pinecone/core-2020-05-10-deduplication huggingface dataset:
Increasing dominance of terrigenous organic matter in circumpolar freshwaters due to permafrost thaw

Climate change and permafrost thaw are unlocking the vast storage of organic carbon held in northern frozen soils. Here we evaluated the effects of thawing ice-rich permafrost on dissolved organic matter (DOM) in freshwaters by optical analysis of 253 ponds across the circumpolar North. For a subset of waters in subarctic Quebec, we also quantified the contribution of terrestrial sources to the DOM pool by stable isotopes. The optical measurements showed a higher proportion of terrestrial carbon and a lower algal contribution to DOM in waters affected by thawing permafrost. DOM composition was largely dominated (mean of 93%) by terrestrial substances at sites influenced by thawing permafrost, while the terrestrial influence was much less in waterbodies located on bedrock (36%) or with tundra soils unaffected by thermokarst processes (42%) in the catchment. Our results demonstrate a strong terrestrial imprint on freshwater ecosystems in degrading ice-rich permafrost catchments, and the likely shift towards increasing dominance of land-derived organic carbon in waters with ongoing permafrost thaw
Hidden in plain sight: The importance of cryptic interactions in marine plankton

Here, we present a range of interactions, which we term “cryptic interactions.” These are interactions that occur throughout the marine planktonic foodweb but are currently largely overlooked by established methods, which mean large‐scale data collection for these interactions is limited. Despite this, current evidence suggests some of these interactions may have perceptible impacts on foodweb dynamics and model results. Incorporation of cryptic interactions into models is especially important for those interactions involving the transport of nutrients or energy. Our aim is to highlight a range of cryptic interactions across the plankton foodweb, where they exist, and models that have taken steps to incorporate these interactions. Additionally, it is discussed where additional research and effort is required to continue advancing our understanding of these cryptic interactions. We call for more collaboration between ecologists and modelers in order to incorporate cryptic interactions into biogeochemical and foodweb models
Characterizing variability in marine protist communities via ARISA fingerprints — a method evaluation

It is important to characterize and understand the diversity of marine protists because of their relevance for\ud
ecosystem functioning. In the era of molecular science, diversity studies have received renewed attention.\ud
High-throughput, cost-intensive next generation sequencing provides deep insight in protist diversity but limits\ud
the volume of studied samples. Protist observations with high spatiotemporal resolution, therefore, require\ud
a quick and cost-effective tool to channelize the large sample volume and help select representatives for diversity\ud
studies. In this study, we evaluated the validity of “Automated Ribosomal Intergenic Spacer Analysis”\ud
(ARISA) as a means of estimating variability in marine protist communities. The evaluation was based on statistical correlation of ARISA data and 454-pyrosequencing data from samples collected in the Southern Ocean\ud
and Arctic Ocean. Here, we provide evidence that differences in ARISA profiles reflect taxon-specific differences observed in 454-pyrosequencing data sets. Calculated similarity indices for the ARISA profiles and 454- pyrosequencing data of 27 marine protist samples revealed strong agreements between the results of both methods regarding the extent of variability among protist communities. We suggest that ARISA might become\ud
an important tool for surveillance of differences in marine protist communities with high spatiotemporal resolution. Furthermore, it might serve as a preselection tool to identify representative samples in large data sets
Assessment of the radio 3H-CH4 tracer technique to measure aerobic methane oxidation in the water column

Microbial methane oxidation rates in ocean and freshwater systems reveal how much of emitted methane from the sediments is oxidized to CO2 and how much can reach the atmosphere directly. The tracer-method using 3H-CH4 provides a way to measure MOX-rates even in water with low methane concentrations without needing any specific instrumentation. We assessed this method by implementing several experiments, collecting data from various environments, and including recent literature concerning the method to identify any uncertainties that should be considered. Our assessment reveals some difficulties of the method but also reassures previous assumptions to be correct. Some of the difficulties are hardly to be avoided, such as incubating all samples at the right in-situ temperature or limiting the variability of MOX-rate measurements in water of low methanotrophic activity. Other details, e.g. quickly measuring the total radioactivity after stopping the incubation, are easy to adapt in each laboratory. And yet other details as shaking during incubation and bottle size seem to be irrelevant. With our study we hope to improve and to encourage future measurements of MOX-rates in different environments and to provide a standard procedure of MOX measurements to make data of MOX better comparable
Stream metabolism and the open diel oxygen method: Principles, practice, and perspectives

