Non-invasive imaging of roots with high resolution X-ray micro-tomography

ray micro-tomography is a well-established technique for non-invasive imaging and evaluation of heterogeneous materials. An inexpensive X-ray micro-tomography system has been designed and built for the specific purposes of examining root growth and root/soil interactions. The system uses a silver target X-ray source with a focal spot diameter of 80 mum, an X-ray image intensifier with a sampling aperture of about 100 mum, and a sample with a diameter of 25 mm. Pre-germinated wheat and rape seeds were grown for up to 8-10 days in plastic containers in a sandy loam soil sieved to < 250 μm, and imaged with the X-ray system at regular intervals. The quality of 3 D image obtained was good allowing the development and growth of both root axes and some first-order laterals to be observed. The satisfactory discrimination between soil and roots enabled measurements of root diameter (wheat values were 0.48-1.22 mm) in individual tomographic slices and, by tracking from slice to slice, root lengths were also measured. The measurements obtained were generally within 10% of those obtained from destructive samples measured manually and with a flat-bed scanner. Further developments of the system will allow more detailed examination of the root: soil interface.

Tracking larval insect movement within soil using high resolution X-ray microtomography

1. In contrast to above-ground insects, comparatively little is known about the behaviour of subterranean insects, due largely to the difficulty of studying them in situ. 2. The movement of newly hatched (neonate) clover root weevil (Sitona lepidus L. Coleoptera: Curculinidae) larvae was studied non-invasively using recently developed high resolution X-ray microtomography. 3. The movement and final position of S. lepidus larvae in the soil was reliably established using X-ray microtomography, when compared with larval positions that were determined by destructively sectioning the soil column. 4. Newly hatched S. lepidus larvae were seen to attack the root rhizobial nodules of their host plant, white clover (Trifolium repens L.). Sitona lepidus larvae travelled between 9 and 27 mm in 9 h at a mean speed of 1.8 mm h(-1). 5. Sitona lepidus larvae did not move through the soil in a linear manner, but changed trajectory in both the lateral and vertical planes.

Exploring the enzymatic landscape: distribution and kinetics of hydrolytic enzymes in soil particle-size fractions

The location of extracellular enzymes within the soil architecture and their association with the various soil components affects their catalytic potential. A soil fractionation study was carried out to investigate: (a) the distribution of a range of hydrolytic enzymes involved in C, N and P transformations, (b) the effect of the location on their respective kinetics, (c) the effect of long-term N fertilizer management on enzyme distribution and kinetic parameters. Soil (silty clay loam) from grassland which had received 0 or 200 kg N ha(-1) yr(-1) was fractionated, and four particle-size fractions (> 200, 200-63, 63-2 and 0. 1-2 mum) were obtained by a combination of wet-sieving and centrifugation, after low-energy ultrasonication. All fractions were assayed for four carbohydrases (beta-cellobiohydrolase, N-acetyl-beta-glucosammidase, beta-glucosidase and beta-xylosidase), acid phosphatase and leucine-aminopeptidase using a microplate fluorimetric assay based on MUB-substrates. Enzyme kinetics (V-max and K-m) were estimated in three particle-size fractions and the unfractionated soil. The results showed that not all particle-size fractions were equally enzymatically active and that the distribution of enzymes between fractions depended on the enzyme. Carbohydrases predominated in the coarser fractions while phosphatase and leucine-aminopeptidase were predominant in the clay-size fraction. The Michaelis constant (K.) varied among fractions, indicating that the association of the same enzyme with different particle-size fractions affected its substrate affinity. The same values of Km were found in the same fractions from the soil under two contrasting fertilizer management regimes, indicating that the Michaelis constant was unaffected by soil changes caused by N fertilizer management. (C) 2004 Elsevier Ltd. All rights reserved.

Does changing the taxonomical resolution alter the value of soil macroinvertebrates as bioindicators of metal pollution?

