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Recent Submissions

  • Seagrass (Halophila stipulacea) invasion enhances carbon sequestration in the Mediterranean Sea.

    Wesselmann, Marlene; Geraldi, Nathan; Duarte, Carlos M.; Garcia-Orellana, Jordi; Diaz Rua, Ruben; Arias-Ortiz, Ariane; Hendriks, Iris E; Apostolaki, Eugenia T; Marbà, Núria (Global change biology, Wiley, 2021-04-12) [Article]
    The introduction and establishment of exotic species often result in significant changes in recipient communities and their associated ecosystem services. However, usually the magnitude and direction of the changes are difficult to quantify because there is no pre-introduction data. Specifically, little is known about the effect of marine exotic macrophytes on organic carbon sequestration and storage. Here, we combine dating sediment cores (210Pb) with sediment eDNA fingerprinting to reconstruct the chronology of pre- and post-arrival of the Red Sea seagrass Halophila stipulacea spreading into the Eastern Mediterranean native seagrass meadows. We then compare sediment organic carbon storage and burial rates before and after the arrival of H. stipulacea and between exotic (H. stipulacea) and native (C. nodosa and P. oceanica) meadows since the time of arrival following a Before-After-Control-Impact (BACI) approach. This analysis revealed that H. stipulacea arrived at the areas of study in Limassol (Cyprus) and West Crete (Greece) in the 1930s and 1970s, respectively. Average sediment organic carbon after the arrival of H. stipulacea to the sites increased in the exotic meadows twofold, from 8.4 ± 2.5 g Corg m−2 year−1 to 14.7 ± 3.6 g Corg m−2 year−1, and, since then, burial rates in the exotic seagrass meadows were higher than in native ones of Cymodocea nodosa and Posidonia oceanica. Carbon isotopic data indicated a 50% increase of the seagrass contribution to the total sediment Corg pool since the arrival of H. stipulacea. Our results demonstrate that the invasion of H. stipulacea may play an important role in maintaining the blue carbon sink capacity in the future warmer Mediterranean Sea, by developing new carbon sinks in bare sediments and colonizing areas previously occupied by the colder thermal affinity P. oceanica.
  • Surface Topography, Bacterial Carrying Capacity, and the Prospect of Microbiome Manipulation in the Sea Anemone Coral Model Aiptasia

    Martins Da Costa, Ruben; Cárdenas, Anny; Loussert-Fonta, Céline; Toullec, Gaëlle; Meibom, Anders; Voolstra, Christian R. (Frontiers in Microbiology, Frontiers Media SA, 2021-04-08) [Article]
    Aiptasia is an emerging model organism to study cnidarian symbioses due to its taxonomic relatedness to other anthozoans such as stony corals and similarities of its microalgal and bacterial partners, complementing the existing Hydra (Hydrozoa) and Nematostella (Anthozoa) model systems. Despite the availability of studies characterizing the microbiomes of several natural Aiptasia populations and laboratory strains, knowledge on basic information, such as surface topography, bacterial carrying capacity, or the prospect of microbiome manipulation is lacking. Here we address these knowledge gaps. Our results show that the surface topographies of the model hydrozoan Hydra and anthozoans differ substantially, whereas the ultrastructural surface architecture of Aiptasia and stony corals is highly similar. Further, we determined a bacterial carrying capacity of ∼104 and ∼105 bacteria (i.e., colony forming units, CFUs) per polyp for aposymbiotic and symbiotic Aiptasia anemones, respectively, suggesting that the symbiotic status changes bacterial association/density. Microbiome transplants from Acropora humilis and Porites sp. to gnotobiotic Aiptasia showed that only a few foreign bacterial taxa were effective colonizers. Our results shed light on the putative difficulties of transplanting microbiomes between cnidarians in a manner that consistently changes microbial host association at large. At the same time, our study provides an avenue to identify bacterial taxa that exhibit broad ability to colonize different hosts as a starting point for cross-species microbiome manipulation. Our work is relevant in the context of microbial therapy (probiotics) and microbiome manipulation in corals and answers to the need of having cnidarian model systems to test the function of bacteria and their effect on holobiont biology. Taken together, we provide import.
  • A step towards the validation of bacteria biotic indices using DNA metabarcoding for benthic monitoring.

