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NASA NTRS2005

Use of a Novel Rover-mounted Fluorescence Imager and Fluorescent Probes to Detect Biological Material in the Atacama Desert in Daylight

We have developed an imaging system, the Fluorescence Imager (FI), for detecting fluorescence signals from sparse microorganisms and biofilms during autonomous rover exploration. The fluorescence signals arise both from naturally occurring chromophores, such as chlorophyll of cyanobacteria and lichens, and from fluorescent probes applied to soil and rocks. Daylight imaging has been accomplished by a novel use of a high-powered flashlamp synchronized to a CCD camera. The fluorescent probes are cell permanent stains that have extremely low intrinsic fluorescence (quantum yields less than 0.01) and a large fluorescence enhancement (quantum yields greater than 0.4) when bound to the target. Each probe specifically targets either carbohydrates, proteins, nucleic acids or membrane lipids, the four classes of macromolecules found in terrestrial life. The intent of the probes is to interrogate the environment for surface and endolithic life forms.

Weinstein, S.↗

NASA NTRS1975

A remote sensing laser fluorometer

A sensor is reported which is able to identify certain specific substances in water by means of their fluorescence spectra. In particular, the sensor detects oil, ligninsulfonates and chlorophyll. The device is able to measure the fluorescence spectra of water at ranges up to 75 m and to detect oil spills on water at altitudes up to 300 m. Blue light from a laser is used to excite the fluorescence of the target. Any light from the ambient background illumination, from the reflected laser light or from the induced fluorescence is gathered by a small telescope focused on the target. Optical filters are used to block the reflected laser light and to select the wavelengths of interest in the fluorescence spectrum of the target. The remaining light is detected with a photomultiplier tube. The amplitude of the laser induced fluorescence in the wavelength interval selected by the optical filters is displayed on a meter or strip chart recorder.

Oneill, R. A.↗

DOE OSTI2023

Energy dissipation efficiency in the CP43 assembly intermediate complex of photosystem II

Photosystem II in oxygenic organisms is a large membrane bound rapidly turning over pigment protein complex. During its biogenesis, multiple assembly intermediates are formed, including the CP43-preassembly complex (pCP43). Here, to understand the energy transfer dynamics in pCP43, we first engineered a His-tagged version of the CP43 in a CP47-less strain of the cyanobacterium Synechocystis 6803. Isolated pCP43 from this engineered strain was subjected to advanced spectroscopic analysis to evaluate its excitation energy dissipation characteristics. These included measurements of steady-state absorption and fluorescence emission spectra for which correlation was tested with Stepanov relation. Comparison of fluorescence excitation and absorptance spectra determined that efficiency of energy transfer from β-carotene to chlorophyll a is 39 %. Time-resolved fluorescence images of pCP43-bound Chl a were recorded on streak camera, and fluorescence decay dynamics were evaluated with global fitting. These demonstrated that the decay kinetics strongly depends on temperature and buffer used to disperse the protein sample and fluorescence decay lifetime was estimated in 3.2–5.7 ns time range, depending on conditions. The pCP43 complex was also investigated with femtosecond and nanosecond time-resolved absorption spectroscopy upon excitation of Chl a and β-carotene to reveal pathways of singlet excitation relaxation/decay, Chl a triplet dynamics and Chl a → β-carotene triplet state sensitization process. The latter demonstrated that Chl a triplet in the pCP43 complex is not efficiently quenched by carotenoids. Finally, detailed kinetic analysis of the rise of the population of β-carotene triplets determined that the time constant of the carotenoid triplet sensitization is 40 ns.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Comprehensive review of photophysical parameters (ε, Φ f , τ s ) of tetraphenylporphyrin (H 2 TPP) and zinc tetraphenylporphyrin (ZnTPP) – Critical benchmark molecules in photochemistry and photosynthesis

