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Permafrost and glaciers in the high Arctic form an impermeable ‘cryospheric cap’ that traps a large reservoir of sub-surface methane and hinders it from reaching the atmosphere. The vulnerability of the cryosphere to climate warming is making releases of this methane possible, but uncertainty in the magnitude and timing makes future predictions of Arctic greenhouse gas emissions difficult. In Svalbard, where air temperatures are rising more than twice as fast as the average for the Arctic, glaciers are retreating and leaving behind an exposed forefield that enables rapid methane escape.We undertook a field survey of unprecedented spatial coverage across central Svalbard to identify methane emission hotspots in glacial forefields, a previously unknown emission source. Here we document how methane-rich groundwater springs that have formed in recently revealed forefields of 78 land-terminating glaciers are bringing deep-seated methane gas to the surface. Waters collected from these springs are supersaturated with methane up to 600,000-times greater than atmospheric equilibration, with strong isotopic evidence of a thermogenic source. We estimate annual emissions of methane degassing from such groundwater springs to be up to 2.31 kt across the Svalbard archipelago. Our findings reveal that climate-driven glacial retreat is facilitating widespread release of methane, a positive feedback loop that is likely to be prevalent across other regions of the rapidly warming Arctic.

In ecosystems, the efficiency of energy transfer from resources to consumers determines the biomass structure of food webs. As a general rule, about 10% of the energy produced in one trophic level makes it up to the next1–3. Recent theory suggests that this energy transfer could be further constrained if rising temperatures increase metabolic growth costs4, although experimental confirmation in whole ecosystems is lacking. Here we quantify nitrogen transfer efficiency—a proxy for overall energy transfer—in freshwater plankton in artificial ponds that have been exposed to seven years of experimental warming. We provide direct experimental evidence that, relative to ambient conditions, 4 °C of warming can decrease trophic transfer efficiency by up to 56%. In addition, the biomass of both phytoplankton and zooplankton was lower in the warmed ponds, which indicates major shifts in energy uptake, transformation and transfer5,6. These findings reconcile observed warming-driven changes in individual-level growth costs and in carbon-use efficiency across diverse taxa4,7–10 with increases in the ratio of total respiration to gross primary production at the ecosystem level11–13. Our results imply that an increasing proportion of the carbon fixed by photosynthesis will be lost to the atmosphere as the planet warms, impairing energy flux through food chains, which will have negative implications for larger consumers and for the functioning of entire ecosystems. In artificial ponds exposed to seven years of experimental warming, energy transfer between two trophic levels of freshwater plankton decreased by 56% and the biomass of both levels was reduced.

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).

Methane is a powerful greenhouse gas but the microbial diversity mediating methylotrophic methanogenesis is not well-characterized. One overlooked route to methane is via the degradation of dimethylsulfide (DMS), an abundant organosulfur compound in the environment. Methanogens and sulfate-reducing bacteria (SRB) can degrade DMS in anoxic sediments depending on sulfate availability. However, we know little about the underlying microbial community and how sulfate availability affects DMS degradation in anoxic sediments. We studied DMS-dependent methane production along the salinity gradient of the Medway Estuary (UK) and characterized, for the first time, the DMS-degrading methanogens and SRB using cultivation-independent tools. DMS metabolism resulted in high methane yield (39%-42% of the theoretical methane yield) in anoxic sediments regardless of their sulfate content. Methanomethylovorans, Methanolobus and Methanococcoides were dominant methanogens in freshwater, brackish and marine incubations respectively, suggesting niche-partitioning of the methanogens likely driven by DMS amendment and sulfate concentrations. Adding DMS also led to significant changes in SRB composition and abundance in the sediments. Increases in the abundance of Sulfurimonas and SRB suggest cryptic sulfur cycling coupled to DMS degradation. Our study highlights a potentially important pathway to methane production in sediments with contrasting sulfate content and sheds light on the diversity of DMS degraders.

