pinecone/core-2020-05-10-deduplication huggingface dataset:
Co-existence of distinct Ostreococcus ecotypes at an oceanic front

Western boundary currents support high primary production and carbon export. Here, we performed a survey of photosynthetic picoeukaryotes in the North Pacific Ocean in four transects crossing the Kuroshio Front. Prasinophyte algae comprised 85% of 18S rRNA gene sequences for photosynthetic taxa in the <5 μm size fraction. The picoplanktonic (<2 μm) genera Micromonas and Ostreococcus comprised 30% and 51% of the total photosynthetic 18S rDNA sequences from five stations. Phylogenetic analysis showed that two Ostreococcus ecotypes, until now rarely found to co‐occur, were both present in the majority of samples. Ostreococcus ecotype OI reached 6,830 ± 343 gene copies mL−1, while Ostreococcus ecotype OII reached 50,190 ± 971 gene copies mL−1 based on qPCR analysis of the 18S rRNA gene. These values are higher than in studies of other oceanographic regions by a factor of 10 for OII. The data suggest that meso‐ and finer‐scale physical dynamics had a significant impact on the populations at the front, either by mingling ecotypes from different source regions at fine scales (∼10s km) or by stimulating their growth through vertical nutrient injections. We investigate this hypothesis with an idealized diffusion‐reaction model, and find that only a combination of mixing and positive net growth can explain the observed distributions and overlap of the two Ostreococcus ecotypes. Our field observations support larger‐scale numerical ocean simulations that predict enhanced biodiversity at western boundary current fronts, and suggest a strategy for systematically testing that hypothesis
Linked sediment and water-column methanotrophy at a man-made gas blowout in the North Sea: Implications for methane budgeting in seasonally stratified shallow seas

Large quantities of the greenhouse gas methane (CH4) are stored in the seafloor. The flux of CH4 from the sediments into the water column and finally to the atmosphere is mitigated by a series of microbial methanotrophic filter systems of unknown efficiency at highly active CH4-release sites in shallow marine settings. Here, we studied CH4-oxidation and the methanotrophic community at a high-CH4-flux site in the northern North Sea (well 22/4b), where CH4 is continuously released since a blowout in 1990. Vigorous bubble emanation from the seafloor and strongly elevated CH4 concentrations in the water column (up to 42 µM) indicated that a substantial fraction of CH4 bypassed the highly active (up to ∼2920 nmol cm−3 d−1) zone of anaerobic CH4-oxidation in sediments. In the water column, we measured rates of aerobic CH4-oxidation (up to 498 nM d−1) that were among the highest ever measured in a marine environment and, under stratified conditions, have the potential to remove a significant part of the uprising CH4 prior to evasion to the atmosphere. An unusual dominance of the water-column methanotrophs by Type II methane-oxidizing bacteria (MOB) is partially supported by recruitment of sedimentary MOB, which are entrained together with sediment particles in the CH4 bubble plume. Our study thus provides evidence that bubble emission can be an important vector for the transport of sediment-borne microbial inocula, aiding in the rapid colonization of the water column by methanotrophic communities and promoting their persistence close to highly active CH4 point sources
Dissolved methane in the Beaufort Sea and the Arctic Ocean, 1992-2009; sources and atmospheric flux

Methane concentration and isotopic composition was measured in ice-covered and ice-free waters of the Arctic Ocean during 11 surveys spanning the years of 1992–1995 and 2009. During ice-free periods, methane flux from the Beaufort shelf varies from 0.14 mg CH4 m−2 d−1 to 0.43 mg CH4 m−2 d−1. Maximum fluxes from localized areas of high methane concentration are up to 1.52 mg CH4 m−2 d−1. Seasonal buildup of methane under ice can produce short-term fluxes of methane from the Beaufort shelf that varies from 0.28 mg CH4 m−2 d−1 to 1.01 mg CH4 m−2 d−1. Scaled-up estimates of minimum methane flux from the Beaufort Sea and pan-Arctic shelf for both ice-free and ice-covered periods range from 0.02 Tg CH4 yr−1 and 0.30 Tg CH4 yr−1, respectively to maximum fluxes of 0.18 Tg CH4 yr−1 and 2.2 Tg CH4 yr−1, respectively. A methane flux of 0.36 Tg CH4 yr−1 from the deep Arctic Ocean was estimated using data from 1993 to 1994. The flux can be as much as 2.35 Tg CH4 yr−1 estimated from maximum methane concentrations and wind speeds of 12 m/s, representing only 0.42% of the annual atmospheric methane budget of ∼ 560 Tg CH4 yr−1. There were no significant changes in methane fluxes during the time period of this study. Microbial methane sources predominate with minor influxes from thermogenic methane offshore Prudhoe Bay and the Mackenzie River delta and may include methane from gas hydrate. Methane oxidation is locally important on the shelf and is a methane sink in the deep Arctic Ocean
The historical dependency of organic carbon burial efficiency

