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Diatom and Environmental Data
Raw data associated with this research. This dataset is associated with the following publication: Yuan, L., R. Mitchell, E. Pilgrim, and N. Smucker. Inferences based on diatom compositions improve estimates of nutrient concentrations in streams. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 952: 176032, (2024).
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Diatom and environmental data
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These raw data associated with this research were collected as part of the United States Environmental Protection Agency's 2018-2019 National Rivers and Streams Assessment (NRSA). The worksheet "Water chemistry data" includes environmental variables examined in this study including total phosphorus (TP), total nitrogen (TN), conductivity, pH, and ecoregion. The worksheet "Diatom ASVs" includes relative abundances of gene sequence reads for each amplicon sequence variant (ASV), which are referred to as taxa. This dataset is associated with the following publication: Smucker, N., E. Pilgrim, C. Nietch, L. Gains-Germain, C. Carpenter, J. Darling, L. Yuan, R. Mitchell, and A. Pollard. Using DNA metabarcoding to characterize national scale diatom-environment relationships and to develop indicators in streams and rivers of the United States. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 939: 173502, (2024).
EPA 2018-2019 National Rivers and Streams Assessment Diatom Diversity and Phosphorus Study
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Raw data associated with EPA 2018-2019 National Rivers and Streams Assessment Diatom Diversity and Phosphorus Study. This dataset is associated with the following publication: Yuan, L., R. Mitchell, A. Pollard, C. Nietch, E. Pilgrim, and N. Smucker. Understanding the effects of phosphorus on diatom richness in rivers and streams using taxon–environment relationships. FRESHWATER BIOLOGY. Blackwell Publishing, Malden, MA, USA, 68(3): 473-486, (2023).
Supplementary material for Lee et al. 2019 Taxonomic harmonization may reveal a stronger association between diatom assemblages and total phosphorus in large datasets
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Diatom data have been collected in large-scale biological assessments in the United States, such as the U.S. Environmental Protection Agency’s National Rivers and Streams Assessment (NRSA). However, the effectiveness of diatoms as indicators may suffer if inconsistent taxon identifications across different analysts obscure the relationships between assemblage composition and environmental variables. To reduce these inconsistencies, we harmonized the 2008–2009 NRSA data from nine analysts by updating names to current synonyms and by statistically identifying taxa with high analyst signal (taxa with more variation in relative abundance explained by the analyst factor, relative to environmental variables). We then screened a subset of samples with QA/QC data and combined taxa with mismatching identifications by the primary and secondary analysts. When these combined “slash groups” did not reduce analyst signal, we elevated taxa to the genus level or omitted taxa in difficult species complexes. We examined the variation explained by analyst in the original and revised datasets. Further, we examined how revising the datasets to reduce analyst signal can reduce inconsistency, thereby uncovering the variation in assemblage composition explained by total phosphorus (TP), an environmental variable of high priority for water managers. To produce a revised dataset with the greatest taxonomic consistency, we ultimately made 124 slash groups, omitted 7 taxa in the small naviculoid (e.g., Sellaphora atomoides) species complex, and elevated Nitzschia, Diploneis, and Tryblionella taxa to the genus level. Relative to the original dataset, the revised dataset had more overlap among samples grouped by analyst in ordination space, less variation explained by the analyst factor, and more than double the variation in assemblage composition explained by TP. Elevating all taxa to the genus level did not eliminate analyst signal completely, and analyst remained the most important predictor for the genera Sellaphora, Mayamaea, and Psammodictyon, indicating that these taxa present the greatest obstacle to consistent identification in this dataset. Although our process did not completely remove analyst signal, this work provides a method to minimize analyst signal and improve detection of diatom association with TP in large datasets involving multiple analysts. Examination of variation in assemblage data explained by analyst and taxonomic harmonization may be necessary steps for improving data quality and the utility of diatoms as indicators of environmental variables. This dataset is associated with the following publication: Lee, S., I. Bishop, S. Spaulding, R. Mitchell, and L. Yuan. Taxonomic harmonization may reveal a stronger association between diatom assemblages and total phosphorus in large datasets.. ECOLOGICAL INDICATORS. Elsevier Science Ltd, New York, NY, USA, 102: 166-174, (2019).
