OceanGliders Oxygen SOP

The live version of this SOP is on the Ocean Gliders community in GITHUB. The home repository of this publication is in the Ocean Best Practices Repository. This standard operating procedure (SOP) document for dissolved oxygen (DO) aims to guide the user through the steps necessary to collect good quality dissolved oxygen data using ocean gliders for both real time and post deployment data streams

CALYPSO 2019 Cruise Report: field campaign in the Mediterranean

This cruise aimed to identify transport pathways from the surface into the interior ocean during the late winter in the Alborán sea between the Strait of Gibraltar (5°40’W) and the prime meridian. Theory and previous observations indicated that these pathways likely originated at strong fronts, such as the one that separates salty Mediterranean water and the fresher water in owing from the Atlantic. Our goal was to map such pathways and quantify their transport. Since the outcropping isopycnals at the front extend to the deepest depths during the late winter, we planned the cruise at the end of the Spring, prior to the onset of thermal stratification of the surface mixed layer.Funding was provided by the Office of Naval Research under Contract No. N000141613130

Altimetry for the future: Building on 25 years of progress

In 2018 we celebrated 25 years of development of radar altimetry, and the progress achieved by this methodology in the fields of global and coastal oceanography, hydrology, geodesy and cryospheric sciences. Many symbolic major events have celebrated these developments, e.g., in Venice, Italy, the 15th (2006) and 20th (2012) years of progress and more recently, in 2018, in Ponta Delgada, Portugal, 25 Years of Progress in Radar Altimetry. On this latter occasion it was decided to collect contributions of scientists, engineers and managers involved in the worldwide altimetry community to depict the state of altimetry and propose recommendations for the altimetry of the future. This paper summarizes contributions and recommendations that were collected and provides guidance for future mission design, research activities, and sustainable operational radar altimetry data exploitation. Recommendations provided are fundamental for optimizing further scientific and operational advances of oceanographic observations by altimetry, including requirements for spatial and temporal resolution of altimetric measurements, their accuracy and continuity. There are also new challenges and new openings mentioned in the paper that are particularly crucial for observations at higher latitudes, for coastal oceanography, for cryospheric studies and for hydrology. The paper starts with a general introduction followed by a section on Earth System Science including Ocean Dynamics, Sea Level, the Coastal Ocean, Hydrology, the Cryosphere and Polar Oceans and the ‘‘Green” Ocean, extending the frontier from biogeochemistry to marine ecology. Applications are described in a subsequent section, which covers Operational Oceanography, Weather, Hurricane Wave and Wind Forecasting, Climate projection. Instruments’ development and satellite missions’ evolutions are described in a fourth section. A fifth section covers the key observations that altimeters provide and their potential complements, from other Earth observation measurements to in situ data. Section 6 identifies the data and methods and provides some accuracy and resolution requirements for the wet tropospheric correction, the orbit and other geodetic requirements, the Mean Sea Surface, Geoid and Mean Dynamic Topography, Calibration and Validation, data accuracy, data access and handling (including the DUACS system). Section 7 brings a transversal view on scales, integration, artificial intelligence, and capacity building (education and training). Section 8 reviews the programmatic issues followed by a conclusion

