P.M. van Bodegom

Effects of alternative electron acceptors and temperature on methanogenesis in rice paddy soils

Soil slurries collected from rice paddies were incubated anaerobically at different temperatures. Changes in the composition of electron acceptors and electron donors in the slurries were monitored daily. During the incubation NO3− was reduced first, followed by Fe3+ and SO42− reduction and methane production. The first two steps in the reduction sequence were exclusive, while competition occurred between sulfate reducers and methanogens. The temperature dependence of the reduction processes was expressed in a Q10 value, which was 2.4 for iron reduction, 1.6 for sulfate reduction and 4.6 for methane production. This means that from 14 °C to 30 °C methane formation rates increased 5.4 times as fast as sulfate reduction rates. This was explained by a change in the competition for acetate and can be due to different temperature responses for acetoclastic methanogens in Qmax or KM than for sulfate reducers. Temperature thus not only influenced conversion rates, but also the competitiveness of organisms. CO2 release during the incubation could be explained with the measured inorganic electron acceptors. Organic electron acceptors do thus not seem important in rice paddies.

Inorganic nitrogen dynamics in fallows and maize on an Oxisol and Alfisol in the highlands of Kenya

Abstract Fallows with naturally regenerated or planted vegetation are important in many subsistence agricultural systems of tropical regions, but the underlying soil processes in fallows are not properly understood. We investigated N dynamics under different fallow vegetation on a Kandiudalfic Eutrudox (2372-mm rain in 16 months) and a Kandic Paleustalf (1266-mm rain in 15 months) in the Kenyan highlands. The treatments, which extended for three cropping seasons (15–16 months), were Zea mays (maize), natural regrowth of vegetation (natural fallow), planted Sesbania sesban (sesbania fallow) and uncultivated soil without vegetation (bare fallow). Inorganic N (nitrate+ammonium-N) to 2-m depth under bare fallow increased by 242 kg N ha −1 year −1 on the Oxisol and 54 kg N ha −1 year −1 on the Alfisol, indicating that N mineralization exceeded N losses. Subsoil inorganic N (0.5–2.0 m) remained relatively unchanged after three crops of unfertilized maize, which produced limited total biomass because of P deficiency. Inorganic N decreased during natural and sesbania fallows, and both fallows similarly depleted subsoil inorganic N. The fallows depleted inorganic N at 0.5–2.0 m by 75–125 kg N ha −1 year −1 down to a minimum N content between 40 and 80 kg N ha −1 . After slashing sesbania and incorporating the above-ground biomass with 154–164 kg N ha −1 , soil inorganic N increased within 2 months by 136 kg N ha −1 on the Oxisol and 148 kg N ha −1 on the Alfisol. Inorganic N decreased after cropping the bare fallow on the Oxisol with maize, indicating that inorganic N was prone to leaching during heavy rains when the maize was small. A considerable part of the N in biomass of the natural fallow was recycled. Much of the total N accumulated by the sesbania fallow was removed with the wood and the amount of N recycled was similar on the Oxisol and Alfisol. We conclude that sesbania fallows can retrieve considerable subsoil inorganic N on deep soils with high subsoil N and effectively cycle this N through its rapidly decomposable biomass to subsequent crops.

Prediction of reducible soil iron content from iron extraction data.

Soils contain various iron compounds that differ in solubility, reducibility and extractability. Moreover, the contribution of the various iron compounds to total iron (Fe) and total Fe concentrations differs highly among soils. As a result, the total reducible Fe content can also differ among soils, and so does the dynamics of iron reduction. These factors complicate the prediction of reducible Fe based on Fe extraction data and hamper the application of process-based models for reduced or waterlogged soils where redox processes play a key-role. This paper presents a theoretical analysis relating reducible to extractable Fe reported in the literature. Predictions made from this theoretical analysis were evaluated in soil incubations using 18 rice paddy soils from all over the world. The incubation studies and the literature study both show that reducible Fe can be related to Fe from some selected, but not all, iron extractions. The combination of measurements for labile Fe(III)oxides (derived from oxalate-extractable Fe) and stabile Fe(III)oxides (derived from dithionite-citrate-extractable Fe) shows highly significant correlations with reducible Fe with high coefficients of determination (r2 = 0.92−0.95 depending on the definition of stabile Fe(III)oxides). Given the high diversity in rice soils used for the incubations, these regression equations will have general applicability. Application of these regression equations in combination with soil database information may improve the predictive ability of process-based models where soil redox processes are important, such as CH4 emission models derived for rice paddies or wetlands.Soils contain various iron compounds that differ in solubility, reducibility and extractability. Moreover, the contribution of the various iron compounds to total iron (Fe) and total Fe concentrations differs highly among soils. As a result, the total reducible Fe content can also differ among soils, and so does the dynamics of iron reduction. These factors complicate the prediction of reducible Fe based on Fe extraction data and hamper the application of process-based models for reduced or waterlogged soils where redox processes play a key-role. This paper presents a theoretical analysis relating reducible to extractable Fe reported in the literature. Predictions made from this theoretical analysis were evaluated in soil incubations using 18 rice paddy soils from all over the world. The incubation studies and the literature study both show that reducible Fe can be related to Fe from some selected, but not all, iron extractions. The combination of measurements for labile Fe(III)oxides (derived from oxalate-extractable Fe) and stabile Fe(III)oxides (derived from dithionite-citrate-extractable Fe) shows highly significant correlations with reducible Fe with high coefficients of determination (r2 = 0.92−0.95 depending on the definition of stabile Fe(III)oxides). Given the high diversity in rice soils used for the incubations, these regression equations will have general applicability. Application of these regression equations in combination with soil database information may improve the predictive ability of process-based models where soil redox processes are important, such as CH4 emission models derived for rice paddies or wetlands.

