Salt marshes play a crucial role in coastal biogeochemical cycles and provide unique ecosystem se... more Salt marshes play a crucial role in coastal biogeochemical cycles and provide unique ecosystem services. Salt marsh biomass, which can strongly influence such services, varies over time in response to hydrologic conditions and other environmental drivers. We used gap-filled monthly observations of Spartina alterniflora aboveground biomass derived from Landsat 5 and Landsat 8 satellite imagery from 1984-2018 to analyze temporal patterns in biomass in comparison to air temperature, precipitation, river discharge, nutrient input, sea level, and drought index for a southeastern US salt marsh. Wavelet analysis and ensemble empirical mode decomposition identified month to multi-year periodicities in both plant biomass and environmental drivers. Wavelet coherence detected cross-correlations between annual biomass cycles and precipitation, temperature, river discharge, nutrient concentrations (NOx and PO43–) and sea level. At longer periods we detected coherence between biomass and all vari...
This dataset is from a sampling campaign completed over the course of 48 hours to investigate the... more This dataset is from a sampling campaign completed over the course of 48 hours to investigate the effects of tidally induced water level variation on aqueous chemistry, dissolved organic matter chemistry, and metabolic potential of microbial communities at the Altamaha River, GA, USA. Filtered surface water (SW) and pore water (PP) samples were collected every three hours in October 2018. This dataset is one of seven companion datasets that were part of the WHONDRS 48 Hour Diel Cycling Study of freshwater rivers. All seven datasets are available on ESS-DIVE; they can be found by searching for WHONDRS 48 Hour.This package contains a variety of chemical and hydrologic variables. All data types are provided in a standard format. Basic geochemistry analyses (e.g., non-purgeable organic carbon concentration, cations, anions, SpC, pH) were conducted, standardized photos were taken, surface water hydrographs were collated from existing instrumentation, and extensive metadata were captured....
Water quality measures for inland and coastal waters are available as discrete samples from profe... more Water quality measures for inland and coastal waters are available as discrete samples from professional and volunteer water quality monitoring programs and higher-frequency, near-continuous data from automated in situ sensors. Water quality parameters also are estimated from model outputs and remote sensing. The integration of these data, via data assimilation, can result in a more holistic characterization of these highly dynamic ecosystems, and consequently improve water resource management. It is becoming common to see combinations of these data applied to answer relevant scientific questions. Yet, methods for scaling water quality data across regions and beyond, to provide actionable knowledge for stakeholders, have emerged only recently, particularly with the availability of satellite data now providing global coverage at high spatial resolution. In this paper, data sources and existing data integration frameworks are reviewed to give an overview of the present status and iden...
Retrieval of aquatic biogeochemical variables, such as the near-surface concentration of chloroph... more Retrieval of aquatic biogeochemical variables, such as the near-surface concentration of chlorophyll-a (Chla) in inland and coastal waters via remote observations, has long been regarded as a challenging task. This manuscript applies Mixture Density Networks (MDN) that use the visible spectral bands available by the Operational Land Imager (OLI) aboard Landsat-8 to estimate Chla. We utilize a database of co-located in situ radiometric and Chla measurements (N = 4,354), referred to as Type A data, to train and test an MDN model (MDNA). This algorithm’s performance, having been proven for other satellite missions, is further evaluated against other widely used machine learning models (e.g., support vector machines), as well as other domain-specific solutions (OC3), and shown to offer significant advancements in the field. Our performance assessment using a held-out test data set suggests that a 49% (median) accuracy with near-zero bias can be achieved via the MDNA model, offering impr...
