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43 results for “diatom communities”
European river typologies fail to capture trends in diatom, fish, and macrophyte community composition
<p>This repository contains files related to the publication: "European river typologies fail to capture trends in diatom, fish, and macrophyte community composition".</p> <p> </p> <p> </p>
Hyporheic diatom community assemblages from Von Guerard Stream, Taylor Valley, McMurdo Dry Valleys, Antarctica in January 2019
In this data package, we present diatom community assemblages from hyporheic sediments collected in January 2019 from six transects across Von Guerard Stream, Taylor Valley, Antarctica. These samples were collected to address questions about the retention and processing of particulate organic matter in the hyporheic zone of McMurdo Dry Valley streams. The six transects were located at pools, riffles, and meanders (three of each geomorphology type) along Von Guerard Stream and extended across the stream channel to the edges of the wetted zone, ranging from 6.6 to 13.6 m in length. At each sampling location, we collected subsurface sediment sample that was preserved in formalin directly after sample collection. We characterized diatom assemblages by counting a total of 300 diatom valves from each preserved diatom sample. This data package is associated with a complementary data package that contains hyporheic sediment chemistry for the same samples.
Fig. 4 in Molecular profiling of 18S rRNA reveals seasonal variation and diversity of diatoms community in the Han River, South Korea
Fig. 4. Principal component analysis (PCA) biplot showing the seasonal variation of (A) all the diatom OTU reads, (B) most frequent diatom OTU detected, sampled in March (spring), June (summer), September (autumn), and December (winter). Calculated based on the number of OTU reads in each sample. Each dot represents diatom OTU recovered in this study.
Fig. 2 in Molecular profiling of 18S rRNA reveals seasonal variation and diversity of diatoms community in the Han River, South Korea
Fig. 2. Rarefaction curves representing the numbers of Operational Taxonomic Units (OTUs) of diatoms vs. the number of tags sampled from pyrosequencing data.
Fig. 1 in Molecular profiling of 18S rRNA reveals seasonal variation and diversity of diatoms community in the Han River, South Korea
Fig. 1. Seasonal variation in water temperature and DO (A), pH and conductivity (B) and TN and TP (C), and cell counts and Chla (D) at the Seongsan Bridge of Han River, Korea.
Fig. 3 in Molecular profiling of 18S rRNA reveals seasonal variation and diversity of diatoms community in the Han River, South Korea
Fig. 3. (A) Proportion of each eukaryotic taxon (eukaryote, phytoplankton, and diatom), (B) relative abundance of phytoplankton, and (C) relative abundance of diatom taxa. These data were calculated by using 18S rRNA pyrosequencing reads. Taxonomic identity of "others" represents taxa with less than 1% composition of total reads.
Genotyping by sequencing for estimating relative abundances of diatom taxa in mock communities
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Pond diatom communities from the McMurdo Sound region of Antarctica, assessed from modern samples (2012-2016) and from historical samples collected during Shackleton’s Nimrod Expedition (1908-1909)
We performed a field survey to characterize diatom communities living in the benthic microbial mats of ponds across the McMurdo Sound region of Antarctica. Samples were collected during the Austral summers of 2012-13, 2013-14, and 2015-16 from the McMurdo Dry Valleys, Cape Royds, and from Hut Ridge near McMurdo Station. We also characterized pond diatom communities in samples collected on various dates from 1908-1909 during Ernest Shackleton’s Nimrod Expedition to compare against modern samples. Historical samples were taken from Cape Royds and the Stranded Moraines, and were analyzed from slides stored at the Natural History Museum, London. This data package includes relative abundance data for diatom species found in these modern and historical samples.
