carbon storage. Until recently, however, a balanced budget of the supply and consumption of organic carbon in the mesopelagic had not been constructed in any region of the ocean, and the processes controlling organic carbon turnover are still poorly understood. Large-scale data syntheses suggest that a wide range of factors can influence remineralisation depth including upper-ocean ecological interactions, and interior dissolved oxygen concentration and temperature. However these analyses do not provide a mechanistic understanding of remineralisation, which increases the challenge of appropriately modelling the mesopelagic carbon dynamics. In light of this, the UK Natural Environment Research Council has funded a programme with this mechanistic understanding as its aim, drawing targeted fieldwork right through to implementation of a new parameterisation for mesopelagic remineralisation within an IPCC class global biogeochemical model. The Controls over Ocean Mesopelagic Interior Carbon Storage (COMICS) programme will deliver new insights into the processes of carbon cycling in the mesopelagic zone and how these influence ocean carbon storage. Here we outline the programme’s rationale, its goals, planned fieldwork and modelling activities, with the aim of stimulating international collaboration.

Laboratory incubations with river-bed sediment collected from riffles and pools were used to quantify potential pathways of dissimilatory nitrate reduction in the hyporheic zone of a groundwater-fed river. Sediments collected from between 5-cm and 86-cm depth in the bed of the River Leith, Cumbria, United Kingdom, were incubated with a suite of 15N-labeled substrates (15NO { , 15NH z , and 14NO { ) to quantify nitrate reduction via denitrification, dissimilatory nitrate reduction to ammonium (DNRA), and anaerobic ammonium oxidation (anammox). Denitrification was the dominant pathway of dissimilatory nitrate reduction in the hyporheic sediments, although recovery of 15N from the ammonium pool indicated that DNRA was also active. The potential for anammox was confirmed by the production of 29N2 during the 15NH z and 14NO { incubation, but it was much smaller than denitrification. Potential rates of denitrification were highest in shallow sediments and decayed exponentially with depth thereafter. There were clear differences in denitrification activity between riffle and pool sediments. After the production of 15N-N2 had stabilized, we added a spike of bacteriological peptone to determine the effect of complex organic substrates on denitrification potential. The potential rate of denitrification increased uniformly at all sediment depths but the total amount of denitrification fueled by the organic substrates decreased markedly with depth, from 90% in the shallow sediments to 30% in the deepest sediments. In addition, a considerable fraction of the 15 NO { could not be accounted for, which suggested that up to 87% of it had been assimilated in the deepest sediments. The hyporheic zone is a key area of biogeochemical activity between the surface water and groundwater of streams and rivers (Boulton et al. 2010). Here exchanges of dissolved and particulate organic matter, oxygen, and nutrients drive the cycling of the key biotic macronutrients (C, H, N, P, S), in turn, sustaining the productivity of the sediment strata in this ‘dynamic ecotone’ at or beneath the river bed (Gilbert et al. 1990). The contribution that biogeochemical activity within the hyporheic zone makes to the river as a whole is, in turn, governed by the balance between surface and subsurface flow and the intensity of subsurface processes (Findlay 1995). One particular biogeochemical process that has received a great deal of attention is denitrification: the biological

We measured denitrification, anaerobic ammonium oxidation (anammox), oxygen uptake, nutrient exchange, and pore-water profiles of oxygen in intact sediments at three sites in the southern North Sea, which we experimentally exposed to different oxygen saturations (ambient and , 33% of air-saturation for oxygen [i.e., our hypoxic treatment]) over 14 months. Denitrification ranged from 1 mmol N m22 h21 to 21 mmol N m22 h21, anammox 0.2 mmol N m22 h21 to 5.7 mmol N m22 h21, and oxygen uptake 47 mmol O2 m22 h21 to 631 mmol O2 m22 h21. The seasonal patterns under ambient oxygen were correlated with those in the hypoxic treatment; though, on the whole, the magnitude of flux was different. On average, under hypoxia, both the penetration and consumption of oxygen decreased by , 50%, denitrification increased by 32%, and anammox remained constant. Anammox accounted for between 10% and 20% of the total N2 production, which agrees with expectations for waters of these depths (30–80 m). Under ambient oxygen the sediments were strong sources of nitrate to the overlying water, 12 mmol NO { m22 h21 on average, but under hypoxia total N mineralization decreased by 46% and nitrate exchanged ceased. Short-term hypoxia alters the balance between available N returned to the overlying water, primarily as NO { , and that removed from the ecosystem as N2 gas. The coastal margins and continental shelves comprise , 9% of the total area of ocean sediments, but are responsible