Abstract Total suspended solids (TSS) concentration is an important biogeochemical parameter for ... more Abstract Total suspended solids (TSS) concentration is an important biogeochemical parameter for water quality management and sediment-transport studies. In this study, we propose a novel semi-analytical method for estimating TSS in clear to extremely turbid waters from remote-sensing reflectance (Rrs). The proposed method includes three sub-algorithms used sequentially. First, the remotely sensed waters are classified into clear (Type I), moderately turbid (Type II), highly turbid (Type III), and extremely turbid (Type IV) water types by comparing the values of Rrs at 490, 560, 620, and 754 nm. Second, semi-analytical models specific to each water type are used to determine the particulate backscattering coefficients (bbp) at a corresponding single wavelength (i.e., 560 nm for Type I, 665 nm for Type II, 754 nm for Type III, and 865 nm for Type IV). Third, a specific relationship between TSS and bbp at the corresponding wavelength is used in each water type. Unlike other existing approaches, this method is strictly semi-analytical and its sub-algorithms were developed using synthetic datasets only. The performance of the proposed method was compared to that of three other state-of-the-art methods using simulated (N = 1000, TSS ranging from 0.01 to 1100 g/m3) and in situ measured (N = 3421, TSS ranging from 0.09 to 2627 g/m3) pairs of Rrs and TSS. Results showed a significant improvement with a Median Absolute Percentage Error (MAPE) of 16.0% versus 30.2–90.3% for simulated data and 39.7% versus 45.9–58.1% for in situ data, respectively. The new method was subsequently applied to 175 MEdium Resolution Imaging Spectrometer (MERIS) and 498 Ocean and Land Colour Instrument (OLCI) images acquired in the 2003–2020 timeframe to produce long-term TSS time-series for Lake Suwa and Lake Kasumigaura, Japan. Performance assessments using MERIS and OLCI matchups showed good agreements with in situ TSS measurements.
The eastern oyster (Crassostrea virginica) is an important proxy for examining historical traject... more The eastern oyster (Crassostrea virginica) is an important proxy for examining historical trajectories of coastal ecosystems. Measurement of ~40,000 oyster shells from archaeological sites along the Atlantic Coast of the United States provides a long-term record of oyster abundance and size. The data demonstrate increases in oyster size across time and a nonrandom pattern in their distributions across sites. We attribute this variation to processes related to Native American fishing rights and environmental variability. Mean oyster length is correlated with total oyster bed length within foraging radii (5 and 10 km) as mapped in 1889 and 1890. These data demonstrate the stability of oyster reefs despite different population densities and environmental shifts and have implications for oyster reef restoration in an age of global climate change.
Abstract Knowledge of light partitioning into different optically active constituents, particular... more Abstract Knowledge of light partitioning into different optically active constituents, particularly chromophoric dissolved organic matter (CDOM) in the ultraviolet (UV) is indispensable for understanding UV dependent biogeochemical issues including photochemical processes in optically complex waters. Herein a new approach is presented to investigate photochemistry by blending two ocean color algorithms, namely the composite SeaUV (Cao et al., 2014) and the SeaCDOM (Cao and Miller, 2015) algorithms, and applying them to visible remote sensing reflectance (Rrs) measured using the Hyperspectral Imager for the Coastal Ocean (HICO). As illustrated using photochemical carbon monoxide (CO) production from CDOM, this model approach allows high resolution examination of UV optical details with estimates of both depth-specific and depth-integrated photoproduction rates in a dynamic estuarine/coastal environment. Decoupled retrievals of inherent and apparent optical properties (i.e. diffuse attenuation coefficient (Kd) and CDOM absorption coefficient (ag)) using two distinct ocean color algorithms over the entire UV spectrum allow a synoptically dynamic view of CDOM's contribution to light attenuation (ag/Kd). This provides new potential to probe UV processes in complex coastal waters on regional as well as global scales using remote sensing of ocean color.
Photogrammetric Engineering and Remote Sensing, 1995
Our spectrometer is a high spectral resolution instrument which has two sensing heads called came... more Our spectrometer is a high spectral resolution instrument which has two sensing heads called cameras. The two cameras were observed to be misregistered relative to one another by up to 6 nm. The cameras were brought to a common wavelength base to correctly compare the data when the two cameras are used in a near-simultaneous mode. The wavelengths were assigned to the respective corresponding camera spectral wavelength bands and spectral bandwidths and sampling intervals calculated for each camera. Spectral bandwidths were larger than expected, but the sampling intervals were in close agreement with manufacturer specifications. Both cameras were calibrated for radiance and irradiance. The calibration coefficients developed during the radiometric calibrations showed an apparent light intensity dependence for wavelengths greater than 1000 nm. A closure experiment was conducted to test the accuracy of radiometric calibrations. Our results showed that estimates of irradiance from both cameras were within 5 percent of each other.
