Jean-Luc Maeght

How to study deep roots—and why it matters

The drivers underlying the development of deep root systems, whether genetic or environmental, are poorly understood but evidence has accumulated that deep rooting could be a more widespread and important trait among plants than commonly anticipated from their share of root biomass. Even though a distinct classification of “deep roots” is missing to date, deep roots provide important functions for individual plants such as nutrient and water uptake but can also shape plant communities by hydraulic lift (HL). Subterranean fauna and microbial communities are highly influenced by resources provided in the deep rhizosphere and deep roots can influence soil pedogenesis and carbon storage.Despite recent technological advances, the study of deep roots and their rhizosphere remains inherently time-consuming, technically demanding and costly, which explains why deep roots have yet to be given the attention they deserve. While state-of-the-art technologies are promising for laboratory studies involving relatively small soil volumes, they remain of limited use for the in situ observation of deep roots. Thus, basic techniques such as destructive sampling or observations at transparent interfaces with the soil (e.g., root windows) which have been known and used for decades to observe roots near the soil surface, must be adapted to the specific requirements of deep root observation. In this review, we successively address major physical, biogeochemical and ecological functions of deep roots to emphasize the significance of deep roots and to illustrate the yet limited knowledge. In the second part we describe the main methodological options to observe and measure deep roots, providing researchers interested in the field of deep root/rhizosphere studies with a comprehensive overview. Addressed methodologies are: excavations, trenches and soil coring approaches, minirhizotrons (MR), access shafts, caves and mines, and indirect approaches such as tracer-based techniques.

Processes driving soil solution chemistry in a flooded rice-cropped vertisol: analysis of long-time monitoring data

Abstract Senegal river water has positive alkalinity (0.55 meq l −1 ) and positive calcite-residual alkalinity (0.30 meq l −1 ). Without leaching, this water presents a possible alkalinization and sodication hazard for the soil. The effect of flooding on soil solution chemistry in an irrigated nondrained vertisol under rice was monitored during 3 years in northern Senegal. During flooding, soil solution redox potential dropped to about −0.15 V, and alkalinity increased to 15 meq l −1 . Mg content increased as well, from about 1 to 5 meq l −1 , whereas Cl and SO 4 contents decreased to very low levels at the end of the growing season (0.05 meq l −1 ). After the fallow, nonflooded period between two crop cycles, the soil solution composition returned to its initial neutral sulfate and chloride composition. The observed cycle in soil solution chemistry could not be explained by water and solute transfer because infiltration rates were very low, due to air entrapment in the soil profile. Geochemical control by calcite and gypsum was excluded during irrigation. Mossbauer spectroscopy showed that iron oxides were both well- and poorly crystallized goethite. Goethite dissolution was assessed by pH–Eh stability diagrams. We explained the increase in alkalinity and Mg concentration in the soil solution partly by the composition of the irrigation water, and partly by the reduction and dissolution of Fe oxides, and Fe 2+ fixation on exchange sites of the clay minerals. These processes were reversed as soon as the soil oxidized. The decline in Cl concentration was attributed to geochemical control through the formation of a GR-Cl − mineral around the porous cups. In that case, Cl should not be used as a natural tracer. Carbonates accumulate in soil solution not only due to iron reduction, but also because of the positive residual alkalinity of the irrigation water. When the soil dries at the end of crop cycle, the carbonate concentration of topsoil will increase and calcite will precipitate. This ongoing process may result in calcium control and ultimately soil alkalinization over the years.

IJ_Rhizo: an open-source software to measure scanned images of root samples

Background and aimsThis 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.MethodsWe 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.ResultsIJ_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.ConclusionsOverall, 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.

Actual and potential salt-related soil degradation in an irrigated rice scheme in the Sahelian zone of Mauritania

Salt-related soil degradation due to irrigation activities is considered a major threat to the sustainability of rice cropping under semi-arid conditions in West Africa. Rice productivity problems related to soil salinity, alkalinity and topographic position were observed in an irrigated rice scheme in southern central Mauritania. Detailed study of soils in a toposequence revealed that highest topsoil salinity and alkalinity were found at the shallow soils ( 2.5 m) and salinity levels remained low due to leaching. Foum Gleita’s irrigation water used is amongst the most alkaline in the Sahel. However, no clear indications of secondary salinization or alkalinization due to irrigation activities were observed. A comparison of historical data revealed no significant changes of topsoil salinity and pH over the last 30 years. The PHREEQC 2.0 model was used to study actual and potential development of soil salinity and alkalinity problems, by simulating excessive concentration of the irrigation water through evaporation. The evolution into a strongly sodic-alkaline solution due to precipitation of Mg-calcite and -silicate minerals did not fit with current composition of ground and surface water, which showed geochemical control of alkalinity at high concentrations. Incorporation of cation exchange processes, using a small (1.0 mmolc per 100 g dry soil) but calcium saturated CEC, resulted in a better fit with field data. Results indicate that the soil’s buffer capacity to

A Geometrical Pore Model for Estimating the Microscopical Pore Geometry of Soil with Infiltration Measurements

