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Recent Submissions

  • Seasonal dynamics of natural Ostreococcus viral infection at the single cell level using VirusFISH.

    M Castillo, Yaiza; Forn, Irene; Yau, Sheree; Moran, Xose Anxelu G.; Alonso-Sáez, Laura; Arandia-Gorostidi, Néstor; Vaqué, Dolors; Sebastián, Marta (Environmental microbiology, Wiley, 2021-04-05) [Article]
    Ostreococcus is a cosmopolitan marine genus of phytoplankton found in mesotrophic and oligotrophic waters, and the smallest free-living eukaryotes known to date, with a cell diameter close to 1 μm. Ostreococcus has been extensively studied as a model system to investigate viral-host dynamics in culture, yet the impact of viruses in naturally occurring populations is largely unknown. Here, we used Virus Fluorescence in situ Hybridization (VirusFISH) to visualize and quantify viral-host dynamics in natural populations of Ostreococcus during a seasonal cycle in the central Cantabrian Sea (Southern Bay of Biscay). Ostreococcus were predominantly found during summer and autumn at surface and 50 m depth, in coastal, mid-shelf and shelf waters, representing up to 21% of the picoeukaryotic communities. Viral infection was only detected in surface waters, and its impact was variable but highest from May to July and November to December, when up to half of the population was infected. Metatranscriptomic data available from the mid-shelf station unveiled that the Ostreococcus population was dominated by the species O. lucimarinus. This work represents a proof of concept that the VirusFISH technique can be used to quantify the impact of viruses on targeted populations of key microbes from complex natural communities. This article is protected by copyright. All rights reserved.
  • Phylogenomics of Porites from the Arabian Peninsula.

    Terraneo, Tullia Isotta; Benzoni, Francesca; Arrigoni, Roberto; Baird, Andrew H; Mariappan, Kiruthiga; Forsman, Zac H; Wooster, Michael K; Bouwmeester, Jessica; Marshell, Alyssa; Berumen, Michael L. (Molecular phylogenetics and evolution, Elsevier BV, 2021-04-04) [Article]
    The advent of high throughput sequencing technologies provides an opportunity to resolve phylogenetic relationships among closely related species. By incorporating hundreds to thousands of unlinked loci and single nucleotide polymorphisms (SNPs), phylogenomic analyses have a far greater potential to resolve species boundaries than approaches that rely on only a few markers. Scleractinian taxa have proved challenging to identify using traditional morphological approaches and many groups lack an adequate set of molecular markers to investigate their phylogenies. Here, we examine the potential of Restriction-site Associated DNA sequencing (RADseq) to investigate phylogenetic relationships and species limits within the scleractinian coral genus Porites. A total of 126 colonies were collected from 16 localities in the seas surrounding the Arabian Peninsula and ascribed to 12 nominal and two unknown species based on their morphology. Reference mapping was used to retrieve and compare nearly complete mitochondrial genomes, ribosomal DNA, and histone loci. De novo assembly and reference mapping to the P. lobata coral transcriptome were compared and used to obtain thousands of genome-wide loci and SNPs. A suite of species discovery methods (phylogenetic, ordination, and clustering analyses) and species delimitation approaches (coalescent-based, species tree, and Bayesian Factor delimitation) suggested the presence of eight molecular lineages, one of which included six morphospecies. Our phylogenomic approach provided a fully supported phylogeny of Porites from the Arabian Peninsula, suggesting the power of RADseq data to solve the species delineation problem in this speciose coral genus.
  • Genomes of the willow-galling sawflies Euura lappo and Eupontania aestiva (Hymenoptera: Tenthredinidae): a resource for research on ecological speciation, adaptation, and gall induction