Ecological indicators are taxa that are affected by, and indicate effects of, anthropogenic environmental stress or disturbance on ecosystems. There is evidence that some species of soil macrofauna (i.e. diameter > 2 min) constitute valuable biological indicators of certain types of soil perturbations. This study aims to determine which level of taxonomic resolution, (species, family or ecological group) is the best to identify indicator of soil disturbance. Macrofauna were sampled in a set of sites encompassing different land-use systems (e.g. forests, pastures, crops) and different levels of pollution. Indicator taxa were sought using the IndVal index proposed by Dufrene and Legendre [Dufrene, M., Legendre, P., 1997. Species assemblages and indicator species: the need for a flexible asymetrical approach. Ecological Monographs 67, 345-3661. This approach is based on a hierarchical typology of sites. The index value changes along the typology and decreases (increases) for generalist (specialist) faunal units (species, families or ecological groups). Of the 327 morphospecies recorded, 19 were significantly associated with a site type or a group of sites (5.8%). Similarly, species were aggregated to form 59 families among which 17 (28.8%) displayed a significant indicator value. Gathering species into 28 broad ecological assemblages led to 14 indicator groups (50%). Beyond the simple proportion of units having significant association with a given level of the site typology, the proportion of specialist and generalist groups changed dramatically when the level of taxonomic resolution was altered. At the species level 84% of the indicator units were specialist, whereas this proportion decreased to 70 and 43% when families and ecological groups were considered. Because specialist groups are the most interesting type of indicators either in terms of conservation or for management purposes we come to the conclusion that the species level is the most accurate taxonomic level in bioindication studies although it requires a high amount of labour and operator knowledge and is time-consuming. (c) 2005 Published by Elsevier Ltd.

Geochemical mapping of carbonate sediments in the Makgadikgadi basin, Botswana using moderate resolution remote sensing data

This paper maps the carbonate geochemistry of the Makgadikgadi Pans region of northern Botswana from moderate resolution (500 m pixels) remotely sensed data, to assess the impact of various geomorphological processes on surficial carbonate distribution. Previous palaeo-environmental studies have demonstrated that the pans have experienced several highstands during the Quaternary, forming calcretes around shoreline embayments. The pans are also a significant regional source of dust, and some workers have suggested that surficial carbonate distributions may be controlled, in part, by wind regime. Field studies of carbonate deposits in the region have also highlighted the importance of fluvial and groundwater processes in calcrete formation. However, due to the large area involved and problems of accessibility, the carbonate distribution across the entire Makgadikgadi basin remains poorly understood. The MODIS instrument permits mapping of carbonate distribution over large areas; comparison with estimates from Landsat Thematic Mapper data show reasonable agreement, and there is good agreement with estimates from laboratory analysis of field samples. The results suggest that palaeo-lake highstands, reconstructed here using the SRTM 3 arc-second digital elevation model, have left behind surficial carbonate deposits, which can be mapped by the MODIS instrument. Copyright (c) 2006 John Wiley & Sons, Ltd.

Convectively coupled equatorial waves in high resolution Hadley centre climate models

Current global atmospheric models fail to simulate well organised tropical phenomena in which convection interacts with dynamics and physics. A new methodology to identify convectively coupled equatorial waves, developed by NCAS-Climate, has been applied to output from the two latest models of the Met Office/Hadley Centre which have fundamental differences in dynamical formulation. Variability, horizontal and vertical structures, and propagation characteristics of tropical convection and equatorial waves, along with their coupled behaviour in the models are examined and evaluated against a previous comprehensive study of observations. It is shown that, in general, the models perform well for equatorial waves coupled with off-equatorial convection. However they perform poorly for waves coupled with equatorial convection. The vertical structure of the simulated wave is not conducive to energy conversion/growth and does not support the correct physical-dynamical coupling that occurs in the real world. The following figure shows an example of the Kelvin wave coupled with equatorial convection. It shows that the models fail to simulate a key feature of convectively coupled Kelvin wave in observations, namely near surface anomalous equatorial zonal winds together with intensified equatorial convection and westerly winds in phase with the convection. The models are also not able to capture the observed vertical tilt structure and the vertical propagation of the Kelvin wave into the lower stratosphere as well as the secondary peak in the mid-troposphere, particularly in HadAM3. These results can be used to provide a test-bed for experimentation to improve the coupling of physics and dynamics in climate and weather models.