Tetraphenylporphyrin (H 2 TPP) and zinc tetraphenylporphyrin (ZnTPP) are widely used benchmark molecules in diverse photochemical studies given facile synthetic access, rich visible-region spectra, and broad structural analogy to chlorophylls. Yet the literature values for each key photophysical parameter – the molar absorption coefficient (ε), fluorescence quantum yield (Φ f ), and also singlet excited-state lifetime (τ S ) – vary over an astonishing range. Here, a comprehensive literature review (~1940–September 2020) encompassing 871 publications is reported for these essential parameters. Each parameter is determined by measurement with distinct instrumentation and suffers idiosyncratic sources of error. The best values for H 2 TPP are ε = 460,000 cm -1 ·M -1 , Φ f = 0.090, and τ S = 12.8 ns in Ar- purged toluene (Φf = 0.070, τS = 9.9 ns in toluene in air); the best values for ZnTPP are ε = 560,000 cm -1 ·M -1 , Φf = 0.030, and τ S = 2.1 ns in Ar-purged toluene (Φ f = 0.029, τ S = 2.0 ns in toluene in air). The choice of values for such parameters has far-reaching consequences in photochemistry ranging from fluorescence (or Förster) resonance energy transfer (FRET) processes to assessments of molecular brightness.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1986

Sunlight induced 685 nm fluorescence imagery

The capability of a new fluorescence method is evaluated using data from an aircraft fluorescence experiment conducted on the Elbe River on August 10-14, 1981. The technique measures chlorophyll concentrations by monitoring sunlight-induced fluorescence at 685 nm. Upwelling radiance spectra and vertical profiles of upwelling radiances are presented and analyzed. The image-processing algorithm used to retrieve fluorescence signals from raw data is described.

Kim, Hongsuk H.↗

NASA NTRS1981

Oceanic Lidar

Instrument concepts which measure ocean temperature, chlorophyll, sediment and Gelbstoffe concentrations in three dimensions on a quantitative, quasi-synoptic basis were considered. Coastal zone color scanner chlorophyll imagery, laser stimulated Raman temperaure and fluorescence spectroscopy, existing airborne Lidar and laser fluorosensing instruments, and their accuracies in quantifying concentrations of chlorophyll, suspended sediments and Gelbstoffe are presented. Lidar applications to phytoplankton dynamics and photochemistry, Lidar radiative transfer and signal interpretation, and Lidar technology are discussed.

Carder, K. L.↗

NASA NTRSDate not supplied

Principal Component and Machine Learning Approach to Gap Fill Hyperspectral Ocean Color Satellite Retrievals

Retrievals of ocean color properties from space are important for monitoring the health of the ocean ecosystem but such retrievals can be limited spatially due to conditions such as clouds, aerosols, and sun glint. Gap filling of ocean color retrievals is typically performed by combining retrievals from multiple satellites or temporally averaging multiple days of retrievals. Despite these techniques large gaps still exist posing challenges for near real time monitoring of events like harmful algae blooms. To address these limitations, we developed a spatial gap filling approach applying machine learning approach to hyperspectral instruments to learn how to perform an atmospheric correction under challenging retrieval conditions. In this approach a principal component analysis is used to decompose the hyperspectral measurements into spectral components that describe the scattering and absorption of the atmosphere mixed with the surface spectral signatures. The coefficients of the principal components are used to train a neural network to predict ocean color properties derived from a standard MODIS ocean color algorithm. We apply the approach to two hyperspectral UV/VIS sensors, the Ozone Monitoring Instrument (OMI) and TROPOspheric Monitoring Instrument (TROPOMI) to show that it can be used to estimate ocean color properties such as chlorophyll, remote sensing reflectance, and fluorescence line height. This method could be used as a gap-filling technique for the future Ocean Color Instrument (OCI) onboard upcoming NASA's Plankton, Aerosol Cloud, ocean Ecosystem (PACE) satellite to provide additional information for monitoring the health of our global oceans. Additionally, it could be applied to the first NASA and Smithsonian geostationary Tropospheric Emissions: Monitoring of Pollution (TEMPO) spectrometer to better understand diurnal variability in inland and coastal ocean ecology.