    Aylagas, Eva; Atalah, Javier; Sánchez-Jerez, Pablo; Pearman, John K.; Casado, Nuria; Asensi, Jorge; Toledo-Guedes, Kilian; Carvalho, Susana (Molecular ecology resources, Wiley, 2021-04-07) [Article]
    Environmental genomics is a promising field for monitoring biodiversity in a timely fashion. Efforts have increasingly been dedicated to the use of bacteria DNA derived data to develop biotic indices for benthic monitoring. However, a substantial debate exists about whether bacteria-derived data using DNA metabarcoding should follow, for example, a taxonomy-based or a taxonomy-free approach to marine bioassessments. Here, we show case the value of DNA-based monitoring using the impact of fish farming as an example of anthropogenic disturbances in coastal areas and compare the performance of taxonomy-based and taxonomy-free approaches in detecting environmental alterations. We analyzed samples collected near to the farm cages and along distance gradients from two aquaculture installations, and at control sites, to evaluate the effect of this activity on bacterial assemblages. Using the putative response of bacterial taxa to stress we calculated the taxonomy-based biotic index microgAMBI. Then, the distribution of individual Amplicon Sequence Variants (ASVs), as a function of a gradient in sediment acid volatile sulfides was used to derive a taxonomy-free bacterial biotic index, specific for this dataset, using a de novo approach based on quantile regression splines. Our results show that microgAMBI revealed a organically enriched environment along the gradient. However, the de novo biotic index outperformed microgAMBI by providing a higher discriminatory power in detecting changes in abiotic factors directly related to fish production, whilst allowing the identification of new ASVs bioindicators. The de novo strategy applied here represents a robust method to define new bioindicators in regions or habitats where no previous information about the response of bacteria to environmental stressors exists.
  • 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.
  • Half of global methane emissions come from highly variable aquatic ecosystem sources

    Rosentreter, Judith A.; Borges, Alberto V.; Deemer, Bridget R.; Holgerson, Meredith A.; Liu, Shaoda; Song, Chunlin; Melack, John; Raymond, Peter A.; Duarte, Carlos M.; Allen, George H.; Olefeldt, David; Poulter, Benjamin; Battin, Tom I.; Eyre, Bradley D (Nature Geoscience, Springer Nature, 2021-04-05) [Article]
    Atmospheric methane is a potent greenhouse gas that plays a major role in controlling the Earth’s climate. The causes of the renewed increase of methane concentration since 2007 are uncertain given the multiple sources and complex biogeochemistry. Here, we present a metadata analysis of methane fluxes from all major natural, impacted and human-made aquatic ecosystems. Our revised bottom-up global aquatic methane emissions combine diffusive, ebullitive and/or plant-mediated fluxes from 15 aquatic ecosystems. We emphasize the high variability of methane fluxes within and between aquatic ecosystems and a positively skewed distribution of empirical data, making global estimates sensitive to statistical assumptions and sampling design. We find aquatic ecosystems contribute (median) 41% or (mean) 53% of total global methane emissions from anthropogenic and natural sources. We show that methane emissions increase from natural to impacted aquatic ecosystems and from coastal to freshwater ecosystems. We argue that aquatic emissions will probably increase due to urbanization, eutrophication and positive climate feedbacks and suggest changes in land-use management as potential mitigation strategies to reduce aquatic methane emissions.
  • 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.
  • Coastal circulation and water transport properties of the Red Sea Project lagoon