This is an Open Access Article. It is published by Wiley on behalf of the Association for the Sciences of Limnology and Oceanography under the Creative Commons Attribution 4.0 International Licence (CC BY). Full detals of this licence are available at: http://creativecommons.org/licenses/by/4.0Many studies have viewed lakes as quasi-static systems with regard to the rate of organic carbon (OC) burial, assuming that the dominant control on BE is sediment mineralization. However, in systems undergoing eutrophication or oligotrophication (i.e., altered nutrient loading), or climatic forcing, the changes in primary production will vary on both longer (> 10 yr) and shorter (seasonal) timescales, influencing the rate of OC accumulation and subsequent permanent burial. Here, we consider the extent to which permanent OC burial reflects changing production in a deep monomictic lake (Rostherne Mere, UK) that has been culturally eutrophied (present TP>200 μg L-1), but has undergone recent reductions in nutrient loading. We compare multi-year dynamics of OC fluxes using sediment traps to longer-term burial rates estimated from two 210Pb-dated sediment cores. The recent sediment record demonstrates that most of the autochthonous OC is preserved (∼95% of OC captured in the deep trap and 86% of the NEP in the contemporary system), contrary to widely held assumptions that this more labile, algal-dominated OC component is not well preserved in lake sediments. A revised method for calculating BE for lakes which have undergone changes in primary productivity in recent decades is developed, which reduces some of problems inherent in existing approaches using historical sediment records averaged over the last 25-150 yr. We suggest that an appreciation of lakes in all biomes as ecosystems responding dynamically to recent human impact and climate change (for example) can improve up-scaled regional and global estimates of lake OC burial
From polar night to midnight sun : diel vertical migration, metabolism and biogeochemical role of zooplankton in a high Arctic fjord (Kongsfjorden, Svalbard)

Zooplankton vertical migration enhances the efficiency of the ocean biological pump by translocating carbon (C) and nitrogen (N) below the mixed layer through respiration and excretion at depth. We measured C and N active transport due to diel vertical migration (DVM) in a Svalbard fjord at 79°N. Multifrequency analysis of backscatter data from an Acoustic Zooplankton Fish Profiler moored from January to September 2014, combined with plankton net data, showed that Thysanoessa spp. euphausiids made up > 90% of the diel migrant biomass. Classical synchronous DVM occurred before and after the phytoplankton bloom, leading to a mismatch with intensive primary production during the midnight sun. Zooplankton DVM resulted in C respiration of 0.9 g m−2 and ammonium excretion of 0.18 g N m−2 below 82 m depth between February and April, and 0.2 g C m−2 and 0.04 g N m−2 from 11 August to 9 September, representing > 25% and > 33% of sinking flux of particulate organic carbon and nitrogen, respectively. Such contribution of DVM active transport to the biological pump in this high-Arctic location is consistent with previous measurements in several equatorial to subarctic oceanic systems of the World Ocean. Climate warming is expected to result in tighter coupling between DVM and bloom periods, stronger stratification of the Barents Sea, and northward advection of boreal euphausiids. This may increase the role of DVM in the functioning of the biological pump on the Atlantic side of the Arctic Ocean, particularly where euphausiids are or will be prevalent in the zooplankton community
Differences in the carbon flows in the benthic food webs of abyssal hill and plain habitats

