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  • 1
    Online Resource
    Online Resource
    Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants
    Wiley ; 2019
    In:  Environmental Microbiology Vol. 21, No. 11 ( 2019-11), p. 4109-4124
    Details
    In: Environmental Microbiology, Wiley, Vol. 21, No. 11 ( 2019-11), p. 4109-4124
    Abstract: Effective and precise grouping of highly similar sequences remains a major bottleneck in the evaluation of high‐throughput sequencing datasets. Amplicon sequence variants (ASVs) offer a promising alternative that may supersede the widely used operational taxonomic units (OTUs) in environmental sequencing studies. We compared the performance of a recently developed pipeline based on the algorithm DADA2 for obtaining ASVs against a pipeline based on the algorithm SWARM for obtaining OTUs. Illumina‐sequencing of 29 individual ciliate species resulted in up to 11 ASVs per species, while SWARM produced up to 19 OTUs per species. To improve the congruency between species diversity and molecular diversity, we applied sequence similarity networks (SSNs) for second‐level sequence grouping into network sequence clusters (NSCs). At 100% sequence similarity in SWARM‐SSNs, NSC numbers decreased from 7.9‐fold overestimation without abundance filter, to 4.5‐fold overestimation when an abundance filter was applied. For the DADA2‐SSN approach, NSC numbers decreased from 3.5‐fold to 3‐fold overestimation. Rand index cluster analyses predicted best binning results between 97% and 94% sequence similarity for both DADA2‐SSNs and SWARM‐SSNs. Depending on the ecological questions addressed in an environmental sequencing study with protists we recommend ASVs as replacement for OTUs, best in combination with SSNs.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    URL: Article
    DOI: 10.1111/emi.v21.11
    DOI: 10.1111/1462-2920.14764
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 2020213-1
    SSG: 12
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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
    Online Resource
    Online Resource
    A Comparison of Different Ciliate Metabarcode Genes as Bioindicators for Environmental Impact Assessments of Salmon Aquaculture
    Wiley ; 2019
    In:  Journal of Eukaryotic Microbiology Vol. 66, No. 2 ( 2019-03), p. 294-308
    Details
    In: Journal of Eukaryotic Microbiology, Wiley, Vol. 66, No. 2 ( 2019-03), p. 294-308
    Abstract: Ciliates are powerful indicators for monitoring the impact of aquaculture and other industrial activities in the marine environment. Here, we tested the efficiency of four different genetic markers (V4 and V9 regions of the SSU rRNA gene, D1 and D2 regions of the LSU rRNA gene, obtained from environmental (e) DNA and environmental (e) RNA ) of benthic ciliate communities for environmental monitoring. We obtained these genetic metabarcodes from sediment samples collected along a transect extending from below salmon cages toward the open sea. These data were compared to benchmark data from traditional macrofauna surveys of the same samples. In beta diversity analyses of ciliate community structures, the V4 and V9 markers had a higher resolution power for sampling sites with different degrees of organic enrichment compared to the D1 and D2 markers. The eDNA and eRNA V4 markers had a higher discriminatory power than the V9 markers. However, results obtained with the eDNA V9 marker corroborated better with the traditional macrofauna monitoring. This allows for a more direct comparison of ciliate metabarcoding with the traditional monitoring. We conclude that the ciliate eDNA V9 marker is the best choice for implementation in routine monitoring programs in marine aquaculture.
