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20 results for “Protist community”
Data from: Is a community state reachable, and why?, and Coexistence and collapse: an experimental investigation of the persistent communities of a protist species pool
<p>Deterministic models have difficulties to take into account stochasticity during community assembly. As a tool to circumvent this problem, we present a qualitative discreteevent model, where consequences of interspecific interactions are described as rules. This model provides a map of all possible future dynamics for a given system, which allows to exhaustively describe the possible pathways during an assembly process. Such a description does not rely on species traits details and is insensitive to stochastic effects. This allows to show that subsets of species are sometimes impossible to reach starting from larger sets of species, and therefore to question the reachability of community states during the system’s dynamics. Applying the model to an experimental dataset studying the collapse of protist communities, we obtain a very good theory-experiment agreement. We finally discuss what the notion of reachability can bring to community assembly.</p>
Fig. 3 in Molecular and Morphological Snapshot Characterisation of the Protist Communities in Contrasting Alpine Glacier Forefields
Fig. 3. Rarefaction analysis derived from the clone libraries of the vegetated transects of Tiefen forefield and Wildstrubel forefield. Dashed lines correspond to 95% confidence intervals.
Fig. 2 in Molecular and Morphological Snapshot Characterisation of the Protist Communities in Contrasting Alpine Glacier Forefields
Fig. 2. Relative abundances (in percentage) of ciliate-related sequences detected in the 18S rRNA gene clone libraries from the vegetated transects of the (a) Tiefen forefield and (b) Wildstrubel forefield. Species names are based on BLAST comparison of the sequences with the NCBI database (first similarity with a known taxonomic group).
Fig. 1 in Molecular and Morphological Snapshot Characterisation of the Protist Communities in Contrasting Alpine Glacier Forefields
Fig. 1. Location of the two sampled forefields of the (a) Tiefen glacier and (b) Wildstrubel glacier. Dots indicate sampling spots (white: unvegetated transects; black: vegetated transects).
Linked collectors and determiners for: Protist community composition in the water column on the East Greenland shelf, May 2022.
Natural history specimen data linked to collectors and determiners held within, "Protist community composition in the water column on the East Greenland shelf, May 2022". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/270fc4bf-3225-4af4-a5c0-dca8652ac37c">https://bionomia.net/dataset/270fc4bf-3225-4af4-a5c0-dca8652ac37c</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/270fc4bf-3225-4af4-a5c0-dca8652ac37c">https://gbif.org/dataset/270fc4bf-3225-4af4-a5c0-dca8652ac37c</a>. Formatted as a Frictionless Data package.
Ecoregional patterns of protist communities in mineral and organic soils: assembly processes, functional traits and diversity of testate amoebae in Northern Eurasia
<p>TA_Traits.csv file includes trait data for testate amoebae. TA_Abundance.csv file includes environmental variables (soil type and region) and relative abundance data of testate amoebae.</p>
Data from: Effects of pesticides on soil bacterial, fungal and protist communities, soil functions and crop quality in vineyards
<p>Pesticides can have unintentional effects on non-target organisms and change biotic communities. Such changes might be particularly important in soil microbial communities which drive many ecosystem functions and may affect crop quality. Here, we investigated, in a 3-year study, how vegetation control (by herbicide application) and soil copper content (from long-term copper-based fungicide application), affect biodiversity and the community structure of soil bacteria, fungi and protists and associated soil functions (respiration, decomposition) in Swiss vineyards. Furthermore, we determined the effects of these two management practices on grape quality as the most direct ecosystem service to farmers. Across all study years, the community composition of microorganisms was affected by herbicide application, however, a significant loss of operational taxonomic units (OTUs) was only observed in fungi and protists. Soil copper content reduced OTU richness of bacteria and protists in some years but had no significant effect on fungal richness. Copper changed the community composition in all three groups of soil microorganisms. While we found no effect of copper on soil functions, herbicide application reduced microbial respiration and biomass by about 39% and 45% respectively. However, decomposition rates remained virtually unchanged by any pesticide. Yeast assimilable nitrogen (YAN) levels in grape must were below the critical threshold of 140 mg/L in 40% of the vineyards without herbicide application and the variety Chasselas , whereas in vineyards with herbicide application it was only 20%. Synthesis and applications: Application of pesticides led to changes in richness and composition of soil microbial communities and directly reduced some soil functions (microbial biomass and respiration), but not all (decomposition). Some grape quality parameters can be indirectly enhanced by pesticide application, highlighting the trade-off between the interests of nature conservation and the interests of the farmer. Balancing these two diverging interests requires the establishment of alternative vineyard management allowing reduced pesticide application.</p>
Data from: Effects of pesticides on soil bacterial, fungal and protist communities, soil functions and crop quality in vineyards
