Limnology and Oceanography: Methods
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Application of the isotope pairing technique in sediments where anammox and denitrification coexist The isotope pairing technique (IPT) is a well‐established 15N method for estimation of denitrification. Presence of anammox, the anaerobic oxidation of NH4 + to N 2 with NO2 − results in violation of central assumptions on which the IPT is built. It is shown that anammox activity causes overestimation of the N 2 production calculated by the IPT. However, experiments with different additions of 15 NO3 − will reveal the problems posed by anammox. Two alternative calculation procedures are presented, which enable a more accurate quantification of anammox and denitrification activity in sediments where the processes coexist. One procedure is based on measurements of 15 N ‐N 2 production in 15 NOx − ‐amended intact sediment cores and data addressing the contribution of anammox to total N 2 production estimated from slurry incubations. The other procedure is based on measurements of 15N 2 production in at least two parallel series of sediment cores incubated with different 15 NOx − additions. The calculation procedure presented is used on field data from four studies where the IPT was used and the potential anammox rate measured. The IPT overestimated total 14N‐N 2 production rates by 0%, 2.5%, 31%, and 82% relative to the revised estimates from the 4 different sites, where anammox accounted for 0%, 6%, 18%, and 69.8%, respectively, of N 2 production. The overestimation of true denitrification was, however, up to several hundred percent. Our analysis suggests however that the IPT does not seriously overestimate N 2 production in estuarine sediments because anammox accounts for <6% of N 2 production in such sediments, according to present knowledge.
Limnology and Oceanography: Methods - Tập 1 Số 1 - Trang 63-73 - 2003
An empirically validated method for characterizing pelagic habitats in the Gulf of Mexico using ocean model data Abstract Mesoscale oceanic features such as eddies generate considerable environmental heterogeneity within the pelagic oceans, but their transient nature makes it difficult to identify both their spatial and temporal extent and their effects on the distribution of pelagic fauna. Simplifying these complex features using a biologically meaningful classification system will likely be a useful first step in understanding the extent of their influence in structuring open‐ocean ecosystems. In this study, we present a tool to classify the pelagic environment in the Gulf of Mexico using sea‐surface height and temperature‐at‐depth data from the 1/25° GOM HYbrid Coordinate Ocean Model (HYCOM). Three “water types” were identified: Loop Current‐origin water (LCOW), Gulf common water (CW), and mixed (MIX) water, where the latter represents an intermediate state during the degradation of LCOW to CW. The HYCOM‐derived classifications were validated against in situ CTD data and microbial samples collected through 2015–2016 by the Deep Pelagic Nekton Dynamics of the Gulf of Mexico (DEEPEND) consortium. The validation data comprised classifications derived from both temperature‐depth (TD) and temperature‐salinity (TS) profiles and from microbial community analyses from the surface to mesopelagic depths. The HYCOM classifications produced an overall agreement rate of 77% with the TS/TD classifications, and 79% with the microbial classifications. With applicability across a wide range of spatial and temporal scales, we believe that the system provides a useful, complementary tool for biological oceanographers and resource managers interested in better understanding the effects of major mesoscale features on the pelagic biota.
Limnology and Oceanography: Methods - Tập 17 Số 6 - Trang 362-375 - 2019
Characterizing dissolved organic matter fluorescence with parallel factor analysis: a tutorial A sub‐fraction of dissolved organic matter fluoresces when excited with ultraviolet light. This property is used to quantify and characterize changes in dissolved organic matter (DOM) in aquatic environments. Detailed mapping of the fluorescence properties of DOM produces excitation emission matrices (EEM), which are well suited to multi‐way data analysis techniques (chemometrics). Techniques such as parallel factor analysis (PARAFAC) are increasingly being applied to characterize DOM fluorescence properties. Here, an introduction to the technique and description of the advantages and pitfalls of its application to DOM fluorescence is presented. Additionally a MATLAB based tutorial and toolbox specific to PARAFAC analysis of DOM fluorescence is presented.
