Transparent soil for imaging the rhizosphere

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

Transparent soil microcosms allow 3D spatial quantification of soil microbiological processes in vivo

The recently developed transparent soil consists of particles of Nafion, a polymer with a low refractive index (RI), which is prepared by milling and chemical treatment for use as a soil analogue. After the addition of a RI-matched solution, confocal imaging can be carried out in vivo and without destructive sampling. In a previous study, we showed that the new substrate provides a good approximation of plant growth conditions found in natural soils. In this paper, we present further development of the techniques for detailed quantitative analysis of images of root-microbe interactions in situ. Using this system it was possible for the first time to analyse bacterial distribution along the roots and in the bulk substrate in vivo. These findings indicate that the coupling of transparent soil with light microscopy is an important advance towards the discovery of the mechanisms of microbial colonisation of the rhizosphere

Identifying spring barley cultivars with differential response to tillage

Cultivars and some cultivar mixtures of spring barley were grown under inversion and non-inversion tillage conditions for three or four years and assessed for disease and yield in order to obtain genotypes that can be used to determine the mechanisms of cultivation adaptation. In general, the higher-yielding cultivars under inversion tillage conditions gave lower yields under non-inversion tillage, whereas low-yielding older cultivars showed relatively smaller reductions in yield under non-inversion tillage. A few cultivars showed preferential yield performance for either inversion or non-inversion tillage and this was irrespective of their overall yield performance. There was no pedigree or breeding programme link between these cultivars and no above-ground gross morphological trait observed was associated with tillage adaptation. Root hairs may contribute to inversion tillage adaptation as a root hair absence mutant was associated with non-inversion adaptation and it is likely that other root-associated traits are responsible also for tillage adaptation. There was no overall cultivar or tillage interaction with rhynchosporium symptoms but a differential tillage interaction may occur in individual years. We have identified clearly contrasting cultivars and tested their across-season robustness with respect to tillage treatment for further detailed mechanistic studies and identification of tillage adaptation traits

Myxospermous seed-mucilage quantity correlates with environmental gradients indicative of water-deficit stress: Plantago species as a model

Abstract Aims Myxospermous seed mucilage is multifunctional and is often found in seeds (or achenes) of species occupying arid environments where the trait may influence seed-dispersal and -germination of seeds. The seed mucilage may also enhance soil-water retention, −hydraulic conductivity and -stability. However, the relationship between seed mucilage quantity, seed germination and seedling traits across environmental gradients which determine water-deficit stress has not yet been ascertained. Methods Therefore, we characterised and tested the relationship between seed mucilage quantity, water-deficit stress responses of seeds and seedlings of 36 accessions of four different Plantago species (P. albicans L., P. coronopus L., P. lagopus L. and P. anceolata L.). These were gathered from six regions across Europe, which presented environmental gradients (of rainfall and temperature), and varying soil qualities. Results Seed mucilage was significantly greater in seeds of accessions experiencing: highest summer temperatures; lowest summer precipitation; soils of the same warm dry regions which had greater capacity to retain water within narrow pore spaces. Under water-deficit stress, seeds with most mucilage exhibited a lower base water potential for germination, suffered least seedling mortality and exhibited the most successful seedling development. Conclusions The findings indicate that seed mucilage quantity appeared as an 'adaptive' trait and there is a relationship between seed-mucilage quantity, seed germination plus seedling survival and development under environmental conditions of highest water-deficit stress

Exercise Training Effects on Inflammatory Gene Expression in White Adipose Tissue of Young Mice

We aimed to determine the effects of 6 wks of exercise on inflammatory markers in mice concomitantly fed either high-fat (HF) or normal chow (NC) diets in young mice. C57BL/6 mice were randomized into (n = 10/group) an NC/sedentary (NC/SED), NC/exercise (NC/EX), HF/SED, and HF/EX groups. Treadmill exercise was performed 5 d/wk at 12 m/min, with 12% grade for 40 min/d. Liver triglycerides and gene expression of F4/80, MCP-1, TNF-α, leptin, and VEGF in visceral white adipose were determined. NC groups had lower body weights after 6 wks versus the HF groups (22.8 ± 0.2 versus 25.7 ± 0.4 g) (P < 0.0001). F4/80 gene expression (indicator of macrophage infiltration) and liver triglycerides were greatest amongst the HF/SED group, with no differences between the remaining groups. VEGF (indicator of angiogenesis) was greatest in the HF/EX versus the other 3 groups (P < 0.05). Exposure of an HF diet in sedentary young mice increased visceral adipose depots and liver triglycerides versus an NC diet. Exercise training while on the HF diet protected against hepatic steatosis and possibly macrophage infiltration within white adipose tissue. This suggests that moderate exercise while on an HF diet can offer some level of protection early on in the development of obesity

