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Author(s): Pat H. Bellamy [1]; Peter J. Loveland [1]; R. Ian Bradley [1]; R. Murray Lark [2]; Guy J. D. Kirk (corresponding author) [1] More than twice as much carbon [...]

Iron toxicity is a major constraint to rice production, particularly in highly weathered soils of inland valleys in sub‐Saharan Africa where the rice growing area is rapidly expanding. There is a wide variation in tolerance of iron toxicity in the rice germplasm. However, the introgression of tolerance traits into high‐yielding germplasm has been slow owing to the complexity of the tolerance mechanisms and large genotype‐by‐environment effects. We review current understanding of tolerance mechanisms, particularly those involving below‐ground plant–soil interactions. Until now these have been less studied than above‐ground mechanisms. We cover processes in the rhizosphere linked to exclusion of toxic ferrous iron by oxidation, and resulting effects on the mobility of nutrient ions. We also cover the molecular physiology of below‐ground processes controlling iron retention in roots and root‐shoot transport, and also plant iron sensing. We conclude that future breeding programmes should be based on well‐characterized molecular markers for iron toxicity tolerance traits. To successfully identify such markers, the complex tolerance response should be broken down into its components based on understanding of tolerance mechanisms, and tailored screening methods should be developed for individual mechanisms. Progress in identifying markers for Fe toxicity tolerance in rice has been slow because of the complexity of tolerance mechanisms and the importance of below‐ground plant‐soil interactions. We review current understanding of these below‐ground processes, including recent advances in the molecular physiology of tolerance. [ABSTRACT FROM AUTHOR]

The use of stable isotope analysis to resolve ecosystem respiration into its plant and soil components rests on how well the end‐member isotope signatures (δ13C) are characterised. In general, it is assumed that end‐member values are constant over time. However, there are necessarily diurnal and other transient variations in end‐members with environmental conditions. We analyse diurnal and seasonal patterns of ecosystem respiration and its δ13C in a C4 grass growing in a C3 soil using fixed and diurnally varying plant and soil δ13C end‐members. We measure the end‐members independently, and we assess the effects of expected variation in values. We show that variation in end‐members within realistic ranges, particularly diurnal changes in the plant end‐member, can cause partitioning errors of 40% during periods of high plant growth. The effect depends on how close the end‐member is to the measured net respiration δ13C, that is, the proportion of the respiration due to that end‐member. We show light‐driven variation in plant end‐members can cause substantial distortion of partitioned soil organic matter (SOM) flux patterns on a diurnal scale and cause underestimation of daily to annual SOM turnover of approximately 25%. We conclude that, while it is not practicable to independently measure the full temporal variation in end‐member values over a growing season, this error may be adjusted for by using a diurnally varying δ13Cplant. Highlights: End‐member δ13C values used to partition ecosystem respiration vary diurnally and seasonallyPatterns of ecosystem respiration and its δ13C in a C4 grass growing in a C3 soil were analysed.Ignoring temporal changes in end‐member δ13C values can cause large errors in partitioningLong‐term data sets with sufficient temporal resolution can be used to correct for this [ABSTRACT FROM AUTHOR]

There is a lack of field methods for measuring plant and soil processes controlling soil organic matter (SOM) turnover over diurnal, seasonal and longer timescales with which to develop datasets for modelling. We describe an automated field system for measuring plant and soil carbon fluxes over such timescales using stable isotope methods, and we assess its performance. The system comprises 24 large (1‐m deep, 0.8‐m diameter) cylindrical lysimeters connected to gas‐flux chambers and instruments. The lysimeters contain intact, naturally structured C3 soil planted with a C4 grass. Fluxes of CO2 and their 13C isotope composition are measured three times daily in each lysimeter, and the isotope composition is used to partition the fluxes between plant and soil sources. We investigate the following potential sources of error in the measurement system and show they do not significantly affect the measured CO2 fluxes or isotope signatures: gas leaks, the rate of gas flow through sampling loops, instrument precision and drift, the concentration dependence of isotope measurements, and the linearity of CO2 accumulation in the chambers and associated isotope fractionation resulting from different rates of 13CO2 and 12CO2 diffusion from the soil. For the loamy grassland soil and US prairie grass (Bouteloua dactyloides) tested, the precision of CO2 flux measurements was ±0.04% and that of the flux partitioning ±0.40%. We give examples of diurnal and seasonal patterns of plant and soil C fluxes and soil temperature and moisture. We discuss the limitations of the isotope methodology for partitioning fluxes as applied in our system. We conclude that the system is suitable for measuring net ecosystem respiration fluxes and their plant and soil components with sufficient precision to resolve diurnal and seasonal patterns. Highlights: We describe an automated system for measuring plant and soil carbon fluxes under field conditions.We exploit the large difference in isotope signatures between C3 and C4 soils and plants to partition the net flux.Possible sources of error are quantified and shown to be small.The system is capable of resolving diurnal and seasonal patterns. [ABSTRACT FROM AUTHOR]