Global quantitative estimations of ecosystem functions are vital. Among those, ecosystem respiration and photosynthesis contribute to carbon cycling and energy flow to food webs. These can be estimated in streams with the open channel diel oxygen method (single or two stations) essentially relying on a mass balance of oxygen over a defined reach. The method is generally perceived as low cost and easy to apply with new drift free optic sensors. Yet, it remains challenging on several key issues reviewed here: measurements of gas transfer at the air-water interface, appropriate mixing of tracers, uncertainty propagation in the calculations, spatial heterogeneity in oxygen concentrations, the derivation of net primary production (NPP) or autotrophic respiration, and the temperature dependence of photosynthesis and respiration. An extremely simple modeling tool is presented in an Excel workbook recommended for teaching the basic principles of the method. The only method able to deal with stream spatial heterogeneity is the method by Demars et al. Example data, Excel workbook, and R script are provided to run stream metabolism calculations. Direct gas exchange determination is essential in shallow turbulent streams, but modeling may be more accurate in large (deep) rivers. Lateral inflows should be avoided or well characterized. New methods have recently been developed to estimate NPP using multiple diel oxygen curves. The metabolic estimates should not be systematically temperature corrected to compare streams. Other recent advances have improved significantly the open channel diel oxygen method, notably the estimation of respiration during daylight hours
A mesocosm concept for the simulation of near-natural shallow underwater climates: The Kiel Outdoor Benthocosms (KOB)

Biogenic, seasonal, and stochastic fluctuations at various scales characterize coastal marine habitats and modulate environmental stress. The relevance of most past studies into climate change impacts is weakened by the usually intentional exclusion of fluctuations from the experimental design. We describe a new outdoor mesocosm system for benthic research (“benthocosms”) which permit the control and manipulation of several environmental variables while admitting all natural in situ fluctuations. This is achieved by continuously measuring the relevant variables (e.g., temperature, pH, O2, CO2) in situ, defining these in real time as reference values in the control software and simulating target climates by delta treatments. The latter constitute the manipulative addition of predefined changes (e.g., “warming”, “acidification”) to the reference values. We illustrate the performance of the system by presenting the environmental data of four seasonal experiments which together represent an entire year. The “Kiel Outdoor Benthocosms” allow realizing near-natural climate change experiments on complex benthic communities under controlled scenarios
Oscillating grid mesocosm for studying oxygen dynamics under controlled unsteady turbulence

In shallow environments, common unsteady flows, such as tides, waves or wind-driven currents modulate the diffusive boundary layer thickness that controls the exchange of electron acceptors for mineralization and oxidation processes in surficial sediment. This study demonstrated the ability of an oscillating grid mesocosm to (1) produce homogenous turbulence at the sediment-water interface of multiple sediment cores (between-core variability<within core variability; 16% on average); (2) simulate diffusive boundary layer thickness dynamics on different timescales by easy control of turbulence intensity and (3) study transient oxygen dynamics of organic matter mineralization under varying turbulent conditions. The relationship between turbulence intensity and oxygen diffusive boundary layer thickness, and oxygen penetration depth in the sediment was investigated with different organic matter enrichments and sediment permeability. Oxygen diffusive boundary layer thickness decreased linearly as URMS increased. Oxygen penetration depth increased with turbulence intensity, and converging to an upper limit with a larger value for low (3.28 mm65.8%) than for high (1.77 mm611.8%) organic matter content in muddy sediment. In sandy sediment, advective flows and resuspension led to a continuous increase of oxygen penetration depth with turbulence intensity, up to 13.2 mm619% for turbulent velocities of 9.6 cm s21. This mesocosm device will enable the experimental study of microbial dynamics under transient oxygen dynamics, to improve early diagenesis modeling under unsteady flow
Update: A non-parametric method for the measurement of size diversity, with emphasis on data standardization. The measurement of the size evenness

A method for the measurement of the size diversity based on the classical Shannon–Wiener expression was proposed as a proxy of the shape of the size distribution. The summatory of probabilities of a discrete variable (such as species relative abundances) in the original Shannon–Wiener expression was substituted by an integral of the probability density function of a continuous variable (such as body size). Here, we propose an update of this method by including the measurement of the size e-evenness, just dividing the exponential of the size diversity by its possible maximum for a given size range. Assuming a domain of the size range of (0,8), for a given logarithmic mean ( math formula) and a logarithmic standard deviation math formula, the distribution with the highest diversity is the Log-Normal. The size e-evenness ranges between 0 and 1 because of the division by the maximum exponential diversity. Size e-evenness is useful to discriminate whether variations in size diversity are due to changes in the shape of the size distribution or caused by differences in size dispersion.Peer ReviewedPostprint (published version
µCT scanning – A novel method for in vivo 3D characterization of zooplankton propagules

