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Two bio-indicators, the Photochemical Reflectance Index (PRI) and solar-induced red and far-red Chlorophyll Fluorescence (SIF), were derived from directional hyperspectral observations and studied in a cornfield on two contrasting days in the growing season. Both red and far-red SIF exhibited higher values on the day when the canopy in the early senescent stage, but only the far-red SIF showed sensitivity to viewing geometry. Consequently, the red/far-red SIF ratio varied greatly among azimuth positions while the largest values were obtained for the "hotspot" at both growth stages. This ratio was lower (approx.0.88 +/- 0.4) in early July than in August when the ratio approached equivalence (near approx.1). In concert, the PRI exhibited stronger responses to both zenith and azimuth angles and different values on the two growth stages. The potential of using these indices to monitor photosynthetic activities needs further investigation

Two bio-indicators, the Photochemical Reflectance Index (PRI) and solar-induced red and far-red Chlorophyll Fluorescence (SIF), were derived from directional hyperspectral observations and studied in a cornfield on two contrasting days in the growing season. Both red and far-red SIF exhibited higher values on the day when the canopy in the early senescent stage, but only the far-red SIF showed sensitivity to viewing geometry. Consequently, the red/far-red SIF ratio varied greatly among azimuth positions while the largest values were obtained for the "hotspot" at both growth stages. This ratio was lower (approx.0.88 +/- 0.4) in early July than in August when the ratio approached equivalence (near approx.1). In concert, the PRI exhibited stronger responses to both zenith and azimuth angles and different values on the two growth stages. The potential of using these indices to monitor photosynthetic activities needs further investigation

The long-term goals for this project are to improve the capability for determining phytoplankton biomass in the ocean from hyperspectral, remotely-sensed chlorophyll a fluorescence and to better understand the variability associated with chlorophyll a fluorescence.

These repository contains all the data and analysis development during 2019 - 2021 in a Doutorate thesis.

This article is from Sensors (Basel, Switzerland) , volume 13 . Abstract Detection of living microalgae cells is very important for ballast water treatment and analysis. Chlorophyll fluorescence is an indicator of photosynthetic activity and hence the living status of plant cells. In this paper, we developed a novel microfluidic biosensor system that can quickly and accurately detect the viability of single microalgae cells based on chlorophyll fluorescence. The system is composed of a laser diode as an excitation light source, a photodiode detector, a signal analysis circuit, and a microfluidic chip as a microalgae cell transportation platform. To demonstrate the utility of this system, six different living and dead algae samples (Karenia mikimotoi Hansen, Chlorella vulgaris, Nitzschia closterium, Platymonas subcordiformis, Pyramidomonas delicatula and Dunaliella salina) were tested. The developed biosensor can distinguish clearly between the living microalgae cells and the dead microalgae cells. The smallest microalgae cells that can be detected by using this biosensor are 3 μm ones. Even smaller microalgae cells could be detected by increasing the excitation light power. The developed microfluidic biosensor has great potential for in situ ballast water analysis.

This volume was digitized and made accessible online due to deterioration of the original print copy.

Chlorophyll fluorescence and hyperspectral reflectance were used to evaluate physiological responses to two common stressors in coastal environments. Chlorophyll content is one indicator of drought and salinity vegetation stress because of its direct role in the photosynthetic process and electron transport. Recent advances in fluorescence spectroscopy have led to the development of numerous reflectance indices that estimate fluorescence emission of vegetation for mapping vegetation stress as chlorophyll content and/or carotenoid content changes. Photoprotection via xanthophyll changes and non-photochemical quenching (qN) have been well correlated to the photochemical reflectance index (PRI) which has been successfully applied at multiple scales and most commonly associated with drought stress. Our objective was to evaluate chlorophyll responses to drought and salinity induced stress in a common shrub species in laboratory experiments and relate to field collected data. Our results indicate that some species do not breakdown chlorophyll during periods of stress, which may be an adaptive in a highly dynamic environment. Variations in PRI were not related to changes in chlorophyll content or the carotenoids/chlorophyll ratio. PRI is an indicator of chronic salinity stress and may be used as an early signal for associated changes due to sea-level rise associated with climate change. Remote sensing of vegetation allows for providing biophysical measurements across landscapes with limited access. However, not all species respond via chlorophyll changes with moderate to high levels of stress and this must be considered as remote sensing of plant signals is applied globally across species.

A provisional biooptical climate of the Northeast Pacific Ocean and Gulf of Alaska in summer combines a regional map of mean remotely sensed K490 (near-surface irradiance attenuation coefficient at 490 nm) with a set of empirical models predicting vertical profiles of irradiance attenuation and in situ chlorophyll-a fluorescence as functions of 1/K490 (m). The K490 seasonal mean was calculated as a composite average of CZCS measurements in this region during June, July, and August in 1979 through 1985.

