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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 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

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.

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.

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.

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.

International audience; Phytoplankton are key components of aquatic ecosystems, fixing CO2 from the atmosphere through photosynthesis and supporting secondary production, yet relatively little is known about how future global warming might alter their biodiversity and associated ecosystem functioning. Here, we explore how the structure, function, and biodiversity of a planktonic metacommunity was altered after five years of experimental warming. Our outdoor mesocosm experiment was open to natural dispersal from the regional species pool, allowing us to explore the effects of experimental warming in the context of metacommunity dynamics. Warming of 4°C led to a 67% increase in the species richness of the phytoplankton, more evenly-distributed abundance, and higher rates of gross primary productivity. Warming elevated productivity indirectly, by increasing the biodiversity and biomass of the local phytoplankton communities. Warming also systematically shifted the taxonomic and functional trait composition of the phytoplankton, favoring large, colonial, inedible phytoplankton taxa, suggesting stronger top-down control, mediated by zooplankton grazing played an important role. Overall, our findings suggest that temperature can modulate species coexistence, and through such mechanisms, global warming could, in some cases, increase the species richness and productivity of phytoplankton communities.

9 pages, 4 figures, 1 table, electronic supplementary material is available at http://rspb.royalsocietypublishing.org/content/279/1740/3011/suppl/DC1, Global warming can affect all levels of biological complexity, though we currently understand least about its potential impact on communities and ecosystems. At the ecosystem level, warming has the capacity to alter the structure of communities and the rates of key ecosystem processes they mediate. Here we assessed the effects of a 4°C rise in temperature on the size structure and taxonomic composition of benthic communities in aquatic mesocosms, and the rates of detrital decomposition they mediated. Warming had no effect on biodiversity, but altered community size structure in two ways. In spring, warmer systems exhibited steeper size spectra driven by declines in total community biomass and the proportion of large organisms. By contrast, in autumn, warmer systems had shallower size spectra driven by elevated total community biomass and a greater proportion of large organisms. Community-level shifts were mirrored by changes in decomposition rates. Temperature-corrected microbial and macrofaunal decomposition rates reflected the shifts in community structure and were strongly correlated with biomass across mesocosms. Our study demonstrates that the 4°C rise in temperature expected by the end of the century has the potential to alter the structure and functioning of aquatic ecosystems profoundly, as well as the intimate linkages between these levels of ecological organization. © 2012 The Royal Society, M.D. was supported by the Aquatic Ecology by Research MSc programme within SBCS, Queen Mary University of London hosted by J.G. G.Y.-D., M.T., D.M.P. and G.W. acknowledge the financial support of NERC (grant nos. NE/F004753/1 and NE/D013305/1), and J.M.M. the financial support of a Ramon y Cajal Fellowship (RYC-2008-03664) and Generalitat de Catalunya grant (2009SGR142). The experiment was made possible thanks to the support of the NERC Fellowship Scheme (NE/C002105/1) awarded to J.M.M., and the hosting of the facilities by the Freshwater Biological Association

The production of N 2 gas via anammox was investigated in sediment slurries at in situ NO 2 − concentrations in the presence and absence of NO 3 − . With single enrichment above 10 μM 14 NO 2 − or 14 NO 3 − and 15 NH 4 + , anammox activity was always linear ( P < 0.05), in agreement with previous findings. In contrast, anammox exhibited a range of activity below 10 μM NO 2 − or NO 3 − , including an elevated response at lower concentrations. With 100 μM NO 3 − , no significant transient accumulation of NO 2 − could be measured, and the starting concentration of NO 2 − could therefore be regulated. With dual enrichment (1 to 20 μM NO 2 − plus 100 μM NO 3 − ), there was a pronounced nonlinear response in anammox activity. Maximal activity occurred between 2 and 5 μM NO 2 − , but the amplitude of this peak varied across the study (November 2003 to June 2004). Anammox accounted for as much as 82% of the NO 2 − added at 1 μM in November 2003 but only for 15% in May 2004 and for 26 and 5% of the NO 2 − added at 5 μM for these two months, respectively. Decreasing the concentration of NO 3 − but holding NO 2 − at 5 μM decreased the significance of anammox as a sink for NO 2 − . The behavior of anammox was explored by use of a simple anammox-denitrification model, and the concept of a biphasic system for anammox in estuarine sediments is proposed. Overall, anammox is likely to be regulated by the availability of NO 3 − and NO 2 − and the relative size or activity of the anammox population.