    Zhan, Peng; Krokos, Georgios; Langodan, Sabique; Guo, Daquan; Dasari, Hari Prasad; Papadopoulos, Vassilis P.; Lermusiaux, Pierre F.J.; Knio, Omar; Hoteit, Ibrahim (Ocean Modelling, Elsevier BV, 2021-03-26) [Article]
    The Red Sea Project (RSP) is based on a coastal lagoon with over 90 pristine islands. The project intends to transform the Red Sea coast into a world-class tourist destination. To better understand the regional dynamics and water exchange scenarios in the lagoon, a high-resolution numerical model is implemented. The general and tidal circulation dynamics are then investigated with a particular focus on the response of the lagoon to strong wind jets. Significant variations in winter and summer circulation patterns are identified. The tidal amplitude inside the lagoon is greater than that outside, with strong tidal currents passing over its surrounding coral reef banks. The lagoon rapidly responds to the strong easterly wind jets that occur mainly in winter; it develops a reverse flow at greater depths, and the coastal water elevation is instantly affected. Lagrangian particle simulations are conducted to study the residence time of water in the lagoon. The results suggest that water renewal is slow in winter. Analysis of the Lagrangian coherent structures (LCS) reveals that water renewal is largely linked to the circulation patterns in the lagoon. In winter, the water becomes restricted in the central lagoon with only moderate exchange, whereas in summer, more circulation is observed with a higher degree of interaction between the central lagoon and external water. The results of LCS also highlight the tidal contribution to stirring and mixing while identifying the hotspots of the phenomenon. Our analysis demonstrates an effective approach for studying regional water mixing and connectivity, which could support coastal management in data-limited regions.
  • Evidence of historical isolation and genetic structuring among broadnose sevengill sharks (Notorynchus cepedianus) from the world’s major oceanic regions

    Schmidt-Roach, Alicia C.J.; Bruels, Christine C.; Barnett, Adam; Miller, Adam D.; Sherman, Craig D.H.; Ebert, David A.; Schmidt-Roach, Sebastian; da Silva, Charlene; Wilke, Christopher G.; Thorburn, Craig; Mangel, Jeffrey C.; Ezcurra, Juan Manuel; Irigoyen, Alejo; Jaureguizar, Andrés Javier; Braccini, Matias; Alfaro-Shigueto, Joanna; Duffy, Clinton; Shivji, Mahmood S. (Reviews in Fish Biology and Fisheries, Springer Nature, 2021-03-26) [Article]
    Cosmopolitan marine pelagic species display variable patterns of population connectivity among the world’s major oceans. While this information is crucial for informing management, information is lacking for many ecologically important species, including apex predators. In this study we examine patterns of genetic structure in the broadnose sevengill shark, Notorynchus cepedianus across its global distribution. We estimate patterns of connectivity among broadnose sevengill shark populations from three major oceanic regions (South Atlantic, Oceania and Eastern Pacific) by contrasting mitochondrial and nuclear DNA haplotype frequencies. We also produced time calibrated Bayesian Inference phylogenetic reconstructions to analyses global phylogeographic patterns and estimate divergence times among distinctive shark lineages. Our results demonstrate significant genetic differentiation among oceanic regions (ΦST = 0.9789, P < 0.0001) and a lack of genetic structuring within regions (ΦST = − 0.007; P = 0.479). Time calibrated Bayesian Inference phylogenetic reconstructions indicate that the observed patterns of genetic structure among oceanic regions are historical, with regional populations estimated to have diverged from a common ancestor during the early to mid-Pleistocene. Our results indicate significant genetic structuring and a lack of gene flow among broadnose sevengill shark populations from the South Atlantic, Oceania and Eastern Pacific regions. Evidence of deep lineage divergences coinciding with the early to mid-Pleistocene suggests historical glacial cycling has contributed to the vicariant divergence of broadnose sevengill shark populations from different ocean basins. These finding will help inform global management of broadnose sevengill shark populations, and provides new insights into historical and contemporary evolutionary processes shaping populations of this ecologically important apex predator.
  • Comparative sensitivity of the early life stages of a coral to heavy fuel oil and UV radiation

