Phytoplankton pigment in situ measurements uncertainty evaluation: an HPLC interlaboratory comparison with a European-scale dataset

Phytoplankton pigment data play a crucial role in ecological studies, enabling the identification of algal groups and estimation of primary production rates. Accurate measurements of chlorophyll a (TChl a) and other marine pigments are essential for the development of bio-optical algorithms and the validation of satellite data products. High-performance liquid chromatography (HPLC) is the gold standard method for quantifying multiple pigments in a single water sample. This study aims to investigate the uncertainties associated with phytoplankton pigment quantification by comparing duplicate sample analyses conducted by two laboratories, the Joint Research Centre of the European Commission (J) and the DHI Group, Denmark (D). The analyses were performed using the same HPLC method. The dataset comprised 957 natural samples collected between 2012 and 2017 from various European seas, representing different trophic conditions with TChl a concentrations ranging from 0.083 to 27.35 mg/m3. The study compared the results of the two independent analyses for TChl a and primary phytoplankton pigments, including chlorophyll b, chlorophyll c, carotens, fucoxanthin, 19′-butanoyloxyfucoxanthin, diadinoxanthin, diatoxanthin, 19′-hexanoyloxyfucoxanthin, peridin, and zeaxanthin. The percent difference between the two analyses was calculated to assess the uncertainties associated with pigment quantification. The mean percent difference observed between the two independent analyses of TChl a was 10.8%. For the primary phytoplankton pigments, the associated mean percent difference was 16.9%. These results meet the requirements of 15% and 25% uncertainties, respectively, which are applicable for the validation of satellite data products. The comparative analysis between the two laboratories demonstrates that the uncertainties associated with phytoplankton pigment quantification are within acceptable ranges for the validation of satellite data products. Moreover, the study investigates the propagation of uncertainties in diagnostic pigment values to phytoplankton indexes, which are derived using pigment-based algorithms to characterize phytoplankton populations according to functional types

Measuring the Asborption Coefficient of Aquatic Particles Retained on Filter Using a Photo-Oxidation Bleaching Technique

This report describes a method for the determination of the particulate absorption coefficient that aims to improve the T-R method of Ferrari and Tassan, (1995, 2002) giving an alternative to the visual deternination of the bleached state of the sample on the filter and introducing a photoxidation bleaching technique to optimize the depigmentation process.JRC.H.3-Global environement monitorin

International Intercomparison of In Situ Chlorophyll-a Measurements for Data Quality Assurance of the Swedish Monitoring Program

Chlorophyll-a is an essential climate variable. Chlorophyll-a in situ measurements are usually used for the validation of satellite images. Previous intercomparisons have shown that there can be substantial differences between in situ laboratories. In order to shed light on these differences, we arranged international chlorophyll-a intercomparisons with eight participating laboratories during 1–2 July 2021. We performed two dedicated transects through Bråviken bay (NW Baltic proper) and sampled four stations in each transect along a chlorophyll-a gradient. We took three surface replicates per laboratory and per station, i.e., 24 samples per laboratory. The samples were filtered through Whatman GF/F filters, and filters were frozen in liquid nitrogen and distributed in dry ice to all laboratories together with chlorophyll-a standards. The results between labs compared quite well. The mean normalized bias (MNB) of the standard measurements ranged between −23% and +19% for all laboratories and −7% to +19% for the Baltic Sea laboratories compared to high-performance liquid chromatography. The MNB of the two Bråviken transects ranged between −23 and +17% for all laboratories (compared to the median of all spectrophotometric and fluorometric measurements) and between −2 and +17% for the Baltic Sea laboratories. On average, the chlorophyll-a concentrations measured by the fluorometric method were about 13% higher than those measured by spectrophotometry, and fluorometry samples tended to have more scatter. The largest uncertainties seem to be caused by variable storage and extraction methods and are not fully captured in this intercomparison. This is demonstrated by analyzing historical comparisons revealing very large uncertainties (root mean square difference (RMSD) up to 109% and bias up to 68%), possibly due to too low filtration volumes and due to different extraction and storage methods. Our recommendation is to flash-freeze samples in liquid nitrogen and store them at −80°C. After storage, they should be extracted and measured at room temperature within 6–24 h. Our results also indicate that ethanol is much more efficient in extracting Chl-a than acetone. Last but not least, we would like to point out that the uncertainties in measuring chlorophyll-a by satellite are now within the range of in situ data, as shown here by comparing the in situ results from this study with published remote sensing results from the literature.publishedVersio

Bio-optical Algorithms for European Seas: Performance and Applicability of Neural-Net Inversion Schemes

