Adsorption and desorption dynamics of citric acid anions in soil

The functional role of organic acid anions (e.g. citrate, oxalate, malonate, etc) in soil has been intensively investigated with special focus either on (i) microbial respiration and soil carbon dynamics, (ii) nutrient solubilization, or (iii) metal detoxification. Considering the potential impact of sorption processes on the functional significance of these effects, comparatively little is known about the adsorption and desorption dynamics of organic acid anions in soils. The aim of this study therefore was to experimentally characterize the adsorption and desorption dynamics of organic acid anions in different soils using citrate as a model carboxylate. Results showed that both adsorption and desorption processes were fast, reaching a steady state equilibrium solution concentration within approximately 1 hour. However, for a given total soil citrate concentration(ctot) the steady state value obtained was critically dependent on the starting conditions of the experiment (i.e. whether most of the citrate was initially present in solution (cl) or held on the solid phase (cs)). Specifically, desorption-led processes resulted in significantly lower equilibrium solution concentrations than adsorption led processes indicating time-dependent sorption hysteresis. As it is not possible to experimentally distinguish between different sorption pools in soil (i.e. fast, slow, irreversible adsorption/desorption), a new dynamic hysteresis model was developed that relies only on measured soil solution concentrations. The model satisfactorily explained experimental data and was able to predict dynamic adsorption and desorption behaviour. To demonstrate its use we applied the model to two relevant scenarios (exudation and microbial degradation), where the dynamic sorption behaviour of citrate occurs. Overall, this study highlights the complex nature of citrate sorption in soil and concludes that existing models need to incorporate both a temporal and sorption hysteresis component to realistically describe the role and fate of organic acids in soil processes

Combined use of empirical data and mathematical modelling to better estimate the microbial turnover of isotopically labelled carbon substrates in soil

The flow of carbon (C) through soil is inherently complex due to the many thousands of different chemical transformations occurring simultaneously within the soil microbial community. The accurate modelling of this C flow therefore represents a major challenge. In response to this, isotopic tracers (e.g. 13C, 14C) are commonly used to experimentally parameterise models describing the fate and residence time of individual C compounds within soil. In this study, we critically evaluated the combined use of experimental 14C labelling and mathematical modelling to estimate C turnover times in soil. We applied 14C-labelled alanine and glucose to an agricultural soil and simultaneously measured their loss from soil solution alongside the rate of microbial C immobilization and mineralization. Our results revealed that chloroform fumigation-extraction (CFE) cannot be used to reliably quantify the amount of isotopically labelled 13C/14C immobilised by the microbial biomass. This is due to uncertainty in the extraction efficiency values (kec) within the CFE methodology which are both substrate and incubation time dependent. Further, the traditional mineralization approach (i.e. measuring 14/13CO2 evolution) provided a poor estimate of substrate loss from soil solution and mainly reflected rates of internal microbial C metabolism after substrate uptake from the soil. Therefore, while isotope addition provides a simple mechanism for labelling the microbial biomass it provides limited information on the behaviour of the substrate itself. We used our experimental data to construct a new empirical model to describe the simultaneous flow of substrate-C between key C pools in soil. This model provided a superior estimate of microbial substrate use and microbial respiration flux in comparison to traditional first order kinetic modelling approaches. We also identify a range of fundamental problems associated with the modelling of isotopic-C in soil, including issues with variation in C partitioning within the community, model pool connectivity and variation in isotopic pool dilution, which make interpretation of any C isotopic flux data difficult. We conclude that while convenient, the use of isotopic data (13C, 14C, 15N) has many potential pitfalls necessitating a critical evaluation of both past and future studies

Linking rhizosphere processes across scales: Opinion

Purpose Simultaneously interacting rhizosphere processes determine emergent plant behaviour, including growth, transpiration, nutrient uptake, soil carbon storage and transformation by microorganisms. However, these processes occur on multiple scales, challenging modelling of rhizosphere and plant behaviour. Current advances in modelling and experimental methods open the path to unravel the importance and interconnectedness of those processes across scales. Methods We present a series of case studies of state-of-the art simulations addressing this multi-scale, multi-process problem from a modelling point of view, as well as from the point of view of integrating newly available rhizosphere data and images. Results Each case study includes a model that links scales and experimental data to explain and predict spatial and temporal distribution of rhizosphere components. We exemplify the state-of-the-art modelling tools in this field: image-based modelling, pore-scale modelling, continuum scale modelling, and functional-structural plant modelling. We show how to link the pore scale to the continuum scale by homogenisation or by deriving effective physical parameters like viscosity from nano-scale chemical properties. Furthermore, we demonstrate ways of modelling the links between rhizodeposition and plant nutrient uptake or soil microbial activity. Conclusion Modelling allows to integrate new experimental data across different rhizosphere processes and scales and to explore more variables than is possible with experiments. Described models are tools to test hypotheses and consequently improve our mechanistic understanding of how rhizosphere processes impact plant-scale behaviour. Linking multiple scales and processes including the dynamics of root growth is the logical next step for future research.Open Access funding enabled and organized by Projekt DEAL.deutsche forschungsgemeinschaftdeutsche forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659natural environment research council (uk)Forschungszentrum Jülich GmbH (4205

