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Sbrana A, Maiello G, Gravina MF, Cicala D, Galli S, Stefani M, Russo T. Environmental DNA metabarcoding reveals the effects of seafloor litter and trawling on marine biodiversity. MARINE ENVIRONMENTAL RESEARCH 2024; 196:106415. [PMID: 38395681 DOI: 10.1016/j.marenvres.2024.106415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024]
Abstract
Environmental DNA (eDNA) techniques are emerging as promising tools for monitoring marine communities. However, they have not been applied to study the integrated effects of anthropogenic pressures on marine biodiversity. This study examined the relationships between demersal community species composition, key environmental features, and anthropogenic impacts such as fishing effort and seafloor litter using eDNA data in the central Tyrrhenian Sea. The results indicated that both fishing effort and seafloor litter influenced species composition and diversity. The adaptive traits of marine species played a critical role in their response to debris accumulation and fishing. Mobile species appeared to use relocation strategies, while sessile species showed flexibility in the face of disturbance. Epibiotic species relied on passive transport. The use of eDNA-based methods is a valuable resource for monitoring anthropogenic impacts during scientific surveys, enhancing our ability to monitor marine ecosystems and more effectively assess the effects of pollution.
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Affiliation(s)
- Alice Sbrana
- Laboratory of Experimental Ecology and Aquaculture - Department of Biology - University of Rome "Tor Vergata", via della Ricerca Scientifica snc, 00133, Rome, Italy; PhD program in Evolutionary Biology and Ecology, University of Rome Tor Vergata, via della Ricerca Scientifica 1, 00133, Rome, Italy.
| | - Giulia Maiello
- School of Biological and Environmental Sciences, Liverpool John Moores University, L33AF, Liverpool, UK
| | - Maria Flavia Gravina
- Laboratory of Experimental Ecology and Aquaculture - Department of Biology - University of Rome "Tor Vergata", via della Ricerca Scientifica snc, 00133, Rome, Italy; CoNISMa, Piazzale Flaminio 9, 00196, Rome, Italy
| | - Davide Cicala
- Laboratory of Experimental Ecology and Aquaculture - Department of Biology - University of Rome "Tor Vergata", via della Ricerca Scientifica snc, 00133, Rome, Italy
| | - Simone Galli
- CoNISMa, Piazzale Flaminio 9, 00196, Rome, Italy
| | - Matteo Stefani
- Laboratory of Experimental Ecology and Aquaculture - Department of Biology - University of Rome "Tor Vergata", via della Ricerca Scientifica snc, 00133, Rome, Italy; PhD program in Evolutionary Biology and Ecology, University of Rome Tor Vergata, via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Tommaso Russo
- Laboratory of Experimental Ecology and Aquaculture - Department of Biology - University of Rome "Tor Vergata", via della Ricerca Scientifica snc, 00133, Rome, Italy; CoNISMa, Piazzale Flaminio 9, 00196, Rome, Italy
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Picardi G, Astolfi A, Chatzievangelou D, Aguzzi J, Calisti M. Underwater legged robotics: review and perspectives. BIOINSPIRATION & BIOMIMETICS 2023; 18. [PMID: 36863018 DOI: 10.1088/1748-3190/acc0bb] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/02/2023] [Indexed: 05/09/2023]
Abstract
Nowadays, there is a growing awareness on the social and economic importance of the ocean. In this context, being able to carry out a diverse range of operations underwater is of paramount importance for many industrial sectors as well as for marine science and to enforce restoration and mitigation actions. Underwater robots allowed us to venture deeper and for longer time into the remote and hostile marine environment. However, traditional design concepts such as propeller driven remotely operated vehicles, autonomous underwater vehicles, or tracked benthic crawlers, present intrinsic limitations, especially when a close interaction with the environment is required. An increasing number of researchers are proposing legged robots as a bioinspired alternative to traditional designs, capable of yielding versatile multi-terrain locomotion, high stability, and low environmental disturbance. In this work, we aim at presenting the new field of underwater legged robotics in an organic way, discussing the prototypes in the state-of-the-art and highlighting technological and scientific challenges for the future. First, we will briefly recap the latest developments in traditional underwater robotics from which several technological solutions can be adapted, and on which the benchmarking of this new field should be set. Second, we will the retrace the evolution of terrestrial legged robotics, pinpointing the main achievements of the field. Third, we will report a complete state of the art on underwater legged robots focusing on the innovations with respect to the interaction with the environment, sensing and actuation, modelling and control, and autonomy and navigation. Finally, we will thoroughly discuss the reviewed literature by comparing traditional and legged underwater robots, highlighting interesting research opportunities, and presenting use case scenarios derived from marine science applications.
