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The environmental distribution of Burkholderia pseudomallei, the causative agent of melioidosis, remains poorly understood. B. pseudomallei is known to have the ability to occupy a variety of environmental niches, particularly in soil. This paper provides novel information about a putative association of soil biogeochemical heterogeneity and the vertical distribution of B. pseudomallei. We investigated (1) the distribution of B. pseudomallei along a 300-cm deep soil profile together with the variation of a range of soil physico-chemical properties; (2) whether correlations between the distribution of B. pseudomallei and soil physico-chemical properties exist and (3) when they exist, what such correlations indicate with regards to the environmental conditions conducive to the occurrence of B. pseudomallei in soils. Unexpectedly, the highest concentrations of B. pseudomallei were observed between 100 and 200 cm below the soil surface. Our results indicate that unravelling the environmental conditions favorable to B. pseudomallei entails considering many aspects of the actual complexity of soil. Important recommendations regarding environmental sampling for B. pseudomallei can be drawn from this work, in particular that collecting samples down to the water table is of foremost importance, as groundwater persistence appears to be a controlling factor of the occurrence of B. pseudomallei in soil. [ABSTRACT FROM AUTHOR]

In the basin of Mekong, over 70 million people rely on unimproved surface water for their domestic requirements. Surface water is often contaminated with fecal matter and yet little information exists on the underlying mechanisms of fecal contamination in tropical conditions at large watershed scales. Our objectives were to (1) investigate the seasonality of fecal contamination using Escherichia coli as fecal indicator bacteria (FIB), and (2) establish links between the fecal contamination in stream water and its controlling factors (hydrology and land use). We present the results of (1) a sampling campaign at the outlet of 19 catchments across Lao PDR, in both the dry and the rainy seasons of 2016, and (2) a 10-day interval monitoring conducted in 2017 and 2018 at three point locations of three rivers (Nam Ou, Nam Suang, and Mekong) in northern Lao PDR. Our results show the presence of fecal contamination at most of the sampled sites, with a seasonality characterized by higher and extreme E. coli concentrations occurring during the rainy season. The highest E. coli concentrations, strongly correlated with total suspended sediment concentrations, were measured in catchments dominated by unstocked forest areas, especially in mountainous northern Lao PDR and in Vientiane province. [ABSTRACT FROM AUTHOR]

Key message: In this study, deep roots of teak tree seem to have acted as a "safety net", allowing trees to maintain their canopy cover longer, thus coping with inter- and intra-seasonal drought. Most deciduous species of dry monsoon forest, such as teak tree (Tectona grandis Linn F.), establish new foliage slightly before, or at the onset of the rainy season, when the upper soil layers are the driest. This phenomenon suggests that trees rely upon deep water storage to cover their need for the new canopy development. Therefore, we hypothesized that deeper rooted trees may display phenological patterns that confer them physiological advantages with regard to access to water. At an upland location in Northern Laos, we characterized 10 mono-specific teak tree plantations corresponding to micro-environments that differed with regard to soil, slope, elevation, and orientation. We compared the leaf phenology of trees, taking into account their age, diameter at breast height (DBH), and rooting pattern down to 3.5 m depth. With at least 5% of its total fine roots below 2 m, teak trees were found to be deep rooted. There was no correlation between the timing of leaf flushing and rooting depth nor with primary production (assessed on the basis of tree girth increase). Leaf flushing was strongly synchronous with rainfall rather pointing out that its primary determinant is the water status of topsoil and near-surface soil horizons that results from seasonal rainfall, even though the mechanism(s) underlying such a process remain to be clarified. However, deeper rooted teak trees tended to maintain a denser canopy cover over longer periods than trees with shallower rooting systems. This suggests that, deep roots may play a role as a "safety net", i.e., providing improved resilience to inter- and intra-seasonal drought events, but do not influence the timing of the leaf flushing. [ABSTRACT FROM AUTHOR]