Linking rhizosphere processes across scales: opinion

Purpose: Simultaneously interacting rhizosphere processes determine emergent plant behaviour, including growth, transpiration, nutrient uptake, soil carbon storage and transformation by microorganisms. However, these processes occur on multiple scales, challenging modelling of rhizosphere and plant behaviour. Current advances in modelling and experimental methods open the path to unravel the importance and interconnectedness of those processes across scales. Methods: We present a series of case studies of state-of-the art simulations addressing this multi-scale, multi-process problem from a modelling point of view, as well as from the point of view of integrating newly available rhizosphere data and images. Results: Each case study includes a model that links scales and experimental data to explain and predict spatial and temporal distribution of rhizosphere components. We exemplify the state-of-the-art modelling tools in this field: image-based modelling, pore-scale modelling, continuum scale modelling, and functional-structural plant modelling. We show how to link the pore scale to the continuum scale by homogenisation or by deriving effective physical parameters like viscosity from nano-scale chemical properties. Furthermore, we demonstrate ways of modelling the links between rhizodeposition and plant nutrient uptake or soil microbial activity. Conclusion: Modelling allows to integrate new experimental data across different rhizosphere processes and scales and to explore more variables than is possible with experiments. Described models are tools to test hypotheses and consequently improve our mechanistic understanding of how rhizosphere processes impact plant-scale behaviour. Linking multiple scales and processes including the dynamics of root growth is the logical next step for future research.Natural Environment Research Council (NERC): NE/S004920/

Compound driven differences in N2 and N2O emission from soil; the role of substrate use efficiency and the microbial community

Organic C is an important control on the process of denitrification, a process that can result in the production and reduction of the potent greenhouse gas nitrous oxide (N2O). This study identified the influence of different low molecular weight C (LMW-C) compounds on the production of nitrous oxide (N2O) and dinitrogen (N2) and the associated role of the size and structure of the microbial community. We examined this following application of glucose, glutamine or citric acid (250 mg C kg−1 dry soil) and 15N-KNO3 (100 mg N kg−1 dry soil) to a sandy loam soil and measured the production of N2 and N2O by denitrifiers using 15N labeling techniques, changes in the bacterial community as measured by T-RFLP on 16SrDNA fragments and changes in the gene copy number of 16SrDNA, nirK, nirS and nosZ over 144 h. Addition of glucose, citric acid and glutamine all increased emissions of 15N-N2 above that found in the control (P < 0.05) while the addition of glucose and glutamine resulted in higher emissions of 14+15N-N2O (P < 0.001) than the addition of citric acid, resulting in a lower 15N-N2O to 15N-N2 ratio in the citric acid treatment. The 16SrDNA gene copy number increased after addition of citric acid and glutamine, whilst 16SrDNA showed significant shifts in community composition in all C treatments although over different time periods. The gene copy number of nosZ only significantly increased at 120 h in the glutamine treatment (P < 0.05) and nirS at 120 h in the citric acid and glutamine treatments (P < 0.05). This suggests that where C is added as a single input, differences in N2 and N2O emissions between LMW-C compounds were not caused by selection for denitrifiers but likely driven by differences in substrate use efficiency and subsequent differences in C partitioning between growth and respiration. The differing influence of the three selected C compounds on denitrification indicates the potential for lowering net N2O emissions through regulation of C compound availability

Enhancing phosphorus and zinc acquisition efficiency in rice: a critical review of root traits and their potential utility in rice breeding

Background: Rice is the world's most important cereal crop and phosphorus (P) and zinc (Zn) deficiency are major constraints to its production. Where fertilizer is applied to overcome these nutritional constraints it comes at substantial cost to farmers and the efficiency of fertilizer use is low. Breeding crops that are efficient at acquiring P and Zn from native soil reserves or fertilizer sources has been advocated as a cost-effective solution, but would benefit from knowledge of genes and mechanisms that confer enhanced uptake of these nutrients by roots. Scope: This review discusses root traits that have been linked to P and Zn uptake in rice, including traits that increase mobilization of P/Zn from soils, increase the volume of soil explored by roots or root surface area to recapture solubilized nutrients, enhance the rate of P/Zn uptake across the root membrane, and whole-plant traits that affect root growth and nutrient capture. In particular, this review focuses on the potential for these traits to be exploited through breeding programmes to produce nutrient-efficient crop cultivars. Conclusions: Few root traits have so far been used successfully in plant breeding for enhanced P and Zn uptake in rice or any other crop. Insufficient genotypic variation for traits or the failure to enhance nutrient uptake under realistic field conditions are likely reasons for the limited success. More emphasis is needed on field studies in mapping populations or association panels to identify those traits and underlying genes that are able to enhance nutrient acquisition beyond the level already present in most cultivars.T. J. Rose, S. M. Impa, M. T. Rose, J. Pariasca-Tanaka, A. Mori, S. Heuer, S. E. Johnson-Beebout and M. Wissuw