Data from: Geo-climatic factors drive diatom community distribution in tropical South American freshwaters
1.Patterns that maintain and generate biodiversity of macro-organisms in the Neotropics are widely discussed in the scientific literature, yet the spatial ecology of microorganisms is largely unknown. The unique character of the tropical Andes and adjacent Amazon lowlands generates a wide gradient of environmental conditions to advance our understanding of what drives community assembly and diversity processes. 2.We analyzed the distribution patterns of benthic diatoms (unicellular siliceous algae) as a model group of microbial passive dispersers, including predictors that describe limnological and geo-climatic gradients for a total of 113 waterbodies (0–28ºS and 58–80ºW), including lakes and streams. Complementary multivariate statistical analyses were performed to correlate i) community composition, and ii) diatom species richness with environmental and spatial factors to infer niche-based and dispersal-based assembly processes, respectively. 3.Results showed that two gradients structured both diatom assemblages and waterbodies, namely climate and landscape configuration. Variance partitioning revealed that broad-scale spatial variables (distance-based Moran's Eigenvectors) outperformed the two environmental components (limnological and geo-climatic), suggesting dispersal-assembled communities. However, diatom assemblages were structured by geo-climatic (regional) factors in certain lakes in the northern and central Andes, although their effects were partially manifested via local variables after the geographical distances were factored out. In a similar way, climatic and topographic structuring homogenized lake and stream communities within ecoregions, as indicated by the strong overlap between the two community types and the weak correlation between biota and limnological variables. Notably, a significant increase in diatom species richness was related to increased water connectivity, interpreted to indicate that a decrease in the remoteness of the system increase species number. 4.Synthesis. We emphasize the strength of macroecological gradients (landscape configuration and climatic factors) in affecting both diatom diversity and community composition in the South American tropics. In this context, our results and the commonalities of ecoregion patterning with groups of macroorganisms (vegetation), suggest the need to integrate microbial ecology into a macroecology framework to unravel mechanisms behind diversity gradients.
Species richness and intraspecific variation interactively shape marine diatom community functioning
<p>The data and code provided here is used to analyze and visualize all data associated with the manuscript "Species richness and intraspecific variation interactively shape marine diatom community functioning" which is under review at L&O Letters and is authored by Patrick K. Thomas, Marrit Jacob, Esteben Acevedo-Trejos, Helmut Hillebrand, and Maren Striebel.</p> <p>Data should be analyzed in R or R studio. The code should execute automatically with no modifications by the user as long as the four csv files are placed in the same working directory that R is set to. The R project (.Rproj) file may also be opened directly to create an R project that is automatically set to the correct directory.</p> <p>ABSTRACT:<br>Biodiversity generally increases productivity in ecosystems; however, this is mediated by the specific functional traits that come with biodiversity loss or gain and how these traits interact with environmental conditions. Most biodiversity studies evaluate effects of species richness alone, despite our increasing understanding that intraspecific diversity can have equally strong impacts. Here, we manipulate both species richness and intraspecific richness (i.e., number of distinct strains) in marine diatom communities to explicitly test the relative importance of species and strain richness for biomass and trait diversity in six distinct temperature/nutrient environments. We show that species and strain richness both have significant effects on biomass and growth rates, but more importantly they interact with each other, indicating that cross-species diversity effects depend on within-species diversity and vice versa. This intertwined relationship thus calls for more integrative approaches quantifying the relative importance of distinct biodiversity components and environmental context on ecosystem functioning.</p>
Data supplementing the article "Benthic diatom communities in an Alpine river impacted by waste water treatment effluents as revealed using DNA metabarcoding" , submitted to Frontiers in Microbiology
<p>These data supplement the article"Benthic diatom communities in an Alpine river impacted by waste water treatment effluents as revealed using DNA metabarcoding" submitted to Frontiers in Microbiology: </p> <p>The directory contains the following files:</p> <p><strong>64 PGM sequencing files (raw data, fastq files) </strong>- one file is provided for each sample by the sequencing platform with demultiplexed DNA reads (raw data prior any bioinformatics treatments).</p> <p><strong>Sample_Names.xlsx</strong> - contains the information relative to the 64 samples including: the ID used in Mothur analyses (corresponding to the name of the fastq files), the sample name and the raw reads number for each sample.</p>
On the biodiversity of diatom communities in lakes of east China: Geochemical effects dominated after eutrophication
