Transparent Soil for Imaging the Rhizosphere

Downie, Helen; Holden, Nicola; Otten, Wilfred; Spiers, Andrew J.; Valentine, Tracy A.; Dupuy, Lionel

doi:10.1371/journal.pone.0044276

Cited by 161 publications

(183 citation statements)

References 44 publications

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“…Several developed high-throughput root phenotyping systems address RSA of roots grown in artificial substrates such as agar or other transparent materials, filter paper or in hydroponics (Nagel et al 2009;Iyer-Pascuzzi et al 2010;Downie et al 2012;Gioia et al 2017). Root trait expression in these systems may, however, deviate from that occurring under natural conditions, where it is influenced by processes involved in the interaction between soil and roots (White et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Phenotyping roots in darkness: disturbance-free root imaging with near infrared illumination

Shi

Junker

Seiler

et al. 2018

Functional Plant Biol.

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Abstract. Root systems architecture (RSA) and size properties are essential determinants of plant performance and need to be assessed in high-throughput plant phenotyping platforms. Thus, we tested a concept that involves near-infrared (NIR) imaging of roots growing along surfaces of transparent culture vessels using special long pass filters to block their exposure to visible light. Two setups were used to monitor growth of Arabidopsis, rapeseed, barley and maize roots upon exposure to white light, filter-transmitted radiation or darkness: root growth direction was analysed (1) through short-term cultivation on agar plates, and (2) using soil-filled transparent pots to monitor long-term responses. White light-triggered phototropic responses were detected for Arabidopsis in setup 1, and for rapeseed, barley and maize roots in setups 1 and 2, whereas light effects could be avoided by use of the NIR filter thus confirming its suitability to mimic darkness. NIR imagederived 'root volume' values correlated well with root dry weight. The root system fractions visible at the different pot sides and in different zones revealed species-and genotype-dependent variation of spatial root distribution and other RSA traits. Following this validated concept, root imaging setups may be integrated into shoot phenotyping facilities in order to enable root system analysis in the context of whole-plant performance investigations.

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Section: Introductionmentioning

confidence: 99%

Phenotyping roots in darkness: disturbance-free root imaging with near infrared illumination

Shi

Junker

Seiler

et al. 2018

Functional Plant Biol.

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“…To the best of our knowledge, little information exists with respect to the 3D spatial location of microbes within the rhizosphere. However, a method using transparent soil has recently been suggested for rhizosphere research that permits the use of normal light transmission microscopy (Downie et al 2012(Downie et al , 2014. This method uses particles of a polymer (Nafion) which become 'invisible' following the addition of a solution with a matching refractive index.…”

Section: Brief Review Of Structural Imagingmentioning

confidence: 99%

“…Particle sizes can be manipulated to obtain different structures for root growth in a 3D porous medium. This method can provide roots whose growth traits are comparable with soil-grown controls (Downie et al 2012), but has the great advantage that light microscopy can be applied for visualisation of microbial colonization and distribution in the rhizosphere (Downie et al 2014). Using multiple fluorescent signals in situ it is possible to study the growth and interactions of biological organisms in a physically complex soil-like environment.…”

Section: Brief Review Of Structural Imagingmentioning

confidence: 99%

Challenges in imaging and predictive modeling of rhizosphere processes

et al. 2016

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Background Plant-soil interaction is central to human food production and ecosystem function. Thus, it is essential to not only understand, but also to develop predictive mathematical models which can be used to assess how climate and soil management practices will affect these interactions. Scope In this paper we review the current developments in structural and chemical imaging of rhizosphere processes within the context of multiscale mathematical image based modeling. We outline areas that need more research and areas which would benefit from more detailed understanding. Conclusions We conclude that the combination of structural and chemical imaging with modeling is an incredibly powerful tool which is fundamental for understanding how plant roots interact with soil. We emphasize the need for more researchers to be attracted to this area that is so fertile for future discoveries. Finally, model building must go hand in hand with experiments. In particular, there is a real need to integrate rhizosphere structural and chemical imaging with modeling for better understanding of the rhizosphere processes leading to models which explicitly account for pore scale processes.

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“…The most promising technique for noninvasive 3D imaging in soil is X-ray computed tomography (CT) and magnetic resonance imaging (MRI) (Metzner et al 2015). There are also other applicable approaches that include selective plane illumination microscopy (SPIM) and optical projection omography (OPT) that are adapted for plants grown in transparent media (Downie et al 2012). Regardless of the method that is used for image acquisition, it is essential to properly analyse the data obtained in a reproducible manner.…”

Section: Root Phenotyping Of Cereal Plantsmentioning

confidence: 99%

Root Phenotyping Pipeline for Cereal Plants

Slota

Małuszyński

Szarejko

2016

Biotechnologies for Plant Mutation Breeding

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The proposed system for the phenotypic analysis of root traits that is presented here enables the precise description of the root growth kinetics of cereal plants. The designed pipeline is composed of a drip irrigation system to supplement plants with a medium, a high-resolution root system scanning facility and a method for comprehensive image analysis. The system enables low-effort, accurate and highly repeatable analysis of features of the root system of cereal seedlings and young plants until the early tillering stage. This system employs an automatic drip irrigation line, which is controlled remotely by a programmable logic controller (PLC). The PLC adapter used facilitates the automated control of all system modules, thus allowing the rate of the medium flow to be adjusted for the supplementation of plants. The system employs measuring sensors for the continuous monitoring of the parameters of the culture medium. This continuous sensing of medium parameters can be applicable for mineral nutrition studies and abiotic stress response testing. The installed drip lines are injected into transparent acrylic tubes (500 mm high, 32/30 mm in outer and inner diameter, with a circular opening in the bottom of 3 mm in diameter) that are filled with glass beads. The acrylic tubes are placed in opaque cover tubes that permit the non-destructive observation of the growth of the root system. Enhanced imaging quality contributes to an increase in the precision of the results that are obtained in the course of the analysis of root parameters using specialised root scanners coupled with the WinRHIZO system. This novel phenotyping pipeline permits noninvasive observation of root system growth adjusted for the subsequent root image acquisition with a reduced background noise. The method combines automated control of plant growth conditions with good imaging quality and high replicability of growth parameters.

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Transparent Soil for Imaging the Rhizosphere

Cited by 161 publications

References 44 publications

Phenotyping roots in darkness: disturbance-free root imaging with near infrared illumination

Phenotyping roots in darkness: disturbance-free root imaging with near infrared illumination

Challenges in imaging and predictive modeling of rhizosphere processes

Root Phenotyping Pipeline for Cereal Plants

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