    Michell, Craig; Wutke, Saskia; Aranda, Manuel; Nyman, Tommi (G3 Genes|Genomes|Genetics, Oxford University Press (OUP), 2021-03-31) [Article]
    Abstract Hymenoptera are a hyperdiverse insect order represented by over 153,000 different species. As many hymenopteran species perform various crucial roles for our environment, such as pollination, herbivory, and parasitism, they are of high economic and ecological importance. There are 99 hymenopteran genomes in the NCBI database, yet only five are representative of the paraphyletic suborder Symphyta (sawflies, woodwasps, and horntails), while the rest represent the suborder Apocrita (bees, wasps, and ants). Here, using a combination of 10X Genomics linked-read sequencing, Oxford Nanopore long-read technology, and Illumina short-read data, we assembled the genomes of two willow-galling sawflies (Hymenoptera: Tenthredinidae: Nematinae: Euurina): the bud-galling species Euura lappo and the leaf-galling species Eupontania aestiva. The final assembly for E. lappo is 259.85 Mbp in size, with a contig N50 of 209.0 kbp and a BUSCO score of 93.5%. The E. aestiva genome is 222.23 Mbp in size, with a contig N50 of 49.7 kbp and an 90.2% complete BUSCO score. De novo annotation of repetitive elements showed that 27.45% of the genome was composed of repetitive elements in E. lappo and 16.89% in E. aestiva, which is a marked increase compared to previously published hymenopteran genomes. The genomes presented here provide a resource for inferring phylogenetic relationships among basal hymenopterans, comparative studies on host-related genomic adaptation in plant-feeding insects, and research on the mechanisms of plant manipulation by gall-inducing insects.
  • Using species connectivity to achieve coordinated large-scale marine conservation efforts in the Red Sea

    Gajdzik, Laura; Green, Alison Lesley; Cochran, Jesse; Hardenstine, Royale; Tanabe, Lyndsey K.; Berumen, Michael L. (Marine Pollution Bulletin, Elsevier BV, 2021-03-18) [Article]
    In the face of increasing anthropogenic threats, coastal nations need to reach common ground for effective marine conservation. Understanding species' connectivity can reveal how nations share resources, demonstrating the need for cooperative protection efforts. Unfortunately, connectivity information is rarely integrated into the design of marine protected areas (MPAs). This is exemplified in the Red Sea where biodiversity is only nominally protected by a non-cohesive network of small-sized MPAs, most of which are barely implemented. Here, we showcase the potential of using connectivity patterns of flagship species to consolidate conservation efforts in the Red Sea. We argue that a large-scale MPA (LSMPA) would more effectively preserve Red Sea species' multinational migration routes. A connectivity-informed LSMPA approach provides thus one avenue to unite coastal nations toward acting for the common good of conservation and reverse the global decline in marine biodiversity.
  • Neotype designation and re-description of Forsskål’s reticulate whipray Himantura uarnak

    Borsa, Philippe; Williams, Collin T.; Mcivor, Ashlie; Hoareau, Thierry B.; Berumen, Michael L. (Marine Biodiversity, Springer Science and Business Media LLC, 2021-03-17) [Article]
    A continuing impediment to the taxonomy of the reticulate whipray Himantura spp. species complex is the absence of a type specimen for H. uarnak (Gmelin [ex Forsskål], 1789). Here, reticulate whipray specimens were sampled from the Jeddah region in the Red Sea, the assumed type locality of H. uarnak, and characterized genetically at the cytochrome-oxidase subunit 1 (CO1) locus. One of these specimens now in the fish collection of the California Academy of Sciences was designated as neotype. The maximum-likelihood phylogeny of all available CO1 gene sequences from the genus Himantura had the following topology: ((H. leoparda, H. uarnak), (H. undulata, (Himantura sp. 2, (H. australis + Himantura sp. 1))), H. tutul), where H. uarnak haplotypes formed a distinct lineage sister to H. leoparda. Based on these CO1 gene sequences, the geographic distribution of H. uarnak includes the eastern Mediterranean, the Red Sea, the East African coast, and the Arabian Sea. At least one lineage in the reticulate whipray species complex remains to be named.
  • A standardisation framework for bio-logging data to advance ecological research and conservation