Simple measures of appropriate levels of soil organic matter are needed for soil evaluation, management and monitoring, based on readily measurable soil properties. We test an index of soil organic matter based on the soil organic carbon (SOC) to clay ratio, defined by thresholds of SOC/clay ratio for specified levels of soil structural quality. The thresholds were originally delineated for a small number of Swiss soils. We assess the index using data from the initial sampling (1978–83) of the National Soil Inventory of England and Wales, covering 3,809 sites under arable land, grassland and woodland. Land use, soil type, annual precipitation and soil pH together explained 21% of the variance in SOC/clay ratio in the dataset, with land use the most important variable. Thresholds of SOC/clay ratio of 1/8, 1/10 and 1/13 indicated the boundaries between "very good", "good", "moderate" and "degraded" levels of structural condition. On this scale, 38.2, 6.6 and 5.6% of arable, grassland and woodland sites, respectively, were degraded. The index gives a method to assess and monitor soil organic matter at national, regional or sub‐regional scales based on two routinely measured soil properties. Given the wide range of soils and land uses across England and Wales in the dataset used to test the index, we suggest it should apply to other European soils in similar climate zones. Highlights: We assess the use of SOC/clay ratios as guidelines for soil management in England and Wales.We use data from 3,809 sites to assess thresholds based on work for Polish, French and Swiss soils.SOC/clay threshold values can indicate degraded and good soil structural condition.The thresholds show the effect of land use and provide an index for use in England and Wales. [ABSTRACT FROM AUTHOR]

Most past research on uranium (U) transport and reaction in the environment has been concerned with groundwater contamination and not with uptake by plants or soil biota, both of which operate over much smaller time and distance scales. We developed and tested a model of U diffusion and reaction in soil at scales appropriate for uptake by plant roots, based on a model we developed in an earlier paper. The model allows for the speciation of U with hydroxyl, carbonate and organic ligands in the soil solution, and the nature and kinetics of sorption reactions with the soil solid. The model predictions were compared with experimentally measured concentration–distance profiles of U in soil adjusted to different pHs and CO2 pressures. Excellent agreement between observed and predicted profiles was obtained using model input parameters measured or otherwise estimated independently of the concentration–distance profiles, showing that the model was a correct description of the system and all important processes were allowed for. The importance of the kinetics of U adsorption and desorption for the timescale of diffusion through the soil is highlighted. The results are discussed in terms of the uptake of U by plant root systems, as modelled in the earlier paper. Highlights: We developed a model of U diffusion and reaction in soil on scales relevant to uptake by plant roots.We tested the model against measured diffusion profiles and obtained excellent agreement.The kinetics of U adsorption–desorption reactions are important.Reaction kinetics measured in shaken suspensions or flow‐through systems are likely to be misleading. [ABSTRACT FROM AUTHOR]

The growth of rice in submerged soils depends on its ability to form continuous gas channels-aerenchyma-through which oxygen (O 2 ) diffuses from the shoots to aerate the roots. Less well understood is the extent to which aerenchyma permits venting of respiratory carbon dioxide (CO 2 ) in the opposite direction. Large, potentially toxic concentrations of dissolved CO 2 develop in submerged rice soils. We show using X-ray computed tomography and image-based mathematical modelling that CO 2 venting through rice roots is far greater than thought hitherto. We found rates of venting equivalent to a third of the daily CO 2 fixation in photosynthesis. Without this venting through the roots, the concentrations of CO 2 and associated bicarbonate (HCO 3 - ) in root cells would have been well above levels known to be toxic to roots. Removal of CO 2 and hence carbonic acid (H 2 CO 3 ) from the soil was sufficient to increase the pH in the rhizosphere close to the roots by 0.7 units, which is sufficient to solubilize or immobilize various nutrients and toxicants. A sensitivity analysis of the model showed that such changes are expected for a wide range of plant and soil conditions., (© 2019 The Authors. Plant, Cell & Environment published by John Wiley & Sons Ltd.)

We sought to explain rice (Oryza sativa) genotype differences in tolerance of zinc (Zn) deficiency in flooded paddy soils and the counter-intuitive observation, made in earlier field experiments, that Zn uptake per plant increases with increasing planting density. We grew tolerant and intolerant genotypes in a Zn-deficient flooded soil at high and low planting densities and found (a) plant Zn concentrations and growth increased with planting density and more so in the tolerant genotype, whereas the concentrations of other nutrients decreased, indicating a specific effect on Zn uptake; (b) the effects of planting density and genotype on Zn uptake could only be explained if the plants induced changes in the soil to make Zn more soluble; and (c) the genotype and planting density effects were both associated with decreases in dissolved CO 2 in the rhizosphere soil solution and resulting increases in pH. We suggest that the increases in pH caused solubilization of soil Zn by dissolution of alkali-soluble, Zn-complexing organic ligands from soil organic matter. We conclude that differences in venting of soil CO 2 through root aerenchyma were responsible for the genotype and planting density effects., (© 2017 John Wiley & Sons Ltd.)