Net emissions of the potent GHG methane from ecosystems represent the balance between microbial methane production (methanogenesis) and oxidation (methanotrophy), each with different sensitivities to temperature. How this balance will be altered by long-term global warming, especially in freshwaters that are major methane sources, remains unknown. Here we show that the experimental warming of artificial ponds over 11 years drives a disproportionate increase in methanogenesis over methanotrophy that increases the warming potential of the gases they emit. The increased methane emissions far exceed temperature-based predictions, driven by shifts in the methanogen community under warming, while the methanotroph community was conserved. Our experimentally induced increase in methane emissions from artificial ponds is, in part, reflected globally as a disproportionate increase in the capacity of naturally warmer ecosystems to emit more methane. Our findings indicate that as Earth warms, natural ecosystems will emit disproportionately more methane in a positive feedback warming loop.\ud \ud

In ecosystems, the efficiency of energy transfer from resources to consumers determines the biomass structure of food webs. As a general rule, about 10% of the energy produced in one trophic level makes it up to the next

In grasslands, N mineralization and nitrification are important processes and are controlled by several factors, including the in situ microbial community composition. Nitrification involves ammonia oxidising archaea (AOA) and bacteria (AOB) and although AOA and AOB co-exist in soils, they respond differently to environmental characteristics and there is evidence of AOA/AOB niche differentiation. Here, we investigated temporal variation in N mineralization and nitrification rates, together with bacterial, archaeal and ammonia-oxidiser communities in grassland soils, on different geologies: clay, Greensand and Chalk. Across geologies, N mineralization and nitrification rates were slower in the autumn than the rest of the year. Turnover times for soil ammonium pools were

Anaerobic oxidation of methane (AOM) reduces methane emissions from marine ecosystems but we know little about AOM in rivers, whose role in the global carbon cycle is increasingly recognized. We measured AOM potentials driven by different electron acceptors, including nitrite, nitrate, sulfate, and ferric iron, and identified microorganisms involved across contrasting riverbeds. AOM activity was confined to the more reduced, sandy riverbeds, whereas no activity was measured in the less reduced, gravel riverbeds where there were few anaerobic methanotrophs. Nitrite-dependent and nitrate-dependent AOM occurred in all sandy riverbeds, with the maximum rates of 61.0 and 20.0 nmol CO2 g−1 (dry sediment) d−1, respectively, while sulfate-dependent and ferric iron-dependent AOM occurred only where methane concentration was highest and the diversity of AOM pathways greatest. Diverse Candidatus Methylomirabilis oxyfera (M. oxyfera)-like bacteria and Candidatus Methanoperedens nitroreducens (M. nitroreducens)-like archaea were detected in the sandy riverbeds (16S rRNA gene abundance of 9.3 × 105 to 1.5 × 107 and 2.1 × 104 to 2.5 × 105 copies g−1 dry sediment, respectively) but no other known anaerobic methanotrophs. Further, we found M. oxyfera-like bacteria and M. nitroreducens-like archaea to be actively involved in nitrite- and nitrate/ferric iron-dependent AOM, respectively. Hence, we demonstrate multiple pathways of AOM in relation to methane, though the activities of M. oxyfera-like bacteria and M. nitroreducens-like archaea are dominant.

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

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.

Oxygen minimum zones (OMZs) contain the largest pools of oceanic methane but its origin and fate are poorly understood. High-resolution (

Lakes and ponds cover only about 4% of the Earth’s non-glaciated surface1, yet they represent disproportionately large sources of methane and carbon dioxide2, 3, 4. Indeed, very small ponds (for example

Anammox, an important N2 loss pathway in marine waters, is not well understood in rivers. In situ measurements of N2 production in UK rivers reveal that anammox can be the dominant N2 loss pathway in permeable but not in impermeable riverbeds. Rivers are an important global sink for excess bioavailable nitrogen: they convert approximately 40% of terrestrial N runoff per year (∼47 Tg) to biologically unavailable N2 gas and return it to the atmosphere1. At present, riverine N2 production is conceptualized and modelled as denitrification2,3,4. Anaerobic ammonium oxidation, known as anammox, is an alternative pathway of N2 production important in marine environments, but its contribution to riverine N2 production is not well understood5,6. Here we use in situ and laboratory measurements of anammox activity using 15N tracers and molecular analyses of microbial communities to evaluate anammox in clay-, sand- and chalk-dominated river beds in the Hampshire Avon catchment, UK during summer 2013. Abundance of the hzo gene, which encodes an enzyme central to anammox metabolism, varied across the contrasting geologies. Anammox rates were similar across geologies but contributed different proportions of N2 production because of variation in denitrification rates. In spite of requiring anoxic conditions, anammox, most likely coupled to partial nitrification, contributed up to 58% of in situ N2 production in oxic, permeable riverbeds. In contrast, denitrification dominated in low-permeability clay-bed rivers, where anammox contributes roughly 7% to the production of N2 gas. We conclude that anammox can represent an important nitrogen loss pathway in permeable river sediments.