    Sequeira, Ana M.M.; O’Toole, Malcolm; Keates, Theresa R.; McDonnell, Laura H.; Braun, Camrin D.; Hoenner, Xavier; Jaine, Fabrice R.A.; Jonsen, Ian D.; Newman, Peggy; Pye, Jonathan; Bograd, Steven J.; Hays, Graeme C.; Hazen, Elliott L; Holland, Melinda; Tsontos, Vardis; Blight, Clint; Cagnacci, Francesca; Davidson, Sarah C.; Dettki, Holger; Duarte, Carlos M.; Dunn, Daniel C.; Eguíluz, V. M.; Fedak, Michael; Gleiss, Adrian C.; Hammerschlag, Neil; Hindell, Mark A.; Holland, Kim; Janekovic, Ivica; McKinzie, Megan K.; Muelbert, Mônica M.C.; Pattiaratchi, Chari; Rutz, Christian; Sims, David W.; Simmons, Samantha E.; Townsend, Brendal; Whoriskey, Frederick; Woodward, Bill; Costa, Daniel P.; Heupel, Michelle R.; Sequeira, Ana M. M.; Harcourt, R.; Weise, Michael (Methods in Ecology and Evolution, Wiley, 2021-03-15) [Article]
    Bio-logging data obtained by tagging animals is key to addressing global conservation challenges. However, the many thousands of existing bio-logging datasets are not easily discoverable, universally comparable, nor readily accessible through existing repositories and across platforms. This slows down ecological research and effective management. A set of universal standards is needed to ensure discoverability, interoperability, and effective translation of bio-logging data into research and management recommendations. We propose a standardisation framework adhering to existing data principles (FAIR: Findable, Accessible, Interoperable, and Reusable; and TRUST: Transparency, Responsibility, User focus, Sustainability and Technology) and involving the use of simple templates to create a data flow from manufacturers and researchers to compliant repositories, where automated procedures should be in place to prepare data availability into four standardised levels: (i) decoded raw data, (ii) curated data, (iii) interpolated data, and (iv) gridded data. Our framework allows for integration of simple tabular arrays (e.g., csv files) and creation of sharable and interoperable network Common Data Form (netCDF) files containing all the needed information for accuracy-of-use, rightful attribution (ensuring data providers keep ownership through the entire process), and data preservation security. We show the standardisation benefits for all stakeholders involved, and illustrate the application of our framework by focusing on marine animals and by providing examples of the workflow across all data levels, providing data examples, including filled templates and code to process data between levels, as well as templates to prepare netCDF files ready for sharing. Adoption of our framework will facilitate collection of Essential Ocean Variables (EOVs) in support of the Global Ocean Observing System (GOOS) and inter-governmental assessments (e.g., the World Ocean Assessment), and will provide a starting point for broader efforts to establish interoperable bio-logging data formats across all fields in animal ecology.
  • Implications of nest relocation for morphology and locomotor performance of green turtle (Chelonia mydas) hatchlings

    Tanabe, Lyndsey K.; Steenacker, Marion; Rusli, Mohd Uzair; Berumen, Michael L. (Ocean & Coastal Management, Elsevier BV, 2021-03-14) [Article]
    Sea turtle scute abnormalities are observed in higher proportion in hatchlings compared to adults, suggesting that hatchlings with a non-modal scute pattern (NMSP) have a lower chance of surviving to adulthood. In this study, we collected 732 newly emerged hatchlings from Redang Island, Malaysia, and compared their scute classification, size, and mass to fitness correlates (self-righting ability, crawling speed, and swimming speed). We investigated the proportion of hatchlings from each nest with NMSP to determine if there was a correlation with incubation duration or clutch relocation. We found relocated clutches at Chagar Hutang Turtle Sanctuary had a significantly shorter incubation duration with a higher proportion of NMSP compared to in situ clutches. Hatchlings’ mass were significantly heavier from in situ clutches compared to relocated clutches, although there were no significant differences of hatchling speed based on scute classification or clutch type. The difference of hatchling mass between in situ and relocated clutches could affect predation and mortality rates on recently emerged hatchlings. These findings have important conservation implications, suggesting that relocation should only be implemented on clutches with a high potential to be disrupted or with a low chance of survival if left in situ. Our findings highlight the need for a standard procedure when clutch relocation is used as a conservation strategy. Relocation should replicate natural nest dimensions by duplicating both nest width and depth, and clutches should be relocated to similar shade conditions as the natural nest.
  • A bibliometric assessment of progress in marine spatial planning

