pinecone/core-2020-05-10-deduplication huggingface dataset:
El Nino southern oscillation and seasonal drought drive riparian input dynamics in a Mediterranean stream

Inland waters substantially contribute to global carbon fluxes, and within them, low-order forested streams are important processors of allochthonous organic matter (OM) inputs. Leaf litter quantity and quality are expected to change in response to global change (e.g., climate change, land use change) but few long-term studies exist to better understand these shifts. The goal of this study was to assess the quantity and quality of OM sources to determine which global and local environmental factors control the dynamics of OM at the reach scale. The study was performed on a Mediterranean stream edged by a deciduous riparian forest over a 10-yr-time period. Riparian inputs, benthic and transported OM, and its carbon and nitrogen content were determined. The quantity of riparian inputs (912 +/- 56 g dry mass m(-2) yr(-1)) was comparable to temperate regions with deciduous riparian forests, but the Mediterranean climate determined the different dynamics of these inputs. El Nino Southern Oscillation was strongly related to the interannual variability in riparian inputs through changes in precipitation. The annual amount of inputs depended on previous cumulated nonflow periods, with successive nonflow periods causing a progressive decrease in riparian inputs. The distribution of inputs throughout the year followed either a unimodal or bimodal pattern according to the absence or presence of a nonflow period in summer. In addition, drought caused lower quality (higher carbon : nitrogen molar ratio) riparian inputs. Changes in the quantity and quality of OM were explained by both present and past local and global factors
Cross-shelf transport, oxygen depletion, and nitrate release within a forming mesoscale eddy in the eastern Indian Ocean

International audienceMesoscale eddies may drive a significant component of cross-shelf transport important in the ecology of shelf ecosystems and adjacent boundary currents. The Leeuwin Current in the eastern Indian Ocean becomes unstable in the austral autumn triggering the formation of eddies. We hypothesized that eddy formation represented the major driver of cross-shelf transport during the autumn. Acoustic Doppler Current Profiler profiles confirmed periodic offshore movement of 2 Sv of shelf waters into the forming eddy from the shelf, carrying a load of organic particles (>0.06 mm). The gap between inflow and outflow then closed, such that the eddy became isolated from further direct input of shelf waters. Drifter tracks supported an anticyclonic surface flow peaking at the eddy perimeter and decreasing in velocity at the eddy center. Oxygen and nutrient profiles suggested rapid remineralization of nitrate mid-depth in the isolated water mass as it rotated, with a total drawdown of oxygen of 3.6 mol m 22 to 350 m. Depletion of oxygen, and release of nitrate, occurred on the timescale of 1 week. We suggest that N supply and N turnover are rapid in this system, such that nitrate is acting primarily as a regenerated nutrient rather than as a source of new nitrogen. We hypothesize that sources of eddy particulate C and N could include particles sourced from coastal primary producers within 500 km such as macrophytes and sea-grasses known to produce copious detritus, which is prone to resuspension and offshore transport
Temporal dynamics of Prochlorococcus cells with the potential for nitrate assimilation in the subtropical Atlantic and Pacific oceans

Utilization of nitrate as a nitrogen source is broadly conserved among marine phytoplankton, yet many strains of Prochlorococcus lack this trait. Among cultured strains, nitrate assimilation has only been observed within two clades of Prochlorococcus: the high-light adapted HLII clade and the low-light adapted LLI clade. To better understand the frequency and dynamics of nitrate assimilation potential among wild Prochlorococcus, we measured seasonal changes in the abundance of cells containing the nitrate reductase gene (narB) in the subtropical North Atlantic and North Pacific oceans. At the Atlantic station, the proportion of HLII cells containing narB varied with season, with the highest frequency observed in stratified waters during the late summer, when inorganic nitrogen concentrations were lowest. The Pacific station, with more persistent stratification and lower N : P ratios, supported a perennially stable subpopulation of HLII cells containing narB. Approximately 20–50% of HLII cells possessed narB under stratified conditions at both sites. Since HLII cells dominate the total Prochlorococcus population in both ecosystems, nitrate potentially supports a significant fraction of the Prochlorococcus biomass in these waters. The abundance of LLI cells containing narB was positively correlated with nitrite concentrations at the Atlantic station. These data suggest that Prochlorococcus may contribute to the formation of primary nitrite maxima through incomplete nitrate reduction and highlight the potential for interactions between Prochlorococcus and sympatric nitrifying microorganisms. Further examination of these relationships will help clarify the selection pressures shaping nitrate utilization potential in low-light and high-light adapted Prochlorococcus.Gordon and Betty Moore Foundation (Grant GBMF495)National Science Foundation (U.S.) (OCE-1153588)National Science Foundation (U.S.) (DBI-0424599
Nonlinear effects of body size and optical attenuation on Diel Vertical Migration by zooplankton

