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  • 1
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    PANGAEA
    In:  Supplement to: Taboada, Sergi; Riesgo, Ana; Wiklund, Helena; Paterson, Gordon L J; Koutsouveli, Vasiliki; Santodomingo, Nadia; Dale, Andrew C; Smith, Craig R; Jones, Daniel O B; Dahlgren, Thomas G; Glover, Adrian G (2018): Implications of population connectivity studies for the design of marine protected areas in the deep sea: An example of a demosponge from the Clarion-Clipperton Zone. Molecular Ecology, 27(23), 4657-4679, https://doi.org/10.1111/mec.14888
    Publication Date: 2023-01-13
    Description: The excel file has two spread-sheets: (i) "Microsatellites-4Areas" including the information of the 11 microsatellites used in the paper for the four different areas we investigated; (ii) "Microsatellites-30Populations" including the information of the 11 microsatellites used in the paper for the 30 different populations we investigated. In the two spread-sheets we include the following columns: "Number of individual" from 1 to 168; "Area" with the names of the areas or populations for every individual; "Sample Code" with the name of the sample used in the paper; "1Ple, 3Ple, 11Ple, 13Ple, 12Ple, 14Ple, 16Ple, 5Ple, 19Ple, 10Ple, and 2Ple" the name of each of the 11 microsatellites gentotyped in our study. In addition to that, we provide a small summary of the "Number of microsatellites", "Number of Individuals", "Number of Areas", "Number of Populations", and "N of individuals per area and population".
    Type: Dataset
    Format: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, 89.7 kBytes
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  • 2
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    PANGAEA
    In:  Supplement to: Bonifácio, Paulo; Martínez Arbizu, Pedro; Menot, Lenaick (2020): Alpha and beta diversity patterns of polychaete assemblages across the nodule province of the eastern Clarion-Clipperton Fracture Zone (equatorial Pacific). Biogeosciences, 17(4), 865-886, https://doi.org/10.5194/bg-17-865-2020
    Publication Date: 2024-02-02
    Description: The dataset contains polychaete abundance data collected from boxcores samples (BC; 0.25 m2) collected in the eastern Clarion Clipperton fracture Zone (northeast Pacific), an area currently being explored for polymetallic nodules. Macrobenthic samples were collected onboard RV Sonne during expedition SO239 in 2015. Four exploration contract areas (BGR, IOM, GSR and Ifremer) and one “Area of Particular Environmental Interest” (APEI#3) were sampled. Between 3 and 8 quantitative box cores were collected in each area. Boxcore samples were sliced in three layers (0-3, 3-5 and 5-10 cm depth) and sieved on a 300 µm mesh. Polychaetes have been counted, sequenced and identified. Identifications were realised based on morphology and DNA (COI, 16S and 18S genes) leading to morphotype in most cases (species-level). DNA sequences are available in Genbank or BOLD databases with their respective codes in this dataset.
    Keywords: Accession number; Area; BC; BC1; BC16; BC19; BC2; BC20; BC21; BC22; BC23; BC24; BC25; BC26; BC28; BC29; BC3; BC30; BC31; BC33; BC34; BC35; BC4; BC5; BC6; BC7; BC8; BC9; Box corer; Comment; Database accession number; Depth, bottom/max; DEPTH, sediment/rock; Depth, top/min; Event label; Identification; JPI Oceans - Ecological Aspects of Deep-Sea Mining; JPIO-MiningImpact; Layer description; Morphotype; North Pacific Ocean; Number of individuals; Sample comment; Sample ID; SO239; SO239_105-1; SO239_106-1; SO239_107-1; SO239_119-1; SO239_12-1; SO239_127-1; SO239_128-1; SO239_137-1; SO239_138-1; SO239_15-1; SO239_159-1; SO239_16-1; SO239_162-1; SO239_169-1; SO239_180-1; SO239_181-1; SO239_182-1; SO239_195-1; SO239_196-1; SO239_203-1; SO239_204-1; SO239_209-1; SO239_21-1; SO239_23-1; SO239_51-1; SO239_57-1; SO239_58-1; SO239_60-1; SO239_88-1; SO239_89-1; SO239_90-1; SO239_94-1; SO239_95-1; SO239_97-1; Sonne_2; Species; Station label
    Type: Dataset
    Format: text/tab-separated-values, 18255 data points
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  • 3
    Publication Date: 2020-02-06
    Description: The Southwest Indian Ridge is an ultraslow-spreading mid-ocean ridge with numerous poorly-explored seamounts. The benthic fauna of seamounts are thought to be highly heterogeneous, within even small geographic areas. Here we report observations from a two-year opportunistic experiment, which was comprised of two deployments of mango wood and whale bones. One was deployed at 732 m on Coral Seamount (~32 °S) and the other at 750 m on Atlantis Bank (~41 °S), two areas with little background faunal knowledge and a significant distance from the continental shelf. The packages mimic natural organic falls, large parcels of food on the deep-sea floor that are important in fulfilling the nutritional needs and providing shelter and substratum for many deep-sea animals. A large number of species colonised the deployments: 69 species at Coral Seamount and 42 species at Atlantis Bank. The two colonising assemblages were different, however, with only 11 species in common. This is suggestive of both differing environmental conditions and potentially, barriers to dispersal between these seamounts. Apart from Xylophaga and Idas bivalves, few organic-fall specialists were present. Several putative new species have been observed, and three new species have been described from the experiments thus far. It is not clear, however, whether this is indicative of high degrees of endemism or simply a result of under-sampling at the regional level.