The emergent rhizosphere: imaging the development of the porous architecture at the root-soil interface

The rhizosphere is the zone of soil infuenced by a plant root and is critical for plant health and nutrient acquisition. All below ground resources must pass through this dynamic zone prior to their capture by plant roots. However, researching the undisturbed rhizosphere has proved very challenging. Here we compare the temporal changes to the intact rhizosphere pore structure during the emergence of a developing root system in diferent soils. High resolution X-ray Computed Tomography (CT) was used to quantify the impact of root development on soil structural change, at scales relevant to individual micro-pores and aggregates (µm). A comparison of micro-scale structural evolution in homogenously packed soils highlighted the impacts of a penetrating root system in changing the surrounding porous architecture and morphology. Results indicate the structural zone of infuence of a root can be more localised than previously reported (µm scale rather than mm scale). With time, growing roots signifcantly alter the soil physical environment in their immediate vicinity through reducing root-soil contact and crucially increasing porosity at the root-soil interface and not the converse as has often been postulated. This ‘rhizosphere pore structure’ and its impact on associated dynamics are discussed

Random Convex Hulls and Extreme Value Statistics

In this paper we study the statistical properties of convex hulls of $N$ random points in a plane chosen according to a given distribution. The points may be chosen independently or they may be correlated. After a non-exhaustive survey of the somewhat sporadic literature and diverse methods used in the random convex hull problem, we present a unifying approach, based on the notion of support function of a closed curve and the associated Cauchy's formulae, that allows us to compute exactly the mean perimeter and the mean area enclosed by the convex polygon both in case of independent as well as correlated points. Our method demonstrates a beautiful link between the random convex hull problem and the subject of extreme value statistics. As an example of correlated points, we study here in detail the case when the points represent the vertices of $n$ independent random walks. In the continuum time limit this reduces to $n$ independent planar Brownian trajectories for which we compute exactly, for all $n$, the mean perimeter and the mean area of their global convex hull. Our results have relevant applications in ecology in estimating the home range of a herd of animals. Some of these results were announced recently in a short communication [Phys. Rev. Lett. {\bf 103}, 140602 (2009)].Comment: 61 pages (pedagogical review); invited contribution to the special issue of J. Stat. Phys. celebrating the 50 years of Yeshiba/Rutgers meeting

Developmental morphology of cover crop species exhibit contrasting behaviour to changes in soil bulk density, revealed by X-ray computed tomography

Plant roots growing through soil typically encounter considerable structural heterogeneity, and local variations in soil dry bulk density. The way the in situ architecture of root systems of different species respond to such heterogeneity is poorly understood due to challenges in visualising roots growing in soil. The objective of this study was to visualise and quantify the impact of abrupt changes in soil bulk density on the roots of three cover crop species with contrasting inherent root morphologies, viz. tillage radish (Raphanus sativus), vetch (Vicia sativa) and black oat (Avena strigosa). The species were grown in soil columns containing a two-layer compaction treatment featuring a 1.2 g cm-3 (uncompacted) zone overlaying a 1.4 g cm-3 (compacted) zone. Three-dimensional visualisations of the root architecture were generated via X-ray computed tomography, and an automated root-segmentation imaging algorithm. Three classes of behaviour were manifest as a result of roots encountering the compacted interface, directly related to the species. For radish, there was switch from a single tap-root to multiple perpendicular roots which penetrated the compacted zone, whilst for vetch primary roots were diverted more horizontally with limited lateral growth at less acute angles. Black oat roots penetrated the compacted zone with no apparent deviation. Smaller root volume, surface area and lateral growth were consistently observed in the compacted zone in comparison to the uncompacted zone across all species. The rapid transition in soil bulk density had a large effect on root morphology that differed greatly between species, with major implications for how these cover crops will modify and interact with soil structure

A new model for root growth in soil with macropores

Abstract: Background and aimsThe use of standard dynamic root architecture models to simulate root growth in soil containing macropores failed to reproduce experimentally observed root growth patterns. We thus developed a new, more mechanistic model approach for the simulation of root growth in structured soil. Methods: In our alternative modelling approach, we distinguish between, firstly, the driving force for root growth, which is determined by the orientation of the previous root segment and the influence of gravitropism and, secondly, soil mechanical resistance to root growth. The latter is expressed by its inverse, soil mechanical conductance, and treated similarly to hydraulic conductivity in Darcy’s law. At the presence of macropores, soil mechanical conductance is anisotropic, which leads to a difference between the direction of the driving force and the direction of the root tip movement. Results: The model was tested using data from the literature, at pot scale, at macropore scale, and in a series of simulations where sensitivity to gravity and macropore orientation was evaluated. Conclusions: Qualitative and quantitative comparisons between simulated and experimentally observed root systems showed good agreement, suggesting that the drawn analogy between soil water flow and root growth is a useful one