Burkholderia pseudomallei is the bacterium that causes melioidosis in humans. While B. pseudomallei is known to be endemic in South East Asia (SEA), the occurrence of the disease in other parts of the tropics points towards a potentially large global distribution. We investigated the environmental factors that influence the presence (and absence) of B. pseudomallei in a tropical watershed in SEA. Our main objective was to determine whether there is a link between the presence of the organism in the hydrographic network and the upstream soil and land-use type. The presence of B. pseudomallei was determined using a specific quantitative real-time PCR assay following enrichment culture. Land use, soil, geomorphology, and environmental data were then analyzed using partial least squares discriminant analysis (PLSDA) to compare the B. pseudomallei positive and negative sites. Soil type in the surrounding catchment and turbidity had a strong positive influence on the presence (acrisols and luvisols) or absence (ferralsols) of B. pseudomallei. Given the strong apparent links between soil characteristics, water turbidity, and the presence/absence of B. pseudomallei, actions to raise public awareness about factors increasing the risk of exposure should be undertaken in order to reduce the incidence of melioidosis in regions of endemicity. [ABSTRACT FROM AUTHOR]

Background and aims: This paper provides an overview of the measuring capabilities of IJ_Rhizo, an ImageJ macro that measures scanned images of washed root samples. IJ_Rhizo is open-source, platform-independent and offers a simple graphic user interface (GUI) for a main audience of non-programmer scientists. Being open-source based, it is also fully modifiable to accommodate the specific needs of the more computer-literate users. A comparison of IJ_Rhizo’s performance with that of the widely used commercial package WinRHIZO™ is discussed. Methods: We compared IJ_Rhizo’s performance with that of the commercial package WinRHIZO™ using two sets of images, one comprising test-line images, the second consisting of images of root samples collected in the field. IJ_Rhizo and WinRHIZO™ estimates were compared by means of correlation and regression analysis. Results: IJ_Rhizo “Kimura” and WinRHIZO™ “Tennant” were the length estimates that were best linearly correlated with each other. Correlation between average root diameter estimates was weaker, due to the sensitivity of this parameter to thresholding and filtering of image background noise. Conclusions: Overall, IJ_Rhizo offers new opportunities for researchers who cannot afford the cost of commercial software packages to carry out automated measurement of scanned images of root samples, without sacrificing accuracy. [ABSTRACT FROM AUTHOR]

Improving access to clean water has the potential to make a major contribution toward poverty reduction in rural communities of Lao P.D.R. This study focuses on stream water quality along a Mekong basin tributary, the Houay Xon that flows within a mountainous, mosaic land-use catchment of northern Lao P.D.R. To compare direct water quality measurements to the perception of water quality within the riparian population, our survey included interviews of villagers. Water quality was found to vary greatly depending on the location along the stream. Overall, it reflected the balance between the stream self-cleaning potential and human pressure on the riparian zone: (i) high bacteria and suspended load levels occurred where livestock are left to free-range within the riparian zone; (ii) very low oxygen content and high bacteriological contamination prevailed downstream from villages; (iii) high concentrations of bacteria were consistently observed along urbanized banks; (iv) low oxygen content were associated with the discharge of organic-rich wastewater from a small industrial plant; (v) very high suspended load and bacteria levels occurred during flood events due to soil erosion from steep cultivated hill slopes. Besides these human induced pollutions we also noted spontaneous enrichments in metals in wetland areas fed by dysoxic groundwater. These biophysical measurements were in agreement with the opinions expressed by the majority of the interviewees who reported poor and decreasing water quality in the Houay Xon catchment. Based on our survey, we propose recommendations to improve or maintain stream water quality in the uplands of northern Lao P.D.R. [ABSTRACT FROM AUTHOR]

Understanding better the interactions between root systems in associated crops is significant for basic knowledge in plant science and to help designing cropping systems. Current research on inter-specific root interactions concentrates on static descriptions of the horizontal extension of root systems or on the dynamics of provoked root encounters. This study considers detailed observations of the dynamics of inter-specific root interactions, in the vertical plane, at both the whole root system and the individual root levels. Corn and young rubber trees were grown in association in artificial conditions that excluded the possibility of competition for resources, using rhizoboxes, i.e. thin containers with a transparent wall. The paper presents novel approaches, such as the study of root system growth trajectories, to document root system development in terms of overall growth rate, colonization of soil space and individual root growth patterns. It was found that (i) corn roots developed towards rubber roots until a contact was established, (ii) rubber roots expanded faster and more vertically in association with corn, (iii) the expansion rates of both root systems varied concomitantly and (iv) inter-specific root encounters resulted in reduced elongation rates in both species. Implications of these results for corn/rubber inter-cropping are discussed. This work advocates in favour of a better understanding of under-ground facilitative effects between species. If understood enough to be manipulated, such knowledge might become a powerful tool for the design of more sustainable and efficient cropping systems. [ABSTRACT FROM AUTHOR]