    Type of Medium: Online Resource
    ISSN: 1066-5234 , 1550-7408
    URL: Issue
    URL: Article
    DOI: 10.1111/jeu.2019.66.issue-2
    DOI: 10.1111/jeu.12670
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 2126326-7
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Marine protist diversity in E uropean coastal waters and sediments as revealed by high‐throughput sequencing
    Wiley ; 2015
    In:  Environmental Microbiology Vol. 17, No. 10 ( 2015-10), p. 4035-4049
    Details
    In: Environmental Microbiology, Wiley, Vol. 17, No. 10 ( 2015-10), p. 4035-4049
    Abstract: Although protists are critical components of marine ecosystems, they are still poorly characterized. Here we analysed the taxonomic diversity of planktonic and benthic protist communities collected in six distant E uropean coastal sites. Environmental deoxyribonucleic acid ( DNA ) and ribonucleic acid ( RNA ) from three size fractions (pico‐, nano‐ and micro/mesoplankton), as well as from dissolved DNA and surface sediments were used as templates for tag pyrosequencing of the V4 region of the 18S ribosomal DNA. Beta‐diversity analyses split the protist community structure into three main clusters: picoplankton‐nanoplankton‐dissolved DNA , micro/mesoplankton and sediments. Within each cluster, protist communities from the same site and time clustered together, while communities from the same site but different seasons were unrelated. Both DNA and RNA ‐based surveys provided similar relative abundances for most class‐level taxonomic groups. Yet, particular groups were overrepresented in one of the two templates, such as marine alveolates ( MALV )‐ I and MALV‐II that were much more abundant in DNA surveys. Overall, the groups displaying the highest relative contribution were Dinophyceae, Diatomea, Ciliophora and Acantharia. Also, well represented were Mamiellophyceae, Cryptomonadales, marine alveolates and marine stramenopiles in the picoplankton, and Monadofilosa and basal F ungi in sediments. Our extensive and systematic sequencing of geographically separated sites provides the most comprehensive molecular description of coastal marine protist diversity to date.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    URL: Article
    DOI: 10.1111/emi.2015.17.issue-10
    DOI: 10.1111/1462-2920.12955
    Language: English
    Publisher: Wiley
    Publication Date: 2015
    detail.hit.zdb_id: 2020213-1
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Transition boundaries for protistan species turnover in hypersaline waters of different biogeographic regions
    Wiley ; 2017
    In:  Environmental Microbiology Vol. 19, No. 8 ( 2017-08), p. 3186-3200
    Details
    In: Environmental Microbiology, Wiley, Vol. 19, No. 8 ( 2017-08), p. 3186-3200
    Abstract: The identification of environmental barriers which govern species distribution is a fundamental concern in ecology. Even though salt was previously identified as a major transition boundary for micro‐ and macroorganisms alike, the salinities causing species turnover in protistan communities are unknown. We investigated 4.5 million high‐quality protistan metabarcodes (V4 region of the SSU rDNA) obtained from 24 shallow salt ponds (salinities 4%–44%) from South America and Europe. Statistical analyses of protistan community profiles identified four salinity classes, which strongly selected for different protistan communities: 4–9%, 14–24%, 27–36% and 38–44%. The proportion of organisms unknown to science is highest in the 14–24% salinity class, showing that environments within this salinity range are an unappreciated reservoir of as yet undiscovered organisms. Distinct higher‐rank taxon groups dominated in the four salinity classes in terms of diversity. As increasing salinities require different cellular responses to cope with salt, our results suggest that different evolutionary lineages of protists have evolved distinct haloadaptation strategies. Salinity appears to be a stronger selection factor for the structuring of protistan communities than geography. Yet, we find a higher degree of endemism in shallow salt ponds compared with less isolated ecosystems such as the open ocean. Thus, rules for biogeographic structuring of protistan communities are not universal, but depend on the ecosystem under consideration.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    URL: Article
    DOI: 10.1111/emi.2017.19.issue-8
    DOI: 10.1111/1462-2920.13805
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2020213-1
    SSG: 12
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  • 6
    Online Resource
    Online Resource
    Factors shaping community patterns of protists and bacteria on a European scale
    Wiley ; 2020
    In:  Environmental Microbiology Vol. 22, No. 6 ( 2020-06), p. 2243-2260
    Details
    In: Environmental Microbiology, Wiley, Vol. 22, No. 6 ( 2020-06), p. 2243-2260
