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  • 1
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    Online Resource
    Metabarcoding reveals high diversity of benthic foraminifera linked to water masses circulation at coastal Svalbard
    Wiley ; 2023
    In:  Geobiology Vol. 21, No. 1 ( 2023-01), p. 133-150
    Details
    In: Geobiology, Wiley, Vol. 21, No. 1 ( 2023-01), p. 133-150
    Abstract: Arctic marine biodiversity is undergoing rapid changes due to global warming and modifications of oceanic water masses circulation. These changes have been demonstrated in the case of mega‐ and macrofauna, but much less is known about their impact on the biodiversity of smaller size organisms, such as foraminifera that represent a main component of meiofauna in the Arctic. Several studies analyzed the distribution and diversity of Arctic foraminifera. However, all these studies are based exclusively on the morphological identification of specimens sorted from sediment samples. Here, we present the first assessment of Arctic foraminifera diversity based on metabarcoding of sediment DNA samples collected in fjords and open sea areas in the Svalbard Archipelago. We obtained a total of 5,968,786 reads that represented 1384 amplicon sequence variants (ASVs). More than half of the ASVs (51.7%) could not be assigned to any group in the reference database suggesting a high genetic novelty of Svalbard foraminifera. The sieved and unsieved samples resolved comparable communities, sharing 1023 ASVs, comprising over 97% of reads. Our analyses show that the foraminiferal assemblage differs between the localities, with communities distinctly separated between fjord and open sea stations. Each locality was characterized by a specific assemblage, with only a small overlap in the case of open sea areas. Our study demonstrates a clear pattern of the influence of water masses on the structure of foraminiferal communities. The stations situated on the western coast of Svalbard that are strongly influenced by warm and salty Atlantic water (AW) are characterized by much higher diversity than stations in the northern and eastern part, where the impact of AW is less pronounced. This high diversity and specificity of Svalbard foraminifera associated with water mass distribution indicate that the foraminiferal metabarcoding data can be very useful for inferring present and past environmental conditions in the Arctic.
    Type of Medium: Online Resource
    ISSN: 1472-4677 , 1472-4669
    URL: Issue
    URL: Article
    DOI: 10.1111/gbi.v21.1
    DOI: 10.1111/gbi.12530
    Language: English
    Publisher: Wiley
    Publication Date: 2023
    detail.hit.zdb_id: 2113509-5
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  • 2
    Online Resource
    Online Resource
    Supervised machine learning outperforms taxonomy‐based environmental DNA metabarcoding applied to biomonitoring
    Wiley ; 2018
    In:  Molecular Ecology Resources Vol. 18, No. 6 ( 2018-11), p. 1381-1391
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 18, No. 6 ( 2018-11), p. 1381-1391
    Abstract: Biodiversity monitoring is the standard for environmental impact assessment of anthropogenic activities. Several recent studies showed that high‐throughput amplicon sequencing of environmental DNA ( eDNA metabarcoding) could overcome many limitations of the traditional morphotaxonomy‐based bioassessment. Recently, we demonstrated that supervised machine learning ( SML ) can be used to predict accurate biotic indices values from eDNA metabarcoding data, regardless of the taxonomic affiliation of the sequences. However, it is unknown to which extent the accuracy of such models depends on taxonomic resolution of molecular markers or how SML compares with metabarcoding approaches targeting well‐established bioindicator species. In this study, we address these issues by training predictive models upon five different ribosomal bacterial and eukaryotic markers and measuring their performance to assess the environmental impact of marine aquaculture on independent data sets. Our results show that all tested markers are yielding accurate predictive models and that they all outperform the assessment relying solely on taxonomically assigned sequences. Remarkably, we did not find any significant difference in the performance of the models built using universal eukaryotic or prokaryotic markers. Using any molecular marker with a taxonomic range broad enough to comprise different potential bioindicator taxa, SML approach can overcome the limits of taxonomy‐based eDNA bioassessment.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.2018.18.issue-6
    DOI: 10.1111/1755-0998.12926
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2406833-0
    SSG: 12
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  • 3
