DOI: 10.5061/dryad.qnk98sfps
title: Data from: High temperatures and low soil moisture synergistically reduce switchgrass yields from marginal field sites and inhibit fermentation

description: 'Marginal lands' are low productivity sites abandoned from
 agriculture for reasons such as low or high soil water content,
 challenging topography, or nutrient deficiency. To avoid competition with
 crop production, cellulosic bioenergy crops have been proposed for
 cultivation on marginal lands, however on these sites they may be more
 strongly affected by environmental stresses such as low soil water
 content. In this study we used rainout shelters to induce low soil
 moisture on marginal lands and determine the effect of soil water stress
 on switchgrass growth and the subsequent production of bioethanol. Five
 marginal land sites that span a latitudinal gradient in Michigan and
 Wisconsin were planted to switchgrass in 2013 and during the 2018-2021
 growing seasons were exposed to reduced precipitation under rainout
 shelters in comparison to ambient precipitation. The effect of reduced
 precipitation was related to the environmental conditions at each site and
 biofuel production metrics (switchgrass biomass yields and composition and
 ethanol production). During the first year (2018), the rainout shelters
 were designed with 60% rain exclusion, which did not affect biomass yields
 compared to ambient conditions at any of the field sites, but decreased
 switchgrass fermentability at the Wisconsin Central - Hancock site. In
 subsequent years, the shelters were redesigned to fully exclude rainfall,
 which led to reduced biomass yields and inhibited fermentation for three
 sites. When switchgrass was grown in soils with large reductions in
 moisture and increases in temperature, the potential for biofuel
 production was significantly reduced, exposing some of the challenges
 associated with producing biofuels from lignocellulosic biomass grown
 under drought conditions.
description: Methods can be found in Chipkar et al. 2023. High temperatures
 and low soil moisture synergistically reduce switchgrass yields from
 marginal field sites and inhibit fermentation. GCB Bioenergy. 
description: # Data From: High temperatures and low soil moisture synergistically
 reduce switchgrass yields from marginal field sites and inhibit
 fermentation This README file was generated on 2024-01-11 by Rebecca Ong.
 ## GENERAL INFORMATION 1. **Title of Dataset:** Data from: High
 temperatures and low soil moisture synergistically reduce switchgrass
 yields from marginal field sites and inhibit fermentation 2. **Author
 Information** A. Principal Investigator Contact Information Name: Rebecca
 Ong Institution: Michigan Technological University Address: Houghton, MI
 USA Email: 3. **Date of data collection (single
 date, range, approximate date):** 2018-2021 4. **Geographic locations of
 data collection:** A. Michigan South–Lux Arbor (latitude: 42.4763,
 longitude: −85.4518, altitude: 295 m a.s.l) B. Michigan Central–Lake City
 (latitude: 44.3095, longitude: −85.2031, altitude: 372 m a.s.l) C.
 Michigan North–Escanaba (latitude: 45.7646, longitude: −87.1838, altitude:
 206 m a.s.l) D. Wisconsin Central–Hancock (latitude: 44.1191, longitude:
 −89.5332, altitude: 332 m a.s.l) E. Wisconsin North–Rhinelander (latitude:
 45.6668, longi- tude: −89.2186, altitude: 498 m a.s.l) 5. **Information
 about funding sources that supported the collection of the data:** A.
 Great Lakes Bioenergy Research Center, U.S. Department of Energy, Office
 of Science, Office of Biological and Environmental Research under Award
 Number DE-SC0018409 B. National Science Foundation Long-term Ecological
 Research Program (DEB 1832042) at the Kellogg Biological Station, and by
 Michigan State University AgBioResearch ## SHARING/ACCESS INFORMATION 1.
 **Licenses/restrictions placed on the data:** CC0 1.0 Universal (CC0 1.0)
 Public Domain 2. **Links to publications that cite or use the data:**
 Chipkar S, Debrauske DJ, Kahmark K, Bohm S, Hussain MZ, Joshi L, Krieg KM,
 Cronk B, Burke E, Cassidy J, Aguado J, Senyk A, Robertson GP, Sato TK,
 Hamilton SK, Thelen KD, and Ong RG. High temperatures and low soil
 moisture synergistically reduce switchgrass yield and inhibit biofuel
 production from marginal field sites. Glob. Change Biol. Bioenergy (2023)
 3. **Links to other publicly accessible locations
 of the data**: None 4. **Links/relationships to ancillary data sets:**
 None 5. **Was data derived from another source?:** Yes. *Field Data:*
 \ *Regional
 Weather Data:* i. Lux Arbor: Battle Creek 5NW, MI
 ii. Lake City: Lake
 City Exp Fa, MI iii.