International audienceWe adopt a trait-based approach to explain Diel Vertical Migration (DVM) across a diverse assemblage of planktonic copepods, utilizing body size as a master trait. We find a reproducible pattern of body size-dependence of day and night depths occupied, and of DVM. Both the smallest surface-dwelling and the largest deeper-dwelling copepods refrain from migrations, while intermediate-sized individuals show pronounced DVM. This pattern apparently arises as a consequence of size-dependent predation risk. In the size classes of migratory copepods the amplitude of DVM is further modulated by optical attenuation in the ocean water column because increased turbidity decreases encounter rates with visually hunting predators. Long-term changes in the ocean optical environment are expected to alter the vertical distributions of many copepods and thus to affect predator-prey encounters as well as oceanic carbon export
Patterns and drivers of carbohydrate budgets in ice algal assemblages from first year Arctic sea ice

© 2016 Association for the Sciences of Limnology and Oceanography.. Ongoing changes in sea ice distribution will have major implications for the ecology of the Arctic Ocean. First year ice (FYI) supports abundant ice-algae communities that produce dissolved and particulate carbohydrates, including extracellular polymeric substances (EPS), which are significant carbon sources, influence ice formation and microbial survival within sea ice, and water column carbon cycling following ice melt. Key drivers of the distribution and composition of these carbohydrates are poorly characterised. Carbohydrates and chlorophyll a concentrations were linearly related in springtime bottom FYI at 36 sites in the Canadian Archipelago region, with high levels of spatial heterogeneity. Nanoeukaryote cell density and phosphate concentration were strong drivers of total and dissolved carbohydrate and uronic acid concentrations. Particulate carbohydrates were strongly related to total bacterial abundance. Dissolved carbohydrates contributed 77% of total carbohydrate: the most abundant (51%) size fraction being dissolved carbohydrates<8 kDa in size, with dissolved EPS contributing 7% to total carbohydrate. Carbohydrate fractions differed in monosaccharide profiles; dissolved components being glucose rich; particulate EPS containing more mannose, xylose, fucose and arabinose. These profiles corresponded to those of cultured sea-ice diatoms. Microbial abundance, silicate, nitrate and phosphate concentration and ice thickness were important environmental drivers, with thicker ice containing relatively more particulate EPS, with thinner ice containing high amounts of glucose-rich smaller-sized carbohydrate moieties. Changes in ice characteristics will alter the relative balance of labile and refractory carbohydrates generated within bottom ice layers, with implications for food webs and carbon turnover in the warming Arctic Ocean
The role of particle associated microbes in remineralisation of faecal pellets in the upper mesopelagic of the Scotia Sea, Antarctica