Solar-stimulated chlorophyll fluorescence measured with the Fraunhofer line depth method has correlated well with vegetation stress in previous studies. However, the instruments used in those studies were limited to a single solar absorption line (e.g. 656.3 nm), obviating the red/far-red ratio (R/FR) method. Optics and detector technology have reached the level whereby multiple, very narrow Fraunhofer lines are resolvable. Thirteen such lines span the visible spectrum in the red to far-red region where chlorophyll fluorescence occurs. Fluorescence intensities at the 13 Fraunhofer line wavelengths were used to model emission spectra. The source data were collected for summer and fall bean crops (Phaseolus vulgaris L.) subjected to various levels of nitrogen fertilization. The intensities were adjusted to account for Fraunhofer line depth and atmospheric transmittance. Multiple R/FR fluorescence ratios, calculated from the modeled fluorescence spectra, correlated strongly with leaf chlorophyll concentration and well with applied nitrogen. The ratio yielding the best correlation with chlorophyll utilized red fluorescence at the 694.5 nm Fraunhofer line and farred fluorescence at the 755.6 nm Fraunhofer line. Twenty R/FR ratios, each evaluated for the maximum differential between low and high (optimal) nitrogen treatments, ranked higher in some cases and lower in others, possibly related to the time of year the crops were grown and the stage of growth of the crops. Ratios with 728.9 nm and 738.9 nm in the denominator consistently ranked in the lowest and next lowest quartile, respectively. Ratios of the 656.3 nm Fraunhofer line and the 755.6 nm line consistently ranked highest for the summer crop. Ratios with 755.6 nm in the denominator ranked in the upper quartile for 10 out of 12 measurement dates. Differences in ratio ranking indicate that physiological conditions may be estimated using selected ratios of Fraunhofer lines within the context of R/FR analysis. A passive instrument designed to monitor R/FR chlorophyll fluorescence (i.e. vegetation stress) from orbit could be built today.

Chlorophyll a fluorescence lifetime was measured for phytoplankton populations inhabiting the three physical zones surrounding the Mississippi River's terminus in the Gulf of Mexico. Observations of river discharge volume, nitrate nitrite, silicate, phosphate, PAR (Photosynthetically Active Radiation) diffuse attenuation within the water column, salinity, temperature, SPM, and chl a concentration were used to characterize the distribution of chl fluorescence lifetime within a given region within restricted periods of time. 33 stations extending from the Mississippi River plume to the shelf break of the Louisiana coast were surveyed for analysis of chlorophyll fluorescence lifetime during two cruises conducted March 31 - April 6, 2000, and October 24 - November 1, 2000. At each station, two to three depths were chosen for fluorescence lifetime measurement to represent the vertical characteristics of the water column. Where possible, samples were taken from just below the surface and from just above and below the pycnocline. All samples collected were within the 1% light level of the water column (the euphotic zone). Upon collection, samples were transferred to amber Nalgene bottles and left in the dark for at least 15 minutes to reduce the effects of non-photochemical quenching and to insure that photosynthetic reaction centers were open. Before measurements within the phase fluorometer were begun, the instrument was allowed to warm up for no less than one hour.

Determining the health and vigor of vegetation using high spectral resolution remote sensing is an important goal which has application to monitoring agriculture and ecosystem productivity and carbon exchange. Two spectral indices used to assess whether vegetation is performing near-optimally or exhibiting symptoms of environmental stress (e.g., drought or nutrient deficiency, non-optimal temperatures, etc.) are the Photochemical Reflectance Index (PRI) and solar-induced red and far-red Chlorophyll Fluorescence (Fs). Both the PRI and Fs capture the dynamics of photoprotection mechanisms within green foliage: the PRI is based on the association of the reflected radiation in the green spectrum with the xanthophyll cycle, whereas Fs measures the emitted radiation in the red and far-red spectrum. Fs was determined from retrievals in the atmospheric oxygen absorption features centered at 688 and 760 nm using a modified Fraunhofer Line Depth (FLD) method. We previously demonstrated diurnal and seasonal PRI differences for sunlit vs. shaded foliage in a conifer forest canopy, as expressed in the hotspot and darkspot of the Bidirectional Reflectance Function (BRF). In a USDA-ARS experimental field site located in Beltsville, MD, USA, measurements were acquired over a corn crop from a nadir view in 2008 with an ASD FieldSpec Pro (Analytical Spectral Devices, Inc., Boulder, CO, USA) to study the behavior of the PRI for sunlit and shaded foliage as captured in reflectance variations associated with the BRF, in a I m tall canopy in the vegetative growth stage. Those observations were compared to simulations obtained from two radiative transfer models. Measurements were then acquired to examine whether the PRI and Fs were influenced by view zenith and azimuth geometries at different times of day. Those measurements were made in 2010 with the Ocean Optics USB4000 Miniature Fiber Optic Spectrometer (Ocean Optics Inc., Dunedin, Florida, USA) at several times during the day on multiple days throughout the growing season. We found that the PRI consistently had higher values, indicating lower stress, in the BRF darkspot associated with shaded foliage than in the hotspot associated with sunlit foliage. We also found that Fs exhibited differences associated with sunlit and shaded canopy sectors, which were most pronounced for the red/far-red Fs ratio. Values indicated greater physiological stress in afternoons compared to mornings, and in the early senescent canopy as compared to the vegetative growth stage, BRFs for both the PRI and the red/far-red Fs ratio were bowl-shaped for the full azimuth sweep of the canopy. These two spectral indices (PRI, Fs ratio) provided complementary information on the photosynthetic function of the corn canopy.