This paper presents a simple geometrical pore model designed to relate characteristic pore radii of the porous network of soils with macroscopic infiltration parameters. The model composed of a stack of spherical hollow elements is described with two radii values: the pore access radius and the actual pore radius. The model was compared to cylindrical pore models and its mathematical consistency was assessed. Soil sorptivity S and the second parameter A of the Philip infiltration equation (1957), have been determined by numerically simulated infiltration. A diagram and an empirical relation have been set in order to relate the pore access and pore radii to the infiltration parameters S and A. The consistency of the model was validated by comparing the predicted sorptivity and hydraulic conductivity values, with the widely used unsaturated soil hydraulic functions (van Genuchten, 1980). The model showed good agreement with experimental infiltration data, and it is therefore concluded that the use of a model with two radii improves the relation between microscopic pore size and macroscopic infiltration parameters.

Seasonal Patterns of Fine Root Production and Turnover in a Mature Rubber Tree (Hevea brasiliensis Müll. Arg.) Stand- Differentiation with Soil Depth and Implications for Soil Carbon Stocks

Fine root dynamics is a main driver of soil carbon stocks, particularly in tropical forests, yet major uncertainties still surround estimates of fine root production and turnover. This lack of knowledge is largely due to the fact that studying root dynamics in situ, particularly deep in the soil, remains highly challenging. We explored the interactions between fine root dynamics, soil depth, and rainfall in mature rubber trees (Hevea brasiliensis Müll. Arg.) exposed to sub-optimal edaphic and climatic conditions. A root observation access well was installed in northern Thailand to monitor root dynamics along a 4.5 m deep soil profile. Image-based measurements of root elongation and lifespan of individual roots were carried out at monthly intervals over 3 years. Soil depth was found to have a significant effect on root turnover. Surprisingly, root turnover increased with soil depth and root half-life was 16, 6–8, and only 4 months at 0.5, 1.0, 2.5, and 3.0 m deep, respectively (with the exception of roots at 4.5 m which had a half-life similar to that found between depths of 1.0 and 2.5 m). Within the first two meters of the soil profile, the highest rates of root emergence occurred about 3 months after the onset of the rainy season, while deeper in the soil, root emergence was not linked to the rainfall pattern. Root emergence was limited during leaf flushing (between March and May), particularly within the first two meters of the profile. Between soil depths of 0.5 and 2.0 m, root mortality appeared independent of variations in root emergence, but below 2.0 m, peaks in root emergence and death were synchronized. Shallow parts of the root system were more responsive to rainfall than their deeper counterparts. Increased root emergence in deep soil toward the onset of the dry season could correspond to a drought acclimation mechanism, with the relative importance of deep water capture increasing once rainfall ceased. The considerable soil depth regularly explored by fine roots, even though significantly less than in surface layers in terms of root length density and biomass, will impact strongly the evaluation of soil carbon stocks.

Vegetation as a driver of temporal variations in slope stability: The impact of hydrological processes

Although vegetation is increasingly used to mitigate landslide risks, how vegetation affects the temporal variability of slope stability is poorly understood, especially in earthquake-prone regions. We combined 3-year long soil moisture monitoring, measurements of soil physical properties and plant functional traits, and numerical modeling to compare slope stability under paired land uses with and without trees in tropical, sub-tropical, and temperate landslide- and earthquake-prone regions. Trees improved stability for 5-12 months per year from drawdown of soil moisture and resulted in less interannual variability in the duration of high-stability periods compared to slopes without trees. Our meta-analysis of published data also showed that slopes with woody vegetation were more stable and less sensitive to climate and soil factors than slopes with herbaceous vegetation. However, estimates of earthquake magnitude necessary to destabilize slopes at our sites suggest that large additional stabilization from trees is necessary for meaningful protection against external triggers.

Melioidosis in Laos

Melioidosis is a serious infectious tropical disease caused by a soil-dwelling bacterium, Burkholderia pseudomallei, transmitted from contaminated soil or surface water. Although endemic in Southeast Asia, it is considered an emerging disease in Lao PDR where it has only been recognised for 15 years, becoming one of the leading causes of community-acquired septicaemia. A research programme has been developed by the Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit in collaboration with the Institut de la Francophonie pour la Medecine Tropicale (IFMT) and the Institut de Recherche pour le Developpement (IRD) to investigate the environmental reservoir of B. pseudomallei in Lao PDR. The first study, conducted in 2009, showed that the geographical distribution of B. pseudomallei was very heterogeneous and not limited to the floodplains of the Mekong River. The soil samples collected in the province of Saravane (southern Laos) was proved the most heavily contaminated. The second study, conducted in 2010, aimed to detect B. pseudomallei in surface water using Moore’s swabs. A high proportion of water samples taken from the Sedone River were positive downstream of a heavily contaminated terrestrial site, suggesting contamination by runoff from land reservoirs. Both environmental reservoir studies of B. pseudomallei pave the way for future research in order to clarify the areas at risk of melioidosis to facilitate preventive measures amongst populations at risk and better care for those infected.