Coupled simulations of the Indian monsoon intraseasonal oscillation using a fine-resolution mixed-layer ocean model

The intraseasonal variability (ISV) of the Indian summer monsoon is dominated by a 30–50 day oscillation between “active” and “break” events of enhanced and reduced rainfall over the subcontinent, respectively. These organized convective events form in the equatorial Indian Ocean and propagate north to India. Atmosphere–ocean coupled processes are thought to play a key role the intensity and propagation of these events. A high-resolution, coupled atmosphere–mixed-layer-oceanmodel is assembled: HadKPP. HadKPP comprises the Hadley Centre Atmospheric Model (HadAM3) and the K Profile Parameterization (KPP) mixed-layer ocean model. Following studies that upper-ocean vertical resolution and sub-diurnal coupling frequencies improve the simulation of ISV in SSTs, KPP is run at 1 m vertical resolution near the surface; the atmosphere and ocean are coupled every three hours. HadKPP accurately simulates the 30–50 day ISV in rainfall and SSTs over India and the Bay of Bengal, respectively, but suffers from low ISV on the equator. This is due to the HadAM3 convection scheme producing limited ISV in surface fluxes. HadKPP demonstrates little of the observed northward propagation of intraseasonal events, producing instead a standing oscillation. The lack of equatorial ISV in convection in HadAM3 constrains the ability of KPP to produce equatorial SST anomalies, which further weakens the ISV of convection. It is concluded that while atmosphere–ocean interactions are undoubtedly essential to an accurate simulation of ISV, they are not a panacea for model deficiencies. In regions where the atmospheric forcing is adequate, such as the Bay of Bengal, KPP produces SST anomalies that are comparable to the Tropical Rainfall Measuring Mission Microwave Imager (TMI) SST analyses in both their magnitude and their timing with respect to rainfall anomalies over India. HadKPP also displays a much-improved phase relationship between rainfall and SSTs over a HadAM3 ensemble forced by observed SSTs, when both are compared to observations. Coupling to mixed-layer models such as KPP has the potential to improve operational predictions of ISV, particularly when the persistence time of SST anomalies is shorter than the forecast lead time.

High Resolution Dynamics Limb Sounder measurements of gravity wave activity in the 2006 Arctic stratosphere

Observations from the High Resolution Dynamics Limb Sounder (HIRDLS) instrument on NASA's Aura satellite are used to quantify gravity wave momentum fluxes in the middle atmosphere. The period around the 2006 Arctic sudden stratospheric warming (SSW) is investigated, during which a substantial elevation of the stratopause occurred. Analysis of the HIRDLS results, together with analysis of European Centre for Medium-Range Weather Forecasting zonal winds, provide direct evidence of wind filtering of the gravity wave spectrum during this period. This confirms previous hypotheses from model studies and further contributes to our understanding of the effects of gravity wave driving on the winter polar stratopause.

High-resolution, unstructured meshes for hydrodynamic models of the Great Barrier Reef, Australia

Accuracy and mesh generation are key issues for the high-resolution hydrodynamic modelling of the whole Great Barrier Reef. Our objective is to generate suitable unstructured grids that can resolve topological and dynamical features like tidal jets and recirculation eddies in the wake of islands. A new strategy is suggested to refine the mesh in areas of interest taking into account the bathymetric field and an approximated distance to islands and reefs. Such a distance is obtained by solving an elliptic differential operator, with specific boundary conditions. Meshes produced illustrate both the validity and the efficiency of the adaptive strategy. Selection of refinement and geometrical parameters is discussed. (c) 2006 Elsevier Ltd. All rights reserved.