This article is from Sensors (Basel, Switzerland) , volume 12 . Abstract Chlorophyll fluorescence can be defined as the red and far-red light emitted by photosynthetic tissue when it is excited by a light source. This is an important phenomenon which permits investigators to obtain important information about the state of health of a photosynthetic sample. This article reviews the current state of the art knowledge regarding the design of new chlorophyll fluorescence sensing systems, providing appropriate information about processes, instrumentation and electronic devices. These types of systems and applications can be created to determine both comfort conditions and current problems within a given subject. The procedure to measure chlorophyll fluorescence is commonly split into two main parts; the first involves chlorophyll excitation, for which there are passive or active methods. The second part of the procedure is to closely measure the chlorophyll fluorescence response with specialized instrumentation systems. Such systems utilize several methods, each with different characteristics regarding to cost, resolution, ease of processing or portability. These methods for the most part include cameras, photodiodes and satellite images.

This article is from PLoS ONE , volume 9 . Abstract Chlorophyll a fluorescence gives information about the plant physiological status due to its coupling to the photosynthetic electron transfer chain and to the further biochemical processes. Environmental stresses, which acts synergistically, disturbs the photosynthesis. The OJIP test, elaborated by Strasser and co-workers, enables comparison of the physiological status of plants grown on polluted vs. control areas. The paper shows that the Chl a measurements are very useful tool in evaluating of heavy metal ions influence on perennial grasses, tested as potential phytoremediators. Among 5 cultivars tested, the highest concentration of Cd and Zn ions, not associated with the yield reduction, was detected in the biomass of tall fescue cv. Rahela. Chl a fluorescence interpreted as double normalized curves pointed out Rahela as the outstanding cultivar under the HM ions stress.

Satellite observation of phytoplankton concentration or chlorophyll-a is an important characteristic, critically integral to monitoring coastal water quality. However, the optical properties of estuarine and coastal waters are highly variable and complex and pose a great challenge for accurate analysis. Constituents such as suspended solids and dissolved organic matter and the overlapping and uncorrelated absorptions in the blue region of the spectrum renders the blue-green ratio algorithms for estimating chlorophyll-a inaccurate. Measurement of sun-induced chlorophyll fluorescence, on the other hand, which utilizes the near infrared portion of the electromagnetic spectrum, may provide a better estimate of phytoplankton concentrations. While modelling and laboratory studies have illustrated both the utility and limitations of satellite baseline algorithms based on the sun induced chlorophyll fluorescence signal, few have examined the empirical validity of these algorithms using a comprehensive long term in situ data set. In an unprecedented analysis of a long term (2003-2011) in situ monitoring data from Tampa Bay, Florida (USA), we assess the validity of the FLH product from the Moderate Resolution Imaging Spectrometer (MODIS) against chlorophyll ]a and a suite of water quality parameters taken in a variety of conditions throughout a large optically complex estuarine system. A systematic analysis of sampling sites throughout the bay is undertaken to understand how the relationship between FLH and in situ chlorophyll-a responds to varying conditions within the estuary including water depth, distance from shore and structures and eight water quality parameters. From the 39 station for which data was derived, 22 stations showed significant correlations when the FLH product was matched with in situ chlorophyll-alpha data. The correlations (r2) for individual stations within Tampa Bay ranged between 0.67 (n=28, pless than 0.01) and-0.457 (n=12, p=.016), indicating that for some areas within the Bay, FLH can be a good predictor of chlorophyll-alpha concentration and hence a useful tool for the analysis of water quality. Overall, the results show a 106% increase in the validity of chlorophyll -a concentration estimates using FLH over the standard the blue-green OC3M algorithm. This analysis also illustrates that the correlations between FLH and in situ chlorophyll -a measurements increases with increasing water depth and distance of the monitoring sites from both the shore and structures. However, due to confounding factors related to the complexity of the estuarine system, a linear improvement in the FLH to chlorophyll ]a relationship was not clearly noted with increasing depth and distance from shore alone. Correlations of FLH with turbidity, nutrients (total nitrogen and total phosphorous) biological oxygen demand, salinity, sea surface temperature correlated positively with FLH concentrations, while dissolved oxygen and pH showed negative correlations. Principle component analyses are employed to further describe the relationships between the multivariate water quality parameters and the FLH product. The majority of sites with higher and very significant correlations (pless than 0.01) also showed high correlation values for nutrients, turbidity and biological oxygen demand. These sites were on average in greater than seven meters of water and over five kilometers from shore. A thorough understanding of the relationship between the MODIS FLH product and in situ water quality parameters will enhance our understanding of the accuracy MODIS fs global FLH algorithm and assist in optimizing its calibration for use in monitoring the quality of estuarine and coastal waters worldwide.

