Limnology and Oceanography: Methods

Cyanobacterial blooms occur frequently in eutrophic lakes and their potentially harmful effects affected the security of drinking water and food sources, biodiversity, and economic activities, and attracted the attention of general public worldwide. Cyanobacteria could move vertically in the water column by regulating their buoyancy, which leads to the assumption of homogeneous water invalid. Ecolight, based on radiative transfer theory, was applied to examine the effects of vertical nonuniform of chlorophyll a concentrations (Chl a(z)) on remote sensing reflectance spectrum (R_rs(λ)) of optically complex inland waters. Simulations for nonuniform water consisting of three Chl a(z) profile classes, including Gaussian, exponential, and power, were compared with simulations for a reference homogeneous water whose Chl a was identical to average value of the nonuniform case. The near‐surface aggregation of phytoplankton are shown to have significant influence on R_rs(λ) and Chl a inversion algorithms. Variations of ΔR_rs(λ) (relative difference of R_rs(λ) between inhomogeneous and homogeneous waters with same average Chl a concentration) mainly depended on the Chl a(z) structure parameters and wavelength. A correction scheme was developed based on the relationships between ΔR_rs(λ) and Chl a(z) structure parameters. With knowledge of Chl a(z) profile parameters, R_rs(λ) of inhomogeneous waters can be corrected to the R_rs(λ) of uniform waters with same average Chl a across the water column. Examples of field data from Lake Chaohu illustrated the effects of phytoplankton variation on the near infrared‐to‐red ratio of R_rs and the R_rs correction performance.

The increasing recognition of the roles that exopolymeric substances (EPS) play in the aquatic environment necessitates obtaining sufficient quantities of purified EPS for exploration of its physical, chemical, and biological properties, as well as for quantitative and structural analysis of its composition. For this purpose, three preconcentration/ purification techniques, i.e., 1) ethanol precipitation, 2) stirred‐cell ultrafiltration, and 3) cross‐flow ultrafiltration, followed by stirred‐cell diafiltration, were compared for their effectiveness to quantitatively isolate EPS from laboratory cultures of Amphora sp. The results showed that the classical ethanol precipitation method was not effective in isolating and concentrating EPS from this seawater culture medium. Stirredcell ultrafiltration appeared best for harvesting EPS from this diatom. However, because of its limitations in terms of time and volume, cross‐flow ultrafiltration needed to be first applied, along with some necessary improvements, followed by a three‐step cartridge soaking and stirred‐cell diafiltration. After cartridge soaking, the yields of the two ultrafiltration methods were comparable. Two different fractions were obtained from EPS of Amphora sp. by anion exchange chromatography and were characterized respectively. Whereas these purified fractions had similar molecular weights of 1000 kDa, their monosaccharide composition was different. In conclusion, cross‐flow ultrafiltration followed by stirred‐cell diafiltration with additional cartridge washing turned out to be the optimal method for EPS separation, based on time, cost, and yield.

This document presents the WAter COlor from Digital Images (WACODI) algorithm, which extracts the color of natural waters from images collected by low‐cost digital cameras, in the context of participatory science and water quality monitoring. SRGB images are converted to the CIE XYZ color space, undergoing a gamma expansion and illumination correction that includes the specular reflection at the air‐water interface. The XYZ values obtained for each pixel of the image are converted to chromaticity coordinates and Hue color angle (α_w), which is a measure of color. Based on the distributions of α_w in sub‐sections of the image, an approximation of the intrinsic color of the water is obtained. This algorithm was applied to images acquired in 2013 during two field campaigns in Northern Europe. The Hue color angles were derived from hyperspectral measurements above and below the surface, carried out simultaneously with image acquisition. When for each station a specific illumination correction was applied, based on the corresponding hyperspectral data, a good fit (r² = 0.93) was obtained between the image and the spectra Hue color angles (slope = 0.98, intercept = −0.03). When a more generic illumination correction was applied to the same images, based on the sky conditions at the time of the image acquisition (either overcast or sunny), a slightly inferior, but still satisfactory fit resulted. Results on the application of the WACODI algorithm to the first images collected by the public via the smartphone application or “APP,” developed within the European FP7 Citclops, are presented at the end of this study.

The isotope pairing technique (IPT) is a well‐established 15N method for estimation of denitrification. Presence of anammox, the anaerobic oxidation of NH₄⁺ to N₂ with NO₂⁻ results in violation of central assumptions on which the IPT is built. It is shown that anammox activity causes overestimation of the N₂ production calculated by the IPT. However, experiments with different additions of ¹⁵NO₃⁻ 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 ¹⁵N‐N₂ production in ¹⁵NO_x⁻‐amended intact sediment cores and data addressing the contribution of anammox to total N₂ production estimated from slurry incubations. The other procedure is based on measurements of 15N₂ production in at least two parallel series of sediment cores incubated with different ¹⁵NO_x⁻ 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‐N₂ 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 N₂ production. The overestimation of true denitrification was, however, up to several hundred percent. Our analysis suggests however that the IPT does not seriously overestimate N₂ production in estuarine sediments because anammox accounts for <6% of N₂ production in such sediments, according to present knowledge.

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.

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.

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 (A_Total; 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 A_Total > 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.

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‐¹⁴CO₂ flux into the ocean remains unchanged. The improved relationship is created using revised global ocean ¹⁴C 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.

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 [¹H]NMR, C/N, and δ¹³C 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.