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Affiliation(s)
- G Picardi
- Instituto de Ciencias del Mar (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), 08003 Barcelona, Spain
- The BioRobotics Institute, Scuola Superiore Sant'Anna, 56127 Pisa, Italy
- Department of Excellence in Robotics & AI, Scuola Superiore Sant'Anna, 56127 Pisa, Italy
| | - A Astolfi
- The BioRobotics Institute, Scuola Superiore Sant'Anna, 56127 Pisa, Italy
- Department of Excellence in Robotics & AI, Scuola Superiore Sant'Anna, 56127 Pisa, Italy
| | - D Chatzievangelou
- Instituto de Ciencias del Mar (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), 08003 Barcelona, Spain
| | - J Aguzzi
- Instituto de Ciencias del Mar (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), 08003 Barcelona, Spain
| | - M Calisti
- Lincoln Institute for Agri-Food Technology, University of Lincoln, Lincoln LN6 7TS, United Kingdom
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Stępień A, Mühlenhardt-Siegel U, Błażewicz M. Diversity of and biogeographic insights into the Atlantic Eocuma (Cumacea: Peracarida). THE EUROPEAN ZOOLOGICAL JOURNAL 2022. [DOI: 10.1080/24750263.2022.2102680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
Affiliation(s)
- A. Stępień
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - U. Mühlenhardt-Siegel
- Universität Hamburg, Leibniz-Institut zur Analyse des Biodiversitätswandels – Standort Hamburg, Hamburg, Germany
| | - M. Błażewicz
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
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4
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Fast and accurate mapping of fine scale abundance of a VME in the deep sea with computer vision. ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2022.101786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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Underwater Hyperspectral Imaging (UHI): A Review of Systems and Applications for Proximal Seafloor Ecosystem Studies. REMOTE SENSING 2021. [DOI: 10.3390/rs13173451] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Marine ecosystem monitoring requires observations of its attributes at different spatial and temporal scales that traditional sampling methods (e.g., RGB imaging, sediment cores) struggle to efficiently provide. Proximal optical sensing methods can fill this observational gap by providing observations of, and tracking changes in, the functional features of marine ecosystems non-invasively. Underwater hyperspectral imaging (UHI) employed in proximity to the seafloor has shown a further potential to monitor pigmentation in benthic and sympagic phototrophic organisms at small spatial scales (mm–cm) and for the identification of minerals and taxa through their finely resolved spectral signatures. Despite the increasing number of studies applying UHI, a review of its applications, capabilities, and challenges for seafloor ecosystem research is overdue. In this review, we first detail how the limited band availability inherent to standard underwater cameras has led to a data analysis “bottleneck” in seafloor ecosystem research, in part due to the widespread implementation of underwater imaging platforms (e.g., remotely operated vehicles, time-lapse stations, towed cameras) that can acquire large image datasets. We discuss how hyperspectral technology brings unique opportunities to address the known limitations of RGB cameras for surveying marine environments. The review concludes by comparing how different studies harness the capacities of hyperspectral imaging, the types of methods required to validate observations, and the current challenges for accurate and replicable UHI research.
