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  • Artikel  (8)
  • Artikel (Open Access)  (8)
  • 1
    Publikationsdatum: 2014-07-01
    Beschreibung: Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world's oceans.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , isiRev
    Format: application/pdf
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 2
    Publikationsdatum: 2019-06-03
    Beschreibung: The deep ocean below 200 m water depth is the least observed, but largest habitat on our planet by volume and area. Over 150 years of exploration has revealed that this dynamic system provides critical climate regulation, houses a wealth of energy, mineral, and biological resources, and represents a vast repository of biological diversity. A long history of deep-ocean exploration and observation led to the initial concept for the Deep-Ocean Observing Strategy (DOOS), under the auspices of the Global Ocean Observing System (GOOS). Here we discuss the scientific need for globally integrated deep-ocean observing, its status, and the key scientific questions and societal mandates driving observing requirements over the next decade. We consider the Essential Ocean Variables (EOVs) needed to address deep-ocean challenges within the physical, biogeochemical, and biological/ecosystem sciences according to the Framework for Ocean Observing (FOO), and map these onto scientific questions. Opportunities for new and expanded synergies among deep-ocean stakeholders are discussed, including academic-industry partnerships with the oil and gas, mining, cable and fishing industries, the ocean exploration and mapping community, and biodiversity conservation initiatives. Future deep-ocean observing will benefit from the greater integration across traditional disciplines and sectors, achieved through demonstration projects and facilitated reuse and repurposing of existing deep-sea data efforts. We highlight examples of existing and emerging deep-sea methods and technologies, noting key challenges associated with data volume, preservation, standardization, and accessibility. Emerging technologies relevant to deep-ocean sustainability and the blue economy include novel genomics approaches, imaging technologies, and ultra-deep hydrographic measurements. Capacity building will be necessary to integrate capabilities into programs and projects at a global scale. Progress can be facilitated by Open Science and Findable, Accessible, Interoperable, Reusable (FAIR) data principles and converge on agreed to data standards, practices, vocabularies, and registries. We envision expansion of the deep-ocean observing community to embrace the participation of academia, industry, NGOs, national governments, international governmental organizations, and the public at large in order to unlock critical knowledge contained in the deep ocean over coming decades, and to realize the mutual benefits of thoughtful deep-ocean observing for all elements of a sustainable ocean.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , peerRev
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 3
    Publikationsdatum: 2020-09-24
    Beschreibung: Deciphering the evolution of marine plankton is typically based on the study of microfossil groups. Cryptic speciation is common in these groups, and large intragenomic variations occur in ribosomal RNA genes of many morphospecies. In this study, we correlated the distribution of ribosomal amplicon sequence variants (ASVs) with paleoceanographic changes by analyzing the highthroughput sequence data assigned to Neogloboquadrina pachyderma in a 140,000-year-old sediment core from the Arctic Ocean. The sedimentary ancient DNA demonstrated the occurrence of various N. pachyderma ASVs whose occurrence and dominance varied through time. Most remarkable was the striking appearance of ASV18, which was nearly absent in older sediments but became dominant during the last glacial maximum and continues to persist today. Although the molecular ecology of planktonic foraminifera is still poorly known, the analysis of their intragenomic variations through time has the potential to provide new insight into the evolution of marine biodiversity and may lead to the development of new and important paleoceanographic proxies.
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , peerRev
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  • 4
    Publikationsdatum: 2016-05-20
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , isiRev
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  • 5
    Publikationsdatum: 2022-05-26
    Beschreibung: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS Biology 12 (2014): e1001889, doi:10.1371/journal.pbio.1001889.
    Beschreibung: Microbial ecology is plagued by problems of an abstract nature. Cell sizes are so small and population sizes so large that both are virtually incomprehensible. Niches are so far from our everyday experience as to make their very definition elusive. Organisms that may be abundant and critical to our survival are little understood, seldom described and/or cultured, and sometimes yet to be even seen. One way to confront these problems is to use data of an even more abstract nature: molecular sequence data. Massive environmental nucleic acid sequencing, such as metagenomics or metatranscriptomics, promises functional analysis of microbial communities as a whole, without prior knowledge of which organisms are in the environment or exactly how they are interacting. But sequence-based ecological studies nearly always use a comparative approach, and that requires relevant reference sequences, which are an extremely limited resource when it comes to microbial eukaryotes. In practice, this means sequence databases need to be populated with enormous quantities of data for which we have some certainties about the source. Most important is the taxonomic identity of the organism from which a sequence is derived and as much functional identification of the encoded proteins as possible. In an ideal world, such information would be available as a large set of complete, well-curated, and annotated genomes for all the major organisms from the environment in question. Reality substantially diverges from this ideal, but at least for bacterial molecular ecology, there is a database consisting of thousands of complete genomes from a wide range of taxa, supplemented by a phylogeny-driven approach to diversifying genomics. For eukaryotes, the number of available genomes is far, far fewer, and we have relied much more heavily on random growth of sequence databases, raising the question as to whether this is fit for purpose.
