Direct biological fixation provides a freshwater sink for N2O.

Nitrous oxide (N2O) is a potent climate gas, with its strong warming potential and ozone-depleting properties both focusing research on N2O sources. Although a sink for N2O through biological fixation has been observed in the Pacific, the regulation of N2O-fixation compared to canonical N2-fixation is unknown. Here we show that both N2O and N2 can be fixed by freshwater communities but with distinct seasonalities and temperature dependencies. N2O fixation appears less sensitive to temperature than N2 fixation, driving a strong sink for N2O in colder months. Moreover, by quantifying both N2O and N2 fixation we show that, rather than N2O being first reduced to N2 through denitrification, N2O fixation is direct and could explain the widely reported N2O sinks in natural waters. Analysis of the nitrogenase (nifH) community suggests that while only a subset is potentially capable of fixing N2O they maintain a strong, freshwater sink for N2O that could be eroded by warming.

Separating natural from human enhanced methane emissions in headwater streams.

Headwater streams are natural sources of methane but are suffering severe anthropogenic disturbance, particularly land use change and climate warming. The widespread intensification of agriculture since the 1940s has increased the export of fine sediments from land to streams, but systematic assessment of their effects on stream methane is lacking. Here we show that excess fine sediment delivery is widespread in UK streams (n = 236) and, set against a pre-1940s baseline, has markedly increased streambed organic matter (23 to 100 g m-2), amplified streambed methane production and ultimately tripled methane emissions (0.2 to 0.7 mmol CH4 m-2 d-1, n = 29). While streambed methane production responds strongly to organic matter, we estimate the effect of the approximate 0.7 °C of warming since the 1940s to be comparatively modest. By separating natural from human enhanced methane emissions we highlight how catchment management targeting the delivery of excess fine sediment could mitigate stream methane emissions by some 70%.

Hydrological properties predict the composition of microbial communities cycling methane and nitrogen in rivers.

Sediment microbial communities drive the biogeochemical cycles that make rivers globally important sources and sinks of carbon (C) and nitrogen (N). The structure of these communities is strongly determined by the local physico-chemical environment. However, we currently lack an understanding of the factors that determine microbial community structures at the catchment scale. Here, we show that the contribution of groundwater to total river flow (quantified as base flow index; BFI) predicts the structure and diversity of the different microbial functional groups that cycle N and C across nine UK rivers, spanning a geological BFI gradient from 0.23 (clay sediment) to 0.95 (chalk gravel sediment). Furthermore, the GC-content (percentage of guanine-cytosine bases in a DNA sequence) and codon-usage bias of ammonia monooxygenase DNA sequences, and the hydrophobicity and net-charge of the corresponding amino acid sequences, were all strongly correlated with BFI, likely reflecting physiological adaptations to different riverbed sediment structure along the BFI gradient. Our results offer an opportunity to overcome the "paradox of scales" that has seen microbial ecologists focus on small- rather than large-scale environmental variables, enabling us to scale-up our understanding of microbial biogeochemistry to the catchment and beyond.

Diversity of dimethylsulfide-degrading methanogens and sulfate-reducing bacteria in anoxic sediments along the Medway Estuary, UK.

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.

Warming impairs trophic transfer efficiency in a long-term field experiment.

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.

Coupled nitrification and N2 gas production as a cryptic process in oxic riverbeds.

The coupling between nitrification and N2 gas production to recycle ammonia back to the atmosphere is a key step in the nitrogen cycle that has been researched widely. An assumption for such research is that the products of nitrification (nitrite or nitrate) mix freely in the environment before reduction to N2 gas. Here we show, in oxic riverbeds, that the pattern of N2 gas production from ammonia deviates by ~3- to 16-fold from that predicted for denitrification or anammox involving nitrite or nitrate as free porewater intermediates. Rather, the patterns match that for a coupling through a cryptic pool, isolated from the porewater. A cryptic pool challenges our understanding of a key step in the nitrogen cycle and masks our ability to distinguish between sources of N2 gas that 20 years' research has sought to identify. Our reasoning suggests a new pathway or a new type of coupling between known pathways in the nitrogen cycle.

Interactions between plant genome size, nutrients and herbivory by rabbits, molluscs and insects on a temperate grassland.

Angiosperm genome sizes (GS) vary ca 2400-fold. Recent research has shown that GS influences plant abundance, and plant competition. There are also tantalizing reports that herbivores may select plants as food dependent on their GS. To test the hypothesis that GS plays a role in shaping plant communities under herbivore pressure, we exploit a grassland experiment that has experimentally excluded herbivores and applied nutrient over 8 years. Using phylogenetically informed statistical models and path analyses, we show that under rabbit grazing, plant species with small GS generated the most biomass. By contrast, on mollusc and insect-grazed plots, it was the plant species with larger GS that increased in biomass. GS was also shown to influence plant community properties (e.g. competitive strategy, total biomass) although the impact varied between different herbivore guilds (i.e. rabbits versus invertebrates) and nutrient inputs. Overall, we demonstrate that GS plays a role in influencing plant-herbivore interactions, and suggest potential reasons for this response, which include the impact of GS on a plant's response to different herbivore guilds, and on a plant's nutrient quality. The inclusion of GS in ecological models has the potential to expand our understanding of plant productivity and community ecology under nutrient and herbivore stress.