 Escanaba: Gladstone, MI (Precipitation); Rapid River SSE (Temperature and
 May 2019 Precipitation)
 iv. Hancock: Hancock
 Exp Farm, WI v.
 Rhinelander: Rhinelander, WI
 6. **Recommended
 citation for this dataset:**\ Chipkar S, Debrauske DJ, Kahmark K, Bohm S,
 Hussain MZ, Joshi L, Krieg KM, Cronk B, Burke E, Cassidy J, Aguado J,
 Senyk A, Robertson GP, Sato TK, Hamilton SK, Thelen KD, and Ong RG.
 (2023). Data from: High temperatures and low soil moisture synergistically
 reduce switchgrass yield and inhibit biofuel production from marginal
 field sites. Dryad Digital Repository.
 ## DATA & FILE
 OVERVIEW 1. **File List:** A. Field_Data.csv B. TempHeatMap.csv C.
 Weather_Data.xlsx D. NIR_Composition_both_years.csv E.
 FermentationHPLCData.csv F. Survival_Analysis_Data.csv G.
 Respirometer_CO2.zip H. MLE_Weather.R I. FermentationDataAnalysis.R J.
 RespirometerCO2Plots.R K. Survival_Analysis.R 2. **Relationship between
 files, if important:** A. MLE_Weather.R requires Field_Data.csv and
 TempHeatMap.csv B. Weather_Data.xlsx includes raw data and calculations
 for 7-day averaged temperatures in TempHeatMap.csv C.
 FermentationDataAnalysis.R requires NIR_Composition_both_years.csv and
 FermentationHPLCData.csv D. RespirometerCO2Plots.R requires the unzipped
 files in Respirometer_CO2.zip E. Survival_Analysis.R requires
 Survival_Analysis_Data.csv 3. **Are there multiple versions of the
 dataset?** No A. If yes, name of file(s) that was updated: NA i. Why was
 the file updated?: NA ii. When was the file updated?: NA
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Field_Data.csv This dataset includes the
 sensor data on soil volumetric water content and soil temperature for
 multiple depths for switchgrass grown under ambient or reduced
 precipitation (rainout shelters). 1. Number of variables: 6 2. Number of
 rows: 1,179,026 3. Variable List: * site: location where the switchgrass
 was harvested (Michigan South - Lux Arbor Reserve, Michigan Central - Lake
 City Exp. Station, Michigan North - Escanaba, Wisconsin Central - Hancock,
 or Wisconsin North - Rhinelander) * treatment: field treatment - whether
 switchgrass was grown under ambient precipitation or a rainout shelter *
 datetime: date and time stamp for sensor readout (yyyy-mm-dd hh:mm:ss) *
 depth: depth of sensor installation in the ground (10 cm or 25 cm) * vwc:
 soil volumetric water content (m^3 water per m^3 of soil) * temperature:
 soil temperature at the sampling depth (°C) 4. Missing data codes: None 5.
 Specialized formats or other abbreviations used: None
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: TempHeatMap.csv This data includes 7-day
 averaged maximum ambient temperatures for each field site and was used to
 generate a heat map of temperatures for each location. NOAA maximum
 temperature weather data was collected at nearby weather stations (links
 to data sources were provided above). 1. Number of variables: 6 2. Number
 of cases/rows: 540 3. Variable List: * Year: year the switchgrass was
 harvested (2018-2021) * Location: location where the switchgrass was
 harvested (MI-South Lux Arbor, MI-Central Lake City, MI-North Escanaba,
 WI-Central Hancock, or WI-North Rhinelander) * Latitude: numeric factor
 grouping sites by similar latitude (1 = South, 2 = Central, 3 = North) *
 State: state where the switchgrass was harvested (MI = Michigan, WI =
 Wisconsin) * Date: start of the 7 day period over which the temperature
 data was averaged - the data appears as headers in the CSV file (mm/dd/yy)
 * Temperature: the maximum ambient temperature, averaged across a 7-day
 period, from regional weather stations 4. Missing data codes: NA (data not
 available) 5. Specialized formats or other abbreviations used: None
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Weather_Data.xlsx Contains raw data and
 calculations for 7-day averaged maximum temperatures in TempHeatMap.csv
 and includes raw data and calculations for cumulative precipitation from
 May-October. Raw data is from NOAA regional weather stations (links
 provided above). Data for each location are provided in separate
 worksheets. 1. Raw Data: * Monthly Accumulated Precipitation (inches) -
 used to calculate cumulative precipitation during the growing season (May
 to October) in inches * Daily Max Temperature (°F) - used to calculate
 7-day averaged maximum temperatures (°C), the date provided marks the
 start of the seven-day period 2. Missing data codes: None. 3. Specialized
 formats or other abbreviations used: None.