Our understanding of the role of freshwaters in the global carbon cycle is being revised, but there is still a lack of data, especially for the cycling of methane, in rivers and streams. Unravelling the role of methanotrophy is key to determining the fate of methane in rivers. Here we focus on the carbon conversion efficiency (CCE) of methanotrophy, that is, how much organic carbon is produced per mole of CH4oxidised, and how this is influenced by variation in methanotroph communities. First, we show that the CCE of riverbed methanotrophs is consistently high (~50%) across a wide range of methane concentrations (~10–7000 nM) and despite a 10-fold span in the rate of methane oxidation. Then, we show that this high conversion efficiency is largely conserved (50%± confidence interval 44–56%) across pronounced variation in the key functional gene (70 operational taxonomic units (OTUs)), particulate methane monooxygenase (pmoA), and marked shifts in the abundance of Type I and Type II methanotrophs in eight replicate chalk streams. These data may suggest a degree of functional redundancy within the variable methanotroph community inhabiting these streams and that some of the variation inpmoAmay reflect a suite of enzymes of different methane affinities which enables such a large range of methane concentrations to be oxidised. The latter, coupled to their high CCE, enables the methanotrophs to sustain net production throughout the year, regardless of the marked temporal and spatial changes that occur in methane.

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.

Aim The average carbon-to-nitrogen-to-phosphorus ratio (C:N:P) of marine algae is known to be tightly coupled to that of the inorganic pools of C, N and P in the ocean interior (i.e. the Redfield ratio), and therefore plays a key role in regulating the C and N cycles in the ocean. The C:N:P ratio of algae also varies substantially, both within and among taxa, in response to variation in the abiotic environment, raising the possibility that biogeochemical controls on the marine C and N cycles may shift as a result of climate change. However, the role of temperature in driving phenotypic variation in stoichiometry within algal taxa, as well as biogeographic variation in particulate C, N and P among oceanic regions, remains largely unresolved. Location Global. Methods To assess the extent to which temperature controls algal stoichiometry we performed two complementary meta-analyses.First,we characterized the global temperature dependence of algal stoichiometry by analysing field data that encompassed 767 estimates of C:N:P from 22 oceanic sites spanning over 130° of latitude. Second, we characterized the within-species acclimation responses of C:N:P stoichiometry to temperature by analysing data that encompassed 17 experiments, 9 species and 4 taxonomic classes. Results The geographic analyses demonstrated that the N:P and C:P ratios of marine algae were best predicted by latitudinal variation in average sea-surface temperature, and that both ratios increased 2.6-fold from 0 to 30 °C. These global-scale temperature responses, which largely reflect geographic variation in the species compositions of algal assemblages, were of similar magnitude to the average within-species response of the N:P and C:P ratios to experimental temperature manipulations. Main conclusions The congruence between field and experimental observations suggests that temperature-dependent physiological mechanisms operating at the subcellularlevelplayanimportantroleindeterminingthestoichiometryof algaein the world’s oceans.

Anthropogenic nitrogen pollution is a critical problem in freshwaters. Although riverbeds are known to attenuate nitrate, it is not known if large woody debris (LWD) can increase this ecosystem service through enhanced hyporheic exchange and streambed residence time. Over a year, we monitored the surface water and pore water chemistry at 200 points along a ~ 50 m reach of a lowland sandy stream with three natural LWD structures. We directly injected 15N-nitrate at 108 locations within the top 1.5 m of the streambed to quantify in situ denitrification, anammox and dissimilatory nitrate reduction to ammonia, which, on average, contributed 85, 10 and 5% of total nitrate reduction, respectively. Total nitrate reducing activity ranged from 0 to 16 µM h−1 and was highest in the top 30 cm of the stream bed. Depth, ambient nitrate and water residence time explained 44% of the observed variation in nitrate reduction; fastest rates were associated with slow flow and shallow depths. In autumn, when the river was in spate, nitrate reduction (in situ and laboratory measures) was enhanced around the LWD compared with non-woody areas, but this was not seen in the spring and summer. Overall, there was no significant effect of LWD on nitrate reduction rates in surrounding streambed sediments, but higher pore water nitrate concentrations and shorter residence times, close to LWD, indicated enhanced delivery of surface water into the streambed under high flow. When hyporheic exchange is too strong, overall nitrate reduction is inhibited due to short flow-paths and associated high oxygen concentrations.

