DNA sequences--already publicly available

DNA barcoding gene sequences and files associated with their analysis

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 represents pulse amplitude modulated (PAM) fluorimetric measurements and other data characterizing the periphytic/biofilm communities inhabiting the stream mesocosm substrates during a test run conducted in 2018. This dataset is associated with the following publication: Katona, L., Y. Vadeboncoeur, C. Nietch, and K. Hossler. A Novel Thin-Film Technique to Improve Accuracy of Fluorescence-Based Estimates for Periphytic Biofilms. WATER. MDPI AG, Basel, SWITZERLAND, 13(11): 1464, (2021).

The U.S. Geological Survey monitored algal biomass accrual and concentrations of metals and other trace elements in stream water and periphytic algae at 3-4 day intervals over a 2-week period at 3 locations within the upper and middle portions of the mining-impacted Clark Fork River, Montana, and at one location on the relatively unimpacted Blackfoot River tributary. This data release makes available trends in major and minor trace element concentrations in surface water and periphytic algae, and corresponding trends in concentrations of autotrophic (chlorophyll a) and heterotrophic (ash-free dry mass) algal biomass collected in late July and early August 2015.

This data set, NPP Multi-Biome: Summary Data from Intensive Studies at 125 Sites, 1936-2006, contains a single shapefile that provides site-level summary statistics from 125 sites in five biomes: boreal forest, grassland, temperate forest, tropical forest, and tundra. The spatial coverage is global and spans the time period from 1936 through 2006. Study periods, and both spatial and temporal resolution vary by site. Data include georeferenced location, elevation, mean annual precipitation, mean annual minimum and maximum air temperature, dominant soil type, ecoregion type, dominant plant species, general vegetation types, annual mean or peak living above- and below-ground biomass, average annual above- and below-ground Net Primary Productivity (NPP), and reference information. Additionally study sampling period and intervals, plot management, and long-term site management history are also provided.

This data set includes water quality data and microbial community abundance tables for periphyton samples from this project. The data set also includes extensive R markdown code used to process the data and generate the results included in the report. This dataset is associated with the following publication: Hagy, J., R. Devereux, K. Houghton, D. Beddick, T. Pierce, and S. Friedman. Developing Microbial Community Indicators of Nutrient Exposure in Southeast Coastal Plain Streams using a Molecular Approach. US EPA Office of Research and Development, Washington, DC, USA, 2018.

This data set contains three files. The first file provides net primary productivity (NPP) estimates, vegetation characteristics, and summary climate data for 720 globally-distributed terrestrial sites. Each site is geographically referenced (latitude/longitude) and classified according to biome (i.e., cropland, desert, forest, grassland, Mediterranean, pasture, plantation, savanna, tundra, and wetlands), where known. The data were extracted and synthesized from scientific literature dating from 1869 to 1982. The majority of references were published in the 1960s and 1970s. The second file provides a summary of climate, vegetation type, species, and type for the 720 records. The third file provides the bibliography of 858 original-source references of data on NPP from Esser et al. (1997). Literature that is not directly cross-referenced to the NPP data set records is marked with an asterisk (*). Of the 720 unique NPP records, about two-thirds have above-ground net primary production (ANPP) estimates that range between 1 and 8,530 g/m2/year dry matter, one-fourth of the sites have estimates for below-ground NPP that range between 0 and 5,828 g/m2/year, and more than half of the sites have total NPP estimates that range from 3 to 9,320 g/m2/year dry matter. The high-range estimates are lower when doubtful values, wetlands estimates, and estimates for crops/pastures and other managed systems are excluded from calculations. Revision Notes: Only the documentation for this data set has been modified. The data files have been checked for accuracy and are identical to those originally published in 1998.

Data available in Science Hub includes measurements used to generate Figures 1, 2, S3, and S4. All other data is reported in the manuscript text. This dataset is associated with the following publication: Li, X., L. Peed, M. Sivaganesan, C. Kelty, C. Nietch, and O. Shanks. Evidence of Genetic Fecal Marker Interactions between Water Column and Periphyton in Artificial Streams. ACS Omega. American Chemical Society, Washington, DC, USA, 3(8): 10107-10113, (2018).

This data set provides two data files (.csv format) containing gridded (0.5-degree) estimates of net primary productivity (NPP), elevation, temperature, precipitation, NDVI, and biome type for selected terrestrial regions of the world. The field data used to develop NPP estimates came from 15 worldwide data sources in several different biomes covering the period 1954-1998. NPP values were developed from natural resource field inventories (e.g., forest, rangeland, crop) at different scales, from plot to county; from data compiled from published literature and high resolution maps; from simulation models using key independent variables; from regression analyses with environmental variables; and by using relationships between remotely-sensed spectral vegetation indices and field observations. The first file, NPP_Gridded_3654_cells_R3.csv with 3,654 0.5-degree grid cells, is suitable for biome level and overall analyses because of a larger sample size. In this file, 36 cells have above-ground net primary production (ANPP) only, 320 cells have total net promary production (TNPP) only, and 3,298 cells have both TNPP and ANPP. The second file, NPP_Gridded_2335_unique_cell_R3s.csv, was derived from the larger file and contains 2,335 0.5-degree grid cells after outliers were excluded, replicate measurements were averaged out for each unique geographic location, and cells classified as water, bare ground, and urban were excluded. This smaller data file is more appropriate for model/data inter-comparisons. Overall, gridded ANPP values ranged from 3 to 890 gC/m2/yr, and gridded TNPP values ranged from 3 to 1,235 gC/m2/yr. The lowest values are for sparsely vegetated ground (e.g., open shrublands) and the highest values are for forests. Revision Notes: This data set has been revised to correct the previously reported temporal coverage of field data measurements that were used to develop NPP estimates and the data set title was also corrected to reflect the date change. Missing value codes were added. Please see the Data Set Revisions section of this document for detailed information.