The report presents and discusses the application of Multi Layer Perceptron (MLP) neural networks to derive Chlorophyll-a concentration (Chl-a), absorption of the yellow substance at 412 nm (ays(412)) and concentration of the total suspended matter (TSM) from remote sensing reflectance Rrs values. MLPs were developed on the basis of data collected within the framework of the Coastal Atmosphere and Sea Time Series (CoASTS) and Bio-Optical mapping of Marine Properties (BiOMaP) programs carried out by the Institute for Environment and Sustainability (IES), JRC of E.C., Italy. Investigated oceanographic regions include the Eastern Mediterranean Sea, the Ligurian Sea, the Northern Adriatic Sea, the Western Black Sea, the English Channel and the Baltic Sea. The study verifies the applicability of MLPs to retrieve ocean color data products in each basin. For instance, the highest accuracy in retrieving Chl-a has been found in the Easter Mediterranean Sea and the Ligurian Sea (14 and 25 %, respectively). In the case of ays(412), the MLP is the most performing in the waters of the English Channel and the Baltic Sea (14 and 13%). Instead, the TSM retrieval is the most accurate in the Black Sea and at the Acqua Alta Oceanographic Tower (14 and 19%). To enhance mission specific ocean color resuls, MLP coefficients are also computed applying band-shift corrections to produce Rrs spectra at wavelengths matching those of SeaWiFS, MODIS and MERIS. Resulting tables of MLP parameters are reported to permit independent applications of neural networks presented in this analysis.JRC.H.3-Global environement monitorin

Regional Bio-optical Relationships and Algorithms for the Adriatic Sea, the Baltic Sea and the English Channel/North Sea Suitable for Ocean Colour Sensors

Regional bio-optical relationships and empirical algorithms were developed on the basis of measurements collected during the CoASTS 1995-2005 bio-optical time-series in the northern coastal Adriatic Sea as well as during ship campaigns performed in coastal regions of the Adriatic Sea, the Baltic Sea and the English Channel/North Sea between 2000 and 2005. The empirical algorithms aim at the retrieval from ocean colour data of the Chlorophyll a and Total Suspended Matter concentrations, of the absorption coefficient of the Coloured Dissolved Organic Matter, of the diffuse attenuation coefficient of downwelling irradiance and of the Secchi depth. Bio-optical relationships relating the marine optically significant components to their absorption or scattering properties are also presented for the investigated coastal areas.JRC.H.3-Global environement monitorin

Molecular epidemiology and genotyping of Chlamydia trachomatis infection in a cohort of young asymptomatic sexually active women (18-25 years) in Milan, Italy.

IntroductionChlamydia trachomatis (Ct) is the most common bacterial cause of sexually transmitted infections (STI) and is associated with severe long-term sequelae in female populations.In Italy Ct infections are not submitted to a screening programme, and its epidemiological profile is understudied. Even scarcer information is available about the genetic diversity on ompA gene, whose sequence defines 18 different genovars.This study aims at evaluating the prevalence of Ct infection in young sexually active asymptomatic women aged 18-25, and characterizing the molecular epidemiology of the different circulating genovars in this population. MethodsCervical samples collected from 909 sexually-active-young women (mean age 21.5 years) were analyzed through molecular assay for the detection of Ct infection. Phylogenetic analysis on the ompA gene was performed on Ct positive samples to identify the circulating genovars. ResultsThe overall prevalence of Ct-infection was 4.4% (95%CI: 3.2-5.9%): 5.3% among women aged 18-21 years and 3.5% among those aged 22-25 years. Phylogenetic analysis has identified 5 different genovars: D, E, F, G, and H. The most common genovar was the E (46%), followed by genovar F and G (18.9% each), D (13.5%), and H (2.7%). ConclusionsThis study underlines the high prevalence of asymptomatic Ct-infections among young women. Overall, about half of asymptomatic infections is sustained by genovar E. The introduction in Italy of a systematic screening program should be considered to allow a better understanding of Ct spreading and providing women with an opportunity for early treatment to protect their sexual and reproductive health

International Intercomparison of In Situ Chlorophyll-a Measurements for Data Quality Assurance of the Swedish Monitoring Program

