Abstracts of the
Coastal Benthic Optical Properties (CoBOP) Program
Effects of Sediment Microfabric on Benthic Optical Properties
Principal Investigator: Mead Allison
PROJECT SUMMARY: Microfabric is defined as the particle size, shape, alignment, sorting, and composition (organic and inorganic) of a sediment. This project proposes to examine the interaction of various inorganic sedimentary parameters on the bidirectional reflectance (BDRF), adsorption, and fluorescence characteristics of sediment seabed surfaces and of shallow sediment layers (to 1-3 cm depth). Planned CoBOP field sites in siliciclastic and carbonate settings will be sampled in "loose" sediment and in seagrass areas. The field effort will be coordinated with localities and time periods when water column light measurements are being made by other CoBOP investigators. Undisturbed seabed samples will be analyzed in the laboratory for microstructural characteristics by thin-section, SEM/TEM, granulometry, and mineralogical techniques. These analytical techniques will support the primary laboratory effort to make spectral measurements of reflectance, transmission and fluorescence of oriented sediment thin-sections on a microspectrometer assembled for the study. This laboratory approach was selected as the best available compromise for making direct measurements of light behavior at, and below, the sediment surface, given present limitations of in situ technology and the mobile, high porosity nature of the optically relevant sediment zone. Empirical data will be integrated with other CoBOP sediment projects to examine how inorganic processes interact with organic components (benthic microalgae, biofilms, DOM) to control the optical signal.
HYPOTHESES: Research efforts will be focused upon testing the following hypotheses that relate to seabed microfabric:
1) Sandy coastal sediments typically contain 10-50% matrix (i.e., the fine-grained sediment fraction) that is incorporated by sedimentation, biofilm trapping, pelletization, infiltration of pore spaces, and internal production. Spatial (lateral and vertical) and temporal variability of the matrix) is the most important control on optical heterogeneity in terrigenous and carbonate sandy coastal sediments. This is due to different origins of the matrix components and a tendency toward preferential alignment of "platy" grains. Further, variations in the mode of fine-grained particle emplacement will be recognizable in microscopic and SEM sections and will influence spectral properties in a predictable fashion.
2) In the absence of matrix, inorganic optical variability of the coarse (sand-size) fraction is primarily a function of mineralogy in quartzo-feldspathic settings and a function of shape/packing in carbonate coastal settings. This is anticipated because of the dominance of near-spherical particles in siliciclastic settings.
3) Preferential alignment of sedimentary particles along bedding planes by a) hydrodynamic sorting by size, shape, and composition; b) by changes in the sediment source function(s); and by c) zonation of benthic microalgal communities are characteristic of energetic, mobile coastal sands and will produce large differences in light properties relative to identical components which have been homogenized.
4) Matrix fluorescence in sandy coastal sediments is spatially heterogeneous on length
scales resolvable by remote sensing methods (~1 cm in the laser line scanner). This is
controlled by covariance of optically "active" inorganic particles (many common
sedimentary minerals fluoresce in the visible band), organic particles (POM) and benthic
microalgae, and dissolved organic matter (DOM) in pore waters. Temporal variations in
inorganic sediment influx and removal (resuspension) will be one significant cause of
spatial patterns change, both by changing the abundance of fluorescent mineral grains and
by the dilution effect of "inactive" sediment grains.
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Spatial and Diel Variability in Photosynthetic and Photoprotective
Pigments in Shallow Benthic Communities
Principal Investigators: Larry Brand and Carol Stephens
INTRODUCTION
As with most environmental parameters, one can expect considerable spatial and temporal variability on a range of scales in the optical properties of shallow benthic communities. Much of this is certainly caused by biological variability. Understanding the causes of this biological variability is the long term goal of ecologists but is, while desirable, ultimately mostly beyond the scope of this project.
We hypothesize however that one component of this variability is fairly predictable and should be able to be detected within the "noise" of natural variability. This component is diel variability in a wide variety of biological properties, which is caused by both external forcing (diel variation in solar energy) and internal forcing (the biological clock). The diel variation in the optical characteristics of the community needs to be known in order to interpret and cross-calibrate optical data collected at different times of the day and night. Spatial variability will be examined to determine how substrate variability affects biological optical properties.
Our overall goal is to document the natural spatial and temporal variability,
particularly diel variability in the photosynthetic and photoprotective pigments and the
fluorescence spectra of photosynthetic organisms found in shallow marine benthic
communities. We are primarily interested in the photosynthetic bacteria, cyanobacteria.,
eukaryotic microalgae, and macroalgae found in the Dry Tortugas, FL and Monterey Bay, CA,
with a secondary interest in the seagrasses and corals.