Salt marshes play a crucial role in coastal biogeochemical cycles and provide unique ecosystem se... more Salt marshes play a crucial role in coastal biogeochemical cycles and provide unique ecosystem services. Salt marsh biomass, which can strongly influence such services, varies over time in response to hydrologic conditions and other environmental drivers. We used gap-filled monthly observations of Spartina alterniflora aboveground biomass derived from Landsat 5 and Landsat 8 satellite imagery from 1984-2018 to analyze temporal patterns in biomass in comparison to air temperature, precipitation, river discharge, nutrient input, sea level, and drought index for a southeastern US salt marsh. Wavelet analysis and ensemble empirical mode decomposition identified month to multi-year periodicities in both plant biomass and environmental drivers. Wavelet coherence detected cross-correlations between annual biomass cycles and precipitation, temperature, river discharge, nutrient concentrations (NOx and PO43–) and sea level. At longer periods we detected coherence between biomass and all vari...
This dataset is from a sampling campaign completed over the course of 48 hours to investigate the... more This dataset is from a sampling campaign completed over the course of 48 hours to investigate the effects of tidally induced water level variation on aqueous chemistry, dissolved organic matter chemistry, and metabolic potential of microbial communities at the Altamaha River, GA, USA. Filtered surface water (SW) and pore water (PP) samples were collected every three hours in October 2018. This dataset is one of seven companion datasets that were part of the WHONDRS 48 Hour Diel Cycling Study of freshwater rivers. All seven datasets are available on ESS-DIVE; they can be found by searching for WHONDRS 48 Hour.This package contains a variety of chemical and hydrologic variables. All data types are provided in a standard format. Basic geochemistry analyses (e.g., non-purgeable organic carbon concentration, cations, anions, SpC, pH) were conducted, standardized photos were taken, surface water hydrographs were collated from existing instrumentation, and extensive metadata were captured....
Water quality measures for inland and coastal waters are available as discrete samples from profe... more Water quality measures for inland and coastal waters are available as discrete samples from professional and volunteer water quality monitoring programs and higher-frequency, near-continuous data from automated in situ sensors. Water quality parameters also are estimated from model outputs and remote sensing. The integration of these data, via data assimilation, can result in a more holistic characterization of these highly dynamic ecosystems, and consequently improve water resource management. It is becoming common to see combinations of these data applied to answer relevant scientific questions. Yet, methods for scaling water quality data across regions and beyond, to provide actionable knowledge for stakeholders, have emerged only recently, particularly with the availability of satellite data now providing global coverage at high spatial resolution. In this paper, data sources and existing data integration frameworks are reviewed to give an overview of the present status and iden...
Retrieval of aquatic biogeochemical variables, such as the near-surface concentration of chloroph... more Retrieval of aquatic biogeochemical variables, such as the near-surface concentration of chlorophyll-a (Chla) in inland and coastal waters via remote observations, has long been regarded as a challenging task. This manuscript applies Mixture Density Networks (MDN) that use the visible spectral bands available by the Operational Land Imager (OLI) aboard Landsat-8 to estimate Chla. We utilize a database of co-located in situ radiometric and Chla measurements (N = 4,354), referred to as Type A data, to train and test an MDN model (MDNA). This algorithm’s performance, having been proven for other satellite missions, is further evaluated against other widely used machine learning models (e.g., support vector machines), as well as other domain-specific solutions (OC3), and shown to offer significant advancements in the field. Our performance assessment using a held-out test data set suggests that a 49% (median) accuracy with near-zero bias can be achieved via the MDNA model, offering impr...