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: NIR_Composition_both_years.csv Contains
 glucan and xylan composition of untreated switchgrass, determined using
 NIR spectroscopy. 1. Number of variables: 6 2. Number of cases/rows: 76 3.
 Variable List: * Location: field site where the switchgrass was harvested
 (Lux Arbor, Lake City, Escanaba, Hancock, or Rhinelander) * Plot: field
 plot at each location where the switchgrass was harvested (1-4) *
 Treatment: field treatment - whether switchgrass was grown under ambient
 precipitation or a rainout shelter * Year: year the switchgrass was
 harvested (2018 or 2020) * Glucan: switchgrass glucan content (% of dry
 biomass) determined using NIR spectroscopy * Xylan: switchgrass xylan
 content (% of dry biomass) determined using NIR spectroscopy 4. Missing
 data codes: None 5. Specialized formats or other abbreviations used: None
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: FermentationHPLCData.csv Contains data from
 HPLC analysis of hydrolysates before and after fermentation, calculated
 values (glucose and xylose consumption and ethanol production), and final
 OD600 (cell culture optical density). 1. Number of variables: 35 2. Number
 of cases/rows: 349 3. Variable List: * FermentationBarcode: a barcode
 specific to the fermentation * HydrolysateBarcode: a barcode specific to
 the batch of hydrolysate used in the fermentation experiment *
 HPLCBarcodePreFerm: a barcode specific to the sample of hydrolysate prior
 to fermentation that was analyzed using HPLC * HPLCBarcodePostFerm: a
 barcode specific to the sample of hydrolysate following fermentation that
 was analyzed using HPLC * Year: switchgrass harvest year (2018 or 2020) *
 Date: date the respirometer fermentation experiment was started (mm/dd/yy)
 * Location: field site where the switchgrass was harvested (Lux Arbor,
 Lake City, Escanaba, Hancock or Rhinelander) or a tag for a control sample
 (Control) * Plot: the field plot for experimental samples (1-4), or a
 descriptor for control hydrolysates (2008 Corn Stover, SynHv2.13, 2010
 Switchgrass, or 2012 Switchgrass) * Treatment: field treatment - whether
 switchgrass was grown under ambient precipitation or a rainout shelter
 (Ambient or Rainout) or a descriptor for control hydrolysates (see Plot
 above) * PreAcetate, PreEthanol, PreFormate, PreGlucose, PreGlycerol,
 PreLactate, PrePyruvate, PreSuccinate, PreXylitol, PreXylose,
 PreCellobiose: concentration of the respective compound in the hydrolysate
 prior to the start of fermentation in grams per liter (g/L) - determined
 using HPLC * PostAcetate, PostEthanol, PostFormate, PostGlucose,
 PostGlycerol, PostLactate, PostPyruvate, PostSuccinate, PostXylitol,
 PostXylose, PostCellobiose: concentration of the respective compound in
 the hydrolysate at the completion of fermentation in grams per liter (g/L)
 - determined using HPLC * GlucoseConsumption, XyloseConsumption: the
 glucose and xylose consumed during the fermentation (PreGlucose -
 PostGlucose or PreXylose - PostXylose) * EthanolProduction: the ethanol
 produced during the fermentation (PostEthanol - PreEthanol) * FinalOD:
 cell density (OD600) measured as the media absorbance at 600 nm at the end
 of fermentation 4. Missing data codes: N/A (data not available) 5.