Until recently, denitrification was thought to be the only significant pathway for N 2 formation and, in turn, the removal of nitrogen in aquatic sediments. The discovery of anaerobic ammonium oxidation in the laboratory suggested that alternative metabolisms might be present in the environment. By using a combination of 15 N-labeled NH 4 + , NO 3 − , and NO 2 − (and 14 N analogues), production of 29 N 2 and 30 N 2 was measured in anaerobic sediment slurries from six sites along the Thames estuary. The production of 29 N 2 in the presence of 15 NH 4 + and either 14 NO 3 − or 14 NO 2 − confirmed the presence of anaerobic ammonium oxidation, with the stoichiometry of the reaction indicating that the oxidation was coupled to the reduction of NO 2 − . Anaerobic ammonium oxidation proceeded at equal rates via either the direct reduction of NO 2 − or indirect reduction, following the initial reduction of NO 3 − . Whether NO 2 − was directly present at 800 μM or it accumulated at 3 to 20 μM (from the reduction of NO 3 − ), the rate of 29 N 2 formation was not affected, which suggested that anaerobic ammonium oxidation was saturated at low concentrations of NO 2 − . We observed a shift in the significance of anaerobic ammonium oxidation to N 2 formation relative to denitrification, from 8% near the head of the estuary to less than 1% at the coast. The relative importance of anaerobic ammonium oxidation was positively correlated ( P < 0.05) with sediment organic content. This report of anaerobic ammonium oxidation in organically enriched estuarine sediments, though in contrast to a recent report on continental shelf sediments, confirms the presence of this novel metabolism in another aquatic sediment system.

We report the complex spatial and temporal dynamics of hyporheic exchange flows (HEFs) and nitrogen exchange in an upwelling reach of a 200 m groundwater‐fed river. We show how research combining hydrological measurement, geophysics and isotopes, with nutrient speciation techniques provides insight on nitrogen pathways and transformations that could not have been captured otherwise, including a zone of vertical preferential discharge of nitrate from deeper groundwater, and a zone of rapid denitrification linking the floodplain with the riverbed. Nitrate attenuation in the reach is dominated by denitrification but is spatially highly variable. This variability is driven by groundwater flow pathways and landscape setting, which influences hyporheic flow, residence time and nitrate removal. We observed the spatial connectivity of the river to the riparian zone is important because zones of horizontal preferential discharge supply organic matter from the floodplain and create anoxic riverbed conditions with overlapping zones of nitrification potential and denitrification activity that peaked 10‐20 cm below the riverbed. Our data show that temporal variability in water pathways in the reach is driven by changes in stage of the order of tens of centimetres and by strength of water flux, which may influence the depth of delivery of dissolved organic carbon. Temporal variability is sensitive to changes to river flows under UK climate projections that anticipate a 14‐15% increase in regional median winter rainfall and a 14‐19% reduction in summer rainfall. Superimposed on seasonal projections is more intensive storm activity that will likely lead to a more dynamic and inherently complex (hydrologically and biogeochemically) hyporheic zone. We recorded direct evidence of suppression of upwelling groundwater (flow reversal) during rainfall events. Such flow reversal may fuel riverbed sediments whereby delivery of organic carbon to depth, and higher denitrification rates in HEFs might act in concert to make nitrate removal in the riverbed more efficient.