Wind-induced resuspension in a shallow lake from Medium Resolution Imaging Spectrometer (MERIS) full-resolution reflectances

A lack of empirical evidence impedes assessment of the spatial and temporal extent of critical conditions for recurring high turbidity in large wind-exposed shallow lakes. Here spatiotemporal variation in total suspended matter (TSM) concentration was captured by processing 30 Envisat Medium Resolution Imaging Spectrometer (MERIS) images of a shallow lake (Markermeer) with a spectral matching algorithm. The TSM maps showed elevated downwind concentrations for moderate winds (from 4 to 9 m

Spectra of a shallow sea-unmixing for class identification and monitoring of coastal waters

Ocean colour-based monitoring of water masses is a promising alternative to monitoring concentrations in heterogeneous coastal seas. Fuzzy methods, such as spectral unmixing, are especially well suited for recognition of water masses from their remote sensing reflectances. However, such models have not yet been applied for water classification and monitoring. In this study, a fully constrained endmember model with simulated endmembers was developed for water class identification in the shallow Wadden Sea and adjacent German Bight. Its performance was examined on in situ measured reflectances and on MERIS satellite data. Water classification by means of unmixing reflectance spectra proved to be successful. When the endmember model was applied to MERIS data, it was able to visualise well-known spatial, tidal, seasonal, and wind-related variations in optical properties in the heterogeneous Wadden Sea. Analyses show that the method is insensitive to small changes in endmembers. Therefore, it can be applied in similar coastal areas. For use in open ocean situations or coastal or inland waters with other specific inherent optical properties, re-simulation of the endmember spectra with local optical properties is required. However, such an adaptation requires only a limited number of local in situ measurements

Validation of a spectral correction procedure for sun and sky reflections in above-water reflectance measurements

A three-component reflectance model (3C) is applied to above-water radiometric measurements to derive remote-sensing reflectance Rrs(l). 3C provides a spectrally resolved offset D(l) to correct for residual sun and sky radiance (Rayleigh- and aerosol-scattered) reflections on the water surface that were not represented by sky radiance measurements. 3C is validated with a data set of matching above- and below-water radiometric measurements collected in the Baltic Sea, and compared against a scalar offset correction D. Correction with D(l) instead of D consistently reduced the (mean normalized root-mean-square) deviation between Rrs(l) and reference reflectances to comparable levels for clear (D: 14.3 +- 2.5 %, D(l): 8.2 +- 1.7 %), partly clouded (D: 15.4 +- 2.1 %, D(l): 6.5 +- 1.4 %), and completely overcast (D: 10.8 +- 1.7 %, D(l): 6.3 +- 1.8 %) sky conditions. The improvement was most pronounced under inhomogeneous sky conditions when measurements of sky radiance tend to be less representative of surface-reflected radiance.Accounting for both sun glint and sky reflections also relaxes constraints on measurement geometry, which was demonstrated based on a semi-continuous daytime data set recorded in an eutrophic freshwater lake in the Netherlands. Rrs(l) that were derived throughout the day varied spectrally by less than 2 % relative standard deviation. Implications on measurement protocols are discussed. An open source software library for processing reflectance measurements was developed and is made publicly available

An optical classification tool for global lake waters

Shallow and deep lakes receive and recycle organic and inorganic substances from within the confines of these lakes, their watershed and beyond. Hence, a large range in absorption and scattering and extreme differences in optical variability can be found between and within global lakes. This poses a challenge for atmospheric correction and bio-optical algorithms applied to optical remote sensing for water quality monitoring applications. To optimize these applications for the wide variety of lake optical conditions, we adapted a spectral classification scheme based on the concept of optical water types. The optical water types were defined through a cluster analysis of in situ hyperspectral remote sensing reflectance spectra collected by partners and advisors of the European Union 7th Framework Programme (FP7) Global Lakes Sentinel Services (GLaSS) project. The method has been integrated in the Envisat-BEAM software and the Sentinel Application Platform (SNAP) and generates maps of water types from image data. Two variations of water type classification are provided: one based on area-normalized spectral reflectance focusing on spectral shape (6CN, six-class normalized) and one that retains magnitude with no modification to the reflectance signal (6C). This resulted in a protocol, or processing scheme, that can also be applied or adapted for Sentinel-3 Ocean and Land Colour Imager (OLCI) datasets. We apply both treatments to MERIS imagery of a variety of European lakes to demonstrate its applicability. The studied target lakes cover a range of biophysical types, from shallow turbid to deep and clear, as well as eutrophic and dark absorbing waters, rich in colored dissolved organic matter (CDOM). In shallow, high-reflecting Dutch and Estonian lakes with high sediment load, 6C performed better, while in deep, low-reflecting clear Italian and Swedish lakes, 6CN performed better. The 6CN classification of in situ data is promising for very dark, high CDOM, absorbing lakes, but we show that our atmospheric correction of the imagery was insufficient to corroborate this. We anticipate that the application of the protocol to other lakes with unknown in-water characterization, but with comparable biophysical properties will suggest similar atmospheric correction (AC) and in-water retrieval algorithms for global lakes

Variability of adjacency effects in sky reflectance measurements

Sky reflectance Rsky is used to correct in situ reflectance measurements in the remote detection of water color. We analyzed the directional and spectral variability in Rsky due to adjacency effects against an atmospheric radiance model. The analysis is based on one year of semi-continuous Rsky observations that were recorded in two azimuth directions. Adjacency effects contributed to Rsky dependence on season and viewing angle and predominantly in the near-infrared (NIR). For our test area, adjacency effects spectrally resembled a generic Vegetation spectrum. The adjacency effect was weakly dependent on the magnitude of Rayleigh- and aerosol-scattered radiance. The reflectance differed between viewing directions 5.4 +/- 6.3% for adjacency effects and 21.0 +/- 19.8% for Rayleigh- and aerosol-scattered Rsky in the NIR. Under which conditions in situ water reflectance observations require dedicated correction for adjacency effects is discussed. We provide an open source implementation of our method to aid identification of such conditions

Effect of FHA and Prn on Bordetella pertussis colonization of mice is dependent on vaccine type and anatomical site.

Bordetella pertussis vaccine escape mutants that lack expression of the pertussis antigen pertactin (Prn) have emerged in vaccinated populations in the last 10-20 years. Additionally, clinical isolates lacking another acellular pertussis (aP) vaccine component, filamentous hemagglutinin (FHA), have been found sporadically. Here, we show that both whole-cell pertussis (wP) and aP vaccines induced protection in the lungs of mice, but that the wP vaccine was more effective in nasal clearance. Importantly, bacterial populations isolated from the lungs shifted to an FHA-negative phenotype due to frameshift mutations in the fhaB gene. Loss of FHA expression was strongly selected for in Prn-deficient strains in the lungs following aP but not wP vaccination. The combined loss of Prn and FHA led to complete abrogation of bacterial surface binding by aP-induced serum antibodies. This study demonstrates vaccine- and anatomical site-dependent adaptation of B. pertussis and has major implications for the design of improved pertussis vaccines