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Micro-colonies developed in the rhizosphere [28]. Since E. As a pathogenic bacteria, E. When using transparent soil, there is a potential problem of moving the bacteria during saturation of the substrate in preparation for imaging but this should not affect attached bacteria such as E. Saturation is, however, a potential limitation of the method if studying microbes that are not attached to surfaces because it is likely that these would be moved during saturation.

In summary, our results show that transparent soil is ideal for imaging studies of certain plant-microbe interactions in situ at the microscopic level. Soil microbes provide numerous important services [30] and their interactions with plants enhance the supply of nutrients, for example by nodulation [31] or by biological fertilization [32]. The transfer of human pathogens in the food chain [27] and spread of crop diseases [33] also involve complex plant-microbe interactions. The use of transparent soil will facilitate quantitative imaging of the dynamics of in situ root-microbe interactions using high resolution imaging with fluorescence for detecting microorganisms expressing fluorescent proteins Fig.

For plant genetics and crop breeding, transparent soil could be integrated with high-throughput screening systems for root traits [34] that may improve nutrient acquisition and reduce the need for fertilizers [35]. Overall, this approach presents new opportunities to unravel the complex processes of plant-soil interactions in situ and in vivo and holds promise for a wide range of applications to aid the understanding of important underlying relationships that underpin the sustainability of our ecosystems.

Nafion was from Ion Power Inc. Acid NR50 and precursor R1 forms were used. After cooling, the particles were washed several times with dH 2 O. The particles were rinsed again multiple times with fresh dH 2 O [36]. To titrate the particles with mineral ions, stock solutions of MSR media were used to immerse the particles. This was repeated until the pH was neutral and stable. Before use, the particles were autoclaved in dH 2 O for sterilisation. The straightness of the line for each image was used as an indicator of the light path distortion by refraction.

The thresholded image was skeletonized and a bounding box around the line was created. Nutrient-titrated Nafion particles were also tested in this way, but with a larger range of sorbitol concentrations. Saturated samples were placed on ceramic plates in glass funnels, which were connected to hanging water columns. Different suctions were achieved by moving the water level in the water column to a specific height.

At each pressure, the water content of the sample was allowed to equilibrate and the mass was recorded to allow calculation of volumetric water content. Data on water retention in vermiculite and sand from other studies were used for comparison with our data on water retention in transparent soil [16] , [37]. Exchangeable cations were extracted using the ammonium acetate method [38] and cation exchange capacity was quantified by subsequent ICP-MS analysis.

To measure anion exchange capacity, sorbed chloride ions were exchanged with nitrate ions and exchange capacity was determined by measuring the extracted chloride ions [39]. Arabidopsis thaliana expressing 35S:LTI6b- EGFP constitutively expressed enhanced green fluorescent protein targeted to the plasma membrane , in the C24 background originally obtained from Dr. Haseloff, University of Cambridge, UK [40] and auxin reporter lines [41] were used for confocal microscopy.

Nicotiana benthamiana tobacco and Latuca sativa lettuce, var. The substrates used for analysing plant growth were 1. The soil was sieved to 3 mm and packed to a density of 1. Horticultural grit sand Gem, UK , with a dry bulk density of 1. Transparent soil, prepared as described below and packed to a density of 1. All plants were excavated, the roots were washed and they were mounted onto acetate sheets for scanning using a flatbed scanner Epson expression XL.

Imaging was carried out after 5 days after sowing. The method used for bacteria-plant interactions allowed colonization of the roots to develop from infected seedlings, rather than from the addition of the inoculum directly to the substrate or the more mature roots. For OPT imaging the samples were prepared in glass cylindrical specimen tubes 2. Duration of growth was dependent on plant species but in general, imaging was performed before the roots reached the base of the tube. Tobacco plants used for OPT were imaged 10 days after sowing. Arabidopsis plants used for confocal imaging were imaged 10—14 days after sowing.

The stage and camera were controlled by software also built in-house, allowing control of the number of images acquired for each sample. The projection images were reconstructed to produce 3D data using a filtered backprojection algorithm with the Iradon function in Matlab The MathWorks, Inc. For CLSM, plants were grown in purpose-built chambers, constructed using a microscope slide and long cover glass with a 4 mm spacer between them on 3 sides and an opening at the top.

The spacer was glued to the slide and cover glass using Araldite glass and ceramic adhesive Huntsman International. The chambers were covered with aluminium foil on the outside during growth to exclude light from the roots. Foil was removed immediately before imaging. The refractive index of the solution matches the refractive index of the Nafion particles used here to provide complete transparency in the substrate.

Sigmaplot 12 Syststat Software, Inc. Image analysis was carried out using Mevislab [43] and Fiji Software [44].