Fecal pellets (FP) are a key component of the biological carbon pump, as they can, under some circumstances, efficiently transfer carbon to depth. Like other forms of particulate organic carbon (POC), they can be remineralized in the ocean interior (particularly in the upper 200 m), or alternatively they can be preserved in the sediments. The controls on the attenuation of FP flux with depth are not fully understood, in particular, the relative contributions of zooplankton fragmentation and microbial/zooplankton respiration to FP loss. Collection of sinking particles using Marine Snow Catchers at three ecologically contrasting sites in the Scotia Sea, Antarctica, revealed large differences in POC flux composition (5–96% FP) and flux attenuation despite similar temperatures. To determine the importance of microbial respiration on FP loss in the upper mesopelagic, we made the first ever measurements of small scale oxygen gradients through the boundary layer at the interface of krill FP collected from the Scotia Sea. Estimated carbon-specific respiration rates of microbes within FP (0.010–0.065 d−1) were too low to account for the observed large decreases in FP flux over the upper 200 m. Therefore, the observed rapid declines in downward FP flux in the upper mesopelagic are more likely to be caused by zooplankton, through coprophagy, coprorhexy, and coprochaly. Microbial respiration is likely to be more important in regions of higher temperatures, and at times of the year, or in depths of the ocean, where zooplankton abundances are low and therefore grazing and fragmentation processes are reduced
Coupled nitrification-denitrification leads to extensive N loss in subtidal permeable sediments

We investigated microbial pathways of nitrogen transformation in highly permeable sediments from the German Bight (South-East North Sea) by incubating sediment cores percolated with 15N-labeled substrates under near in situ conditions. In incubations with added math formula, production of math formula occurred while the sediment was oxic, indicating ammonia oxidation. Similarly, math formula production during math formula incubations indicated nitrite oxidation. Taken together these findings provide direct evidence of high nitrification rates within German Bight sands. The production of 15N-N2 on addition of math formula revealed high denitrification rates within the sediment under oxic and anoxic conditions. Denitrification rates were strongly and positively correlated with oxygen consumption rates, suggesting that denitrification is controlled by organic matter availability. Nitrification and denitrification rates were of the same magnitude and the rapid production of 15N-N2 in incubations with added math formula confirmed close coupling of the two processes. Areal rates of N-transformation were estimated taking advective transport of substrates into account and integrating volumetric rates over modeled oxygen and nitrate penetration depths, these ranged between 22 μmol N m−2 h−1 and 94 μmol N m−2 h−1. Furthermore, results from the 15N-labeling experiments show that these subtidal permeable sediments are, in sharp contrast to common belief, a substantial source of N2O. Our combined results show that nitrification fuels denitrification by providing an additional source of nitrate, and as such masks true N-losses from these highly eutrophic sediments. Given the widespread occurrence of anthropogenically influenced permeable sediments, coupled benthic nitrification–denitrification might have an important but so far neglected role in N-loss from shelf sediments
Drivers of fluorescent dissolved organic matter in the global epipelagic ocean

Catalá, Teresa S. ... et. al.-- 19 pages, 7 figures, 1 table, supporting information https://dx.doi.org/10.1002/lno.10281Fluorescent dissolved organic matter (FDOM) in open surface waters (< 200 m) of the Atlantic, Pacific, and Indian oceans was analysed by excitation-emission matrix (EEM) spectroscopy and parallel factor analysis (PARAFAC). A four-component PARAFAC model was fit to the EEMs, which included two humic- (C1 and C2) and two amino acid-like (C3 and C4) components previously identified in ocean waters. Generalized-additive models (GAMs) were used to explore the environmental factors that drive the global distribution of these PARAFAC components. The explained variance for the humic-like components was substantially larger (> 70%) than for the amino acid-like components (< 35%). The environmental variables exhibiting the largest effect on the global distribution of C1 and C2 were apparent oxygen utilisation followed by chlorophyll a. Positive non-linear relationships between both predictor variables and the two humic-like PARAFAC components suggest that their distribution are biologically controlled. Compared with the dark ocean (> 200 m), the relationships of C1 and C2 with AOU indicate a higher C1/AOU and C2/AOU ratios of the humic-like substances in the dark ocean than in the surface ocean where a net effect of photobleaching is also detected. C3 (tryptophan-like) and C4 (tyrosine-like) variability was mostly dictated by salinity (S), by means of positive non-linear relationships, suggesting a primary physical control of their distributions at the global surface ocean scale that could be related to the changing evaporation-precipitation regime. Remarkably, bacterial biomass (BB) only contributed to explain a minor part of the variability of C1 and C4T.S.C acknowledges funding through a predoctoral fellowship (reference AP2009-2138) from the Ministerio de Educación, Cultura y Deporte. [...] J. Otero was supported by “Junta para la Ampliación de Estudios” Fellowship (JAE-Doc program 2011) from the CSIC and ESF. M. Nieto-Cid was funded by the EU FP/-IOF project FeBOL-220172 and the CSIC Program “Junta para la Ampliación de Estudios” co-financed by the ESF. B. Horstkotte was supported by JAE 2010 Postdoctoral fellowship from the CSIC. This study was financed by the Malaspina 2010 circumnavigation expedition (grant number CSD2008–00077)Peer Reviewe
Reply to comment: Prey perception in feeding-current feeding copepods

