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Taxonomic Revision of the Genus Trictenotoma Gray, 1832 (Coleoptera: Trictenotomidae). Part 3 – Species from the Philippine Archipelago, with Description of a New Species
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RBINS Staff Publications 2021
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Food nutrient availability affects epibiont prevalence and richness in natural Daphnia populations
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RBINS Staff Publications 2020
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Quality-control tests for OC4, OC5 and NIR-red satellite chlorophyll-a algorithms applied to coastal waters
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Reliable satellite estimates of chlorophyll-a concentration (Chl-a) are needed in coastal waters for applications such as eutrophication monitoring. However, because of the optical complexity of coastal waters, retrieving accurate Chl-a is still challenging. Many algorithms exist and give quite different performance for different optical conditions but there is no clear definition of the limits of applicability of each algorithm and no clear basis for deciding which algorithm to apply to any given image pixel (reflectance spectrum). Poor quality satellite Chl-a data can easily reach end-users. To remedy this and provide a clear decision on when a specific Chl-a algorithm can be used, we propose simple quality control tests, based on MERIS water leaving reflectance (ρw) bands, to determine on a pixel-by-pixel basis if any of three popular and complementary algorithms can be used. The algorithms being tested are: 1. the OC4 blue-green band ratio algorithm which was designed for open ocean waters; 2. the OC5 algorithm which is based on look-up tables and corrects OC4 overestimation in moderately turbid waters and 3. a near infrared-red (NIR-red) band ratio algorithm designed for eutrophic waters. Using a dataset of 348 in situ Chl-a / MERIS matchups, the conditions for reliable performance of each of the selected algorithms are determined. The approach proposed here looks for the best compromise between the minimization of the relative difference between In situ measurements and satellite estimations and the number of pixels processed. Conditions for a reliable application of OC4 and OC5 depend on ρw412/ρw443 and ρw560, used as proxies of coloured dissolved organic matter and suspended particulate matter (SPM), as compared to ρw560/ρw490, used as a proxy for Chl-a. Conditions for reliable application of the NIR-red band ratio algorithm depend on Chl-a and SPM. These conditions are translated into pixel-based quality control (QC) tests with appropriately chosen thresholds. Results show that by removing data which do not pass QC, the performance of the three selected algorithms is significantly improved. After combining these algorithms, 70\% of the dataset could be processed with a median absolute percent difference of 30.5\%. The QC tests and algorithm merging methodology were then tested on four MERIS images of European waters. The OC5 algorithm was found to be suitable for most pixels, except in very turbid and eutrophic waters along the coasts where the NIR-red band ratio algorithm helps to fill the gap. Finally, a test was performed on an OLCI-S3A image. Although some validations of water reflectance are still needed for the OLCI sensors, results show similar behavior to the MERIS applications which suggests that when applied to OLCI data the present methodology will help to accurately estimate Chl-a in coastal waters for the next decade.
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RBINS Staff Publications 2022
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Monitoring of high biomass Phaeocystis globosa blooms in the Southern North Sea by in situ and future spaceborne hyperspectral radiometry
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Phaeocystis globosa (P. globosa hereafter) is a phytoplankton species which commonly blooms at high biomass in April–May in the Southern North Sea and forms undesirable foam which accumulates on the beaches. Monitoring of this species is required by EU directives. Measurement of phytoplankton species composition has historically been made by pigment or microscopic analysis of water samples, which is spatially sparse and temporally infrequent e.g. weekly/monthly. In-water instruments such as flow cytometers can provide very high frequency data but at high acquisition and maintenance cost. Automated in situ above water radiometry has the potential to provide very high frequency data at single locations but requires very careful design of processing algorithms in turbid waters with high non-algal absorption. Spaceborne radiometry could provide both very good spatial coverage and moderate/high frequency of data, e.g. daily/weekly, but accurate determination of phytoplankton species composition is considerably more difficult in turbid waters than in open ocean waters. Prior studies based on a limited number of shipborne reflectance measurements suggested feasibility of P. globosa detection in turbid waters from hyperspectral radiometry. The availability of a new autonomous above water hyperspectral radiometer system has enabled further refinement and intensive testing of these techniques. From a time-series of 4356 water reflectance spectra measured near Ostend harbour in Belgian coastal waters from 2020/04/01 to 2020/08/18, two existing algorithms for P. globosa detection were successfully applied. Results show a high biomass P. globosa bloom occurring in late-April/early-May as found every year in water sample analyses for Belgian coastal waters. The high temporal resolution of the radiometric data allows to capture the evolution of the bloom at time scales sufficiently short (hourly and daily) compared to growth/decay and tidal processes. The challenges of extending the methods to future spaceborne instruments are also tested by simulating the impact of errors in sensor inter-band calibration, atmospheric correction and radiometric noise. Results show that because of their spectral coherence, atmospheric correction errors impact only slightly P. globosa detection whereas inaccuracy in inter-band calibration and radiometric noise are much more problematic as they affect each spectral band independently. Because radiometric noise should be reduced in the new generation of hyperspectral sensors and can always be reduced by spatial binning, the inter-band relative calibration uncertainty appears to be the main challenge for spaceborne mission design. Indeed, it was demonstrated that inter-band calibration error should be 0.25\% and ideally 0.1\% at top of the atmosphere highlighting the need for particular attention to inter-band calibration in sensor design and post processing treatments including vicarious calibration.