    Type: Article , PeerReviewed
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  • 4
    Publication Date: 2024-02-07
    Description: Highlights • All known observations for Area of Particular Environmental Interest 6 presented. • Assess morphology, sediments, nodules, oceanography, biogeochemistry and ecology. • APEI-6 partially representative of nearby exploration areas yet clear differences. • Present scientific synthesis and management implications for Clarion Clipperton Zone. To protect the range of habitats, species, and ecosystem functions in the Clarion Clipperton Zone (CCZ), a region of interest for deep-sea polymetallic nodule mining in the Pacific, nine Areas of Particular Environmental Interest (APEIs) have been designated by the International Seabed Authority (ISA). The APEIs are remote, rarely visited and poorly understood. Here we present and synthesise all available observations made at APEI-6, the most north eastern APEI in the network, and assess its representativity of mining contract areas in the eastern CCZ. The two studied regions of APEI-6 have a variable morphology, typical of the CCZ, with hills, plains and occasional seamounts. The seafloor is predominantly covered by fine-grained sediments, and includes small but abundant polymetallic nodules, as well as exposed bedrock. The oceanographic parameters investigated appear broadly similar across the region although some differences in deep-water mass separation were evident between APEI-6 and some contract areas. Sediment biogeochemistry is broadly similar across the area in the parameters investigated, except for oxygen penetration depth, which reached 〉2 m at the study sites within APEI-6, deeper than that found at UK1 and GSR contract areas. The ecology of study sites in APEI-6 differs from that reported from UK1 and TOML-D contract areas, with differences in community composition of microbes, macrofauna, xenophyophores and metazoan megafauna. Some species were shared between areas although connectivity appears limited. We show that, from the available information, APEI-6 is partially representative of the exploration areas to the south yet is distinctly different in several key characteristics. As a result, additional APEIs may be warranted and caution may need to be taken in relying on the APEI network alone for conservation, with other management activities required to help mitigate the impacts of mining in the CCZ.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 5
    Publication Date: 2024-02-07
    Description: Abyssal seafloor communities cover more than 60% of Earth’s surface. Despite their great size, abyssal plains extend across modest environmental gradients compared to other marine ecosystems. However, little is known about the patterns and processes regulating biodiversity or potentially delimiting biogeographical boundaries at regional scales in the abyss. Improved macroecological understanding of remote abyssal environments is urgent as threats of widespread anthropogenic disturbance grow in the deep ocean. Here, we use a new, basin-scale dataset to show the existence of clear regional zonation in abyssal communities across the 5,000 km span of the Clarion–Clipperton Zone (northeast Pacific), an area targeted for deep-sea mining. We found two pronounced biogeographic provinces, deep and shallow-abyssal, separated by a transition zone between 4,300 and 4,800 m depth. Surprisingly, species richness was maintained across this boundary by phylum-level taxonomic replacements. These regional transitions are probably related to calcium carbonate saturation boundaries as taxa dependent on calcium carbonate structures, such as shelled molluscs, appear restricted to the shallower province. Our results suggest geochemical and climatic forcing on distributions of abyssal populations over large spatial scales and provide a potential paradigm for deep-sea macroecology, opening a new basis for regional-scale biodiversity research and conservation strategies in Earth’s largest biome.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 6
    Publication Date: 2024-02-07