Nitrogen (N) and/or phosphorus (P) availability can limit growth of primary producers across most of the world's aquatic and terrestrial ecosystems. These constraints are commonly overcome in agriculture by applying fertilizers to improve yields. However, excessive anthropogenic N and P inputs impact natural environments and have far-reaching ecological and evolutionary consequences, from individual species up to entire ecosystems. The extent to which global N and P cycles have been perturbed over the past century can be seen as a global fertilization experiment with significant redistribution of nutrients across different ecosystems. Here we explore the effects of N and P availability on stoichiometry and genomic traits of organisms, which, in turn, can influence: (i) plant and animal abundances; (ii) trophic interactions and population dynamics; and (iii) ecosystem dynamics and productivity of agricultural crops. We articulate research priorities for a deeper understanding of how bioavailable N and P move through the environment and exert their ultimate impacts on biodiversity and ecosystem services.

Biological oceanic processes, principally the surface production, sinking and interior remineralization of organic particles, keep atmospheric CO2 lower than if the ocean was abiotic. The remineralization length scale (RLS, the vertical distance over which organic particle flux declines by 63%, affected by particle respiration, fragmentation and sinking rates) controls the size of this effect and is anomalously high in oxygen minimum zones (OMZ). Here we show in the Eastern Tropical North Pacific OMZ 70% of POC remineralization is due to microbial respiration, indicating that the high RLS is the result of lower particle fragmentation by zooplankton, likely due to the almost complete absence of zooplankton particle interactions in OMZ waters. Hence, the sensitivity of zooplankton to ocean oxygen concentrations can have direct implications for atmospheric carbon sequestration. Future expansion of OMZs is likely to increase biological ocean carbon storage and act as a negative feedback on climate change., The downward transfer of organic carbon from the surface to the deep ocean is increased in oxygen minimum zones relative to oxic waters. Here, the authors show reduced interactions of zooplankton with sinking particles owing to low oxygen are likely the primary reason for the observed high transfer of carbon.

Phytoplankton photosynthesis is a critical flux in the carbon cycle, accounting for approximately 40% of the carbon dioxide fixed globally on an annual basis and fuelling the productivity of aquatic food webs. However, rapid evolutionary responses of phytoplankton to warming remain largely unexplored, particularly outside the laboratory, where multiple selection pressures can modify adaptation to environmental change. Here, we use a decade-long experiment in outdoor mesocosms to investigate mechanisms of adaptation to warming (+4 °C above ambient temperature) in the green alga Chlamydomonas reinhardtii, in naturally assembled communities. Isolates from warmed mesocosms had higher optimal growth temperatures than their counterparts from ambient treatments. Consequently, warm-adapted isolates were stronger competitors at elevated temperature and experienced a decline in competitive fitness in ambient conditions, indicating adaptation to local thermal regimes. Higher competitive fitness in the warmed isolates was linked to greater photosynthetic capacity and reduced susceptibility to photoinhibition. These findings suggest that adaptive responses to warming in phytoplankton could help to mitigate projected declines in aquatic net primary production by increasing rates of cellular net photosynthesis. Isolates of the green alga Chlamydomonas reinhardtii adapted to a decade of chronic warming in outdoor mesocosms have higher competitive fitness than ambient controls, due to greater photosynthetic capacity and reduced susceptibility to photoinhibition

The role that hydrology plays in governing the interactions between dissolved organic carbon (DOC) and nitrogen in rivers draining lowland, agricultural landscapes is currently poorly understood, yet important to assess given the potential changes to production and delivery of DOC and nitrate arising from climate change. We measured DOC and nitrate concentrations in river water of six reaches of the lowland River Hampshire Avon (Wiltshire, southern UK) in order to quantify the relationship between Baseflow Index (BFI) and DOC : nitrate molar ratios across contrasting geologies (Chalk, Greensand and clay). We found a significant positive relationship between nitrate and Baseflow Index (p

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.

