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NASA NTRS2001

Optical Measurements and Modeling to Estimate Concentrations and Fluxes of Organic Matter in the Southern Ocean

This project was a collaboration between two Principal Investigators, Dr. Dariusz Stramski and Dr. Greg Mitchell of Scripps Institution of Oceanography, University of California San Diego. Our overall goal was to conduct optical measurements and modeling to estimate concentrations of organic matter in the Southern Ocean in support of the U.S. JGOFS Process Study in this region. Key variables and processes of high relevance to accomplish the JGOFS goals include time and space resolution of phytoplankton pigments, particulate organic carbon, and the formation and export of organic carbon. Our project focused on establishing the fundamental relationships for parameterization of these variables and processes in terms of the optical properties of seawater, and developing understanding of why the Southern Ocean differs from other low-latitude systems, or has differentiation within. Our approach builds upon historical observations that optical properties provide a useful proxy for key reservoirs of organic matter such as chlorophyll alpha (Chl) and particulate organic carbon (POC) concentrations, which are of relevance to the JGOFS objectives. We carried out detailed studies of in situ and water sample optical properties including spectral reflectance, absorption, beam attenuation, scattering, and backscattering coefficients. We evaluated the ability to estimate Chl from the spectral reflectance (ocean color) in the Southern Ocean. We examined relationships between the ocean optical properties and particulate organic carbon. We developed, for the first time, an algorithm for estimating particulate organic carbon concentration in the surface ocean from satellite imagery of ocean color. With this algorithm, we obtained maps of POC distribution in the Southern Ocean showing the seasonal progression of POC in the austral spring-summer season. We also developed a semianalytical reflectance model for the investigated polar waters based on our field measurements of absorption and backscattering coefficients and Chl-dependent parameterizations of these coefficients. With this model, libraries of expected reflectance spectra for various chlorophyll concentrations can be generated with high spectral resolution for specific oceanic regions. In addition, our semianalytical reflectance model provided insight into the mechanisms which drive the empirical relationships between the ocean color and chlorophyll concentration. Our optical approach to the study of pigment and carbon concentrations will be directly relevant to development of system models and long-term monitoring of the Southern Ocean.

Stramski, Dariusz↗

NASA NTRS2001

Bio-Optical Measurement and Modeling of the California Current and Polar Oceans

The principal goals of our research are to validate standard or experimental products through detailed bio-optical and biogeochemical measurements, and to combine ocean optical observations with advanced radiative transfer modeling to contribute to satellite vicarious radiometric calibration and advanced algorithm development. To achieve our goals requires continued efforts to execute complex field programs globally, as well as development of advanced ocean optical measurement protocols. We completed a comprehensive set of ocean optical observations in the California Current, Southern Ocean, Indian Ocean requiring a large commitment to instrument calibration, measurement protocols, data processing and data merger. We augmented separately funded projects of our own, as well as others, to acquire ill situ data sets we have collected on various global cruises supported by separate grants or contracts. In collaboration with major oceanographic ship-based observation programs funded by various agencies (CalCOFI, US JGOFS, NOAA AMLR, INDOEX and Japan/East Sea) our SIMBIOS effort has resulted in data from diverse bio-optical provinces. For these global deployments we generate a high-quality, methodologically consistent, data set encompassing a wide-range of oceanic conditions. Global data collected in recent years have been integrated with our on-going CalCOFI database and have been used to evaluate SeaWiFS algorithms and to carry out validation studies. The combined database we have assembled now comprises more than 700 stations and includes observations for the clearest oligotrophic waters, highly eutrophic blooms, red-tides and coastal case 2 conditions. The data has been used to validate water-leaving radiance estimated with SeaWiFS as well as bio-optical algorithms for chlorophyll pigments. The comprehensive data is utilized for development of experimental algorithms (e.g. high-low latitude pigment transition, phytoplankton absorption, and cDOM). During this period we completed 9 peer-reviewed publications in high quality journals, and presented aspects of our work at more than 10 scientific conferences.

