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98 results for “freshwater communities”
Cascading effects of algal warming in a freshwater community
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Data from: Auxotrophy and intra-population complementary in the 'interactome' of a cultivated freshwater model community
Microorganisms are usually studied either in highly complex natural communities or in isolation as monoclonal model populations that we manage to grow in the laboratory. Here, we uncover the biology of some of the most common and yet-uncultured bacteria in freshwater environments using a mixed culture from Lake Grosse Fuchskuhle. From a single shotgun metagenome of a freshwater mixed culture of low complexity, we recovered four high-quality metagenome-assembled genomes (MAGs) for metabolic reconstruction. This analysis revealed the metabolic interconnectedness and niche partitioning of these naturally dominant bacteria. In particular, vitamin- and amino acid biosynthetic pathways were distributed unequally with a member of Crenarchaeota most likely being the sole producer of vitamin B12 in the mixed culture. Using coverage-based partitioning of the genes recovered from a single MAG intrapopulation metabolic complementarity was revealed pointing to 'social' interactions for the common good of populations dominating freshwater plankton. As such, our MAGs highlight the power of mixed cultures to extract naturally occurring 'interactomes' and to overcome our inability to isolate and grow the microbes dominating in nature.
Data from: Native freshwater species get out of the way: Prussian carp (Carassius gibelio) impacts both fish and benthic invertebrate communities in North America
Prussian Carp (Carassius gibelio) are one of the most noxious non-native species in Eurasia. Recently, Prussian Carp, a non-native freshwater fish species, were genetically confirmed in Alberta, Canada and have been rapidly expanding their range in North America since establishment. Given their rapid range expansion, there is an increasing need to determine how Prussian Carp may impact native species. We assessed the severity of the Prussian Carp invasion by 1) determining their impact on fish communities, 2) assessing their impact on benthic invertebrate communities, 3) evaluating if Prussian Carp alter abiotic conditions, and 4) identifying where we find higher abundances of Prussian Carp. When Prussian Carp were established, we found significant changes to the fish community. Correspondingly, the degree of impact to benthic invertebrate communities was related to the stage of invasion (none, early, or recent), where changes in fish communities were significantly concordant with changes in benthic invertebrate communities. Finally, we found that higher abundances of Prussian Carp were significantly associated with lower abundances of a majority of native fish species. Altogether, using three lines of evidence, we determine that Prussian Carp can have wide ranging impacts on freshwater ecosystems in North America, pressing the need for management intervention.
Supplementary material 1 from: Biessy L, Pearman JK, Waters S, Vandergoes MJ, Wood SA (2022) Metagenomic insights to the functional potential of sediment microbial communities in freshwater lakes. Metabarcoding and Metagenomics 6: e79265. https://doi.org/10.3897/mbmg.6.79265
Figures S1–S6
Supplementary material 2 from: Biessy L, Pearman JK, Waters S, Vandergoes MJ, Wood SA (2022) Metagenomic insights to the functional potential of sediment microbial communities in freshwater lakes. Metabarcoding and Metagenomics 6: e79265. https://doi.org/10.3897/mbmg.6.79265
Tables S1, S2
Elevation in tropical sky islands as the common driver in structuring genes and communities of freshwater organisms
<p>Output files from pyRAD v.3.0 for four ddRAD sequenced Sumatran mayfly species.</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
Environmental filters of freshwater fish community assembly along elevation and latitudinal gradients
Aim <p>The aim was to identify drivers of historical freshwater fish community assembly by testing for interactions between functional traits and two climatic gradients, namely elevation and latitude. Many studies conclude that environmental filtering is the dominant process of community-wide trait convergence at high elevations and high latitudes, but a full understanding of which specific filters cause trait convergence is lacking.</p> Location <p>Great Plains–Rocky Mountains, USA.</p> Time period <p>1960–2018.</p> Major taxa studied <p>Freshwater fish.</p> Methods <p>Using 2,539 stream fish community surveys documenting the native distributions of 51 species, we evaluated trait–environment relationships (trade-offs) and trait–dispersion relationships (standardized effect sizes from null models) along elevation and latitudinal gradients in four functional trait categories. We tested whether elevation and latitude exhibited similar trait–environment and trait–dispersion relationships using four functional trait categories (life history, habitat, trophic and locomotion). We predicted that elevation and latitude would have similar relationships owing to shared environmental filters of cold stress and dispersal constraints.</p> Results <p>Life history was the only trait category to display evidence of increased environmental filtering along both gradients, with trait dispersion more constrained at high elevations and high latitudes. Trade-offs revealed that periodic strategies (high fecundity, low juvenile survivorship) decreased with elevation and increased with latitude, whereas equilibrium strategies (low fecundity, high juvenile survivorship) declined along both gradients. Despite the observation of predictable trade-offs for habitat, trophic and locomotion trait strategies, there was little evidence for environmental filtering of these traits at high elevations and high latitudes.</p> Main conclusions <p>Elevation and latitude appear to be environmental filters of freshwater fish community assembly when mediated through life-history strategies, which is likely to be attributable to thermal constraints on growth and reproduction. Our results support the role of environmental filtering in trait convergence patterns along climatic gradients, and we identify cold stress as one specific filter of community assembly.</p>
Data from: Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms
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Data from: Auxotrophy and intra-population complementary in the 'interactome' of a cultivated freshwater model community
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Environmental filters of freshwater fish community assembly along elevation and latitudinal gradients
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Data from: Native freshwater species get out of the way: Prussian carp (Carassius gibelio) impacts both fish and benthic invertebrate communities in North America
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A mesocosm experiment testing the combined effects on plankton community of a terrestrial organic matter runoff and a warming in small freshwater reservoirs
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Optimising environmental DNA biomonitoring for Kakadu National Park's freshwater fish communities
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Data from: Salinization triggers a trophic cascade in experimental freshwater communities with varying food-chain length
The application of road deicing salts in northern regions worldwide is changing the chemical environment of freshwater ecosystems. Chloride levels in many lakes, streams, and wetlands exceed the chronic and acute thresholds established by the United States and Canada for the protection of freshwater biota. Few studies have identified the impacts of deicing salts in stream and wetland communities and none have examined impacts in lake communities. We tested how relevant concentrations of road salt (15, 100, 250, 500, and 1000 mg Cl− L−1) interacted with experimental communities containing two or three trophic levels (i.e. no fish vs. predatory fish). We hypothesized that road salt and fish would have a negative synergistic effect on zooplankton, which would then induce a trophic cascade. We tested this hypothesis in outdoor mesocosms containing filamentous algae, periphyton, phytoplankton, zooplankton, several macroinvertebrate species, and fish. We found that the presence of fish and high salt had a negative synergistic effect on the zooplankton community, which in turn caused an increase in phytoplankton. Contributing to the magnitude of this trophic cascade was a direct positive effect of high salinity on phytoplankton abundance. Cascading effects were limited with respect to impacts on the benthic food web. Periphyton and snail grazers were unaffected by the salt-induced trophic cascade, but the biomass of filamentous algae decreased as a result of shading effects from phytoplankton. We also found direct negative effects of high salinity on the biomass of filamentous algae and amphipods (Hyalella azteca) and the mortality of banded mystery snails (Viviparus georgianus) and fingernail clams (Sphaerium simile). Clam mortality was dependent on the presence of fish, suggesting a non-consumptive interactive effect with salt. Our results indicate that globally increasing concentrations of road salt can alter community structure via both direct and indirect effects.
Data from: Salinization triggers a trophic cascade in experimental freshwater communities with varying food-chain length
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.