    Abstract: Factors shaping community patterns of microorganisms are controversially discussed. Physical and chemical factors certainly limit the survival of individual taxa and maintenance of diversity. In recent years, a contribution of geographic distance and dispersal barriers to distribution patterns of protists and bacteria has been demonstrated. Organismic interactions such as competition, predation and mutualism further modify community structure and maintenance of distinct taxa. Here, we address the relative importance of these different factors in shaping protists and bacterial communities on a European scale using high‐throughput sequencing data obtained from lentic freshwater ecosystems. We show that community patterns of protists are similar to those of bacteria. Our results indicate that cross‐domain organismic factors are important variables with a higher influence on protists as compared with bacteria. Abiotic physical and chemical factors also contributed significantly to community patterns. The contribution of these latter factors was higher for bacteria, which may reflect a stronger biogeochemical coupling. The contribution of geographical distance was similar for both microbial groups.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    URL: Article
    DOI: 10.1111/emi.v22.6
    DOI: 10.1111/1462-2920.14992
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2020213-1
    SSG: 12
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  • 7
    Online Resource
    Online Resource
    Aquatic food webs in deep temperate lakes: Key species establish through their autecological versatility
    Wiley ; 2021
    In:  Molecular Ecology Vol. 30, No. 4 ( 2021-02), p. 1053-1071
    Details
    In: Molecular Ecology, Wiley, Vol. 30, No. 4 ( 2021-02), p. 1053-1071
    Abstract: Microbial planktonic communities are the basis of food webs in aquatic ecosystems since they contribute substantially to primary production and nutrient recycling. Network analyses of DNA metabarcoding data sets emerged as a powerful tool to untangle the complex ecological relationships among the key players in food webs. In this study, we evaluated co‐occurrence networks constructed from time‐series metabarcoding data sets (12 months, biweekly sampling) of protistan plankton communities in surface layers (epilimnion) and bottom waters (hypolimnion) of two temperate deep lakes, Lake Mondsee (Austria) and Lake Zurich (Switzerland). Lake Zurich plankton communities were less tightly connected, more fragmented and had a higher susceptibility to a species extinction scenario compared to Lake Mondsee communities. We interpret these results as a lower robustness of Lake Zurich protistan plankton to environmental stressors, especially stressors resulting from climate change. In all networks, the phylum Ciliophora contributed the highest number of nodes, among them several in key positions of the networks. Associations in ciliate‐specific subnetworks resembled autecological species‐specific traits that indicate adaptions to specific environmental conditions. We demonstrate the strength of co‐occurrence network analyses to deepen our understanding of plankton community dynamics in lakes and indicate biotic relationships, which resulted in new hypotheses that may guide future research in climate‐stressed ecosystems.
    Type of Medium: Online Resource
    ISSN: 0962-1083 , 1365-294X
    URL: Issue
    URL: Article
    DOI: 10.1111/mec.v30.4
    DOI: 10.1111/mec.15776
    RVK:
    WA 15000
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2020749-9
    detail.hit.zdb_id: 1126687-9
    SSG: 12
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  • 8
    Online Resource
    Online Resource
    Purine metabolism controls innate lymphoid cell function and protects against intestinal injury
    Wiley ; 2018
    In:  Immunology & Cell Biology Vol. 96, No. 10 ( 2018-11), p. 1049-1059
    Details
    In: Immunology & Cell Biology, Wiley, Vol. 96, No. 10 ( 2018-11), p. 1049-1059
    Abstract: Inflammatory bowel disease ( IBD ) is a condition of chronic inflammatory intestinal disorder with increasing prevalence but limited effective therapies. The purine metabolic pathway is involved in various inflammatory processes including IBD . However, the mechanisms through which purine metabolism modulates IBD remain to be established. Here, we found that mucosal expression of genes involved in the purine metabolic pathway is altered in patients with active ulcerative colitis ( UC ), which is associated with elevated gene expression signatures of the group 3 innate lymphoid cell ( ILC 3)–interleukin ( IL )‐22 pathway. In mice, blockade of ectonucleotidases ( NTPD ases), critical enzymes for purine metabolism by hydrolysis of extracellular adenosine 5′‐triphosphate ( eATP ) into adenosine, exacerbates dextran‐sulfate sodium‐induced intestinal injury. This exacerbation of colitis is associated with reduction of colonic IL ‐22‐producing ILC 3s, which afford essential protection against intestinal inflammation, and is rescued by exogenous IL ‐22. Mechanistically, activation of ILC 3s for IL ‐22 production is reciprocally mediated by eATP and adenosine. These findings reveal that the NTPD ase‐mediated balance between eATP and adenosine regulates ILC 3 cell function to provide protection against intestinal injury and suggest potential therapeutic strategies for treating IBD by targeting the purine– ILC 3 axis.
    Type of Medium: Online Resource
    ISSN: 0818-9641 , 1440-1711
    URL: Issue
    URL: Article
    DOI: 10.1111/imcb.2018.96.issue-10
    DOI: 10.1111/imcb.12167
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2011707-3
    SSG: 12
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