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  • 1
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    An acquisition, curation and management workflow for sustainable, terabyte-scale marine image analysis (2018)
    Nature Research
    In:  Scientific Data, 5 (180181).
    Details
    Publication Date: 2021-03-19
    Description: Optical imaging is a common technique in ocean research. Diving robots, towed cameras, drop-cameras and TV-guided sampling gear: all produce image data of the underwater environment. Technological advances like 4K cameras, autonomous robots, high-capacity batteries and LED lighting now allow systematic optical monitoring at large spatial scale and shorter time but with increased data volume and velocity. Volume and velocity are further increased by growing fleets and emerging swarms of autonomous vehicles creating big data sets in parallel. This generates a need for automated data processing to harvest maximum information. Systematic data analysis benefits from calibrated, geo-referenced data with clear metadata description, particularly for machine vision and machine learning. Hence, the expensive data acquisition must be documented, data should be curated as soon as possible, backed up and made publicly available. Here, we present a workflow towards sustainable marine image analysis. We describe guidelines for data acquisition, curation and management and apply it to the use case of a multi-terabyte deep-sea data set acquired by an autonomous underwater vehicle.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1038/sdata.2018.181
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 2
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    Sensitivities to global change drivers may correlate positively or negatively in a foundational marine macroalga (2019)
    Nature Research
    In:  Scientific Reports, 9 (1). Art.Nr. 4653.
    Details
    Publication Date: 2022-01-31
    Description: Ecological impact of global change is generated by multiple synchronous or asynchronous drivers which interact with each other and with intraspecific variability of sensitivities. In three near-natural experiments, we explored response correlations of full-sibling germling families of the seaweed Fucus vesiculosus towards four global change drivers: elevated CO2 (ocean acidification, OA), ocean warming (OW), combined OA and warming (OAW), nutrient enrichment and hypoxic upwelling. Among families, performance responses to OA and OW as well as to OAW and nutrient enrichment correlated positively whereas performance responses to OAW and hypoxia anti-correlated. This indicates (i) that families robust to one of the three drivers (OA, OW, nutrients) will also not suffer from the two other shifts, and vice versa and (ii) families benefitting from OAW will more easily succumb to hypoxia. Our results may imply that selection under either OA, OW or eutrophication would enhance performance under the other two drivers but simultaneously render the population more susceptible to hypoxia. We conclude that intraspecific response correlations have a high potential to boost or hinder adaptation to multifactorial global change scenarios.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1038/s41598-019-51099-8
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 3
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    Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals (2017)
    Nature Research
    In:  Scientific Reports, 7 (1). Art.No. 6442.
    Details
    Publication Date: 2020-02-06
    Description: Despite the importance of deep-sea corals, our current understanding of their ecology and evolution is limited due to difficulties in sampling and studying deep-sea environments. Moreover, a recent re-evaluation of habitat limitations has been suggested after characterization of deep-sea corals in the Red Sea, where they live at temperatures of above 20 °C at low oxygen concentrations. To gain further insight into the biology of deep-sea corals, we produced reference transcriptomes and studied gene expression of three deep-sea coral species from the Red Sea, i.e. Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. Our analyses suggest that deep-sea coral employ mitochondrial hypometabolism and anaerobic glycolysis to manage low oxygen conditions present in the Red Sea. Notably, we found expression of genes related to surface cilia motion that presumably enhance small particle transport rates in the oligotrophic deep-sea environment. This is the first study to characterize transcriptomes and in situ gene expression for deep-sea corals. Our work offers several mechanisms by which deep-sea corals might cope with the distinct environmental conditions present in the Red Sea As such, our data provide direction for future research and further insight to organismal response of deep-sea coral to environmental change and ocean warming.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1038/s41598-017-05572-x
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 4
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    Transcriptomes and expression profiling of deep-sea corals from the Red Sea provide insight into the biology of azooxanthellate corals (2017)
    Nature Research
    In:  Scientific Reports, 7 (1). Art.No. 6442.
    Details
    Publication Date: 2020-02-06
    Description: Despite the importance of deep-sea corals, our current understanding of their ecology and evolution is limited due to difficulties in sampling and studying deep-sea environments. Moreover, a recent re-evaluation of habitat limitations has been suggested after characterization of deep-sea corals in the Red Sea, where they live at temperatures of above 20 °C at low oxygen concentrations. To gain further insight into the biology of deep-sea corals, we produced reference transcriptomes and studied gene expression of three deep-sea coral species from the Red Sea, i.e. Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. Our analyses suggest that deep-sea coral employ mitochondrial hypometabolism and anaerobic glycolysis to manage low oxygen conditions present in the Red Sea. Notably, we found expression of genes related to surface cilia motion that presumably enhance small particle transport rates in the oligotrophic deep-sea environment. This is the first study to characterize transcriptomes and in situ gene expression for deep-sea corals. Our work offers several mechanisms by which deep-sea corals might cope with the distinct environmental conditions present in the Red Sea As such, our data provide direction for future research and further insight to organismal response of deep-sea coral to environmental change and ocean warming.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1038/s41598-017-05572-x
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 5
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    Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments (2018)
    Nature Research
    In:  Scientific Data, 5 . p. 180154.