    Chalastani, Vasiliki I.; Tsoukala, Vasiliki K.; Coccossis, Harry; Duarte, Carlos M. (Marine Policy, Elsevier BV, 2021-03-13) [Article]
    Marine/maritime spatial planning (MSP) is a process to optimise marine space allocation to various activities and the environment by avoiding negative interactions, improving synergies, thereby helping the advance towards a sustainable ocean economy. A bibliometric progress assessment of MSP was performed for the period 2003–2019 to analyse 1323 papers published in the ISI Web of Science and Scopus databases. The analysis revealed that MSP is a relatively new, however rapidly growing research field, as the number of MSP publications increased exponentially, at about 44% per year, between 2003 and 2019. The dominance of the journal “Marine Policy” on MSP publications and the presence of leading authors with government-related positions (i.e. 11%, n = 981) indicate the linkage of MSP to policy and governance. Almost 70% of the MSP publications are case-based indicating MSP's practical orientation. More than half of the authors leading MSP publications are affiliated in Europe, while the majority of reported MSP case studies are undertaken within the European Union. Most, 63%, of all MSP studies (n = 1323) approach the matter in a qualitative manner, whereas only 22% of the quantitative and/or modelling studies (n = 489) are describing MSP applications, suggesting that the development of MSP quantitative and/or modelling methodologies is still at its infancy. The dominance of ecologists among the leading authors of MSP publications outlines the ecosystem-based approach used to address MSP. This bibliometric study draws the landscape of the current state and trends of MSP, outlines gaps and indicates the roadmap for further developments to assist MSP processes.
  • Climate-driven impacts of exotic species on marine ecosystems

    Bennett, Scott; Santana-Garcon, Julia; Marbà, Núria; Jorda, Gabriel; Anton Gamazo, Andrea; Apostolaki, Eugenia T; Cebrian, Just; Geraldi, Nathan; Krause-Jensen, Dorte; Lovelock, Catherine E; Martinetto, Paulina; Pandolfi, John M.; Duarte, Carlos M. (Global Ecology and Biogeography, Wiley, 2021-03-12) [Article]
    Aim: Temperature is fundamental to the physiological and ecological performance of marine organisms, but its role in modulating the magnitude of ecological impacts by exotic species remains unresolved. Here, we examine the relationship between thermal regimes in the range of origin of marine exotic species and sites of measured impact, after human-induced introduction. We compare this relationship with the magnitude of impact exerted by exotic species on native ecosystems. Location: Global. Time period: 1977–2017 (meta-analysis). Major taxa studied: Marine exotic species. Methods: Quantitative impacts of exotic species in marine ecosystems were obtained from a global database. The native range of origin of exotic species was used to estimate the realized thermal niche for each species and compared with the latitude and climatic conditions in recipient sites of recorded impact of exotic species. The difference in median temperatures between recipient sites and the thermal range of origin (i.e., thermal midpoint anomaly) was compared with the magnitude of effect sizes by exotic species on native species, communities and ecosystems. Results: Recorded impacts occurred predominantly within the thermal niche of origin of exotic species, albeit with a tendency toward higher latitudes and slightly cooler conditions. The severity of impacts by exotic species on abundance of native taxa displayed a hump-shaped relationship with temperature. Peak impacts were recorded in recipient sites that were 2.2°C cooler than the thermal midpoint of the range of origin of exotic species, and impacts decreased in magnitude toward higher and lower thermal anomalies. Main conclusions: Our findings highlight how temperature and climatic context influence ecological impacts by exotic species in marine ecosystems and the implications for existing and novel species interactions under climate change.
  • Fish Growth Trajectory Tracking via Reinforcement Learning in Precision Aquaculture

    Chahid, Abderrazak; Ndoye, Ibrahima; Majoris, John E.; Berumen, Michael L.; Laleg-Kirati, Taous-Meriem (arXiv, 2021-03-12) [Preprint]
    This paper studies the fish growth trajectory tracking via reinforcement learning under a representative bioenergetic growth model. Due to the complex aquaculture condition and uncertain environmental factors such as temperature, dissolved oxygen, un-ionized ammonia, and strong nonlinear couplings, including multi-inputs of the fish growth model, the growth trajectory tracking problem can not be efficiently solved by the model-based control approaches in precision aquaculture. To this purpose, we formulate the growth trajectory tracking problem as sampled-data optimal control using discrete state-action pairs Markov decision process. We propose two Q-learning algorithms that learn the optimal control policy from the sampled data of the fish growth trajectories at every stage of the fish life cycle from juveniles to the desired market weight in the aquaculture environment. The Q-learning scheme learns the optimal feeding control policy to fish growth rate cultured in cages and the optimal feeding rate control policy with an optimal temperature profile for the aquaculture fish growth rate in tanks. The simulation results demonstrate that both Q-learning strategies achieve high trajectory tracking performance with less amount feeding rates.
  • Red Sea fish market assessments indicate high species diversity and potential overexploitation