Chlorophyll a fluorescence lifetime was measured for phytoplankton populations inhabiting the three physical zones surrounding the Mississippi River's terminus in the Gulf of Mexico. Observations of river discharge volume, nitrate + nitrite, silicate, phosphate, PAR (Photosynthetically Active Radiation) diffuse attenuation within the water column, salinity, temperature, SPM, and chl a concentration were used to characterize the distribution of chl fluorescence lifetime within a given region within restricted periods of time. 33 stations extending from the Mississippi River plume to the shelf break of the Louisiana coast were surveyed for analysis of chlorophyll fluorescence lifetime during two cruises conducted March 31 - April 6, 2000, and October 24 - November 1, 2000. At each station, two to three depths were chosen for fluorescence lifetime measurement to represent the vertical characteristics of the water column. Where possible, samples were taken from just below the surface and from just above and below the pycnocline. All samples collected were within the 1% light level of the water column (the euphotic zone). Upon collection, samples were transferred to amber Nalgene bottles and left in the dark for at least 15 minutes to reduce the effects of non-photochemical quenching and to insure that photosynthetic reaction centers were open. Before measurements within the phase fluorometer were begun, the instrument was allowed to warm up for no less than one hour.

The FLuorescence Explorer (FLEX) satellite concept is one of six semifinalist mission proposals selected in 2006 for pre-Phase studies by the European Space Agency (ESA). The FLEX concept proposes to measure passive solar induced chlorophyll fluorescence (SIF) of terrestrial ecosystems. A new spectral vegetation Fluorescence Model (FluorMOD) was developed to include the effects of steady state SIF on canopy reflectance. We used our laboratory and field measurements previously acquired from foliage and canopies of corn (Zea mays L.) under controlled nitrogen (N) fertilization to parameterize and evaluate FluorMOD. Our data included biophysical properties, fluorescence (F) and reflectance spectra for leaves; reflectance spectra of canopies and soil; solar irradiance; plot-level leaf area index; and canopy SIF emissions determined using the Fraunhofer Line Depth principal for the atmospheric telluric oxygen absorption features at 688 nm (O2-beta) and 760 nm (O2-alpha). FluorMOD simulations implemented in the default "look-up-table" mode did not reproduce the observed magnitudes of leaf F, canopy SIF, or canopy reflectance. However, simulations for all of these parameters agreed with observations when the default FluorMOD information was replaced with measurements, although N treatment responses were underestimated. Recommendations were provided to enhance FluorMOD's potential utility in support of SIF field experiments and studies of agriculture and ecosystems.

The FLuorescence Explorer (FLEX) satellite concept is one of six semifinalist mission proposals selected in 2006 for pre-Phase studies by the European Space Agency (ESA). The FLEX concept proposes to measure passive solar induced chlorophyll fluorescence (SIF) of terrestrial ecosystems. A new spectral vegetation Fluorescence Model (FluorMOD) was developed to include the effects of steady state SIF on canopy reflectance. We used our laboratory and field measurements previously acquired from foliage and canopies of corn (Zea mays L.) under controlled nitrogen (N) fertilization to parameterize and evaluate FluorMOD. Our data included biophysical properties, fluorescence (F) and reflectance spectra for leaves; reflectance spectra of canopies and soil; solar irradiance; plot-level leaf area index; and canopy SIF emissions determined using the Fraunhofer Line Depth principal for the atmospheric telluric oxygen absorption features at 688 nm (O2-beta) and 760 nm (O2-alpha). FluorMOD simulations implemented in the default "look-up-table" mode did not reproduce the observed magnitudes of leaf F, canopy SIF, or canopy reflectance. However, simulations for all of these parameters agreed with observations when the default FluorMOD information was replaced with measurements, although N treatment responses were underestimated. Recommendations were provided to enhance FluorMOD's potential utility in support of SIF field experiments and studies of agriculture and ecosystems.

No abstract available