Due to a combination of local methanogenesis and high background concentrations in the groundwater, water in the River Lambourn is 51 times supersaturated with methane (162 nmol CH4 L−1). Pore-water concentrations of methane in the gravels of the riverbed were much lower throughout the year (71 nmol CH4 L−1), suggesting significant methane oxidation. To investigate the potential for methane oxidation as a novel chemosynthetic source of carbon to the food web, we made simultaneous measurements, in laboratory chambers, of primary production, respiration, and methane oxidation associated with the gravels. Biomass-specific net primary production was up to 2.7 µmol O2 mg−1 chlorophyll (Chl) h−1 and was similarly high for respiration (2.7 µmmol O2 mg−1 Chl h−1). We also found active methane (CH4) oxidation with the rate increasing in proportion to concentration. At the maximum rate of 0.18 µmol CH4 mg−1 Chl h−1 and a growth efficiency of 0.8, net carbon fixation via methane oxidation was equivalent to 6% of the carbon fixed via net photosynthetic primary production. However, production via methane oxidation could be proportionately much greater under the shade of the profuse instream or riparian vegetation, deep in the gravels, and especially during winter, when light is limiting (< 25 µmol quanta m−2 s−1).

We measured the δ13C values of dominant primary consumers and their potential food sources in a groundwater-fed lowland river. The δ13C of most consumers, such as Gammarus and Simulium, reflected that of the dominant forms of photosynthetic production, whereas the cased larvae of two caddis flies (Agapetus and Silo) were consistently 13C depleted (mean δ13C: -41.2% and -40.4%, respectively) throughout the year. The river water was supersaturated (approximately 50 times atmospheric) with methane, reflecting both supersaturation in the groundwater and local production in fine sediments. We measured appreciable rates of methane oxidation, relative to water only controls, in the biofilms on gravel, on the caddis fly cases, and on the bottom of larger rocks. In addition, there was a marked difference in the ratio of methane-oxidizing potential to chlorophyll across those substrata. This ratio was below detection in the biofilm (i.e., no methane oxidation) on the tops of rocks, greater on the bottom of rocks, and maximal for the gravels and the caddis cases. If the caddis larvae acquire most of their carbon by grazing the tops of such rocks (where they are normally found), then they must acquire their depleted δ13C values by occasionally grazing biofilm where the ratio of methane oxidation to chlorophyll was much greater, and the most likely candidate is from their own or conspecific cases. Grazing methane-oxidizing bacteria could provide the caddis larvae with up to 30% of their carbon, which could represent a true subsidy from an ancient groundwater source.