Supplementary material for Lee et al. 2019 Taxonomic harmonization may reveal a stronger association between diatom assemblages and total phosphorus in large datasets
공공데이터포털
Diatom data have been collected in large-scale biological assessments in the United States, such as the U.S. Environmental Protection Agency’s National Rivers and Streams Assessment (NRSA). However, the effectiveness of diatoms as indicators may suffer if inconsistent taxon identifications across different analysts obscure the relationships between assemblage composition and environmental variables. To reduce these inconsistencies, we harmonized the 2008–2009 NRSA data from nine analysts by updating names to current synonyms and by statistically identifying taxa with high analyst signal (taxa with more variation in relative abundance explained by the analyst factor, relative to environmental variables). We then screened a subset of samples with QA/QC data and combined taxa with mismatching identifications by the primary and secondary analysts. When these combined “slash groups” did not reduce analyst signal, we elevated taxa to the genus level or omitted taxa in difficult species complexes. We examined the variation explained by analyst in the original and revised datasets. Further, we examined how revising the datasets to reduce analyst signal can reduce inconsistency, thereby uncovering the variation in assemblage composition explained by total phosphorus (TP), an environmental variable of high priority for water managers. To produce a revised dataset with the greatest taxonomic consistency, we ultimately made 124 slash groups, omitted 7 taxa in the small naviculoid (e.g., Sellaphora atomoides) species complex, and elevated Nitzschia, Diploneis, and Tryblionella taxa to the genus level. Relative to the original dataset, the revised dataset had more overlap among samples grouped by analyst in ordination space, less variation explained by the analyst factor, and more than double the variation in assemblage composition explained by TP. Elevating all taxa to the genus level did not eliminate analyst signal completely, and analyst remained the most important predictor for the genera Sellaphora, Mayamaea, and Psammodictyon, indicating that these taxa present the greatest obstacle to consistent identification in this dataset. Although our process did not completely remove analyst signal, this work provides a method to minimize analyst signal and improve detection of diatom association with TP in large datasets involving multiple analysts. Examination of variation in assemblage data explained by analyst and taxonomic harmonization may be necessary steps for improving data quality and the utility of diatoms as indicators of environmental variables. This dataset is associated with the following publication: Lee, S., I. Bishop, S. Spaulding, R. Mitchell, and L. Yuan. Taxonomic harmonization may reveal a stronger association between diatom assemblages and total phosphorus in large datasets.. ECOLOGICAL INDICATORS. Elsevier Science Ltd, New York, NY, USA, 102: 166-174, (2019).
LMR spatial temporal analysis data
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This file includes the following data for 25 stream sites in the Little Miami River watershed: diatom operational taxonomic units with their numbers and relative abundances of rbcL gene sequence reads, watershed land cover, and nutrient concentration and conductivity data. This dataset is associated with the following publication: Yuan, L., N. Smucker, C. Nietch, and E. Pilgrim. Quantifying spatial and temporal relationships between diatoms and nutrients in streams strengthens evidence of nutrient effects from monitoring data. Freshwater Science. The Society for Freshwater Science, Springfield, IL, 41(1): 100-112, (2022).
LMR watershed temporal DNA metabarcoding 2016 study
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LMR watershed temporal DNA metabarcoding 2016 study. This dataset is associated with the following publication: Smucker, N., E. Pilgrim, H. Wu, C. Nietch, J. Darling, M. Molina, B. Johnson, and L. Yuan. Characterizing temporal variability in streams supports nutrient indicator development using diatom and bacterial DNA metabarcoding. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 831: 154960, (2022).
LMR watershed temporal DNA metabarcoding 2016 study
공공데이터포털
LMR watershed temporal DNA metabarcoding 2016 study. This dataset is associated with the following publication: Smucker, N., E. Pilgrim, H. Wu, C. Nietch, J. Darling, M. Molina, B. Johnson, and L. Yuan. Characterizing temporal variability in streams supports nutrient indicator development using diatom and bacterial DNA metabarcoding. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, NETHERLANDS, 831: 154960, (2022).
