Transparent soil for imaging the rhizosphere

• Published in: PloS one Vol. 7; no. 9; p. e44276
• Main Authors: Downie, Helen, Holden, Nicola, Otten, Wilfred, Spiers, Andrew J, Valentine, Tracy A, Dupuy, Lionel X
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 11-09-2012; Public Library of Science (PLoS)
• Subjects: Agriculture; Bacteria - metabolism; Biology; Cell division; Climate change; Colonies; Colonization; Dietary minerals; Disease transmission; E coli; Escherichia coli; Fluorescence; Fluorescent dyes; Fluorescent indicators; Food security; Food supply; Genetics; Humans; Imaging; Imaging, Three-Dimensional - methods; Medical imaging; Microbiology; Microorganisms; Microscopy; Microscopy, Confocal; Minerals; Optical properties; Particle size; Particulates; Plant growth; Plant Roots - growth & development; Plant Roots - microbiology; Pore size; Porosity; Refractometry; Rhizosphere; Soil; Soil biology; Soil Microbiology; Soil microorganisms; Soil testing; Substrates; Tomography; Vermiculite; United Kingdom > UK
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0044276

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.