The results of a modelling study to investigate the mechanisms controlling macroalgal growth within the Medway estuary, UK, are presented. Intertidal zone bathymetry, tidal dynamics and turbidity control the time available for nutrient uptake and photosynthesis, and were used as a basis for predicting areas where macroalgae will grow. Tidal bed stress was also considered as a controlling factor for the presence of the less robust green macroalgae species. Two approaches to predicting macroalgal distributions were applied: (1) a simple ‘suitability index’ method based on tidal flooding and drying, taking account of the conflict between time available for nutrient uptake and for photosynthesis; and (2) a biological macroalgal growth model that includes a detailed treatment of nutrient uptake and plant growth. The former approach assigns a value between zero and one for the suitability of a location for macroalgal occurrence, while the latter predicts the full macroalgal growth dynamics over an annual cycle. Tidal bed stress was included in both approaches as an independent modifier of macroalgal occurrence/growth. Results were compared with aerial survey maps of observed vegetation cover and time series of measured biomass density. Both approaches gave good predictions of non-species-specific vegetation cover in the intertidal zone of the Medway. Tidal bed stress was found to be a strong predictor of the specific occurrence of Enteromorpha spp. and Ulva spp., with these species favouring areas of low tidal energy. It was concluded that light and a lack of suitable regions with low tidal bed stress, rather than nutrients, were the main factors limiting excessive growth of Enteromorpha spp. and Ulva spp. in the estuary. Although this study was focussed on the Medway, the results are likely to be applicable to a broad range of relatively turbid, meso- and macro-tidal estuaries.

We assayed sediment for the anammox reaction at 40 sites from 9 estuaries during the summer of 2004. The anammox reaction was detected at all sites with its potential contribution to the production of N 2 (ra, %) ranging from 3 % (> 2 nmol N 2 ml -1 wet sediment for anammox after 24 h), below this, though still detectable, anammox was underestimated with 15 NH 4 + . The decrease in the estimate for anammox with 15 NH 4 + relative to 15 NO 3 - was partly explained by a decrease in the recovery of N 2 gas, probably as a result of significant dissimilatory nitrate reduction to ammonium (DNRA) in some of the slurries. The potential interference from DNRA in the anammox assay, however, would be low, with the probability of anamox making 30 N 2 (A 30 N 2 ) being about 1.4 %. Our findings provide firm evidence that the anammox reaction is widespread in estuarine sediments.

We measured the production of N2 gas from anammox and denitrification simultaneously in intact sediment cores at six sites along a transect of the continental shelf (50 m) and deeper slope (2000 m) in the North Atlantic. Maximum rates of total N2 production were measured on the shelf and were largely due to denitrification, with anammox contributing, on average, 33% of this production. On the continental slope, the production of N2 gas decreased but the proportion due to anammox reached a maximum of 65%. This change in both amount and dominant pathway of N2 production could be explained largely by the concentration of organic carbon at each site. With increasing carbon the total production of N2 increased rapidly while the response of anammox was not significant. On the continental slope, total N2 production fell below 2 mmol N m22 h21 and anammox was strongly related (r 5 0.95) to denitrification but the relative magnitude of anammox to denitrification (1.65 : 1) suggested that anammox could not be fuelled by NO { from denitrification alone. On the shelf, however, where total N2 production was predominantly greater than 2 mmol N m22 h21, no relationship between anammox and denitrification was found and anammox remained constant at 1.4 mmol N m22 h21. Despite the constancy and greater availability of NO { and lower temperatures on the continental slope, the significance of anammox to the

Summary 1. The emission of biogenic gases, particularly methane, is usually associated with wetlands rather than clean streams. Here, we investigated methane production from a southern English chalk stream, where increased sedimentation, compounded by extensive macrophyte growth, may have altered ecosystem function. 2. Cover of the channel by the dominant macrophyte, Ranunculus penicillatus, peaked in August, when plant beds were associated with low water velocity and the accumulation of sediment (90%) of the methane flux is transported to the atmosphere through the Ranunculus stems. 5. Although the total flux of methane from U.K. chalk streams is probably relatively modest (estimated at 3.2 × 10−6 Tg CH4 year−1), this phenomenon changes our perception of the health of these ecosystems and indicates another deleterious side effect of agriculture.