Mitchell, B. Greg↗

NASA NTRS2001

Bio-Optical Measurement and Modeling of the California Current and Polar Oceans

This Sensor Intercomparison and Merger for Biological and Interdisciplinary Oceanic Studies (SIMBIOS) project contract supports in situ ocean optical observations in the California Current, Southern Ocean, Indian Ocean as well as merger of other in situ data sets we have collected on various global cruises supported by separate grants or contracts. The principal goals of our research are to validate standard or experimental products through detailed bio-optical and biogeochemical measurements, and to combine ocean optical observations with advanced radiative transfer modeling to contribute to satellite vicarious radiometric calibration and advanced algorithm development. In collaboration with major oceanographic ship-based observation programs funded by various agencies (CalCOFI, US JGOFS, NOAA AMLR, INDOEX and Japan/East Sea) our SIMBIOS effort has resulted in data from diverse bio-optical provinces. For these global deployments we generate a high-quality, methodologically consistent, data set encompassing a wide-range of oceanic conditions. Global data collected in recent years have been integrated with our on-going CalCOFI database and have been used to evaluate Sea-Viewing Wide Field-of-view Sensor (SeaWiFS) algorithms and to carry out validation studies. The combined database we have assembled now comprises more than 700 stations and includes observations for the clearest oligotrophic waters, highly eutrophic blooms, red-tides and coastal case two conditions. The data has been used to validate water-leaving radiance estimated with SeaWiFS as well as bio optical algorithms for chlorophyll pigments. The comprehensive data is utilized for development of experimental algorithms (e.g., high-low latitude pigment transition, phytoplankton absorption, and cDOM).

Mitchell, B. Greg↗

NASA NTRS2001

Covariation of Mesoscale Ocean Color and Sea-Surface Temperature Patterns in the Sargasso Sea

During the lifetime of the Coastal Zone Color Scanner, there were 21 instances in which both satellite-derived ocean color and sea-surface temperature are simultaneously available over large areas of the Sargasso Sea. These images reveal close correspondence between mesoscale structures observed in temperature and pigment fields. In general, higher (lower) pigment biomass occurs in mesoscale features consisting of cold (warm) temperature anomalies. This relationship is consistent with the idea that upward displacement of isopycnals at the base of the euphotic zone by mesoscale eddies is an important mechanism of nutrient supply in the region.

McGillicuddy, Dennis J., Jr.↗

NASA NTRS2002

Seasonal to Decadal-Scale Variability in Satellite Ocean Color and Sea Surface Temperature for the California Current System

Support for this project was used to develop satellite ocean color and temperature indices (SOCTI) for the California Current System (CCS) using the historic record of CZCS West Coast Time Series (WCTS), OCTS, WiFS and AVHRR SST. The ocean color satellite data have been evaluated in relation to CalCOFI data sets for chlorophyll (CZCS) and ocean spectral reflectance and chlorophyll OCTS and SeaWiFS. New algorithms for the three missions have been implemented based on in-water algorithm data sets, or in the case of CZCS, by comparing retrieved pigments with ship-based observations. New algorithms for absorption coefficients, diffuse attenuation coefficients and primary production have also been evaluated. Satellite retrievals are being evaluated based on our large data set of pigments and optics from CalCOFI.

Mitchell, B. Greg↗

NASA NTRS2001

Covariation of Mesoscale Ocean Color and Sea-Surface Temperature Patterns in the Sargasso Sea

McGillicuddy, D. J.↗

NASA NTRS2002

Sources of Variability in Chlorophyll Analysis by Fluorometry and High-Performance Liquid Chromatography in a SIMBIOS Inter-Calibration Exercise

The purpose of this technical report is to provide current documentation of the Sensor Intercomparison and Merger for Biological and Interdisciplinary Oceanic Studies (SIMBIOS) Project activities, NASA Research Announcement (NRA) research status, satellite data processing, data product validation, and field calibration. This documentation is necessary to ensure that critical information is related to the scientific community and NASA management. This critical information includes the technical difficulties and challenges of validating and combining ocean color data from an array of independent satellite systems to form consistent and accurate global bio-optical time series products. This technical report is not meant as a substitute for scientific literature. Instead, it will provide a ready and responsive vehicle for the multitude of technical reports issued by an operational project. This particular document focus on the variability in chlorophyll pigment measurements resulting from differences in methodologies and laboratories conducting the pigment analysis.

