Improved Underwater Excitation-Emission Matrix Fluorometer

A compact, high-resolution, two-dimensional excitation-emission matrix fluorometer (EEMF) has been designed and built specifically for use in identifying and measuring the concentrations of organic compounds, including polluting hydrocarbons, in natural underwater settings. Heretofore, most EEMFs have been designed and built for installation in laboratories, where they are used to analyze the contents of samples collected in the field and brought to the laboratories. Because the present EEMF can be operated in the field, it is better suited to measurement of spatially and temporally varying concentrations of substances of interest. In excitation-emission matrix (EEM) fluorometry, fluorescence is excited by irradiating a sample at one or more wavelengths, and the fluorescent emission from the sample is measured at multiple wavelengths. When excitation is provided at only one wavelength, the technique is termed one-dimensional (1D) EEM fluorometry because the resulting matrix of fluorescence emission data (the EEM) contains only one row or column. When excitation is provided at multiple wavelengths, the technique is termed two-dimensional (2D) EEM fluorometry because the resulting EEM contains multiple rows and columns. EEM fluorometry - especially the 2D variety - is well established as a means of simultaneously detecting numerous dissolved and particulate compounds in water. Each compound or pool of compounds has a unique spectral fluorescence signature, and each EEM is rich in information content, in that it can contain multiple fluorescence signatures. By use of deconvolution and/or other mixture-analyses techniques, it is often possible to isolate the spectral signature of compounds of interest, even when their fluorescence spectra overlap. What distinguishes the present 2D EEMF over prior laboratory-type 2D EEMFs are several improvements in packaging (including a sealed housing) and other aspects of design that render it suitable for use in natural underwater settings. In addition, the design of the present 2D EEMF incorporates improvements over the one prior commercial underwater 2D EEMF, developed in 1994 by the same company that developed the present one. Notable advanced features of the present EEMF include the following: 1) High sensitivity and spectral resolution are achieved by use of an off-the-shelf grating spectrometer equipped with a sensor in the form of a commercial astronomical- grade 256 532-pixel charge-coupled-device (CCD) array. 2) All of the power supply, timing, control, and readout circuits for the illumination source and the CCD, ancillary environmental monitoring sensors, and circuitry for controlling a shutter or filter motor are custom-designed and mounted compactly on three circuit boards below a fourth circuit board that holds the CCD (see figure). 3) The compactness of the grating spectrometer, CCD, and circuit assembly makes it possible to fit the entire instrument into a compact package that is intended to be maneuverable underwater by one person. 4) In mass production, the cost of the complete instrument would be relatively low - estimated at approximately $30,000 at 2005 prices

Modeling the spectral shape of absorption by chromophoric dissolved organic matter

A single exponential model of the form ag(λ)∝e -seλ was evaluated in the context of its application and interpretation in describing absorption by chromophoric dissolved organic matter (CDOM), ag, as a function of wavelength, λ. The spectral slope, se, is often used as a proxy for CDOM composition, including the ratio of fulvic to humic acids and molecular weight. About three-quarters of the variability in se values from the literature could be explained by the different spectral ranges used in each study. Dependency on different spectral ranges resulted from the relatively weak performance of the single exponential as a descriptor of ag(λ) in comparison to other models that allow for greater spectral curvature. Consequently, actual variability in the spectral shape of absorption, and thus the composition of CDOM, from widely varying water types appears less than currently thought. The usefulness of five other models in describing CDOM absorption spectra in the visible domain was also evaluated. Six data sets collected with an ac9 in-situ spectrophotometer from around the coastal United States were used in the analysis. All models considered performed better than the conventional single exponential model, with the exception of a double exponential model, where the second exponential term contributed little new information in the fit. Statistically, the most useful model (judged by an analysis of variance) in the visible range was a hyperbolic model of the form: a g(λ)∝λ-sh. Although the hyperbolic model was less dependent on the spectral range used in the fit, some dependency remained. The most representative model for describing ag(λ) from the six regions considered in this study, with ag at 412 nm as input, was: ag(λ)=ag(412)(λ/412) -6.92. This spectral relationship may be suitable for remote sensing semi-analytical models which must compute a spectrum from a single estimate of CDOM absorption in the blue derived from a remotely sensed water-leaving radiance signal