Spatial separation of anaerobic ammonium oxidation and nitrite-dependent anaerobic methane oxidation in permeable riverbeds.

Anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) play important roles in nitrogen and carbon cycling in fresh waters but we do not know how these two processes compete for their common electron acceptor, nitrite. Here, we investigated the spatial distribution of anammox and n-damo across a range of permeable riverbed sediments. Anammox activity and gene abundance were detected in both gravel and sandy riverbeds and showed a simple, common vertical distribution pattern, while the patterns in n-damo were more complex and n-damo activity was confined to the more reduced, sandy riverbeds. Anammox was most active in surficial sediment (0-2 cm), coincident with a peak in hzsA gene abundance and nitrite. In contrast, n-damo activity peaked deeper down (4-8 cm) in the sandy riverbeds, coincident with a peak in n-damo 16S rRNA gene abundance and higher methane concentration. Pore water nitrite, methane and oxygen were key factors influencing the distribution of these two processes in permeable riverbeds. Furthermore, both anammox- and n-damo- activity were positively correlated with denitrification activity, suggesting a role for denitrification in supplying both processes with nitrite. Our data reveal spatial separation between anammox and n-damo in permeable riverbed sediments that potentially avoids them competing for nitrite.

Extreme drought pushes stream invertebrate communities over functional thresholds.

Functional traits are increasingly being used to predict extinction risks and range shifts under long-term climate change scenarios, but have rarely been used to study vulnerability to extreme climatic events, such as supraseasonal droughts. In streams, drought intensification can cross thresholds of habitat loss, where marginal changes in environmental conditions trigger disproportionate biotic responses. However, these thresholds have been studied only from a structural perspective, and the existence of functional nonlinearity remains unknown. We explored trends in invertebrate community functional traits along a gradient of drought intensity, simulated over 18 months, using mesocosms analogous to lowland headwater streams. We modelled the responses of 16 traits based on a priori predictions of trait filtering by drought, and also examined the responses of trait profile groups (TPGs) identified via hierarchical cluster analysis. As responses to drought intensification were both linear and nonlinear, generalized additive models (GAMs) were chosen to model response curves, with the slopes of fitted splines used to detect functional thresholds during drought. Drought triggered significant responses in 12 (75%) of the a priori-selected traits. Behavioural traits describing movement (dispersal, locomotion) and diet were sensitive to moderate-intensity drought, as channels fragmented into isolated pools. By comparison, morphological and physiological traits showed little response until surface water was lost, at which point we observed sudden shifts in body size, respiration mode and thermal tolerance. Responses varied widely among TPGs, ranging from population collapses of non-aerial dispersers as channels fragmented to irruptions of small, eurythermic dietary generalists upon extreme dewatering. Our study demonstrates for the first time that relatively small changes in drought intensity can trigger disproportionately large functional shifts in stream communities, suggesting that traits-based approaches could be particularly useful for diagnosing catastrophic ecological responses to global change.

Active pathways of anaerobic methane oxidation across contrasting riverbeds.

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.

Reach-scale river metabolism across contrasting sub-catchment geologies: Effect of light and hydrology.

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 Temperature Dependence of Phytoplankton Stoichiometry: Investigating the Roles of Species Sorting and Local Adaptation.

The elemental composition of phytoplankton (C:N:P stoichiometry) is a critical factor regulating nutrient cycling, primary production and energy transfer through planktonic food webs. Our understanding of the multiple direct and indirect mechanisms through which temperature controls phytoplankton stoichiometry is however incomplete, increasing uncertainty in the impacts of global warming on the biogeochemical functioning of aquatic ecosystems. Here, we use a decade-long warming experiment in outdoor freshwater ponds to investigate how temperature-driven turnover in species composition and shifts in stoichiometric traits within species through local thermal adaptation contribute to the effects of warming on seston stoichiometry. We found that experimental warming increased seston C:P and N:P ratios, while the C:N ratio was unaffected by warming. Temperature was also the dominant driver of seasonal variation in seston stoichiometry, correlating positively with both C:P and N:P ratios. The taxonomic composition of the phytoplankton community differed substantially between the warmed and ambient treatments indicating that warming resulted in differential sorting of species from the regional pool. Furthermore, taxonomic composition also changed markedly over the year within each of the warmed and ambient treatments, highlighting substantial temporal turnover in species. To investigate whether local adaptation also played an important role in shaping the effects of warming on seston stoichiometry, we isolated multiple strains of the cosmopolitan alga, Chlamydomonas reinhardtii from across the warmed and ambient mesocosms. We found that warmed isolates had higher C:P and N:P ratios, shifts that were comparable in direction and magnitude to the effects of warming on seston stoichiometry. Our results suggest that both species sorting and local adaptation are likely to play important roles in shaping the effects of warming on bulk phytoplankton stoichiometry and indicate that major shifts in aquatic biogeochemistry should be expected in a warmer world.