    Shellem, Claire T.; Ellis, Joanne; Coker, Darren James; Berumen, Michael L. (Fisheries Research, Elsevier BV, 2021-03-11) [Article]
    In many parts of the world, particularly remote and underdeveloped regions, reports of fisheries catch, effort, and landing data are limited. In order to implement effective fishing regulations to protect natural stocks, understanding fishing pressure, key target species, catch composition, and value of each species is vital. In regions where published data is limited, and the sampling of numerous small boats and landing sites is not feasible, fish market surveys represent an opportunity to obtain key fisheries data. This study therefore aims to obtain species-specific prices and market composition for fish landed in the central Red Sea by surveying local fish markets. We conducted 11 surveys at two major Red Sea fish markets to ascertain key fisheries metrics using market data as a proxy for catch data. Results indicate that a high proportion of the market composition is generated by 46 species from six family-level groups, Serranidae, Labridae, scarine labrids, Carangidae, Lethrinidae, and Lutjanidae, contributing to 87 % of the total market biomass. Species-specific values ranged from 4.50 USD/kg to 26.44 USD/kg, with market surveys highlighting the economic value of three local serranid species: Plectropomus pessuliferus marisrubri, Plectropomus areolatus and Variola louti, all valued at more than 25 USD/kg, and a labrid: Cheilinus undulatus, valued at 26.44 USD/kg. The Serranidae family represents 47 % of the total biomass and 55 % of the potential revenue in the market, while also indicating potentially overfished reefs due to the high occurrence of smaller species and undersized individuals of higher priced serranid species. Many of the high-valued serranids were below the size at sexual maturity. Target species exhibited small body size and decreasing abundance, potentially indicating a “shrinking baseline” scenario occurring in the Saudi Arabian artisanal coral reef fishery. These results indicate that introducing effective fisheries legislation and management is necessary for the longevity and sustainability of the reef-based fishery in the Saudi Arabian Red Sea. Implementing catch quotas, size limits, and seasonal restrictions are potential mechanisms that could be used to facilitate positive change within this vulnerable fishery.
  • Flexibility in Red Sea Tridacna maxima -Symbiodiniaceae associations supports environmental niche adaptation

    Rossbach, Susann; Hume, Benjamin; Cardenas, Anny; Perna, Gabriela; Voolstra, Christian R.; Duarte, Carlos M. (Ecology and Evolution, Wiley, 2021-03-11) [Article]
    Giant clams (Tridacninae) are important members of Indo-Pacific coral reefs and among the few bivalve groups that live in symbiosis with unicellular algae (Symbiodiniaceae). Despite the importance of these endosymbiotic dinoflagellates for clam ecology, the diversity and specificity of these associations remain relatively poorly studied, especially in the Red Sea. Here, we used the internal transcribed spacer 2 (ITS2) rDNA gene region to investigate Symbiodiniaceae communities associated with Red Sea Tridacna maxima clams. We sampled five sites spanning 1,300 km (10° of latitude, from the Gulf of Aqaba, 29°N, to the Farasan Banks, 18°N) along the Red Sea's North-South environmental gradient. We detected a diverse and structured assembly of host-associated algae with communities demonstrating region and site-specificity. Specimens from the Gulf of Aqaba harbored three genera of Symbiodiniaceae, Cladocopium, Durusdinium, and Symbiodinium, while at all other sites clams associated exclusively with algae from the Symbiodinium genus. Of these exclusively Symbiodinium-associating sites, the more northern (27° and 22°) and more southern sites (20° and 18°) formed two separate groupings despite site-specific algal genotypes being resolved at each site. These groupings were congruent with the genetic break seen across multiple marine taxa in the Red Sea at approximately 19°, and along with our documented site-specificity of algal communities, contrasted the panmictic distribution of the T. maxima host. As such, our findings indicate flexibility in T. maxima-Symbiodiniaceae associations that may explain its relatively high environmental plasticity and offers a mechanism for environmental niche adaptation.
  • Flexibility in Red Sea Tridacna maxima -Symbiodiniaceae associations supports environmental niche adaptation