Optical measurements of small deeply penetrating bubble populations generated by breaking waves in the Southern Ocean

Bubble size distributions ranging from 0.5 to 125 μm radius were measured optically during high winds of 13 m s−1 and large-scale wave breaking as part of the Southern Ocean Gas Exchange Experiment. Very small bubbles with radii less than 60 µm were measured at 6–9 m depth using optical measurements of the near-forward volume scattering function and critical scattering angle for bubbles (∼80°). The bubble size distributions generally followed a power law distribution with mean slope values ranging from 3.6 to 4.6. The steeper slopes measured here were consistent with what would be expected near the base of the bubble plume. Bubbles, likely stabilized with organic coatings, were present for time periods on the order of 10–100 s at depths of 6–9 m. Here, relatively young seas, with an inverse wave age of approximately 0.88 and shorter characteristic wave scales, produced lower bubble concentrations, shallower bubble penetration depths, and steep bubble size distribution slopes. Conversely, older seas, with an inverse wave age of 0.70 and longer characteristic wave scales, produced relatively higher bubble concentrations penetrating to 15 m depth, larger bubble sizes, and shallower bubble size distribution slopes. When extrapolated to 4 m depth using a previously published bubble size distribution, our estimates suggest that the deeply penetrating small bubbles measured in the Southern Ocean supplied ∼36% of the total void fraction and likely contributed to the transfer and supersaturation of low-solubility gases

Microscale Quantification of the Absorption by Dissolved and Particulate Material in Coastal Waters with an ac-9

Measuring coastal and oceanic absorption coefficients of dissolved and particulate matter in the visible domain usually requires a methodology for amplifying the natural signal because conventional spectrophotometers lack the necessary sensitivity. The WET Labs ac-9 is a recently developed in situ absorption and attenuation meter with a precision better than ±0.001 m−1 in the raw signal, which is sufficient to make these measurements in pristine samples. Whereas the superior sensitivity of the ac-9 has been well documented, the accuracy of in situ measurements for bio-optical applications has not been rigorously evaluated. Obtaining accurate results with an ac-9 requires careful attention to calibration procedures because baselines drift as a result of the changing optical properties of several ac-9 components. To correct in situ measurements for instrument drift, a pressurized flow procedure was developed for calibrating an ac-9 with optically clean water. In situ, micro- (cm) to fine- (m) scale vertical profiles of spectral total absorption, at(λ), and spectral absorption of dissolved materials, ag(λ), were then measured concurrently using multiple meters, corrected for drift, temperature, salinity, and scattering errors and subsequently compared. Particulate absorption, ap(λ), was obtained from at(λ) − ag(λ). CTD microstructure was simultaneously recorded. Vertical profiles of ag(λ), at(λ), and ap(λ) were replicated with different meters within ±0.005 m−1, and spectral relationships compared well with laboratory measurements and hydrographic structure

Assessing uncertainties in scattering correction algorithms for reflective tube absorption measurements made with a WET Labs ac-9

In situ absorption measurements collected with a WET Labs ac-9 employing a reflective tube approach were scatter corrected using several possible methods and compared to reference measurements made by a PSICAM to assess performance. Overall, two correction methods performed best for the stations sampled: one using an empirical relationship between the ac-9 and PSICAM to derive the scattering error (ε) in the nearinfrared (NIR), and one where ε was independently derived from concurrent measurements of the volume scattering function (VSF). Application of the VSF-based method may be more universally applicable, although difficult to routinely apply because of the lack of commercially available VSF instrumentation. The performance of the empirical approach is encouraging as it relies only on the ac meter measurement and may be readily applied to historical data, although there are inevitably some inherent assumptions about particle composition that hinder universal applicability. For even the best performing methods, residual errors of 20% or more were commonly observed for many water types. For clear ocean waters, a conventional baseline subtraction with the assumption of negligible near-IR absorption performed as well or better than the above methods because propagated uncertainties were lower than observed with the proportional method

