Soil organic carbon is significantly associated with the pore geometry, microbial diversity and enzyme activity of the macro-aggregates under different land uses.

Microbial activity strongly influences the stabilization of soil organic matter (SOM), and is affected by the abiotic properties within soil aggregates, which tend to differ between land uses. Here, we assessed the effects of SOM and pore geometry on the diversity and activity of microbial communities within aggregates formed under different land uses (undisturbed, plantation, pasture, and cropping). X-ray micro-computed tomography (µCT) revealed that macro-aggregates (2-8 mm) of undisturbed soils were porous, highly-connected, and had 200% more macro-pores compared with those from pasture and cropping soils. While the macro-aggregates of undisturbed soils had greater soil organic carbon (SOC) contents and N-acetyl ß-glucosaminidase, ß-glucosidase, and phosphatase activities, those of cropped soils harboured more diverse bacterial communities. Organic carbon was positively associated with the porosity of the macro-aggregates, which was negatively associated with microbial diversity and positively associated with enzyme activity. Thus, the biophysical processes in macro-aggregates may be important for SOC stabilization within the macro-aggregates.

The impact of carbon addition on the organisation of rhizosheath of chickpea.

Spatio-temporal development of the rhizosheath during root elongation has the potential to modify the function of the rhizosphere under abiotic stress. We quantified the impact of carbon (i.e. glucose) addition on the development and function of rhizosheath of drought tolerant and sensitive chickpea (Cicer arietinum L.) by integrating soil pore volume obtained from X-ray microtomography (µCT), soil physical and microbial respiration measures, and measurements of root traits. Structural equation modelling indicated the feedback mechanisms between added carbon, root traits, pore geometry, and soil functions differed between the cultivars in a fashion congruent with the concept of soil as a self-organising system that interacts with an introduced root system. The drought tolerant cultivar partitioned more photosynthetically fixed carbon to the roots, had more root hairs and more porous rhizosheath, as compared with the sensitive cultivar.

Plant roots redesign the rhizosphere to alter the three-dimensional physical architecture and water dynamics.

The mechanisms controlling the genesis of rhizosheaths are not well understood, despite their importance in controlling the flux of nutrients and water from soil to root. Here, we examine the development of rhizosheaths from drought-tolerant and drought-sensitive chickpea varieties; focusing on the three-dimensional characterization of the pore volume (> 16 µm voxel spatial resolution) obtained from X-ray microtomography, along with the characterization of mucilage and root hairs, and water sorption. We observe that drought-tolerant plants generate a larger diameter root, and a greater and more porous mass of rhizosheath, which also has a significantly increased water sorptivity, as compared with bulk soil. Using lattice Boltzmann simulations of soil permeability, we find that the root activity of both cultivars creates an anisotropic structure in the rhizosphere, in that its ability to conduct water in the radial direction is significantly higher than in the axial direction, especially in the drought-tolerant cultivar. We suggest that significant differences in rhizosheath architectures are sourced not only by changes in structure of the volumes, but also from root mucilage, and further suggest that breeding for rhizosheath architectures and function may be a potential future avenue for better designing crops in a changing environment.

An image processing and analysis tool for identifying and analysing complex plant root systems in 3D soil using non-destructive analysis: Root1.

The objective of this study was to develop a flexible and free image processing and analysis solution, based on the Public Domain ImageJ platform, for the segmentation and analysis of complex biological plant root systems in soil from x-ray tomography 3D images. Contrasting root architectures from wheat, barley and chickpea root systems were grown in soil and scanned using a high resolution micro-tomography system. A macro (Root1) was developed that reliably identified with good to high accuracy complex root systems (10% overestimation for chickpea, 1% underestimation for wheat, 8% underestimation for barley) and provided analysis of root length and angle. In-built flexibility allowed the user interaction to (a) amend any aspect of the macro to account for specific user preferences, and (b) take account of computational limitations of the platform. The platform is free, flexible and accurate in analysing root system metrics.

Visualization of xylem embolism by X-ray microtomography: a direct test against hydraulic measurements.