Inputs of detritus from the surface ocean are an important driver of community dynamics in the deep sea. The assessment of the flow of carbon through the benthic food web gives insight into how the community is sustained, and its resilience to fluctuations in food supply. We used a linear inverse model to compare the carbon flow through the food webs on an abyssal hill and the nearby plain at the Porcupine Abyssal Plain sustained observatory (4850 m water depth; northeast Atlantic), to examine the partitioning of detrital input in these substantially different megafaunal communities. We found minimal variation in carbon flows at the plain over two years, but differences in the detrital inputs and in the processing of that carbon input between the hill and plain habitats. Suspension feeding dominated metazoan carbon processing on the hill, removing nearly all labile detritus input to the system. By contrast, half of all labile detritus was deposited and available for deposit feeders on the abyssal plain. This suggests that the biomass on the hill is dependent on a more variable carbon supply than the plain. The presence of millions of abyssal hills globally suggests that the high benthic biomass and respiration, and reduced deposition of detritus may be pervasive, albeit with varying intensity
Regulation of benthic oxygen fluxes in permeable sediments of the coastal ocean

Large areas of the oceanic shelf are composed of sandy sediments through which reactive solutes are transported via porewater advection fueling active microbial communities. The advective oxygen transport in permeable sands of the North Sea was investigated under in situ conditions using a new benthic observatory to assess the dynamic interaction of hydrodynamics, sediment morphodynamics, and oxygen penetration depth. During 16 deployments, concurrent measurement of current velocity, sediment topography, and porewater oxygen concentration were carried out. In all cases the oxyclines were found at depths of 1–6 cm, correlating with the topography of stationary and migrating bedforms (ripples). Different conditions in terms of bottom water currents and bedform migration led to fluctuating oxygen penetration depths and, hence, highly variable redox conditions in up to 2.5 cm thick layers beneath the surface. Volumetric oxygen consumption rates of surface sediments were measured on board in flow-through reactors. Bedform migration was found to reduce consumption rates by up to 50%, presumably caused by the washout of organic carbon that is otherwise trapped in the pore space of the sediment. Based on the observations we found oxygen penetration depths to be largely controlled by oxygen consumption rates, grain size, and current velocity. These controlling variables are summarized by an adapted Damköhler number which allows for prediction of oxygen penetretion depths based on a simple scaling law. By integrating the oxygen consumption rates over the oxygen penetration depth, oxygen fluxes of 8–34 mmol m−2 d−1 were estimate
Thaumarchaeal ecotype distributions across the equatorial Pacific Ocean and their potential roles in nitrification and sinking flux attenuation

Thaumarchaea are among the most abundant microbial groups in the ocean, but controls on their abundance and the distribution and metabolic potential of different subpopulations are poorly constrained. Here, two ecotypes of ammonia-oxidizing thaumarchaea were quantified using ammonia monooxygenase (amoA) genes across the equatorial Pacific Ocean. The shallow, or water column “A” (WCA), ecotype was the most abundant ecotype at the depths of maximum nitrification rates, and its abundance correlated with other biogeochemical indicators of remineralization such as NO3 : Si and total Hg. Metagenomes contained thaumarchaeal genes encoding for the catalytic subunit of the urease enzyme (ureC) at all depths, suggesting that members of both WCA and the deep, water column “B” (WCB) ecotypes may contain ureC. Coupled urea hydrolysis-ammonia oxidation rates were similar to ammonia oxidation rates alone, suggesting that urea could be an important source of ammonia for mesopelagic ammonia oxidizers. Potential inducement of metal limitation of both ammonia oxidation and urea hydrolysis was demonstrated via additions of a strong metal chelator. The water column inventory of WCA was correlated with the depth-integrated abundance of WCB, with both likely controlled by the flux of sinking particulate organic matter, providing strong evidence of vertical connectivity between the ecotypes. Further, depth-integrated amoA gene abundance and nitrification rates were correlated with particulate organic nitrogen flux measured by contemporaneously deployed sediment traps. Together, the results refine our understanding of the controls on thaumarchaeal distributions in the ocean, and provide new insights on the relationship between material flux and microbial communities in the mesopelagic
The differential response of kelp to swell and infragravity wave motion