    Nordborg, F. Mikaela; Brinkman, Diane L.; Ricardo, Gerard F.; Agusti, Susana; Negri, Andrew P. (Science of the Total Environment, Elsevier BV, 2021-03-23) [Article]
    During an oil spill, shallow, tropical coral reefs are likely to be simultaneously exposed to high intensities of ultraviolet radiation (UVR), which can exacerbate the toxicity of petroleum oils. While successful recruitment of corals is critical for reef recovery following disturbances, the sensitivity of several early life stages of coral to petroleum hydrocarbons has not been investigated, particularly for UVR co-exposure. Here we present the first dataset on the relative sensitivity of three early life stages (gametes, embryos and planula larvae) in a model broadcast spawning coral species, Acropora millepora, to the dissolved fraction of a heavy fuel oil (HFO), both in the absence and presence of UVR. All early life stages were negatively impacted by HFO exposure but exhibited distinct sensitivities. Larval metamorphosis was the most sensitive endpoint assessed with a 10% effect concentration of 34 μg L−1 total aromatic hydrocarbons (TAH) in the absence of UVR. The impact on fertilisation success was highly dependent on sperm density, while the fragmentation of embryos masked embryo mortality. Larval metamorphosis was conclusively the most reliable endpoint for use in risk assessments of the endpoints investigated. Putative critical target lipid body burdens (CTLBBs) were calculated for each life stages, enabling a comparison of their sensitivities against species in the Target Lipid Model (TLM) database. A. millepora had a putative CTLBB of 4.4 μmol g−1 octanol for larval metamorphosis, indicating it is more sensitive than any species currently included in the TLM database. Coexposure to UVR reduced toxicity thresholds by 1.3-fold on average across the investigated life stages and endpoints. This increase in sensitivity in the presence of UVR highlights the need to incorporate UVR co-exposure (where ecologically relevant) when assessing oil toxicity thresholds, otherwise the risks posed by oil spills to shallow coral reefs are likely to be underestimated.
  • Three-dimensional simulation of shoaling internal solitary waves and their influence on particle transport in the southern Red Sea

    Guo, Daquan; Zhan, Peng; Hoteit, Ibrahim (Journal of Geophysical Research: Oceans, American Geophysical Union (AGU), 2021-03-22) [Article]
    The shoaling process of a group of internal solitary waves (ISWs) in the southern Red Sea is simulated with a 3D, non-hydrostatic, high-resolution MIT general circulation model (MITgcm). The breaking and dissipation processes are well reproduced, in which a positive tail forms behind and locally moves the interface upward, causing the transformation of wave polarity as it moves onshore. With the step-like structure followed, the wave eventually evolve into smaller water bores. Combined with the parameters of the leading wave slope (Sw) of about 0.07 and topography slope (S) of about 0.01, the shoaling is suggested to follow a mild breaking process. The particle transport during the shoaling process is further examined quantitatively using the Connectivity modelling system (CMS). 38400 particles are released at six different vertical layers in the main shoaling domain. Most of the particles are transported up-and-down following the wave oscillation process then settle within 10-20 m around the original released depth. For the particles inside the breaking area, the oscillation process becomes more complex and intensified, and eventually a great portion of these particles settle far away from their released locations. The time-integrated transport distance, Ti, and the direct transport distance, Ts, are also analyzed. With Ti almost 20 times to Ts in vertical, continuous up-and-down movements are suggested during the shoaling process.
  • 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 Nature, 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.
  • Ethylene involvement in the regulation of heat stress tolerance in plants.

    Poór, Peter; Nawaz, Kashif; Gupta, Ravi; Ashfaque, Farha; Khan, M Iqbal R (Plant cell reports, Springer Nature, 2021-03-13) [Article]
    Because of the rise in global temperature, heat stress has become a major concern for crop production. Heat stress deteriorates plant productivity and alters phenological and physiological responses that aid in precise monitoring and sensing of mild-to-severe transient heat stress. Plants have evolved several sophisticated mechanisms including hormone-signaling pathways to sense heat stimuli and acquire heat stress tolerance. In response to heat stress, ethylene, a gaseous hormone, is produced which is indispensable for plant growth and development and tolerance to various abiotic stresses including heat stress. The manipulation of ethylene in developing heat stress tolerance targeting ethylene biosynthesis and signaling pathways has brought promising out comes. Conversely increased ethylene biosynthesis and signaling seem to exhibit inhibitory effects in plant growth responses from primitive to maturity stages. This review mainly focuses on the recent studies of ethylene involvement in plant responses to heat stress and its functional regulation, and molecular mechanism underlying the plant responses in the mitigation of heat-induced damages. Furthermore, this review also describes the crosstalk between ethylene and other signaling molecules under heat stress and approaches to improve heat stress tolerance in plants.
  • 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.

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