Measuring pH variability using an experimental sensor on an underwater glider

Autonomous underwater gliders offer the capability of measuring oceanic parameters continuously at high resolution in both vertical and horizontal planes, with timescales that can extend to many months. An experimental ion sensitive field effect transistor (ISFET) sensor measuring pH on the total scale was attached to a glider during the REP14 – MED experiment in June 2014 in the northwestern Mediterranean Sea. During the deployment, pH was sampled at depths of up to 1000 m, along an 80 km transect over a period of 12 days. Water samples were collected from a nearby ship and analysed for dissolved inorganic carbon concentration and total alkalinity to derive pH for validating the ISFET measurements. The vertical resolution of the pH sensor was good (1 to 2 m), but stability was poor, and the sensor drifted in a non-monotonous fashion. In order to remove the sensor drift, a time-dependent, depth-invariant offset was applied throughout the water column for each dive, reducing the spread of the data by approximately two thirds. Furthermore, the ISFET sensor required temperature and pressure-based corrections, which were achieved using linear regression. Correcting for this decreased the apparent sensor pH variability by a further 13 to 31 %. Sunlight caused an apparent sensor pH decrease of up to 0.1 in surface waters around local noon, highlighting the importance of shielding the sensor away from light in future deployments. The corrected pH from the ISFET sensor is presented along with potential temperature, salinity, potential density anomalies (σθ), and dissolved oxygen concentrations (c(O2)) measured by the glider, providing insights into physical and biogeochemical variability in this region. pH maxima were identified at the depth of the summer chlorophyll maximum, where high c(O2) values were also found. Longitudinal pH variations at depth (σθ > 28.8 kg m−3) highlighted variability of water masses in this region. Higher pH was observed where salinity was > 38.65, and lower pH was found where salinity ranged between 38.3 and 38.65. It seemed that the higher pH was associated with saltier Levantine Intermediate Water. Furthermore, shoaling isopycnals closer to shore coinciding with low pH, high salinity, low c(O2) waters may be indicative of upwelling

Bright ligand-activatable fluorescent protein for high-quality multicolor live-cell super-resolution microscopy

We introduce UnaG as a green-to-dark photoswitching fluorescent protein capable of high-quality super-resolution imaging with photon numbers equivalent to the brightest photoswitchable red protein. UnaG only fluoresces upon binding of a fluorogenic metabolite, bilirubin, enabling UV-free reversible photoswitching with easily controllable kinetics and low background under Epi illumination. The on- and off-switching rates are controlled by the concentration of the ligand and the excitation light intensity, respectively, where the dissolved oxygen also promotes the off-switching. The photo-oxidation reaction mechanism of bilirubin in UnaG suggests that the lack of ligand-protein covalent bond allows the oxidized ligand to detach from the protein, emptying the binding cavity for rebinding to a fresh ligand molecule. We demonstrate super-resolution single-molecule localization imaging of various subcellular structures genetically encoded with UnaG, which enables facile labeling and simultaneous multicolor imaging of live cells. UnaG has the promise of becoming a default protein for high-performance super-resolution imaging. Photoconvertible proteins occupy two color channels thereby limiting multicolour localisation microscopy applications. Here the authors present UnaG, a new green-to-dark photoswitching fluorescent protein for super-resolution imaging, whose activation is based on a noncovalent binding with bilirubin

High-resolution observations in the western Mediterranean Sea: the REP14-MED experiment

The observational part of the REP14-MED experiment was conducted in June 2014 in the Sardo-Balearic Basin west of Sardinia (western Mediterranean Sea). Two research vessels collected high-resolution oceanographic data by means of hydrographic casts, towed systems, and underway measurements. In addition, a vast amount of data was provided by a fleet of 11 ocean gliders, time series were available from moored instruments, and information on Lagrangian flow patterns was obtained from surface drifters and one profiling float. The spatial resolution of the observations encompasses a spectrum over 4 orders of magnitude from (10¹ m) to (10⁵ m), and the time series from the moored instruments cover a spectral range of 5 orders from (10¹ s) to (10⁶ s). The objective of this article is to provide an overview of the huge data set which has been utilised by various studies, focusing on (i) water masses and circulation, (ii) operational forecasting, (iii) data assimilation, (iv) variability of the ocean, and (v) new payloads for gliders

Metabolically active microbial communities in marine sediment under high-CO2 and low-pH extremes

Sediment-hosting hydrothermal systems in the Okinawa Trough maintain a large amount of liquid, supercritical and hydrate phases of CO2 in the seabed. The emission of CO2 may critically impact the geochemical, geophysical and ecological characteristics of the deep-sea sedimentary environment. So far it remains unclear whether microbial communities that have been detected in such high-CO2 and low-pH habitats are metabolically active, and if so, what the biogeochemical and ecological consequences for the environment are. In this study, RNA-based molecular approaches and radioactive tracer-based respiration rate assays were combined to study the density, diversity and metabolic activity of microbial communities in CO2-seep sediment at the Yonaguni Knoll IV hydrothermal field of the southern Okinawa Trough. In general, the number of microbes decreased sharply with increasing sediment depth and CO2 concentration. Phylogenetic analyses of community structure using reverse-transcribed 16S ribosomal RNA showed that the active microbial community became less diverse with increasing sediment depth and CO2 concentration, indicating that microbial activity and community structure are sensitive to CO2 venting. Analyses of RNA-based pyrosequences and catalyzed reporter deposition-fluorescence in situ hybridization data revealed that members of the SEEP-SRB2 group within the Deltaproteobacteria and anaerobic methanotrophic archaea (ANME-2a and -2c) were confined to the top seafloor, and active archaea were not detected in deeper sediments (13–30 cm in depth) characterized by high CO2. Measurement of the potential sulfate reduction rate at pH conditions of 3–9 with and without methane in the headspace indicated that acidophilic sulfate reduction possibly occurs in the presence of methane, even at very low pH of 3. These results suggest that some members of the anaerobic methanotrophs and sulfate reducers can adapt to the CO2-seep sedimentary environment; however, CO2 and pH in the deep-sea sediment were found to severely impact the activity and structure of the microbial community