We present field measurements of the movement of the giant kelp Macrocystis pyrifera under wave forcing. We resolve the depth and frequency-dependent responses along the stipe and find different and counterintuitive patterns of response at the infragravity and swell wave forcing frequencies. At swell frequencies, tilting of the stipe is largest toward the holdfast, whereas at infragravity frequencies, the stipe tilting is largest closer to the water surface. It is postulated that the stretching of blades and subsequent pull on the stipe is, in part, responsible for these patterns. This conclusion is supported by results of manipulative experiments, which show a more along-stipe uniform response after removal of blades from the kelp. The length of the kelp also exerts a strong control on the relative magnitudes of movements in the different frequency bands, with the swell band becoming more important relative to the infragravity band for shorter length kelp. These results indicate that kelp will differentially dissipate energy over both frequencies and varying depths within the water column. The variety of movement responses over differing wave forcing frequencies may also imply that there exist differing rates of breakage for kelp exposed to hydrodynamics stressors of multiple frequencies
Predation on Atlantic herring (Clupea harengus ) eggs by the resident predator community in coastal transitional waters

Atlantic herring (Clupea harengus) migrates from offshore to coastal areas to spawn and their eggs and larvae may substantially increase prey resources for resident predators. We combined an in situ predator exclusion experiment using eggs naturally spawned on submerged aquatic vegetation and field observations of predator abundance to estimate the magnitude of predation mortality of herring eggs. During our predator exclusion experiment, performed in an important spawning ground in the southwest Baltic Sea, 20% of the herring eggs were consumed resulting in an extrapolated predation of 42% of all eggs between spawning and hatch. Abundance and stomach content analyses indicated that one predator (threespine stickleback, Gasterosteus aculeatus) was responsible for the majority of the predation impact. Predation mortality estimates from this in situ study were more than 10-fold higher than those of an empirical egg predation model for the same predator in the same region. Our findings highlight the potential of resident predators to regulate the survival of early life stages of ocean-going fishes that rely on the nursery functions of inshore transitional waters
Molecular composition of dissolved organic matter in the Mediterranean Sea

14 pages, 5 figuresThe molecular composition of marine dissolved organic matter (DOM) is still poorly understood, particularly\ud
in the Mediterranean Sea. In this work, DOM from the open Mediterranean Sea and the adjacent Northeast\ud
Atlantic Ocean was isolated by solid-phase extraction (SPE-DOM) and molecularly characterized using\ud
Fourier-transform ion cyclotron resonance mass spectrometry. We assessed the gradual reworking of the SPEDOM\ud
transported by the shallow overturning circulation of the Mediterranean Sea by following the increase\ud
in molecular weight (120 Da), oxygenation (15%), degradation index (Ideg 122%), and the proportional\ud
decrease of unsaturated aliphatic compounds (134%) along the Levantine Intermediate Water. This reworked\ud
SPE-DOM that leaves the Mediterranean Sea through the Strait of Gibraltar strongly contrasts with the fresh\ud
material transported by the inflow of Atlantic water (Ideg 225%). In the deep eastern and western overturning\ud
cells, the molecular composition of the deep waters varied according to their area and/or time of formation.\ud
SPE-DOM of the waters formed in the Aegean Sea during the Eastern Mediterranean Transient (EMT)\ud
was more processed than the DOM in pre-EMT waters formed in the Adriatic Sea (molecular weight and the\ud
proportion of unsaturated aliphatic compounds were increased by 5 Da and 9%, respectively). Furthermore,\ud
pre-EMT waters contain more reworked SPE-DOM (Ideg 17%) than post-EMT waters formed also in the Adriatic\ud
Sea. In summary, our study shows that the Mediterranean Sea constitutes a laboratory basin where degradation\ud
processes and diagenetic transformations of DOM can be observed on close spatial and temporal\ud
scalesPeer reviewe
Macroalgae may mitigate ocean acidification effects on mussel calcification by increasing pH and its fluctuations