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Data from: Temperature and carbon dioxide interactively drive shifts in the compositional and functional structure of peatland protist communities
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Data from: Environmental monitoring through protist NGS metabarcoding: assessing the impact of fish farming on benthic foraminifera communities
The measurement of species diversity represents a powerful tool for assessing the impacts of human activities on marine ecosystems. Traditionally, the impact of fish farming on the coastal environment is evaluated by monitoring the dynamics of macrobenthic infaunal populations. However, taxonomic sorting and morphology-based identification of the macrobenthos demands highly trained specialists and is extremely time-consuming and costly, what makes it unsuitable for large-scale biomonitoring efforts involving numerous samples. Here, we propose to alleviate this laborious task by developing protist metabarcoding tools based on next-generation sequencing (NGS) of environmental DNA and RNA extracted from sediment samples. In this study, we analysed the response of benthic foraminiferal communities to the variation of environmental gradients associated with salmon farms in Scotland. We investigated the foraminiferal diversity based on ribosomal minibarcode sequences generated by the Illumina NGS technology. We compared the molecular data with morphospecies counts and with environmental gradients, including distance to cages and Redox used as a proxy for sediment oxygenation. Our study revealed high variations between foraminiferal communities collected in the vicinity of fish farms and at distant locations. We found evidence for alpha diversity loss in strongly impacted sites, especially visible in the RNA data. We also detected some candidate bioindicator foraminiferal species. Based on this proof-of-concept study, we conclude that NGS metabarcoding using foraminifera and other protists has considerable potential to become a new tool for surveying the impact of aquaculture and other industrial activities in the marine environment.
Supplementary material 4 from: Boenigk J, Wodniok S, Bock C, Beisser D, Hempel C, Grossmann L, Lange A, Jensen M (2018) Geographic distance and mountain ranges structure freshwater protist communities on a European scalе. Metabarcoding and Metagenomics 2: e21519. https://doi.org/10.3897/mbmg.2.21519
Richness is shown for different elevations. The number of lakes within this elevation range is indicated. While mean richness ranges around 750 OTUs it drops to around 400 OTUs at high elevations. The transition seems to be around or slightly below 1400m.
Data from: Environmental monitoring through protist NGS metabarcoding: assessing the impact of fish farming on benthic foraminifera communities
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Data from: Evidence for an active rare biosphere within freshwater protists community
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Data from: Bacteria, protists and fungi may hold clues of seamount impact on diversity and connectivity of deep-sea pelagic communities
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Dataset_2020_Biogeosciences_Protists and collembolans alter microbial community composition, C dynamics and soil aggregation in simplified consumer - prey systems
<p>Dataset associated to the publication: Erktan, A., Rillig, M.C., Carminati, A., Jousset, A., Scheu, S. (2020) Protists and collembolans alter microbial community composition, C dynamics and soil aggregation in simplified consumer - prey systems, Biogeosciences, accepted the 27/08/2020.</p>
Supplementary material 2 from: Boenigk J, Wodniok S, Bock C, Beisser D, Hempel C, Grossmann L, Lange A, Jensen M (2018) Geographic distance and mountain ranges structure freshwater protist communities on a European scalе. Metabarcoding and Metagenomics 2: e21519. https://doi.org/10.3897/mbmg.2.21519
Lake characteristics and diversity indices
Supplementary material 3 from: Boenigk J, Wodniok S, Bock C, Beisser D, Hempel C, Grossmann L, Lange A, Jensen M (2018) Geographic distance and mountain ranges structure freshwater protist communities on a European scalе. Metabarcoding and Metagenomics 2: e21519. https://doi.org/10.3897/mbmg.2.21519
Bray distance matrix
Supplementary material 1 from: Boenigk J, Wodniok S, Bock C, Beisser D, Hempel C, Grossmann L, Lange A, Jensen M (2018) Geographic distance and mountain ranges structure freshwater protist communities on a European scalе. Metabarcoding and Metagenomics 2: e21519. https://doi.org/10.3897/mbmg.2.21519
Sample Identifier for molecular analyses
Fig. 1 in Review paper The Role of Bacterial-based Protist Communities in Aquatic and Soil Ecosystems and the Carbon Biogeochemical Cycle, with Emphasis on Naked Amoebae
Fig. 1. Protocol for respiration and microbial biomass experiments. Respiration was measured with an infrared CO gas analyzer, glu2 cose (444 µg/g soil) in solution was added as a supplement. Microbial assays for naked amoebae used a culture observation method (COM) for living amoebae routinely employed in our laboratory (e.g. Anderson 2000), glutaraldehyde-fixed portions of the soil sample were examined microscopically for bacteria and heterotrophic nanoflagellates using a fluorescent staining technique (Anderson et al. 2001). For experiments of one-week duration, sampling was done on Days 1, 4, and 8. For two-week duration experiments, sampling was done on Days 1, 8, and 15.
Data from: Not all are free-living: high-throughput DNA metabarcoding reveals a diverse community of protists parasitizing soil metazoa
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