The distribution of radionuclides and some trace metals in the water columns of the Japan and Bonin trenches

Presented here is the first detailed geochemical data set on the U/Th series Th, Pa, Ac, and Pb isotopes and artificial fallout radionuclides (Sr-90, Cs-137, and Pu isotopes), and some trace elements (V, Zn, Cd, Cu, Mn, and Ni) in two water columns of the Japan and Bonin trenches down to the bottom depths of 7585 m and 9750 m, respectively. Hydrographic properties such as temperature, salinity, dissolved oxygen, and nutrient content within the trench valley remain constant at the same levels as those in the bottom water of the Northwest Pacific basin (typically similar to 6000 m in depth). The radionuclide activities and most trace metal concentrations are also not very different from those in the overlying water at depths of around 5000-6000 m. This means that any chemical alteration which sea water undergoes during its residence within the trench was not obviously detected by the techniques used here. The suggestion follows that the trench water is rather freely communicating by isopycnal mixing with the bottom water overlying the Northwest Pacific abyssal plain. The trench waters contain high Pu-239,Pu-240 activities throughout, indicating that Pu is actively regenerating from rapidly sinking, large particles at the bottom interface, probably due to a change in the oxidation state. On the other hand, the vertical profiles of Pb-210 and Pa-231 show lower activities within the trench than those in the overlying deep waters, suggesting that the effect of boundary and bottom scavenging is significant in controlling their oceanic distributions. However, none of the trace metals studied here obviously follows the behaviour of the above nuclides. The Th-228 data show scattering within the Bonin Trench that is largely ascribable to analytical errors. If, however we accept that the scatter of Th-228 data is real and the variation is caused solely by decay of its parent Ra-228, We,,, set an upper limit of similar to 5 years for the renewal time of the trench water.La première série détaillée de données géochimiques obtenues dans deux colonnes d'eau des fosses du Japon et des îles Bonin, respectivement jusqu'à 7585 m et 9750 m, est présentée ici. Elle porte sur la série uranium/thorium, sur les isotopes de thorium, protactinium, actinium et plomb et sur les retombées des nucléides radioactifs artificiels (strontium-90, césium-137 et plutonium) ainsi que sur quelques éléments à l'état de traces (vanadium, zinc, cadmium, cuivre, manganèse et nickel). Les caractéristiques hydrologiques telles que température, salinité, oxygène dissous et teneurs en nutriments prennent les mêmes valeurs aux mêmes profondeurs, dans les fosses comme dans l'eau de fond du bassin nord-occidental du Pacifique (typiquement, vers 6000 m). De même, les valeurs de l'activité des nucléides radioactifs et les concentrations de la plupart des traces métalliques ne sont pas très différentes dans la fosse et dans l'eau sus-jacente, vers 5000–6000 m. Si, au cours de son transit dans la fosse, l'eau a subi une modification chimique, celle-ci n'a pas été détectée par les techniques utilisées. Cela suggère que l'eau de la fosse communique assez librement par mélange isopycne avec l'eau de fond qui couvre la plaine abyssale dans le nord-ouest du Pacifique. Partout dans les eaux de la fosse l'activité du 239, 240Pu est élevée, ce qui indique que le plutonium est activement régénéré à partir des grosses particules qui sédimentent rapidement sur le fond, probablement par un changement de leur état d'oxydation. De plus les profils verticaux de 210Pb et 231Pa indiquent des activités plus faibles dans la fosse que dans les eaux profondes sus-jacentes, suggérant que l'effet de barrière et le balayage sur le fond sont significatifs dans la répartition de ces éléments dans l'océan. Aucun des éléments-traces étudiés ici ne se comporte comme les nucléides radioactifs. Dans la fosse des îles Bonin, les données de 228Th montrent une dispersion qui est due essentiellement aux erreurs analytiques. Cependant, si la dispersion est réelle et résulte uniquement de la désintégration du 228Ra, on peut fixer une limite supérieure d'environ cinq ans pour le temps de renouvellement de l'eau dans la fosse

Autonomous Underwater Vehicle Survey Design for Monitoring Carbon Capture and Storage Sites

Long-term monitoring of sub-seabed Carbon Capture and Storage (CCS) sites will require systems that are flexible, independent, and have long-endurance. In this presentation we will discuss the utility of autonomous underwater vehicles equipped with different sensor packages in monitoring storage sites. We will present data collected using Autosub AUV, as part of the ECO2 project, from the Sleipner area of the North Sea. The Autosub AUV was equipped with sidescan sonar, an EM2000 multibeam systems, a Chirp sub-bottom profiler, and a variety of chemical sensors. Our presentation will focus on survey design, and the simultaneous use of multiple sensor packages in environmental monitoring on the continental shelf