Ocean acidification (OA) is generally assumed to negatively impact calcification rates of marine organisms. At a local scale however, biological activity of macrophytes may generate pH fluctuations with rates of change that are orders of magnitude larger than the long-term trend predicted for the open ocean. These fluctuations may in turn impact benthic calcifiers in the vicinity. Combining laboratory, mesocosm and field studies, such interactions between OA, the brown alga Fucus vesiculosus, the sea grass Zostera marina and the blue mussel Mytilus edulis were investigated at spatial scales from decimetres to 100s of meters in the western Baltic. Macrophytes increased the overall mean pH of the habitat by up to 0.3 units relative to macrophyte-free, but otherwise similar, habitats and imposed diurnal pH fluctuations with amplitudes ranging from 0.3 to more than 1 pH unit. These amplitudes and their impact on mussel calcification tended to increase with increasing macrophyte biomass to bulk water ratio. At the laboratory and mesocosm scales, biogenic pH fluctuations allowed mussels to maintain calcification even under acidified conditions by shifting most of their calcification activity into the daytime when biogenic fluctuations caused by macrophyte activity offered temporal refuge from OA stress. In natural habitats with a low biomass to water body ratio, the impact of biogenic pH fluctuations on mean calcification rates of M. edulis was less pronounced. Thus, in dense algae or seagrass habitats, macrophytes may mitigate OA impact on mussel calcification by raising mean pH and providing temporal refuge from acidification stress
Phosphorus and nitrogen starvation reveal life-cycle specific responses in the metabolome of Emiliania huxleyi (Haptophyta)

The coccolithophore Emiliania huxleyi is a microalga with biogeochemical and biotechnological relevance, due to its high abundance in the ocean and its ability to form intricate calcium carbonate structures. Depletion of macronutrients in oceanic waters is very common and will likely enhance with advancing climate change. We present the first comprehensive metabolome study analyzing the effect of phosphorus (P) and nitrogen (N) starvation on the diploid and haploid life-cycle stage, applying various metabolome analysis methods to gain new insights in intracellular mechanisms to cope with nutrient starvation. P-starvation led to an accumulation of many generic and especially N-rich metabolites, including lipids, osmolytes, and pigments. This suggests that P-starvation primarily arrests cell-cycling due to lacking P for nucleic acid synthesis, but that enzymatic functionality is widely preserved. Also, the de-epoxidation ratio of the xanthophyll cycle was upregulated in the diploid stage under P-starvation, indicating increased nonphotochemical quenching, a response typically observed under high light stress. In contrast, N-starvation resulted in a decrease of most central metabolites, also P-containing ones, especially in the diploid stage, indicating that most enzymatic functionality ceased. The two investigated nutrient starvation conditions caused significantly different responses, contrary to previous assumptions derived from transcriptomic studies. Data highlight that instantaneous biochemical flux is a more dominant driver of the metabolome than the transcriptomically rearranged pathway patterns. Due to the fundamental nature of the observed responses it may be speculated that microalgae with similar nutrient requirements can cope better with P-starvation than with N-starvation
Limitation of dimethylsulfoniopropionate synthesis at high irradiance in natural phytoplankton communities of the Tropical Atlantic

Predictions of the ocean-atmosphere flux of dimethyl sulfide will be improved by understanding what controls seasonal and regional variations in dimethylsulfoniopropionate (DMSP) production. To investigate the influence of high levels of irradiance including ultraviolet radiation (UVR), on DMSP synthesis rates (μDMSP) and inorganic carbon fixation (μPOC) by natural phytoplankton communities, nine experiments were carried out at different locations in the low nutrient, high light environment of the northeastern Tropical Atlantic. Rates of μDMSP and μPOC were determined by measuring the incorporation of inorganic 13C into DMSP and particulate organic carbon. Based on measurements over discrete time intervals during the day, a unique μDMSP vs. irradiance (P vs. E) relationship was established. Comparison is made with the P vs. E relationship for μPOC, indicating that light saturation of μDMSP occurs at similar irradiance to μPOC and is closely coupled to carbon fixation on a diel basis. Photoinhibition during the middle of the day was exacerbated by exposure to UVR, causing an additional 55–60% inhibition of both μDMSP and μPOC at the highest light levels. In addition, decreased production of DMSP in response to UVR-induced photoxidative stress, contrasted with the increased net synthesis of photoprotective xanthophyll pigments. Together these results indicate that DMSP production by phytoplankton in the tropical ocean is not regulated in the short term by the necessity to control increasing photooxidative stress as irradiance increases during the day. The study provides new insight into the regulation of resource allocation into this biogeochemically important, multi-functional compatible solute