Altimetry for the future: building on 25 years of progress

In 2018 we celebrated 25 years of development of radar altimetry, and the progress achieved by this methodology in the fields of global and coastal oceanography, hydrology, geodesy and cryospheric sciences. Many symbolic major events have celebrated these developments, e.g., in Venice, Italy, the 15th (2006) and 20th (2012) years of progress and more recently, in 2018, in Ponta Delgada, Portugal, 25 Years of Progress in Radar Altimetry. On this latter occasion it was decided to collect contributions of scientists, engineers and managers involved in the worldwide altimetry community to depict the state of altimetry and propose recommendations for the altimetry of the future. This paper summarizes contributions and recommendations that were collected and provides guidance for future mission design, research activities, and sustainable operational radar altimetry data exploitation. Recommendations provided are fundamental for optimizing further scientific and operational advances of oceanographic observations by altimetry, including requirements for spatial and temporal resolution of altimetric measurements, their accuracy and continuity. There are also new challenges and new openings mentioned in the paper that are particularly crucial for observations at higher latitudes, for coastal oceanography, for cryospheric studies and for hydrology. The paper starts with a general introduction followed by a section on Earth System Science including Ocean Dynamics, Sea Level, the Coastal Ocean, Hydrology, the Cryosphere and Polar Oceans and the “Green” Ocean, extending the frontier from biogeochemistry to marine ecology. Applications are described in a subsequent section, which covers Operational Oceanography, Weather, Hurricane Wave and Wind Forecasting, Climate projection. Instruments’ development and satellite missions’ evolutions are described in a fourth section. A fifth section covers the key observations that altimeters provide and their potential complements, from other Earth observation measurements to in situ data. Section 6 identifies the data and methods and provides some accuracy and resolution requirements for the wet tropospheric correction, the orbit and other geodetic requirements, the Mean Sea Surface, Geoid and Mean Dynamic Topography, Calibration and Validation, data accuracy, data access and handling (including the DUACS system). Section 7 brings a transversal view on scales, integration, artificial intelligence, and capacity building (education and training). Section 8 reviews the programmatic issues followed by a conclusion

Viabilité du phytoplancton et des algues de glace dans la mer de Beaufort (Arctique canadien)