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RBINS Staff Publications 2022
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Suitability of multisensory satellites for long-term chlorophyll assessment in coastal waters: A case study in optically-complex waters of the temperate region
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We investigated the use of multisensory satellite data to determine long-term changes in surface chlorophyll concentrations using a 19-year (1998–2016) time series of chlorophyll data in the Danish Kattegat region of the Baltic Sea. Merged satellite estimates (SeaWiFS-MODIS/Aqua-MERIS-VIIRS) were compared with in situ ship based time series from four monitoring stations situated with increasing distance from land and nutrient sources. In situ and satellite derived estimates showed similar trend in chlorophyll with several fold higher values closer to land. Satellites aligned very well with in situ estimates in the open water stations but showed significant differences in magnitude and inter-annual variability, in particular in shallow coastal waters. Some systematic deviation was observed with satellite underestimating the growing season average for the earlier periods (1998–2002) and overestimating for the later period (2012–2016) compared to in situ estimates. Comparing growing season chlorophyll means over the 19 year period showed increasing magnitude and variability in nearshore and shallower areas, most pronounced for the satellite derived chlorophyll. Satellites overestimated chlorophyll in nearshore areas 2–4 fold, despite excluding shallow nearshore areas with possible benthic interferences from the analyses. This bias needs further validation and requires correction to improve the overall applicability of satellites for long-term monitoring of chlorophyll in the Kattegat region. From analysis of normalized data, we developed a simple correction model, which reduced deviations considerably between methods, underlying the importance of in situ data for application of satellite observations. While significant deviations were observed from in situ data, satellites are clearly advantageous in the much higher temporal and high spatial coverage they provide. Multisensory satellites can, however, not be used currently as a standalone technique for long-term assessment of chlorophyll. They require validation with in situ measurements, which provide essential data for calibration, validation and correction of satellite based estimates. A complementary use of multisensory satellite and in situ measurements therefore remains essential to assess trends in the ecological status of optically complex waters such as the Kattegat region of the Baltic Sea.
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RBINS Staff Publications 2022
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Organic Matter Composition of Biomineral Flocs and Its Influence on Suspended Particulate Matter Dynamics Along a Nearshore to Offshore Transect
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The seasonal variation in concentration of transparent exopolymer particles (TEPs), particulate organic carbon (POC) and particulate organic nitrogen (PON) were investigated together with floc size and the concentration of suspended particulate matter (SPM) along the cross-shore gradient, from the high turbid nearshore toward the low-turbid offshore waters in the Southern Bight of the North Sea. Our data demonstrate that biophysical flocculation cannot be explained by these heterogeneous parameters, but requires a distinction between a more reactive labile (“fresh”) and a less reactive refractory (“mineral-associated”) fraction. Based on all data, we separated the labile and mineral-associated POC, PON, and TEP using a semi-empirical model approach. The model's estimates of fresh and mineral-associated organic matter (OM) show that great parts of the POC, PON, and TEP are associated with suspended minerals, which are present in the water column throughout the year, whereas the occurrence of fresh TEP, POC, and PON is restricted to spring and summer months. In spite of a constantly high abundance of total TEP throughout the entire year, it is its fresh fraction that promotes the formation of larger and faster sinking biomineral flocs, thereby contributing to reducing the SPM concentration in the water column over spring and summer. Our results show that the different components of the SPM, such as minerals, extracellular OM and living organisms, form an integrated dynamic system with direct interactions and feedback controls.