Adaptation of phytoplankton to a decade of experimental warming linked to increased photosynthesis.

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.

Origin and fate of methane in the Eastern Tropical North Pacific oxygen minimum zone.

Oxygen minimum zones (OMZs) contain the largest pools of oceanic methane but its origin and fate are poorly understood. High-resolution (<15 m) water column profiles revealed a 300 m thick layer of elevated methane (20-105 nM) in the anoxic core of the largest OMZ, the Eastern Tropical North Pacific. Sediment core incubations identified a clear benthic methane source where the OMZ meets the continental shelf, between 350 and 650 m, with the flux reflecting the concentration of methane in the overlying anoxic water. Further incubations characterised a methanogenic potential in the presence of both porewater sulphate and nitrate of up to 88 nmol g-1day-1 in the sediment surface layer. In these methane-producing sediments, the majority (85%) of methyl coenzyme M reductase alpha subunit (mcrA) gene sequences clustered with Methanosarcinaceae (⩾96% similarity to Methanococcoides sp.), a family capable of performing non-competitive methanogenesis. Incubations with 13C-CH4 showed potential for both aerobic and anaerobic methane oxidation in the waters within and above the OMZ. Both aerobic and anaerobic methane oxidation is corroborated by the presence of particulate methane monooxygenase (pmoA) gene sequences, related to type I methanotrophs and the lineage of Candidatus Methylomirabilis oxyfera, known to perform nitrite-dependent anaerobic methane oxidation (N-DAMO), respectively.

Nitrous oxide as a function of oxygen and archaeal gene abundance in the North Pacific.

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.

Modelling flow and inorganic nitrogen dynamics on the Hampshire Avon: Linking upstream processes to downstream water quality.

Managing diffuse pollution in catchments is a major issue for environmental managers planning to meet water quality standards and comply with the EU Water Framework Directive. A major source of diffuse pollution is from nitrogen, with high nitrate concentrations affecting water supplies and in-stream ecology. A dynamic, process based model of flow, nitrate and ammonium (INCA-N) has been applied to the Hampshire Avon as part of the NERC Macronutrient Cycles Programme to link upstream and downstream measurements of water chemistry. The model has been calibrated and validated against Environment Agency discharge and solute chemistry data, as well as a data set collected from a river site immediately upstream of the estuary tidal limit. Upstream measurements of denitrification at six sites have been used to evaluate nitrate removal rates in vegetated and non-vegetated conditions. Results show that sediments underlying vegetation were associated with significantly higher rates of nitrate removal than un-vegetated sediments (with an average increase of 245%). These data have been used to scale up rates of nitrate loss to the whole catchment scale and have been implemented via the model. The effects of streambed geology and macrophyte cover on catchment-scale nitrogen dynamics are explored and nutrient fluxes entering the estuary are evaluated. The model is used to test a strategy for nitrogen reduction assessed using a nitrate vulnerable zone (NVZ) methodology. It suggests that nitrate and ammonium concentrations could be reduced by 10% in 10years and much lower nitrogen level can be achieved but only over a long time period.

Genome size and ploidy influence angiosperm species' biomass under nitrogen and phosphorus limitation.

Angiosperm genome sizes (GS) range c. 2400-fold, and as nucleic acids are amongst the most phosphorus- (P) and nitrogen (N)-demanding cellular biomolecules, we test the hypothesis that a key influence on plant biomass and species composition is the interaction between N and P availability and plant GS. We analysed the impact of different nutrient regimes on above-ground biomass of angiosperm species with different GS, ploidy level and Grime's C-S-R (competitive, stress-tolerant, ruderal) plant strategies growing at the Park Grass Experiment (Rothamsted, UK), established in 1856. The biomass-weighted mean GS of species growing on plots with the addition of both N and P fertilizer were significantly higher than that of plants growing on control plots and plots with either N or P. The plants on these N + P plots are dominated by polyploids with large GS and a competitive plant strategy. The results are consistent with our hypothesis that large genomes are costly to build and maintain under N and P limitation. Hence GS and ploidy are significant traits affecting biomass growth under different nutrient regimes, influencing plant community composition and ecosystem dynamics. We propose that GS is a critical factor needed in models that bridge the knowledge gap between biodiversity and ecosystem functioning.

Five Years of Experimental Warming Increases the Biodiversity and Productivity of Phytoplankton.

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.