To measure the elongation rate of individual roots in soil remains a challenge. A novel method for estimating elongation rates of excavated roots is presented. Morphological markers are identified along the tip of excavated roots, and their distance relative to the apex is measured. These markers correspond to developmental stages which follow known temporal patterns. Hence, their distance relative to the apex reflects root elongation during the period corresponding to their development. The method was tested on maize roots grown in a range of conditions and substrates. It was found that distances from markers to apices were proportional, with some variability, to elongation rates. Remarkably, the linear relationships between these distances were neither affected by substrate, nor by growing conditions. Using several markers allows covering time periods ranging from 0.3 day to 3 days as well as cross validation of estimates. Provided further testing, under a wider range of environmental conditions, is conducted, the concepts presented in this paper may serve to define a new measurement technique. [ABSTRACT FROM AUTHOR]

In this issue of Plant and Soil Nakaji et al. ( Plant Soil, this volume, ) report a novel approach for automatically identifying roots and other rhizosphere components in rhizosphere images acquired using a multi-spectral (visible—VIS- and near-infrared—NIR-) imaging system. The images are acquired through a root-window observation device and the study highlights the perspectives offered by this imaging system. An outstanding outcome of this research is that the new approach can be applied to effectively separate soil litter from the purely mineral phase and distinguish root tissues that differ in physiological status, i.e. live (different age classes), senescent and dead. If achievable routinely, such a detailed classification of rhizosphere components could greatly improve our appraisal of root turnover and associated organic matter input to the soil, information of paramount importance for an improved understanding of many essential processes such as global geochemical cycles. Minirhizotrons (MR) systems have been increasingly used in global change studies because they are a convenient way to frequently and nondestructively quantify root length production and mortality (Norby and Jackson, New Phytol, 147:3–12, ; Hendrick and Pregitzer, Ecology, 73:1094–1104, ). However, the MR technique still has many limitations, including the lack of a standard, accurate and rapid procedure to extract and classify rhizosphere components from the MR images obtained. The recent work by Nakaji et al. ( Plant Soil, this volume, ) provides convincing evidence that the inclusion of a VIS-NIR multi-spectral capability into conventional MR systems could substantially improve this method, and extend its adoption by the wider plant scientist community as a standard research tool. [ABSTRACT FROM AUTHOR]

Roots modify the properties of soil in their immediate vicinity. Individually, fine roots (<1 mm in diameter) have little effect on soil properties, but this is offset by the fact that they make up most of a plant’s total root length. Roots growing near the soil surface may influence soil detachment. Slope conditions are also known to influence root growth. A field study conducted in a small watershed of Northern Lao People’s Democratic Republic (PDR) during the 2005 rainy season assessed putative interactions between shallow fine roots, slope angle and soil detachment under three land uses: shifting cultivation, fallow and tree plantations. We used auger sampling and root windows to measure root length density and 1-m2 microplots to monitor water infiltration, runoff and soil detachment. Annual crops and plantation trees did not explore shallow soil horizons as thoroughly as fallow species. Under both crop and fallow, RLD in the top 5 cm decreased as slope increased. This pattern could be linked, either as a cause or a consequence, to slope-related changes in infiltration regimes. In contrast, no clear relation between fine root development and soil detachment was found. [ABSTRACT FROM AUTHOR]