1. Pesticides can have strong deleterious impacts in fresh waters, but understanding how these effects cascade through natural ecosystems, from microbes to apex predators, is limited because research that spans multiple levels of biological organisation is rare. 2. We report how an accidental insecticide spill altered the structure and functioning of a river across levels ranging from genes to ecosystems. We quantified the impacts on assemblages of microbes, diatoms, macroinvertebrates and fish and measured leaf-litter decomposition rates and microbial functional potential at upstream control and downstream impacted sites 2 months after the spill. 3. Both direct and indirect impacts were evident across multiple levels of organisation and taxa, from the base of the food web to higher trophic levels. At the molecular level, differences in functional gene abundance within the impacted sites reflected a combination of direct and indirect effects of the pesticide, via elevated abundances of microbial populations capable of using chlorpyrifos as a resource (i.e. direct effect) and oxidising ammonia released by decaying macroinvertebrate carcasses (i.e. indirect effect). 4. At the base of the food chains, diatom taxa found only in the impacted sites were an order-of- magnitude larger in cell size than the largest comparable taxa in control communities, following the near extirpation of their consumers. Population biomass of the key detritivore Gammarus pulex was markedly lower, as was the rate of litter decomposition in the impacted sites. This was partially compensated for, however, by elevated microbial breakdown, suggesting another indirect food-web effect of the toxic spill. 5. Although many species exhibited population crashes or local extirpation, total macroinvertebrate biomass and abundance were largely unaffected due to a compensatory elevation in small tolerant taxa such as oligochaetes, and/or taxa which were in their adult aerial life stage at the time of the spill (e.g. chironomids) and thus avoided contact with the polluted waters and were able to repopu- late the river quickly. Mass–abundance scaling of trophic links between consumers and resources revealed extensive restructuring within the food web. 6. This case study shows that pesticides can affect food-web structure and ecosystem functioning, both directly and indirectly across levels of biological organisation. It also demonstrates how an integrated assessment approach, as adopted here, can elucidate links between microbiota, macroinvertebrates and fish, for instance, thus improving our understanding of the range of biological consequences of chemical contamination in natural ecosystems.

Anammox, i.e. the anaerobic oxidation of NH4 + with NO2 - to N2, has redefined our understanding of nitrogen cycling in aquatic ecosystems. The isotope pairing technique (IPT) is the dominant tool for quantifying denitrification in intact sediments, but it cannot distinguish anammox from denitrification as sources of N2 and may, where anammox is significant, lead to large errors in the estimate of true N2 production. In a previous study, the IPT was revised in theory and a solution was proposed whereby the parameter r14, i.e. the ratio of 14 NO3 - to 15 NO3 - in the NO3 - reduction zone is used to correct the IPT in the presence of anammox. We begin by exploring the limitations of the 2 indirect techniques previously proposed for estimating r14. The first, based on the contribution of anammox to N2 production (ra) in sediment slurry incubations, underestimates anammox and cannot fully correct the IPT. The second, derived from the production of 15 N-N2 gas as a function of 15 NO3 - concentration, although valid in sieved sediment, was ineffective in natural intact sediments. In con- trast, a newly developed direct technique based on the 15 N-labelling of N2O, corrects the IPT in the presence of significant anammox (48% of N2 formation) in natural sediment and can even distinguish between anammox and denitrification in estuarine sediment with a lower anammox contribution (21%). We contrast these findings with sediments where anammox is minimal (

Sediment characteristics, sediment respiration (oxygen uptake and sulphate reduction) and sediment–water nutrient exchange, in conjunction with water column structure and phytoplankton biomass were measured at five stations across the western Irish Sea front in August 2000. The transition from thermally stratified (surface to bottom temperature difference of 2.3 °C) to isothermal water (14.3 °C) occurred over a distance of 13 km. The influence of the front on phytoplankton biomass was limited to a small region of elevated near surface chlorophyll (2.23 mg m −3 ; 50% > biomass in mixed waters). The front clearly marked the boundary between depositional sediments (silt/clays) with elevated sediment pigment levels (≈60 mg m −2 ) on the western side, to pigment impoverished ( −2 ) sand, through to coarse sand and shell fragments on the eastern side. Maximal rates of sedimentary respiration on the western stratified side of the front e.g. oxygen uptake S2 (852 μmol O 2 m −2 h −1 ) and sulphate reduction at S1 (149 μmol SO 4 2− m −2 h −1 ), coupled to significant efflux of nitrate and silicate at the western stations indicate closer benthic–pelagic coupling in the western Irish Sea. Whether this simply reflects the input of phytodetritus from the overlying water column or entrapment and settlement of pelagic production from other regions of the Irish Sea cannot yet be resolved.

