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Michelle Baker

Utah State University | Professor

Subject Areas: aquatic ecology, biogeochemistry, hydrology

 Recent activity

ABSTRACT:

This resource contains the results of a diphenhydramine dose-response experiment conducted on stream biofilms at a site on the Logan River in northern Utah. We grew stream biofilms on inorganic (fritted glass disc) and organic (cellulose sponge) substrates in the river for 20 days. The biofilm-colonized substrates were then placed as caps on contaminant exposure substrates (CES), 1-oz plastic cups filled with agar amended with diphenhydramine at a series of concentrations (control, 0.5 mM, 0.75 mM, 1.25m M, 2.5 mM, 15 mM). CES were then deployed in the river for 20 days.

At the end of the CES deployment, the biofilm-colonized substrates were used to perform a series of in-stream incubations. We measured respiration and productivity using a modified light-dark bottle incubation method and nitrogen fixation rates 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_diphenhydramine” 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 diphenhydramine treatment and substrate type. The Word document “methods_diphenhydramine” describes the analytical methods used to measure chlorophyll and ash-free dry mass.

We characterized light availability and nutrient concentrations at the study site. The Word document “methods_diphenhydramine” describes the methods used to measure site characteristics and the analytical methods used to measure nutrient concentrations. The CSV file “site_characteristics_diphenhydramine” contains percent canopy openness, transmitted PAR, transmitted solar shortwave radiation, total nitrogen, total phosphorus, ammonium, nitrate, soluble reactive phosphorus, dissolved total iron, and dissolved ferrous iron concentrations.

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ABSTRACT:

This resource contains the results of a nutrient uptake incubation experiment conducted at a mountain and urban site on the Logan River in northern Utah. The experiments were performed with biofilms grown for 14-15 days on nutrient diffusing substrates (NDS), 1-oz plastic cups filled with agar and capped with a fritted glass disc. We performed the nutrient uptake experiment by incubating biofilm-colonized discs in clear plastic jars filled with stream water spiked with nitrogen (N) and phosphorus (P) at a series of concentrations. The CSV file "nutrient uptake treatments" lists the treatments used in the nutrient uptake experiment at each site. Biofilms were incubated in situ for 2 hours at midday. Samples for dissolved nutrient analysis were collected from the nutrient treatment solutions used to fill the jars and from each jar at the end of the incubation. The dissolved oxygen concentration in each jar was measured at the start and end of the incubation. We calculated nutrient uptake rates as the rate of loss in water nutrients and net primary production as the change in dissolved oxygen concentration. We measured biofilm biomass as chlorophyll a. The CSV file “nutrient uptake results” contains summary statistics (mean, standard deviation, count) of nutrient uptake rates, net primary production rates, and chlorophyll a concentrations in nutrient uptake treatments at each site. The Word document “nutrient uptake analytical methods” contains the analytical methods used to measure nutrient concentrations.

We also examined biofilm nutrient limitation at each site using NDS. We constructed nutrient limitation NDS by filling 1-oz plastic cups with agar amended with either no nutrients (control), 0.5 M NH4-N (N), 0.5 M PO4-P (P), or 0.5 M NH4-N + 0.5 M PO4-P (N+P). NDS were then capped with a fritted glass disc and placed in the stream at each site during the same period that NDS for the nutrient uptake experiment were deployed. Biofilm biomass was measured as chlorophyll a and ash-free dry mass. The CSV file “nutrient limitation results” contains summary statistics of chlorophyll a concentration and ash-free dry mass in each nutrient treatment at each site. The Word document “nutrient uptake analytical methods” contains the analytical methods used to measure chlorophyll and ash-free dry mass.

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ABSTRACT:

This resource contains the results of a 13C-hemicellulose DNA stable isotope probing (DNA-SIP) experiment that tested how nutrients and light exposure influence hemicellulose decomposition and hemicellulose-degrading bacterial populations. We conducted our experiment with stream biofilms grown on nutrient diffusing substrates (NDS) in the Middle Provo River (Utah), at a site below Jordanelle Reservoir (June 1, 2016 - June 20, 2016). To construct the nutrient diffusing substrates, we filled 1-oz plastic cups with unamended agar and then capped the agar with a fritted glass disc, which served as a platform for biofilm colonization. To assess potential nutrient limitation of the stream biofilms grown for our hemicellulose DNA-SIP experiment, we also deployed NDS containing agar amended with either no nutrients (control), nitrogen (N; 0.5 M NH4-N), phosphorus (P; 0.5 M PO4-P), or N and P (N+P) and measured biomass (chlorophyll a, ash-free dry mass) and calculated Autotrophic Index values. The CSV file “hemicellulose DNA-SIP nutrient limitation” contains summary statistics (mean, standard deviation, count) of chlorophyll, ash-free dry mass, and Autotrophic Index values on each nutrient treatment. The Word document “hemicellulose DNA-SIP analytical methods” describes the analytical methods used to measure chlorophyll and ash-free dry mass. To characterize conditions at the site, we collected water column samples for total and dissolved nutrient analyses and calculated degree days from time series water temperature data collected as part of the NSF-funded iUTAH project (Award number 1208732). The CSV file “hemicellulose DNA-SIP site characteristics” reports degree days and water column concentrations of total nitrogen (TN), total phosphorus (TP), ammonium (NH4-N), nitrate (NO3-N + NO2-N), and soluble reactive phosphorus (SRP-P) (nutrient concentrations are mean of 3 replicates). The Word document “hemicellulose DNA-SIP analytical methods” describes the analytical methods used to measure nutrient concentrations.