Dataset 1: Studies included in literature review
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This dataset contains the results of a literature review of experimental nutrient addition studies to determine which nutrient forms were most often measured in the scientific literature. To obtain a representative selection of relevant studies, we searched Web of Science™ using a search string to target experimental studies in artificial and natural lotic systems while limiting irrelevant papers. We screened the titles and abstracts of returned papers for relevance (experimental studies in streams/stream mesocosms that manipulated nutrients). To supplement this search, we sorted the relevant articles from the Web of Science™ search alphabetically by author and sequentially examined the bibliographies for additional relevant articles (screening titles for relevance, and then screening abstracts of potentially relevant articles) until we had obtained a total of 100 articles. If we could not find a relevant article electronically, we moved to the next article in the bibliography. Our goal was not to be completely comprehensive, but to obtain a fairly large sample of published, peer-reviewed studies from which to assess patterns. We excluded any lentic or estuarine studies from consideration and included only studies that used mesocosms mimicking stream systems (flowing water or stream water source) or that manipulated nutrient concentrations in natural streams or rivers. We excluded studies that used nutrient diffusing substrate (NDS) because these manipulate nutrients on substrates and not in the water column. We also excluded studies examining only nutrient uptake, which rely on measuring dissolved nutrient concentrations with the goal of characterizing in-stream processing (e.g., Newbold et al., 1983). From the included studies, we extracted or summarized the following information: study type, study duration, nutrient treatments, nutrients measured, inclusion of TN and/or TP response to nutrient additions, and a description of how results were reported in relation to the research-management mismatch, if it existed. Below is information on how the search was conducted: Search string used for Web of Science advanced search Search conducted on 27 September 2016. TS= (stream* OR creek* OR river* OR lotic OR brook OR headwater OR tributary) AND TS = (mesocosm OR flume OR "artificial stream" OR "experimental stream" OR "nutrient addition") AND TI= (nitrogen OR phosphorus OR nutrient OR enrichment OR fertilization OR eutrophication)
Dataset 1: Studies included in literature review
공공데이터포털
This dataset contains the results of a literature review of experimental nutrient addition studies to determine which nutrient forms were most often measured in the scientific literature. To obtain a representative selection of relevant studies, we searched Web of Science™ using a search string to target experimental studies in artificial and natural lotic systems while limiting irrelevant papers. We screened the titles and abstracts of returned papers for relevance (experimental studies in streams/stream mesocosms that manipulated nutrients). To supplement this search, we sorted the relevant articles from the Web of Science™ search alphabetically by author and sequentially examined the bibliographies for additional relevant articles (screening titles for relevance, and then screening abstracts of potentially relevant articles) until we had obtained a total of 100 articles. If we could not find a relevant article electronically, we moved to the next article in the bibliography. Our goal was not to be completely comprehensive, but to obtain a fairly large sample of published, peer-reviewed studies from which to assess patterns. We excluded any lentic or estuarine studies from consideration and included only studies that used mesocosms mimicking stream systems (flowing water or stream water source) or that manipulated nutrient concentrations in natural streams or rivers. We excluded studies that used nutrient diffusing substrate (NDS) because these manipulate nutrients on substrates and not in the water column. We also excluded studies examining only nutrient uptake, which rely on measuring dissolved nutrient concentrations with the goal of characterizing in-stream processing (e.g., Newbold et al., 1983). From the included studies, we extracted or summarized the following information: study type, study duration, nutrient treatments, nutrients measured, inclusion of TN and/or TP response to nutrient additions, and a description of how results were reported in relation to the research-management mismatch, if it existed. Below is information on how the search was conducted: Search string used for Web of Science advanced search Search conducted on 27 September 2016. TS= (stream* OR creek* OR river* OR lotic OR brook OR headwater OR tributary) AND TS = (mesocosm OR flume OR "artificial stream" OR "experimental stream" OR "nutrient addition") AND TI= (nitrogen OR phosphorus OR nutrient OR enrichment OR fertilization OR eutrophication)
Diatom Assemblages as Indicators of Water Quality in Freshwater Habitats of Guam
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This data package was created 2025-12-03 10:49:12 by NPSTORET and includes selected project, location, and result data. Data are from William J. Zolan and J. A. Marsh's (University of Guam Water and Energy Research Institute of the Western Pacific) 1981 Project Completion Report (Technical Report #29) entitled "Diatom Assemblages as Indicators of Water Quality in Freshwater Habitats of Guam." This diatom survey of various Guam freshwater sites, including those known to be polluted, identified which diatoms were the predominant species in the periphyton according to habitat and water quality, and may be used as biological indicators of increased pollution concentrations. The study also provided ranges of common species diversity indices for the periphyton assemblages. Only water quality data and a diatom species list are presented here. Data contained in WAPA_NPSTORET_BE.ACCDB (NPSTORET back-end file) were filtered to include: Organization: - WAPA: War in the Pacific National Historical Park Project: - WAPA0025: Diatom Assemblages as Indicators of Water Quality in Freshwater Habitats of Guam Station: - Include Trip QC And All Station Visit Results Value Status: - Accepted or Certified (exported as Final) or Final The data package is organized into six data tables: - Projects.csv - describes the purpose and background of the monitoring efforts - Locations.csv - documents the attributes of the monitoring locations/stations - Results.csv - contains the field measurements, observations, and/or lab analyses for each sample/event/data grouping - HUC.csv - enumerates the domain of allowed values for 8-digit and 12-digit hydrologic unit codes utilized by the Locations data table - Characteristics.csv - enumerates the domain of characteristics available in NPSTORET to identify what was sampled, measured or observed in Results - Taxon.csv - enumerates the domain of taxa available in NPSTORET to identify the organism sampled for Results Period of record for filtered data is 1978-10-03 to 1979-07-23. This data package is a snapshot in time of one National Park Service project. The most current data for this project, which may be more or less extensive than that in this data package, can be found on the Water Quality Portal at: https://www.waterqualitydata.us/data/Result/search?project=WAPA0025&mimeType=csv&zip=yes&dataProfile=biological&providers=STORET