    Rossbach, Susann; Hume, Benjamin; Cardenas, Anny; Perna, Gabriela; Voolstra, Christian R.; Duarte, Carlos M. (Ecology and Evolution, Wiley, 2021-03-11) [Article]
    Giant clams (Tridacninae) are important members of Indo-Pacific coral reefs and among the few bivalve groups that live in symbiosis with unicellular algae (Symbiodiniaceae). Despite the importance of these endosymbiotic dinoflagellates for clam ecology, the diversity and specificity of these associations remain relatively poorly studied, especially in the Red Sea. Here, we used the internal transcribed spacer 2 (ITS2) rDNA gene region to investigate Symbiodiniaceae communities associated with Red Sea Tridacna maxima clams. We sampled five sites spanning 1,300 km (10° of latitude, from the Gulf of Aqaba, 29°N, to the Farasan Banks, 18°N) along the Red Sea's North-South environmental gradient. We detected a diverse and structured assembly of host-associated algae with communities demonstrating region and site-specificity. Specimens from the Gulf of Aqaba harbored three genera of Symbiodiniaceae, Cladocopium, Durusdinium, and Symbiodinium, while at all other sites clams associated exclusively with algae from the Symbiodinium genus. Of these exclusively Symbiodinium-associating sites, the more northern (27° and 22°) and more southern sites (20° and 18°) formed two separate groupings despite site-specific algal genotypes being resolved at each site. These groupings were congruent with the genetic break seen across multiple marine taxa in the Red Sea at approximately 19°, and along with our documented site-specificity of algal communities, contrasted the panmictic distribution of the T. maxima host. As such, our findings indicate flexibility in T. maxima-Symbiodiniaceae associations that may explain its relatively high environmental plasticity and offers a mechanism for environmental niche adaptation.
  • Inclusivity is key to progressing coral biodiversity research: Reply to comment by Bonito et al. 2021.

    Wepfer, Patricia H; Nakajima, Yuichi; Sutthacheep, Makamas; Radice, Veronica Z; Richards, Zoe; Ang, Put; Terraneo, Tullia Isotta; Fujimura, Atsushi; Toonen, Robert J; Mikheyev, Alexander S; Mitarai, Satoshi; Economo, Evan P (Molecular phylogenetics and evolution, Elsevier BV, 2021-03-08) [Article]
    1.1. Wepfer et al. reply to comment by Bonito et al. 2021 Bonito et al. (2021) provide a wide-ranging critique of our recent phylogeographic study (Wepfer et al. 2020) of the coral genus Galaxea, using the opportunity to offer their views about best practices in coral taxonomy and related topics. First of all, we agree with Bonito et al. that our original paper did not provide adequate information about the specimen vouchers. However, photographs and polyp samples were taken in the field, and 69 of the samples have colony fragments linked to museum accessions or are publicly available through research institutions. We have now deposited the photos and data for our study in a Dryad archive (https://doi.org/10.5061/dryad.vdncjsxsr), but the fact that this archive was not associated with the paper initially is an oversight on our part. For logistical and practical reasons, it was not possible to take skeletal samples from many regions. We agree with Bonito et al. that this situation is not ideal, as we discussed in our original paper, and the gold standard for evolutionary studies is to produce vouchered museum collections that can be used for other work such as taxonomic revisions. Other recent studies on coral phylogenetics (e.g., Cowman et al., 2020) have lacked museum-vouchered specimen information, photographs of all the sequenced specimens, or remarks about specific morphological differences in relation to comparative type material, so we all must strive to improve this situation in the future.
  • Enabling a large-scale assessment of litter along Saudi Arabian red sea shores by combining drones and machine learning.

    Martin, Cecilia; Zhang, Qiannan; Zhai, Dongjun; Zhang, Xiangliang; Duarte, Carlos M. (Environmental pollution (Barking, Essex : 1987), Elsevier BV, 2021-03-02) [Article]
    Beach litter assessments rely on time inefficient and high human cost protocols, mining the attainment of global beach litter estimates. Here we show the application of an emerging technique, the use of drones for acquisition of high-resolution beach images coupled with machine learning for their automatic processing, aimed at achieving the first national-scale beach litter survey completed by only one operator. The aerial survey had a time efficiency of 570 ± 40 m2 min-1 and the machine learning reached a mean (±SE) detection sensitivity of 59 ± 3% with high resolution images. The resulting mean (±SE) litter density on Saudi Arabian shores of the Red Sea is of 0.12 ± 0.02 litter items m-2, distributed independently of the population density in the area around the sampling station. Instead, accumulation of litter depended on the exposure of the beach to the prevailing wind and litter composition differed between islands and the main shore, where recreational activities are the major source of anthropogenic debris.
  • Integrative systematics of the scleractinian coral genera Caulastraea, Erythrastrea and Oulophyllia