Soil water uptake by plant roots results from the complex interplay between plant and soil which modulates and determines transport processes at a range of spatial and temporal scales: at small scales, uptake rates are determined by local soil and root hydraulic properties but, at the plant scale, local processes interact within the root system and are integrated through the hydraulic architecture of the root system and plant transpiration. However, because of the inherent complexity of the root system (both structural and functional), plant roots are commonly account for with synthetic but over-simplifying descriptors, valid at a given spatial scale. In this article, we present a model describing both soil and plant processes involved in water uptake at the scale of the whole root system with explicit account of individual roots. This is achieved through the unifying concepts of root system architecture and hydraulic continuity between the soil and plant. The model is based on a combination of architectural, root system hydraulic and soil water transfer modelling. The model can reproduce qualitatively and quantitatively laboratory experimental data obtained from imaging of water uptake by light transmission (cf. Garrigues et al., Water uptake by plant roots: I-Formation and propagation of a water extraction front in mature root systems as evidenced by 2D light transmission imaging. Plant and soil (2006, this issue) or X-ray imaging for two soil types (a sand/clay mix and a sandy clay loam) and different narrow-leaf lupin root systems (taprooted and fibrous), using independently measured soil–plant parameters. Results of the experiments and modelling reported in this paper concur to show that a water extraction front formed on the root system. This uptake front’s spatial extension and propagation were closely related to the local dependence between root and soil hydraulic properties and root axial conductance. Hence, a sharp front formed in the sand/clay mix but was much more attenuated in the sandy loam. Comparison between taprooted and fibrous root systems grown in a sand/clay mix, show that the taprooted architecture induced a more spatially concentrated uptake zone (near the soil surface) with higher flux rates, but with xylem water potential at the base of the root system twice as low than in the fibrous architecture. Modelling provided evidence that hydraulic lift might have occurred when transpiration declined, particularly in soil prone to abrupt variations in soil water potential (sand/clay mix). Finally, such a model, explicitly coupling root system-soil water transfers, can be useful to study water uptake in relation with root architectural traits, distribution of root hydraulic conductance or influence of heterogeneous conditions (localised irrigation, root clumping). [ABSTRACT FROM AUTHOR]

Soil water extraction by plant roots results from plant and soil transport processes interacting at different space and time scales. At the single root scale, local soil hydraulic status and plant physiology strongly control water uptake. At the whole root system level, these local, spatially interacting processes, are integrated and modulated depending on the root system hydraulics and plant transpiration. Most often, architectural and physiological characteristics of the root system are poorly taken into account in water uptake studies. This work aims at (i) studying root water extraction by mature root systems from the single root to the whole root system scale and (ii) providing experimental data for the assessment of a detailed model of water transport in the soil–root system presented in a companion paper (Doussan et al., Plant Soil 2006, this issue). Based on the dynamic imaging of soil water depletion around roots, we examined the influence of root system architecture and soil hydraulic properties on water uptake. We worked with narrow-leaf lupin plants whose root system architecture ranged from taprooted to fasciculate. Plants were grown in large thin containers (rhizotron) filled with a translucent sand/clay mix growing medium. Water transfer in the soil, together with root water uptake, were monitored in laboratory experiments by means of 2D light transmission imaging. This technique enables the mapping of the soil water content at high spatial and temporal resolutions. Throughout water uptake events, we clearly observed and quantified the formation and movement of a water extraction front and of high gradients of soil water content next to the roots. The data obtained also demonstrate that water uptake is never restricted to a specific portion of a root and that the contribution of a specific portion of a root to the overall uptake varies with time and with the position of the root within the root system. Finally, we found that different root system architectures induced different water uptake patterns. [ABSTRACT FROM AUTHOR]

Direct and simultaneous observation of root growth and plant water uptake is difficult because soils are opaque. X-ray imaging techniques such as projection radiography or Computer Tomography (CT) offer a partial alternative to such limitations. Nevertheless, there is a trade-off between resolution, large field-of-view and 3-dimensionality: With the current state of the technology, it is possible to have any two. In this study, we used X-ray transmission through thin-slab systems to monitor transient saturation fields that develop around roots as plants grow. Although restricted to 2-dimensions, this approach offers a large field-of-view together with high spatial and dynamic resolutions. To illustrate the potential of this technology, we grew peas in 1 cm thick containers filled with soil and imaged them at regular intervals. The dynamics of both the root growth and the water content field that developed around the roots could be conveniently monitored. Compared to other techniques such as X-ray CT, our system is relatively inexpensive and easy to implement. It can potentially be applied to study many agronomic problems, such as issues related to the impact of soil constraints (physical, chemical or biological) on root development. [ABSTRACT FROM AUTHOR]