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  • The time course of molecular acclimation to seawater in a euryhaline fish.

    Bonzi, Lucrezia C; Monroe, Alison; Lehmann, Robert; Berumen, Michael L.; Ravasi, Timothy; Schunter, Celia (Scientific reports, Springer Science and Business Media LLC, 2021-09-14) [Article]
    The Arabian pupfish, Aphanius dispar, is a euryhaline fish inhabiting both inland nearly-freshwater desert ponds and highly saline Red Sea coastal lagoons of the Arabian Peninsula. Desert ponds and coastal lagoons, located respectively upstream and at the mouths of dry riverbeds ("wadies"), have been found to potentially become connected during periods of intense rainfall, which could allow the fish to migrate between these different habitats. Flash floods would therefore flush Arabian pupfish out to sea, requiring a rapid acclimation to a greater than 40 ppt change in salinity. To investigate the molecular pathways of salinity acclimation during such events, a Red Sea coastal lagoon and a desert pond population were sampled, with the latter exposed to a rapid increase in water salinity. Changes in branchial gene expression were investigated via genome-wide transcriptome measurements over time from 6 h to 21 days. The two natural populations displayed basal differences in genes related to ion transport, osmoregulation and immune system functions. These mechanisms were also differentially regulated in seawater transferred fish, revealing their crucial role in long-term adaptation. Other processes were only transiently activated shortly after the salinity exposure, including cellular stress response mechanisms, such as molecular chaperone synthesis and apoptosis. Tissue remodelling processes were also identified as transient, but took place later in the timeline, suggesting their importance to long-term acclimation as they likely equip the fish with lasting adaptations to their new environment. The alterations in branchial functional pathways displayed by Arabian pupfish in response to salinity increases are diverse. These reveal a large toolkit of molecular processes important for adaptation to hyperosmolarity that allow for successful colonization to a wide variety of different habitats.
  • Comprehensive analytical approaches reveal species-specific search strategies in sympatric apex predatory sharks

    Calich, Hannah J.; Rodríguez, J. P.; Eguíluz, V. M.; Hammerschlag, Neil; Pattiaratchi, Charitha; Duarte, Carlos M.; Sequeira, Ana M.M. (Ecography, Wiley, 2021-09-14) [Article]
    Animals follow specific movement patterns and search strategies to maximize encounters with essential resources (e.g. prey, favourable habitat) while minimizing exposures to suboptimal conditions (e.g. competitors, predators). While describing spatiotemporal patterns in animal movement from tracking data is common, understanding the associated search strategies employed continues to be a key challenge in ecology. Moreover, studies in marine ecology commonly focus on singular aspects of species' movements, however using multiple analytical approaches can further enable researchers to identify ecological phenomena and resolve fundamental ecological questions relating to movement. Here, we used a set of statistical physics-based methods to analyze satellite tracking data from three co-occurring apex predators (tiger, great hammerhead and bull sharks) that predominantly inhabit productive coastal regions of the northwest Atlantic Ocean and Gulf of Mexico. We analyzed data from 96 sharks and calculated a range of metrics, including each species' displacements, turning angles, dispersion, space-use and community-wide movement patterns to characterize each species' movements and identify potential search strategies. Our comprehensive approach revealed high interspecific variability in shark movement patterns and search strategies. Tiger sharks displayed near-random movements consistent with a Brownian strategy commonly associated with movements through resource-rich habitats. Great hammerheads showed a mixed-movement strategy including Brownian and resident-type movements, suggesting adaptation to widespread and localized high resource availability. Bull sharks followed a resident movement strategy with restricted movements indicating localized high resource availability. We hypothesize that the species-specific search strategies identified here may help foster the co-existence of these sympatric apex predators. Following this comprehensive approach provided novel insights into spatial ecology and assisted with identifying unique movement and search strategies. Similar future studies of animal movement will help characterize movement patterns and also enable the identification of search strategies to help elucidate the ecological drivers of movement and to understand species' responses to environmental change.
  • Symbiodinium microadriaticum (coral microalgal endosymbiont)