The hyporheic zone of riverbed sediments has the potential to attenuate nitrate from upwelling, polluted groundwater. However, the coarse-scale (5 – 10 cm) measurement of nitrogen biogeochemistry in the hyporheic zone can often mask fine-scale (

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.

Environmental anaerobic ammonium oxidation (anammox) was demonstrated for the first time in 2002, using 15 N labeling, in homogenized sediment from the Skagerrak, where it accounted for up to 67% of N 2 production. We returned to some of these original sites in 2010 to make measurements of nitrogen and carbon cycling under conditions more representative of those in situ , quantifying anammox and denitrification, together with oxygen penetration and consumption, in intact sediment cores. Overall, oxygen consumption and N 2 production decayed with water depth, as expected, but the drop in N 2 production was relatively more pronounced. Whereas we confirmed the dominance of N 2 production by anammox (72% and 77%) at the two deepest sites (∼700 m of water), anammox was conspicuously absent from two shallower sites (∼200 m and 400 m). At the shallower sites, we could measure no anammox activity with either intact or homogeneous sediment, and quantitative PCR (16S rRNA) gave a negligible abundance of anammox bacteria in the anoxic layers. Such an absence of anammox, especially at one locale where it was originally demonstrated, is hard to reconcile. Despite the dominance of anammox at the deepest sites, anammox activity could not make up for the drop in denitrification, and assuming Redfield ratios for the organic matter being mineralized, the estimated retention of fixed N actually increased to 90% to 97% of that mineralized, whereas it was 80% to 86% at the shallower sites.

Emergent vegetation in river beds can play a significant role in nutrient cycling in riverine sediments. We analysed and compared pore water NO3 − concentration gradients in the sediments of the River Leith, Cumbria, UK, in the presence and absence of emergent vegetation (dominated by Sparganium spp.). High resolution (1 cm interval), in situ, vertical profiles of NO3 − to 30 cm depth were measured using deployment of diffusive equilibrium in thin films probes on four occasions from July to September 2010. We found significantly (p

We examined the influence of river stage on subsurface hydrology and pore water chemistry within the hyporheic zone of a groundwater-fed river during the summer baseflow period of 2011. We found river stage and geomorphologic environment to control chemical patterns in the hyporheic zone. At high river stage, the flux of upwelling water in the shallow sediments (> 20 cm) decreased at samples sites in the upper section of our study reach and increased substantially at sites in the lower section. This differential response is attributed to the contrasting geomorphology of these sub-reaches which affects the rate of the rise and fall of river stage relative to subsurface head. At sites where streamward vertical flux decreased, concentration profiles of a conservative environmental tracer suggest surface water infiltration into the riverbed below depths recorded at low river stage. An increase in vertical flux at sites in the lower sub-reach is attributed to the movement of lateral subsurface waters originating from the adjacent floodplain. This lateral-moving water preserved or decreased the vertical extent of the hyporheic mixing zone observed at low river stage. Down welling surface water appeared to be responsible for elevated dissolved organic carbon (DOC) and Mn concentrations in shallow sediments (0 – 20 cm); however, lateral subsurface flows were probably important for elevated concentrations of these solutes at deeper levels. Results suggest that DOC delivered to hyporheic sediments during high river stage from surface water and lateral subsurface sources could enhance heterotrophic microbial activities. This article is protected by copyright. All rights reserved.

Water pathways through permeable riverbeds are multi-dimensional, including lateral hyporheic exchange flows as well as vertical (upwelling and downwelling) fluxes. The influence of different pathways of water on solute patterns and the supply of nitrate and other redox-sensitive chemical species in the riverbed is poorly understood but could be environmentally significant. For example, nitrate-rich upwelling water in the gaining reaches of groundwater-fed rivers has the potential to supply significant quantities of nitrate through the riverbed to surface waters, constraining opportunities to deliver the goals of the EU Water Framework Directive to achieve ‘good ecological status’. We show that patterns in porewater chemistry in the armoured river bed of a gaining reach (River Leith, Cumbria) reflect the spatial variability in different sources of water; oxic conditions being associated with preferential discharge from groundwater and reducing conditions with longitudinal and lateral fluxes of water due to water movement from riparian zones and/or hyporheic exchange flows. Our findings demonstrate the important control of both vertical and lateral water fluxes on patterns of redox-sensitive chemical species in the river bed. Furthermore, under stable, baseflow conditions (