    Description: Highlights: • Characterization of enzymes from bone-degrading marine microbiomes. • Enzymes degrade sialo/glyco-proteins at multiple conditions of pH and temperatures. • Enzyme cocktails are useful for valorising bone residues in biorefinery industry. Abstract: Many microorganisms feed on the tissue and recalcitrant bone materials from dead animals, however little is known about the collaborative effort and characteristics of their enzymes. In this study, microbial metagenomes from symbionts of the marine bone-dwelling worm Osedax mucofloris, and from microbial biofilms growing on experimentally deployed bone surfaces were screened for specialized bone-degrading enzymes. A total of 2,043 taxonomically (closest match within 40 phyla) and functionally (1 proteolytic and 9 glycohydrolytic activities) diverse and non-redundant sequences (median pairwise identity of 23.6%) encoding such enzymes were retrieved. The taxonomic assignation and the median identity of 72.2% to homologous proteins reflect microbial and functional novelty associated to a specialized bone-degrading marine community. Binning suggests that only one generalist hosting all ten targeted activities, working in synergy with multiple specialists hosting a few or individual activities. Collagenases were the most abundant enzyme class, representing 48% of the total hits. A total of 47 diverse enzymes, representing 8 hydrolytic activities, were produced in Escherichia coli, whereof 13 were soluble and active. The biochemical analyses revealed a wide range of optimal pH (4.0–7.0), optimal temperature (5–65 °C), and of accepted substrates, specific to each microbial enzyme. This versatility may contribute to a high environmental plasticity of bone-degrading marine consortia that can be confronted to diverse habitats and bone materials. Through bone-meal degradation tests, we further demonstrated that some of these enzymes, particularly those from Flavobacteriaceae and Marinifilaceae, may be an asset for development of new value chains in the biorefinery industry.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
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  • 7
    Publication Date: 2024-02-07
    Description: The marine bone biome is a complex assemblage of macro- and microorganisms; however, the enzymatic repertoire to access bone-derived nutrients remains unknown. The bone matrix is a composite material made up mainly of organic collagen and inorganic hydroxyapatite. We conducted field experiments to study microbial assemblages that can use organic bone components as nutrient source. Bovine and turkey bones were deposited at 69 m depth in a Norwegian fjord (Byfjorden, Bergen). Metagenomic sequence analysis was used to assess the functional potential of microbial assemblages from bone surface and the bone-eating worm Osedax mucofloris, which is a frequent colonizer of whale falls and known to degrade bone. The bone microbiome displayed a surprising taxonomic diversity revealed by the examination of 59 high-quality metagenome-assembled genomes from at least 23 bacterial families. Over 700 genes encoding enzymes from 12 relevant enzymatic families pertaining to collagenases, peptidases, and glycosidases putatively involved in bone degradation were identified. Metagenome-assembled genomes (MAGs) of the class Bacteroidia contained the most diverse gene repertoires. We postulate that demineralization of inorganic bone components is achieved by a timely succession of a closed sulfur biogeochemical cycle between sulfur-oxidizing and sulfur-reducing bacteria, causing a drop in pH and subsequent enzymatic processing of organic components in the bone surface communities. An unusually large and novel collagen utilization gene cluster was retrieved from one genome belonging to the gammaproteobacterial genus Colwellia.
    Type: Article , PeerReviewed
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  • 8
    Publication Date: 2024-02-12
    Description: The abyssal Clarion‐Clipperton Zone (CCZ), Pacific Ocean, is an area of commercial importance owing to the growing interest in mining high‐grade polymetallic nodules at the seafloor for battery metals. Research into the spatial patterns of faunal diversity, composition, and population connectivity is needed to better understand the ecological impacts of potential resource extraction. Here, a DNA taxonomy approach is used to investigate regional‐scale patterns of taxonomic and phylogenetic alpha and beta diversity, and genetic connectivity, of the dominant macrofaunal group (annelids) across a 6 million km 2 region of the abyssal seafloor.