    Voolstra, Christian R.; Aranda, Manuel; Zhan, Ye; Dekker, Job (Trends in Genetics, Elsevier BV, 2021-09-11) [Article]
    Photosynthetic microalgae, from the family Symbiodiniaceae, engage in endosymbioses with marine invertebrates, including stony corals. More generally, dinoflagellates are ubiquitous protists and the main primary producers in the oceans. Despite their ecological and economic importance, their biology remains enigmatic. Here we assembled 94 chromosome-scale scaffolds of the ancestral Symbiodiniaceae species Symbiodinium microadriaticum. Contrary to the random order of genes typically found in eukaryotic cells, genes are enriched toward the ends of chromosomes in alternating unidirectional blocks that are sometimes enriched for genes of specific biological processes. These gene blocks are coexpressed and separated by structural boundaries where transcription converges. These structural domains, in turn, comprise the transcription-dependent basic building blocks of the chromosomes that fold as linear rods. Such a highly ordered structure linking gene orientation, transcription, and spatial organization of chromosomes is exceptional.
  • Testing angular velocity as a new metric for metabolic demands of slow-moving marine fauna: a case study with Giant spider conchs Lambis truncata

    Hopkins, Lloyd W.; Geraldi, Nathan; Pope, Edward C.; Holton, Mark D.; Lurgi, Miguel; Duarte, Carlos M.; Wilson, Rory P. (Animal Biotelemetry, Springer Science and Business Media LLC, 2021-09-07) [Article]
    Abstract Background Quantifying metabolic rate in free-living animals is invaluable in understanding the costs of behaviour and movement for individuals and communities. Dynamic body acceleration (DBA) metrics, such as vectoral DBA (VeDBA), are commonly used as proxies for the energy expenditure of movement but are of limited applicability for slow-moving species. It has recently been suggested that metrics based on angular velocity might be better suited to characterise their energetics. We investigated whether a novel metric—the ‘Rate of change of Rotational Movement (RocRM)’, calculated from the vectoral sum of change in the pitch, roll and yaw/heading axes over a given length of time, is a suitable proxy for energy expenditure. Results We found that RocRM can be used as an alternative energy expenditure proxy in a slow-moving benthic invertebrate. Eleven Giant spider conchs Lambis truncata (collected in the Red Sea) were instrumented with multiple channel (Daily Diary) tags and kept in sealed chambers for 5 h while their oxygen consumption, V̇O2, was measured. We found RocRM to be positively correlated with V̇O2, this relationship being affected by the time-step (i.e. the range of the calculated differential) of the RocRM. Time steps of 1, 5, 10 and 60 s yielded an explained variability of between 15 and 31%. The relationship between V̇O2 and VeDBA was not statistically significant, suggesting RocRM to provide more accurate estimations of metabolic rates in L. truncata. Conclusions RocRM proved to be a statistically significant predictor of V̇O2 where VeDBA did not, validating the approach of using angular-based metrics over dynamic movement-based ones for slower moving animals. Further work is required to validate the use of RocRM for other species, particularly in animals with minimally dynamic movement, to better understand energetic costs of whole ecosystems. Unexplained variability in the models might be a consequence of the methodology used, but also likely a result of conch activity that does not manifest in movement of the shell. Additionally, density plots of mean RocRM at each time-step suggest differences in movement scales, which may collectively be useful as a species fingerprint of movement going forward.
  • Sustainable and Eco-Friendly Coral Restoration through 3D Printing and Fabrication

    Albalawi, Hamed I.; Khan, Zainab N.; Valle-Pérez, Alexander U.; Kahin, Kowther M.; Hountondji, Maria; Alwazani, Hibatallah; Schmidt-Roach, Sebastian; Bilalis, Panagiotis; Aranda, Manuel; Duarte, Carlos M.; Hauser, Charlotte (ACS Sustainable Chemistry & Engineering, American Chemical Society (ACS), 2021-09-02) [Article]
    Coral reef degradation is a rising problem, driven by marine heatwaves, the spread of coral diseases, and human impact by overfishing and pollution. Our capacity to restore coral reefs lags behind in terms of scale, effectiveness, and cost-efficiency. While common restoration efforts rely on the formation of carbonate skeletons on structural frames for supported coral growth, this technique is a rate-limiting step in the growth of scleractinian corals. Reverse engineering and additive manufacturing technologies offer an innovative shift in approach from the use of concrete blocks and metal frames to sophisticated efforts that use scanned geometries of harvested corals to fabricate artificial coral skeletons for installation in coral gardens and reefs. Herein, we present an eco-friendly and sustainable approach for coral fabrication by merging three-dimensional (3D) scanning, 3D printing, and molding techniques. Our method, 3D CoraPrint, exploits the 3D printing technology to fabricate artificial natural-based coral skeletons, expediting the growth rate of live coral fragments and quickening the reef transplantation process while minimizing nursery costs. It allows for flexibility, customization, and fast return time with an enhanced level of accuracy, thus establishing an environmentally friendly, scalable model for coral fabrication to boost restorative efforts around the globe.
  • Diel dynamics of dissolved organic matter and heterotrophic prokaryotes reveal enhanced growth at the ocean's mesopelagic fish layer during daytime