A diagenetic model is presented which considers nitrate reduction by both denitrification and Dissimilatory Nitrate Reduction to Ammonium (DNRA). This work builds on an existing model (Kelly-Gerreyn et al 1999; Mar Ecol Prog Ser 177:37-50). Previous models have assumed nitrate reduction to be solely due to denitrification. This paper questions the reliability of this assumption in coastal areas and suggests that DNRA can account for a high proportion of nitrate reduction. Data from a North Sea estuary (the lower Gt. Ouse, Norfolk, UK) containing high nutrient concentrations (mean 406 μM NO 3 - ) are used to derive a relationship between temperature and the proportioning of nitrate reduction driven by nitrate from the overlying water into denitrification and DNRA. The relationship is assumed to apply to total nitrate reduction. The result is a function which shows that DNRA and denitrification occur at all temperatures but that DNRA is the favoured pathway at the extremes of the observed temperatures ( 17°C) while denitrification is favoured only in a narrow range of temperatures (14 to 17°C). The mechanism is probably an adaptive response of different nitrate-reducing bacteria to temperature. This temperature relationship is implemented in the model and used to successfully simulate both observed rates of uncoupled denitrification (4 to 228 μmolN m -2 h -1 ), denitrification fuelled by nitrate in the overlying water (D w ), and calculated rates of DNRA fuelled by nitrate in the overlying water (DNRA w ) (measured nitrate flux - measured D w rate). In contrast, standard diagenetic formulae for nitrate reduction (i.e. by denitrification only) cannot satisfactorily reproduce the D w rates observed in these sediments. It is concluded that temperature is an important controlling factor for partitioning nitrate reduction into DNRA and denitrification in the lower Gt. Ouse sediments. This temperature effect implies that during an extended warm summer in temperate estuaries receiving high nitrate inputs, nitrate reduction may contribute to, rather than counteract, a eutrophication event. Diagenetic models of the nitrogen cycle in coastal areas should include DNRA.

Seasonal measurements of organic matter mineralisation by oxygen uptake and denitrification were carried out from July 1996 to March 1998 along a -200 km transect of the River Thames estuary, UK. There was a distinct gradient of decreasing rates of organic matter mineralisation seaward, which was related to the concentration of suspended solids and sedimentary organic carbon (C) at each site. There was clear seasonality and highest rates of oxygen uptake (10 056 pmol O 2 m -2 h -1 ) at the muddy sites, but lower rates and non-temperature-dependent oxygen uptake at the sandier sites. Denitrification, both that driven by nitrate from the overlying water (D w ) and that coupled to nitrification in the sediment (D n ), followed a similar trend to oxygen uptake, from negligible rates of approximately 1 pmol N m -2 h -1 for both D w and D n at the furthest offshore site, Site 12, to 11 407 and 8209 pmol N m -2 h -1 , respectively, at the inner muddy Site 1. The Thames estuary is heterotrophic and a very efficient organic C filter, trapping and remineralising 77% of its organic C-input. Attenuation of fluvial nitrate loads was regulated by freshwater flow. Minimal attenuation (3 %) occurred during peak flows (i.e. during periods of shortest freshwater flushing time) and > 100 % attenuation during periods of lowest freshwater flow (longest flushing times). Including the sewage treatment works (STWs) nitrate load in this calculation reduced the degree of attenuation of the nitrate load to, on average, 11%. Annual rates of D w and D n for an inner area of 125 km 2 were 112 and 85 Mmol N yr -1 , respectively, with a total rate of 196 Mmol N yr -1 (2744 t), which was equivalent to 9% of the total dissolved inorganic nitrogen (DIN) load for 1995-96. A mean denitrification rate (D w ) of 0.64 mol N m -2 yr -1 , based on measurements in 4 east coast estuaries, was used to estimate a total rate of denitrification for the entire area of UK east coast estuaries. The total rate of 0.81 Gmol N yr -1 represented 16% attenuation of the total fluvial discharge of nitrate (-6 Gmol N yr -1 ) to the UK's east coast estuaries (1995-96) and hence a 16% reduction in the UK nitrate load to the North Sea.