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  • 9
    Publication Date: 2024-05-14
    Description: This paper represents a continuation of taxonomic publications on the benthic fauna of polymetallic nodule fields in the eastern Clarion-Clipperton Zone (CCZ) using material collected during baseline environmental survey work targeting two exploration contract areas (“UK-1” and “OMS”) and one Area of Particular Environmental Interest, “APEI-6.” Families Poecilochaetidae Hannerz, 1956 and Spionidae Grube, 1850 of the annelid suborder Spioniformia were studied here. Taxonomic data are presented for 25 species from 98 records as identified by a combination of morphological and genetic approaches. Although sub-optimal morphological condition can prevent new species being formally described, it is essential that morphological, molecular, and voucher data are made available for future surveys. Descriptions of two new species— Poecilochaetus brenkei sp. nov. and Laonice shulseae sp. nov.—increase the number of formally described new annelid species from the areas targeted in this study to 15 and CCZ-wide to 46. We also discuss the commonly reported “cosmopolitan” deep-sea spionid Aurospio dibranchiata Maciolek, 1981, which we show represents several genetically distinct species (three of these from CCZ area alone) but without reliable morphological characters to separate them. Molecular data provide evidence that 15 out of 25 species reported here have a wide distribution within the eastern CCZ and that Aurospio sp. “NHM_2186” and the known species Prionospio amarsupiata Neal & Altamira in Paterson et al. 2016 may be cosmopolitan. Lastly, the molecular data provide insights into relationships within Spioniformia, suggesting that both Poecilochaetidae and Trochochaetidae belong within Spionidae.
    Type: Article , PeerReviewed
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  • 10
    Publication Date: 2022-05-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Govindarajan, A. F., Kallstrom, B., Selander, E., Ostrnan, C., & Dahlgren, T. G. The highly toxic and cryptogenic clinging jellyfish Gonionemus sp. (Hydrozoa, Limnomedusae) on the Swedish west coast. Peerj, 7, (2019): e6883, doi:10.7717/peerj.6883.
    Description: The clinging jellyfish Gonionemus sp. is a small hydromedusa species known historically from the Swedish west coast but not reported in recent times. This species is thought to be native to the northwest Pacific where it is notorious for causing severe stings in humans and is considered invasive or cryptogenic elsewhere. This year, unlike in the past, severe stings in swimmers making contact with Gonionemus sp. medusae occurred in Swedish waters from a sheltered eelgrass bed in the inner Skagerrak archipelago. To the best of our knowledge, this is only the second sting record of Gonionemus sp. from the Northeast Atlantic—with the first record occurring off the Belgian coast in the 1970s. Stinging Gonionemus sp. medusae have also been recently reported from the northwestern Atlantic coast, where, like on the Swedish coast, stings were not reported in the past. We analyzed sea surface temperature data from the past 30 years and show that 2018 had an exceptionally cold spring followed by an exceptionally hot summer. It is suggested that the 2018 temperature anomalies contributed to the Swedish outbreak. An analysis of mitochondrial COI sequences showed that Swedish medusae belong to the same clade as those from toxic populations in the Sea of Japan and northwest Atlantic. Gonionemus sp. is particularly prone to human-mediated dispersal and we suggest that it is possible that this year’s outbreak is the result of anthropogenic factors either through a climate-driven northward range shift or an introduction via shipping activity. We examined medusa growth rates and details of medusa morphology including nematocysts. Two types of penetrating nematocysts: euryteles and b-mastigophores were observed, suggesting that Gonionemus sp. medusae are able to feed on hard-bodied organisms like copepods and cladocerans. Given the now-regular occurrence and regional spread of Gonionemus sp. in the northwest Atlantic, it seems likely that outbreaks in Sweden will continue. More information on its life cycle, dispersal mechanisms, and ecology are thus desirable.
    Description: Funding was provided by the Swedish Research Council (VR) to Erik Selander “Signals in the Sea” and from the Faculty of Science of Uppsala University to Carina Östman. Funding for the DNA sequencing analysis was provided by the Kathleen M. and Peter E. Naktenis Family Foundation and the Borrego Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
    Keywords: Sea grass ; Zostera ; Taxonomy ; Biogeography ; Climate change ; Burn ; Nematocyst ; Ultrastructure ; Microscope ; Tentacle
    Repository Name: Woods Hole Open Access Server
    Type: Article
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