    Moran, Xose Anxelu G.; García, Francisca C.; Røstad, Anders; Silva, Luis; Al-Otaibi, Najwa; Irigoien, Xabier; Calleja, Maria L. (Science of The Total Environment, Elsevier BV, 2021-09) [Article]
    Contrary to epipelagic waters, where biogeochemical processes closely follow the light and dark periods, little is known about diel cycles in the ocean's mesopelagic realm. Here, we monitored the dynamics of dissolved organic matter (DOM) and planktonic heterotrophic prokaryotes every 2 h for one day at 0 and 550 m (a depth occupied by vertically migrating fishes during light hours) in oligotrophic waters of the central Red Sea. We additionally performed predator-free seawater incubations of samples collected from the same site both at midnight and at noon. Comparable in situ variability in microbial biomass and dissolved organic carbon concentration suggests a diel supply of fresh DOM in both layers. The presence of fishes in the mesopelagic zone during daytime likely promoted a sustained, longer growth of larger prokaryotic cells. The specific growth rates were consistently higher in the noon experiments from both depths (surface: 0.34 vs. 0.18 d-1, mesopelagic: 0.16 vs. 0.09 d-1). Heterotrophic prokaryotes in the mesopelagic layer were also more efficient at converting extant DOM into new biomass. These results suggest that the ocean's twilight zone receives a consistent diurnal supply of labile DOM from diel vertical migrating fishes, enabling an unexpectedly active community of heterotrophic prokaryotes.
  • Host under epigenetic control: A novel perspective on the interaction between microorganisms and corals

    Barno, Adam R.; Villela, Helena D. M.; Aranda, Manuel; Thomas, Torsten; Peixoto, Raquel S (BioEssays, Wiley, 2021-08-31) [Article]
    Coral reefs have been challenged by the current rate and severity of environmental change that might outpace their ability to adapt and survive. Current research focuses on understanding how microbial communities and epigenetic changes separately affect phenotypes and gene expression of corals. Here, we provide the hypothesis that coral-associated microorganisms may directly or indirectly affect the coral's phenotypic response through the modulation of its epigenome. Homologs of ankyrin-repeat protein A and internalin B, which indirectly cause histone modifications in humans, as well as Rv1988 histone methyltransferase, and the DNA methyltransferases Rv2966c, Mhy1, Mhy2, and Mhy3 found in coral-associated bacteria indicate that there are potential host epigenome-modifying proteins in the coral microbiome. With the ideas presented here, we suggest that microbiome manipulation may be a means to alter a coral's epigenome, which could aid the current efforts to protect coral reefs.
  • Widespread bleaching in the One Tree Island lagoon (Southern Great Barrier Reef) during record-breaking temperatures in 2020

    Nolan, Megan K. B.; Schmidt-Roach, Sebastian; Davis, Andrew R.; Aranda, Manuel; Howells, Emily J. (Environmental Monitoring and Assessment, Springer Science and Business Media LLC, 2021-08-21) [Article]
    The global marine environment has been impacted significantly by climate change. Ocean temperatures are rising, and the frequency, duration and intensity of marine heatwaves are increasing, particularly affecting coral reefs. Coral bleaching events are becoming more common, with less recovery time between events. Anomalous temperatures at the start of 2020 caused widespread bleaching across the Great Barrier Reef (GBR), extending to southern, previously less affected reefs such as One Tree Island. Here, nine video transects were conducted at One Tree Island, in the Capricorn Bunker Group, and analysed for community composition and diversity, and the extent of bleaching across taxa. Average live hard coral cover across the area was 11.62%, and almost half of this was identified as severely bleached. This bleaching event is concerning as it occurred in an area previously considered a potential refuge for corals and associated fauna from the risks of climate warming. Due to the global impacts of COVID-19 during 2020, this report provides one of potentially few monitoring efforts of coral bleaching.
  • Enhancing the heat tolerance of reef-building corals to future warming