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Cordier T, Alonso‐Sáez L, Apothéloz‐Perret‐Gentil L, Aylagas E, Bohan DA, Bouchez A, Chariton A, Creer S, Frühe L, Keck F, Keeley N, Laroche O, Leese F, Pochon X, Stoeck T, Pawlowski J, Lanzén A. Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap. Mol Ecol 2021; 30:2937-2958. [PMID: 32416615 PMCID: PMC8358956 DOI: 10.1111/mec.15472] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/25/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023]
Abstract
A decade after environmental scientists integrated high-throughput sequencing technologies in their toolbox, the genomics-based monitoring of anthropogenic impacts on the biodiversity and functioning of ecosystems is yet to be implemented by regulatory frameworks. Despite the broadly acknowledged potential of environmental genomics to this end, technical limitations and conceptual issues still stand in the way of its broad application by end-users. In addition, the multiplicity of potential implementation strategies may contribute to a perception that the routine application of this methodology is premature or "in development", hence restraining regulators from binding these tools into legal frameworks. Here, we review recent implementations of environmental genomics-based methods, applied to the biomonitoring of ecosystems. By taking a general overview, without narrowing our perspective to particular habitats or groups of organisms, this paper aims to compare, review and discuss the strengths and limitations of four general implementation strategies of environmental genomics for monitoring: (a) Taxonomy-based analyses focused on identification of known bioindicators or described taxa; (b) De novo bioindicator analyses; (c) Structural community metrics including inferred ecological networks; and (d) Functional community metrics (metagenomics or metatranscriptomics). We emphasise the utility of the three latter strategies to integrate meiofauna and microorganisms that are not traditionally utilised in biomonitoring because of difficult taxonomic identification. Finally, we propose a roadmap for the implementation of environmental genomics into routine monitoring programmes that leverage recent analytical advancements, while pointing out current limitations and future research needs.
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Affiliation(s)
- Tristan Cordier
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
| | - Laura Alonso‐Sáez
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
| | | | - Eva Aylagas
- Red Sea Research Center (RSRC)Biological and Environmental Sciences and Engineering (BESE)King Abdullah University of Science and Technology (KAUST)ThuwalSaudi Arabia
| | - David A. Bohan
- AgroécologieINRAEUniversity of BourgogneUniversity Bourgogne Franche‐ComtéDijonFrance
| | | | - Anthony Chariton
- Department of Biological SciencesMacquarie UniversitySydneyNSWAustralia
| | - Simon Creer
- School of Natural SciencesBangor UniversityGwyneddUK
| | - Larissa Frühe
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | | | - Nigel Keeley
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Olivier Laroche
- Benthic Resources and Processes GroupInstitute of Marine ResearchTromsøNorway
| | - Florian Leese
- Aquatic Ecosystem ResearchFaculty of BiologyUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Xavier Pochon
- Coastal & Freshwater GroupCawthron InstituteNelsonNew Zealand
- Institute of Marine ScienceUniversity of AucklandWarkworthNew Zealand
| | - Thorsten Stoeck
- Department of EcologyTechnische Universität KaiserslauternKaiserslauternGermany
| | - Jan Pawlowski
- Department of Genetics and EvolutionScience IIIUniversity of GenevaGenevaSwitzerland
- ID‐Gene EcodiagnosticsGenevaSwitzerland
- Institute of OceanologyPolish Academy of SciencesSopotPoland
| | - Anders Lanzén
- AZTIMarine ResearchBasque Research and Technology Alliance (BRTA)Spain
- Basque Foundation for ScienceIKERBASQUEBilbaoSpain
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Aguzzi J, Flexas MM, Flögel S, Lo Iacono C, Tangherlini M, Costa C, Marini S, Bahamon N, Martini S, Fanelli E, Danovaro R, Stefanni S, Thomsen L, Riccobene G, Hildebrandt M, Masmitja I, Del Rio J, Clark EB, Branch A, Weiss P, Klesh AT, Schodlok MP. Exo-Ocean Exploration with Deep-Sea Sensor and Platform Technologies. ASTROBIOLOGY 2020; 20:897-915. [PMID: 32267735 DOI: 10.1089/ast.2019.2129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