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Root tracking used an algorithm by Friman et al [45]. Skeletonization and edge detection was carried out using the standard Mevislab algorithms developed respectively by Milo Hindennach and Olaf Konrad and Wolf Spindler. Snapshots of volume renderings of confocal scans of Arabidopsis thaliana roots expressing GFP in plasma membranes grey in transparent soil with sulphorhdamine-B-dyed particles orange.

Lateral root emerging from primary root.

The Rhizosphere: an interaction between plant roots and soil biology

Section of primary root and root hairs in contact with Nafion particle. In situ 3D image of branched Arabidopsis thaliana roots expressing GFP in plasma membranes green in transparent soil with sulphorhdamine-B-dyed particles red. In situ 3D image of Arabidopsis thaliana root with emrging lateral root expressing GFP in plasma membranes green in transparent soil with sulphorhdamine-B-dyed particles orange. In situ 3D image of Arabidopsis thaliana root with root hairs expressing GFP in plasma membranes green with Nafion particle of transparent soil orange.

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Yossef A. Performed the experiments: HD. Browse Subject Areas? Click through the PLOS taxonomy to find articles in your field. Abstract Understanding of soil processes is essential for addressing the global issues of food security, disease transmission and climate change. Introduction The ability of plants and microorganisms to successfully exploit soil resources underpins the survival of all terrestrial life. Results and Discussion Making Soils Transparent using Refractive Index Matching At the boundary of two transparent materials with different refractive indices, the path of light is distorted through refraction.

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Interactions of beneficial and detrimental root-colonizing filamentous microbes with plant hosts

Mimicking Physical and Chemical Properties of Soil We have also sought to mimic physical and chemical properties important for supporting plant and microbial growth in soils in the transparent soil system. Root Growth in Transparent Soil Transparent soil can be used for a large range of other applications. Figure 2. Imaging roots and microorganisms in transparent soil using OPT and confocal microscopy. Application of Transparent Soil to the Study of Root Bacteria Interactions We have applied transparent soil to study the mechanisms of transmission of food-borne human pathogens on fresh produce plants using GFP-labelled Escherichia coli OH7.

New Opportunities for Plant Sciences Soil microbes provide numerous important services [30] and their interactions with plants enhance the supply of nutrients, for example by nodulation [31] or by biological fertilization [32]. Analysis of Plant Growth in Different Substrates The substrates used for analysing plant growth were 1.

Theodore Friedmann. Pierre Pontarotti. Plant Biochemistry. The Alkaloids. Geoffrey A. Plant Developmental Biology - Biotechnological Perspectives. Eng Chong Pua. Biocommunication of Fungi. Physiology and Genetics. Timm Anke. Root Genomics. Antonio Costa de Oliveira. Biological Nitrogen Fixation. Frans J. Molecular Techniques in Crop Improvement. Abiotic Stress Adaptation in Plants. Ashwani Pareek. Lise Jouanin. Tom Gerats. Growth, Differentiation and Sexuality. Biocommunication of Plants.

Developmental Timing. Ann E Rougvie. Signaling and Communication in Plant Symbiosis. Silvia Perotto.

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Low-Oxygen Stress in Plants. Francesco Licausi. Temperature and Plant Development. Keara Franklin. Genomics of Soil- and Plant-Associated Fungi. Benjamin A. Stress Ecology. Christian E.

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Maria Romeralo. Charles Darwin. Polyploidy and Genome Evolution. Douglas E. Post-Genome Biology of Primates. Hiroo Imai. The Biology of Plant-Insect Interactions. Chandrakanth Emani. Plants with Seeds. Roger Prior. Forest Health. John D. Plant Acclimation to Environmental Stress. Biocommunication in Soil Microorganisms. Tropical Ecosystems and Ecological Concepts. Patrick L. Palm Trees of the Amazon and their Uses. Alfred Russel Wallace. Genetics and Genomics of Brachypodium. John P. Seed Genomics. Philip W.

Conversation Pieces. Mark Carnall. Root Hairs. Anne Mie C. Adrian P. Rhizosphere ecology and phytoprotection in soils naturally suppressive to Thielaviopsis black root rot of tobacco. Effect of clay mineralogy on iron bioavailability and rhizosphere transcription of 2,4-diacetylphloroglucinol biosynthetic genes in biocontrol Pseudomonas protegens. Plant Microbe Interact.

Baehler, E. Use of green fluorescent protein-based reporters to monitor balanced production of antifungal compounds in the biocontrol agent Pseudomonas fluorescens CHA0. Bangera, M. Characterization of a genomic locus required for synthesis of the antibiotic 2,4-diacetylphloroglucinol by the biological control agent Pseudomonas fluorescens Q Bao, Y. An improved Tn7-based system for the single-copy insertion of cloned genes into chromosomes of gram-negative bacteria.

Gene , — Berendsen, R. The rhizosphere microbiome and plant health. Trends Plant Sci.