    Details
    Publication Date: 2021-04-23
    Description: Prochlorococcus and Synechococcus are the dominant primary producers in marine ecosystems and perform a significant fraction of ocean carbon fixation. These cyanobacteria interact with a diverse microbial community that coexists with them. Comparative genomics of cultivated isolates has helped address questions regarding patterns of evolution and diversity among microbes, but the fraction that can be cultivated is miniscule compared to the diversity in the wild. To further probe the diversity of these groups and extend the utility of reference sequence databases, we report a data set of single cell genomes for 489 Prochlorococcus, 50 Synechococcus, 9 extracellular virus particles, and 190 additional microorganisms from a diverse range of bacterial, archaeal, and viral groups. Many of these uncultivated single cell genomes are derived from samples obtained on GEOTRACES cruises and at well-studied oceanographic stations, each with extensive suites of physical, chemical, and biological measurements. The genomic data reported here greatly increases the number of available Prochlorococcus genomes and will facilitate studies on evolutionary biology, microbial ecology, and biological oceanography.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1038/sdata.2018.154
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 6
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    Integrating experimental and distribution data to predict future species patterns (2019)
    Nature Research
    In:  Scientific Reports, 9 (1). Art.Nr. 1821.
    Details
    Publication Date: 2022-01-31
    Description: Predictive species distribution models are mostly based on statistical dependence between environmental and distributional data and therefore may fail to account for physiological limits and biological interactions that are fundamental when modelling species distributions under future climate conditions. Here, we developed a state-of-the-art method integrating biological theory with survey and experimental data in a way that allows us to explicitly model both physical tolerance limits of species and inherent natural variability in regional conditions and thereby improve the reliability of species distribution predictions under future climate conditions. By using a macroalga-herbivore association (Fucus vesiculosus - Idotea balthica) as a case study, we illustrated how salinity reduction and temperature increase under future climate conditions may significantly reduce the occurrence and biomass of these important coastal species. Moreover, we showed that the reduction of herbivore occurrence is linked to reduction of their host macroalgae. Spatial predictive modelling and experimental biology have been traditionally seen as separate fields but stronger interlinkages between these disciplines can improve species distribution projections under climate change. Experiments enable qualitative prior knowledge to be defined and identify cause-effect relationships, and thereby better foresee alterations in ecosystem structure and functioning under future climate conditions that are not necessarily seen in projections based on non-causal statistical relationships alone.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1038/s41598-018-38416-3
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 7
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    Earthquake and typhoon trigger unprecedented transient shifts in shallow hydrothermal vents biogeochemistry (2019)
    Nature Research
    In:  Scientific Reports, 9 (Article number 16926).
    Details
    Publication Date: 2022-01-31
    Description: Shallow hydrothermal vents are of pivotal relevance for ocean biogeochemical cycles, including seawater dissolved heavy metals and trace elements as well as the carbonate system balance. The Kueishan Tao (KST) stratovolcano off Taiwan is associated with numerous hydrothermal vents emitting warm sulfur-rich fluids at so-called White Vents (WV) and Yellow Vent (YV) that impact the surrounding seawater masses and habitats. The morphological and biogeochemical consequences caused by a M5.8 earthquake and a C5 typhoon (“Nepartak”) hitting KST (12th May, and 2nd–10th July, 2016) were studied within a 10-year time series (2009–2018) combining aerial drone imagery, technical diving, and hydrographic surveys. The catastrophic disturbances triggered landslides that reshaped the shoreline, burying the seabed and, as a consequence, native sulfur accretions that were abundant on the seafloor disappeared. A significant reduction in venting activity and fluid flow was observed at the high-temperature YV. Dissolved Inorganic Carbon (DIC) maxima in surrounding seawater reached 3000–5000 µmol kg−1, and Total Alkalinity (TA) drawdowns were below 1500–1000 µmol kg−1 lasting for one year. A strong decrease and, in some cases, depletion of dissolved elements (Cd, Ba, Tl, Pb, Fe, Cu, As) including Mg and Cl in seawater from shallow depths to the open ocean followed the disturbance, with a recovery of Mg and Cl to pre-disturbance concentrations in 2018. The WV and YV benthic megafauna exhibited mixed responses in their skeleton Mg:Ca and Sr:Ca ratios, not always following directions of seawater chemical changes. Over 70% of the organisms increased skeleton Mg:Ca ratio during rising DIC (higher CO2) despite decreasing seawater Mg:Ca ratios showing a high level of resilience. KST benthic organisms have historically co-existed with such events providing them ecological advantages under extreme conditions. The sudden and catastrophic changes observed at the KST site profoundly reshaped biogeochemical processes in shallow and offshore waters for one year, but they remained transient in nature, with a possible recovery of the system within two years.