One of Saturn's largest moons, Enceladus, possesses a vast extraterrestrial ocean (i.e., exo-ocean) that is increasingly becoming the hotspot of future research initiatives dedicated to the exploration of putative life. Here, a new bio-exploration concept design for Enceladus' exo-ocean is proposed, focusing on the potential presence of organisms across a wide range of sizes (i.e., from uni- to multicellular and animal-like), according to state-of-the-art sensor and robotic platform technologies used in terrestrial deep-sea research. In particular, we focus on combined direct and indirect life-detection capabilities, based on optoacoustic imaging and passive acoustics, as well as molecular approaches. Such biologically oriented sampling can be accompanied by concomitant geochemical and oceanographic measurements to provide data relevant to exo-ocean exploration and understanding. Finally, we describe how this multidisciplinary monitoring approach is currently enabled in terrestrial oceans through cabled (fixed) observatories and their related mobile multiparametric platforms (i.e., Autonomous Underwater and Remotely Operated Vehicles, as well as crawlers, rovers, and biomimetic robots) and how their modified design can be used for exo-ocean exploration.
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Affiliation(s)
- J Aguzzi
- Instituto de Ciencias del Mar (ICM-CSIC), Barcelona, Spain
- Stazione Zoologica Anton Dohrn, Naples, Italy
| | - M M Flexas
- California Institute of Technology, Pasadena, California, USA
| | - S Flögel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | - C Lo Iacono
- Instituto de Ciencias del Mar (ICM-CSIC), Barcelona, Spain
- National Oceanographic Center (NOC), University of Southampton, Southampton, United Kingdom
| | | | - C Costa
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria (CREA)-Centro di ricerca Ingegneria e Trasformazioni agroalimentari - Monterotondo, Rome, Italy
| | - S Marini
- Stazione Zoologica Anton Dohrn, Naples, Italy
- National Research Council of Italy (CNR), Institute of Marine Sciences, La Spezia, Italy
| | - N Bahamon
- Instituto de Ciencias del Mar (ICM-CSIC), Barcelona, Spain
- Centro de Estudios Avanzados de Blanes (CEAB-CSIC), Blanes, Spain
| | - S Martini
- Sorbonne Université, CNRS, Laboratoire d'Océanographie de Villefranche, Villefranche-sur-mer, France
| | - E Fanelli
- Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - R Danovaro
- Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - S Stefanni
- Stazione Zoologica Anton Dohrn, Naples, Italy
| | | | - G Riccobene
- Istituto Nazionale di Fisica Nucleare (INFN), Laboratori Nazionali del Sud, Catania, Italy
| | - M Hildebrandt
- German Research Center for Artificial Intelligence (DFKI), Bremen, Germany
| | - I Masmitja
- SARTI, Universitat Politècnica de Catalunya (UPC), Barcelona, Spain
| | - J Del Rio
- SARTI, Universitat Politècnica de Catalunya (UPC), Barcelona, Spain
| | - E B Clark
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - A Branch
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | - A T Klesh
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - M P Schodlok
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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Picardi G, Chellapurath M, Iacoponi S, Stefanni S, Laschi C, Calisti M. Bioinspired underwater legged robot for seabed exploration with low environmental disturbance. Sci Robot 2020; 5:5/42/eaaz1012. [DOI: 10.1126/scirobotics.aaz1012] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 04/06/2020] [Indexed: 12/12/2022]
Abstract
Robots have the potential to assist and complement humans in the study and exploration of extreme and hostile environments. For example, valuable scientific data have been collected with the aid of propeller-driven autonomous and remotely operated vehicles in underwater operations. However, because of their nature as swimmers, such robots are limited when closer interaction with the environment is required. Here, we report a bioinspired underwater legged robot, called SILVER2, that implements locomotion modalities inspired by benthic animals (organisms that harness the interaction with the seabed to move; for example, octopi and crabs). Our robot can traverse irregular terrains, interact delicately with the environment, approach targets safely and precisely, and hold position passively and silently. The capabilities of our robot were validated through a series of field missions in real sea conditions in a depth range between 0.5 and 12 meters.