Biofilms grown on unamended NDS were used to perform the hemicellulose DNA-SIP experiment. Biofilm-colonized discs were placed in clear glass jars containing filter-sterilized river water amended with 13C-hemicellulose (approximately 540 µmol C L-1). We tested eight combinations of nutrient (control, N, P, N+P) and light exposure (light, dark) treatments. Nutrient treatments were applied by adding N (2.5 mg NH4-N L-1) and/or P (0.36 mg PO4-P L-1) to the appropriate jars. To apply the light exposure treatments, we wrapped dark treatment jars in aluminum foil and left the light treatment jars unwrapped. We incubated jars for 10 days on a shaker table (50 rpm) in a growth chamber held at a temperature of 12°C set to a 15-hour photoperiod, which was illuminated using cool white fluorescent bulbs (4200 K color temperature, Sylvania Supersaver, Osram Sylvania Products Inc.). The average photosynthetically active radiation, measured with a LI-COR LI-190 quantum sensor, was 27.3 µE m-2 sec-1. We collected biofilms and water samples from each treatment on day 0 and day 10. Biofilms were frozen for DNA-SIP analyses. Water samples were collected for dissolved organic carbon (DOC) concentration and dissolved organic matter (DOM) fluorescence characterization analyses. We used DOC and DOM data to calculate Fluorescence Index (FI), Freshness Index (BIX), Humification Index (HIX) and specific ultraviolet absorbance (SUVA254; calculated by dividing the absorbance at 254 nm by the DOC concentration). The CSV file “hemicellulose DNA-SIP DOC and DOM” contains summary statistics of DOC and DOM data in each hemicellulose incubation treatment. The Word document “hemicellulose DNA-SIP analytical methods” describes the analytical methods used to measure DOC and DOM.

DNA-SIP analyses were conducted by first extracting genomic DNA from each biofilm-colonized disc. We next separated the DNA in each sample by density using ultracentrifugation (58,000 rpm, 20°C, at least 72 hours). We collected 28 density fractions from the resulting gradient with a fraction recovery system and pooled the low density fractions containing unlabeled DNA and high density fractions containing 13C labeled DNA in each sample. We then composited the low and high density fractions from all samples within each hemicellulose incubation treatment. We performed target metagenomics of the 16S rRNA gene. The Word document “hemicellulose DNA-SIP analytical methods” describes the DNA-SIP community composition analysis methods. The CSV file “hemicellulose DNA-SIP shared OTU” lists the number of sequences for each OTU in the low and high density fractions of each hemicellulose incubation treatment. The CSV file “hemicellulose DNA-SIP taxonomy” contains OTU classification information.

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ABSTRACT:

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 CSV files “bacteria_otu_CES” and “eukaryotes_otu_CES” list the number of sequences of each bacterial and eukaryotic OTU, respectively, in contaminant treatments. The CSV files “bacteria_tax_CES” and “eukaryotes_tax_CES” contain taxonomic classification information for bacterial and eukaryotic OTUs, respectively.

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 low- and high-flow periods. The masses of 16 pharmaceuticals which had sorbed onto the POCIS were measured using high performance liquid chromatography combined with tandem mass spectrometry. We used the resulting pharmaceutical masses and uptake rates reported in the literature to calculate the time-weighted average concentration of each pharmaceutical. Average daily discharge was calculated using time series discharge data collected by the iUTAH project. The CSV file “POCIS_CES” contains time-weighted average concentrations of 16 pharmaceuticals and average daily discharge at each site during low- and high-flow periods.

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Generic Generic
Effects of nutrient and pharmaceutical additions on stream biofilm biomass, function, and community composition
Created: July 16, 2016, 5:54 p.m.
Authors: Elizabeth Ogata · Donald Long · Michelle Baker · Zachary Aanderud · Emma Rosi · Trevor Smart

ABSTRACT:

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 CSV files “bacteria_otu_CES” and “eukaryotes_otu_CES” list the number of sequences of each bacterial and eukaryotic OTU, respectively, in contaminant treatments. The CSV files “bacteria_tax_CES” and “eukaryotes_tax_CES” contain taxonomic classification information for bacterial and eukaryotic OTUs, respectively.

