title: Transparent soil for imaging the rhizosphere.
abstract: Understanding of soil processes is essential for addressing the global issues of food security, disease transmission and climate change. However, techniques for observing soil biology are lacking. We present a heterogeneous, porous, transparent substrate for in situ 3D imaging of living plants and root-associated microorganisms using particles of the transparent polymer, Nafion, and a solution with matching optical properties. Minerals and fluorescent dyes were adsorbed onto the Nafion particles for nutrient supply and imaging of pore size and geometry. Plant growth in transparent soil was similar to that in soil. We imaged colonization of lettuce roots by the human bacterial pathogen Escherichia coli O157:H7 showing micro-colony development. Micro-colonies may contribute to bacterial survival in soil. Transparent soil has applications in root biology, crop genetics and soil microbiology.
authors.affiliation: The James Hutton Institute, Invergowrie, Dundee, United Kingdom.
authors.forename: Helen
authors.initials: H
authors.lastname: Downie
authors.forename: Nicola
authors.initials: N
authors.lastname: Holden
authors.forename: Wilfred
authors.initials: W
authors.lastname: Otten
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Spiers
authors.forename: Tracy A
authors.initials: TA
authors.lastname: Valentine
authors.forename: Lionel X
authors.initials: LX
authors.lastname: Dupuy
mesh_terms: D001419:Bacteria / Q000378:metabolism; D006801:Humans; D021621:Imaging, Three-Dimensional / Q000379:methods*; D018613:Microscopy, Confocal; D018517:Plant Roots / Q000254:growth & development / Q000382:microbiology; D012031:Refractometry; D058441:Rhizosphere; D012987:Soil; D012988:Soil Microbiology; D014054:Tomography
chemical_list: D012987:Soil