Sedimentary organic matter mineralisation (oxygen uptake), nitrogen (N) loss (denitrification) and nutrient exchange were measured seasonally in areas of both high and low Enteromorpha sp. and Ulva sp. cover at 6 sites in 2 harbours on the south coast of England. Measurements of macroalgal and phytoplankton photosynthesis were also carried out. Sedimentary carbon (C) and N cycling was most rapid at the sites with a heavy cover of macroalgae. Macroalgae were responsible, on average, for 57% of total dark oxygen uptake, with sediment bacterial respiration accounting for the remaining 43 %. Dark rates of nutrient uptake for Enteromorpha sp. and Ulva sp. were equivalent to 70% of those in the light. Denitrification rates were low (D w [NO 3 - from overlying water] 98%) remained within the system. External inputs of nutrients (N and P) to the harbours may have supported the spring growth of macroalgae, but it seemed unlikely that they were capable of supporting the summer peaks in algal biomass and rapid rates of N turnover. More likely the intense recycling (ammonification) of organically bound N within the sediments, coupled to a minimum loss via denitrification, provided a sustained and sufficient N supply for the macroalgae.

Fluvial and sewage loading of N and P to Liverpool Bay (England) elevated winter con- centrations of dissolved inorganic N (29.2 µM) and P (1.7 µM) and molar ratios of N:P (17.0) and N:Si (6.0) compared to Irish coastal waters (9.5 µM N, 0.8 µM P; N:P 12.0 N:Si 1.9). At the enriched site in Liverpool Bay, enhanced spring production (up to 3165.8 mg C m -2 d -1 ) summer production (471.8 to 971.5 mg C m -2 d -1 ) and biomass (4.1 to 13.6 mg chorophyll m -3 ) was dominated by diatoms. Annual production at this site was estimated as 182 g C m -2 compared to 97 g C m -2 at the Irish coastal sta- tion. Enrichment and shifts in nutrient ratios did not favour flagellate growth compared to growth of diatoms in Liverpool Bay. Low amounts of sediment phytopigments (9.2 to 26 mg m -2 ), low concen- trations of pore water Si (mean, 9.8 µM), and a negligible summer benthic efflux of Si (1.0 µmol m -2 h -1 ) suggested little phytodetrital input to sediments in Liverpool Bay and that summer diatom pro- duction required an allochthonous supply of Si. At the Irish coastal station, coupling between benthic and water-column processes ensured that benthic efflux of Si was sufficient to support the bulk of summer diatom production. Water-column recycling of N was an order of magnitude greater than sediment recycling of N at both coastal sites.