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Affiliation(s)
- G. Picardi
- The BioRobotics Institute, Scuola Superiore Sant’Anna, Pisa, Italy
- Department of Excellence in Robotics & AI, Scuola Superiore Sant’Anna, Pisa, Italy
| | - M. Chellapurath
- The BioRobotics Institute, Scuola Superiore Sant’Anna, Pisa, Italy
- Department of Excellence in Robotics & AI, Scuola Superiore Sant’Anna, Pisa, Italy
- Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - S. Iacoponi
- The BioRobotics Institute, Scuola Superiore Sant’Anna, Pisa, Italy
- Department of Excellence in Robotics & AI, Scuola Superiore Sant’Anna, Pisa, Italy
| | - S. Stefanni
- Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - C. Laschi
- The BioRobotics Institute, Scuola Superiore Sant’Anna, Pisa, Italy
- Department of Excellence in Robotics & AI, Scuola Superiore Sant’Anna, Pisa, Italy
| | - M. Calisti
- The BioRobotics Institute, Scuola Superiore Sant’Anna, Pisa, Italy
- Department of Excellence in Robotics & AI, Scuola Superiore Sant’Anna, Pisa, Italy
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Ecological variables for developing a global deep-ocean monitoring and conservation strategy. Nat Ecol Evol 2020; 4:181-192. [PMID: 32015428 DOI: 10.1038/s41559-019-1091-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 12/19/2019] [Indexed: 11/09/2022]
Abstract
The deep sea (>200 m depth) encompasses >95% of the world's ocean volume and represents the largest and least explored biome on Earth (<0.0001% of ocean surface), yet is increasingly under threat from multiple direct and indirect anthropogenic pressures. Our ability to preserve both benthic and pelagic deep-sea ecosystems depends upon effective ecosystem-based management strategies and monitoring based on widely agreed deep-sea ecological variables. Here, we identify a set of deep-sea essential ecological variables among five scientific areas of the deep ocean: (1) biodiversity; (2) ecosystem functions; (3) impacts and risk assessment; (4) climate change, adaptation and evolution; and (5) ecosystem conservation. Conducting an expert elicitation (1,155 deep-sea scientists consulted and 112 respondents), our analysis indicates a wide consensus amongst deep-sea experts that monitoring should prioritize large organisms (that is, macro- and megafauna) living in deep waters and in benthic habitats, whereas monitoring of ecosystem functioning should focus on trophic structure and biomass production. Habitat degradation and recovery rates are identified as crucial features for monitoring deep-sea ecosystem health, while global climate change will likely shift bathymetric distributions and cause local extinction in deep-sea species. Finally, deep-sea conservation efforts should focus primarily on vulnerable marine ecosystems and habitat-forming species. Deep-sea observation efforts that prioritize these variables will help to support the implementation of effective management strategies on a global scale.
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10
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Cross-disciplinarity in the advance of Antarctic ecosystem research. Mar Genomics 2018; 37:1-17. [DOI: 10.1016/j.margen.2017.09.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 09/20/2017] [Accepted: 09/20/2017] [Indexed: 01/01/2023]
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11
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Research on climate-change impact on Southern Ocean and Antarctic ecosystems after the UN Paris climate conference—“now more than ever” or “set sail to new shores”? Polar Biol 2016. [DOI: 10.1007/s00300-016-2059-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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