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    Changes in the foliar fungal community between oak leaf flushes along a latitudinal gradient in Europe
    Wiley ; 2022
    In:  Journal of Biogeography Vol. 49, No. 12 ( 2022-12), p. 2269-2280
    Details
    In: Journal of Biogeography, Wiley, Vol. 49, No. 12 ( 2022-12), p. 2269-2280
    Abstract: Leaves support a large diversity of fungi, which are known to cause plant diseases, induce plant defences or influence leaf senescence and decomposition. To advance our understanding of how foliar fungal communities are structured and assembled, we assessed to what extent leaf flush and latitude can explain the within‐ and among‐tree variation in foliar fungal communities. Location A latitudinal gradient spanning c . 20 degrees in latitude in Europe. Taxa The foliar fungal community associated with a foundation tree species, the pedunculate oak Quercus robur . Methods We examined the main and interactive effects of leaf flush and latitude on the foliar fungal community by sampling 20 populations of the pedunculate oak Quercus robur across the tree's range. We used the ITS region as a target for characterization of fungal communities using DNA metabarcoding. Results Species composition, but not species richness, differed between leaf flushes. Across the latitudinal gradient, species richness was highest in the central part of the oak's distributional range, and foliar fungal community composition shifted along the latitudinal gradient. Among fungal guilds, the relative abundance of plant pathogens and mycoparasites was lower on the first leaf flush, and the relative abundance of plant pathogens and saprotrophs decreased with latitude. Conclusions Changes in community composition between leaf flushes and along the latitudinal gradient were mostly a result of species turnover. Overall, our findings demonstrate that leaf flush and latitude explain 5%–22% of the small‐ and large‐scale spatial variation in the foliar fungal community on a foundation tree within the temperate region. Using space‐for‐time substitution, we expect that foliar fungal community structure will change with climate warming, with an increase in the abundance of plant pathogens and mycoparasites at higher latitudes, with major consequences for plant health, species interactions and ecosystem dynamics.
    Type of Medium: Online Resource
    ISSN: 0305-0270 , 1365-2699
    URL: Issue
    URL: Article
    DOI: 10.1111/jbi.v49.12
    DOI: 10.1111/jbi.14508
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2020428-0
    detail.hit.zdb_id: 188963-1
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  • 4
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    Molecular Identification of Algal Endosymbionts in Large Miliolid Foraminifera: 2. Dinoflagellates
    Wiley ; 2001
    In:  Journal of Eukaryotic Microbiology Vol. 48, No. 3 ( 2001-05), p. 368-373
    Details
    In: Journal of Eukaryotic Microbiology, Wiley, Vol. 48, No. 3 ( 2001-05), p. 368-373
    Abstract: ABSTRACT. Large miliolid foraminifers of the subfamily Soritinae bear symbiotic dinoflagellates morphologically similar to the species of the “ Symbiodinium ” complex, commonly found in corals and other marine invertebrates. Soritid foraminifers are abundant in coral reefs and it has been proposed that they share their symbionts with other dinoflagellate‐bearing reef dwellers. In order to test this hypothesis, we have analysed partial large subunit ribosomal DNA sequences from dinoflagellates symbionts obtained from 28 foraminiferal specimens, and compared them to the corresponding sequences of Symbiodinium ‐like endosymbionts from various groups of invertebrates. Phylogenetic analysis of our data shows that all soritid symbionts belong to the “ Symbiodinium ” species complex, within which they form seven different molecular types (Fr1–Fr7). Only one of these types (Fr1) branches within a group of invertebrate symbionts, previously described as type C. The remaining six types form sister groups to coral symbionts previously designed as types B, C, and D. Our data indicate a high genetic diversity and specificity of Symbiodinium ‐like symbionts in soritids. Except for type C, we have found no evidence for the transmission of symbionts between foraminifers and other symbiont‐bearing invertebrates from the same localities. However, exchanges must have occurred frequently between the different species of Soritinae, as suggested by the lack of host specificity and some biogeographical patterns observed in symbiont distribution. Our data suggest that members of the subfamily Soritinae acquired their symbionts at least three times during their history, each acquisition being followed by a rapid diversification and independent radiation of symbionts within the foraminiferal hosts.