RÉSUMÉ: Cette thèse examine pour la première fois l'influence de diverses variables environnementales, dont l'éclairement, sur la photo-physiologie et la viabilité cellulaire des communautés algales de la mer de Beaufort lors de la transition entre le printemps et l'été. Nous avons d'abord comparé deux techniques permettant de déterminer la viabilité cellulaire (pourcentage de cellules vivantes (% LC) et de cellules mortes) : la méthode de digestion cellulaire (CDA, sans colorant) et le kit BacLight ™ (une méthode de coloration). Au début de cette thèse, aucune étude n'avait encore été publiée sur la possibilité d'appliquer ces méthodes aux algues polaires. Pour la diatomée pelmale Nitzschia ji-igida, une espèce associée à la glace de mer, les deux méthodes ont donné des résultats similaires. La méthode CDA a donc été choisie pour comparer le % LC retrouvé sous des sites aux couverts de neige variables (mince et moyen) et ainsi étudier l'influence de l'éclairement sur la viabilité des communautés naturelles d'algues de glace. En général, les plus faibles % LC étaient trouvés sous les minces couverts de neige (ca. 30%). L'influence de l'éclairement sur la viabilité des algues cellulaires a aussi été étudiée en exposant des cultures discontinues d'une diatomée centrale, Attheya septentrionalis, à différentes intensités lumineuses en laboratoire. Après quatre jours d'exposition à des intensités lumineuses fortes pour cette algue de glace (170-180 umol photons m-2 S-1), le % LC a diminué jusqu'à 10%. La méthode CDA apparaît donc comme une teclmique valide pour déterminer la viabilité cellulaire des algues polaires et son utilisation a permis de fournir de précieuses informations quant à l'influence de l'éclairement sur les communautés algales arctiques. Les changements de la composition taxonomique et de l'état photo-physiologique des communautés algales associées à la couche inférieure de la glace dans la mer de Beaufort ont été examinés au printemps. En utilisant l'information fournie par les marqueurs pigmentaires chémotaxonomiques, nous avons démontré que les diatomées de Type 2 (type pigmentaire probablement associé à des diatomées pennales) dominent le bloom d'algues de glace au printemps et sont ensuite remplacées par les chlorophytes, les prasinophytes et les dinoflagellés à la fin du bloom. Les conditions de couverture de neige affectent significativement la composition de la communauté algale seulement au commencement du bloom. À ce moment, les sites avec un épais couvert de neige et un faible éclairement étaient caractérisés par la présence de diatomées de Type 1 (diatomées centrales) et de chlorophytes, lesquels n'étaient pas présents sous les couverts de neige plus minces. Un éclairement plus élevé sous les conditions de mince couverture neigeuse a favorisé la présence de diatomées de Type 2. Nous avons aussi observé des différences significatives dans les pigments photoprotecteurs entre les trois différents couverts de neige au commencement du bloom, la photoprotection étant accrue sous les faibles couverts de neige. Cette réponse, et le fait que la variable environnementale la mieux corrélée avec le ratio de pigments photoprotecteurs/pigments photosynthétiques soit l'éclairement moyen à la base de la glace pendant les 3 jours précédents l'échantillonnage, suggèrent que la neige reste en place suffisamment longtemps pour permettre à la photo-acclimatation de prendre place. Les conditions de faible couvert de neige ont toutefois favorisé la croissance des algues de glace au commencement du bloom puisque la biomasse de chlorophylle a (chl a) y était plus grande. À cet accroissement de biomasse algale était associée une augmentation des concentrations de pigments de dégradation de la chl a, peut-être en lien avec la présence d'espèces présentant de fortes concentrations internes de chlorophyllide a (possiblement les diatomées pelmales). Cette étude souligne l'importance du rôle de la lumière dans le contrôle des communautés d'algues de glace de l'Arctique pendant le printemps, avant la fin du bloom. L'extrapolation de nos résultats en fonction du réchauffement climatique actuel de l'Arctique suggère que le bloom printanier d'algues de glace pourrait bénéficier d'une réduction du couvert de neige (influence bénéfique de la lumière au commencement du bloom), mais pourrait être de plus courte durée en raison d'une saison de glace raccourcie et possiblement d'une mortalité accrue associée à un éclairement plus important. La viabilité cellulaire du phytoplancton a été examinée dans les eaux de surface de la mer de Beaufort pendant la transition printemps/été. Le pourcentage de cellules vivantes était très variable. Cette variabilité s'expliquait partiellement par les différences dans la composition des communautés et était influencée par la température de l'eau et par l'éclairement, avec des tendances distinctes pour les stations couvertes de glace et les stations d'eau libre. La performance photo synthétique et le % LC diminuaient avec une augmentation de l'éclairement, suggérant un effet négatif des fortes intensités lumineuses sur la condition physiologique des cellules. Pour les stations couvelies de glace, les plus faibles % LC étaient associés aux températures de fonte de glace, alors qu'ils s'associaient plutôt aux fortes intensités lumineuses dans les stations d'eau libre. Un pigment que nous avons appelé « simili »-pyrophéophorbide a et qui devra être mieux identifié avec des techniques appropriées (telles que le LC-MS) a montré un potentiel comme marqueur pigmentaire pour la perte de viabilité cellulaire dans l'environnement arctique. Cette étude souligne la complexité des réponses des communautés algales naturelles lorsqu'elles doivent