Correction of profiles of in-situ chlorophyll fluorometry for the contribution of fluorescence originating from non-algal matter

In situ chlorophyll fluorometers have been widely employed for more than half a century, and to date, it still remains the most used instrument to estimate chlorophyll-a concentration in the field, especially for measurements onboard autonomous observation platforms, e.g., Bio-Argo floats and gliders. However, in deep waters (> 300 m) of some specific regions, e.g., subtropical gyres and the Black Sea, the chlorophyll fluorescence profiles frequently reveal “deep sea red fluorescence” features. In line with previous studies and through the analysis of a large data set (cruise transect in the South East Pacific and data acquired by 82 Bio- Argo floats), we show that the fluorescence signal measured by a humic-like DOM fluorometer is highly correlated to the “deep sea red fluorescence.” Both fluorescence signals are indeed linearly related in deep waters. To remove the contribution of non-algal organic matter from chlorophyll fluorescence profiles, we introduce a new correction. Rather that removing a constant value (generally the deepest chlorophyll a fluorescence value from the profile, i.e., so-called “deep-offset correction”), we propose a correction method which relies on DOM fluorometry and on its variation with depth. This new method is validated with chlorophyll concentration extracted from water samples and further applied on the Bio-Argo float data set. More generally, we discuss the potential of the proposed method to become a standard and routine procedure in quality-control and correction of chlorophyll a fluorescence originating from Bio-Argo network

Recommendations for obtaining unbiased chlorophyll estimates from in situ chlorophyll fluorometers: A global analysis of WET Labs ECO sensors

Chlorophyll fluorometers provide the largest in situ global data set for estimating phytoplankton biomass because of their ease of use, size, power consumption, and relatively low price. While in situ chlorophyll a (Chl) fluorescence is proxy for Chl a concentration, and hence phytoplankton biomass, there exist large natural variations in the relationship between in situ fluorescence and extracted Chl a concentration. Despite this large natural variability, we present here a global validation data set for the WET Labs Environmental Characterization Optics (ECO) series chlorophyll fluorometers that suggests a factor of 2 overestimation in the factory calibrated Chl a estimates for this specific manufacturer and series of sensors. We base these results on paired High Pressure Liquid Chromatography (HPLC) and in situ fluorescence match ups for which non-photochemically quenched fluorescence observations were removed. Additionally, we examined matches between the factory-calibrated in situ fluorescence and estimates of chlorophyll concentration determined from in situ radiometry, absorption line height, NASA’s standard ocean color algorithm as well as laboratory calibrations with phytoplankton monocultures spanning diverse species that support the factor of 2 bias. We therefore recommend the factor of 2 global bias correction be applied for the WET Labs ECO sensors, at the user level, to improve the global accuracy of chlorophyll concentration estimates and products derived from them. We recommend that other fluorometer makes and models should likewise undergo global analyses to identify potential bias in factory calibration

Calibration procedures and first data set of Southern Ocean chlorophyll a profiles collected by elephant seals equipped with a newly developed CTD-fluorescence tags

In-situ observation of the marine environment has traditionally relied on ship-based platforms. The obvious consequence is that physical and biogeochemical properties have been dramatically undersampled, especially in the remote Southern Ocean (SO). The difficulty in obtaining in situ data represents the major limitations to our understanding, and interpretation of the coupling between physical forcing and the biogeochemical response. Southern elephant seals (Mirounga leonina) equipped with a new generation of oceanographic sensors can measure ocean structure in regions and seasons rarely observed with traditional oceanographic platforms. Over the last few years, seals have allowed for a considerable increase in temperature and salinity profiles from the SO. However we were still lacking information on the spatio-temporal variation of phytoplankton concentration. This information is critical to assess how the biological productivity of the SO, with direct consequences on the amount of CO2 "fixed" by the biological pump, will respond to global warming. In this research program, we use an innovative sampling fluorescence approach to quantify phytoplankton concentration at sea. For the first time, a low energy consumption fluorometer was added to Argos CTD-SRDL tags, and these novel instruments were deployed on 27 southern elephant seals between 25 December 2007 and the 4 February 2011. As many as 3388 fluorescence profiles associated with temperature and salinity measurements were thereby collected from a vast sector of the Southern Indian Ocean. This paper address the calibration issue of the fluorometer before being deployed on elephant seals and present the first results obtained for the Indian Sector of the Southern Ocean.This in situ system is implemented in synergy with satellite ocean colour radiometry. Satellite-derived data is limited to the surface layer and is restricted over the SO by extensive cloud cover. However, with the addition of these new tags, we're able to assess the 3 dimension distribution of phytoplankton concentration by foraging southern elephant seals. This approach reveals that for the Indian sector of the SO, the surface chlorophyll a (chl a) concentrations provided by MODIS were underestimated by a factor of the order of 2–3 compared to in situ measurements. The scientific outcomes of this program include an improved understanding of both the present state and variability in ocean biology, and the accompanying biogeochemistry, as well as the delivery of real-time and open-access data to scientists