    Type of Medium: Online Resource
    ISSN: 1066-5234 , 1550-7408
    URL: Issue
    URL: Article
    DOI: 10.1111/jeu.2001.48.issue-3
    DOI: 10.1111/j.1550-7408.2001.tb00326.x
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2001
    detail.hit.zdb_id: 2126326-7
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  • 5
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    Molecular Phylogeny and Morphology of Leannia veloxifera n. gen. et sp. Unveils a New Lineage of Monothalamous Foraminifera
    Wiley ; 2015
    In:  Journal of Eukaryotic Microbiology Vol. 62, No. 3 ( 2015-05), p. 353-361
    Details
    In: Journal of Eukaryotic Microbiology, Wiley, Vol. 62, No. 3 ( 2015-05), p. 353-361
    Abstract: Monothalamous (single‐chambered) foraminifera have long been considered as the “poor cousins” of multichambered species, which calcareous and agglutinated tests dominate in the fossil record. This view is currently changing with environmental DNA surveys showing that the monothalamids may be as diverse as hard‐shelled foraminifera. Yet, the majority of numerous molecular lineages revealed by e DNA studies remain anonymous. Here, we describe a new monothalamous species and genus isolated from the sample of sea grass collected in Gulf of Eilat (Red Sea). This new species, named Leannia veloxifera , is characterized by a tiny ovoid theca (about 50–100 μm) composed of thin organic wall, with two opposite apertures. The examined individuals are multinucleated and show very active reticulopodial movement. Phylogenetic analyses of SSU r DNA , actin, and beta‐tubulin (ß‐tubulin) show that the species represents a novel lineage branching separately from other monothalamous foraminifera. Interestingly, the SSU r DNA sequence of the new species is very similar to an environmental foraminiferal sequence from Bahamas, suggesting that the novel lineage may represent a group of shallow‐water tropical allogromiids, poorly studied until now.
    Type of Medium: Online Resource
    ISSN: 1066-5234 , 1550-7408
    URL: Issue
    URL: Article
    DOI: 10.1111/jeu.2015.62.issue-3
    DOI: 10.1111/jeu.12190
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2015
    detail.hit.zdb_id: 2126326-7
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  • 6
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    A Marine Dinoflagellate, Amphidinium eilatiensis n. sp., from the Benthos of a Mariculture Sedimentation Pond in Eilat, Israel
    Wiley ; 2003
    In:  The Journal of Eukaryotic Microbiology Vol. 50, No. 6 ( 2003-11), p. 439-448
    Details
    In: The Journal of Eukaryotic Microbiology, Wiley, Vol. 50, No. 6 ( 2003-11), p. 439-448
    Type of Medium: Online Resource
    ISSN: 1066-5234 , 1550-7408
    URL: Issue
    URL: Article
    DOI: 10.1111/jeu.2003.50.issue-6
    DOI: 10.1111/j.1550-7408.2003.tb00270.x
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2003
    detail.hit.zdb_id: 2126326-7
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  • 7
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    Unexpected Foraminiferal Diversity Revealed by Small‐subunit rDNA Analysis of Antarctic Sediment
    Wiley ; 2004
    In:  Journal of Eukaryotic Microbiology Vol. 51, No. 2 ( 2004-03), p. 173-179
    Details
    In: Journal of Eukaryotic Microbiology, Wiley, Vol. 51, No. 2 ( 2004-03), p. 173-179
    Abstract: ABSTRACT. Studies of benthic Foraminifera typically rely on the morphological identification of dried specimens. This approach can introduce sampling bias against small, delicate, or morphologically ambiguous forms. To overcome this limitation, we extracted total DNA from sediment followed by PCR using group‐ and species‐specific primers. Phylogenetic analyses revealed that approximately ninety percent of the PCR products represented previously undescribed sequence types that group with undersampled members of the allogromiid Foraminifera. We also used a modification of this technique to track individual species in sediment fractions too fine for normal morphological identification, and to confirm species placement of morphologically ambiguous foraminiferans. We were able to identify the DNA of several large foraminiferal species in fine fractions in a seasonally‐dependent manner, indicating that in some seasons the majority of the standing stock of these species exists as gametes/juveniles. The approach outlined here represents a powerful strategy for exploring the total diversity of benthic foraminiferal communities.
