This readme.txt file was generated on <2023.09.18> by Hailey Sauer ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset Data for Reduced snow and increased nutrients show enhanced ice-associated photoautotrophic growth using a modified experimental under-ice design 2. Author Information Principal Investigator Contact Information Name: Lesley Knoll Institution: Miami University Address: 700 E. High St, Oxford, OH 45056 Email: knolllb@miamioh.edu Associate or Co-investigator Contact Information Name: Hailey Sauer Institution: University of Minnesota - Twin Cities Address: 1445 Gortner Ave, St. Paul, MN 55108 Email: breis014@umn.edu 3. Date of data collection: 2021-02-18 - 2021-03-15 4. Geographic location of data collection: Lake Itasca, Minnesota, USA 5. Information about funding sources that supported the collection of the data: H.M.S. received support from NSF grant #1948058. 6. Overview of the data (abstract): We modified an existing stream method to create a novel under-ice approach by deploying nutrient diffusing substrates (single nutrient amendments, nitrogen or phosphorus; combined enrichment of nitrogen and phosphorus) under two different light scenarios (snow covered, reduced light; snow removed, increased light) near the water-ice interface to mimic the habitat of ice-associated photoautotrophs. The data associated with the nutrient diffusing substrates are: chlorophyll a concentrations, 16S, and 18S. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC0 1.0 Universal (https://creativecommons.org/publicdomain/zero/1.0/) 2. Links to publications that cite or use the data: Knoll, L.B., B. Fry, N.M. Hayes, and H.M. Sauer. 2023. Reduced snow and increased nutrients show enhanced ice-associated photoautotrophic growth using a modified experimental under-ice design. Limnology and Oceanography. https://doi.org/10.1002/lno.12469 3. Was data derived from another source? No If yes, list source(s): 4. Terms of Use: Data Repository for the U of Minnesota (DRUM) By using these files, users agree to the Terms of Use. https://conservancy.umn.edu/pages/drum/policies/#terms-of-use --------------------- DATA & FILE OVERVIEW --------------------- 1. File List A. Filename: NDS_chl.csv Short description: chlorophyll-a concentrations across snow treatments and nutrient treatments for the 21 day experiment and 25 day experiment. B. Filename: 16S_Sequences zipped folder Short description: folder containing 8 fastq files for 4 paired-end 16S V4 amplicon sequencing samples. Files are named based on their nutrient treatment replication and are for the 25 day experiment. Files are named with the following convention: LakeName_NutrientTreatment_ReplicateNumber_InternalLabel_R1/R2_001.fastq (where R1 is the forward read and R2 is the reverse read) C. Filename: 18S_Sequences zipped folder Short description: folder containing 8 fastq files for 4 paired-end 18S V9 amplicon sequencing samples. Files are named based on their nutrient treatment replication and are for the 25 day experiment. Files are named with the following convention: LakeName_NutrientTreatment_ReplicateNumber_InternalLabel_R1/R2_001.fastq (where R1 is the forward read and R2 is the reverse read) 2. Relationship between files: The main dataset is "NDS_chl.csv" and has chlorophyll-a concentrations for all NDS deployed in the experiment. The 18S_Sequences and 16S_Sequences are the 18S and 16S data from a subset of NDS. -------------------------- METHODOLOGICAL INFORMATION -------------------------- 1. Description of methods used for collection/generation of data: See publication (in review) 2. Methods for processing the data: See publication for full methods (in review). Condensed methods (from in review manuscript): Our experiment was conducted in Lake Itasca, a mesotrophic, dimictic lake in northern Minnesota, USA. We regulated snow cover (i.e., light) and nutrients available to photoautotrophs in situ. Two frames were deployed under natural snow cover and ice (hereafter, snow covered) and two frames were deployed under ice only (hereafter, snow removed). All experimental frames were deployed on 18 February 2021 and ice formed over the holes by the next morning. Two experimental frames (one snow removed, one snow covered) were retrieved on 11 March 2021 (21 day experiment) and the final two (one snow removed, one snow covered) were retrieved on 15 March 2021 (25 day experiment). We anticipated the final two frames would incubate in the water for 30 days. Although there was snowfall (12.7 cm) on 11 March, a few sunny and warm days melted the remaining snow by 