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Bertani, G. Studies on lysogenesis I. PubMed Abstract Google Scholar. Bithell, S. Predicting take-all severity in second-year wheat using soil DNA concentrations of Gaeumannomyces graminis var. Plant Dis. Blankenfeldt, W. Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens.

Blumer, C. Mechanism, regulation, and ecological role of bacterial cyanide biosynthesis. Brandt, K. Decreased abundance and diversity of culturable Pseudomonas spp. FEMS Microbiol. Cha, J. Microbial and biochemical basis of a Fusarium wilt-suppressive soil. ISME J. Chin-A-Woeng, T. Phenazines and their role in biocontrol by Pseudomonas bacteria. New Phytol. Biocontrol by phenazinecarboxamide-producing Pseudomonas chlororaphis PCL of tomato root rot caused by Fusarium oxysporum f.

Introduction of the phzH gene of Pseudomonas chlororaphis PCL extends the range of biocontrol ability of phenazinecarboxylic acid producing Pseudomonas spp. The Pseudomonas chlororaphis PCL sigma regulator psrA represses the production of the antifungal metabolite phenazinecarboxamide. Chng, S. Take-all decline in New Zealand wheat soils and the microorganisms associated with the potential mechanisms of disease suppression. Plant Soil , — Cook, J. The role of bacteria in the biological control of Gaeumannomyces graminis by suppressive soils.

Cullen, D. Development and validation of conventional and quantitative polymerase chain reaction assays for the detection of storage rot potato pathogens, Phytophthora erythroseptica, Pythium ultimum and Phoma foveata. Detection of plant-modulated alterations in antifungal gene expression in Pseudomonas fluorescens CHA0 on roots by flow cytometry. Plant- and microbe-derived compounds affect the expression of genes encoding antifungal compounds in a pseudomonad with biocontrol activity.

DeCoste, N. Relative and absolute quantitative real-time PCR-based quantifications of hcnC and phlD gene transcripts in natural soil spiked with Pseudomonas sp. Duffy, B. Zinc improves biocontrol of Fusarium crown and root rot of tomato by Pseudomonas fluorescens and represses the production of pathogen metabolites inhibitory to bacterial antibiotic biosynthesis. Phytopathology 87, — Environmental factors modulating antibiotic and siderophore biosynthesis by Pseudomonas fluorescens biocontrol strains. Flisch, R. Principles for fertilisation in arable and fodder production in German.

Agrarforschung 16, 1— Flury, P. Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics. Frapolli, M. Denaturing gradient gel electrophoretic analysis of dominant 2,4-diacetylphloroglucinol biosynthetic phlD alleles in fluorescent Pseudomonas from soils suppressive or conducive to black root rot of tobacco.

Garbeva, P. Effect of above-ground plant species on soil microbial community structure and its impact on suppression of Rhizoctonia solani AG3. Quantitative detection and diversity of the pyrrolnitrin biosynthetic locus in soil under different treatments. Haas, D. Biological control of soil-borne pathogens by fluorescent pseudomonads. Take-all or nothing. Fluorescent pseudomonads as biocontrol agents for sustainable agricultural systems.

Hwang, J. Pyrrolnitrin production by Burkholderia cepacia and biocontrol of Rhizoctonia stem rot of poinsettia. Control 25, 56— Jousset, A. Plants respond to pathogen infection by enhancing the antifungal gene expression of root-associated bacteria. Predator-prey chemical warfare determines the expression of biocontrol genes by rhizosphere-associated Pseudomonas fluorescens. Full-genome sequence of the plant growth-promoting bacterium Pseudomonas protegens CHA0. Genome Announc. Keel, C. Suppression of root diseases by Pseudomonas fluorescens CHA0: importance of the bacterial secondary metabolite 2,4-diacetylphloroglucinol.

Iron sufficiency, a prerequisite for the suppression of tobacco black root rot by Pseudomonas fluorescens strain CHA0 under gnotobiotic conditions. Phytopathology 79, — Kim, J. Application of PCR primer sets for detection of Pseudomonas sp. King, E. Two simple media for the demonstration of pyocyanin and fluorescein. Kirner, S. Functions encoded by pyrrolnitrin biosynthetic genes from Pseudomonas fluorescens. Klein, E. Soil suppressiveness to fusarium disease: shifts in root microbiome associated with reduction of pathogen root colonization.

Phytopathology , 23— Koch, B. A panel of Tn7-based vectors for insertion of the gfp marker gene or for delivery of cloned DNA into Gram-negative bacteria at a neutral chromosomal site. Methods 45, — Kyselkova, M. Landa, B. Differential ability of genotypes of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens strains to colonize the roots of pea plants.