    Arrigoni, Roberto; Huang, Danwei; Berumen, Michael L.; Budd, Ann F.; Montano, Simone; Richards, Zoe; Terraneo, Tullia Isotta; Benzoni, Francesca (Zoologica Scripta, Wiley, 2021-03-02) [Article]
    Modern systematics integrating molecular and morphological data has greatly improved our understanding of coral evolutionary relationships during the last two decades and led to a deeply revised taxonomy of the order Scleractinia. The family Merulinidae (Cnidaria: Scleractinia) was recently subjected to a series of revisions following this integrated approach but the phylogenetic affinities of several genera ascribed to it remain unknown. Here, we partially fill this gap through the study of 89 specimens belonging to all 10 valid species from four genera (Caulastraea, Erythrastrea, Oulophyllia and Dipsastraea) collected from 14 localities across the Indo-Pacific realm. Four molecular loci (histone H3, COI, ITS and IGR) were sequenced, and a total of 44 skeletal morphological characters (macromorphology, micromorphology and microstructure) were analysed. Molecular phylogenetic analyses revealed that the phaceloid Caulastraea species are split into two distinct lineages. A species previously ascribed to the genus Dipsastraea, Dipsastraea maxima, is also recovered in one on these lineages. Furthermore, Erythrastrea is nested within Oulophyllia. The molecular reconstructions of evolutionary relationships are further corroborated by multiscale morphological evidence. To resolve the taxonomy of these genera, Astraeosmilia is resurrected to accommodate Astraeosmilia connata, Astraeosmilia curvata, Astraeosmilia tumida and Astraeosmilia maxima, with Caulastraea retaining Caulastraea furcata and Caulastraea echinulata. Based on the examination of type material, Erythrastrea flabellata is considered an objective synonym of Lobophyllia wellsi, which is transferred to Oulophyllia following the obtained morpho-molecular results. This work further confirms that an integrated morpho-molecular approach based on a rigorous phylogenetic framework is fundamental for an objective classification that reflects the evolutionary history of scleractinian corals.
  • Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline

    Michoud, Gregoire; Ngugi, David; Barozzi, Alan; Merlino, Giuseppe; Calleja Cortes, Maria de Lluch; Delgado-Huertas, Antonio; Moran, Xose Anxelu G.; Daffonchio, Daniele (The ISME Journal, Springer Science and Business Media LLC, 2021-03-01) [Article]
    AbstractDeep-sea hypersaline anoxic basins are polyextreme environments in the ocean’s interior characterized by the high density of brines that prevents mixing with the overlaying seawater, generating sharp chemoclines and redoxclines up to tens of meters thick that host a high concentration of microbial communities. Yet, a fundamental understanding of how such pycnoclines shape microbial life and the associated biogeochemical processes at a fine scale, remains elusive. Here, we applied high-precision sampling of the brine–seawater transition interface in the Suakin Deep, located at 2770 m in the central Red Sea, to reveal previously undocumented fine-scale community structuring and succession of metabolic groups along a salinity gradient only 1 m thick. Metagenomic profiling at a 10-cm-scale resolution highlighted spatial organization of key metabolic pathways and corresponding microbial functional units, emphasizing the prominent role and significance of salinity and oxygen in shaping their ecology. Nitrogen cycling processes are especially affected by the redoxcline with ammonia oxidation processes being taxa and layers specific, highlighting also the presence of novel microorganisms, such as novel Thaumarchaeota and anammox, adapted to the changing conditions of the chemocline. The findings render the transition zone as a critical niche for nitrogen cycling, with complementary metabolic networks, in turn underscoring the biogeochemical complexity of deep-sea brines.
  • Seaweed farms provide refugia from ocean acidification.