Wave-induced light field fluctuations in measured irradiance depth profiles: A wavelet analysis

Rapid variations in the intensities of light are commonly observed in profiles of downwelling plane irradiance in the ocean. These fluctuations are often treated as noise and filtered out. Here an effort is made to extract the pertinent statistics to quantify the light field fluctuations from vertical profiles of irradiance measured under clear skies. The irradiance data are collected in oceanic and coastal waters using a traditional free-fall downwelling plane irradiance sensor. The irradiance profiles are transformed into time-frequency domain with a wavelet technique. Two signatures including the dominant frequency (<3.5 Hz) and the coefficient of variation of irradiance fluctuations along the water column are identified from the variance spectrum. Both the dominant frequency and the amplitude decrease as the inverse square root of depth, consistent with simple models of wave focusing and data from other studies. Mechanisms contributing to the observed variations and the observational uncertainties are discussed

A review of mechanically stimulated bioluminescence of marine plankton and its applications

Bioluminescence is ubiquitous in marine ecosystems and found in uni- and multicellular organisms. Bioluminescent displays can be used to deter predators, attract mates, and lure and hunt prey. Mechanically stimulated flash kinetics of zooplankton and dinoflagellates are life stage-dependent and species-specific, and could prove effective at identification and monitoring biodiversity in bioluminescent species. Here, we provide a comprehensive review of mechanically stimulated bioluminescence for the main dinoflagellate and zooplankton clades in marine environments and assemble known flash kinetics and spectral emission data. Instruments and methods used in measuring bioluminescence are also discussed. Applications, research gaps, perspectives, and biases in approaches to studying bioluminescence are identified. Moreover, emission kinetics of most zooplankton are very poorly known and constitute a critical gap. Lastly, available knowledge is interpreted in terms of potential future changes in global bioluminescence driven by climate change

Evaluation of a flow cytometry method to determine size and real refractive index distributions in natural marine particle populations

A flow cytometric (FC) method was developed to retrieve particle size distributions (PSDs) and real refractive index (nr) information in natural waters. Geometry and signal response of the sensors within the flow cytometer (CytoSense, CytoBuoy b.v., Netherlands) were characterized to form a scattering inversion model based on Mie theory. The procedure produced a mesh of diameter and nrisolines where each particle is assigned the diameter and nrvalues of the closest node, producing PSDs and particle real refractive index distributions. The method was validated using polystyrene bead standards of known diameter and polydisperse suspensions of oil with known nr, and subsequently applied to natural samples collected across a broad range of UK shelf seas. FC PSDs were compared with independent PSDs produced from data of two LISST-100X instruments (type B and type C). PSD slopes and features were found to be consistent between the FC and the two LISST-100X instruments, but LISST concentrations were found in disagreement with FC concentrations and with each other. FC nrvalues were found to agree with expected refractive index values of typical marine particle components across all samples considered. The determination of particle size and refractive index distributions enabled by the FC method has potential to facilitate identification of the contribution of individual subpopulations to the bulk inherent optical properties and biogeochemical properties of the particle population

Temporal and spatial occurrence of thin phytoplankton layers in relation to physical processes

In 1996 three cruises were conducted to simultaneously quantify the fine-scale optical and physical structure of the water column. Data from 120 profiles were used to investigate the temporal occurrence and spatial distribution of thin layers of phytoplankton as they relate to variations in physical processes. Thin layers ranged in thickness from a few centimeters to a few meters. They may extend horizontally for kilometers and persist for days. Thin layers are a recurring feature in the marine environment; they were observed and measured in 54% of our profiles. Physical processes are important in the temporal and spatial distribution of thin layers. Thin layer depth was closely associated with depth and strength of the pycnocline. Over 71% of all thin layers were located at the base of, or within, the pycnocline. The strong statistical relationships between thin layers and physical structure indicate that we cannot understand thin layer dynamics without understanding both local circulation patterns and regional physical forcing