The role that hydrology plays in governing the interactions between dissolved organic carbon (DOC) and nitrogen in rivers draining lowland, agricultural landscapes is currently poorly understood. In light of the potential changes to the production and delivery of DOC and nitrate to rivers arising from climate change and land use management, there is a pressing need to improve our understanding of hydrological controls on DOC and nitrate dynamics in such catchments. We measured DOC and nitrate concentrations in river water of six reaches of the lowland river Hampshire Avon (Wiltshire, southern UK) in order to quantify the relationship between BFI (BFI) and DOC : nitrate molar ratios across contrasting geologies (Chalk, Greensand, and clay). We found a significant positive relationship between nitrate and BFI (p 5 throughout the year, whilst groundwater-dominated reaches underlain by Chalk, with a high BFI have DOC : nitrate ratios in surface waters that are an order of magnitude lower (

Oceanic oxygen minimum zones are strong sources of the potent greenhouse gas N2O but its microbial source is unclear. We characterized an exponential response in N2O production to decreasing oxygen between 1 and 30 μmol O2 l−1 within and below the oxycline using 15NO2−, a relationship that held along a 550 km offshore transect in the North Pacific. Differences in the overall magnitude of N2O production were accounted for by archaeal functional gene abundance. A one-dimensional (1D) model, parameterized with our experimentally derived exponential terms, accurately reproduces N2O profiles in the top 350 m of water column and, together with a strong 45N2O signature indicated neither canonical nor nitrifier–denitrification production while statistical modelling supported production by archaea, possibly via hybrid N2O formation. Further, with just archaeal N2O production, we could balance high-resolution estimates of sea-to-air N2O exchange. Hence, a significant source of N2O, previously described as leakage from bacterial ammonium oxidation, is better described by low-oxygen archaeal production at the oxygen minimum zone's margins., Understanding the production processes behind oceanic sources of nitrous oxide (N2O), a potent greenhouse gas, is of critical importance. Here, the authors reveal an archaeal-mediated N2O production pathway in the North Pacific, which increases exponentially with decreasing oxygen.

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.

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.

Expansion of commercial agriculture in equatorial regions has significant implications for regional nitrogen (N) budgets. Here we investigate changes in N availability and turnover in Southeast Asia following the replacement of tropical forest with oil palm plantations along a chronosequence of oil palm maturity (3-months to 15-year-old stands) and secondary to primary forest succession in Sabah, Malaysian Borneo. Ten sites were sampled during March and April 2012 and rates of gross ammonium ( NH 4 + ) and nitrate ( NO 3 − ) production (mineralisation and nitrification) and consumption ( n = 8), potential denitrification and “anaerobic ammonium oxidation” (“anammox”) ( n = 12) were determined using 15 N isotope additions to soil cores and slurries respectively. Gross mineralisation rates (0.05–3.08 g N m −2 d −1 ) remained unchanged in oil palm relative to forests. However, a significant reduction in gross nitrification (0.04–2.31 g N m −2 d −1 ) and an increase in NH 4 + immobilisation disrupt the pathway to nitrogen gas (N 2 ) production substantially reducing (by > 90%) rates of denitrification and “anammox” in recently planted oil palm relative to primary forest. Potential nitrous oxide (N 2 O) emissions were greater than potential N 2 production and remained unchanged across the chronosequence indicating a potentially increased ratio of N 2 O:N 2 emission when soils were first disturbed. These results are an important precursor to studies that could yield improved estimates of regional N turnover and loss in Southeast Asia which will have global implications for N biogeochemical cycling.