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Colored Dissolved Organic Matter in Sediments and Seagrass Beds
and its Impact on Shallow Water Benthic Optical Properties
Principal Investigator: David J. Burdige
Abstract
The optical properties of shallow water coastal environments are a complex function of physical and biogeochemical processes occurring both in the sediments and in the water column. Developing models of the optical properties of these environments requires further knowledge of the processes affecting light alteration and modification by biogeochemical reactions in the surficial sediments and at the sediment-water interface. The goal of this proposal is to examine one aspect of this problem, namely the impact of dissolved organic matter (DOM) in sediment pore waters on benthic optical properties. In particular, I propose to examine the processes affecting the production of colored and fluorescent dissolved organic matter (CFDOM) in sediment pore waters, the mechanism(s) by which this material may be transported out of the sediments, and the impact of pore water CFDOM on the optical properties of the shallow water benthos (i.e., both the sediments, the sediment-water interface and the waters overlying the sediment, including the benthic boundary layer).
Proposed Objectives
The overall goals of this project are to examine the processes affecting the production of colored and fluorescent dissolved organic matter (CFDOM) in sediment pore waters, its transport out of sediments, and the impact of pore water CFDOM on the optical properties of the shallow water benthos (i.e., both the sediments, the sediment-water interface and the waters overlying the sediment, including the benthic boundary layer). The specific questions I propose to examine in this proposal are:
1. What are the optical properties of CFDOM in pore waters and near the sediment-water interface (i.e., the benthic boundary layer)? Can we relate the two?
2. Does the presence and benthic flux of pore water CFDOM influence the light field of the sediment-water interface? the sediments?
3. What is the "optical fate" of pore water CFDOM at or just above the sediment-water interface?
To address these questions I will use a combination of field measurements and
experiments, all carried out in close cooperation and coordination with other funded CoBOP
researchers.
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Coastal Benthic Optical Properties of Coral Environments:
ROV/AUV Optical Classification
Principal Investigators: Kendall L. Carder and Dave K. Costello
1.0 INTRODUCTION/STATEMENT OF SCIENTIFIC AGENDA
This proposal requests funds for a continuation of our work begun under ONR grant
Coastal Benthic Optical Properties of Coral Environments: ROV/AUV Optical Classification. The primary goals and objectives remain the same:
1) Development of remote sensing models to quantify optical properties of the water column and bottom.
2) Develop the means to rapidly measure the optical properties of the coastal ocean and bottom.
3) Develop a means of rapidly and remotely classifying bottom features on the basis of the elastic and inelastic bottom albedo.
However, the work proposed for the next stage of the project has been expanded and is strongly weighted toward field operations with enhanced data acquisition abilities to enable hyperspectral, optical modeling of coastal marine environments.
Some of the ongoing scientific questions to be addressed include the following:
1) Under what conditions can chlorophyll a and colored dissolved organic matter (CDOM) concentrations be quantified remotely (from airborne or spaceborne hyperspectral sensors)?
2) Under what conditions can bathymetry be remotely determined using hyperspectral data from waters of varying bottom albedo, turbidity, and absorption properties?
3) Under what conditions can benthic plant classification (benthic diatom and algal mats, seagrasses, green and red macrophytes, and corals) be performed remotely?
4) Under what conditions can bottom sediment type (calcareous/quartz sand, clay, mud) or structure (reef, rock, man-made) be classified remotely?
The expanded work proposed here is required in order to interpret hyperspectral, remote sensing data for coastal waters to test radiative transfer models. This primarily involves four additional areas of investigation:
1) the bidirectional reflectance distribution function (BRDF)
2) the upwelling attenuation coefficient for bottom-reflected radiance
3) hyperspectral modeling in homogenous and vertically structured waters for
uniform and contrasting bottom albedos.
4) 3-dimensional Monte Carlo modeling of grass and coral canopies: scattering effects on apparent BRDF.
5) the enhancement of the elastic bottom albedo through inelastic processes
(fluorescence).
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UAV Borne Hyperspectral Imaging System
for Benthic and Littoral Applications
Principal Investigators: John A. Antoniades and Curttis O. Davis
Abstract
Recent experience with aircraft imaging spectrometers has demonstrated their suitability for assessing water column and bottom optical properties in the littoral zone. Here we propose building an imaging spectrometer optimized for the coastal ocean that is suitable for operation on manned or unmanned aircraft. The system includes the hardware and software necessary for complete remote operation during UAV flights. The Ocean PHILLS will be operated on the ONR Pelican or other platform to support the CoBOP experiment and to test algorithms for water column and benthic optical properties.
Objectives
1. A PHILLS aircraft imaging spectrometer optimized for the coastal ocean has been designed for aircraft operation. The PHILLS instruments are small compact systems suitable for UAV operation. Here we propose building an Ocean PHILLS modified to be capable of fully remote operation for use on a UAV.
2. However, the sensor alone is not adequate for littoral and benthic studies. Two approaches will be provided for processing and analysis of the data. First, laboratory calibrations and atmospheric correction will be applied which have been developed based on the experience with AVIRIS data (Gao et al., 1993) and that are being adapted for the PHILLS data under current funding. Then existing models (e.g., Lee et al., 1994) can be applied to separate water column and benthic optical properties.