Limnology and Oceanography: Methods - Tập 6 Số 11 - Trang 572-579 - 2008
Inner filter correction of dissolved organic matter fluorescence The fluorescence of dissolved organic matter (DOM) is suppressed by a phenomenon of self‐quenching known as the inner filter effect (IFE). Despite widespread use of fluorescence to characterize DOM in surface waters, the advantages and constraints of IFE correction are poorly defined. We assessed the effectiveness of a commonly used absorbance‐based approach (ABA), and a recently proposed controlled dilution approach (CDA) to correct for IFE. Linearity between corrected fluorescence and total absorbance (ATotal ; the sum of absorbance at excitation and emission wavelengths) across the full excitation‐emission matrix (EEM) in dilution series of four samples indicated both ABA and CDA were effective to an absorbance of at least 1.5 in a 1 cm cell, regardless of wavelength positioning. In regions of the EEMs where signal to background noise (S/N) was low, CDA correction resulted in more variability than ABA correction. From the ABA algorithm, the onset of significant IFE (>5%) occurs when absorbance exceeds 0.042. In these cases, IFE correction is required, which was the case for the vast majority (97%) of lakes in a nationwide survey (n= 554). For highly absorbing samples, undesirably large dilution factors would be necessary to reduce absorbance below 0.042. For rare EEMs with ATotal > 1.5 (3.0% of the lakes in the Swedish survey), a 2‐fold dilution is recommended followed by ABA or CDA correction. This study shows that for the vast majority of natural DOM samples the most commonly applied ABA algorithm provides adequate correction without prior dilution.
Limnology and Oceanography: Methods - Tập 11 Số 12 - Trang 616-630 - 2013
Relationship between wind speed and gas exchange over the ocean revisited The relationship between gas exchange and wind speed is used extensively for estimating bulk fluxes of atmospheric gases across the air‐sea interface. Here, I provide an update on the frequently used method of Wanninkhof (1992). The update of the methodology reflects advances that have occurred over the past two decades in quantifying the input parameters. The general principle of obtaining a relationship constrained by the globally integrated bomb‐14 CO2 flux into the ocean remains unchanged. The improved relationship is created using revised global ocean 14 C inventories and improved wind speed products. Empirical relationships of the Schmidt number, which are necessary to determine the fluxes, are extended to 40°C to facilitate their use in the models. The focus is on the gas exchange of carbon dioxide, but the suggested functionality can be extended to other gases at intermediate winds (≈4−15 m s−1 ). The updated relationship, expressed as k = 0.251 <U2 > (Sc/660)−0.5 where k is the gas transfer velocity, <U2 > is the average squared wind speed, and Sc is the Schmidt number, has a 20% uncertainty. The relationship is in close agreement with recent parameterizations based on results from gas exchange process studies over the ocean.
Limnology and Oceanography: Methods - Tập 12 Số 6 - Trang 351-362 - 2014
A simple and efficient method for the solid‐phase extraction of dissolved organic matter (SPE‐DOM) from seawater A simple protocol is presented for the solid‐phase extraction of dissolved organic matter (SPE‐DOM) from seawater using commercially prepacked cartridges. The method does not require major instrumentation and can be performed in the field. Modified styrene divinyl benzene polymer type sorbents (Varian PPL and ENV) and sorbents of a silica structure bonded with different hydrocarbon chains (Varian C8, C18, C18OH, and C18EWP) were considered. Except for C18OH, which heavily contaminated the samples, none of the sorbents leached significant amounts of dissolved organic carbon (DOC) or nitrogen (DON). Samples from the North Brazil shelf with strong mixing gradients of terrigenous and marine DOM were used to compare the various sorbents. PPL was the most efficient—on average, 62% of DOC was recovered as salt‐free extracts. C18 was found to be most efficient among the silica‐based sorbents, but it showed only two‐thirds of the extraction efficiency of PPL. As indicated by [1 H]NMR, C/N, and δ13 C analyses, PPL extracted a more representative proportion of DOM than C18. Therefore, PPL was used for comparative studies in the Gulf of Mexico and Antarctica. From brackish marsh and river waters, 65% and 62% of total DOC, respectively, could be extracted. For purely marine DOM in Antarctica and the deep sea, the extraction efficiency was lower (43% on average). The efficiency of the new method to isolate marine DOM is better than or similar to highly laborious methods. A further advantage is the complete desalination of the sample. The isolation of a major DOM fraction, which is salt‐free, offers many possibilities to further characterize DOM by advanced analytical techniques.