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RBINS Staff Publications 2022
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Comparing life history traits and tolerance to changing environments of two oyster species (Ostrea edulis and Crassostrea gigas) through Dynamic Energy Budget theory
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To predict the response of the European flat oyster (Ostrea edulis) and Pacific cupped oyster (Crassostrea gigas/Magallana gigas) populations to environmental changes, it is key to understand their life history traits. The Dynamic Energy Budget (DEB) theory is a mechanistic framework that enables the quantification of the bioenergetics of development, growth and reproduction from fertilization to death across different life stages. This study estimates the DEB parameters for the European flat oyster, based on a comprehensive dataset, while DEB parameters for the Pacific cupped oyster were extracted from the literature. The DEB parameters for both species were validated using growth rates from laboratory experiments at several constant temperatures and food levels as well as with collected aquaculture data from the Limfjorden, Denmark, and the German Bight. DEB parameters and the Arrhenius temperature parameters were compared to get insight in the life history traits of both species. It is expected that increasing water temperatures due to climate change will be beneficial for both species. Lower assimilation rates and high energy allocation to soma explain O. edulis’ slow growth and low reproductive output. Crassostrea gigas’ high assimilation rate, low investment in soma and extremely low reserve mobility explains the species’ fast growth, high tolerance to starvation and high reproductive output. Hence, the reproductive strategies of both species are considerably different. Flat oysters are especially susceptible to unfavourable environmental conditions during the brooding period, while Pacific oysters’ large investment in reproduction make it well adapted to highly diverse environments. Based on the life history traits, aquaculture and restoration of O. edulis should be executed in environments with suitable and stable conditions.
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RBINS Staff Publications 2022
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Global satellite water classification data products over oceanic, coastal, and inland waters
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Satellites have generated extensive data of remote sensing reflectance spectra (Rrs(λ)) covering diverse water classes or types across global waters. Spectral classification of satellite Rrs(λ) data allows for the distinguishing and grouping of waters with characteristic bio-optical/biogeochemical features that may influence the productivity of a given water body. This study reports new satellite water class products (Level-2 and Level-3) from the Visible Infrared Imaging Radiometer Suite (VIIRS). We developed and implemented a hyperspectral scheme that accounts for the Rrs(λ) spectral shapes and globally resolves oceanic, coastal, and inland waters into 23 water classes. We characterized the light absorption and scattering coefficients, chlorophyll-a concentration, diffuse attenuation coefficient, and suspended particulate matter for individual water classes. It is shown that the water classes are separable by their distinct bio-optical and biogeochemical properties. Furthermore, validation result suggests that the VIIRS water class products are accurate globally. Finally, we examined the spatial and temporal variability of the water classes in case studies for a demonstration of applications. The water class data in open oceans reveal that the subtropical ocean gyres have experienced dramatic expansion over the last decade. In addition, the water class data appear to be a valuable (and qualitative) indicator for water quality in coastal and inland waters with compelling evidence. We stress that this new satellite product is an excellent addition to the aquatic science database, despite the need for continuous improvement toward perfection.