3. The PHILLS project has developed the Optical Real-time Adaptive Signature
Identification System (ORASIS; Bowles et al., in press) for automated endmember
determination and subpixel demixing of arbitrary scenes. ORASIS exploits data obtained by
broad band hyperspectral imagers to identify objects not only by absorption band
characteristics, which are severely modified by the water, but also by the small
differences in the continuum reflectance of the dissolved substances. These small
differences are responsible for the unique fingerprints associated with dissolved organic
matter, resuspended sediments, etc.
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MICROBIAL BIOFILMS: A parameter "masking" the
apparent optical spectral properties of surfaces.
Principal Investigator: Alan W. Decho
Successful closure between inherent and apparent properties of objects for radiative transfer modelling is a major goal of the CoBOP project. Fluorescence emission and spectral reflection provide two important sources for the detection of upwelling scalar irradiance, and in the final interpretation of objects.
Virtually all surfaces placed in seawater will acquire a "microbial biofilm" coating especially in sediment and seagrass systems. Biofilms consist of microbial cells (i.e. bacteria or microalgae) enclosed within a matrix of mucous "exopolymer" molecules. The presence of a biofilm coating constitutes a potentially important light-altering parameter which may contribute to differences observed between inherent and apparent optical properties of an object or surface. Even a relatively thin (10-100 mm) biofilm, due to its high sorptive capabilities, may concentrate significant amounts of optically-active dissolved organic matter (DOM) from the surrounding water. The inherent properties of biofilm exopolymers may modify optical scattering, reflectance and fluorescence, and alter optical spectra of both micro- and macroscale structures.
My proposed studies focus on three biofilm processes which alter fluorescence and spectral reflection, and may "mask" the inherent optical properties of sediments, objects and seagrasses:
(1) Sorptive-concentration of DOM by biofilms, acts a "Photon-sink", to Absorb Light: The biofilm acts as a "Sorptive Sponge" which concentrates DOM from seawater. Sorption of optically-active DOM in a biofilm may significantly reduce the incident light reaching a substrate, and alter its resulting spectral reflectance.
(2) Biofilm may "Quench" fluorescence emissions of an underlying substrate, and "Mask" its optical signature: Emission of fluorescent signals by an underlying substrate will be "quenched" by DOM concentrated within overlying biofilm coating. Additionally, fluorescent cells within the biofilm may produce their own "Masking" Fluorescence Signature, different from that of the underlying substrate.
(3) Biofilm exopolymers in Sediments may "Enhance Scattering of Incident Light and Reflection": Exopolymers are a binding agent in sediments, and may affect light scattering and penetration. These processes will modify optical spectra and bidirectional reflectance of light from sediments. To understand (and predict) variability in these effects, field measurements and manipulative "sediment-coating" experiments will be conducted at different times of the year and under different conditions (e.g. diel, sediment vs. seagrass, carbonate vs siliceous sediments).
Biofilms interact with important biological, chemical, and geological features of
coastal benthic systems. Investigating the masking effects of biofilms will be central to
understanding the optical properties of coastal sediment and seagrass systems. Finally,
these data will be used to develop "biofilm correction factors" which adjust for
masking effects in radiative transfer models, and reach closure between inherent and
apparent optical properties.
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Influence of Sedimentary and Seagrass Microbial Communities
on Shallow Water Benthic Optical Properties
Principal Investigator: Frederick C. Dobbs
An overall goal of the Coastal Ocean Benthic Optical Properties (CoBOP) program is to produce a working radiative-transfer model for selected sub-littoral zone environments. It is anticipated that the model will be derived from first Principals, that is, it will predict the inherent optical properties of the benthic environment given input from microbiology, geochemistry, sedimentology, and physics. In the context of microbiology, it will be important to investigate the entire community of microorganisms associated with the benthic environments of focus--sediments and seagrass. For several reasons, before incoming light reaches the sediment or seagrass blades and prior to any light returning to the water column, it must pass through a microbial "gateway" that may affect its quantity and quality.
I anticipate two distinct contributions to the CoBOP program. The first is scientific and will use lipid analyses to characterize and quantify the microbial communities living in sediments and on the blades of seagrasses. Two study sites, one in the Dry Tortugas (a carbonate environment) and the other in Monterey Bay (a siliciclastic environment) will be occupied one to two times per year during the three-year project. Data from this proposed investigation, together with the first-Principals information collected by other CoBOP sediment researchers, will be delivered to the optical modelers and integrated into their radiative-transfer models.
The second contribution is administrative, one in which I anticipate coordinating the sediment research team (microbiology, sedimentology, geochemistry, physics) and acting as its liaison to ONR personnel, as well as liaison to the coordinators of other CoBOP research teams (seagrass, coral reef, instrumentation, modeling).