Quantification of methane oxidation in the rice rhizosphere using 13C-labelled methane

In this paper isotope ratio mass spectrometry is used to determine the methane (CH4) oxidation fraction in the rhizosphere of intact rice plant-soil systems. Earlier studies on quantification of the methane oxidation were based on inhibition or incubation procedures which strongly interfered with the plant-soil system and resulted in a large variability of the reported fractions, while other studies considered stable isotopes at natural abundance levels to investigate methanotrophy in the rhizosphere of rice. The current work is the first that used 13C-labelled CH4 as additive and calculated the oxidation fraction from the ratio between the added 13C-labelled CH4 and its oxidation product 13CO2. Both labelled gases could be distinguished from the natural abundance percentages. The oxidation fraction for methane was found to be smaller than 7%, suggesting that former approaches overestimate the methane oxidation fraction.

Upscaling regional emissions of greenhouse gases from rice cultivation: methods and sources of uncertainty.

One of the important sources of greenhouse gases is the emission of methane from rice fields. Methane emission from rice fields is the result of a complex array of soil processes involving plant-microbe interactions. The cumulative effects of these processes at the level of individual plants influence the global atmospheric composition and make it necessary to expand our research focus from small plots to large landscapes and regions. However, present extrapolations (‘upscaling’) are tenuous at best because of methodological and practical problems. The different steps taken to calculate regional emission strengths are discussed and illustrated by calculations for a case-study in the Philippines. The applicability of high quality, process-based, models of methane emission at the level of individual plants is limited for regional analysis by their large data requirements. Simplified models can be used at the regional level but are not able to capture the complex emission situation. Data availability and model accuracy are therefore often difficult to match. Other common sources of uncertainty are the quality of input data. A critical evaluation of input data should be made in every upscaling study to assess the suitability for calculating regional emissions. For the case-study we show effects of differences in input data caused by data source and interpolation technique. The results from the case-study and similar studies in literature indicate that upscaling techniques are still troublesome and a cause of large uncertainties in regional estimates. The results suggest that some of the stumbling blocks in the conventional upscaling procedure are almost impassable in the near future. Based on these results, a plea is made for meso-level measurements to calibrate and validate upscaling methods in order to be better able to quantify and reduce uncertainties in regional emission estimates.

Radial oxygen loss, a plastic property of dune slack plant species

Mean and environmentally induced differences in radial oxygen loss (ROL) were investigated for three pioneer species (i.e. Schoenus nigricans L., Juncus articulatus L. and Samolus valerandi L.) and two late-successional dune slack species (i.e. Calamagrostis epigejos L. and Carex flacca Schreber). These species were grown in a factorial design at conditions differing in moisture, light, nutrient availability and Fe2+ and Mn2+ concentrations. On average, ROL was twice as low for late-successional species compared to pioneer species, but it increased on average by a factor 1.5 for these species upon flooding while ROL was unaffected by flooding in pioneer species. Other effects of treatments on pioneer and late-successional species groups were insignificant. Species-specific plasticity in ROL was stronger than that of the species groups and varied highly with the different combinations of – interactions between – environmental cultivation conditions flooding, concentrations of Fe2+ and Mn2+, nutrient and light levels, but was not affected by differences in relative growth rates. Moreover, ROL activity was almost 20×, and significantly, higher for seedlings than for adults of Schoenus nigricans. This implies that ROL of a species depends on the stage of the life cycle and on growth conditions, something that should be considered when determining ROL. ROL activity of most species increased at (a combination of) high nutrient and at low light levels: ROL activity was strongly negatively correlated to the root/shoot ratio, which was presumably caused by a higher gas transport capacity compared to root oxygen consumption at low root/shoot ratios. The plasticity in ROL leads to a highly dynamic rhizosphere in which the oxygen influx is a function of plant species and particularly of the interactions between plant species and environmental conditions.