The description and calibration of a reaction-diffusion model of early diagenesis are presented. Unlike previous models it has been developed for a temperate latitude estuary (Gt Ouse, UK) impacted by high nitrate concentrations (annual mean 700 μM). Five variables, O 2 , NO 3 - , NH 4 + , SO 4 2- and S 2- , are modelled from the steady state distributions of bulk total organic carbon (TOC) (i.e. a 1-G model). Three methods for deriving the first order rate constant, k, for TOC mineralisation are tested: (1) data calculated k values [i.e. (depth integrated total mineralisation rate) + (depth integrated TOC inventory)]; (2) an exponential formulation, k z = k 0 e -αz (k 0 = k at sediment surface, a = reactivity coefficient of decrease, z = depth); and (3) use of separate k values for individual mineralisation pathways. Method 1 underestimates observed fluxes of solutes across the sediment-water interface (SWI) by up to an order of magnitude. This is due to an inappropriate use of the calculated kin the model. The calculation of k yields an overall net value which implicitly accounts for all factors acting on mineralisation. Such factors (e.g. oxidant limitation of organic decay) are explicitly modelled. Consequently, k is significantly reduced by factors applied to it in the model which have previously been accounted for in the calculation. In Method 2, measured NO 3 - fluxes are overestimated by up to a factor of 7. To reproduce measured benthic oxygen demands and sulphate reduction rates, a cannot be simultaneously fitted to the NO 3 - fluxes. The high overlying NO 3 - concentrations result in model denitrification that cannot reproduce the degree of limitation that actually occurs. Method 3 reproduces the data (i.e. both stoichiometrically derived mineralisation rates and measured solute fluxes at the SWI) to a high degree (r > 0.99, p < 0.001), but at the expense of increasing the degrees of freedom in the model and conceptual simplicity. These results cast doubt over the universal applicability of diagenetic models for estuarine systems exposed to high NO 3 - concentrations. It is concluded that the use of commonly calculated first order rate constants (Method 1) and the frequently used exponential function (Method 2) in diagenetic models cannot be relied upon to reproduce observations in high NO 3 - estuaries. Previous stoichiometric calculations suggested that all of the measured ammonium fluxes across the SWI in the Gt Ouse could be accounted for with oxygen, nitrate and sulphate reduction alone. With these latter processes the model (Method 3) underestimates the observed ammonium fluxes by up to 44 % at 3 out of 4 sites. This suggests that other mineralisation pathways (e.g. nitrate ammonification) are active in the Great Ouse sediments.

The impact of the spring bloom on benthic remineralisation rates was studied in offshore waters of the western Irish Sea during 1998. Initiation of the spring bloom coincided with the onset of thermal stratification at the end of April. Peak chlorophyll biomass (6.48 mg chl m -3 ) and algal standing stock (145.0 mg chl m -2 ) were measured on May 11, and the bloom lasted approximately 1 mo. Sediment oxygen uptake increased to 1658 μmol m -2 h -1 for a short period in early May, which was followed by increased denitrification (up to 48 μmol N m -2 h -1 ) in late May and early July. Subsequently sulphate reduction increased (up to 83 μmol SO 4 2- m -2 h -1 ) in early July. Efflux of nitrate remained low but constant (10 μmol m -2 h -1 ) throughout the study, accounting for 27 % of ammonified organic N, with the remaining 63% being denitrified. Sediment depth profiles of chlorophyll and phaeopigment showed deep (>30 cm) mixing of phytodetritus into the sediment in early July, which may explain the high rates of sulphate reduction measured at this time. Evidence of a large phytodetrital flux to the benthos during spring 1998 was limited. Deepening of chlorophyll isopleths suggested sinking of algae in early May, although sediment pigment concentrations indicated a continual but low input. Benthic oxygen consumption represented 46 % of total spring phytoplankton production or 61% of new production and approximately balanced the calculated flux of detrital carbon (C) to the benthos. The impact of detrital C (assumed to be largely phytodetritus immediately after the spring bloom) on the benthos was short lived, being rapidly remineralised, and in turn little spring production would have been available for secondary production, e.g. Nephrops norvegica. In such years, benthic production, particularly that of N. norvegica, must be supported by phytoplankton production which takes place after the bloom or by detrital C which is advected into the area following the breakdown of the gyre.