Using machine learning and Biogeochemical-Argo (BGC-Argo) floats to assess biogeochemical models and optimize observing system design

Numerical models of ocean biogeochemistry are becoming the major tools used to detect and predict the impact of climate change on marine resources and to monitor ocean health. However, with the continuous improvement of model structure and spatial resolution, incorporation of these additional degrees of freedom into fidelity assessment has become increasingly challenging. Here, we propose a new method to provide information on the model predictive skill in a concise way. The method is based on the conjoint use of a k-means clustering technique, assessment metrics, and Biogeochemical-Argo (BGC-Argo) observations. The k-means algorithm and the assessment metrics reduce the number of model data points to be evaluated. The metrics evaluate either the model state accuracy or the skill of the model with respect to capturing emergent properties, such as the deep chlorophyll maximums and oxygen minimum zones. The use of BGC-Argo observations as the sole evaluation data set ensures the accuracy of the data, as it is a homogenous data set with strict sampling methodologies and data quality control procedures. The method is applied to the Global Ocean Biogeochemistry Analysis and Forecast system of the Copernicus Marine Service. The model performance is evaluated using the model efficiency statistical score, which compares the model–observation misfit with the variability in the observations and, thus, objectively quantifies whether the model outperforms the BGC-Argo climatology. We show that, overall, the model surpasses the BGC-Argo climatology in predicting pH, dissolved inorganic carbon, alkalinity, oxygen, nitrate, and phosphate in the mesopelagic and the mixed layers as well as silicate in the mesopelagic layer. However, there are still areas for improvement with respect to reducing the model–data misfit for certain variables such as silicate, pH, and the partial pressure of CO2 in the mixed layer as well as chlorophyll-a-related, oxygen-minimum-zone-related, and particulate-organic-carbon-related metrics. The method proposed here can also aid in refining the design of the BGC-Argo network, in particular regarding the regions in which BGC-Argo observations should be enhanced to improve the model accuracy via the assimilation of BGC-Argo data or process-oriented assessment studies. We strongly recommend increasing the number of observations in the Arctic region while maintaining the existing high-density of observations in the Southern Oceans. The model error in these regions is only slightly less than the variability observed in BGC-Argo measurements. Our study illustrates how the synergic use of modeling and BGC-Argo data can both provide information about the performance of models and improve the design of observing systems.</p

Two databases derived from BGC-Argo float measurements for marine biogeochemical and bio-optical applications

Since 2012, an array of 105 Biogeochemical-Argo (BGC-Argo) floats has been deployed across the world’s oceans to assist in filling observational gaps that are required for characterizing open-ocean environments. Profiles of biogeochemical (chlorophyll and dissolved organic matter) and optical (single-wavelength particulate optical backscattering, downward irradiance at three wavelengths, and photosynthetically available radiation) variables are collected in the upper 1000m every 1 to 10 days. The database of 9837 vertical profiles collected up to January 2016 is presented and its spatial and temporal coverage is discussed. Each variable is quality controlled with specifically developed procedures and its time series is quality-assessed to identify issues related to biofouling and/or instrument drift. A second database of 5748 profile-derived products within the first optical depth (i.e., the layer of interest for satellite remote sensing) is also presented and its spatiotemporal distribution discussed. This database, devoted to field and remote ocean color applications, includes diffuse attenuation coefficients for downward irradiance at three narrow wavebands and one broad waveband (photosynthetically available radiation), calibrated chlorophyll and fluorescent dissolved organic matter concentrations, and single wavelength particulate optical backscattering. To demonstrate the applicability of these databases, data within the first optical depth are compared with previously established bio-optical models and used to validate remotely derived bio-optical products. The quality-controlled databases are publicly available from the SEANOE (SEA scieNtific Open data Edition) publisher at https://doi.org/10.17882/49388 and https://doi.org/10.17882/47142 for vertical profiles and products within the first optical depth, respectively

Low Clinical Burden of 2009 Pandemic Influenza A (H1N1) Infection during Pregnancy on the Island of La Réunion