VanHeukelem, Laurie↗

NASA NTRS2004

High Spectral Resolution MODIS Algorithms for Ocean Chlorophyll in Case II Waters

The Case 2 chlorophyll a algorithm is based on a semi-analytical, bio-optical model of remote sensing reflectance, R(sub rs)(lambda), where R(sub rs)(lambda) is defined as the water-leaving radiance, L(sub w)(lambda), divided by the downwelling irradiance just above the sea surface, E(sub d)(lambda,0(+)). The R(sub rs)(lambda) model (Section 3) has two free variables, the absorption coefficient due to phytoplankton at 675 nm, a(sub phi)(675), and the absorption coefficient due to colored dissolved organic matter (CDOM) or gelbstoff at 400 nm, a(sub g)(400). The R(rs) model has several parameters that are fixed or can be specified based on the region and season of the MODIS scene. These control the spectral shapes of the optical constituents of the model. R(sub rs)(lambda(sub i)) values from the MODIS data processing system are placed into the model, the model is inverted, and a(sub phi)(675), a(sub g)(400) (MOD24), and chlorophyll a (MOD21, Chlor_a_3) are computed. Algorithm development is initially focused on tropical, subtropical, and summer temperate environments, and the model is parameterized in Section 4 for three different bio-optical domains: (1) high ratios of photoprotective pigments to chlorophyll and low self-shading, which for brevity, we designate as 'unpackaged'; (2) low ratios and high self-shading, which we designate as 'packaged'; and (3) a transitional or global-average type. These domains can be identified from space by comparing sea-surface temperature to nitrogen-depletion temperatures for each domain (Section 5). Algorithm errors of more than 45% are reduced to errors of less than 30% with this approach, with the greatest effect occurring at the eastern and polar boundaries of the basins. Section 6 provides an expansion of bio-optical domains into high-latitude waters. The 'fully packaged' pigment domain is introduced in this section along with a revised strategy for implementing these variable packaging domains. Chlor_a_3 values derived semi-analytically and Chlor_a_2 values derived empirically using the O Reilly et al. OC3M algorithm from MODIS Terra radiances are compared to field chlorophyll-a concentrations in Sections 7 and 8.

Carder, Kendall L.↗

NASA NTRS2003

Bio-Optical and Geochemical Properties of the South Atlantic Subtropical Gyre

An investigation of the bio-optical properties of the South Atlantic subtropical gyre (SASG) was conducted using data primarily from the UK Atlantic Meridional Transect (AMT) program and SeaWiFS. The AMT cruises extend from the UK to the Falklands Islands (sailing on the RRS James Clark Ross) with the purpose of improving our knowledge of surface layer hydrography, biogeochemical processes, ecosystem dynamics and food webs across basin scales in the Atlantic Ocean. Two objectives of the AMT program relevant to this study are the characterization of biogeochemical provinces and the analysis of optical and pigment parameters in connection with remote sensing ocean color data. The primary focus of this NASA Technical Memorandum is on the variability of the vertical distribution of phytoplankton pigments and associated absorption properties across the SASG, and their relevance to remote sensing algorithms. Therefore, a subset of the AMT data within the SASG from all available cruises was used in the analyses. One of the challenges addressed here is the determination of the SASG geographic boundaries. One of the major problems is to reconcile the properties of biogeochemical provinces. We use water mass analysis, dynamics of ocean currents, and meridional gradients of bio-optical properties, to identify the SASG boundaries.