The fate of nitrogen (N) in the bottom sediments of the upper Great Ouse estuary, England, was examined over the course of a year. The sedirnents were consistent sinks for NO3from the overlying river water, and were weak sources of NH,'. Simultaneous measurements of oxygen uptake, nutrient exchange and sulphate reduction, when combined with the measured C:N ratios of the sediment organic matter, permitted calculation of the amount of N released within the sediment by organic matter mineralisation. With the exception of a site w ~ t h thixotropic sediment, at all other sites the amount of inorganic N entering the sedlment by transport from the overlying water and by internal ammonification of organic matter was not matched by measured exports of N from the sedirnents. We calculate that >90% of the flux of N through the sediment was lost as gases, and that 50'L of the N ammonified from organic matter must have been converted to gases by coupled nitrification-denitrification within the sediments. When compared to the total flux of N through the entire estuary, any N loss by denitrification in the sediments of the upper estuary was minor (-1 X) because of the small surface area of sediment to freshwater flow

The purpose of this research was to investigate the potential causes of low oxygen levels in the bottom water of the Oyster Grounds region of the shallow southern North Sea, an area which provides suitable conditions for low oxygen levels to develop. At the end of the summer stratified period, relevant biogeochemical processes were investigated using a combination of sedimentary and water column rate measurements. Phytoplankton nitrate and ammonium uptake was measured throughout the water column using (15)N labelled isotopes and showed ammonium uptake dominated in the upper and bottom mixed layer with a maximum 294.4 micromol N m(-3)h(-1). In the deep chlorophyll maximum at the thermocline, primary production was dominated by nitrate uptake, with an average of 35.0 micromol N m(-3)h(-1), relative to ammonium uptake, with an average of 24.6 micromol N m(-3)h(-1). This high relative nitrate uptake will in part result in exportable new production to the isolated bottom mixed layer and sediments, as opposed to regenerated ammonium driven uptake. This biomass export was indicated by significant benthic oxygen consumption rates in the stratified region (782-1275 micromol O(2)m(-2)h(-1)micromol N m(-3)h(-1)) long after the end of the spring bloom. The sediments were also an active net source of nitrate, ammonium, phosphate and silicate into the bottom mixed layer of 4.4, 8.4, 2.3 and 68.8 micromol m(-2)h(-1), respectively. The export of new production within the thermocline to the bottom mixed layer and the consequent sediment oxygen consumption in the isolated bottom mixed layer in the Oyster Grounds are expected to have contributed to the low bottom water oxygen concentrations of 2.07 mg l(-1) (64.7 micromol l(-1)) measured. The long stratified period associated with this low oxygen is predicted to occur more regularly in the future and continued monitoring of this ecologically important region is therefore essential if the causes of these potentially damaging low oxygen levels are to be fully understood.

Benthic trawling has a recognised impact on sediment whole organism communities, yet little is known about its impact on sediment biogeochemistry. On 2 cruises in October 2001 and July 2002, we measured sediment characteristics (particle size distribution, porosity and organic matter (OM)) and sediment metabolism (oxygen uptake, denitrification, sulphate reduction and sediment- water nutrient exchange) along gradients of trawling activity at 14 sites in 2 regions of the southern North Sea: one with low tidal disturbance but high trawling disturbance (Outer Silver Pit, OSP), the other with high tidal disturbance but lower trawling disturbance (Thames). There was no measurable impact of trawling activity on oxygen uptake, denitrification or nutrient exchange in either region. In contrast, at the high trawling disturbance sites in the OSP only, there was both a shift in particle size distribution (towards fines) and a greater rate of sulphate reduction (volume specific rates 0.83 and 0.49 nmol SO4 2- cm -3 h -1 at high and low impact sites, respectively), but not in the Thames. In addi- tion, areal rates of sulphate reduction were positively correlated with both silt content (i.e. associated with organics) and long-term trawling in the OSP but not in the Thames. Biogeochemical processes in the upper layers of sediment, both oxic and suboxic, seemed unaffected by trawling in the long- term. In deeper anoxic sediment, however, mineralisation via sulphate reduction may be stimulated by the extra disturbance, at least in areas where tidal energy is slight.