Abstract Total suspended solids (TSS) concentration is an important biogeochemical parameter for ... more Abstract Total suspended solids (TSS) concentration is an important biogeochemical parameter for water quality management and sediment-transport studies. In this study, we propose a novel semi-analytical method for estimating TSS in clear to extremely turbid waters from remote-sensing reflectance (Rrs). The proposed method includes three sub-algorithms used sequentially. First, the remotely sensed waters are classified into clear (Type I), moderately turbid (Type II), highly turbid (Type III), and extremely turbid (Type IV) water types by comparing the values of Rrs at 490, 560, 620, and 754 nm. Second, semi-analytical models specific to each water type are used to determine the particulate backscattering coefficients (bbp) at a corresponding single wavelength (i.e., 560 nm for Type I, 665 nm for Type II, 754 nm for Type III, and 865 nm for Type IV). Third, a specific relationship between TSS and bbp at the corresponding wavelength is used in each water type. Unlike other existing approaches, this method is strictly semi-analytical and its sub-algorithms were developed using synthetic datasets only. The performance of the proposed method was compared to that of three other state-of-the-art methods using simulated (N = 1000, TSS ranging from 0.01 to 1100 g/m3) and in situ measured (N = 3421, TSS ranging from 0.09 to 2627 g/m3) pairs of Rrs and TSS. Results showed a significant improvement with a Median Absolute Percentage Error (MAPE) of 16.0% versus 30.2–90.3% for simulated data and 39.7% versus 45.9–58.1% for in situ data, respectively. The new method was subsequently applied to 175 MEdium Resolution Imaging Spectrometer (MERIS) and 498 Ocean and Land Colour Instrument (OLCI) images acquired in the 2003–2020 timeframe to produce long-term TSS time-series for Lake Suwa and Lake Kasumigaura, Japan. Performance assessments using MERIS and OLCI matchups showed good agreements with in situ TSS measurements.
The eastern oyster (Crassostrea virginica) is an important proxy for examining historical traject... more The eastern oyster (Crassostrea virginica) is an important proxy for examining historical trajectories of coastal ecosystems. Measurement of ~40,000 oyster shells from archaeological sites along the Atlantic Coast of the United States provides a long-term record of oyster abundance and size. The data demonstrate increases in oyster size across time and a nonrandom pattern in their distributions across sites. We attribute this variation to processes related to Native American fishing rights and environmental variability. Mean oyster length is correlated with total oyster bed length within foraging radii (5 and 10 km) as mapped in 1889 and 1890. These data demonstrate the stability of oyster reefs despite different population densities and environmental shifts and have implications for oyster reef restoration in an age of global climate change.
Abstract Knowledge of light partitioning into different optically active constituents, particular... more Abstract Knowledge of light partitioning into different optically active constituents, particularly chromophoric dissolved organic matter (CDOM) in the ultraviolet (UV) is indispensable for understanding UV dependent biogeochemical issues including photochemical processes in optically complex waters. Herein a new approach is presented to investigate photochemistry by blending two ocean color algorithms, namely the composite SeaUV (Cao et al., 2014) and the SeaCDOM (Cao and Miller, 2015) algorithms, and applying them to visible remote sensing reflectance (Rrs) measured using the Hyperspectral Imager for the Coastal Ocean (HICO). As illustrated using photochemical carbon monoxide (CO) production from CDOM, this model approach allows high resolution examination of UV optical details with estimates of both depth-specific and depth-integrated photoproduction rates in a dynamic estuarine/coastal environment. Decoupled retrievals of inherent and apparent optical properties (i.e. diffuse attenuation coefficient (Kd) and CDOM absorption coefficient (ag)) using two distinct ocean color algorithms over the entire UV spectrum allow a synoptically dynamic view of CDOM's contribution to light attenuation (ag/Kd). This provides new potential to probe UV processes in complex coastal waters on regional as well as global scales using remote sensing of ocean color.
Photogrammetric Engineering and Remote Sensing, 1995
Our spectrometer is a high spectral resolution instrument which has two sensing heads called came... more Our spectrometer is a high spectral resolution instrument which has two sensing heads called cameras. The two cameras were observed to be misregistered relative to one another by up to 6 nm. The cameras were brought to a common wavelength base to correctly compare the data when the two cameras are used in a near-simultaneous mode. The wavelengths were assigned to the respective corresponding camera spectral wavelength bands and spectral bandwidths and sampling intervals calculated for each camera. Spectral bandwidths were larger than expected, but the sampling intervals were in close agreement with manufacturer specifications. Both cameras were calibrated for radiance and irradiance. The calibration coefficients developed during the radiometric calibrations showed an apparent light intensity dependence for wavelengths greater than 1000 nm. A closure experiment was conducted to test the accuracy of radiometric calibrations. Our results showed that estimates of irradiance from both cameras were within 5 percent of each other.
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Papers by John Schalles