    Howells, Emily J.; Abrego, David; Liew, Yi Jin; Burt, John A.; Meyer, Eli; Aranda, Manuel (Science Advances, American Association for the Advancement of Science (AAAS), 2021-08-20) [Article]
    Reef-building corals thriving in extreme thermal environments may provide genetic variation that can assist the evolution of populations to rapid climate warming. However, the feasibility and scale of genetic improvements remain untested despite ongoing population declines from recurrent thermal stress events. Here, we show that corals from the hottest reefs in the world transfer sufficient heat tolerance to a naïve population sufficient to withstand end-of-century warming projections. Heat survival increased up to 84% when naïve mothers were selectively bred with fathers from the hottest reefs because of strong heritable genetic effects. We identified genomic loci associated with tolerance variation that were enriched for heat shock proteins, oxidative stress, and immune functions. Unexpectedly, several coral families exhibited survival rates and genomic associations deviating from origin predictions, including a few naïve purebreds with exceptionally high heat tolerance. Our findings highlight previously uncharacterized enhanced and intrinsic potential of coral populations to adapt to climate warming.
  • Coral microbiome manipulation elicits metabolic and genetic restructuring to mitigate heat stress and evade mortality

    Santoro, Erika P.; Borges, Ricardo M.; Espinoza, Josh L.; Freire, Marcelo; Messias, Camila S. M. A.; Villela, Helena D. M.; Pereira, Leandro M.; Vilela, Caren L. S.; Rosado, João G.; Cardoso, Pedro M.; Rosado, Phillipe M.; Assis, Juliana M.; Duarte, Gustavo A. S.; Perna, Gabriela; Rosado, Alexandre S.; Macrae, Andrew; Dupont, Christopher L.; Nelson, Karen E.; Sweet, Michael; Voolstra, Christian R.; Peixoto, Raquel S (Science Advances, American Association for the Advancement of Science (AAAS), 2021-08-13) [Article]
    Beneficial microorganisms for corals (BMCs) ameliorate environmental stress, but whether they can prevent mortality and the underlying host response mechanisms remains elusive. Here, we conducted omics analyses on the coral Mussismilia hispida exposed to bleaching conditions in a long-term mesocosm experiment and inoculated with a selected BMC consortium or a saline solution placebo. All corals were affected by heat stress, but the observed “post-heat stress disorder” was mitigated by BMCs, signified by patterns of dimethylsulfoniopropionate degradation, lipid maintenance, and coral host transcriptional reprogramming of cellular restructuration, repair, stress protection, and immune genes, concomitant with a 40% survival rate increase and stable photosynthetic performance by the endosymbiotic algae. This study provides insights into the responses that underlie probiotic host manipulation. We demonstrate that BMCs trigger a dynamic microbiome restructuring process that instigates genetic and metabolic alterations in the coral host that eventually mitigate coral bleaching and mortality.
  • Integrating environmental variability to broaden the research on coral responses to future ocean conditions