BACKGROUND: Pregnant women have been identified as a group at risk, both for respiratory complications than for the admissions to the Intensive Care Unit (ICU) during the 2009 H1N1 influenza pandemic (pdm). The purpose of this prospective register-based cohort-study was to characterize the clinical virulence of the pdm (H1N1/09)v during pregnancy in La Réunion. METHODS/PRINCIPAL FINDINGS: Over a twelve-week pdm wave (13 July to 3 October 2009), 294 pregnant women presented with an influenza-like illness (ILI) to one of the three maternity departments of the South Reunion area, Indian Ocean. Out of these, 278 were checked by RT-PCR for influenza viruses (157 positive and 121 negative, of whom, 141 with pdm flu and 132 with ILIs of non pdm origin, 5 untyped). The median body temperature was higher in women experiencing pdm flu than in those with non pdm ILI (38.9 degrees C versus 38.3 degrees C, P<0.0001), without evidence linked to circulating viremia. Oseltamivir was given for 86% of pdm flu cases in a median time inferior than 48 hrs (range 0-7 days). The hospitalization rate for pdm flu was of 60% and not associated with underlying conditions. Six viral pneumonia and fourteen asthma attacks were observed among 84 hospitalized pdm flu cases, of whom, only one led to the ICU for an acute lung injury. No maternal death occurred during the pdm wave. None adverse pregnancy outcome was associated with pdm flu. No congenital birth defect, nor early-onset neonatal influenza infection was attributable to pdm flu exposure. CONCLUSIONS/SIGNIFICANCE: This report mitigates substantially the presumed severity of pandemic H1N1/09 influenza infection during pregnancy. The reasons for which the clinical burden of H1N1/09 influenza virus may differ worldwide raise questions about a differential local viral-strain effect and public health preparedness, notably in timely access to special care and antiviral treatments

Physical forcing and physical/biochemical variability of the Mediterranean Sea: a review of unresolved issues and directions for future research

This paper is the outcome of a workshop held in Rome in November 2011 on the occasion of the 25th anniversary of the POEM (Physical Oceanography of the Eastern Mediterranean) program. In the workshop discussions, a number of unresolved issues were identified for the physical and biogeochemical properties of the Mediterranean Sea as a whole, i.e., comprising the Western and Eastern sub-basins. Over the successive two years, the related ideas were discussed among the group of scientists who participated in the workshop and who have contributed to the writing of this paper. Three major topics were identified, each of them being the object of a section divided into a number of different sub-sections, each addressing a specific physical, chemical or biological issue: 1. Assessment of basin-wide physical/biochemical properties, of their variability and interactions. 2. Relative importance of external forcing functions (wind stress, heat/moisture fluxes, forcing through straits) vs. internal variability. 3. Shelf/deep sea interactions and exchanges of physical/biogeochemical properties and how they affect the sub-basin circulation and property distribution. Furthermore, a number of unresolved scientific/methodological issues were also identified and are reported in each sub-section after a short discussion of the present knowledge. They represent the collegial consensus of the scientists contributing to the paper. Naturally, the unresolved issues presented here constitute the choice of the authors and therefore they may not be exhaustive and/or complete. The overall goal is to stimulate a broader interdisciplinary discussion among the scientists of the Mediterranean oceanographic community, leading to enhanced collaborative efforts and exciting future discoveries

Spatial and temporal distribution patterns of Anopheles arabiensis breeding sites in La Reunion Island - multi-year trend analysis of historical records from 1996-2009

<p>Abstract</p> <p>Background</p> <p>An often confounding facet of the dynamics of malaria vectors is the aquatic larval habitat availability and suitable conditions under which they can thrive. Here, we investigated the impact of environmental factors on the temporal and spatial distribution of larval habitats of <it>Anopheles </it><it>arabiensis </it>in different locations on La Reunion Island.</p> <p>Methods</p> <p>A retrospective examination was made from archival data which provided the complete enumeration of <it>An. arabiensis </it>breeding habitats in three distinct geographic zones - extending North-east, West and South of the island over 14 years, from January 1996 to December 2009. Data on the occurrence and the number of active larval habitats at each of a total of 4376 adjacent ellipsoid grid cells (216,506 square meters each) were used (1) to provide the geographic extent of breeding site availability from year to year and (2) to analyze associations with prevailing environmental factors, habitat types, and locations.</p> <p>Results</p> <p><it>Anopheles arabiensis </it>utilized a spectrum of man-made and natural aquatic habitats, most of which were concentrated primarily in the rock pools located in ravines and river fringes, and also in the large littoral marshes and within the irrigated agricultural zones. The numbers of breeding site per sampling grid differed significantly in different parts of the island. In contrast to an originally more widespread distribution across the island in the 1950s, detailed geographic analyses of the data obtained in the period extending from 1996-2009 showed an intriguing clustered distribution of active breeding sites in three discontinuous geographic zones, in which aquatic habitats availability fluctuates with the season and year. Seasonality in the prevalence of anopheles breeding sites suggests significant responsiveness to climatic factors.</p> <p>Conclusions</p> <p>The observed retreat of <it>An. arabiensis </it>distribution range to lower altitudinal zones (< 400 m) and the upward shift in the most remote littoral areas in the northeast and southwest regions suggest the possible influence of biogeographic factors, changes in land use and control operations. The results of this study would allow for a more rational implementation of control strategies across the island.</p