Signorini, S. R.↗

NASA NTRS1990

Carbonate petrography, kerogen distribution, and carbon and oxygen isotope variations in an early Proterozoic transition from limestone to iron-formation deposition, Transvaal Supergroup, South Africa

The transition zone comprises Campbellrand microbialaminated (replacing "cryptalgalaminate") limestone and shale, with minor dolomite, conformably overlain by the Kuruman Iron Formation of which the basal part is characterized by siderite-rich microbanded iron-formation with minor magnetite and some hematite-containing units. The iron-formation contains subordinate intraclastic and microbialaminated siderite mesobands and was deposited in deeper water than the limestones. The sequence is virtually unaltered with diagenetic mineral assemblages reflecting a temperature interval of about 110 degrees to 170 degrees C and pressures of 2 kbars. Carbonate minerals in the different rock types are represented by primary micritic precipitates (now recrystallized to microsparite), early precompactional sparry cements and concretions, deep burial limpid euhedral sparites, and spar cements precipitated from metamorphic fluids in close contact with diabase sills. Paragenetic pathways of the carbonate minerals are broadly similar in all lithofacies with kerogen intimately associated with them. Kerogen occurs as pigmentation in carbonate crystals, as reworked organic detritus in clastic-textured carbonate units, and as segregations of kerogen pigment around late diagenetic carbonate crystals. Locally kerogen may also be replaced by carbonate spar. Carbon isotope compositions of the carbonate minerals and kerogen are dependent on their mode of occurrence and on the composition of the dominant carbonate species in a specific lithofacies. Integration of sedimentary, petrographic, geochemical, and isotopic results makes it possible to distinguish between depositional, early diagenetic, deep burial, and metamorphic effects on the isotopic compositions of the carbonate minerals and the kerogen in the sequence. Major conclusions are that deep burial thermal decarboxylation led to 13C depletion in euhedral ferroan sparites and 13C enrichment in kerogen (organic carbon). Metamorphic sparites are most depleted in 13C. Carbonates in oxide-rich iron-formations are more depleted in 13C than those in siderite-rich iron-formation whereas the kerogens in oxide banded iron-formations (BIF) are more enriched. This implies that the siderite-rich iron-formations were not derived from oxide-rich iron-formation through reduction of ferric iron by organic matter. Organic matter oxidation by ferric iron did, however, decrease the abundance of kerogen in oxide-rich iron-formation and led to the formation of isotopically very light sparry carbonates. Siderite and calcmicrosparite both represent recrystallized primary micritic precipitates but differ in their 13C composition, with the siderites depleted in 13C by 4.6 per mil on average relative to calcmicrosparite. This means that the siderites were precipitated from water with dissolved inorganic carbon depleted in 13C by about 9 per mil relative to that from which the limestones precipitated. This implies an ocean system stratified with regard to total carbonate, with the deeper water, from which siderite-rich iron-formation formed, depleted in 13C. Iron-formations were deposited in areas of very low organic matter supply. Depletion of 13C may, therefore, derive not from degradation of organic matter but from hydrothermal activity, a conclusion which is supported by 18O composition of the carbonate minerals and trace element and rare earth element (REE) compositions of the iron-formations.

NASA Discipline Number 52-30↗

NASA NTRS1989

Carbon isotope fractionation by thermophilic phototrophic sulfur bacteria: evidence for autotrophic growth in natural populations

Purple phototrophic bacteria of the genus Chromatium can grow as either photoautotrophs or photoheterotrophs. To determine the growth mode of the thermophilic Chromatium species, Chromatium tepidum, under in situ conditions, we have examined the carbon isotope fractionation patterns in laboratory cultures of this organism and in mats of C. tepidum which develop in sulfide thermal springs in Yellowstone National Park. Isotopic analysis (13C/12C) of total carbon, carotenoid pigments, and bacteriochlorophyll from photoautotrophically grown cultures of C. tepidum yielded 13C fractionation factors near -20%. Cells of C. tepidum grown on excess acetate, wherein synthesis of the Calvin cycle enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase ribulose bisphosphate carboxylase) was greatly repressed, were isotopically heavier, fractionation factors of ca. -7% being observed. Fractionation factors determined by isotopic analyses of cells and pigment fractions of natural populations of C. tepidum growing in three different sulfide thermal springs in Yellowstone National Park were approximately -20%, indicating that this purple sulfur bacterium grows as a photoautotroph in nature.