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 low- and high-flow periods. The masses of 16 pharmaceuticals which had sorbed onto the POCIS were measured using high performance liquid chromatography combined with tandem mass spectrometry. We used the resulting pharmaceutical masses and uptake rates reported in the literature to calculate the time-weighted average concentration of each pharmaceutical. Average daily discharge was calculated using time series discharge data collected by the iUTAH project. The CSV file “POCIS_CES” contains time-weighted average concentrations of 16 pharmaceuticals and average daily discharge at each site during low- and high-flow periods.

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Generic Generic
Stream biofilm 13C-hemicellulose DNA stable isotope probing experiment
Created: Aug. 6, 2016, 4:43 p.m.
Authors: Elizabeth Ogata · Sandra Udy · Michelle Baker · Zachary Aanderud

ABSTRACT:

This resource contains the results of a 13C-hemicellulose DNA stable isotope probing (DNA-SIP) experiment that tested how nutrients and light exposure influence hemicellulose decomposition and hemicellulose-degrading bacterial populations. We conducted our experiment with stream biofilms grown on nutrient diffusing substrates (NDS) in the Middle Provo River (Utah), at a site below Jordanelle Reservoir (June 1, 2016 - June 20, 2016). To construct the nutrient diffusing substrates, we filled 1-oz plastic cups with unamended agar and then capped the agar with a fritted glass disc, which served as a platform for biofilm colonization. To assess potential nutrient limitation of the stream biofilms grown for our hemicellulose DNA-SIP experiment, we also deployed NDS containing agar amended with either no nutrients (control), nitrogen (N; 0.5 M NH4-N), phosphorus (P; 0.5 M PO4-P), or N and P (N+P) and measured biomass (chlorophyll a, ash-free dry mass) and calculated Autotrophic Index values. The CSV file “hemicellulose DNA-SIP nutrient limitation” contains summary statistics (mean, standard deviation, count) of chlorophyll, ash-free dry mass, and Autotrophic Index values on each nutrient treatment. The Word document “hemicellulose DNA-SIP analytical methods” describes the analytical methods used to measure chlorophyll and ash-free dry mass. To characterize conditions at the site, we collected water column samples for total and dissolved nutrient analyses and calculated degree days from time series water temperature data collected as part of the NSF-funded iUTAH project (Award number 1208732). The CSV file “hemicellulose DNA-SIP site characteristics” reports degree days and water column concentrations of total nitrogen (TN), total phosphorus (TP), ammonium (NH4-N), nitrate (NO3-N + NO2-N), and soluble reactive phosphorus (SRP-P) (nutrient concentrations are mean of 3 replicates). The Word document “hemicellulose DNA-SIP analytical methods” describes the analytical methods used to measure nutrient concentrations.

Biofilms grown on unamended NDS were used to perform the hemicellulose DNA-SIP experiment. Biofilm-colonized discs were placed in clear glass jars containing filter-sterilized river water amended with 13C-hemicellulose (approximately 540 µmol C L-1). We tested eight combinations of nutrient (control, N, P, N+P) and light exposure (light, dark) treatments. Nutrient treatments were applied by adding N (2.5 mg NH4-N L-1) and/or P (0.36 mg PO4-P L-1) to the appropriate jars. To apply the light exposure treatments, we wrapped dark treatment jars in aluminum foil and left the light treatment jars unwrapped. We incubated jars for 10 days on a shaker table (50 rpm) in a growth chamber held at a temperature of 12°C set to a 15-hour photoperiod, which was illuminated using cool white fluorescent bulbs (4200 K color temperature, Sylvania Supersaver, Osram Sylvania Products Inc.). The average photosynthetically active radiation, measured with a LI-COR LI-190 quantum sensor, was 27.3 µE m-2 sec-1. We collected biofilms and water samples from each treatment on day 0 and day 10. Biofilms were frozen for DNA-SIP analyses. Water samples were collected for dissolved organic carbon (DOC) concentration and dissolved organic matter (DOM) fluorescence characterization analyses. We used DOC and DOM data to calculate Fluorescence Index (FI), Freshness Index (BIX), Humification Index (HIX) and specific ultraviolet absorbance (SUVA254; calculated by dividing the absorbance at 254 nm by the DOC concentration). The CSV file “hemicellulose DNA-SIP DOC and DOM” contains summary statistics of DOC and DOM data in each hemicellulose incubation treatment. The Word document “hemicellulose DNA-SIP analytical methods” describes the analytical methods used to measure DOC and DOM.