    Ziegler, Maren; Anton Gamazo, Andrea; Klein, Shannon; Rädecker, Nils; Geraldi, Nathan; Schmidt-Roach, Sebastian; Saderne, Vincent; Mumby, Peter J.; Cziesielski, Maha Joana; Martin, Cecilia; Frölicher, Thomas L.; Pandolfi, John M.; Suggett, David J.; Aranda, Manuel; Duarte, Carlos M.; Voolstra, Christian R. (Global Change Biology, Wiley, 2021-08-13) [Article]
    Our understanding of the response of reef-building corals to changes in their physical environment is largely based on laboratory experiments, analysis of long-term field data, and model projections. Experimental data provide unique insights into how organisms respond to variation of environmental drivers. However, an assessment of how well experimental conditions cover the breadth of environmental conditions and variability where corals live successfully, is missing. Here, we compiled and analyzed a globally distributed dataset of in situ seasonal and diurnal variability of key environmental drivers (temperature, pCO2, and O2) critical for the growth and livelihood of reef-building corals. Using a meta-analysis approach, we compared the variability of environmental conditions assayed in coral experimental studies to current and projected conditions in their natural habitats. We found that annual temperature profiles projected for the end of the 21st century were characterized by distributional shifts in temperatures with warmer winters and longer warm periods in the summer, not just peak temperatures. Further, short-term hourly fluctuations of temperature and pCO2 may regularly expose corals to conditions beyond the projected average increases for the end of the 21st century. Coral reef sites varied in the degree of coupling between temperature, pCO2, and dissolved O2, which warrants site-specific, differentiated experimental approaches depending on the local hydrography and influence of biological processes on the carbonate system and O2 availability. Our analysis highlights that a large portion of the natural environmental variability at short and long time scales is underexplored in experimental designs, which may provide a path to extend our understanding on the response of corals to global climate change.
  • A prevalent neglect of environmental control in mammalian cell culture calls for best practices

    Klein, Shannon; Alsolami, Samhan M.; Steckbauer, Alexandra; Arossa, Silvia; Parry, Anieka; Ramos Mandujano, Gerardo; Alsayegh, Khaled; Izpisua Belmonte, Juan Carlos; Li, Mo; Duarte, Carlos M. (Nature Biomedical Engineering, Springer Science and Business Media LLC, 2021-08-13) [Article]
    Human cell lines, first cultured in the 1950s1, are indispensable in biomedical research. Today, a wide range of cell types are available, and sophisticated advanced ‘omics’ and visualization techniques allow for the routine assessment of cell identity and cellular responses2. However, the culture methods have remained relatively unchanged. Major advances in culture systems were made over three decades ago3,4, yet the old standard approach of batch cell culture — the culture of cells either in suspension or as adherent monolayers of cells in standard media5,6,7 — remains the predominant method in biomedical research.
  • Model predictive control paradigms for fish growth reference tracking in precision aquaculture

    Chahid, Abderrazak; Ndoye, Ibrahima; Majoris, John E.; Berumen, Michael L.; Laleg-Kirati, Taous-Meriem (Journal of Process Control, Elsevier BV, 2021-08-12) [Article]
    In precision aquaculture, the primary goal is to maximize biomass production while minimizing production costs. This objective can be achieved by optimizing factors that have a strong influence on fish growth, such as feeding rate, temperature, and dissolved oxygen. This paper provides a comparative study of four model predictive control (MPC) strategies for fish growth reference tracking under a representative bioenergetic growth model in precision aquaculture. We propose to evaluate four candidate MPC formulations for fish growth reference tracking based on the receding horizon. The first MPC formulation tracks a desired fish growth trajectory while penalizing the feed ration, temperature, and dissolved oxygen. The second MPC optimization strategy directly optimizes the feed conversion ratio (FCR), which is the ratio between food quantity and fish weight gain at each sampling time. This FCR-like optimization strategy minimizes the feed while maximizing the predicted growth state's deviation from the given reference growth trajectory. The third MPC formulation includes a tradeoff between the growth rate trajectory tracking, the dynamic energy, and food cost. The last MPC formulation aims to maximize the fish growth rate while minimizing the costs. Numerical simulations that integrate a realistic bioenergetic fish growth model of Nile tilapia (Oreochromis niloticus) are illustrated to examine the comparative performance of the four proposed optimal control strategies. A sensitivity analysis is conducted to study the robustness of these MPC strategies with respect to the effect of the prediction horizon, the regularization term, and the additive input disturbances to the process. The obtained results show great potential and flexibility to meet the fish farmers’ needs depending on the type of fish, selling price, culture duration, and feed cost.
  • New Insights From Transcriptomic Data Reveal Differential Effects of CO2 Acidification Stress on Photosynthesis of an Endosymbiotic Dinoflagellate in hospite