Non-NASA Center↗

NASA NTRS1992

Forster energy transfer in chlorosomes of green photosynthetic bacteria

Energy transfer properties of whole cells and chlorosome antenna complexes isolated from the green sulfur bacteria Chlorobium limicola (containing bacteriochlorophyll c), Chlorobium vibrioforme (containing bacteriochlorophyll d) and Pelodictyon phaeoclathratiforme (containing bacteriochlorophyll e) were measured. The spectral overlap of the major chlorosome pigment (bacteriochlorophyll c, d or, e) with the bacteriochlorophyll a B795 chlorosome baseplate pigment is greatest for bacteriochlorophyll c and smallest for bacteriochlorophyll e. The absorbance and fluorescence spectra of isolated chlorosomes were measured, fitted to gaussian curves and the overlap factors with B795 calculated. Energy transfer times from the bacteriochlorophyll c, d or e to B795 were measured in whole cells and the results interpreted in terms of the Forster theory of energy transfer.

NASA Program Exobiology↗

NASA NTRS2000

[Characteristics of super dwarf wheat metabolism in microgravity]

Metabolism of sLt during Russian-US experiment GREENHOUSE-2 (July 9, 1996-January 17, 1997) within the MIR/NASA space research program and in laboratory Svet experiments in 1995-1996 was studied. Chemical, biochemical and pigment analyses of the flight and laboratory plants were made after the first (dry biomass) and second vegetation (photosynthetically active 41-d old plants). Data on the composition of leaves and stems of ground and flight wheat do not attest any biologically significant shifts in plant metabolism. There were slight changes in accumulation and migration of several macro- and microelements, protein nitrogen and phosphororganic compounds in microgravity. Lowered content of lignin, a critical supportive element for cellular walls was observed only during early stages of vegetation. In the Mir experiment, concentrations of photosynthetically active pigments also decreased a little but the chlorophyills-carotenoids balance was not upset.

Non-NASA Center↗

NASA NTRS1998

The origin and evolution of oxygenic photosynthesis

The evolutionary developments that led to the ability of photosynthetic organisms to oxidize water to molecular oxygen are discussed. Two major changes from a more primitive non-oxygen-evolving reaction center are required: a charge-accumulating system and a reaction center pigment with a greater oxidizing potential. Intermediate stages are proposed in which hydrogen peroxide was oxidized by the reaction center, and an intermediate pigment, similar to chlorophyll d, was present.

Review, Tutorial↗

NASA NTRS1994

Provisional bilateral symmetry in Xenopus eggs is established during maturation

Dorsal-ventral patterning in the Xenopus egg becomes established midway through the first cell cycle during a 30 degree rotation of the subcortical yolk mass relative to the egg cortex. This 'rotation of symmetrisation' is microtubule dependent, and its direction is thought to be cued by the usually eccentric sperm centrosome. The fact that parthenogenetically activated eggs also undergo a directed rotation, despite the absence of a sperm centrosome, suggests that an endogenous asymmetry in the unfertilised egg supports the directed polymerisation of microtubules in the vegetal cortex, in the way that an eccentric sperm centrosome would in fertilised eggs. Consistent with this idea, we noticed that the maturation spot is usually located an average of more than 15 degrees from the geometric centre of the pigmented animal hemisphere. In parthenogenetically activated eggs, this eccentric maturation spot can be used to predict the direction of rotation. Although in most fertilised eggs the yolk mass rotates toward the sperm entry point (SEP) meridian, occasionally this relationship is perturbed significantly; in such eggs, the maturation spot is never on the same side of the egg as the SEP. In oocytes tilted 90 degrees from upright during maturation in vitro, the maturation spot developed 15 degrees or more from the centre of the pigmented hemisphere, always displaced towards the point on the equator that was up during maturation. This experimentally demonstrated lability is consistent with an off-axis oocyte orientation during oogenesis determining its eccentric maturation spot position, and, in turn, its endogenous rotational bias.