    Type of Medium: Online Resource
    ISSN: 1066-5234 , 1550-7408
    URL: Issue
    URL: Article
    DOI: 10.1111/jeu.2004.51.issue-2
    DOI: 10.1111/j.1550-7408.2004.tb00542.x
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2004
    detail.hit.zdb_id: 2126326-7
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  • 8
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    Assessing SSU rDNA Barcodes in Foraminifera: A Case Study using Bolivina quadrata
    Wiley ; 2018
    In:  Journal of Eukaryotic Microbiology Vol. 65, No. 2 ( 2018-03), p. 220-235
    Details
    In: Journal of Eukaryotic Microbiology, Wiley, Vol. 65, No. 2 ( 2018-03), p. 220-235
    Abstract: The Small Subunit Ribosomal RNA gene ( SSU rDNA ) is a widely used tool to reconstruct phylogenetic relationships among foraminiferal species. Recently, the highly variable regions of this gene have been proposed as DNA barcodes to identify foraminiferal species. However, the resolution of these barcodes has not been well established, yet. In this study, we evaluate four SSU rDNA hypervariable regions (37/f, 41/f, 43/e, and 45/e) as DNA barcodes to distinguish among species of the genus Bolivina , with particular emphasis on Bolivina quadrata for which ten new sequences ( KY468817 – KY468826 ) were obtained during this study. Our analyses show that a single SSU rDNA hypervariable sequence is insufficient to resolve all Bolivina species and that some regions (37/f and 41/f) are more useful than others (43/e and 45/e) to distinguish among closely related species. In addition, polymorphism analyses reveal a high degree of variability. In the context of barcoding studies, these results emphasize the need to assess the range of intraspecific variability of DNA barcodes prior to their application to identify foraminiferal species in environmental samples; our results also highlight the possibility that a longer SSU rDNA region might be required to distinguish among species belonging to the same taxonomic group (i.e. genus).
    Type of Medium: Online Resource
    ISSN: 1066-5234 , 1550-7408
    URL: Issue
    URL: Article
    DOI: 10.1111/jeu.2018.65.issue-2
    DOI: 10.1111/jeu.12471
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2126326-7
    SSG: 12
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  • 9
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    Molecular Phylogenetic Analysis Places Percolomonas cosmopolites within Heterolobosea: Evolutionary Implications
    Wiley ; 2004
    In:  Journal of Eukaryotic Microbiology Vol. 51, No. 5 ( 2004-09), p. 575-581
    Details
    In: Journal of Eukaryotic Microbiology, Wiley, Vol. 51, No. 5 ( 2004-09), p. 575-581
    Abstract: Percolomonas cosmopolitus is a common free‐living flagellate of uncertain phylogenetic position that was placed within the Heterolobosea on the basis of ultrastructure studies. To test the relationship between Percolomonas and Heterolobosea, we analysed the primary structure of the actin and small‐subunit ribosomal RNA (SSU rRNA) genes of P. cosmopolitus as well as the predicted secondary structure of the SSU rRNA. Percolomonas shares common secondary structure patterns of the SSU rRNA with heterolobosean taxa, which, together with the results of actin gene analysis, confirms that it is closely related to Heterolobosea. Phylogenetic reconstructions based on the sequences of the SSU rRNA gene suggest Percolomonas belongs to the family Vahlkampliidae. The first Bayesian analysis of a large taxon sampling of heterolobosean SSU rRNA genes clarifies the phylogenetic relationships within this group.
    Type of Medium: Online Resource
    ISSN: 1066-5234 , 1550-7408
    URL: Issue
    URL: Article
    DOI: 10.1111/jeu.2004.51.issue-5
    DOI: 10.1111/j.1550-7408.2004.tb00294.x
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2004
    detail.hit.zdb_id: 2126326-7
    SSG: 12
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  • 10
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    A molecular perspective on the phylogeny of amoeboid protists
    Wiley ; 2005
    In:  The Journal of Eukaryotic Microbiology Vol. 52, No. 2 ( 2005-03), p. 7S-27S
    Details
    In: The Journal of Eukaryotic Microbiology, Wiley, Vol. 52, No. 2 ( 2005-03), p. 7S-27S
    Type of Medium: Online Resource
    ISSN: 1066-5234 , 1550-7408
    URL: Issue
    URL: Article
    DOI: 10.1111/jeu.2005.52.issue-2
    DOI: 10.1111/j.1550-7408.2005.05202003_1_11.x
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2005
    detail.hit.zdb_id: 2126326-7
    SSG: 12
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