faire face à des changements environnementaux. Il semble que les diatomées se portaient mieux que d'autres groupes pendant la période de fonte de glace entre le printemps et l'été, montrant qu'elles semblent occuper des niches écologiques spécifiques dans lesquelles elles sont favorisées. Cette thèse a identifié l'éclairement, la température et la stratification de la colonne d'eau comme des facteurs envirolmementaux importants qui influencent la condition physiologique et la viabilité des algues de l'Arctique. -- Mots clés : Arctique, algues de glace, phytoplancton, mort cellulaire, indice d' activité photo synthétique, pigments, CHEMT AX, photoprotection. --ABSTRACT: This thesis examines for the first time the influence of irradiance and other environmental factors on the photo-physiology and cell viability of algal communities in the Canadian Beaufort Sea during the spring-summer transition. We tested the applicability of two techniques to determine cell viability (as percentages of living (% LC) and dead cells): the cell digestion assay (CDA, non-staining) and the BacLight™ Kit (a staining method). At the beginning of this thesis, no study had been published on the applicability of these methods on polar algae. The two methods gave similar results when applied to the sea ice pennate diatom Nitzschiafi-igida. The influence of irradiance on the viability of natural ice algal communities was investigated by comparing sites with various snow cover depths and measuring % LC with the CDA. In general, lower % LC values were found under the lowest snow cover depths (ca. 30%). The influence of irradiance on algal cell viability was also examined by exposing batch cultures of the centric diatom Attheya septentrionalis to various irradiances in the laboratory. After 4 days of exposure to irradiances considered high for this ice algal species (170-180 umol photons m-2 S-1), % LC decreased down to 10%. The CDA method is a valid technique to de termine viability of polar algae and it provided valuable data on the influence of light on Arctic algal communities. Changes in the taxonomic composition and the photo-physiological state of the bottom ice algal community of the Beaufort Sea were studied during the spring. Using information on chemotaxonomic marker pigments, we showed that diatoms Type 2 (pigment type likely associated with pennate diatoms) dominate the sea ice aigal bloom during spring, followed by seasonal replacement with chlorophytes, prasinophytes and dinoflagellates during the post-bloom period. Snow cover conditions affected community composition only during the early bloom, when the low irradiance, high snow cover sites were characterized by the presence of diatoms Type 1 (centric diatoms) and chlorophytes which were not detected in the other snow cover sites. Higher irradiances under low snow cover conditions favoured the presence of diatoms Type 2. We also observed significant differences in photoprotective pigments among the three snow cover conditions in early bloom, with enhanced photoprotection under low snow cover. This response, and the fact that the ratio of photoprotective to photosynthetic pigments was best correlated with the average bottom ice irradiance over the preceding three days, suggests that snow remained in place long enough for photoacclimation to take place. These conditions favoured the growth of sea ice algae, since the chlorophyll a (chl a) biomass was greater under low snow cover conditions in the early bloom period. This was also associated with an increase in chl a degradation pigments possibly related to the presence of species with particularly abundant chlorophyllide a (possibly pennate diatoms). This study highlights the important role of light in controlling the algal communities in Arctic sea ice during spring, before the demise of the ice algal bloom. Extrapolation of our results to continued climate wanning in the Arctic suggests that the ice algae spring bloom could benefit from a reduction of the snow cover (beneficial influence of light early on) but may be cut short by the shorter ice season and possibly by the increased mortality of sea ice algae associated with increased irradiance. Phytoplankton cell viability was examined in the surface waters of the Beaufort Sea during the spring-summer transition. The percentage of living cells varied widely, this variation being explained partly by differences in the community composition and was influenced by water temperature and irradiance with distinct trends for ice-covered and open-water stations. Photosynthetic perfonnance and the relative abundance of living cells decreased with increasing irradiance, suggesting a detrimental effect of high irradiances on the physiological condition of cells. The lower % LC values were related to melting temperatures at ice-covered stations and to the highest irradiances at open-water stations. A pigment that we called pyropheophorbide a-"like" and that will need to be fully identified with appropriate techniques (such as LC-MS), shows potential as a marker pigment for the loss of cell viability in this environrnent. This study highlights the complexity of the responses of natural communities coping with changes of the environmental variables. However diatoms seemed to thrive better than other groups during the spring-summer melting conditions, showing that they seem to occupy specific ecological niches in which they are favored. This thesis identified irradiance, temperature and stratification as important environmental factors influencing the physiological conditions and viability of Arctic algae. -- Keywords : lce algae, phytoplankton, cell death, photosynthetic activity index, pigments, CHEMTAX, photoprotection