    Herrera, Marcela; Liew, Yi Jin2021-06-15; Venn, Alexander; Tambutté, Eric; Zoccola, Didier; Tambutté, Sylvie; Cui, Guoxin; Aranda, Manuel (Frontiers in microbiology, Frontiers Media SA, 2021-08-05) [Article]
    Ocean acidification (OA) has both detrimental as well as beneficial effects on marine life; it negatively affects calcifiers while enhancing the productivity of photosynthetic organisms. To date, many studies have focused on the impacts of OA on calcification in reef-building corals, a process particularly susceptible to acidification. However, little is known about the effects of OA on their photosynthetic algal partners, with some studies suggesting potential benefits for symbiont productivity. Here, we investigated the transcriptomic response of the endosymbiont Symbiodinium microadriaticum (CCMP2467) in the Red Sea coral Stylophora pistillata subjected to different long-term (2 years) OA treatments (pH 8.0, 7.8, 7.4, 7.2). Transcriptomic analyses revealed that symbionts from corals under lower pH treatments responded to acidification by increasing the expression of genes related to photosynthesis and carbon-concentrating mechanisms. These processes were mostly up-regulated and associated metabolic pathways were significantly enriched, suggesting an overall positive effect of OA on the expression of photosynthesis-related genes. To test this conclusion on a physiological level, we analyzed the symbiont’s photochemical performance across treatments. However, in contrast to the beneficial effects suggested by the observed gene expression changes, we found significant impairment of photosynthesis with increasing pCO2. Collectively, our data suggest that over-expression of photosynthesis-related genes is not a beneficial effect of OA but rather an acclimation response of the holobiont to different water chemistries. Our study highlights the complex effects of ocean acidification on these symbiotic organisms and the role of the host in determining symbiont productivity and performance.
  • Projecting coral responses to intensifying marine heatwaves under ocean acidification

    Klein, Shannon; Geraldi, Nathan; Anton Gamazo, Andrea; Schmidt-Roach, Sebastian; Ziegler, Maren; Cziesielski, Maha Joana; Martin, Cecilia; Rädecker, Nils; Frölicher, Thomas L.; Mumby, Peter J.; Pandolfi, John M.; Suggett, David J.; Voolstra, Christian R.; Aranda, Manuel; Duarte, Carlos. M. (Global Change Biology, Wiley, 2021-08-03) [Article]
    Over this century, coral reefs will run the gauntlet of climate change as marine heatwaves (MHWs) become more intense and frequent, and ocean acidification (OA) progresses. However, we still lack a quantitative assessment of how, and to what degree, OA will moderate the responses of corals to MHWs as they intensify throughout this century. Here, we first projected future MHW intensities for tropical regions under three future greenhouse gas emissions scenarios (RCP2.6, RCP4.5, and RCP8.5) for the near-term (2021-2040), mid-century (2041-2060), and late-century (2081-2100). We then combined these MHW intensity projections with a global dataset of 1,788 experiments to assess coral attribute performance and survival under the three emissions scenarios for the near term, mid-century, and late century in the presence and absence of OA. Although warming and OA had predominately additive impacts on the coral responses, the contribution of OA in affecting most coral attribute responses was minor relative to the dominant role of intensifying MHWs. However, the addition of OA led to greater decreases in photosynthesis and survival under intermediate and unrestricted emissions scenarios for the mid and late century than if intensifying MHWs were considered as the only driver. These results indicate that the role OA in affecting coral responses to intensifying MHWs temperatures is specific to the coral attribute examined and the extremity of temperatures tested. Specifically, intensifying MHWs and OA will cause increasing instances of coral bleaching and substantial declines in coral productivity, calcification, and survival within the next two decades under the low and intermediate emissions scenarios. These projections suggest that corals must rapidly adapt or acclimatize to projected ocean conditions to persist, which is far more likely under a low emissions scenario and with increasing efforts to manage reefs to enhance resilience.
  • A prediction and imputation method for marine animal movement data

