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

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, a[subscript]t(λ), and spectral absorption of dissolved materials, a[subscript]g(λ), were then measured concurrently using multiple meters, corrected for drift, temperature, salinity, and scattering errors and subsequently compared. Particulate absorption, a[subscript]p(λ), was obtained from a[subscript]t(λ) − a[subscript]g(λ). CTD microstructure was simultaneously recorded. Vertical profiles of a[subscript]g(λ), a[subscript]t(λ), and a[subscript]p(λ) were replicated with different meters within ±0.005 m⁻¹, and spectral relationships compared well with laboratory measurements and hydrographic structur

Characteristics, Distribution and Persistence of Thin Layers Over a 48 Hour Period

The biological and physical processes contributing to planktonic thin layer dynamics were examined in a multidisciplinary study conducted in East Sound, Washington, USA between June 10 and June 25, 1998. The temporal and spatial scales characteristic of thin layers were determined using a nested sampling strategy utilizing 4 major types of platforms: (1) an array of 3 moored acoustical instrument packages and 2 moored optical instrument packages that recorded distributions and intensities of thin layers; (2) additional stationary instrumentation deployed outside the array comprised of meteorological stations, wave-tide gauges, and thermistor chains; (3) a research vessel anchored 150 m outside the western edge of the array; (4) 2 mobile vessels performing basin-wide surveys to define the spatial extent of thin layers and the physical hydrography of the Sound. We observed numerous occurrences of thin layers that contained locally enhanced concentrations of material; many of the layers persisted for intervals of several hours to a few days. More than one persistent thin layer may be present at any one time, and these spatially distinct thin layers often contain distinct plankton assemblages. The results suggest that the species or populations comprising each distinct thin layer have responded to different sets of biological and/or physical processes. The existence and persistence of planktonic thin layers generates extensive biological heterogeneity in the water column and may be important in maintaining species diversity and overall community structure

Hyperspectral temperature and salt dependencies of absorption by water and heavy water in the 400-750 nm spectral range

The temperature and salt dependencies of absorption by liquid water (H₂O) and heavy water (D₂O) were determined using a hyperspectral absorption and attenuation meter (WET Labs, AC-S). Sodium chloride (NaCl) was used as a proxy for seawater salts. There was no significant temperature (ψₜ) or salt (ψₛ) dependency of absorption at wavelengths 550 nm, ψₜ exhibited peaks at ~604, 662, and 740 nm. A small negative trough in ψₛ occurred at ~590 nm, followed by a small positive peak ~620 nm, a larger negative trough at ~720 nm, and a strong positive peak at ~755 nm. The salt dependency of absorption by heavy water, ψₛᴴ, exhibited a negative power-law shape with very low ψₛᴴ, at wavelengths >550 nm. Our experiments with NaCl, clean open ocean seawater, and artificial seawater support the hypothesis that salts modify the absorption spectra of seawater by modifying the molecular matrix and vibrations of pure water

Spectral particulate attenuation and particle size distribution in the bottom boundary layer of a continental shelf

Spectral attenuation and absorption coefficients of particulate matter and collocated hydrographic measurements were obtained in the Mid-Atlantic Bight during the fall of 1996 and the spring of 1997 as part of the Coastal Mixing and Optics experiment. Within the bottom boundary layer (BBL) the magnitude of the beam attenuation decreased and its spectral shape became steeper with distance from the bottom. Concurrently, the slope of the particulate size distribution (PSD) was found to increase with distance from the bottom. Changes in the PSD shape and the magnitude of the beam attenuation as functions of distance from the bottom in the BBL are consistent with particle resuspension and settling in the BBL, two processes that are dependent on particle size and density. For particles of similar density, resuspension and settling would result in a flattening of the PSD and an increase in the beam attenuation toward the bottom. In both fall and spring the magnitude of the particle attenuation coefficient correlates with its spectral shape, with a flatter shape associated with higher values of the attenuation. This observation is consistent with idealized optical theory for polydispersed nonabsorbing spheres. According to this theory, changes in the steepness of the particle size distribution (particle concentration as a function of size) will be associated with changes in the steepness of the attenuation spectra as a function of wavelength; a flatter particle size distribution will be associated with a flatter attenuation spectrum. In addition, the observed ranges of the beam attenuation spectral slope and PSD exponent are found to be consistent with this theory

Biophysical forcing of particle production and distribution during a spring bloom in the North Atlantic

Abstract: The beam attenuation serves as a proxy for particulate matter and is a key parameter in visibility algorithms for the aquatic environment. It is well known, however, that the beam attenuation is a function of the acceptance angle of the transmissometer used to measure it. Here we compare eight different transmissometers with four different acceptance angles using four different deployment strategies and sites, and find that their mean attenuation values differ markedly and in a consistent way with instrument acceptance angle: smaller acceptance angles provide higher beam attenuation values. This difference is due to variations in scattered light collected with different acceptance angles and is neither constant nor easy to parameterize. Variability (in space or time) in the ratios of beam attenuations measured by two different instruments correlates, in most cases, with the particle size parameter (as expected from Mie theory), but this correlation is often weak and can be the opposite of expectations based on particle size changes. We recommended careful consideration of acceptance angle in applications of beam transmission data especially when comparing data from different instruments

Biophysical forcing of particle production and distribution during a spring bloom in the North Atlantic

Abstract: The beam attenuation serves as a proxy for particulate matter and is a key parameter in visibility algorithms for the aquatic environment. It is well known, however, that the beam attenuation is a function of the acceptance angle of the transmissometer used to measure it. Here we compare eight different transmissometers with four different acceptance angles using four different deployment strategies and sites, and find that their mean attenuation values differ markedly and in a consistent way with instrument acceptance angle: smaller acceptance angles provide higher beam attenuation values. This difference is due to variations in scattered light collected with different acceptance angles and is neither constant nor easy to parameterize. Variability (in space or time) in the ratios of beam attenuations measured by two different instruments correlates, in most cases, with the particle size parameter (as expected from Mie theory), but this correlation is often weak and can be the opposite of expectations based on particle size changes. We recommended careful consideration of acceptance angle in applications of beam transmission data especially when comparing data from different instruments

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community’s functional capabilities. Here we describe PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this ‘predictive metagenomic’ approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available