Zachary Fasnacht↗

NASA NTRSDate not supplied

A Principal Component and Machine Learning Approach to Spatially Gap Fill Hyperspectral Ocean Color Satellite Retrievals

Retrievals of ocean color properties from space are important for monitoring the health of the ocean ecosystem but such retrievals tend to be limited in spatial coverage due to conditions such as clouds, aerosols, and sun glint. Gap filling of ocean color retrievals is typically performed by combining retrievals from multiple satellites or temporally averaging multiple days of retrievals but despite these techniques large gaps still exist posing challenges for near real time monitoring of events like harmful algae blooms. To address these limitations, we propose a spatial gap filling approach using machine learning to learn how to perform an atmospheric correction under challenging retrieval conditions. In this approach a principal component analysis is used to decompose the hyperspectral measurements into spectral features that describe the scattering and absorption of the atmosphere as well as the underlying surface. The coefficients of the principal components are then used to train a neural network to predict ocean color properties derived from a standard ocean color algorithm such as the MODIS atmospheric correction algorithm. This machine learning approach is independent of a priori information and does not rely on any radiative transfer modeling. We apply the approach to two hyperspectral UV/VIS instruments, the Ozone Monitoring Instrument (OMI) and TROPOspheric Monitoring Instrument (TROPOMI) to show that it can be used to estimate ocean color properties such as chlorophyll, remote sensing reflectance, and fluorescence line height. This method could be used as a gap-filling technique for the future Ocean Color Instrument (OCI) which will be onboard NASA's Plankton, Aerosol Cloud, ocean Ecosystem (PACE) ocean color satellite to provide additional information for monitoring the health of our global oceans. Additionally, it could be applied to the geostationary satellite Tropospheric Emissions: Monitoring of Pollution (TEMPO) to better understand diurnal variability in ocean ecology.

MODIS atmospheric correction algorithm↗

DOE OSTI2023

River Geomorphology Affects Biogeochemical Responses to Hydrologic Events in a Large River Ecosystem

Shifts in the frequency and intensity of high discharge events due to climate change may have important consequences for the hydrology and biogeochemistry of rivers. However, our understanding of event-scale biogeochemical dynamics in large rivers lags that of small streams. To fill this gap, we used high-frequency sensor data collected during four consecutive summers from a main channel and backwater site of the Upper Mississippi River. We identified high discharge events and calculated event concentration-discharge responses for both physical-chemical (nitrate, turbidity, and fluorescent dissolved organic matter) and biological (chlorophyll-a and cyanobacteria) constituents using metrics of hysteresis and slope. We found a range of responses across events, particularly for nitrate. Although fluorescent dissolved organic matter (FDOM) and turbidity exhibited more consistent responses across events, contrasting hysteresis metrics indicated that FDOM was flushed to the river from more distant sources than turbidity. Biological responses (chlorophyll a and cyanobacteria) differed more between sites than physical and chemical constituents. Lastly, we found that the event characteristics best explaining concentration responses differed between sites, with event magnitude more frequently related to responses in the main channel, and antecedent wetness conditions associated with response variation in the backwater. Furthermore, our results indicate that event responses in large rivers are distinct across the diverse habitats and biogeochemical components of a large floodplain river, which has implications for local and downstream ecosystems as the climate shifts.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2024

Narragansett Bay Water Resources: Using Earth Observations to Identify Trends in Harmful Algal Blooms in Narragansett Bay