Combining upscaling and downscaling of methane emissions from rice fields: methodologies and preliminary results

The uncertainty in the methane (CH4) source strength of rice fields is among the highest of all sources in the global CH4 budget. Methods to estimate the source strength of rice fields can be divided into two scaling categories: bottom-up (upscaling) and top-down (downscaling). A brief review of upscaling and downscaling methodologies is presented. The combination of upscaling and downscaling methodologies is proposed as a potential method to reduce the uncertainty in the regional CH4 source strength of rice fields. Some preliminary results based on upscaling and downscaling are presented and the limitations of the approaches are discussed. The first case study focuses on upscaling by using a field-scale model in combination with spatial databases to calculate CH4 emissions for the island of Java. The reliability of upscaling results is limited by the uncertainty in model input parameters such as soil properties and organic carbon management. Because controlling variables such as harvested rice area may change on relatively short time scales, a land use change model (CLUE) was used to quantify the potential land use changes on Java in the period 1994–2010. The predicted changes were evaluated using the CH4 emission model. Temporal scaling by coupling land use change models and emission models is necessary to answer policy-related questions on future greenhouse gas emissions. In a downscaling case study, we investigate if inverse modeling can constrain the emissions from rice fields by testing a standard CH4 from rice scenario and a low CH4 from rice scenario (80 and 30 Tg CH4 yr−1, respectively). The results of this study are not yet conclusive; to obtain fine-resolution CH4 emission estimates over the Southeast Asian continent, the monitoring network atmospheric mixturing ratios need to be extended and located closer to the continental sources.

Modeling Methane Emissions from Rice Fields: Variability, Uncertainty, and Sensitivity Analysis of Processes Involved

Estimates of global methane (CH4) emissions, to which rice cropping systems contribute significantly, are uncertain. T The variability and uncertainty of variables governing emission rates and the sensitivity of emissions to these variables determine the accuracy of CH4 emission estimates. A good tool for quantification of sensitivities is a process-based model. This paper describes a model that has been validated previously by experimental data. Variability and uncertainty in processes and variables underlying CH4 emissions are reviewed and the sensitivities of modeled CH4 emission estimates for process variables are tested. The sensitivity analysis is carried out for two sites in the Philippines at which CH4 emissions have been measured for several years. The sensitivities of the model are compared with measured sensitivities, both as a function of input parameters. The model sensitivity analysis shows that the system is not sensitive to mechanisms of CH4 production or the pathway of gas transport through the plant. Methane emissions are very sensitive, however, to the description of substrate supply (both from the soil and from organic fertilizers). Unfortunately, this description also represents a main uncertainty. Uncertainty in CH4 emission estimates will thus remain large as long as this process is not well quantified.

Gas transport through the root-shoot transition zone of rice tillers

Rice plants (Oryza sativa L.) are mainly cultivated in flooded paddy fields and are thus dependent on oxygen transport through the plant to maintain aerobic root metabolism. This gas transport is effectuated through the aerenchyma of roots and shoots. However, the efficiency of gas transport through the root–shoot transition zone is disputed and there are indications that the root–shoot transition zone may represent one of the largest resistances for gas transport. Therefore, we present gas conductance measurements of the root–shoot transition of individual rice tillers measured using SF6. SF6 was detected with a highly advanced laser based photoacoustic detection scheme allowing sensitive, high resolution measurements. In conjunction with these measurements, various plant morphological parameters were quantified. These measurements indeed indicate that the conductance at the root–shoot transition may be much smaller than the conductance of root and shoot aerenchyma within the rice plant. Conductance was strongly correlated to tiller transverse area. After elimination of tiller area from the conductance equation, the resulting permeance coefficient was still correlated to tiller area, but negatively and related to the process of radial tiller expansion. In addition, a decrease in the permeance coefficient was also observed for increasing distance from the plant centre. No correlation was found with tiller type or age of the mother tiller. Incorporation of estimates of the conductance of the root–shoot transition zone coupled to plant morphological parameters will allow considerable improvement of understanding and models on gas transport through plants.