    Type: Article , PeerReviewed
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    Format: other
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    DOI: 10.1038/s41598-019-53314-y
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 8
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    Winter weather controls net influx of atmospheric CO2 on the north-west European shelf (2019)
    Nature Research
    In:  Scientific Reports, 9 (1). Art.Nr. 20153.
    Details
    Publication Date: 2022-01-31
    Description: Shelf seas play an important role in the global carbon cycle, absorbing atmospheric carbon dioxide (CO2) and exporting carbon (C) to the open ocean and sediments. The magnitude of these processes is poorly constrained, because observations are typically interpolated over multiple years. Here, we used 298500 observations of CO2 fugacity (fCO2) from a single year (2015), to estimate the net influx of atmospheric CO2 as 26.2 ± 4.7 Tg C yr−1 over the open NW European shelf. CO2 influx from the atmosphere was dominated by influx during winter as a consequence of high winds, despite a smaller, thermally-driven, air-sea fCO2 gradient compared to the larger, biologically-driven summer gradient. In order to understand this climate regulation service, we constructed a carbon-budget supplemented by data from the literature, where the NW European shelf is treated as a box with carbon entering and leaving the box. This budget showed that net C-burial was a small sink of 1.3 ± 3.1 Tg C yr−1, while CO2 efflux from estuaries to the atmosphere, removed the majority of river C-inputs. In contrast, the input from the Baltic Sea likely contributes to net export via the continental shelf pump and advection (34.4 ± 6.0 Tg C yr−1).
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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    DOI: 10.1038/s41598-019-56363-5
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 9
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    In search for the sources of plastic marine litter that contaminates the Easter Island Ecoregion (2019)
    Nature Research
    In:  Scientific Reports, 9 (1). Art.Nr. 19662.
    Details
    Publication Date: 2022-01-31
    Description: Subtropical gyres are the oceanic regions where plastic litter accumulates over long timescales, exposing surrounding oceanic islands to plastic contamination, with potentially severe consequences on marine life. Islands’ exposure to such contaminants, littered over long distances in marine or terrestrial habitats, is due to the ocean currents that can transport plastic over long ranges. Here, this issue is addressed for the Easter Island ecoregion (EIE). High-resolution ocean circulation models are used with a Lagrangian particle-tracking tool to identify the connectivity patterns of the EIE with industrial fishing areas and coastline regions of the Pacific basin. Connectivity patterns for “virtual” particles either floating (such as buoyant macroplastics) or neutrally-buoyant (smaller microplastics) are investigated. We find that the South American shoreline between 20°S and 40°S, and the fishing zone within international waters off Peru (20°S, 80°W) are associated with the highest probability for debris to reach the EIE, with transit times under 2 years. These regions coincide with the most-densely populated coastal region of Chile and the most-intensely fished region in the South Pacific. The findings offer potential for mitigating plastic contamination reaching the EIE through better upstream waste management. Results also highlight the need for international action plans on this important issue.
    Type: Article , PeerReviewed
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    DOI: 10.1038/s41598-019-56012-x
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 10
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    Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization (2017)
    Nature Research
    In:  The ISME Journal, 11 (11). pp. 2465-2478.
    Details
    Publication Date: 2020-06-18
    Description: Marine sponges are ancient metazoans that are populated by distinct and highly diverse microbial communities. In order to obtain deeper insights into the functional gene repertoire of the Mediterranean sponge Aplysina aerophoba, we combined Illumina short-read and PacBio long-read sequencing followed by un-targeted metagenomic binning. We identified a total of 37 high-quality bins representing 11 bacterial phyla and two candidate phyla. Statistical comparison of symbiont genomes with selected reference genomes revealed a significant enrichment of genes related to bacterial defense (restriction-modification systems, toxin-antitoxin systems) as well as genes involved in host colonization and extracellular matrix utilization in sponge symbionts. A within-symbionts genome comparison revealed a nutritional specialization of at least two symbiont guilds, where one appears to metabolize carnitine and the other sulfated polysaccharides, both of which are abundant molecules in the sponge extracellular matrix. A third guild of symbionts may be viewed as nutritional generalists that perform largely the same metabolic pathways but lack such extraordinary numbers of the relevant genes. This study characterizes the genomic repertoire of sponge symbionts at an unprecedented resolution and it provides greater insights into the molecular mechanisms underlying microbial-sponge symbiosis.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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    Format: other
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    DOI: 10.1038/ismej.2017.101
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    OceanRep: Article in a Scientific Journal - peer-reviewed
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