    Li, Xinqing; Sindihebura, Tanguy Tresor; Zhou, Lei; Duarte, Carlos M.; Costa, Daniel P.; Hindell, Mark A.; McMahon, Clive; Muelbert, Mônica M.C.; Zhang, Xiangliang; Peng, Chengbin (PeerJ Computer Science, PeerJ, 2021-08-03) [Article]
    Data prediction and imputation are important parts of marine animal movement trajectory analysis as they can help researchers understand animal movement patterns and address missing data issues. Compared with traditional methods, deep learning methods can usually provide enhanced pattern extraction capabilities, but their applications in marine data analysis are still limited. In this research, we propose a composite deep learning model to improve the accuracy of marine animal trajectory prediction and imputation. The model extracts patterns from the trajectories with an encoder network and reconstructs the trajectories using these patterns with a decoder network. We use attention mechanisms to highlight certain extracted patterns as well for the decoder. We also feed these patterns into a second decoder for prediction and imputation. Therefore, our approach is a coupling of unsupervised learning with the encoder and the first decoder and supervised learning with the encoder and the second decoder. Experimental results demonstrate that our approach can reduce errors by at least 10% on average comparing with other methods.
  • Distribution and temporal trends in the abundance of nesting sea turtles in the Red Sea

    Shimada, Takahiro; Meekan, Mark G.; Baldwin, Robert; Al-Suwailem, Abdulaziz M.; Clarke, Christopher; Santillan, August Santillan; Duarte, Carlos M. (Biological Conservation, Elsevier BV, 2021-08-03) [Article]
    Mobile species often aggregate at predictable places and times to ensure that individuals find mates and breed in suitable habitats. Sea turtles demonstrate this life history trait, which can make these species highly susceptible to population declines if nesting habitats are lost or degraded. Conservation management thus requires knowledge of where and when turtles nest and changes in abundance in these habitats through time. Here, we compiled new and published data and used a novel analysis to describe seasonality, annual abundance and spatial distribution of nesting green (Chelonia mydas) and hawksbill (Eretmochelys imbricata) turtles in data-deficient populations that inhabit the Red Sea. Major new rookeries were identified for green turtles at Jazirat1 Mashabah (113 and 179 nesting females in 2018 and 2019) and for hawksbill turtles at Jazirat Al Waqqadi (79 nesting females in 2018), both of which are located on nearshore islands of the Kingdom of Saudi Arabia in an area subject to industrial, residential and ecotourism developments. An upward trend in annual abundance of nesting sea turtles was estimated at some sites including Ras Al Baridi (Saudi Arabia), a major rookery of green turtles in the Red Sea, where the annual numbers increased from 14–110 individuals in 1982–1995 to 178 and 330 individuals in 2018 and 2019. This integrative work provides the most up-to-date, comprehensive information on nesting sea turtles in the Red Sea and documents a critical baseline for sea turtle conservation and future management effort.
  • Consensus Guidelines for Advancing Coral Holobiont Genome and Specimen Voucher Deposition

    Voolstra, Christian R.; Quigley, Kate M.; Davies, Sarah W.; Parkinson, John Everett; Peixoto, Raquel S.; Aranda, Manuel; Baker, Andrew C.; Barno, Adam R.; Barshis, Daniel J.; Benzoni, Francesca; Bonito, Victor; Bourne, David G.; Buitrago-López, Carol; Bridge, Tom C.L.; Chan, Cheong Xin; Combosch, David J.; Craggs, Jamie; Frommlet, Jörg C.; Herrera, Santiago; Quattrini, Andrea M.; Röthig, Till; Reimer, James D.; Rubio-Portillo, Esther; Suggett, David J.; Villela, Helena; Ziegler, Maren; Sweet, Michael (Frontiers in Marine Science, Frontiers Media SA, 2021-08-03) [Article]
    Coral research is being ushered into the genomic era. To fully capitalize on the potential discoveries from this genomic revolution, the rapidly increasing number of high-quality genomes requires effective pairing with rigorous taxonomic characterizations of specimens and the contextualization of their ecological relevance. However, to date there is no formal framework that genomicists, taxonomists, and coral scientists can collectively use to systematically acquire and link these data. Spurred by the recently announced “Coral symbiosis sensitivity to environmental change hub” under the “Aquatic Symbiosis Genomics Project” - a collaboration between the Wellcome Sanger Institute and the Gordon and Betty Moore Foundation to generate gold-standard genome sequences for coral animal hosts and their associated Symbiodiniaceae microalgae (among the sequencing of many other symbiotic aquatic species) - we outline consensus guidelines to reconcile different types of data. The metaorganism nature of the coral holobiont provides a particular challenge in this context and is a key factor to consider for developing a framework to consolidate genomic, taxonomic, and ecological (meta)data. Ideally, genomic data should be accompanied by taxonomic references, i.e., skeletal vouchers as formal morphological references for corals and strain specimens in the case of microalgal and bacterial symbionts (cultured isolates). However, exhaustive taxonomic characterization of all coral holobiont member species is currently not feasible simply because we do not have a comprehensive understanding of all the organisms that constitute the coral holobiont. Nevertheless, guidelines on minimal, recommended, and ideal-case descriptions for the major coral holobiont constituents (coral animal, Symbiodiniaceae microalgae, and prokaryotes) will undoubtedly help in future referencing and will facilitate comparative studies. We hope that the guidelines outlined here, which we will adhere to as part of the Aquatic Symbiosis Genomics Project sub-hub focused on coral symbioses, will be useful to a broader community and their implementation will facilitate cross- and meta-data comparisons and analyses.
  • Localized effects of offshore aquaculture on water quality in a tropical sea.