Objectives
Microbiology:
* Determine the biomass and composition of sedimentary microorganisms at field sites in the Dry Tortugas and Monterey Bay
* Assess seasonal and interannual variations in these microbial communities
* Similarly, determine the biomass, composition, and temporal variation (seasonal and interannual) of microorganisms associated with seagrass blades in the Dry Tortugas (Thallassia spp.) and in Monterey Bay (Zostera marina).
* In concert with other CoBOP researchers, assess how the microbial community affects the flux of photons to and from the sediments and eelgrass blades and how temporal changes in the microbiological community influence temporal changes in benthic optical characteristics
Administration:
*Coordinate various sediment biologists, geochemists, and geologists
*Serve as liaison from the sediment group to ONR personnel as well as to the coral
reef, seagrass, modeling, and instrumentation groups.
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Processes Affecting the Variability of Fluorescence Signals
from Benthic Targets in Shallow Waters
Principal Investigator: Paul G. Falkowski
Summary
The major theme of this proposal is to understand processes that contribute to fluorescence emission from benthic targets in the coastal and shallow waters with the overarching goal of developing parameterization schemes that optically detect anthropogenic objects. This effort is part of the larger CoBOP DRI. The proposed research has three basic tasks: (1) To analyze data obtained from in situ fluorescence detectors, especially the scuba-based Fast Repetition Rate Fluorometer and to iteratively improve the instrumentation and retrieval algorithms in support of CoBOP field measurements. (2) To measure fluorescence lifetimes in the subnanosecond time domain from model organisms. This task will be carried out at the National Synchrotron Light Source (NSLS) at BNL, and will provide the fundamental knowledge for the interpretation of in situ lifetime measurements. (3) To examine both NASA Shuttle and high orbital visible and near IR channels to correlate spectral emission/absorption characteristics deduced on small scales to large scales. This latter task will examine the first order applicability of CoBOP optical models to sub-tropical and tropical shallow water benthic environments.
Goals of the proposed research:
The goals of the proposed research are threefold:
1. To identify the sources of variations in the effective absorption cross sections of the target molecules, fluorescence lifetimes (and by inference, quantum yields) of individual chromophores, and to provide an interpretive understanding of how physical, chemical, and biological variability affects these optical properties.
2. To determine the extent and variability in the coupling of absorbed radiation to the fluorescence emission spectrum, and the development of biophysical radiative transfer models that predict the latter from the former in a variety of benthic environments.
3. To develop an understanding of the spatial and temporal variability in benthic and
optical signals.
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Smart Sensor for Extended Range Optical Imaging
Principal Investigator: Jules S. Jaffe
Abstract
This proposal requests funds to develop and test, via experimental construction, a new idea for an extended range underwater optical imaging system. The system is a semi-solid state version of a laser scanning system that has proven itself as the best imaging system in the ocean today. Our novel contribution is to replace the scanning receiver with a high speed solid state array which has the capability to measure time varying radiance. By measuring and analyzing the time evolving radiance that is incident on the elements of the imaging array we will create an image of both the reflectance and also the distances of the objects that are in the field of view of the sensor. This combination of extended range imaging of reflectance in conjunction with topography has important consequences for identifying buried objects, like mines, which are typically covered with a layer of sediment. In addition, the replacement of the mechanical elements with solid state ones will permit the fabrication of a more reliable, less expensive, and more flexible imaging system. The system thus provides more information at a reduced price than existing laser line scan systems.
Specific Program Goals
The specific goal of this program is to come up with a "proof of concept"
demonstration unit which is a prototype of an extended range imaging system. The system
will be assembled in the lab in year 1 from existing commercially available components in
order to gain familiarity with the technology and to uncover any hidden problems that we
do not anticipate right now. In year two, we will fabricate a seagoing version of the
system that will be deployed on a towed body. This first system will be only one
dimensional and it will permit a visual swath mapping system, similar to the existing
laser line scan system. In year 2 we will also start the development of a 2-dimensional
version of the system which will be used to record 2-dimensional images rather that a
single line image as above. In year 3, we will deploy the 2-dimensional imaging system in
the ocean as a proof of the concept for this phase of the development. If we are
successful, we will have demonstrated that an inexpensive, flexible and reliable extended
range imaging system can be developed. This will have great impact on future NAVY systems
as this sensor will be inexpensive enough for it to be incorporated, routinely in these
systems. System results will be analyzed to characterize the performance of the system.
Accuracy in the range resolution of the system will be judged by deploying targets of
known relief. Images will be inspected for clarity using well known measures such as
signal-to-noise of the MTF of the system as a function of range and turbidity of the
water.
