Anomalies in the carbonate system of Red Sea coastal habitats

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Baldry, K., Saderne, V., McCorkle, D. C., Churchill, J. H., Agust, S., & Duarte, C. M. Anomalies in the carbonate system of Red Sea coastal habitats. Biogeosciences, 17(2), (2020): 423-439, doi:10.5194/bg-17-423-2020.We use observations of dissolved inorganic carbon (DIC) and total alkalinity (TA) to assess the impact of ecosystem metabolic processes on coastal waters of the eastern Red Sea. A simple, single-end-member mixing model is used to account for the influence of mixing with offshore waters and evaporation–precipitation and to model ecosystem-driven perturbations on the carbonate system chemistry of coral reefs, seagrass meadows and mangrove forests. We find that (1) along-shelf changes in TA and DIC exhibit strong linear relationships that are consistent with basin-scale net calcium carbonate precipitation; (2) ecosystem-driven changes in TA and DIC are larger than offshore variations in >70 % of sampled seagrass meadows and mangrove forests, changes which are influenced by a combination of longer water residence times and community metabolic rates; and (3) the sampled mangrove forests show strong and consistent contributions from both organic respiration and other sedimentary processes (carbonate dissolution and secondary redox processes), while seagrass meadows display more variability in the relative contributions of photosynthesis and other sedimentary processes (carbonate precipitation and oxidative processes). The results of this study highlight the importance of resolving the influences of water residence times, mixing and upstream habitats on mediating the carbonate system and coastal air–sea carbon dioxide fluxes over coastal habitats in the Red Sea.This research has been supported by the King Abdullah University of Science and Technology (KAUST) (grant nos. BAS/1/1071-01-01 and BAS/1/1072-01-01) and the Investment in Science fund at WHOI

Subsurface chlorophyll maxima reduce the performance of non-photochemical quenching corrections in the Southern Ocean

Non-photochemical quenching (NPQ) within phytoplankton cells often causes the daytime suppression of chlorophyll fluorescence in the Southern Ocean. This is problematic and requires accurate correction when chlorophyll fluorescence is used as a proxy for chlorophyll-a concentration or phytoplankton abundance. In this study, we reveal that Southern Ocean subsurface chlorophyll maxima (SCMs) are the largest source of uncertainty when correcting for NPQ of chlorophyll fluorescence profiles. A detailed assessment of NPQ correction methods supports this claim by taking advantage of coincident chlorophyll fluorescence and chlorophyll concentration profiles. The best performing NPQ correction methods are conditional methods that consider the mixed layer depth (MLD), subsurface fluorescence maximum (SFM) and depth of 20% surface light. Compared to existing methods, the conditional methods proposed halve the bias in corrected chlorophyll fluorescence profiles and improve the success of replicating a SFM relative to chlorophyll concentration profiles. Of existing methods, the X12 and P18 methods, perform best overall, even when considering methods supplemented by beam attenuation or backscatter data. The widely-used S08 method, is more varied in its performance between profiles and its application introduced on average up to 2% more surface bias. Despite the significant improvement of the conditional method, it still underperformed in the presence of an SCM due to 1) changes in optical properties at the SCM and 2) large gradients of chlorophyll fluorescence across the pycnocline. Additionally, we highlight that conditional methods are best applied when uncertainty in chlorophyll fluorescence yields is within 50%. This highlights the need to better characterize the bio-optics of SCMs and chlorophyll fluorescence yields in the Southern Ocean, so that chlorophyll fluorescence data can be accurately converted to chlorophyll concentration in the absence of in situ water sampling

A biological ocean data reformatting effort

Abstract Biological ocean data collected from ships find reuse in aggregations of historical data. These data are heavily relied upon to document long term change, validate satellite algorithms for ocean biology and are useful in assessing the performance of autonomous platforms and biogeochemical models. Existing aggregate products have largely been restricted to the surface ocean, omit physical data or have limited biological data. We present the first version of a BIOlogical ocean data reforMATting Effort (BIO-MATE) to begin to fill a gap in subsurface bio-physical data aggregates in a reproducible way. BIO-MATE uses open-source R software that reformats openly sourced published datasets from oceanographic voyages. These reformatted biological and physical data from underway sensors, profiling sensors, pigments analysis and particulate organic carbon analysis are stored in an interoperable BIO-MATE data product for easy access and use. Specific QA/QC protocols can now be easily applied to the BIO-MATE data product to support a variety of surface and subsurface applications

Characterization of the CO2 system in a coral reef, a seagrass meadow and a mangrove forest in the central Red Sea

The data are one year (summer 2016 - summer 2017) of continuous pH (seafet), Salinity, and temperature measurements in a seagrass, coral reef and mangrove ecosystem of the Red Sea. Monthly statistics of pH, Salinity and Temperature are also provided for the three ecosystems. Full characterization of the carbonate system was done every 15 days on discrete samples from measurement of dissolved inorganic carbon and total alkalinity. In a subset of samples, the pH was also measured spectrophotometrically to compare with the pH from the Seafet sensors. At the coral reef site, the SeaFET mooring started the 16.06.2016 and was interrupted the 09.05.2017 because of sensor malfunction, with three interruptions for maintenance, between the 31.08.2016 and the 30.09.2016, the 11 and the 18.11.2016 and the 27 and the 30.03.2017. The CTD moorings were conducted in parallel to the SeaFET moorings. At the seagrass site, a malfunction of the CTD caused a gap of data between the 12.11.2016 and the 20.01.2017, two more interruptions for maintenance occurred between the 03 and the 09.03.2017 and between the 11 and the 20.06.2017. At the coral reef site, two interruptions for maintenance occurred between the 05 and the 17.11.2017 and between the 03 and the 09.06.2017