Phytoplankton size structure impacts ocean food-web dynamics and biogeochemical cycling, and is thus an important ecological indicator that can be utilised to quantitatively evaluate the state of marine ecosystems. Potential alterations to size structure are predicted to occur in tropical regions under future scenarios of climate change. Therefore, there is an increasing requirement for the synoptic monitoring of phytoplankton size structure in marine systems. The Red Sea remains a comparatively unexplored tropical marine ecosystem, particularly with regards to its large-scale biological dynamics. Using an in situ pigment dataset acquired in the Red Sea, we parameterise a two-component, abundance-based phytoplankton size model and apply it to remotely-sensed observations of chlorophyll-a (Chl-a) concentration, to infer Chl-a in two size classes of phytoplankton, small cells <2 μm in size (picophytoplankton) and large cells >2 μm in size. Satellite-derived estimates of phytoplankton size structure are in good agreement with corresponding in situ measurements and also capture the spatial variability related to regional mesoscale dynamics. Our analysis reveals that, for the estimation of Chl-a in the two size classes, the model performs comparably or in some cases better, to validations in other oceanic regions. Our model parameterisation will be useful for future studies on the seasonal and interannual variability of phytoplankton size classes in the Red Sea, which may ultimately be relevant for understanding trophic linkages between phytoplankton size structure and fisheries, and the development of marine management strategies.

Nitrous oxide (N2O) is a climate-relevant atmospheric trace gas. It is produced as an intermediate of the nitrogen cycle. The open and coastal oceans are major sources of atmospheric N2O. However, its oceanic distribution is still largely unknown. Here we present the first measurements of the water column distribution of N2O in the Gulf of Aqaba and the Red Sea. Samples for N2O depth profiles were collected at the time-series site Station A in the northern Gulf of Aqaba (June and September 2003, and February 2004) and at several stations in the central Red Sea (October 2014, January and August 2016). Additionally, we measured N2O concentrations in brine pool samples collected in the northern and central Red Sea (January 2005 and August 2016). In the Gulf of Aqaba, N2O surface concentrations ranged from 6 to 8 nmol L−1 (97–111% saturation) and were close to the equilibrium with the overlying atmosphere. A pronounced temporal variability of the N2O water column distribution was observed. We suggest that this variability is a reflection of the interplay between N2O production by nitrification and its consumption by N2 fixation in the layers below 150 m during summer. N2O surface concentrations and saturations in the central Red Sea basin ranged from 2 to 9 nmol L−1 (43–155% saturation). A pronounced temporal variability with significant supersaturation in October 2014 and undersaturation in January and August 2016 was observed in the surface layer. In October 2014, N2O in the water column seemed to result from production via nitrification. Low N2O water column concentrations in January and August 2016 indicated a significant removal of N2O. We speculate that either in-situ consumption or remote loss processes of N2O such as denitrification in coastal regions were responsible for this difference. Strong meso- and submesoscale processes might have transported the coastal signals across the Red Sea. In addition, enhanced N2O concentrations of up to 39 nmol L−1 were found at the seawater-brine pool interfaces which point to an N2O production via nitrification and/or denitrification at low O2 concentrations. Our results indicate that the Red Sea and the Gulf of Aqaba are unique natural laboratories for the study of N2O production and consumption pathways under extreme conditions in one of the warmest and most saline region of the global oceans.

The diversity of free-living dinoflagellates in the coastal areas of the central Red Sea, Saudi Arabia, was studied from April 2016 to March 2017. A total of 106 dinoflagellates belonging to 36 genera, 20 families and 7 orders were identified and characterized using light microscopy. Of these, 47 taxa were potentially harmful, and 60 taxa were recorded for the first time from the Red Sea. The unexpectedly high species diversity, including new records, was due to the benthic species. The monthly variability of planktonic species records exhibited negative correlations with temperature and salinity, although in most cases, the links between them were insignificant. Subsequently, the dinoflagellates checklist for the entire Red Sea was updated and showed that there were currently 395 taxa and 66 genera. The results of this study provide a solid foundation for future studies of dinoflagellate biodiversity in the Red Sea, particularly for benthic and harmful species.