DNA-SIP analyses were conducted by first extracting genomic DNA from each biofilm-colonized disc. We next separated the DNA in each sample by density using ultracentrifugation (58,000 rpm, 20°C, at least 72 hours). We collected 28 density fractions from the resulting gradient with a fraction recovery system and pooled the low density fractions containing unlabeled DNA and high density fractions containing 13C labeled DNA in each sample. We then composited the low and high density fractions from all samples within each hemicellulose incubation treatment. We performed target metagenomics of the 16S rRNA gene. The Word document “hemicellulose DNA-SIP analytical methods” describes the DNA-SIP community composition analysis methods. The CSV file “hemicellulose DNA-SIP shared OTU” lists the number of sequences for each OTU in the low and high density fractions of each hemicellulose incubation treatment. The CSV file “hemicellulose DNA-SIP taxonomy” contains OTU classification information.

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Generic Generic

ABSTRACT:

This resource contains the results of a nutrient uptake incubation experiment conducted at a mountain and urban site on the Logan River in northern Utah. The experiments were performed with biofilms grown for 14-15 days on nutrient diffusing substrates (NDS), 1-oz plastic cups filled with agar and capped with a fritted glass disc. We performed the nutrient uptake experiment by incubating biofilm-colonized discs in clear plastic jars filled with stream water spiked with nitrogen (N) and phosphorus (P) at a series of concentrations. The CSV file "nutrient uptake treatments" lists the treatments used in the nutrient uptake experiment at each site. Biofilms were incubated in situ for 2 hours at midday. Samples for dissolved nutrient analysis were collected from the nutrient treatment solutions used to fill the jars and from each jar at the end of the incubation. The dissolved oxygen concentration in each jar was measured at the start and end of the incubation. We calculated nutrient uptake rates as the rate of loss in water nutrients and net primary production as the change in dissolved oxygen concentration. We measured biofilm biomass as chlorophyll a. The CSV file “nutrient uptake results” contains summary statistics (mean, standard deviation, count) of nutrient uptake rates, net primary production rates, and chlorophyll a concentrations in nutrient uptake treatments at each site. The Word document “nutrient uptake analytical methods” contains the analytical methods used to measure nutrient concentrations.

We also examined biofilm nutrient limitation at each site using NDS. We constructed nutrient limitation NDS by filling 1-oz plastic cups with agar amended with either no nutrients (control), 0.5 M NH4-N (N), 0.5 M PO4-P (P), or 0.5 M NH4-N + 0.5 M PO4-P (N+P). NDS were then capped with a fritted glass disc and placed in the stream at each site during the same period that NDS for the nutrient uptake experiment were deployed. Biofilm biomass was measured as chlorophyll a and ash-free dry mass. The CSV file “nutrient limitation results” contains summary statistics of chlorophyll a concentration and ash-free dry mass in each nutrient treatment at each site. The Word document “nutrient uptake analytical methods” contains the analytical methods used to measure chlorophyll and ash-free dry mass.

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Generic Generic
Stream biofilm diphenhydramine dose-response experiment
Created: Oct. 1, 2017, 2:53 p.m.
Authors: Elizabeth Ogata · Donald Long · Michelle Baker · Zachary Aanderud · Emma Rosi

ABSTRACT:

This resource contains the results of a diphenhydramine dose-response experiment conducted on stream biofilms at a site on the Logan River in northern Utah. We grew stream biofilms on inorganic (fritted glass disc) and organic (cellulose sponge) substrates in the river for 20 days. The biofilm-colonized substrates were then placed as caps on contaminant exposure substrates (CES), 1-oz plastic cups filled with agar amended with diphenhydramine at a series of concentrations (control, 0.5 mM, 0.75 mM, 1.25m M, 2.5 mM, 15 mM). CES were then deployed in the river for 20 days.

At the end of the CES deployment, the biofilm-colonized substrates were used to perform a series of in-stream incubations. We measured respiration and productivity using a modified light-dark bottle incubation method and nitrogen fixation rates 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_diphenhydramine” 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 diphenhydramine treatment and substrate type. The Word document “methods_diphenhydramine” describes the analytical methods used to measure chlorophyll and ash-free dry mass.

We characterized light availability and nutrient concentrations at the study site. The Word document “methods_diphenhydramine” describes the methods used to measure site characteristics and the analytical methods used to measure nutrient concentrations. The CSV file “site_characteristics_diphenhydramine” contains percent canopy openness, transmitted PAR, transmitted solar shortwave radiation, total nitrogen, total phosphorus, ammonium, nitrate, soluble reactive phosphorus, dissolved total iron, and dissolved ferrous iron concentrations.

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