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  • 1
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 46 (1999), S. 0 
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Reticulomyxa filosa is a freshwater protist possessing fine granular, branching and anastomosing pseudopodia and therefore traditionally placed in the class Granuloreticulosea, order Athalamida, as a sister group to the order Foraminiferida. Recent studies have revealed remarkable similarities in pseudopodial motility and ultrastructure between R. filosa and foraminifera (e.g. Allogromia laticollaris), prompting us to conduct a molecular phylogenetic analysis of these seemingly disparate organisms. We sequenced the complete small-subunit of the ribosomal DNA of the cultured strain of R. filosa and compared it to the corresponding sequences of other protists including 12 species of foraminifera. We also sequenced and analyzed the actin coding genes from R. filosa and two species of foraminifera, Allogromia sp. and Ammonia sp. the analysis of both data sets clearly shows that R. filosa branches within the clade of foraminifera, suggesting that R. filosa is in fact a freshwater naked foraminiferan.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    [s.l.] : Macmillan Magazines Ltd.
    Nature 399 (1999), S. 27-27 
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] It is generally assumed that the first fossil appearance of a group of organisms corresponds to its evolutionary origin. But we have molecular evidence that extant members of the most abundant microfossil-forming group, the Foraminifera, include ‘naked’ amoeboid species, indicating ...
    Type of Medium: Electronic Resource
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  • 3
    ISSN: 1432-1432
    Keywords: Foraminifera ; Sequence dissimilarity ; LSU rRNA gene ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract An unusually high divergence was observed in the ribosomal RNA genes of a free-living population of foraminifera belonging to the genusAmmonia. The sequences of a large-subunit (LSU) rDNA expansion segment D1 and flanking regions were obtained from 20 specimens namedAmmonia sp. 1 andAmmonia sp. 2. The sequence divergence between the two species averages 14%. Within each species it ranges from 0.2% to 7.1% inAmmonia sp. 1 and from 0.7% to 2.3% inAmmonia sp. 2. We did not find two specimens having identical sequences. Moreover, in opposition to the generally acaepted view, rDNA sequence variations were also found within a single individual. The variations among several rDNA copies in a single specimen ofAmmonia may reach up to 4.9%. Most of the observed variations result from multiplication of CA or TA serial repeats occurring in two particularly variable regions. For single base changes, C-T transitions are most frequently observed. We discuss the evolution of expansion segments and their use for phylogenetic studies.
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1432-1432
    Keywords: Key words: Planktonic foraminifera — Molecular phylogenetics — Rates of substitution — Ribosomal DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Planktonic foraminifera are marine protists, whose calcareous shells form oceanic sediments and are widely used for stratigraphic and paleoenvironmental analyses. The fossil record of planktonic foraminifera is compared here to their molecular phylogeny inferred from ribosomal DNA sequences. Eighteen partial SSU rDNA sequences from species representing all modern planktonic families (Globigerinidae, Hastigerinidae, Globorotaliidae, Candeinidae) were obtained and compared to seven sequences representing the major groups of benthic foraminifera. The phylogenetic analyses indicate a polyphyletic origin for the planktonic foraminifera. The Candeinidae, the Globorotaliidae, and the clade Globigerinidae + Hastigerinidae seem to have originated independently, at different epochs in the evolution of foraminifera. Inference of their relationships, however, is limited by substitution rates of heterogeneity. Rates of SSU rDNA evolution vary from 4.0 × 10−9 substitutions/site/year in the Globigerinidae to less than 1.0 × 10−9 substitutions/site/year in the Globorotaliidae. These variations may be related to different levels of adaptation to the planktonic mode of life. A clock-like evolution is observed among the Globigerinidae, for which molecular and paleontological data are congruent. Phylogeny of the Globorotaliidae is clearly biased by rapid rates of substitution in two species (G. truncatulinoides and G. menardii). Our study reveals differences in absolute rates of evolution at all taxonomic levels in planktonic foraminifera and demonstrates their effect on phylogenetic reconstructions.
    Type of Medium: Electronic Resource
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  • 5
    Publication Date: 2014-07-01
    Description: 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
    Type: Article , isiRev
    Format: application/pdf
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  • 6
    Publication Date: 2019-06-03
    Description: 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
    Type: Article , peerRev
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  • 7
    Publication Date: 2016-05-20
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 8
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in 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.
    Description: 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.
    Description: 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.
    Keywords: Deep sea ; Ocean observation ; Blue economy ; Essential ocean variables ; Biodiversity ; Ocean sensors
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 9
    Publication Date: 2022-05-26
    Description: © 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.
    Description: 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.
    Description: 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
    Type: Article
    Format: application/msword
    Format: application/pdf
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