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Coastal Benthic Optical Properties (CoBOP) of Coral Reef Environments:
Effects of Changes in the Spectral Quality and Quantity of the Underwater Light Field
and Elevated Temperatures on Small Scale (0.01 to 0.1 m) Optical Properties of Corals
Principal Investigator: Michael P. Lesser
Scope of Project
Coral reefs have one of the highest rates of primary productivity and biodiversity
measured for any natural ecosystem. Additionally, they are important sites of calcium
carbon deposition and a long-term sink for carbon dioxide. Corals, in particular, provide
a substantial amount of the reef framework along with various forms of calcareous algae.
This framework is home to many species of photosynthetic organisms that span several
taxonomic groups. Despite the perception of a homogeneous environment, the rates of
photosynthesis, respiration, and calcification of coral reef primary producers are greatly
effected by changes in light (both ultraviolet and visible), nutrients, dissolved gases,
temperature, and flow regime. Monitoring changes in the metabolic rates of corals over
large spatial scales, even larger than meters, is technically difficult. For areas less
than a meter we presently have the capability to measure metabolic rates of corals and
associated reef organisms. One way to assess the primary productivity of coral reefs on
larger spatial and temporal scales is to take an optical approach. Any optical approach to
monitoring coral reef productivity must include a mechanistic approach to the underlying
reasons for changes in the optical signal(s) of choice. Part of the optical approach is to
obtain optical closure, assessing which photons are absorbed, reflected, or re-emitted as
fluorescence. Areas of high absorbance reflect the presence of primary producers
containing photosynthetic and accessory pigments. The mechanistic understanding of the
optical reflectance and fluorescence signatures of a benthic community permits other types
of reef classification. A high percentage of the surface cover of coral reefs consists of
dead reef and calcium carbonate sands. The optical approach will also be able to delineate
between living and dead reef structures. Against this background signal from the natural
environment comes the optical signal of man-made objects placed on the bottom. These
structures are subject to fouling by many species of primary producers such as algal
turfs, cyanobacteria, and macroalgae. If we understand the optical signals of coral reefs,
and the mechanistic causes for changes in those signals, both taxonomically and
physiologically, we might then be able to distinguish between the optical signature of
man-made objects versus the natural signal using a variety of tools already available or
being developed.
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Spatial and Temporal Measurements of Benthic Optical Properties
Principal Investigator: Robert Maffione
ABSTRACT
We propose to intensively study the light field that interacts with the benthic environment in optically shallow waters. This study will involve long-time series measurements, with a benthic mooring, of light field parameters near the bottom, the irradiance reflectance of the bottom, and the light field penetrating the top layer of sediments. The three major bottom types, sediments, corals, and seagrasses, will be investigated. Seagrass studies will include measurements of the light field incident on the seagrass, penetrating through the seagrass canopy, and incident at the base of the seagrass. The measured light-field parameters will include the full three-dimensional vector irradiance, scalar irradiance, and the radiance distribution. Irradiance measurements will be spectral, covering the wavelength range from 350 to 700 nm. A surface buoy will measure the spectral irradiance incident on the water's surface, as well as wind speed and air temperature. In addition to light field parameters, the bottom mooring will measure water temperature, three-axis current velocity, surface wave spectra, turbidity and fluorescence. Bottom mooring measurements will be supplemented with routine measurements from a boat of the water column inherent optical properties (IOP's).
The bottom mooring we propose to build is referred to as BSAP, for Benthic Stationary
Autonomous Profiler. BSAP measurements will provide critical data for developing and
verifying shallow-water radiative transfer models and for furthering our understanding of
the interaction of the benthos with the light field. For example, one-dimensional
radiative transfer models, such as Hydrolight, compute the light field given a set of
boundary conditions and the IOP's of the water column. Thus to verify Hydrolight's output,
we must measure it. This is a static process, but it is the first step that must be taken
towards verifying our approaches to modeling shallow-water radiative transfer. We know,
however. that the interaction of the light field with the benthos is a dynamic process -
it changes over time. To better understand this dynamic process so that we can begin to
develop predictive models of shallow-water optics, we need to gather long time series
data. BSAP will provide this. In addition, our periodic visits to the mooring site will
give us many opportunities to gather a complete set of data to achieve closure.
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Coastal Benthic Optical Properties:
Characteristics and Processes Related to Optical Properties
of Benthic Marine Organisms and Substrates
Principal Investigator: Charles H. Mazel
SUMMARY
This proposal concerns research to be carried out in support of the ONR Departmental Research Initiative in Coastal Benthic Optical Properties (CoBOP). The general issues to be addressed in this effort are:
1. detailed investigation of the fluorescence properties of coral reef organisms. This will include measurement of the excitation/emission properties of the pigments; collaboration in biochemical identification of the pigments; investigation of temporal variations in the optical characteristics; and investigation of the biological conditions and processes that determine the fluorescence properties.
2. measurement of the optical properties (fluorescence and reflectance) of a more general range of benthic organisms and substrates. This will provide data that will support the efforts of those working on optical models aimed at achieving optical closure, and the associated researchers working on other aspects of the general benthic optics problem (sediment and seagrass environments),
3. coordination of coral reef research sub-group data collection and presentation.