Coastal ph variability in the Balearic sea

ASLO 2021 Aquatic Sciences Meeting, 22–27 June, VirtualThe Mediterranean Sea is one of the most fragile ecosystems in the world to increases in carbon dioxide (CO2) emissions due to its distinct physical and biogeochemical characteristics. However, until recently, only two permanent stations were monitoring trends in pH in this basin; the Mediterranean Ocean Observing System for the Environment station (DYFAMED) in the Ligurian Sea and the Gibraltar Fixed Timeseries (GIFT) mooring line in the Strait of Gibraltar. Evaluating trends in pH in coastal systems can be complex, as the measured signal is influenced by a multitude of drivers, including watershed processes, nutrient inputs, and changes in ecosystem structure and metabolism. Interaction between ocean acidification due to anthropogenic CO2 emissions and dynamic local drivers of coastal ecosystems cause high variability of pH in coastal waters. Therefore, it is crucial to disentangle local drivers and elucidate pH trends in coastal stations. Here we evaluate data from high-resolution autonomous sensors in surface waters in the Balearic Sea, in two stations with different anthropogenic pressures. These sites belong to the Balearic Ocean Acidification Time Series (BOATS), with sites at the Balearic Islands Coastal Ocean Observing and Forecasting System (SOCIB) fixed station (Palma Bay, Spain) and Cabrera National Park. We compare the seasonal variability of coastal surface waters with over two years of data from a SAMI (Sunburst LLC.) pH sensor. Reconstruction of pH data with other available biogeochemical parameters is applied to evaluate the robustness of found patternsN

Snow cover affects ice algal pigment composition in the coastal Arctic Ocean during spring

Specific pigments produced by algae and their degradation products can provide considerable information on the taxonomic composition and photo-physiological state of algal communities. However, no previous study has looked at ice algal pigment composition in the high Arctic. We examined the bottom ice algal pigment composition in the Canadian Beaufort Sea under various snow cover conditions during the spring bloom (March to June 2008). During the early and peak bloom periods, pennate diatoms (pigment Type 2, containing chlorophyll [chl] c2 and c3) dominated the chl a biomass. Diatoms containing chl c1 (pigment Type 1) and chlorophytes were only present under high snow cover. A more diverse community was observed during the post-bloom when only low snow cover sites remained due to snow melt, with higher relative contributions of chlorophytes, prasinophytes and dinoflagellates, associated with the loss of diatoms, along with increased abundance of large empty diatoms (from microscopy) and with signs of a deteriorating physiological condition (increases in chlorophyllide a and the allomer of chl a). The ratio of photoprotective to photosynthetic pigments was generally higher at low snow cover sites, increasing seasonally with the bottom ice irradiance. Low snow cover sites differed also by having more Type 2 diatoms, increased photoprotection and greater chl a biomass during the early bloom. In addition, these sites showed increases in chl a degradation pigments that may be due to the presence of chlorophyllide-rich pennate diatoms, since the increasing biomass suggests healthy physiological conditions at that time. This study highlights the important influence of light and the light-acclimation plasticity in Arctic sea ice algae. © Inter-Research 2013.Peer Reviewe

Coastal pH variability in the Balearic Sea

[Description of methods used for collection/generation of data] In both stations a SAMI-pH (Sunburst Sensors LCC) was attached, at 1 m in the Bay of Palma and at 4 m depth in Cabrera. The pH sensors were measuring pH, in the total scale (pHT), hourly since December 2018 in the Bay of Palma and since November 2019 in Cabrera. The sensor precision and accuracy are < 0.001 pH and ± 0.003 pH units, respectively. Monthly maintenance of the sensors was performed including data download and surface cleaning. Temperature and salinity for the Cabrera mooring line was obtained starting November 2019 with a CT SBE37 (Sea-Bird Scientific©). Accuracy of the CT is ± 0.002 ∘C for temperature and ± 0.003 mS cm−1−1 for conductivity. Additionally, oxygen data from a SBE 63 (Sea-Bird Scientific ©) sensor attached to the CT in Cabrera were used. Accuracy of oxygen sensors is ± 2% for the SBE 63.[Methods for processing the data] Periodically water samplings for dissolved oxygen (DO), pH in total scale at 25 ∘C (pH25) and total alkalinity (TA) were obtained during the sensor maintenance campaigns. DO and (pH25) samples were collected in order to validate the data obtained by the sensors. DO concentrations were evaluated with the Winkler method modified by Benson and Krause by potentiometric titration with a Metrohm 808 Titrando with a accuracy of the method of ± 2.9 μmol kg−1μmol kg−1 and with an obtained standard deviation from the sensors data and the water samples collected of ± 5.9 μmol kg−1μmol kg−1. pH25T25 data was obtained by the spectrophotometric method with a Shimadzu UV-2501 spectrophotometer containing a 25 ∘C-thermostated cells with unpurified m-cresol purple as indicator following the methodology established by Clayton and Byrne by using Certified Reference Material (CRM Batch #176 supplied by Prof. Andrew Dickson, Scripps Institution of Oceanography, La Jolla, CA, USA). The accuracy obtained from the CRM Batch was of ± 0.0051 pH units and the precision of the method of ± 0.0034 pH units. The mean difference between the SAMI-pH and discrete samples was of 0.0017 pH units.Funding for this work was provided by the projects RTI2018-095441-B-C21 (SuMaEco) and, the BBVA Foundation project Posi-COIN and the Balearic Islands Government projects AAEE111/2017 and SEPPO (2018). SF was supported by a “Margalida Comas” postdoctoral scholarship, also from the Balearic Islands Government. FFP was supported by the BOCATS2 (PID2019-104279GB-C21) project funded by MCIN/AEI/10.13039/501100011033.This work is a contribution to CSIC’s Thematic Interdisciplinary Platform PTI WATER:iOS.Peer reviewe