 Specialized formats or other abbreviations used: None
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Survival_Analysis_Data.csv Contains data
 needed for survival analysis of the fermentation experiments 1. Number of
 variables: 14 2. Number of cases/rows: 292 3. Variable List: *
 FermentationBarcode: a barcode specific to the fermentation * Location:
 field site where the switchgrass was harvested (Lux Arbor, Lake City,
 Escanaba, Hancock or Rhinelander) or a tag for a control sample (Control)
 * Plot: the field plot for experimental samples (1-4), or a descriptor for
 control hydrolysates (2008 Corn Stover, SynHv2.13, 2010 Switchgrass, or
 2012 Switchgrass) * Treatment: field treatment - whether switchgrass was
 grown under ambient precipitation or a rainout shelter (Ambient or
 Rainout) or a descriptor for control hydrolysates (see Plot above) * Year:
 switchgrass harvest year (2018 or 2020) * MaxVolume: maximum CO2
 production (mL) during respirometer fermentation * MaxVolumeTime: time
 (hr) at which maximum CO2 production occurred * MaxSlope: maximum rate of
 CO2 production (mL/hr) * StartMaxSlopeVol: the starting CO2 volume (mL)
 for which the maximum rate of CO2 production was calculated *
 StartMaxSlopeTime: the starting fermentation time (hr) for which the
 maximum rate of CO2 production was calculated * EndMaxSlopeVol: the final
 CO2 volume (mL) for which the maximum rate of CO2 production was
 calculated * EndMaxSlopeTime: the final fermentation time (hr) for which
 the maximum rate of CO2 production was calculated * LagTime: the time (hr)
 at which fermentation lag phase ended; fermentations that failed to reach
 the end of lag phase by the end of the fermentation (Low CO2 in MaxSlope)
 had the Lag Time coded as the ending time for fermentation, which was
 necessary for the survival analysis * Status: censoring variable used to
 specify whether a fermentation had reached the end of lag phase or not by
 the end of the experiment (0 = censored, 1 = reached end of lag phase) 4.
 Missing data codes: None 5. Specialized formats or other abbreviations
 used: Low CO2 - indicates the maximum slope was not able to be calculated
 and the fermentation did not reach the end of lag phase by the end of the
 experiment
 \#########################################################################
 DATA-SPECIFIC INFORMATION FOR: Respirometer_CO2.zip Zipped folder of 33
 CSV files with time-series CO2 production data from respirometer
 fermentation experiments. These files are intended to be kept in the same
 folder and analyzed using RespirometerCO2Plots.R. 1. Number of variables:
 9 2. Number of cases/rows: varies by file 3. Header Variable List: *
 HydrolysateBarcode: a barcode specific to the batch of hydrolysate used in
 the fermentation experiment * FermentationBarcode: a barcode specific to
 the fermentation * Location: field site where the switchgrass was
 harvested (Lux Arbor, Lake City, Escanaba, Hancock or Rhinelander) or a
 tag for a control sample (2008 Corn Stover, SynHv2.13, 2010 Switchgrass,
 or 2012 Switchgrass) * HarvestYr: switchgrass harvest year (2018 or 2020)
 or N/A for control samples * Plot: the field plot for experimental samples
 (1-4), or N/A for control samples * Treatment: field treatment - whether
 switchgrass was grown under ambient precipitation or a rainout shelter
 (Ambient or Rainout) or a descriptor for control hydrolysates (Control -
 CS, SynH, Control - Drought, Control - Normal) * Date: date the
 respirometer fermentation experiment was started (mm/dd/yy) * Replicate:
 letter code indicating different replicates of the same untreated sample
 (there is no relationship between the same letter for different untreated
 samples) 4. Numeric Data: * Column A: time (hr) when the data was
 collected * Columns B - Z: cumulative CO2 production (mL) 5. Missing data
 codes: None 6. Specialized formats or other abbreviations used: CS = corn
 stover, SynH = synthetic hydrolysate, Control - Normal = 2010 Switchgrass,
 Control - Drought = 2012 switchgrass
 \#########################################################################
 ## DETAILS ON R CODE R Code was used for statistical analysis and to
 generate figures used in the paper. All files are also posted in GitHub
 () and Zenodo (). All code was run using RStudio Version 2023.06.1+524 (2023.06.1+524). 1. **MLE_Weather.R**\ R code used to generate plots and statistics for soil properties and weather data. Requires Field_Data.csv and TempHeatMap.csv files and the readr, tidyverse, lubridate, ggh4x, reshape2, viridisLite, and viridis packages. 2. **FermentationDataAnalysis.R**\ R code used to generate bar graphs and conducts ANOVAs for lignocellulosic biomass and hydrolysate composition and fermentation ethanol production and glucose consumption. Requires NIR_Composition_both_years.csv and FermentationHPLCData.csv and the readr, reshape2, ggplot2, ggpubr, and dplyr packages. 3. **RespirometerCO2Plots.R**\ R code used to aggregate data from multiple CSV files into a single dataframe and then generate faceted line plots of replicates and average CO2 production from respirometer fermentation experiments. Requires the unzipped files in Respirometer_CO2.zip stored in the same folder, and the tidyverse, ggnewscale, and ggh4x packages. 4. **Survival_Analysis.R**\ R code used to generate faceted survival plots annotated with p-values from a paired t-test. Requires Survival_Analysis_Data.csv and the readr, survival, ggplot2, survminer, and tidyverse packages.