    Dunne, Aislinn; Carvalho, Susana; Moran, Xose Anxelu G.; Calleja, Maria Ll; Jones, Burton (Marine pollution bulletin, Elsevier BV, 2021-07-30) [Article]
    Aquaculture production has increased steadily in many tropical countries over the past few decades, although impact assessments have been frequently neglected. We investigated the impacts of an offshore barramundi fish farm on water quality in the southern-central Red Sea, a traditionally understudied tropical, oligotrophic, and semi-enclosed basin. Inorganic nutrients, particulate matter, chlorophyll-a, and heterotrophic bacteria were measured periodically over 8 months around the farm. Water down-current from the farm had, on average, more heterotrophic bacteria and chlorophyll-a than up-current (11% and 34% higher, respectively). Ratios of dissolved inorganic nitrogen:phosphorus down-current from the farm were lower than ratios up-current (mean 9.8 vs 16.0, respectively). Phosphate, inorganic nitrogen, and particulate matter showed patterns of enrichment associated with the farm after a fish feeding event. Strategies such as feed optimization and considering hydrodynamics in site selection may improve water quality for future fish farms in Saudi Arabia and other tropical countries.
  • Assessment of Red Sea temperatures in CMIP5 models for present and future climate

    Agulles, Miguel; Jorda, Gabriel; Hoteit, Ibrahim; Agusti, Susana; Duarte, Carlos M. (PLOS ONE, Public Library of Science (PLoS), 2021-07-30) [Article]
    The increase of the temperature in the Red Sea basin due to global warming could have a large negative effect on its marine ecosystem. Consequently, there is a growing interest, from the scientific community and public organizations, in obtaining reliable projections of the Red Sea temperatures throughout the 21st century. However, the main tool used to do climate projections, the global climate models (GCM), may not be well suited for that relatively small region. In this work we assess the skills of the CMIP5 ensemble of GCMs in reproducing different aspects of the Red Sea 3D temperature variability. The results suggest that some of the GCMs are able to reproduce the present variability at large spatial scales with accuracy comparable to medium and high-resolution hindcasts. In general, the skills of the GCMs are better inside the Red Sea than outside, in the Gulf of Aden. Based on their performance, 8 of the original ensemble of 43 GCMs have been selected to project the temperature evolution of the basin. Bearing in mind the GCM limitations, this can be an useful benchmark once the high resolution projections are available. Those models project an averaged warming at the end of the century (2080–2100) of 3.3 ±> 0.6°C and 1.6 ±> 0.4°C at the surface under the scenarios RCP8.5 and RCP4.5, respectively. In the deeper layers the warming is projected to be smaller, reaching 2.2 ±> 0.5°C and 1.5 ±> 0.3°C at 300 m. The projected warming will largely overcome the natural multidecadal variability, which could induce temporary and moderate decrease of the temperatures but not enough to fully counteract it. We have also estimated how the rise of the mean temperature could modify the characteristics of the marine heatwaves in the region. The results show that the average length of the heatwaves would increase ~15 times and the intensity of the heatwaves ~4 times with respect to the present conditions under the scenario RCP8.5 (10 time and 3.6 times, respectively, under scenario RCP4.5).

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