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  • 1
    Electronic Resource
    Electronic Resource
    Examination of the Montastraea annularis Species Complex (Cnidaria: Scleractinia) Using ITS and COI Sequences (1999)
    Springer
    Marine biotechnology 1 (1999), S. 89-97 
    Details
    ISSN: 1436-2236
    Keywords: Key words:Montastraea, ITS, COI, speciation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract The Caribbean coral Montastraea annularis has recently been proposed to be a complex of at least three sibling species. To test the validity of this proposal, we sequenced the ITS region of the nuclear ribosomal RNA gene family (ITS-1, 5.8S, and ITS-2), and a portion of the mitochondrial DNA gene cytochrome c oxidase subunit I (COI) from the three proposed species (M. annularis, M. faveolata, and M. franksi) from Florida reefs. The ITS fragment was 665 nucleotides long and had 19 variable sites, of which 6 were parsimony-informative sites. None of these sites was fixed within the proposed species. The COI fragment was 658 nucleotides long with only two sites variable in one individual. Thus, under both the biological species concept and the phylogenetic species concept, the molecular evidence gathered in this study indicates the Montastraea annularis species complex to be a single evolutionary entity as opposed to three distinct species. The three proposed Montastraea species can interbreed, ruling out prezygotic barriers to gene flow (biological species concept), and the criterion of monophyly is not satisfied if hybridization is occurring among taxa (phylogenetic species concept).
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00011756
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    Paper (German National Licenses)
    Fulltext
  • 2
    Electronic Resource
    Electronic Resource
    Comparison of Four Mendelian Loci of the California Sea Hare (Aplysia californica) from Populations of the Coast of California and the Sea of Cortez (2000)
    Springer
    Marine biotechnology 2 (2000), S. 449-455 
    Details
    ISSN: 1436-2236
    Keywords: Key words:Aplysia californica, gene flow, mendelian markers, population structure, California coast.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract: Aplysia californica is a species widely used in neurobiology, and specimens are collected from a wide range of places along its distribution range. A. californica is endemic to the coast of California and the Gulf of California. On the west coast, this is an unusual distribution range relative to other benthic species from that region. Four polymorphic nuclear Mendelian markers were identified (three single-copy nuclear DNA loci and one microsatellite) for an initial survey of genetic variation of wild populations. F ST values not significantly different from 0 (overall F ST= 0.0148) suggest there was no geographic genetic population subdivision in 177 individuals examined.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s101260000020
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    Paper (German National Licenses)
    Fulltext
  • 3
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    A communal catalogue reveals Earth’s multiscale microbial diversity (2017)
    Nature Research
    In:  Nature, 551 (7681). pp. 457-463.
    Details
    Publication Date: 2020-02-06
    Description: Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1038/nature24621
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 4
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    A community perspective on the concept of marine holobionts: current status, challenges, and future directions (2021)
    PeerJ
    Details
    Publication Date: 2024-02-07
    Description: Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever.
    Type: Article , PeerReviewed , info:eu-repo/semantics/article
    Format: text
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 5
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    Unraveling the functional dark matter through global metagenomics (2023)
    Nature Research
    Details
    Publication Date: 2024-02-07
    Description: Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities1,2. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database3. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.
    Type: Article , PeerReviewed
    Format: text
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    OceanRep: Article in a Scientific Journal - peer-reviewed
  • 6
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    Threatened corals provide underexplored microbial habitats (2021)
    In:  http://aquaticcommons.org/id/eprint/14805 | 403 | 2014-02-27 20:19:32 | 14805 | United States National Ocean Service
    Details
    Publication Date: 2021-06-25
    Description: Contemporary in-depth sequencing of environmental samples has provided novel insights into microbial community structures, revealing that their diversity had been previously underestimated. Communities in marine environments are commonly composed of a few dominant taxa and a high number of taxonomically diverse, low-abundance organisms. However, studying the roles and genomic information of these “rare” organisms remains challenging, because little is known about their ecological niches and the environmental conditions to which they respond. Given the current threat to coral reef ecosystems, we investigated the potential of corals to provide highly specialized habitats for bacterial taxa including those that are rarely detected or absent in surrounding reef waters. The analysis of more than 350,000 small subunit ribosomal RNA (16S rRNA) sequence tags and almost 2,000 nearly full-length 16S rRNA gene sequences revealed that rare seawater biosphere members are highly abundant or even dominant in diverse Caribbean corals. Closely related corals (in the same genus/family) harbored similar bacterial communities. At higher taxonomic levels, however, the similarities of these communities did not correlate with the phylogenetic relationships among corals, opening novel questions about the evolutionary stability of coral-microbial associations. Large proportions of OTUs (28.7–49.1%) were unique to the coral species of origin. Analysis of the most dominant ribotypes suggests that many uncovered bacterial taxa exist in coral habitats and await future exploration. Our results indicate that coral species, and by extension other animal hosts, act as specialized habitats of otherwise rare microbes in marine ecosystems. Here, deep sequencing provided insights into coral microbiota at an unparalleled resolution and revealed that corals harbor many bacterial taxa previously not known. Given that two of the coral species investigated are listed as threatened under the U.S. Endangered Species Act, our results add an important microbial diversity-based perspective to the significance of conserving coral reefs.