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RBINS Staff Publications 2022
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Validation of Landsat 8 high resolution Sea Surface Temperature using surfers
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Nearshore coastal waters are highly dynamic in both space and time. They can be difficult to sample using conventional methods due to their shallow depth, tidal variability, and the presence of strong currents and breaking waves. High resolution satellite sensors can be used to provide synoptic views of Surface Temperature (ST), but the performance of such ST products in the nearshore zone is poorly understood. Close to the shoreline, the ST pixels can be influenced by mixed composition of water and land, as a result of the sensor’s spatial resolution. This can cause thermal adjacency effects due to the highly different diurnal temperature cycles of water bodies and land. Previously, temperature data collected during surfing sessions has been proposed for validation of moderate resolution (1 km pixel size) satellite ST products. In this paper we use surfing temperature data to validate three high resolution (100 m resampled to 30 m pixel size) ST products derived from the Thermal InfraRed Sensor (TIRS) on board Landsat 8 (L8). ST was derived from Collection 1 and 2 Level 1 data (C1L1 and C2L1) using the Thermal Atmospheric Correction Tool (TACT), and was obtained from the standard Collection 2 Level 2 product (USGS C2L2). This study represents one of the first evaluations of the new C2 products, both L1 and L2, released by USGS at the end of 2020. Using automated matchup and image quality control, 88 matchups between L8/TIRS and surfers were identified, distributed across the North-Western semihemisphere. The unbiased Root Mean Squared Difference (uRMSD) between satellite and in situ measurements was generally ¡ 2 K, with warm biases (Mean Average Difference, MAD) of 1.7 K (USGS C2L2), 1.3 K (TACT C1L1) and 0.8 K (TACT C2L1). Large interquartile ranges of ST in 5 × 5 satellite pixels around the matchup location were found for several images, especially for the summer matchups around the Californian coast. By filtering on target stability the number of matchups reduced to 31, which halved the uRMSD across the three methods (to around 1.1K), MAD were much lower, i.e. 1.1 K (USGS C2L2), 0.6 K (TACT C1L1), and 0.2 K (TACT C2L1). The larger biases of the C2L2 product compared to TACT C2L1 are caused as a result of: (1) a lower emissivity value for water targets used in USGS C2L2, and (2) differences in atmospheric parameter retrieval, mainly from differences in upwelling atmospheric radiance and lower atmospheric transmittance retrieved by USGS C2L2. Additionally, tiling artefacts are present in the C2L2 product, which originate from a coarser atmospheric correction process. Overall, the L8/TIRS derived ST product compares well with in situ measurements made while surfing, and we found the best performing ST product for nearshore coastal waters to be the Collection 2 Level 1 data processed with TACT.
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RBINS Staff Publications 2022
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On the Seasonal Dynamics of Phytoplankton Chlorophyll-a Concentration in Nearshore and Offshore Waters of Plymouth, in the English Channel: Enlisting the Help of a Surfer
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The role of phytoplankton as ocean primary producers and their influence on global biogeochemical cycles makes them arguably the most important living organisms in the sea. Like plants on land, phytoplankton exhibit seasonal cycles that are controlled by physical, chemical, and biological processes. Nearshore coastal waters often contain the highest levels of phytoplankton biomass. Yet, owing to difficulties in sampling this dynamic region, less is known about the seasonality of phytoplankton in the nearshore (e.g., surf zone) compared to offshore coastal, shelf and open ocean waters. Here, we analyse an annual dataset of chlorophyll-a concentration—a proxy of phytoplankton biomass—and sea surface temperature (SST) collected by a surfer at Bovisand Beach in Plymouth, UK on a near weekly basis between September 2017 and September 2018. By comparing this dataset with a complementary in-situ dataset collected 7 km offshore from the coastline (11 km from Bovisand Beach) at Station L4 of the Western Channel Observatory, and guided by satellite observations of light availability, we investigated differences in phytoplankton seasonal cycles between nearshore and offshore coastal waters. Whereas similarities in phytoplankton biomass were observed in autumn, winter and spring, we observed significant differences between sites during the summer months of July and August. Offshore (Station L4) chlorophyll-a concentrations dropped dramatically, whereas chlorophyll-a concentrations in the nearshore (Bovsiand Beach) remained high. We found chlorophyll-a in the nearshore to be significantly positively correlated with SST and PAR over the seasonal cycle, but no significant correlations were observed at the offshore location. However, offshore correlation coefficients were found to be more consistent with those observed in the nearshore when summer data (June–August 2018) were removed. Analysis of physical (temperature and density) and chemical variables (nutrients) suggest that the offshore site (Station L4) becomes stratified and nutrient limited at the surface during the summer, in contrast to the nearshore. However, we acknowledge that additional experiments are needed to verify this hypothesis. Considering predicted changes in ocean stratification, our findings may help understand how the spatial distribution of phytoplankton phenology within temperate coastal seas could be impacted by climate change. Additionally, this study emphasises the potential for using marine citizen science as a platform for acquiring environmental data in otherwise challenging regions of the ocean, for understanding ecological indicators such as phytoplankton abundance and phenology. We discuss the limitations of our study and future work needed to explore nearshore phytoplankton dynamics.
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RBINS Staff Publications 2022