3 pages, 1 figure, supporting information https://dx.doi.org/10.1002/lno.10293We reply to the comments of Paffenhöfer and Jiang (2016) who argues that remote chemical prey perception is necessary for feeding-current feeding copepods to fulfill their nutritional requirements in a dilute ocean, that remote chemical prey detection may only be observed at very low prey concentrations, and that chemical prey perception is feasible if prey cells release dissolved organic material in short-lasting but intense bursts. We demonstrate that mechanoreception at a very short range is sufficient to sustain a living, even in a dilute ocean. Further, if chemoreception requires that prey cells have short intense leakage burst, only a very small fraction of prey cells would be available to the copepod at any instance in time and, thus would be inefficient at low prey concentration. Finally, we report a few new observations of prey capture in two species of copepods, Temora longicornis and Centropages hamatus, offered a 45-μm sized dinoflagellate at very low concentration. The observed short prey detection distances, up to a few prey cell radii, are consistent with mechanoreception and we argue briefly that near-field mechanoreception is the most likely and common prey perception mechanism in calanoid copepodsPeer Reviewe
Chemoautotrophy and anoxygenic photosynthesis within the water column of a large meromictic tropical lake (Lake Kivu, East Africa)

We quantified chemoautotrophic and anoxygenic photosynthetic microbial production in the water column of Lake Kivu, a permanently stratified tropical lake situated amidst volcanic activity, and aimed to identify the microorganisms involved in these processes through the analysis of their phospholipid fatty acid (PLFA) content and stable isotope (13C) labelling of PLFA in a set of incubation experiments. Data demonstrate the existence of a biogeochemically active chemoautotrophic bacterial community in the redoxcline of Lake Kivu (50–70 m). PLFA data indicate that the bacterial communities are structured vertically in the water column, with a large dissimilarity between the oxic and anoxic waters. Maximum volumetric dark CO2 fixation rates measured in Lake Kivu were in the same range as values reported from H2S-rich marine redoxclines, such as the Black and Baltic Seas, and the Cariaco Basin. Similarly, maximal chemoautotrophic activities in Lake Kivu were observed in sulfidic waters, just below the oxycline. Anoxygenic photosynthetic production was never observed in the main basin of Lake Kivu. However, anoxygenic phototrophs largely dominated CO2 fixation in the illuminated redoxcline of Kabuno Bay, a shallower ferruginous sub-basin. Overall, this study supports the idea that chemoautotrophs and/or anoxygenic photoautotrophs might play an important role in the flow of carbon and energy in permanently stratified tropical ecosystems. In Lake Kivu, these processes significantly contribute to organic matter biosynthesis and exert an indirect control on oxygenic photoautotrophs by shortcircuiting the vertical transport of nutrients to the illuminated and oxygenated surface waters.Peer reviewe
Feedback between sediment and light for seagrass: where is it important?