X-ray microtomography (microCT) is becoming a valuable noninvasive tool for advancing our understanding of plant-water relations. Laboratory-based microCT systems are becoming more affordable and provide better access than synchrotron facilities. However, some systems come at the cost of comparably lower signal quality and spatial resolution than synchrotron facilities. In this study, we evaluated laboratory-based X-ray microCT imaging as a tool to nondestructively analyse hydraulic vulnerability to drought-induced embolism in a woody plant species. We analysed the vulnerability to drought-induced embolism of benchtop-dehydrated Eucalyptus camaldulensis plants using microCT and hydraulic flow measurements on the same sample material, allowing us to directly compare the two methods. Additionally, we developed a quantitative procedure to improve microCT image analysis at limited resolution and accurately measure vessel lumens. Hydraulic measurements matched closely with microCT imaging of the current-year growth ring, with similar hydraulic conductivity and loss of conductivity due to xylem embolism. Optimized thresholding of vessel lumens during image analysis, based on a physiologically meaningful parameter (theoretical conductivity), allowed us to overcome common potential constraints of some lab-based systems. Our results indicate that estimates of vulnerability to embolism provided by microCT visualization agree well with those obtained from hydraulic measurements on the same sample material.

Root hair length and rhizosheath mass depend on soil porosity, strength and water content in barley genotypes.

Selecting plants with improved root hair growth is a key strategy for improving phosphorus-uptake efficiency in agriculture. While significant inter- and intra-specific variation is reported for root hair length, it is not known whether these phenotypic differences are exhibited under conditions that are known to affect root hair elongation. This work investigates the effect of soil strength, soil water content (SWC) and soil particle size (SPS) on the root hair length of different root hair genotypes of barley. The root hair and rhizosheath development of five root hair genotypes of barley (Hordeum vulgare L.) was compared in soils with penetrometer resistances ranging from 0.03 to 4.45 MPa (dry bulk densities 1.2-1.7 g cm(-3)). A "short" (SRH) and "long" root hair (LRH) genotype was selected to further investigate whether differentiation of these genotypes was related to SWC or SPS when grown in washed graded sand. In low-strength soil (<1.43 MPa), root hairs of the LRH genotype were on average 25 % longer than that of the SRH genotype. In high-strength soil, root hair length of the LRH genotype was shorter than that in low-strength soil and did not differ from that of the SRH genotype. Root hairs were shorter in wetter soils or soils with smaller particles, and again SRH and LRH did not differ in hair length. Longer root hairs were generally, but not always, associated with larger rhizosheaths, suggesting that mucilage adhesion was also important. The root hair growth of barley was found to be highly responsive to soil properties and this impacted on the expression of phenotypic differences in root hair length. While root hairs are an important trait for phosphorus acquisition in dense soils, the results highlight the importance of selecting multiple and potentially robust root traits to improve resource acquisition in agricultural systems.

Root hairs improve root penetration, root-soil contact, and phosphorus acquisition in soils of different strength.

Root hairs are a key trait for improving the acquisition of phosphorus (P) by plants. However, it is not known whether root hairs provide significant advantage for plant growth under combined soil stresses, particularly under conditions that are known to restrict root hair initiation or elongation (e.g. compacted or high-strength soils). To investigate this, the root growth and P uptake of root hair genotypes of barley, Hordeum vulgare L. (i.e. genotypes with and without root hairs), were assessed under combinations of P deficiency and high soil strength. Genotypes with root hairs were found to have an advantage for root penetration into high-strength layers relative to root hairless genotypes. In P-deficient soils, despite a 20% reduction in root hair length under high-strength conditions, genotypes with root hairs were also found to have an advantage for P uptake. However, in fertilized soils, root hairs conferred an advantage for P uptake in low-strength soil but not in high-strength soil. Improved root-soil contact, coupled with an increased supply of P to the root, may decrease the value of root hairs for P acquisition in high-strength, high-P soils. Nevertheless, this work demonstrates that root hairs are a valuable trait for plant growth and nutrient acquisition under combined soil stresses. Selecting plants with superior root hair traits is important for improving P uptake efficiency and hence the sustainability of agricultural systems.

Ecological succession, hydrology and carbon acquisition of biological soil crusts measured at the micro-scale.