15 March. Thus, the experiment ended early. We assessed light and nutrient limitation of ice-associated photoautotrophs by modifying a nutrient diffusing substrata (NDS) stream method in which plastic containers were filled with agar either amended with nutrients (nutrient treatments) or lacking nutrient amendments (control) covered by a fritted glass disc to measure photoautotrophic biomass via chlorophyll-a concentration. Each experimental frame held 20 NDS with 5 replicates per nutrient treatment: Control (no nutrients added), + N (0.5 mol L-1 N added as NaNO3 and NH4Cl), + P (0.5 mol L-1 P added as KH2PO4), and + N & P (0.5 mol L-1 N added as NaNO3 and NH4Cl and 0.5 mol L-1 P added as KH2PO4, Fig. 1A, 1B). Immediately after retrieving NDS, we removed each fritted glass disc and placed each in a 50 mL centrifuge tube. All tubes were stored at -20 ˚C until analysis of chlorophyll-a and DNA. We extracted chlorophyll-a from the glass frits with 95% ethanol. Samples were centrifuged (5000 RPM, 15 minutes) and analyzed on a Turner Trilogy fluorometer (Turner Designs, San Jose, CA) equipped with a chlorophyll-a non-acidification module. We saved the ethanol extracted chlorophyll-a for DNA analysis on eight samples (two of each nutrient treatment from snow covered conditions from the 25 day experiment). We pelleted samples and extracted DNA from the pellet using a Qiagen PowerLyzer PowerSoil DNA extraction kit following manufacturer protocols. We were only able to recover enough DNA from four of the eight samples for sequencing (2 +NP, 1 +N and 1 +P). We performed negative controls for each round of DNA extractions by carrying out extractions on blanks, using only reagents without a sample. We determined final bulk DNA concentrations using a Qubit dsDNA HS Assay kit and Qubit Fluorometer. While we detected no DNA in any of our negative controls, we still attempted to prepare libraries and sequence them. Positive controls included a Zymo mock community (16S SSU, hereafter 16S) and snow algae cultures (18S SSU, hereafter 18S). We prepared sequencing libraries using a 2-step PCR wherein the first PCR amplified the region of interest (16S V4 and 18S V9) and the second PCR added barcodes and Illumina adapters to the amplicons. Our final datasets following post-processing contained 81,619 sequences across 1,866 taxa (16S-V4) and 139,920 sequences across 45,006 taxa (18S-V9). We then further filtered both datasets to remove singletons, rarefied to 99% of the lowest sampling depth per region (16S - 4,534 per sample; 18S - 7,658 per sample), and converted counts to relative abundance. 3. Instrument- or software-specific information needed to interpret the data: None 4. Standards and calibration information, if appropriate: NA 5. Environmental/experimental conditions: Snow treatments: 1) Snow-covered (ambient snow conditions; dark) and snow-removed (daily snow removal by shovel; light). Nutrient treatments: Control (no nutrients added), + N (0.5 mol L-1 N added as NaNO3 and NH4Cl), + P (0.5 mol L-1 P added as KH2PO4), and + N & P (0.5 mol L-1 N added as NaNO3 and NH4Cl and 0.5 mol L-1 P added as KH2PO4). 6. Describe any quality-assurance procedures performed on the data: Data have been closely reviewed. No data were removed from the "NDS-chl.csv" file. Sequencing data are raw reads from Illumina and have undergone no quality-assurance in their current, uploaded form. 7. People involved with sample collection, processing, analysis and/or submission: Authors: Lesley Knoll, Benton Fry, Nicole Hayes, and Hailey Sauer. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: NDS_chl.csv ----------------------------------------- 1. Number of variables: 6 2. Number of cases/rows: 80 3. Missing data codes: none 4. Variable List 1. Name: end.date Description: Date the experimental incubation ended in M/DD/YYYY format. All experiments were initiated on 18-Feb-2021. 2. Name: length Description: Number of days of the experimental incubation period. 3. Name: nutrient.treatment Description: Nutrient treatment for each nutrient diffusing substrate. Control (no amendment), N+ (nitrogen added), P+ (phosphorus added) and NP+ (nitrogen and phosphorus added). 4. Name: snow.treatment Description: Snow treatment for each nutrient diffusing substrate: dark (snow-covered; ambient snow cover) and light (snow-removed). 5. Name: frame Desciption: Frame identification number for each nutrient diffusing substrate. 6. Name: chl Description: Chlorophyll-a concentrations (micrograms/cm2) at the end of the incubation for each nutrient diffusing substrate.