The primary research method will be in situ measurement. This will be supplemented by laboratory measurements for optical measurements that are beyond the current state-of-the-art for in situ implementation. Measurement of optical properties will cover all pigments, both fluorescent and nonfluorescent. Detailed biochemical and biological characterization will focus on the non-photosynthetic fluorescent pigments. The nature of these substances is still not known. Nor are the temporal variations (at either short or long time scales) in the fluorescent properties, or the underlying processes that modify these properties.
The work will be carried out as a part of the coordinated CoBOP program. Particularly
close collaboration is anticipated with some researchers (e.g. Mike Lesser for
biochemistry and optical measurements related to photosynthesis), and the data will be
coordinated with that of the research team as a whole.
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Radiative Transfer Modeling for CoBOP
Principal Investigator: Curt Mobley
BACKGROUND
The Coastal Benthic Optical Properties (CoBOP) program takes optical oceanography and radiative transfer theory into a new domain - shallow water with highly variable bottom topography and bottom optical properties. Because of the spatial inhomogeneity of the bottom optical properties, the light field within the water will vary in all three spatial dimensions. In addition to the light-field effects induced by elastic scattering from the bottom, fluorescence by different bottom substances such as corals, benthic diatoms, or sea grasses can significantly alter the spectral character of the light field. These fluorescence effects can be important to both passive and active remote sensing systems. Radiative transfer questions related to these three dimensional and bottom-inelastic effects have never been addressed.
Instrumentation to be developed for the CoBOP field experiments will make measurements
of the near-bottom light field and of bottom physical and optical properties with
unprecedented temporal, spatial, directional. and wavelength resolution. Radiative
transfer numerical models provide the closing link between these various measurements. The
CoBOP program provides numerous opportunities for collaborations where heretofore
radiative transfer has seldom or naively been applied to problems such as primary
production by seagrasses or light absorption and reflection by sediments.
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Analysis of hyperspectral coastal ocean color data
Principal Investigator: William Philpot
1 . Introduction
Numerous methods have been developed for extracting water quality information from spectral data. Most have been designed to use data from multispectral sensor systems with spectrally discontinuous bands and relatively wide spectral bandwidths with each spectral band being treated as an independent variable. Band differences, band ratios, principal component analysis, and most other algebraic operations fall into this category. The assumption that the spectral bands are independent is entirely appropriate for multispectral data and procedures based on that assumption have been successfully applied to multispectral data for open ocean waters (Gordon and Morel, 1983).
Multispectral methods are more difficult to apply to coastal or inland water spectra. Where the optically important water components covary or where only a few distinct components control the spectral variability of the water-leaving radiance, multispectral methods still have value even when hyperspectral data are available (Carder et al., 1993; Gould and Arnone, 1994; Lee, 1994). However, as the number of optically important components increases, extracting useful information about the optical components of the water is not only likely to require hyperspectral data but more appropriate analysis methods as well.
Hyperspectral data, consisting of spectrally contiguous bands, each with a relatively narrow bandwidth, have a better chance of capturing subtle details in the spectra of coastal waters. The assumption of band-to-band independence does not hold for this data and the standard multispectral analysis methods are not entirely suitable. Nonetheless, researchers in remote sensing have tended to use or modify the multispectral methods to select an optimal set of bands or to generate new algorithms (Hamilton et al., 1993; Lee and Landgrebe, 1993). While there have been some attempts to apply techniques that attempt to make better use of the band-to-band dependencies (Campbell and Esaias, 1983; Philpot, 1991), there is far more potential to be developed.
We propose to develop spectral techniques for ocean color analysis that are explicitly
designed for use with hyperspectral data. In particular, we propose to apply spectral
decomposition methods to hyperspectral remote sensing data, to identify the major
components of the spectra and, hopefully, to relate the spectral components to optically
important water properties, e.g., pigment concentration, DOM, CDOM (Bricaud et al., 1988;
Bricaud and Stramski, 1990; Kiefer and SooHoo, 1982; Yentsch et al., 1985; Yentsch and
Yentsch, 1984). The major focus of our efforts will be on the airborne, hyperspectral
imaging system that is scheduled to be flown during the planned Dry Tortugas field
experiment; however, the techniques that we develop should be equally applicable to any
high-resolution spectral data.
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Composition, Texture and Diagenesis of Carbonate Sediments:
Effects on Benthic Optical Properties
Principal Investigator: R. Pamela Reid
Statement of the Problem
Light in aquatic ecosystems has been studied intensively in the water columns of lakes and oceans (see for example the Dec. 1989 issue of Limnology and Oceanography). In contrast, knowledge of the optical properties of benthic environments is limited. Sorting out how geologic and biologic parameters of bottom sediment interrelate to determine spectral reflectance and its contribution to the upwelling component of scalar irradiance will be of critical importance in understanding the variability of optical properties of the sea floor in space and time and in modeling radiative transfer in shallow water.