The hydrological characteristics of biological soil crusts (BSCs) are not well understood. In particular the relationship between runoff and BSC surfaces at relatively large (>1 m(2)) scales is ambiguous. Further, there is a dearth of information on small scale (mm to cm) hydrological characterization of crust types which severely limits any interpretation of trends at larger scales. Site differences and broad classifications of BSCs as one soil surface type rather than into functional form exacerbate the problem. This study examines, for the first time, some hydrological characteristics and related surface variables of a range of crust types at one site and at a small scale (sub mm to mm). X-ray tomography and fine scale hydrological measurements were made on intact BSCs, followed by C and C isotopic analyses. A 'hump' shaped relationship was found between the successional stage/sensitivity to physical disturbance classification of BSCs and their hydrophobicity, and a similar but 'inverse hump' relationship exists with hydraulic conductivity. Several bivariate relationships were found between hydrological variables. Hydraulic conductivity and hydrophobicity of BSCs were closely related but this association was confounded by crust type. The surface coverage of crust and the microporosity 0.5 mm below the crust surface were closely associated irrespective of crust type. The δ (13)C signatures of the BSCs were also related to hydraulic conductivity, suggesting that the hydrological characteristics of BSCs alter the chemical processes of their immediate surroundings via the physiological response (C acquisition) of the crust itself. These small scale results illustrate the wide range of hydrological properties associated with BSCs, and suggest associations between the ecological successional stage/functional form of BSCs and their ecohydrological role that needs further examination.

Non-destructive quantification of cereal roots in soil using high-resolution X-ray tomography.

One key constraint to further understanding plant root development is the inability to observe root growth in situ due to the opaque nature of soil. Of the present non-destructive techniques, computed tomography (CT) is best able to capture the complexities of the edaphic environment. This study compared the accuracy and impact of X-ray CT measurement of in situ root systems with standard technology (soil core washing and WinRhizo analysis) in the context of treatments that differed in the vertical placement of phosphorus fertilizers within the soil profile. Although root lengths quantified using WinRhizo were 8% higher than that observed in the same plants using CT, measurements of root length by the two methodologies were highly correlated. Comparison of scanned and unscanned plants revealed no effect of repeated scanning on plant growth and CT was not able to detect any changes in roots between phosphorus treatments that was observed using WinRhizo. Overall, the CT technique was found to be fast, safe, and able to detect roots at high spatial resolutions. The potential drawbacks of CT relate to the software to digitally segment roots from soil and air, which will improve significantly as automated segmentation algorithms are developed. The combination of very fast scans and automated segmentation will allow CT methodology to realize its potential as a high-throughput technique for the quantification of roots in soils.

Anomalous diffusion of heterogeneous populations characterized by normal diffusion at the individual level.

The characterization of the dispersal of populations of non-identical individuals is relevant to most ecological and epidemiological processes. In practice, the movement is quantified by observing relatively few individuals, and averaging to estimate the rate of dispersal of the population as a whole. Here, we show that this can lead to serious errors in the predicted movement of the population if the individuals disperse at different rates. We develop a stochastic model for the diffusion of heterogeneous populations, inspired by the movement of the parasitic nematode Phasmarhabditis hermaphrodita. Direct observations of this nematode in homogeneous and heterogeneous environments reveal a large variation in individual behaviour within the population as reflected initially in the speed of the movement. Further statistical analysis shows that the movement is characterized by temporal correlations and in a heterogeneously structured environment the correlations that occur are of shorter range compared with those in a homogeneous environment. Therefore, by using the first-order correlated random walk techniques, we derive an effective diffusion coefficient for each individual, and show that there is a significant variation in this parameter among the population that follows a gamma distribution. Based on these findings, we build a new dispersal model in which we maintain the classical assumption that individual movement can be described by normal diffusion, but due to the variability in individual dispersal rates, the diffusion coefficient is not constant at the population level and follows a continuous distribution. The conclusions and methodology presented are relevant to any heterogeneous population of individuals with widely different diffusion rates.

Root phenomics of crops: opportunities and challenges.

