Data from: High temperatures and low soil moisture synergistically reduce switchgrass yields from marginal field sites and inhibit fermentation
Data files
Jan 11, 2024 version files 93.15 MB
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FermentationHPLCData.csv
81.87 KB
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Field_Data.csv
92.43 MB
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NIR_Composition_both_years.csv
3.56 KB
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README.md
17.16 KB
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Respirometer_CO2.zip
266.03 KB
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Survival_Analysis_Data.csv
28.21 KB
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TempHeatMap.csv
31.42 KB
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Weather_Data.xlsx
295.94 KB
Abstract
'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.
README: 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
Title of Dataset: Data from: High temperatures and low soil moisture synergistically reduce switchgrass yields from marginal field sites and inhibit fermentation
Author Information
A. Principal Investigator Contact Information
Name: Rebecca Ong
Institution: Michigan Technological University
Address: Houghton, MI USA
Email: rgong1@mtu.eduDate of data collection (single date, range, approximate date): 2018-2021
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)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
Licenses/restrictions placed on the data: CC0 1.0 Universal (CC0 1.0) Public Domain
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) https://doi.org/
Links to other publicly accessible locations of the data: None
Links/relationships to ancillary data sets: None
Was data derived from another source?: Yes.
Field Data: https://data.sustainability.glbrc.org/datatables/572
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Regional Weather Data:
i. Lux Arbor: Battle Creek 5NW, MI https://www.weather.gov/wrh/climate?wfo=grr
ii. Lake City: Lake City Exp Fa, MI https://www.weather.gov/wrh/climate?wfo=apx
iii. Escanaba: Gladstone, MI (Precipitation); Rapid River SSE (Temperature and May 2019 Precipitation) https://www.weather.gov/wrh/climate?wfo=mqt
iv. Hancock: Hancock Exp Farm, WI https://www.weather.gov/wrh/climate?wfo=grb
v. Rhinelander: Rhinelander, WI https://www.weather.gov/wrh/climate?wfo=grbRecommended 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. https://doi.org/10.5061/dryad.qnk98sfps
DATA & FILE OVERVIEW
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.RRelationship 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.csvAre 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
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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).
Number of variables: 6
Number of rows: 1,179,026
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)
Missing data codes: None
Specialized formats or other abbreviations used: None
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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).
Number of variables: 6
Number of cases/rows: 540
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
Missing data codes: NA (data not available)
Specialized formats or other abbreviations used: None
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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.
- 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
Missing data codes: None.
Specialized formats or other abbreviations used: None.
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DATA-SPECIFIC INFORMATION FOR: NIR_Composition_both_years.csv
Contains glucan and xylan composition of untreated switchgrass, determined using NIR spectroscopy.
Number of variables: 6
Number of cases/rows: 76
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
Missing data codes: None
Specialized formats or other abbreviations used: None
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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).
Number of variables: 35
Number of cases/rows: 349
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
Missing data codes: N/A (data not available)
Specialized formats or other abbreviations used: None
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DATA-SPECIFIC INFORMATION FOR: Survival_Analysis_Data.csv
Contains data needed for survival analysis of the fermentation experiments
Number of variables: 14
Number of cases/rows: 292
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)
Missing data codes: None
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
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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.
Number of variables: 9
Number of cases/rows: varies by file
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)
- Numeric Data:
* Column A: time (hr) when the data was collected
* Columns B - Z: cumulative CO2 production (mL)
Missing data codes: None
Specialized formats or other abbreviations used:
CS = corn stover, SynH = synthetic hydrolysate, Control - Normal = 2010 Switchgrass, Control - Drought = 2012 switchgrass
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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 (https://github.com/rebeccaongmtu/switchgrass-rainout-shelter-paper) and Zenodo (https://doi.org/10.5281/zenodo.10278446). All code was run using RStudio Version 2023.06.1+524 (2023.06.1+524).
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.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.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.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.
Methods
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.