Here we evaluate a new field methodology for the deployment of Diffusive Equilibrium in Thin Films (DET, protected in stainless steel holders) in coarse riverbed sediments based on that originally developed for fine-grained sediments and soils. Concentration gradients of NO3 −, NH4+ and dissolved Mn were measured at cm resolution. We observed fine scale changes in NO3−, NH4+, and Mn concentrations in the river bed (0–30 cm) that were only evident at high resolution and compared them to profiles of NO3− and NH4+ obtained with low resolution multilevel piezometers. The range in concentrations of NO3− and NH4+measured through DET was larger than those measured at coarse resolution through pore water sampling from multilevel piezometer in the riverbed over the 30 cm depth. According to the results, high resolution profiles of redox sensitive chemical species in riverbeds could help in identifying and resolving hotspots of biogeochemical activity. Measurements of NH4+ using DET were higher than measurements in pore water collected from the multilevel samplers. Further studies are needed to establish whether there is a systematic bias associated with either procedure for the measurement of NH4+.

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

Variations in the overall and depth-specific significance of anammox were measured using (15) N isotope experiments in both bioirrigated and undisturbed sediments of the Medway Estuary, UK. This was performed over two surveys, alongside FISH experiments, to identify and track shifts in the relative abundance of anammox organisms with depth. In Survey 1 (initially screening for the presence of anammox), the potential for anammox (ra) decreased from 32% upstream to 6% downstream. In Survey 2, depth-specific values of ra varied between a maximum of 37% upstream and a minimum of 4% downstream. This was linked to a small population of anammox organisms accounting for 1-8% of total bacteria with depth in Survey 1 and 1-3% in Survey 2. The relationship between the relative abundance of anammox cells and the potential contribution of anammox to total N(2) production did not however correlate. In Survey 2, infaunal disruption of the sediment substrata, and concomitant fluctuations of O(2) over depth, did not appear to inhibit the potential for anammox, even at the most bioturbated site. Moreover, deficits detected in the retrieval of (15) N gas from denitrification in Survey 2 may imply potential links between dissimilatory nitrate reduction to ammonium and anammox in estuarine sediments.

The relative magnitudes of, and factors controlling, denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were measured in the soil of a re-connected temperate floodplain divided into four different land management zones (grazing grassland, hay meadow, fritillary meadow and a buffer zone). Soil samples were collected from each zone to measure their respective potentials for nitrate attenuation using 15N both at the surface and at depth in the soil column and additional samples were collected to measure the lability of the organic carbon. Denitrification capacity ranged between 0.4 and 4.2 (μmol N g(-1) dry soil d(-1)) across the floodplain topsoil and DNRA capacity was an order of magnitude lower (0.01-0.71 μmol N g(-1) d(-1)). Land management practice had a significant effect on denitrification but no significant effects were apparent for DNRA. In this nitrogen-rich landscape, spatial heterogeneity in denitrification was explained by differences in lability and the magnitude of organic carbon associated with different management practices (mowing and grazing). The lability of organic carbon was significantly higher in grazing grassland in comparison to other ungrazed areas of the floodplain, and consequently denitrification capacity was also highest in this area. Our results indicate that bacteria capable of DNRA do survive in frequently flooded riparian zones, and to a limited extent, compete with denitrification for nitrate, acting to retain and recycle nitrogen in the floodplain. Exponential declines in both denitrification and DNRA capacity with depth in the floodplain soils of a hay meadow and buffer zone were controlled primarily by the organic carbon content of the soils. Furthermore, grazing could be employed in re-connected, temperate floodplains to enhance the potential for nitrate removal from floodwaters via denitrification.

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

Methane (CH(4)) and carbon dioxide (CO(2)) are the dominant gaseous end products of the remineralization of organic carbon and also the two largest contributors to the anthropogenic greenhouse effect. We investigated whether warming altered the balance of CH(4) efflux relative to gross primary production (GPP) and ecosystem respiration (ER) in a freshwater mesocosm experiment. Whole ecosystem CH(4) efflux was strongly related to temperature with an apparent activation energy of 0.85 eV. Furthermore, CH(4) efflux increased faster than ER or GPP with temperature, with all three processes having sequentially lower activation energies. Warming of 4 degrees C increased the fraction of GPP effluxing as CH(4) by 20% and the fraction of ER as CH(4) by 9%, in line with the offset in their respective activation energies. Because CH(4) is 21 times more potent as a greenhouse gas, relative to CO(2), these results suggest freshwater ecosystems could drive a previously unknown positive feedback between warming and the carbon cycle.