Hydrographic and atmospheric forcing set fundamental constraints on the biogeochemistry of aquatic ecosystems and manifest in patterns of resource (nutrient) availability and recycling, species composition of communities, trophic dynamics, and ecosystem metabolism. In the Red Sea, gradients in environmental conditions and primary production have been ascribed to fluctuations in Gulf of Aden Water inflow, upwelling/mixing, and regenerated nutrient utilization i.e. rapidly recycled nitrogen in upper layers. However, the understanding of upper layer dynamics and related changes in plankton communities, metabolism and carbon and nitrogen export is limited. We surmised that stratification and mesoscale eddies modulate the nutrient availability and taxonomic identity of plankton communities in the central Red Sea. Based on remote-sensing data of sea level anomalies and high resolution in situ profiling (ScanFish) we selected stations for hydrographic CTD profiles, water sampling (nutrients, seawater stable oxygen isotopes [δ18OSW]), phytoplankton and zooplankton collections. In fall 2014, strong stratification subjected the plankton community to an overall nitrogen and phosphorus shortage. The nutrient deficiency increased numbers of heterotrophic dinoflagellates, microzooplankton, and diazotrophs (Trichodesmium, diatom-diazotroph associations [DDAs]), albeit largely decreased phytoplankton and mesozooplankton abundances. In spring 2015, mesoscale eddies increased the nutrient availability, and the thermohaline characteristics and low δ18OSW point to the interaction of eddies with Gulf of Aden Surface Water (GASW). Cyclonic eddies and, most likely, the availability of nutrients associated with the GASW, increased the abundances of autotrophs (diatoms, Prasinophytes) and supported larger numbers of zooplankton and their larvae. We demonstrate that the interplay of stratification, advection of Gulf of Aden water and mesoscale eddies are key to better understand changes in plankton community composition, ecosystem metabolism, and macronutrient export in the Red Sea in space and time.

The Red Sea is a unique body of water, hosting some of the most productive and diverse coral reefs. Human populations along coasts of the Red Sea were initially sparse due to the hot and arid climate surrounding it, but this is changing with improved desalination techniques, accessible energy, and increased economic interest in coastal areas. In addition to increasing pressure on reefs from coastal development, global drivers, primarily ocean acidification and seawater warming, are threatening coral reefs of the region. While reefs in southern sections of the Red Sea live near or above their maximum temperature tolerance and have experienced bleaching events in the recent past, coral reefs in northern sections are considered a coral reef refugia from global warming and acidification, at least for the coming decades. Such differential sensitivities along the latitudinal gradient of the Red Sea require differential solutions and management. In an effort to identify the appropriate solutions to conserve and maintain resilience of these reefs along a latitudinal gradient, we used a SWOT analysis (strengths/weaknesses/opportunities/threats) to frame the present situation and to propose policy solutions as useful planning procedures. We highlight the need for immediate action to secure the northern sections of the Red Sea as a coral reef climate change refuge by management and removal of local stressors. There is a need to strengthen the scientific knowledge base for proper management and to encourage regional collaboration on environmental issues. Based on scientific data, solutions such as marine protected areas, fishing regulation, and reef restoration approaches were ranked for five distinct latitudinal sections in the Red Sea and levels of interventions are recommended.

Lagrangian tracking of passive tracers in a stochastic velocity field within a sequential ensemble data assimilation framework is challenging due to the exponential growth in the number of particles. This growth arises from describing the behavior of velocity over time as a set of possible combinations of the different realizations, before and after each assimilation cycle. This paper addresses the problem of efficiently advecting particles in stochastic flow fields, whose statistics are prescribed by an underlying ensemble, in a parallel computational framework (openMP). To this end, an efficient algorithm for forward and backward tracking of passive particles in stochastic flow-fields is presented. The algorithm, which employs higher order particle advection schemes, presents a mechanism for controlling the growth in the number of particles. The mechanism uses an adaptive binning procedure, while conserving the zeroth, first and second moments of probability (total probability, mean position, and variance). The adaptive binning process offers a tradeoff between speed and accuracy by limiting the number of particles to a desired maximum. To validate our method, we conducted various forward and backward particles tracking experiments within a realistic high-resolution ensemble assimilation setting of the Red Sea, focusing on the effect of the maximum number of particles, the time step, the variance of the ensemble, the travel time, the source location, and history of transport.

In this study, we investigated the in situ responses of Red Sea picophytoplankton, the dominant phytoplankton group in the oligotrophic ocean, to two toxic polycyclic aromatic hydrocarbons (PAHs), phenanthrene and pyrene. The experiments were conducted across a latitudinal gradient of the Saudi Arabian Red Sea, an area sensitive to oil pollution. We observed significant adverse effects on the growth and abundance of the picocyanobacteria Synechococcus and picoeukaryotes, at all stations sampled. Prochlorococcus, which was abundant only at one of the stations, also appeared to be affected. Pyrene was found to be more toxic to phytoplankton at all stations. In general, picoeukaryotes exhibited higher sensitivity to PAHs than Synechococcus. Populations in the highly oligotrophic Northern region of the Red Sea were more tolerant to PAHs, presumably influenced by the natural selection of more resistant strains of phytoplankton due to the prolonged exposure to PAHs. Toxicity threshold values estimated here are higher than those reported for picophytoplankton from other oligotrophic marine waters and exceed by far the natural levels of PAHs in many oceans. Our findings reveal a possible adaptation of picophytoplankton populations to oil-related contaminants, which may clearly influence their spatial distribution patterns in the Red Sea.