    Keywords: Biology ; Ecology ; Fisheries
    Repository Name: AquaDocs
    Type: article , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: e9554
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    PAPER (OA)
  • 7
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    A community perspective on the concept of marine holobionts: current status, challenges, and future directions (2021)
    In:  EPIC3PeerJ, 9, pp. e10911, ISSN: 2167-8359
    Details
    Publication Date: 2021-11-17
    Description: Host-microbe interactions play crucial roles in marine ecosystems. However, we still have very little understanding of the mechanisms that govern these relationships, the evolutionary processes that shape them, and their ecological consequences. The holobiont concept is a renewed paradigm in biology that can help to describe and understand these complex systems. It posits that a host and its associated microbiota with which it interacts, form a holobiont, and have to be studied together as a coherent biological and functional unit to understand its biology, ecology, and evolution. Here we discuss critical concepts and opportunities in marine holobiont research and identify key challenges in the field. We highlight the potential economic, sociological, and environmental impacts of the holobiont concept in marine biological, evolutionary, and environmental sciences. Given the connectivity and the unexplored biodiversity specific to marine ecosystems, a deeper understanding of such complex systems requires further technological and conceptual advances, e.g., the development of controlled experimental model systems for holobionts from all major lineages and the modeling of (info)chemical-mediated interactions between organisms. Here we propose that one significant challenge is to bridge cross-disciplinary research on tractable model systems in order to address key ecological and evolutionary questions. This first step is crucial to decipher the main drivers of the dynamics and evolution of holobionts and to account for the holobiont concept in applied areas, such as the conservation, management, and exploitation of marine ecosystems and resources, where practical solutions to predict and mitigate the impact of human activities are more important than ever.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev , info:eu-repo/semantics/article
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    PAPER (OA)
  • 8
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    Fv/Fm for cultured Clade A & B Symbiodinium with 2 treatments measured over a range of temperatures (2019)
    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Details
    Publication Date: 2022-10-31
    Description: Dataset: Symbiodinium Fv/Fm over a temperature gradient
    Description: Coral photosynthetic endosymbionts (Symbiodinium) are phylogenetically very diverse, yet the extent of inter- and intraspecific functional variation within clades remains largely underexplored. Understanding this variability will be critical for future research on climate change mediated responses. A properly functioning thylakoid membrane is essential for optimal photosynthetic performance both in free-living and in hospite conditions. Here we analyze the thylakoid membrane melting points of 13 Symbiodinium strains from species in Clades B and A, grown at both control (26 °C) and high temperature (31 °C). We observed a broad range of responses to thermal stress regardless of taxonomic rank. Our results support and augment a growing body of literature demonstrating that functional differences among Symbiodinium spp. are as distinct at lower taxonomic levels (i.e. interspecific) as they are among major clades. These findings highlight the importance of assessing the variability of plastid traits across the Symbiodinium tree. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/732890
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1442206, NSF Division of Ocean Sciences (NSF OCE) OCE-1642311
    Keywords: Symbiodinium ; Thermal tolerance ; Phenotypic plasticity ; Photochemical efficiency ; Thylakoid membrane ; Thermal stress ; Symbiotic dinoflagellates ; Coral bleaching
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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  • 9
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    Photosystem II (PSII) photochemical efficiency (Yield PSII) recorded at noon (ΔF/Fm') and at dusk (Fv/Fm) on random coral colonies of Orbicella faveolata from Varadero and Rosario reefs, Colombia, May 2017 (2020)
    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Details
    Publication Date: 2022-05-26
    Description: Dataset: Reciprocal transplant expt. - PSII of random colonies
    Description: Photosystem II (PSII) photochemical efficiency (Yield PSII) recorded at noon (ΔF/Fm') and at dusk (Fv/Fm) on random coral colonies of Orbicella faveolata for a reciprocal transplant experiment, from Varadero and Rosario reefs, Colombia, May 2017 For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/786548
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1642311
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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  • 10
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    Photosynthesic parameters (calculated alpha, Pmax, Respiration, Ek and Ec) for each P-E curve for coral Orbicella faveolata from Rosaria and Varadero reef sites and Cartagena Bay, Colombia, 2016 and 2017 (2020)
    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Details
    Publication Date: 2022-05-26
    Description: Dataset: Reciprocal transplant expt. - Photosynthetic parameters
    Description: This dataset contains the results of the photosynthetic parameters calculated based on the analysis of the P-E curves from coral fragment of the species Orbicella faveolata used in the transplant experiment between three sites: Varadero (10°18'23.3"N, 75°35'08.0"W), Rosario (10°11'12.1"N, 75°44'43.0"W) and Abanico (10°18'5.80"N, 75°34'37.10"W). The tag number/color of each fragment, the date of data collection, and the sites of origin and destination are specified. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/719161
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1642311
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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