A feedback between seagrass presence, suspended sediment and benthic light can induce bistability between two ecosystem states: one where the presence of seagrass reduces suspended sediment concentrations to increase benthic light availability thereby favoring growth, and another where seagrass absence increases turbidity thereby reducing growth. This literature review identifies (1) how the environmental and seagrass meadow characteristics influence the strength and direction (stabilizing or destabilizing) of the seagrass-sediment-light feedback, and (2) how this feedback has been incorporated in ecosystem models proposed to support environmental decision making. Large, dense seagrass meadows in shallow subtidal, non-eutrophic systems, growing in sediments of mixed grain size and subject to higher velocity flows, have the greatest potential to generate bistability via the seagrass-sediment-light feedback. Conversely, seagrass meadows of low density, area and height can enhance turbulent flows that interact with the seabed, causing water clarity to decline. Using a published field experiment as a case study, we show that the seagrass-sediment-light feedback can induce bistability only if the suspended sediment has sufficient light attenuation properties. The seagrass-sediment-light feedback has been considered in very few ecosystem models. These models have the potential to identify areas where bistability occurs, which is information that can assist in spatial prioritization of conservation and restoration efforts. In areas where seagrass is present and bistability is predicted, recovery may be difficult once this seagrass is lost. Conversely, bare areas where seagrass presence is predicted (without bistability) may be better targets for seagrass restoration than bare areas where bistability is predicted
Carbon cycling in the deep eastern North Pacific benthic food web: Investigating the effect of organic carbon input

The deep ocean benthic environment plays a role in long-term carbon sequestration. Understanding carbon cycling in the deep ocean floor is critical to evaluate the impact of changing climate on the oceanic systems. Linear inverse modeling was used to quantify carbon transfer between compartments in the benthic food web at a long time-series study site in the abyssal northeastern Pacific (Station M). Linear inverse food web models were constructed for three separate years in the time-series when particulate organic carbon (POC) flux was relatively high (1990: 0.63 mean mmol C m?2 d?1), intermediate (1995: 0.24) and low (1996: 0.12). Carbon cycling in all years was dominated by the flows involved in the microbial loop; dissolved organic carbon uptake by microbes (0.80–0.95 mean mmol C m?2 d?1), microbial respiration (0.52–0.61), microbial biomass dissolution (0.09–0.18) and the dissolution of refractory detritus (0.46–0.65). Moreover, the magnitude of carbon flows involved in the microbial loop changed in relation to POC input, with a decline in contribution during the high POC influxes, such as those recently experienced at Station M. Results indicate that during high POC episodic pulses the role of faunal mediated carbon cycling would increase. Semi-labile detritus dominates benthic faunal diets and the role of labile detritus declined with increased total POC input. Linear inverse modeling represents an effective framework to analyze high-resolution time-series data and demonstrate the impact of climate change on the deep ocean carbon cycle in a coastal upwelling system.\ud
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H+-driven increase in CO2 uptake and decrease in HCO3- uptake explain coccolithophores' acclimation responses to ocean acidification

Recent ocean acidification (OA) studies revealed that seawater [H+] rather than [CO2] or [HCO3-] regulate short-term responses in carbon fluxes of Emiliania huxleyi. Here, we investigated whether acclimation to altered carbonate chemistry modulates this regulation pattern and how the carbon supply for calcification is affected by carbonate chemistry. We acclimated E. huxleyi to present-day (ambient [CO2], [HCO3-], and pH) and OA conditions (high [CO2], ambient [HCO3-], low pH). To differentiate between the CO2 and pH/H+ effects, we also acclimated cells to carbonation (high [CO2] and [HCO3-], ambient pH) and acidification (ambient [CO2], low [HCO3-], and pH). Under these conditions, growth, production of particulate inorganic and organic carbon, as well as carbon and oxygen fluxes were measured. Under carbonation, photosynthesis and calcification were stimulated due to additional inline image uptake, whereas growth was unaffected. Such stimulatory effects are not apparent after short-term carbonation, indicating that cells adjusted their carbon acquisition during acclimation. Being driven by H+, these regulations can, however, not explain typical OA effects. Under acidification and OA, photosynthesis stayed constant, whereas calcification and growth decreased. Similar to the short-term responses toward high [H+], CO2 uptake significantly increased, but inline image uptake decreased. This antagonistic regulation in CO2 and inline image uptake can explain why photosynthesis, being able to use CO2 and inline image, often benefits from OA, whereas calcification, being mostly dependent on inline image, often decreases. We identified H+ as prime driver of coccolithophores' acclimation responses toward OA. Acidified conditions seem to put metabolic burdens on the cells that result in decreased growth