Many zooplankton species produce dormant stages to bridge episodes that are unfavorable for juveniles and adults. Although a variety of methods has been used to study the morphology and internal structure of these propagules, surprisingly little is known about links between propagule traits and life history characteristics such as dormancy, hatching behavior and fitness of emerging larvae. A major constraint is that most available methods are lethal to the embryo and processing can generate visual artefacts. Here, we investigate the potential of High Resolution X-ray Computed Tomography (HRXCT or mCT scanning) to compile whole mount 3D reconstructions of the propagules of three zooplankton species that differ in size (200–1200 lm) and shape (spherical eggs vs. semi-circular ephippia). Our results show that mCT scanning is a suitable technique for whole mount reconstruction of propagules. In addition, by combining the scanning procedure with a laboratory hatching experiment we showed that while eggs that were exposed to mCT scanning had significantly lower hatching fractions and lower motility of hatchlings than control eggs, some of the scanned eggs or larvae could still be used in subsequent life table experiments. Overall, mCT scanning represents a valuable, non-invasive technique for internal and external characterization of zooplankton propagules and to study associations between propagule structure and life history traits.status: publishe
Processing of multibeam water column image data for automated bubble/seep detection and repeated mapping

Water Column Imaging Multibeam Echosounder Systems (MBES) are effective and sensitive tools for investigating free gas (bubble) release and its rise through the water column. The main advantages of MBES are the detection range and lateral coverage in the water column and at the seafloor; furthermore, they are becoming increasingly available on research vessels worldwide. However, high noise levels and systematic artefacts due to side-lobe induced signal interference degrade MBES Water Column Images (WCIs) and hampered automated bubble detection and related gas seepage investigations. We present a new technique advancing automated detection of bubble streams and moving toward a quantitative gas-release assessment. It is shown that bubble streams can be detected reliably by their spatio-temporal behavior even when they are discontinuous in WCI data. Using assumptions about the bubble rising trajectories, bubble release spots at the seafloor can be traced even if the source location is obscured by acoustic noise or unwanted acoustic targets. A map with acoustic response and source locations of bubbles being released can be produced and serves as a starting point for more detailed quantitative analyses. The efficiency of the method has been assessed at a methane seep site in the Dutch North Sea. Multiple survey lines are merged to a detailed acoustic map of the area. Processed results are in good agreement with manual investigations of the WCI data as well as ROV-based video analysis
A novel membrane inlet-infrared gas analysis (MI-IRGA) system for monitoring of seawater carbonate system

Increased atmospheric CO 2 concentrations are driving changes in ocean chemistry at unprecedented rates resulting in ocean acidification, which is predicted to impact the functioning of marine biota, in particular of marine calcifiers. However, the precise understanding of such impacts relies on an analytical system that determines the mechanisms and impact of elevated pCO 2 on the physiology of organisms at scales from species to entire communities. Recent work has highlighted the need within experiments to control all aspects of the carbonate system to resolve the role of different inorganic carbon species on the physiological responses observed across taxa in real-time. Presently however, there are limited options available for continuous quantification of physiological responses, coupled with real-time calculation of the seawater carbonate chemistry system within microcosm environments. Here, we describe and characterise the performance of a novel pCO 2 membrane equilibrium system (the Membrane Inlet Infra-Red Gas Analyser, MI-IRGA) integrated with a continuous pH and oxygen monitoring platform. The system can detect changes in the seawater carbonate chemistry and determine organism physiological responses, while providing the user with real-time control over the microcosm system. We evaluate the systems control, response time and associated error, and demonstrate the flexibility of the system to operate under field conditions and within a laboratory. We use the system to measure physiological parameters (photosynthesis and respiration) for the corals Pocillipora damicornis and Porites cylindrica; in doing so we present a novel dataset examining the interactive role of temperature, light and pCO 2 on the physiology of P. cylindrica
Planktotrons: A novel indoor mesocosm facility for aquatic biodiversity and food web research

We established a new indoor mesocosm facility, 12 fully controlled “Planktotrons”, designed to conduct marine and freshwater experiments for biodiversity and food web approaches using natural or artificial, benthic or planktonic communities. The Planktotrons are a unique and custom-tailored facility allowing long-term experiments. Wall growth can be inhibited by a rotating gate paddle with silicone lips. Additionally, temperature and light intensity are individually controllable for each Planktotron and the large volume (600 L) enables high-frequency or volume-intense measurements. In a pilot freshwater experiment various trophic levels of a pelagic food web were maintained for up to 90 d. First, an artificially assembled phytoplankton community of 11 species was inoculated in all Planktotrons. After 22 d, two ciliates were added to all, and three Daphnia species were added to six Planktotrons. After 72 d, dissolved organic matter (DOM, an alkaline soil extract) was added as an external disturbance to six of the 12 Planktotrons, involving three Planktotrons stocked with Daphnia and three without, respectively. We demonstrate the suitability of the Planktotrons for food web and biodiversity research. Variation among replicated Planktotrons (n = 3 minimum) did not differ from other laboratory systems and field experiments. We investigated population dynamics and interactions among the different trophic levels, and found them affected by the sequence of ciliate and Daphnia addition and the disturbance caused by addition of DOM
Using stable isotopes and gas concentrations for independent constraints on microbial methane oxidation at Arctic Ocean temperatures