Reliable techniques for screening large numbers of plants for root traits are still being developed, but include aeroponic, hydroponic and agar plate systems. Coupled with digital cameras and image analysis software, these systems permit the rapid measurement of root numbers, length and diameter in moderate (typically <1000) numbers of plants. Usually such systems are employed with relatively small seedlings, and information is recorded in 2D. Recent developments in X-ray microtomography have facilitated 3D non-invasive measurement of small root systems grown in solid media, allowing angular distributions to be obtained in addition to numbers and length. However, because of the time taken to scan samples, only a small number can be screened (typically <10 per day, not including analysis time of the large spatial datasets generated) and, depending on sample size, limited resolution may mean that fine roots remain unresolved. Although agar plates allow differences between lines and genotypes to be discerned in young seedlings, the rank order may not be the same when the same materials are grown in solid media. For example, root length of dwarfing wheat (Triticum aestivum L.) lines grown on agar plates was increased by ~40% relative to wild-type and semi-dwarfing lines, but in a sandy loam soil under well watered conditions it was decreased by 24-33%. Such differences in ranking suggest that significant soil environment-genotype interactions are occurring. Developments in instruments and software mean that a combination of high-throughput simple screens and more in-depth examination of root-soil interactions is becoming viable.

Visualization, modelling and prediction in soil microbiology.

The introduction of new approaches for characterizing microbial communities and imaging soil environments has benefited soil microbiology by providing new ways of detecting and locating microorganisms. Consequently, soil microbiology is poised to progress from simply cataloguing microbial complexity to becoming a systems science. A systems approach will enable the structures of microbial communities to be characterized and will inform how microbial communities affect soil function. Systems approaches require accurate analyses of the spatio-temporal properties of the different microenvironments present in soil. In this Review we advocate the need for the convergence of the experimental and theoretical approaches that are used to characterize and model the development of microbial communities in soils.

Modelling nematode movement using time-fractional dynamics.

We use a correlated random walk model in two dimensions to simulate the movement of the slug parasitic nematode Phasmarhabditis hermaphrodita in homogeneous environments. The model incorporates the observed statistical distributions of turning angle and speed derived from time-lapse studies of individual nematode trails. We identify strong temporal correlations between the turning angles and speed that preclude the case of a simple random walk in which successive steps are independent. These correlated random walks are appropriately modelled using an anomalous diffusion model, more precisely using a fractional sub-diffusion model for which the associated stochastic process is characterised by strong memory effects in the probability density function.

Three-dimensional microorganization of the soil-root-microbe system.

Soils contain the greatest reservoir of biodiversity on Earth, and the functionality of the soil ecosystem sustains the rest of the terrestrial biosphere. This functionality results from complex interactions between biological and physical processes that are strongly modulated by the soil physical structure. Using a novel combination of biochemical and biophysical indicators and synchrotron microtomography, we have discovered that soil microbes and plant roots microengineer their habitats by changing the porosity and clustering properties (i.e., spatial correlation) of the soil pores. Our results indicate that biota act to significantly alter their habitat toward a more porous, ordered, and aggregated structure that has important consequences for functional properties, including transport processes. These observations support the hypothesis that the soil-plant-microbe complex is self-organized.

Root cap influences root colonisation by Pseudomonas fluorescens SBW25 on maize.

We investigated the influence of root border cells on the colonisation of seedling Zea mays roots by Pseudomonas fluorescens SBW25 in sandy loam soil packed at two dry bulk densities. Numbers of colony forming units (CFU) were counted on sequential sections of root for intact and decapped inoculated roots grown in loose (1.0 mg m(-3)) and compacted (1.3 mg m(-3)) soil. After two days of root growth, the numbers of P. fluorescens (CFU cm(-1)) were highest on the section of root just below the seed with progressively fewer bacteria near the tip, irrespective of density. The decapped roots had significantly more colonies of P. fluorescens at the tip compared with the intact roots: approximately 100-fold more in the loose and 30-fold more in the compact soil. In addition, confocal images of the root tips grown in agar showed that P. fluorescens could only be detected on the tips of the decapped roots. These results indicated that border cells, and their associated mucilage, prevented complete colonization of the root tip by the biocontrol agent P. fluorescens, possibly by acting as a disposable surface or sheath around the cap.

The effects of soil horizons and faunal excrement on bacterial distribution in an upland grassland soil.