The optically clear water of carbonate environments, which characterize shallow shelves and submarine platforms in low latitudes, is ideal for investigating interactions of light with the benthos. My proposed research will focus on physical and chemical properties of carbonate sediment with the goal of determining feedback mechanisms between these sedimentologic characteristics, benthic organic production and light.
Proposed Research
Objectives and Hypotheses
The proposed research will investigate the composition, texture and diagenesis of shallow-water carbonate sediments. Measurements of physical and chemical sedimentologic properties will be integrated with biologic and optical measurements made by collaborating investigators in the CoBOP Program and used to model benthic light fields. Hypotheses that will be tested are as follows:
1. Light is modified at the sediment-water interface as a function of grain composition and texture (i.e. size, shape, surface roughness, density, and packing). These sedimentologic parameters will affect both the light fields within the sediment and the spectral reflectance of the sediment.
2. Substrate and corresponding light fields within the sediment determine benthic biological community structure and organic production. The organic components, in turn, interact with carbonate grains, causing diagenetic alteration. Grains of equivalent grain size but different diagenetic state have distinct optical signatures.
3. Relationships between downwelling light, physical and chemical sedimentologic
properties, light fields within the sediment, and benthic biological production are
predictable and can be used to model spectral reflectance.
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Inelastic Light Scattering in the Coastal Zone and in Benthic Environments
Principal Investigator: Kenneth J. Voss
LONG RANGE SCIENTIFIC OBJECTIVES
My work involves experimentally investigating the interrelationships and variability of optical properties in the ocean and atmosphere. My goal is to define the variability of the optical properties, particularly those dealing with light scattering, and to improve the prediction capabilities of image and radiative transfer models used in the ocean.
My near term objectives have been 1) to quantify the role and importance of inelastic scattering in the natural in-water radiation field, 2) to improve the measurement capability of measuring the in-water and above-water spectral radiance distribution, and 3) to investigate the variability of the Point Spread Function (PSF) as it relates to the imaging properties of the ocean. This last work has recently focused on aspects of the PSF relating to the littoral zone, including effects due to layering of the optical properties on the PSF.
PROPOSED RESEARCH
Our work in this period will continue the inelastic scattering measurements in two
areas, coastal waters with high DOM concentrations, and the benthic environment (as part
of the CoBOP program). In addition, as part of our CoBOP efforts we will be designing and
constructing an instrument to make in situ bi-directional reflectance measurements.
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The Impact of Bottom Roughness and Bioturbation Intensity
on Benthic Optical Properties
Principal Investigator: Rob Wheatcroft
I. Long-Range Scientific Objectives
The ultimate objective of this research program is to identify and obtain a predictive understanding of the physical and biological processes responsible for the formation and maintenance of the microtopography (decimeter to millimeter) of the sea floor. To achieve this goal, it is necessary to study formative processes occurring on the sediment surface (e.g., biogenic mound formation, ripple development), as well as processes occurring within the seabed (e.g., bioturbation, compaction) which generally lessen microtopography. The approach to these areas of interest is predominantly field-oriented, with a secondary emphasis on model development.
II. Scientific Objectives of this Proposal
The objective of this proposal, which is submitted as a part of the Coastal Benthic
Optical Properties (CoBOP) DRI, is to study the impact of bottom roughness (biological and
physical) and bioturbation on benthic optical properties. I specifically propose to
conduct a field study at a sediment - seagrass site within Dry Tortugas National Park in
which co-located measurements of bottom roughness and sediment bioturbation rate will be
made on multiple spatial (cm to 10's m) and temporal (hour to seasonal) scales. Data
collection and analysis will be made in conjunction with researchers studying aspects of
carbonate sedimentology (Pamela Reid, University of Miami; Mead Allison, Texas A & M
University), the microdistribution, diel variability and spectral properties of epibenthic
microalgae (Larry Brand, University of Miami), the microdistribution of nonphotosynthetic
microbes (Fred Dobbs, Old Dominion University), as well as the optical properties of the
near-bottom region (Robert Maffione and Curt Mobley, SRI; Ken Voss, University of Miami).
Insight obtained in this study will have important ramifications for diverse oceanographic
problems including high-frequency acoustics, sediment transport, benthic ecology and,
especially, the near-bottom light field.
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CoBOP Coral Reefs: Optical closure of a coral reef submarine light field.
Principal Investigators: Charles S. Yentsch and David A. Phinney
ABSTRACT
This program of research will supply the basic optical data for the development of optical remote sensing algorithms which will allow the determination of biomass, diversity and primary production of benthic coral, seagrass and macroalgal communities.
The focus of the program is the measurement of spectral signatures of reflectance and fluorescence for the major groups of benthic organisms solar induced photosynthesis and bio-fouling of man-made materials. The effect of boundary layer flow on the variability of water column optical properties will also be investigated. The program strongly argues that with knowledge of the contribution of in-water optical properties and the spectral reflectance and fluorescence of the benthic organisms, water leaving radiances contain ecological information concerning the biomass, diversity and primary production of benthic communities.
