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Effects of nutrient and pharmaceutical additions on stream biofilm biomass, function, and community composition

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Created: Jul 16, 2016 at 5:54 p.m.
Last updated: Aug 14, 2019 at 10:38 p.m.
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This resource contains the results of an experiment to test the effects of nutrients and pharmaceuticals on stream biofilms at montane and urban sites in the Logan River, Red Butte Creek, and Middle Provo River watersheds located in northern Utah. We constructed contaminant exposure substrates (CES) by filling 1-oz plastic cups with agar amended with individual and combined additions of nutrients (nitrogen, phosphorus, iron) and pharmaceuticals (caffeine, diphenhydramine). The CSV file “treatments_CES” lists the contaminant treatments included in the CES experiment. We capped the agar with an inorganic (fritted glass disc) or organic (cellulose sponge) substrate to select for biofilm assemblages dominated by autotrophic and heterotrophic microbes, respectively, and then deployed CES in the river at each site for 18 - 26 days.

At the end of the deployment period, we used biofilms grown on CES to perform a series of in-stream incubations. We measured respiration and productivity using a modified light-dark bottle incubation method and nitrogen fixation using an acetylene reduction assay. We measured biofilm biomass (chlorophyll a, ash-free dry mass) and calculated Autotrophic Index values (calculated as chlorophyll a concentration divided by ash-free dry mass). The CSV file “biomass_function_CES” contains summary statistics (mean, standard deviation, count) of respiration rates, gross primary production rates, nitrogen fixation rates, chlorophyll a concentrations, ash-free dry mass, and Autotrophic Index values of biofilms on each contaminant treatment and substrate type at our study sites. The Word document “methods_CES” describes the analytical methods used to measure chlorophyll and ash-free dry mass.

To examine microbial community composition of biofilms grown on CES, were used target metagenomics of the 16S rRNA and 18S rRNA genes to identify bacterial and eukaryotic taxa, respectively. The Word document "methods_CES" describes our sequence analysis methods. The folders "bacteria_fastq" and "eukaryotes_fastq" contain the bacterial and eukaryotic fastq files, respectively and the CSV files "bacteria_design_CES" and "eukaryotes_design_CES" describe the contaminant treatment and study location for each sample. The CSV files “bacteria_tax_CES” and “eukaryotes_tax_CES” contain taxonomic classification information for bacterial and eukaryotic OTUs, respectively. The CSV files “bacteria_otu_CES” and “eukaryotes_otu_CES” list the number of sequences of each bacterial and eukaryotic OTU, respectively, in contaminant treatments, with both datasets rarefied to the smallest sample size (bacteria = 27,704 sequences; eukaryotes = 1,523 sequences). The CSV file "bacteria_abun_photo_core_CES" lists bacterial OTUs that were abundant (≥0.1% relative abundance) and rare (<0.1 relative abundance) and potential photoautotrophs and potential heterotrophs. The file also lists bacterial OTUs that were identified as core taxa in each contaminant treatment by land-use combination, where core taxa were defined as OTUs present in at least 75% of samples in a specific grouping.

We characterized light availability, water temperature, and nutrient concentrations at each study site. The Word document "methods_CES" describes our methods for measuring these site characteristics and the analytical methods used to measure nutrient concentrations. The CSV file “site_characteristics_CES” contains percent canopy openness, transmitted incoming PAR, transmitted solar shortwave radiation, degree days, total nitrogen, total phosphorus, ammonium, nitrate, soluble reactive phosphorus, total dissolved iron, and total ferrous iron concentrations at each site.

We examined water column pharmaceutical concentrations at one site on each river using Polar Organic Contaminant Integrative Samplers (POCIS). POCIS were deployed for 20-26 days during summer and fall 2015. The masses of 19 pharmaceuticals which had sorbed onto the POCIS were measured using high performance liquid chromatography combined with tandem mass spectrometry. The CSV file “POCIS_CES” reports concentrations of pharmaceuticals that accumulated in each POCIS (expressed as ng/POCIS) and time-weighted average concentrations of pharmaceuticals (expressed as ng/L), calculated using the resulting pharmaceutical masses and uptake rates reported in the literature. Average daily discharge was calculated using time series discharge data collected by the iUTAH project.

Subject Keywords



Coordinate System/Geographic Projection:
WGS 84 EPSG:4326
Coordinate Units:
Decimal degrees
Place/Area Name:
Multiple Watersheds
North Latitude
East Longitude
South Latitude
West Longitude


Start Date:
End Date:


Additional Metadata

Name Value
Observed variables in "POCIS_CES" CSV file average daily discharge (m3/s), caffeine concentration (ng/L), diphenhydramine concentration (ng/L), 1,7-dimethylxanthine concentration (ng/L), acetaminophen concentration (ng/L), amphetamine concentration (ng/L), carbamazepine concentration (ng/L), cimetidine concentration (ng/L), cotinine concentration (ng/L), MDA concentration (ng/L), MDMA concentration (ng/L), methamphetamine concentration (ng/L), morphine concentration (ng/L), sulfamethazine concentration (ng/L), sulfamethoxazole concentration (ng/L), thiabendazole concentration (ng/L), azithromycin concentration (ng/L), phenazone concentration (ng/L), sulfachloropyridazine concentration (ng/L), trimethoprim concentration (ng/L)
Observed variables in "biomass_function_CES" CSV file gross primary production (mg O2/m2/hr), respiration (mg O2/m2/hr), nitrogen fixation rate (ug N2/m2/hr), chlorophyll a concentration (chl; mg/m2), ash-free dry mass (g/m2), Autotrophic Index (calculated as ash-free dry mass (mg/m2) divided by chlorophyll a concentration (mg/m2))
Observed variables in "site_characteristics_CES" CSV file total nitrogen (mg N/L), total phosphorus (mg P/L), ammonium (mg NH4-N/L), nitrate (mg NO3-N+NO2-N/L), soluble reactive phosphorus (mg SRP-P/L), total dissolved iron (ug/L), dissolved ferrous iron (ug/L), percent canopy openness, transmitted photosynthetically active radiation (umols/m2/day), transmitted solar shortwave radiation (W/m2/day)


Funding Agencies

This resource was created using funding from the following sources:
Agency Name Award Title Award Number
National Science Foundation iUTAH-innovative Urban Transitions and Aridregion Hydro-sustainability 1208732

How to Cite

Ogata, E., D. Long, Z. Aanderud, M. Baker, E. Rosi, T. Smart (2019). Effects of nutrient and pharmaceutical additions on stream biofilm biomass, function, and community composition, HydroShare,

This resource is shared under the Creative Commons Attribution CC BY.


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