The density and spatial location of bacteria were investigated within different horizons of an upland grassland soil before and after a liming treatment to increase the numbers of large soil fauna. Bacterial cells were located by image analysis of stained thin sections and densities calculated from these data. Excrement from macro- and meso-fauna was identified using micromorphology and the densities of bacteria on specific areas of excrement measured by image analysis. There were significant differences among horizons in the density of bacterial cells, with the minimum density found in the horizon with least evidence of earthworm activity, but no difference in density between the organic H and organo-mineral Ah horizons. Soil improvement by liming significantly increased bacterial densities in all three horizons, with the greatest increase found in the horizon with the smallest density before liming. There were no differences in bacterial density between areas dominated by excrement from earthworms and excrement from enchytraeids, although densities in both areas were significantly increased by liming. Variability in bacterial density at spatial scales of less than 1 mm was linked to the occurrence of excrement. Bacterial densities within areas of both types of excrement were significantly greater than those in the surrounding soil. However, the frequency distribution of the ratios of density in excrement to that in the soil was bimodal, with a majority of occurrences having a ratio near 1 and only some 20-30% having a much larger ratio. These variations can probably be explained by variations in the age of the excrement and its suitability as a substrate.

Towards an evolutionary ecology of life in soil.

The soil-microbe system is one of the most diverse components of the terrestrial ecosystem. The origin of this diversity, and its relation to the life-sustaining processes that are mediated by the resident microbial community, is still poorly understood. The inherent complexities necessitate a theoretical framework that integrates ecological and evolutionary approaches and which embraces the physical heterogeneity of the soil environment. Such a framework is currently lacking, although recent advances in theory and experimentation are beginning to identify the essential ingredients. Here, we review and evaluate the relevance of current modelling approaches, and propose a new synthesis of an evolutionary ecology of life in soil. Key elements include an account of dispersal, horizontal gene transfer, and the consideration of the physical and biological components of soil as an integrated complex adaptive system.

Spinning-induced rhabdomyolysis: a case report.

Exercise induced rhabdomyolysis has previously been described as occurring in unfit adults or those attempting exhaustive exercise, but is rarely seen in previously fit adults undertaking moderate exercise. This case report describes what we believe to be the first reported case of exercise induced rhabdomyolysis due to the patient completing a 'spinning class' at her local gymnasium. The report also covers diagnosis and management of this condition.

Spatial distribution of bacterial communities and their relationships with the micro-architecture of soil.

Biological soil thin-sections and a combination of image analysis and geostatistical tools were used to conduct a detailed investigation into the distribution of bacteria in soil and their relationship with pores. The presence of spatial patterns in the distribution of bacteria was demonstrated at the microscale, with ranges of spatial autocorrelation of 1 mm and below. Bacterial density gradients were found within bacterial patches in topsoil samples and also in one subsoil sample. Bacterial density patches displayed a mosaic of high and low values in the remaining subsoil samples. Anisotropy was detected in the spatial structure of pores, but was not detected in relation to the distribution of bacteria. No marked trend as a function of distance to the nearest pore was observed in bacterial density values in the topsoil, but in the subsoil bacterial density was greatest close to pores and decreased thereafter. Bacterial aggregation was greatest in the cropped topsoil, though no consistent trends were found in the degree of bacterial aggregation as a function of distance to the nearest pore. The implications of the results presented for modelling and predicting bacterial activity in soil are discussed.

Effect of bulk density on the spatial organisation of the fungus Rhizoctonia solani in soil.

Abstract The mycelial growth form of eucarpic fungi allows for a highly effective spatial exploration of the soil habitat. However, understanding mycelial spread through soil has been limited by difficulties of observation and quantification of fungi as they spread through this matrix. We report on a study on the effects of soil structure by altering the soil bulk density, on the spatial exploration of soil by the fungus Rhizoctonia solani using a soil thin-sectioning technique. First we quantified fungal densities in microscopic images (0.44 mm(2)). At this scale, hyphae were either absent, or present as minor fragments, typically occupying less than 1% surface area of the thin section. From contiguous microscopic images we then produced large-scale (6.21 cm(2)) spatial distribution maps of fungal hyphae. These maps were superimposed onto soil structural maps, which quantify the degree of porosity in each microscopic image. Alterations in soil structure by changing the bulk density are shown to affect the distribution of the fungus within the soil. The volume of soil explored by the fungus increased with increasing bulk density. This was associated with a shift from a few large pore spaces to more evenly distributed small-scale pores. Fungal hyphae were present in all porosity classes within each bulk density, including areas that contain less than 5% visible pore space. However, fungal hyphae were more often found in areas with a higher porosity, in particular at low soil bulk densities. The results show that soil structure is a major component in the spatial exploration of soil by fungi.