    Beschreibung: This project was funded by the Gordon and Betty Moore Foundation (GBMF; Grants GBMF2637 and GBMF3111) to the National Center for Genome Resources (NCGR) and the National Center for Marine Algae and Microbiota (NCMA).
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Format: application/msword
    Format: application/pdf
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  • 6
    Publikationsdatum: 2022-10-26
    Beschreibung: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Levin, L. A., Bett, B. J., Gates, A. R., Heimbach, P., Howe, B. M., Janssen, F., McCurdy, A., Ruhl, H. A., Snelgrove, P., Stocks, K., I., Bailey, D., Baumann-Pickering, S., Beaverson, C., Benfield, M. C., Booth, D. J., Carreiro-Silva, M., Colaco, A., Eble, M. C., Fowler, A. M., Gjerde, K. M., Jones, D. O. B., Katsumata, K., Kelley, D., Le Bris, N., Leonardi, A. P., Lejzerowicz, F., Macreadie, P., I., McLean, D., Meitz, F., Morato, T., Netburn, A., Pawlowski, J., Smith, C. R., Sun, S., Uchida, H., Vardaro, M. F., Venkatesan, R., & Weller, R. A. Global observing needs in the deep ocean. Frontiers in Marine Science, 6, (2019):241, doi: 10.3389/fmars.2019.00241.
    Beschreibung: The deep ocean below 200 m water depth is the least observed, but largest habitat on our planet by volume and area. Over 150 years of exploration has revealed that this dynamic system provides critical climate regulation, houses a wealth of energy, mineral, and biological resources, and represents a vast repository of biological diversity. A long history of deep-ocean exploration and observation led to the initial concept for the Deep-Ocean Observing Strategy (DOOS), under the auspices of the Global Ocean Observing System (GOOS). Here we discuss the scientific need for globally integrated deep-ocean observing, its status, and the key scientific questions and societal mandates driving observing requirements over the next decade. We consider the Essential Ocean Variables (EOVs) needed to address deep-ocean challenges within the physical, biogeochemical, and biological/ecosystem sciences according to the Framework for Ocean Observing (FOO), and map these onto scientific questions. Opportunities for new and expanded synergies among deep-ocean stakeholders are discussed, including academic-industry partnerships with the oil and gas, mining, cable and fishing industries, the ocean exploration and mapping community, and biodiversity conservation initiatives. Future deep-ocean observing will benefit from the greater integration across traditional disciplines and sectors, achieved through demonstration projects and facilitated reuse and repurposing of existing deep-sea data efforts. We highlight examples of existing and emerging deep-sea methods and technologies, noting key challenges associated with data volume, preservation, standardization, and accessibility. Emerging technologies relevant to deep-ocean sustainability and the blue economy include novel genomics approaches, imaging technologies, and ultra-deep hydrographic measurements. Capacity building will be necessary to integrate capabilities into programs and projects at a global scale. Progress can be facilitated by Open Science and Findable, Accessible, Interoperable, Reusable (FAIR) data principles and converge on agreed to data standards, practices, vocabularies, and registries. We envision expansion of the deep-ocean observing community to embrace the participation of academia, industry, NGOs, national governments, international governmental organizations, and the public at large in order to unlock critical knowledge contained in the deep ocean over coming decades, and to realize the mutual benefits of thoughtful deep-ocean observing for all elements of a sustainable ocean.