Microbial oxidation of methane in oxic water bodies is an important control on the amount of dissolved methane which is released from the ocean to the atmosphere. We explored the use of stable isotope methane spikes to quantify methane oxidation rates in Arctic seawater samples. A Picarro G2201-i cavity ring-down spectrometer was used to determine methane concentration and isotope ratios from headspace samples in foil incubators. The methane mass balance and the change in stable isotope ratios served as independent constraints on methane oxidation. For a fractionation factor of 1.025 oxidation rate constants determined with both methods agreed within 20% for small changes in isotope ratio (e.g., 10‰). For large changes in isotope ratio (e.g., 90‰), which was outside the calibration range, methods diverged. Rate constants down to 0.01 / d could be resolved with high statistical support. Stable isotope infrared spectroscopy to determine methane oxidation in foil incubators (ISMOFI) was successfully tested on under ice seawater from Utqiagvik, Alaska, by repeated sampling from each incubation vessel. Depending on the amount of isotope spike added, we determined oxidation rates of 0.15 ± 0.02 nmol / (L*d) at in situ methane concentration and a maximal oxidation potential of 271 ± 41 nmol / (L*d). The ISMOFI method permits variable incubation durations from days to months in a single incubator. The method is transportable and applicable in a variety of field or seagoing laboratory environments, and it avoids the use of hazardous substances such as radioisotopes and toxic chemicals
A fast and sensitive method for the continuous in situ determination\ud
of dissolved methane and its d13C-isotope ratio in surface waters

A fast and sensitive method for the continuous determination of methane (CH4) and its stable carbon isotopic\ud
values (d13C-CH4) in surface waters was developed by applying a vacuum to a gas/liquid exchange\ud
membrane and measuring the extracted gases by a portable cavity ring-down spectroscopy analyser\ud
(M-CRDS). The M-CRDS was calibrated and characterized for CH4 concentration and d13C-CH4 with synthetic\ud
water standards. The detection limit of the M-CRDS for the simultaneous determination of CH4 and d13CCH4\ud
is 3.6 nmol L21 CH4. A measurement precision of CH4 concentrations and d13C-CH4 in the range of\ud
1.1%, respectively, 1.7& (1r) and accuracy (1.3%, respectively, 0.8& [1r]) was achieved for single measurements\ud
and averaging times of 10 min. The response time s of 5765 s allow determination of d13C-CH4 values\ud
more than twice as fast than other methods. The demonstrated M-CRDS method was applied and tested\ud
for Lake Stechlin (Germany) and compared with the headspace-gas chromatography and fast membrane CH4\ud
concentration methods. Maximum CH4 concentrations (577 nmol L21) and lightest d13C-CH4 (235.2&) were\ud
found around the thermocline in depth profile measurements. The M-CRDS-method was in good agreement\ud
with other methods. Temporal variations in CH4 concentration and d13C-CH4 obtained in 24 h measurements\ud
indicate either local methane production/oxidation or physical variations in the thermocline. Therefore,\ud
these results illustrate the need of fast and sensitive analyses to achieve a better understanding of\ud
different mechanisms and pathways of CH4 formation in aquatic environments
A versatile optode system for oxygen, carbon dioxide, and pH measurements in seawater with integrated battery and logger

Herein, we present a small and versatile optode system with integrated battery and logger for monitoring of O-2, pH, and pCO(2) in seawater. Three sensing materials designed for seawater measurements are optimized with respect to dynamic measurement range and long-term stability. The spectral properties of the sensing materials were tailored to be compatible with a commercially available laboratory oxygen logger that was fitted into a pressure housing. Interchangeable sensor caps with appropriate "sensing chemistry" are conveniently attached to the end of the optical fiber. This approach allows using the same instrument for multiple analytes, which offers great flexibility and minimizes hardware costs. Applications of the new optode system were demonstrated by recording depth profiles for the three parameters during a research cruise in the Baltic Sea and by measuring surface water transects of pH. The optode was furthermore used to monitor the concentration of dissolved oxygen in a seagrass meadow in the Limfjord, Denmark, and sensor packages consisting of pO(2), pH, and pCO(2) were deployed in the harbors of Kiel, Germany, and Southampton, England, for 6 d. The measurements revealed that the system can resolve typical patterns in seawater chemistry related to spatial heterogeneities as well as temporal changes caused by biological and tidal activity