Cell death in lake phytoplankton communities

1. The fraction of living and dead phytoplankton cells in seven Florida lakes was assessed by using the cell digestion assay, a non-staining membrane permeability test. The cell digestion assay is an effective method to analyse cell viability in complex natural phytoplankton communities. 2. The lakes examined ranged widely in phytoplankton abundance and community composition. The variability in the percentage of living cells (% LC) was high among the taxonomic groups forming the different phytoplankton communities, ranging from 19.7% to 98% LC. 3. All cells within single cyanobacteria filaments were determined to be either dead or alive, suggesting physiological integration of the cells within colonies. 4. Within each lake, the dominant taxa generally exhibited the highest proportion of living cells. A high proportion of living cells was found to be a characteristic of the different taxa forming the communities of eutrophic lakes. The average value for the % LC for all groups comprising the phytoplankton communities in each of the lakes ranged from 29.9 ± 7.2 to 80.4 ± 4.0 (mean ± SE) and varied strongly and positively with chlorophyll a concentration. 5. These results suggest phytoplankton cell death to be an important process structuring phytoplankton communities in lakes, particularly in oligotrophic ones. © 2006 The Authors.Peer Reviewe

Lagrangian flow properties along filament-like structures and its impact on the distribution and composition of phytoplankton

Trabajo presentado en la Ocean Sciences Meeting, celebrada en San Diego del 16 al 21 de febrero de 2020.Physical factors induced by the turbulent flow play a crucial role in regulating marine ecosystems. Here we show that the combination of complementary Lagrangian diagnostics provides an improved description of the geometrical and kinetic properties of the flow, which facilitates the interpretation of physical mechanisms affecting phytoplankton composition, dynamics and patchiness. The influence of small-scale dynamics (O(3.5-25) km, i.e. spanning upper submesoscale and mesoscale processes) on phytoplankton in surface waters derived from satellite chlorophyll-a (chl a) is studied using Lagrangian metrics computed from High-Frequency Radar currents over the Ibiza Channel. Attracting small-scale flow structures are associated to filaments of accumulated negative divergence where particles and chl a standing stocks cluster. Regions of accumulated positive divergence, representing large accumulated upward vertical velocities and suggesting accrued injection of subsurface nutrients, match areas with large chl a concentrations. Furthermore the composition of phytoplankton community was studied regarding the sustained kinematic properties of the flow during the formation of an intense filament. In this regard new metrics accounting for the Lagrangian evolution of the turbulent and topological properties along fluid parcel trajectories have been developed. Here we provide observational evidences, during the SHEBEX cruise (May 2015) in the western Mediterranean and altimetry-derived Lagrangian computations, that fluid parcels associated with high Lagrangian turbulent kinetic energy and Lagrangian positive vorticity host higher relative abundance of larger pennate diatoms (i.e. Pseudo-nitzschia spp). Our findings indicate that the combination of these diagnostics provides an improved description of the turbulent dynamics showing that the Lagrangian properties of the flow have important biological consequences.Peer reviewe