NASA Discipline Number 40-20↗

NASA NTRS2003

Demonstration of a Porous Tube Hydroponic System to Control Plant Moisture and Growth

Accurate remote detection of plant health indicators such as moisture, plant pigment concentrations, photosynthetic flux, and other biochemicals in canopies is a major goal in plant research. Influencing factors include complex interactions between wavelength dependent absorbing and scattering features from backgrounds as well as canopy biochemical and biophysical constituents. Accurately controlling these factors in outdoor field studies is difficult. Early testing of a porous tube plant culture system has indicated that plant biomass production, biomass partitioning, and leaf moisture of plants can be controlled by precisely managing the root water potential. Managing nutrient solution chemistry can also control plant pigments, biochemical concentrations, plant biomass production, and photosynthetic rates. A test bed was developed which utilized the porous tube technology with the intent of evaluating remote sensing systems, spectral analyses procedures, gas-exchange, and fluorescence measurements for their ability to detect small differences in plant water status. Spectral analysis was able to detect small differences in the mean leaf water content between the treatments. However these small differences were not detectable in the gas-exchange or fluorescence measurements.

Dreschel, T. W.↗

NASA NTRS2006

Bucky Paper as a Support Membrane in Retinal Cell Transplantation

A method for repairing a retinal system of an eye, using bucky paper on which a plurality of retina pigment epithelial cells and/or iris pigment epithelial cells and/or stem cells is deposited, either randomly or in a selected cell pattern. The cell-covered bucky paper is positioned in a sub-retinal space to transfer cells to this space and thereby restore the retina to its normal functioning, where retinal damage or degeneration, such as macular degeneration, has occurred.

Loftus, David J.↗

NASA NTRS2006

Chlorophyll Fluorescence Emissions of Vegetation Canopies From High Resolution Field Reflectance Spectra

A two-year experiment was performed on corn (Zea mays L.) crops under nitrogen (N) fertilization regimes to examine the use of hyperspectral canopy reflectance information for estimating chlorophyll fluorescence (ChlF) and vegetation production. Fluorescence of foliage in the laboratory has proven more rigorous than reflectance for correlation to plant physiology. Especially useful are emissions produced from two stable red and far-red chlorophyll ChlF peaks centered at 685V10 nm and 735V5 nm. Methods have been developed elsewhere to extract steady state solar induced fluorescence (SF) from apparent reflectance of vegetation canopies/landscapes using the Fraunhofer Line Depth (FLD) principal. Our study utilized these methods in conjunction with field-acquired high spectral resolution canopy reflectance spectra obtained in 2004 and 2005 over corn crops, as part of an ongoing multi-year experiment at the USDA/Agriculture Research Service in Beltsville, MD. A spectroradiometer (ASD-FR Fieldspec Pro, Analytical Spectral Devices, Inc., Boulder, CO) was used to measure canopy radiances 1 m above plant canopies with a 22deg field of view and a 0deg nadir view zenith angle. Canopy and plant measurements were made at the R3 grain fill reproductive stage on 3-4 replicate N application plots provided seasonal inputs of 280, 140, 70, and 28 kg N/ha. Leaf level measurements were also made which included ChlF, photosynthesis, and leaf constituents (photosynthetic pigment, carbon (C), and N contents). Crop yields were determined at harvest. SIF intensities for ChlF were derived directly from canopy reflectance spectra in specific narrowband regions associated with atmospheric oxygen absorption features centered at 688 and 760 nm. The red/far-red S F ratio derived from these field reflectance spectra successfully discriminated foliar pigment levels (e.g., total chlorophyll, Chl) associated with N application rates in both corn crops. This canopy-level spectral ratio was also positively correlated to the foliar C/N ratio (r = 0.89, n = go), as was a leaf-level steady state fluorescence ratio (Fs/Chl, r = 0.92). The latter ratio was inversely correlated with crop grain yield (Kg 1 ha) (r = 0.9). This study has relevance to future passive satellite remote sensing approaches to monitoring C dynamics from space.

Middleton, E. M.↗