Images, data, and statistical analysis scripts for review article on cover crop roots

Images, data, and statistical analysis scripts for review article on cover crop roots.

Optimization of root traits to provide enhanced ecosystem services in agricultural systems: a focus on cover crops - [https://doi.org/10.1111/pce.14247]

• Research site, planting, and growth
  • 10/2020 - 04/26/2021 cover crop field trial. DDPSC FRS at Planthaven Farm, O'Fallon, MO 63366 (latitude 38.848240°, longitude -90.686640°). 
  • The field was tilled before sowing of cover crops. Seed for each cover crop were spread in using a push seed spreader and were lightly irrigated.
  • Alfalfa (Medicago sativa), dundale pea (Pisum sativum), milkvetch (Astragalus canadensis, Astragalus bisulcatus), crimson clover (Trifolium incarnatum), hairy vetch (Vicia villosa), mustard (Brassica juncea var Mighty Mustard, var Kodiak), barley (Hordeum vulgare), wheat (Triticum aestivum, winter, spring), winter rye (Secale cereale), and triticale (× Triticosecale Wittmack).

• Field harvest measurements

  • Four canopy images were taken across each cover crop row using a Canon 5DS R camera. Images were taken from above each plot at 5ft height manually. Green color was thresholded from the canopy images in batch using OpenCV python script and the percent green cover calculated (Jupiter notebook).

  • Five soil monoliths were excavated using a "shovelomics" approach with an average monolith size of 25.4cm x 25.4cm x 20 cm. The remaining four soil monoliths were destructively analyzed.

  • One soil monolith was imaged using a Canon 50D DLSR camera in a photogrammetry shed. All photogrammetric analysis was conducted using Pix4D mapper software (Pix4D S.A. Prilly, Switzerland), and point cloud cleaning was conducted in CloudCompare V2. 10.2.

  • Cover crop shoots from the remaining soil monoliths were cut and placed into a paper bag for dry biomass determination (60oC for 5 days). A cover crop shoot count was conducted for each monolith with each tiller considered as a shoot for the grasses (barley, wheat, triticale). After cover crop shoot harvesting, a photo was then taken of each soil monolith with remaining weed biomass. A weed score was assigned to each image by one trained researcher with a score 1 low weeds to 5 high weed presence.

  • Soil monoliths were the soaked briefly in water and then the soil washed using a hose keeping the roots. Roots were then scanned on an Epson Expression 12000XL Photo Scanner with transparency unit. Images labeled with "_part" were samples with too many roots for scanning and so were separately weighed. Dry root biomass was taken for the scanned and unscanned roots separately. Root length was determined from images using software RhizoVision Explorer (https://doi.org/10.5281/zenodo.4095629), total root length was estimated using scanned root length and scanned dry biomass with unscanned root biomass.

  • Along each cover crop plot a 10ft trench was dug using a Yanmar Excavator Vi020-6 perpendicular to the row with each trench fully bisecting the plot. Trench was one bucket wide (19 inches) and approximately 36 inches deep in the middle of the row. The five deepest roots that could be observed in the trench wall was measured manually with a tape measure for each cover crop. A garden trowel and shovel were used to excavate and confirm roots in trench wall.

  • Data was analyzed using R Statistics script and raw data used for data processing and figure generation (2021PlantHavenCovercrop_dataprocessing.R). PCA analysis was conducted using the “FactoMineR” package (Husson et al. 2019) to explore the relationships between the traits within the dataset and clustered by family.

Individual ZIP file contents:

• 2021PlantHavenCovercrop_CanopyImages.zip – Raw canopy images, processed percent green cover images, and Jupiter notebook python script (2021PlantHavenCovercrop_ImageBatchColorThreshold.ipynb).
• 2021PlantHavenCovercrop_RootFlatbedImages.zip – Raw flatbed root scans of cover crops and processed images using RhizoVision Explorer.
• 2021PlantHavenCovercrop_SoilMonolithWeedImages.zip – Images of soil monoliths after cover crop shoot biomass was removed.
• 2021PlantHavenCovercrop_dataprocessing.zip – R Statistics script and raw data used for data processing and figure generation (2021PlantHavenCovercrop_dataprocessing.R).
• 2021PlantHavenCovercrop_ShootPhotogrammetry.zip – 3D models of cover crop shoots from excavated soil monoliths. The .bin files can be opened using CloudCompare app.