<p><strong>Aim:</strong> Over the last century, lakes all over the world have experienced significant eutrophication and become more susceptible to critical transitions. This has prompted a growing need to understand how community dynamics shift following ecological perturbations. This study aims to elucidate the present status, spatial patterns and determinants of biological diversity, and how they have changed in response to alterations driven by eutrophication.</p> <p><strong>Location:</strong> Lakes of East China, mostly in the Yangtze River Basin</p> <p><strong>Taxa:</strong> Bacillariophyceae (163 species in 33 genres) </p> <p><strong>Methods:</strong> The environmental conditions of over sixty lakes were assessed based on parameters such as water quality, physical characteristics and biogeochemical constituents. Surface sediment samples and high-resolution sediment records were collected to quantify the biodiversity of diatom communities, and Principle Component Analysis (PCA) was used to determine the major environmental gradients. Meanwhile, linear regression, Canonical Correlation Analysis and Mantel tests were used to quantify the correlations between variables.</p> <p><strong>Results:</strong> Biodiversity metrics showed no distinct geographic patterns, although areas near large lakes showed comparatively high evenness. Smaller pairwise dissimilarities were observed among hypereutrophic lakes in comparison to lakes with a lower trophic status. The past century has witnessed a decrease in both pairwise dissimilarity and the standard deviation of Evenness. A significant statistical association was found between dissimilarity and ionic concentration and composition in the surface sediment of lakes, rather than nutrient levels.</p> <p><strong>Main conclusions:</strong> Following regional eutrophication and human disturbance, a significant reduction in biodiversity differentiation was observed in lakes located in East China. Currently, the dominant factor in determining the beta diversity of diatom communities is geochemical conditions rather than nutrient concentrations. Long-term stress caused by cultural eutrophication may also have altered the dominant determinant of regional biodiversity and diatom community dynamics.</p>
Data from: Geo-climatic factors drive diatom community distribution in tropical South American freshwaters
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On the biodiversity of diatom communities in lakes of east China: Geochemical effects dominated after eutrophication
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Data from: Integrating water quality monitoring and diatom community trends to determine landscape-level change in protected lakes.
<p>These data represent water quality measurements and diatom counts from surface sediments collected from lakes in five National Park units in the Great Lakes Region (USA) between 2005 and 2018. Water quality measurements were made three times annually during the growing season; data are presented as growing season means. Surface sediment samples were collected from the same lakes every 3-5 years over more than a decade to analyze diatom community turnover. Diatom data are presented as proportions relative to total diatom counts in each sample; only taxa occuring at 2% or greater in a given park were included. </p>
Original data of diatom communities in two alpine lakes of eastern China
<p>This study explored ecological responses of Erye and Sanye lakes to climate change and atmospheric deposition based on multi-proxy sedimentary records in the Taibai Mountain (eastern China). Diatom communities of the two study lakes shifted from large-sized benthic taxa to small fragilariod species after the mid-20th century, synchronous with an increase in diatom production and a decrease in mean length of diatom valves. Changes in diatom communities were significantly correlated with nitrogen deposition in both lakes and climate warming in the upstream lake. </p>
Supplementary material 1 from: Mora D, Carmona J, Jahn R, Zimmermann J, Abarca N (2017) Epilithic diatom communities of selected streams from the Lerma-Chapala Basin, Central Mexico, with the description of two new species. PhytoKeys 88: 39-69. https://doi.org/10.3897/phytokeys.88.14612
Diatom taxa list from the Lerma-Chapala Basin, Central Mexico and identification references : Explanation note: Diatom taxa list from the Lerma‒Chapala Basin, Central Mexico
Metadata from "Multiple stressors in tropical streams: nitrate interactions mediate diatom community responses in experimental streams"
<p>These are datasets on benthic diatom communities sampled in outdoor experimental stream mesocosms in Brazil (ExStream system) under the influence of multiple stressors related to agriculture. The data also include information on the three stressors: sediment (two levels), nitrate (four levels), and water flow (two levels) in a full factorial design.</p> <p>In addition to the datasets, we also provide the R codes used to investigate the individual and interactive effects of the stressors on the benthic diatom communities, analyzing diversity attributes. The dataset also contains chlorophyll-a concentrations.</p>
Original data of diatom communities in two alpine lakes of eastern China
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Data from: Integrating water quality monitoring and diatom community trends to determine landscape-level change in protected lakes.
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