RESEARCH GOALS
1) Determine the influence of boundary layer flow on the variability in optical proper-ties of coastal waters. What are the effects of tidal and secondary flows, non-tidal flow and internal waves?
2) Determine the reflectance and fluorescence spectral signatures of corals, seagrasses, macroalgae and unconsolidated sediments in meter scale patches and as individual organisms. Specific emphasis will be placed on the changes in spectral reflectance and fluorescence as a function of depth.
3) Chlorophyll and phycoerythrin fluorescence emission as indicators of physiological status and photosynthetic kinetics measured by fluorescence decay as a function of time.
4) Measurement of spectral reflectance and fluorescence from bio-colonization of
selected surfaces.
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Inherent Optical Properties in the Benthic Environment
Principal Investigators: J. Ronald V. Zaneveld and W. Scott Pegau
ABSTRACT
Little is known about the optical characteristics of various bottom types. In order to correctly solve the equation of radiative transfer the spectral absorption and bidirectional scattering characteristics of the bottom must be known. We propose to modify recently developed instrumentation so that they can be operated by divers. This allows optical micro environments to be investigated. These devices are the 9 wavelength absorption and attenuation meter (ac-9), the spectral absorption and fluorescence meter (SAFire) and the intermediate and large angle scattering sensor (ILASS). They lend themselves to diver-operated realizations, as they all are flow-through devices.
We propose to study the small scale (temporal and spatial) structure of the IOP in benthic regimes. We will work with other scientists in the project to determine what particulate and dissolved material properties cause the observed variations in the IOP. We would like to see if the distribution of the IOP (including fluorescence) can be used to detect small scale benthic structures including man-made objects. We are interested in studying how the particulate and dissolved material distributions are affected by small scale benthic structures including anthropogenic objects. In turn we want to determine how the small scale variations in the IOP affect radiative transfer and visibility in benthic environments.
QUESTIONS TO BE ADDRESSED
1. What is the small scale (temporal and spatial) structure of the complete set of IOP in benthic regimes?
2. What particulate and dissolved material properties cause the observed variations in the IOP? Can the IOP be inverted to give cm scale distributions of particulate and dissolved material properties?
3. How are the particulate and dissolved material distributions affected by small scale benthic structures including anthropogenic objects? And conversely, can the distribution of the IOP (including fluorescence) be used to detect small scale benthic structures including man-made objects?
4. How do the small scale variations in the IOP affect radiative transfer and
visibility in benthic environments?
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Radiative Transfer in Seagrass Canopies
Principal Investigator: Richard C. Zimmerman
I. PROPOSAL SUMMARY OF INFORMATION
A. Statement of Objectives
The proposed study will develop a model of radiative transfer for seagrass canopies that includes canopy architecture, impacts of water motion and bottom reflectance below the canopy. This model will enable the quantitative prediction of upward spectral radiation from vegetated surfaces, allowing remote sensing optical technologies to assist in the search for submerged objects of anthropogenic origin and the rapid mapping of seagrass resource distribution and abundance in optically shallow waters. Also, the results of the proposed study will improve significantly our ability to evaluate irradiance levels within seagrass canopies, a task necessary to determine accurately light requirements and photosynthetic productivity of these ecologically important ecosystems.
B. Statement of Approach
The proposed objectives will be accomplished through (i) modeling of radiative transfer theory provided by Hydrolight (in collaboration with C. Mobley), (ii) laboratory studies of the inherent optical properties of individual seagrass leaves, such as spectral absorbance, fluorescence and reflectance, and (iii) development of diver-operated instruments for in situ measurement of leaf area index (L) to compliment optical data generated by the Benthic Stationary Autonomous Profiler (BSAP, in collaboration with R. Maffione). The laboratory and field investigations proposed here will provide extensive data sets to parameterize and test a bio-optical model of seagrass canopies based on the radiative transfer theory developed by C. Mobley, as part of Hydrolight. This combination of theoretical and experimental approaches, and instrument development will permit quantitative assessment of the degree to which closure has been achieved in our understanding of radiative transfer in shallow coastal ecosystems vegetated by seagrasses.
C. Statement of Significance
The proposed research will improve significantly our ability to exploit the reflectance
and scattering (both elastic and inelastic) properties of submerged plant canopies for the
development of radiative transfer theory for shallow coastal waters. This improved theory
will lead to the application of waterborne and airborne remote sensing technology to
search for submerged objects and to map shallow coastal environments. This study will also
improve our ability to determine photosynthetic rates of seagrass canopies from measures
of above-canopy irradiance (EPAR), significantly increasing the reliability of production
models necessary for the protection and preservation of important seagrass ecosystems that
are currently under severe pressure from anthropogenic modification of coastal marine
environments.
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