Narragansett Bay in Rhode Island is known for its quahog, or hard-shell clam, shellfisheries. However, increased levels in harmful algal blooms (HABs) and high phytoplankton biomass events pose threats to quahog populations, creating conditions that limit quahog growth and reproduction. Quahog shortages, along with public health concerns associated with contamination of shellfish from HAB-produced neurotoxins, have contributed to shellfishery closures. NASA DEVELOP partnered with the Environmental Protection Agency’s National Health and Environmental Effects Research Laboratory and Rhode Island’s Department of Environmental Management to use Earth observations and the partners’ in-situ data to visualize phytoplankton bloom events within the bay. We used Sentinel-3 Ocean and Land Color Instrument (OLCI), Landsat 8 and 9 Operational Land Imager (OLI)data to track several proxies of phytoplankton biomass from June 2016 to October 2023. Multiple sensors and in situ datasets were used to assess the feasibility of monitoring phytoplankton biomass accurately in the relatively small sized Narragansett Bay. We determined that Phytoplankton fluorescence line height was the best parameter to monitor phytoplankton biomass in the bay. Although the relatively small size of the bay and the optical complexity of these nearshore waters can pose a challenge, this assessment showed that Earth observations can be a useful complement to the in-situ monitoring of phytoplankton biomass in Narragansett Bay.

Sentinel-3↗

NASA NTRS2018

Estimation of Terrestrial Global Gross Primary Production (GPP) with Satellite Data-Driven Models and Eddy Covariance Flux Data

We estimate global terrestrial gross primary production (GPP) based on models that use satellite data within a simplified light-use efficiency framework that does not rely upon other meteorological inputs. Satellite-based geometry-adjusted reflectances are from the MODerate-resolution Imaging Spectroradiometer (MODIS) and provide information about vegetation structure and chlorophyll content at both high temporal (daily to monthly) and spatial (1 km) resolution. We use satellite-derived solar-induced fluorescence (SIF) to identify regions of high productivity crops and also evaluate the use of downscaled SIF to estimate GPP. We calibrate a set of our satellite-based models with GPP estimates from a subset of distributed eddy covariance flux towers (FLUXNET 2015). The results of the trained models are evaluated using an independent subset of FLUXNET 2015 GPP data. We show that variations in light-use efficiency (LUE) with incident PAR are important and can be easily incorporated into the models. Unlike many LUE-based models, our satellite-based GPP estimates do not use an explicit parameterization of LUE that reduces its value from the potential maximum under limiting conditions such as temperature and water stress. Even without the parameterized downward regulation, our simplified models are shown to perform as well as or better than state-of-the-art satellite data-driven products that incorporate such parameterizations. A significant fraction of both spatial and temporal variability in GPP across plant functional types can be accounted for using our satellite-based models. Our results provide an annual GPP value of 140 Pg C year 1 for 2007 that is within the range of a compilation of observation-based, model, and hybrid results, but is higher than some previous satellite observation-based estimates

CO2↗

DOE OSTI2022

The Influence of Microbial Priming Effects on the Hydro-bio-geochemistry of Large River Reservoirs

River-tributary confluences, where diverse organic matter (OM) sources mix, are considered aquatic critical zones for biogeochemical cycling. Here we evaluate dissolved OM composition and bioavailability in the mainstem of the Columbia River and three of its tributaries (Snake, Yakima, and Walla Walla rivers) along a hydrologic gradient in the Columbia River drainage basin using a variety of bulk and molecular level measurements. Field replicates and mixtures representing river-tributary confluences were incubated in the dark for 15 days to investigate the response of the microbial community to varying OM quantity/composition. The Columbia, Snake, and Yakima rivers did not differ in dissolved organic carbon (DOC), fluorescent dissolved OM (fDOM), or Chlorophyll-a (Chl-a) concentrations. However, the Walla Walla River had significantly greater DOC, fDOM, and Chl-a concentrations, indicative of greater contributions from algal DOM. FT-ICR-MS spectra for Walla Walla had significantly more peaks corresponding to amino sugars, carbohydrates and proteins while the Columbia River had more peaks for lignin, unsaturated hydrocarbons, and condensed aromatics. When incubated for 15 days in the dark, total DOC did not decrease for any of the river samples. DOC did decrease, however, in a mix representing the confluence of the Columbia and Walla Walla rivers, suggesting the microbial consortia of the Columbia River were primed by the Walla Walla River OM. OM composition was significantly different for several compound classes (e.g., lignin, protein, and tannin) following the incubations of unmixed river and tributary samples. However, the microbial community in the Walla Walla-Columbia mixture appeared to be indiscriminate of the molecular structure of the DOM as the compound class distribution did not change significantly. This provides preliminary evidence that the heterotrophs in river-tributary critical zones remineralize diverse OM structures.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS2004