    Xiao, Xi; Agusti, Susana; Yu, Yan; Huang, Yuzhou; Chen, Weizhou; Hu, Jing; Li, Chao; Li, Ke; Wei, Fangyi; Lu, Yitian; Xu, Caicai; Chen, Zepan; Liu, Shengping; Zeng, Jiangning; Wu, Jiaping; Duarte, Carlos M. (The Science of the total environment, Elsevier BV, 2021-02-28) [Article]
    Seaweed farming has been proposed as a strategy for adaptation to ocean acidification, but evidence is largely lacking. Changes of pH and carbon system parameters in surface waters of three seaweed farms along a latitudinal range in China were compared, on the weeks preceding harvesting, with those of the surrounding seawaters. Results confirmed that seaweed farming is efficient in buffering acidification, with Saccharina japonica showing the highest capacity of 0.10 pH increase within the aquaculture area, followed by Gracilariopsis lemaneiformis (ΔpH = 0.04) and Porphyra haitanensis (ΔpH = 0.03). The ranges of pH variability within seaweed farms spanned 0.14-0.30 unit during the monitoring, showing intense fluctuations which may also help marine organisms adapt to enhanced pH temporal variations in the future ocean. Deficit in pCO2 in waters in seaweed farms relative to control waters averaged 58.7 ± 15.9 μatm, ranging from 27.3 to 113.9 μatm across farms. However, ΔpH did not significantly differ between day and night. Dissolved oxygen and Ωarag were also elevated in surface waters at all seaweed farms, which are benefit for the survival of calcifying organisms. Seaweed farming, which unlike natural seaweed forests, is scalable and is not dependent on suitable substrate or light availability, could serve as a low-cost adaptation strategy to ocean acidification and deoxygenation and provide important refugia from ocean acidification.
  • The global network of ports supporting high seas fishing

    Rodríguez, J. P.; Fernández-Gracia, Juan; Duarte, Carlos M.; Irigoien, Xabier; Eguíluz, V. M. (Science Advances, American Association for the Advancement of Science (AAAS), 2021-02-26) [Article]
    Fisheries in waters beyond national jurisdiction (“high seas”) are difficult to monitor and manage. Their regulation for sustainability requires critical information on how fishing effort is distributed across fishing and landing areas, including possible border effects at the exclusive economic zone (EEZ) limits. We infer the global network linking harbors supporting fishing vessels to fishing areas in high seas from automatic identification system tracking data in 2014, observing a modular structure, with vessels departing from a given harbor fishing mostly in a single province. The top 16% of these harbors support 84% of fishing effort in high seas, with harbors in low- and middle-income countries ranked among the top supporters. Fishing effort concentrates along narrow strips attached to the boundaries of EEZs with productive fisheries, identifying a free-riding behavior that jeopardizes efforts by nations to sustainably manage their fisheries, perpetuating the tragedy of the commons affecting global fishery resources.
  • Influences of physical and biogeochemical variability of the central Red Sea during winter.

    Zarokanellos, Nikolaos; Jones, Burton (Journal of Geophysical Research: Oceans, American Geophysical Union (AGU), 2021-02-14) [Article]
    The central Red Sea (CRS) has been characterized by significant eddy activity throughout the year. Weakened wintertime stratification contributes to enhanced vertical exchange. In winter 2014-2015, an extended glider time series in the CRS captured this variability. Surface cooling and stronger winds resulted in deepening of the mixed layer (ML) to nearly 90 m. The vertical distributions of density and oxygen suggest that the ML did not penetrate into the nutricline. However, mixing events dispersed phytoplankton from the deep CHL maximum (DCM) throughout the ML increasing nearsurface chlorophyll. Following the mixing events a mesoscale cyclonic eddy (CE) grew and intensified causing weakening of stratification and a decrease in the ML depth within the eddy. Where the CE interfaced with an adjacent anticyclonic eddy (AE), the CE DCM subducted beneath the shallower AE DCM leading to a local integrated chlorophyll maximum. Low salinity water containing relative high chlorophyll and CDOM concentrations, originating from the Gulf of Aden, appeared in late winter. Mesoscale eddy activity resulted in an 160 m upward displacement of the nutricline to ∼60 m, well within the euphotic layer. Remote sensing imagery indicates that these eddies contribute to horizontal dispersion, including exchange between the open sea and coastal coral reefs. When the phytoplankton is distributed through the ML, clear diel variability was evident in the temporal CHL distribution. Because not all of the biogeochemical responses were apparent at the surface, sustained glider observations were essential to understand the temporal and spatial scales and their impact on these processes.

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