A fully parallel ensemble data assimilation and forecasting system has been developed for the Red Sea based on the MIT general circulation model (MITgcm) to simulate the Red Sea circulation and the Data Assimilation Research Testbed (DART) ensemble assimilation software. An important limitation of operational ensemble assimilation systems is the risk of ensemble members’ collapse. This could happen in those situations when the filter update step imposes large corrections on one, or more, of the forecasted ensemble members that are not fully consistent with the model physics. Increasing the ensemble size is expected to improve the assimilation system performances, but obviously increases the risk of members’ collapse. Hardware failure or slow numerical convergence encountered for some members should also occur more frequently. In this context, the manual steering of the whole process appears as a real challenge and makes the implementation of the ensemble assimilation procedure uneasy and extremely time consuming.This paper presents our efforts to build an efficient and fault-tolerant MITgcm-DART ensemble assimilation system capable of operationally running thousands of members. Built on top of Decimate, a scheduler extension developed to ease the submission, monitoring and dynamic steering of workflow of dependent jobs in a fault-tolerant environment, we describe the assimilation system implementation and discuss in detail its coupling strategies. Within Decimate, only a few additional lines of Python is needed to define flexible convergence criteria and to implement any necessary actions to the forecast ensemble members, as for instance (i) restarting faulty job in case of job failure, (ii) changing the random seed in case of poor convergence or numerical instability, (iii) adjusting (reducing or increasing) the number of parallel forecasts on the fly, (iv) replacing members on the fly to enrich the ensemble with new members, etc.We demonstrate the efficiency of the system with numerical experiments assimilating real satellites sea surface height and temperature observations in the Red Sea.

The absorption coefficient of chromophoric dissolved organic matter (CDOM) is a major variable used in developing robust bio-optical models and understanding biogeochemical processes. Over the last decade, the optical properties of CDOM in the open sea have been intensely studied. However, their variations in clear water are poorly documented, particularly in the Red Sea, owing to the absence of in situ measurements. We performed several cruises in the Red Sea to investigate the spatial distribution of the absorption coefficient of CDOM. The spectral absorption coefficients were determined from 400nm to 740nm using a WETLabs ac-s hyper-spectral spectrophotometer. In general, we found a latitudinal gradient in the CDOM absorption coefficient at 443nm (aCDOM(443)) from south to north that is likely influenced by the exchange of water through the strait of Bab-el-Mandeb and the thermohaline circulation of the Red Sea. However, high aCDOM(443) values were observed in the northern Red Sea due to the existence of a sub-mesoscale feature that may induce an increase in phytoplankton production and lead to CDOM production. The aCDOM(443) covaried with the chlorophyll a concentration ([Chl a],) despite a high scatter. Furthermore, the aCDOM(443) for a given [Chl a] concentration was higher than those predicted by global ocean bio-optical models. This study advances our understanding of CDOM concentration in the Red Sea and may help improve the accuracy of the algorithms used to obtain CDOM absorption from ocean color.

This study confirms the presence of the toxigenic benthic dinoflagellates Gambierdiscus belizeanus and Ostreopsis spp. in the central Red Sea. To our knowledge, this is also the first report of these taxa in coastal waters of Saudi Arabia, indicating the potential occurrence of ciguatera fish poisoning (CFP) in that region. During field investigations carried out in 2012 and 2013, a total of 100 Turbinaria and Halimeda macroalgae samples were collected from coral reefs off the Saudi Arabian coast and examined for the presence of Gambierdiscus and Ostreopsis, two toxigenic dinoflagellate genera commonly observed in coral reef communities around the world. Both Gambierdiscus and Ostreopsis spp. were observed at low densities (<200 cells g−1 wet weight algae). Cell densities of Ostreopsis spp. were significantly higher than Gambierdiscus spp. at most of the sampling sites, and abundances of both genera were negatively correlated with seawater salinity. To assess the potential for ciguatoxicity in this region, several Gambierdiscus isolates were established in culture and examined for species identity and toxicity. All isolates were morphologically and molecularly identified as Gambierdiscus belizeanus. Toxicity analysis of two isolates using the mouse neuroblastoma cell-based assay for ciguatoxins (CTX) confirmed G. belizeanus as a CTX producer, with a maximum toxin content of 6.50±1.14×10−5pg P-CTX-1 eq. cell−1. Compared to Gambierdiscus isolates from other locations, these were low toxicity strains. The low Gambierdiscus densities observed along with their comparatively low toxin contents may explain why CFP is unidentified and unreported in this region. Nevertheless, the presence of these potentially toxigenic dinoflagellate species at multiple sites in the central Red Sea warrants future study on their possible effects on marine food webs and human health in this region.