Chlorophyll-a is an essential climate variable. Chlorophyll-a in situ measurements are usually used for the validation of satellite images. Previous intercomparisons have shown that there can be substantial differences between in situ laboratories. In order to shed light on these differences, we arranged international chlorophyll-a intercomparisons with eight participating laboratories during 1–2 July 2021. We performed two dedicated transects through Bråviken bay (NW Baltic proper) and sampled four stations in each transect along a chlorophyll-a gradient. We took three surface replicates per laboratory and per station, i.e., 24 samples per laboratory. The samples were filtered through Whatman GF/F filters, and filters were frozen in liquid nitrogen and distributed in dry ice to all laboratories together with chlorophyll-a standards. The results between labs compared quite well. The mean normalized bias (MNB) of the standard measurements ranged between −23% and +19% for all laboratories and −7% to +19% for the Baltic Sea laboratories compared to high-performance liquid chromatography. The MNB of the two Bråviken transects ranged between −23 and +17% for all laboratories (compared to the median of all spectrophotometric and fluorometric measurements) and between −2 and +17% for the Baltic Sea laboratories. On average, the chlorophyll-a concentrations measured by the fluorometric method were about 13% higher than those measured by spectrophotometry, and fluorometry samples tended to have more scatter. The largest uncertainties seem to be caused by variable storage and extraction methods and are not fully captured in this intercomparison. This is demonstrated by analyzing historical comparisons revealing very large uncertainties (root mean square difference (RMSD) up to 109% and bias up to 68%), possibly due to too low filtration volumes and due to different extraction and storage methods. Our recommendation is to flash-freeze samples in liquid nitrogen and store them at −80°C. After storage, they should be extracted and measured at room temperature within 6–24 h. Our results also indicate that ethanol is much more efficient in extracting Chl-a than acetone. Last but not least, we would like to point out that the uncertainties in measuring chlorophyll-a by satellite are now within the range of in situ data, as shown here by comparing the in situ results from this study with published remote sensing results from the literature

Ocean Colour Calibration and Validation: The JRC contribution to Copernicus

Copernicus Sentinel-3 missions, including the ongoing Sentinel-3A and -3B and the future Sentinel-3C and -3D, offer an unprecedented opportunity for long-term ocean colour observations to support global environmental and climate investigations. Nevertheless, any ocean colour mission incorporates calibration and validation activities essential for the indirect calibration of the space sensor and the validation of data products. These calibration and validation activities are largely centered on the production of highly accurate in situ reference measurements relying on state of the art measurement methods and instrumentation. Since the start of the operational ocean colour missions in 1997, the JRC sustained the required calibration and validation activities by developing unique expertise and setting up specific measurement programs and infrastructures. This expertise, measurement programs and infrastructures, currently support the Copernicus ocean colour calibration and validation tasks through the delivery and exploitation of in situ reference data essential for the quality control of satellite data products. This Technical Report aims at providing: i. a general introduction to the ocean colour paradigm; ii. an extended synopsis of requirements and strategies for satellite ocean colour missions with a detailed focus on the JRC experimental activities carried out during the last decades; and finally iii. a discussion supporting the need for a sustained support of the JRC laboratory and field measurement programs assisting the production and exploitation of in situ reference data for the validation of Sentinel-3 ocean colour products. The Report, mostly through section 2, should naturally satisfy readers interested in appraising the specific JRC activities performed to support ocean colour calibration and validation. The same Report through sections 1 and 3, should also satisfy the need for more essential information supporting the need for sustaining the JRC ocean colour validation activities currently embedded in the Copernicus Earth Observation program of major relevance for global marine and climate investigations.JRC.D.2-Water and Marine Resource

Molecular characterization and phylogenetic analysis of human influenza A viruses in three consecutive seasons with different epidemiological profiles

Introduction. Influenza activity and influenza virus circulation were observed in Lombardy (northern Italy) during three con- secutive seasons and the molecular characteristics of circulating viruses analysed to control for introduction of new variants. Methods. The molecular characterization of 38 isolates, namely 20 A/H3N2 and 18 A/H1N1 influenza strains from the 2005/06, 2006/07 and 2007/08 seasons, was performed by sequence analy- sis of the globular head region of the HA protein (HA1 subunit), specific for influenza virus A/H3 and A/H1. Results and discussion. The last three influenza seasons in the study region were characterized by medium-low activity. A typical co-circulation of several variants was shown for A/H3 viruses for approximately two years and were subsequently almost entirely substituted by new emerging variants. Vice versa, A/H1 viruses had a more homogeneous circulation with a single lineage clearly dominating each season. The HA sequences of the A/H3 and the A/H1 viruses isolated in the last three seasons fell into 4 and 3 principal phylogenetic groups, respectively. No evidence of positive or negative selection in the sequence align- ments was observed. Conclusions. Molecular characterization of the influenza viruses in three consecutive seasons highlighted considerable heteroge- neity in their HA sequences. A careful surveillance of genetic changes in the HA1 domain during seasonal influenza epidemics may reveal immune escape and provide early information on newly emerging strains with epidemiologic inference

Viable Newcastle Disease Vaccine Strains in a Pharmaceutical Dump

To assess the viability of discarded and buried vaccine strains, we examined vaccines that had been buried for >20 years in an industrial waste dump in the city of Milan, Italy. Viability results showed potential biological risk associated with uncontrolled burial of pharmaceutical industry waste, including some live vaccines