    Beschreibung: Preparation of this manuscript was supported by NNX16AJ87A (NASA) Consortium for Ocean Leadership, Sub-Award No. SA16-33. AC was supported by FCT-Investigador contract (IF/00029/2014/CP1230/CT0002). LL was supported by a NASA subaward from the Consortium for Ocean Leadership. AG and HR were supported by Horizon 2020, EU Project “EMSO Link” grant ID 731036. AG, BB, DJ, and HR contributions were supported by the UK Natural Environment Research Council Climate Linked Atlantic Section Science project (NE/R015953/1). JP was funded by the Swiss Network for International Studies, and the Swiss National Science Foundation (grant 31003A_179125). TM was supported by Program Investigador FCT (IF/01194/2013), IFCT Exploratory Project (IF/01194/2013/CP1199/CT0002), H2020 Atlas project (GA 678760), and the H2020 MERCES project (GA 689518). This is PMEL contribution number 4965.
    Schlagwort(e): Deep sea ; Ocean observation ; Blue economy ; Essential ocean variables ; Biodiversity ; Ocean sensors
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 7
    Publikationsdatum: 2023-05-02
    Beschreibung: DNA sequencing shows that species of the genera Notorotalia, Porosorotalia and Buccella form a distinct branch (Notorotaliidae) of Rotaloidea, and cluster as sister to Elphidiidae. In this review we report on the sequencing of three species of Buccella (from the Arctic Ocean, Patagonia and Chile) and one each of Notorotalia (New Zealand) and Porosorotalia (Chile). This information has been combined with all the morphological descriptive information on species of these genera plus the genera Cristatavultus and Parrellina to provide a global synthesis of living species of the Notorotaliidae. We recognize 11 species of the southern hemisphere genus Notorotalia, which has a centre of diversity around New Zealand (8 species). A second southern-hemisphere-restricted genus, restricted to eastern Australia is Parrellina (3 species) although specimens (possibly introduced) have been recorded from the Mediterranean Sea. Cristatavultus has a single species, with a tropical west Pacific distribution.We synonymize Cribrorotalia under Porosorotalia, which has a disjunct distribution with one species in the northwest Pacific and a second around the southern parts of South America. Buccella is the most diverse and widespread genus (16 species recognized) with its greatest abundance in the Arctic Ocean and around subantarctic-temperate South America. Five species of Buccella live in a belt along the west coast of central America, from USAto Peru, with some spillage into the Caribbean Sea and Gulf of Mexico. Two new species of Buccella are recognized: B. dejardini (from South Georgia) and Buccella n. sp. A (from Chile).
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , peerRev
    Format: application/pdf
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  • 8
    Publikationsdatum: 2024-05-30
    Beschreibung: Foraminifera are a species-rich phylum of rhizarian protists that are highly abundant in most marine environments. Molecular methods such as metabarcoding have revealed a high, yet undescribed diversity of Foraminifera. However, so far only one molecular marker, the 18S ribosomal RNA, was available for metabarcoding studies on Foraminifera. Primers that allow amplification of foraminiferal mitochondrial cytochrome oxidase I (COI) and identification of Foraminifera species were recently published. Here we test the performance of these primers for the amplification of whole foraminiferal communities, and compare their performance to that of the highly degenerate LerayXT primers, which amplify the same COI region in a wide range of eukaryotes. We applied metabarcoding to 48 samples taken along three transects spanning a North Sea beach in the Netherlands from dunes to the low tide level, and analysed both sediment samples and meiofauna samples, which contained taxa between 42 mm and 1 mm in body size obtained by decantation from sand samples. We used single-cell metabarcoding (Girard et al., 2022) to generate a COI reference library containing 32 species of Foraminifera, and used this to taxonomically annotate our community metabarcoding data. Our analyses show that the highly degenerate LerayXT primers do not amplify Foraminifera, while the Foraminifera primers are highly Foraminifera- specific, with about 90% of reads assigned to Foraminifera and amplifying taxa from all major groups, i.e., monothalamids, Globothalamea, and Tubothalamea. We identified 176 Foraminifera ASVs and found a change in Foraminifera community composition along the beach transects from high tide to low tide level, and a dominance of single-chambered monothalamid Foraminifera. Our results highlight that COI metabarcoding can be a powerful tool for assessing Foraminiferal communities.
    Schlagwort(e): Foraminifera ; Metabarcoding ; Beach ; Community composition ; Intertidal ; Molecular ; biodiversity
    Repository-Name: National Museum of Natural History, Netherlands
    Materialart: info:eu-repo/semantics/article
    Format: application/pdf
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