Limnology and Oceanography: Methods - Tập 6 Số 6 - Trang 230-235 - 2008
Online δ<sup>13</sup>C analysis of volatile fatty acids in sediment/porewater systems by liquid chromatography-isotope ratio mass spectrometry
Limnology and Oceanography: Methods - Tập 4 Số 10 - Trang 346-357 - 2006
Evaluation of diagnostic pigments to estimate phytoplankton size classes Abstract Phytoplankton accessory pigments are commonly used to estimate phytoplankton size classes, particularly during development and validation of biogeochemical models and satellite ocean color‐based algorithms. The diagnostic pigment analysis (DPA) is based on bulk measurements of pigment concentrations and relies on assumptions regarding the presence of specific pigments in different phytoplankton taxonomic groups. Three size classes are defined by the DPA: picoplankton, nanoplankton, and microplankton. Until now, the DPA has not been evaluated against an independent approach that provides phytoplankton size calculated on a per‐cell basis. Automated quantitative cell imagery of microplankton and some nanoplankton, used in combination with conventional flow cytometry for enumeration of picoplankton and nanoplankton, provide a novel opportunity to perform an independent evaluation of the DPA. Here, we use a data set from the North Atlantic Ocean that encompasses all seasons and a wide range of chlorophyll concentrations (0.18–5.14 mg m−3 ). Results show that the DPA overestimates microplankton and picoplankton when compared to cytometry data, and subsequently underestimates the contribution of nanoplankton to total biomass. In contrast to the assumption made by the DPA that the microplankton size class is largely made up of diatoms and dinoflagellates, imaging‐in‐flow cytometry shows significant presence of diatoms and dinoflagellates in the nanoplankton size class. Additionally, chlorophyll b is commonly attributed solely to picoplankton by the DPA, but Chl b ‐containing phytoplankton are observed with imaging in both nanoplankton and microplankton size classes. We suggest revisions to the DPA equations and application of uncertainties when calculating size classes from diagnostic pigments.
Limnology and Oceanography: Methods - Tập 18 Số 10 - Trang 570-584 - 2020
An interlaboratory comparison for the quantification of aqueous dimethylsulfide An interlaboratory comparison (ILC) was conducted to evaluate the proficiency of multiple laboratories to quantify dimethylsulfide (DMS) in aqueous solution. Ten participating laboratories were each supplied with blind duplicate test solutions containing dimethylsulfoniopropionate hydrochloride (DMSP HCl) dissolved in acidified artificial seawater. The test solutions were prepared by the coordinating laboratory from a DMSP HCl reference material that was synthesized and purity certified for this purpose. A concentration range was specified for the test solutions and the participating laboratories were requested to dilute them as required for their analytical procedure, together with the addition of excess alkali under gas‐tight conditions to convert the DMSP to DMS. Twenty‐two DMS concentrations and their estimated expanded measurement uncertainties (95% confidence level) were received from the laboratories. With two exceptions, the within‐laboratory variability was 5% or less and the between‐laboratory variability was ~ 25%. The magnitude of expanded measurement uncertainties reported from all participants ranged from 1% to 33% relative to the result. The information gained from this pilot ILC indicated the need for further test sample distribution studies of this type so that participating laboratories can identify systematic errors in their analysis procedures and realistically evaluate their measurement uncertainty. The outcome of ILC studies provides insights into the comparability of data in the global surface seawater DMS database.
Limnology and Oceanography: Methods - Tập 12 Số 11 - Trang 784-794 - 2014
Quantifying nitrogen assimilation rates of individual phytoplankton species and plankton groups during harmful algal blooms via sorting flow cytometry Abstract While 15 N‐labeled nitrogen (N) compounds have been used to quantify N uptake rates by plankton communities for decades, accurately ascribing those rates to individual populations or species has been a challenge. Here, we apply sorting flow cytometry combined with species‐specific immuno‐detection of a harmful alga, Aureococcus anophagefferens , to contrast the nutritional ecology of this alga with co‐occurring picoplankton (picoeukaryotes, cyanobacteria, heterotrophic bacteria) during brown tides. The method was iteratively refined to yield close agreement (85–101%) between plankton community 15 N uptake quantified via traditional filtration and this novel sorting method. Sorting of plankton revealed that the δ15 N values of A. anophagefferens and phycocyanin‐containing cyanobacteria were more enriched (∼ 10‰) than the values of other picoeukaryotes and heterotrophic bacteria that decreased to < 0‰ after A. anophagefferens abundance declined, suggesting that these plankton utilized isotopically lighter nitrogen sources (e.g., recycled nutrients or fertilizer). A. anophagefferens utilized multiple forms of nitrogen (e.g., nitrate, ammonium, urea) during blooms and their uptake rates of ammonium and urea were highest during blooms. However, A. anophagefferens urea uptake rates on a per cell basis were fivefold faster than all other groups, affirming the nutritionally strategic uptake of urea to fuel brown tides. This study presents a novel approach to successfully sort a single algal species from a plankton community for the purpose of assessing nitrogen uptake and highlights a promising and powerful approach for investigating and contrasting the nutritional ecology of bloom‐causing species and co‐occurring plankton populations during harmful algal blooms.
Limnology and Oceanography: Methods - Tập 15 Số 8 - Trang 706-721 - 2017
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