Latz, E. Plant identity drives the expression of biocontrol factors in a rhizosphere bacterium across a plant diversity gradient. Lebreton, L. Linear relationship between Gaeumannomyces graminis var. Lemanceau, P. Gnanamanickam Dordrecht: Springer , — The occurrence of pathogen suppressive soils in Sweden in relation to soil biota, soil properties, and farming practices. Soil Ecol. Lugtenberg, B. Plant-growth-promoting rhizobacteria.

Martin, F. Association of chemical and biological factors in soils suppressive to Pythium ultimum. Phytopathology 76, — Mascher, F. Maurhofer, M. Cross talk between 2,4-diacetylphloroglucinol-producing biocontrol pseudomonads on wheat roots. Influence of enhanced antibiotic production in Pseudomonas fluorescens strain CHA0 on its disease suppressive capacity. Phytopathology 82, — Mavrodi, D. A seven-gene locus for synthesis of phenazinecarboxylic acid by Pseudomonas fluorescens Accumulation of the antibiotic phenazinecarboxylic acid in the rhizosphere of dryland cereals.

Recent insights into the diversity, frequency and ecological roles of phenazines in fluorescent Pseudomonas spp. Mavrodi, O. Irrigation differentially impacts populations of indigenous antibiotic-producing Pseudomonas spp. Mazurier, S. Phenazine antibiotics produced by fluorescent pseudomonads contribute to natural soil suppressiveness to Fusarium wilt.

Mendes, R. The rhizosphere microbiome: significance of plant-beneficial, plant-pathogenic and human-pathogenic microorganisms. Deciphering the rhizosphere microbiome for disease-suppressive bacteria. Science , — Mercado-Blanco, J. Interactions between plants and beneficial Pseudomonas spp. Antonie van Leeuwenhoek 92, — Meyer, J. Interplay between wheat cultivars, biocontrol pseudomonads, and soil. Nesemann, K. Draft genome sequence of the phenazine-producing Pseudomonas fluorescens strain Notz, R. Fusaric acid-producing strains of Fusarium oxysporum alter 2,4-diacetylphloroglucinol biosynthetic gene expression in Pseudomonas fluorescens CHA0 in vitro and in the rhizosphere of wheat.

Biotic factors affecting expression of the 2,4-diacetylphloroglucinol biosynthesis gene phlA in Pseudomonas fluorescens biocontrol strain CHA0 in the rhizosphere. Phytopathology 91, — Novinscak, A. Effect of soil clay content on RNA isolation and on detection and quantification of bacterial gene transcripts in soil by quantitative reverse transcription-PCR.

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Ownley, B. Identification and manipulation of soil properties to improve the biological control performance of phenazine-producing Pseudomonas fluorescens. Control and host-dependent activation of insect toxin expression in a root-associated biocontrol pseudomonad. Pierson, L. Cloning and heterologous expression of the phenazine biosynthetic locus from Pseudomonas aureofaciens R Core Team Vienna: R Foundation for Statistical Computing. Raaijmakers, J. Effect of population density of Pseudomonas fluorescens on production of 2,4-diacetylphloroglucinol in the rhizosphere of wheat.

Phytopathology 89, — Diversity and natural functions of antibiotics produced by beneficial and plant pathogenic bacteria. Soil immune responses. The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms. Frequency of antibiotic-producing Pseudomonas spp. Ramette, A.

Genetic diversity and biocontrol potential of fluorescent pseudomonads producing phloroglucinols and hydrogen cyanide from Swiss soils naturally suppressive or conducive to Thielaviopsis basicola -mediated black root rot of tobacco. Rochat, L. Combination of fluorescent reporters for simultaneous monitoring of root colonization and antifungal gene expression by a biocontrol pseudomonad on cereals with flow cytometry.

Sambrook, J. Molecular Cloning: A Laboratory Manual. Schnider-Keel, U. The sigma factor AlgU AlgT controls exopolysaccharide production and tolerance towards desiccation and osmotic stress in the biocontrol agent Pseudomonas fluorescens CHA0. Autoinduction of 2, 4-diacetylphloroglucinol biosynthesis in the biocontrol agent Pseudomonas fluorescens CHA0 and repression by the bacterial metabolites salicylate and pyoluteorin. Stanisich, V. A mutant sex factor of Pseudomonas aeruginosa. Agrarforschung 14, — Stutz, E. Naturally occurring fluorescent pseudomonads involved in suppression of black root rot of tobacco.

Tamietti, G. Physiological responses of tomato plants grown in Fusarium suppressive soil. Thomashow, L. Role of a phenazine antibiotic from Pseudomonas fluorescens in biological control of Gaeumannomyces graminis var. Untergasser, A. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res. Vieira, J. Voisard, C. Cyanide production by Pseudomonas fluorescens helps suppress black root rot of tobacco under gnotobiotic conditions. EMBO J.