Contrasting Inherent Optical Properties and Carbon Metabolism Between Five Northeastern (USA) Estuary-plume Systems

We have recently developed the ability to rapidly assess Surface inherent optical properties (IOP), oxygen concentration and pCO2 in estuarine-plume systems using flow-through instrumentation. During the summer of 2004, several estuarine-plume systems were surveyed which include the Pleasant (ME), Penobscot (ME), Kennebec-Androscoggin (ME), Merrimack (NH-MA) and Hudson (NY). Continuous measurements of surface chlorophyll and colored dissolved organic carbon (CDOM) fluorescence, beam attenuation, temperature, salinity, oxygen and pC02 were taken at each system along a salinity gradient from fresh water to near oceanic endmembers. CTD and IOP profiles were also taken at predetermined surface salinity intervals. These were accompanied by discrete determinations of chlorophyll (HPLC and fluorometric), total suspended solids (TSS), dissolved organic carbon (DOC) and alkalinity. IOP data were calibrated using chlorophyll, DOC and TSS data to enable the retrieval of these constituents from IOP data. Considerable differences in the data sets were observed between systems. These ranged from the DOC-enriched, strongly heterotrophic Pleasant River System to the high-chlorophyll autotrophic Merrimack River System. Using pCO2 and oxygen saturation measurements as proxies for water column metabolism, distinct relationships were found between trophic status and inherent optical properties. The nature of these relationships varies between systems and is likely a function of watershed and estuarine attributes including carbon and nutrient loading, in-situ production and related autochthonous inputs of DOC and alkalinity. Our results suggest that IOP data may contain significant information about the trophic status of estuarine and plume systems.

Vandemark, Doug↗

NASA NTRS2000

Advances in Fluorescence Sensing Systems for the Remote Assessment of Nitrogen Supply in Field Corn

The studies described herein were conducted to better define changes in fluorescence properties of leaves from field grown corn (Zea mays L.) as they relate to varying levels of nitrogen (N) fertilization. This research was directed toward: 1) providing a remote non-destructive sensing technique to aid in the determination of optimal rates of N fertilization in corn crops and, 2) defining parameters for further development of fluorescence instrumentation to be operated remotely at field canopy levels. Fluorescence imaging bands centered in the blue (450 nm), green (525 nm), red (680 nm), and far-red (740 nm) and ratios of these bands were compared with the following plant parameters: rates of photosynthesis, N:C ratio, pigment concentrations, and grain yields. Both the fluorescence and physiological measures exhibited similar curvilinear responses to N fertilization level while significant linear correlations were obtained among fluorescence bands and band ratios to certain physiological measures of plant productivity. The red / blue, red / green, far-red / blue, far-red /green fluorescence ratios are well suited for remote observation and provided high correlations to grain yield, LAI, N:C, and chlorophyll contents. The results from this investigation indicate that fluorescence technology could aid in the determination of N fertilization requirements for corn. This discussion will also address design concepts and preliminary field trials of a mobile field-based Laser Induced Fluorescence Imaging System (LIFIS) capable of simultaneously acquiring images of four fluorescence emission bands from areas of plant canopies equaling 1 sq m and greater without interference of ambient solar radiation.

Corp, L. A.↗

NASA NTRS2001

Interpretation of Observations of Trans-Spectral Phenomena Acquired Using Hyperspectral Sensors Aboard a Remotely Operated Vehicle in Exuma Sound

Hyper-spectral (512-channel) optical data acquired during a relatively deep (102m) dive of our ROSEBUD Remotely Operated Vehicle (ROV) in the clear waters of Exuma Sound, Bahamas provided the opportunity to investigate the trans-spectral shift of photonic energy (inelastic scattering) as a function of water depth. Results show a convolution of several spectral processes (e.g. absorption, scattering) involving water molecules, dissolved material and particulates as well as trans-spectral (inelastic) processes involving fluorescence by water molecules (Raman), dissolved material and chlorophyll. The spectral signatures of these convolved causes and effects allow deconvolution with a hyperspectral approach. Intrinsic to the convolution was the ability to position the vehicle at depths where Raman fluorescence dominated at red wavelengths. Results show that the calculated Raman absorption coefficients are generally consistent with historical values (i.e. 0.9 x 10(sup)-4 at 525 nm excitation) and that an angstrom exponent of 5 is more appropriate than the often cited value of 4.

Costello, D.↗

NASA NTRS1988

Three color laser fluorometer for studies of phytoplankton fluorescence

A three-color laser fluorometer has been developed for field work operations. Using two tunable dye lasers (excitation wavelengths at 440 nm and 530 nm), broadband wavelength optical filters were selected to obtain maximum fluorescence sensitivity at wavelengths greater than 675 nm (chlorophyll) and 575 + or - 15 nm (phycoerythrin). The laser fluorometer permits the measurement of phytoplankton pigments under static or flowing conditions and more closely resembles the time scales (ns) and energy levels (mW) of other laser-induced fluorescence instruments.

Phinney, David A.↗

DOE OSTI2025

Database of low‐temperature absorption and fluorescence spectra of native photosynthetic tetrapyrrole macrocycles

Low-temperature (77 K) absorption and fluorescence spectra of 12 naturally occurring photosynthetic tetrapyrrole macrocycles have been recorded in a frozen glass (2-methyltetrahydrofuran). The compounds encompass distinct chromophore classes: porphyrin, chlorophyll c 2 ; chlorin, chlorophylls a, b, d, f and bacteriochlorophylls c, d, e, f; and bacteriochlorin, bacteriochlorophylls a, b, g. The spectra are compared with those of the same pigment in liquid solution (predominantly 2-methyltetrahydrofuran) at room temperature (293 K). The measured Stokes shifts at 77 K across the 12 macrocycles range from ~30 to 300 cm −1 . The spectral data in digital form are made available as part of the PhotochemCAD databases. Literature searches have revealed extensive published data for Chl a (often in biological matrices) but at best rather limited data for less common macrocycles. The availability of a systematic collection of curated spectral data collected at low temperature should be useful for a variety of assessments, including reconstruction of absorption spectra of (bacterio)chlorophyll-containing protein complexes, vibrational analysis of absorption and fluorescence spectra, and calculations where knowledge of energy levels is important.

Niedzwiedzki, Dariusz M. [Washington University in↗

DOE OSTI2020

Impacts of Hurricane Disturbance on Water Quality across the Aquatic Continuum of a Blackwater River to Estuary Complex

Hurricanes cause landscape-scale disturbances that affect biogeochemical cycling and water quality in coastal ecosystems. During Hurricane Irma’s passage through northern Florida, water movements driven by wind velocities up to 105 km h-1 caused a salinity peak in an estuary/blackwater river complex. Water quality was monitored across the 15 km site to detect the magnitude and duration of disturbance. Saline water intruded 15 km inland into a freshwater portion of the river that peaked at a salinity of 2 psu. Due to the volume of precipitation from the hurricane, significant runoff of freshwater and dissolved organic matter (DOM) caused a decrease in salinity, dissolved oxygen (DO), and Chlorophyll-a concentrations while increasing turbidity and fluorescent dissolved organic matter (fDOM). The disturbance caused rapid changes observed by in-situ water quality monitors over a 3-week period, but some effects persisted for longer periods as shown by 3-month weekly water sampling. This disturbance caused shifts in DOM loading, altered salinity dynamics, and reshaped landscapes due to wind and wave surge both in upland marsh and downstream estuary. Hurricane disturbance temporarily and abruptly alters the aquatic continuum, and observations of system response can help us understand the mechanisms associated with ecosystem resilience and recovery.

54 ENVIRONMENTAL SCIENCES↗