Phototrophic Biofilm Decomposition Enhances Dissimilatory Nitrate Reduction to Ammonia in Paddy Soil

The movement of ammonium due to diffusion in paddy soils in Taiwan was investigated in the laboratory. The movement of ammonium in flooded soils was inversely proportional to the concentration of ammonium in the soil solution, which was a function of the quantity of ammonium present, the content of solid matter in a unit volume of soil (bulk density), and the adsorptive property of soil. Although there was a considerable variation in the value of both the ammonium adsorption and bulk density of soils, the adsorptive property was more variable. Therefore, the adsorptive property seemed to be the most influencial factor on the movement of ammonium in flooded soils, where the property had a close relation to the cationexchange capacity. The bulk density of flooded soils in the field could be reproduced in glass tubes under percolating condition in the laboratory. The values of bulk density determined on paddy soils after harvesting or on air-dry soils were considerably different from those in the flooded soils in the field. A simple determination method of bulk density was proposed for paddy soils.

Syringic acid (SA) is a novel biological nitrification inhibitor (BNIs) discovered in rice root exudates with significant inhibition of Nitrosomonas strains. However, the inhibitory effect of SA on nitrification and nitrous oxide (N2O) emissions in different soils and the environmental factors controlling the degree of inhibition have not been studied. Using 14-day microcosm incubation, we investigated the effects of different concentrations of SA on nitrification activity, abundance of ammonia-oxidizing microorganisms, and N2O emissions in three typical agricultural soils. The nitrification inhibitory efficacy of SA was strongest in acidic red soil, followed by weakly acidic paddy soil, with no significant effect in an alkaline calcareous soil. Potential nitrification activity (PNA) were also greatly reduced by SA additions in paddy and red soil. Pearson correlation analysis showed that the inhibitory efficacy of SA might be negatively correlated with soil pH and positively correlated with clay percentage. SA treatments significantly reduced N2O emissions by 69.1-79.3% from paddy soil and by 40.8%-46.4% from red soil, respectively, but no effect was recorded in the calcareous soil. SA addition possessed dual inhibition of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) abundance in paddy and red soil. Structural equation modelling revealed that soil ammonium (NH4 +) and dissolved organic carbon content (DOC) were the key variables explaining AOA and AOB abundance and subsequent N2O emissions. Our results support the potential for the use of the BNI SA in mitigating N2O emissions and enhancing N utilization in red and paddy soils.

The effects of lanthanum on nitrification and ammonification in three Chinese soils were evaluated through an incubation experiment. Soils were collected from experimental plots under rice/rape rotation in Yingtan, Jiangxi province (red soil), under rice/wheat rotation in Wuxi, Jiangsu province (paddy soil), and under corn/wheat rotation in Fengqiu, Henan province (Fluvo-aquic soil). Soil nitrification was stimulated slightly by La at lower concentrations, and the stimulation rate reached about 20% in red soil at 150 mg La kg−1 dry soil, and 14% in fluvo-aquic soil at 300 mg La kg−1 dry soil. When more La was added in soils, nitrification was inhibited, with a maximum inhibition rate of 42, 44 and 66% in red soil, fluvo-aquic soil, and paddy soil, respectively. Soil ammonification was not significantly different between control and up to 600 mg La kg−1 dry soil in red soil, but it was significantly reduced in doses of 900 and 1200 mg La kg−1 dry soil. Significant reduction in soil ammonification was also found in doses from 60 to 1200 mg La kg−1 dry soil except for 600 mg La kg−1 dry soil in fluvo-aquic soil. In contrast the ammonification in paddy soil was strongly stimulated by La, reaching about 25 times that of control at 900 mg La kg−1 dry soil. We assumed that application of La accelerates the transformation of nitrogen in soils at low dosage, and the currently applied dosage in agriculture in China cannot inhibit soil nitrification and ammonification even after long term successive application.

In Situ Dissimilatory Nitrate Reduction to Ammonium in a Paddy Soil Fertilized with Liquid Cattle Waste

Ammonium-induced stimulatory, inhibitory, and/or neutral effects on soil methane oxidation have been attributable to the ammonium concentration and mineral forms, confounded by other edaphic properties (e.g., pH, salinity), as well as the site-specific composition of the methanotrophic community. We hypothesize that this inconsistency may stem from the discrepancy in the cation adsorption capacity of the soil. We postulate that the effects of ammonium on the methanotrophic activity in soil are more accurately portrayed by relating methane uptake rates to the soluble ammonium (bioavailable), rather than the exchangeable (total) ammonium. To reduce adsorption (exchangeable) sites for ammonium in a paddy soil, two successive pre-incubation steps were introduced resulting in a 1000-fold soil dilution (soil enrichment), to be compared to a soil slurry (tenfold dilution) incubation. Ammonium was supplemented as NH4Cl at 0.5–4.75gL−1 after pre-incubation. While NH4Cl significantly stimulated the methanotrophic activity at all concentrations in the soil slurry incubation, methane uptake showed a dose-dependent effect in the soil enrichment. The trend in methane uptake could be explained by the soluble ammonium concentration, which was proportionate to the supplemented ammonium in the soil enrichment. In the soil slurry incubation, a fraction (36–63%) of the supplemented ammonium was determined to be adsorbed to the soil. Accordingly, Methylosarcina was found to predominate the methanotrophic community after the incubation, suggesting the relevance of this methanotroph at elevated ammonium levels (< 3.25gL−1 NH4Cl). Collectively, our results showed that the soluble, rather than the exchangeable ammonium concentration, is relevant when determining the effects of ammonium on methane oxidation, but this does not exclude other (a)biotic factors concurrently influencing methanotrophic activity.

Electron shuttle potential of biochar promotes dissimilatory nitrate reduction to ammonium in paddy soil

Tetracycline and sulfamethazine alter dissimilatory nitrate reduction processes and increase N2O release in rice fields

Clay-fixed ammonium () plays an important role in the dynamics and availability of soil nitrogen (N), acting as a sink or source of exchangeable . However, quantitative information about exchange processes between exchangeable and fixed is limited. In this study, we developed a method to sequentially extract exchangeable and fixed , and evaluated whether fixed acts as a sink or source of exchangeable in a paddy soil. A paddy soil was subjected to anaerobic incubation for 70 days with and without the application of powdered rice (Oryza sativa L. cv. Hinohikari) straw as a pre-treatment, and with and without air-drying as a post-treatment. By the anaerobic incubation, the content of weakly fixed increased significantly with a significant increase in exchangeable , implying that exchangeable in the paddy soil is the main pool as a source of weakly fixed . On the other hand, a significant decrease in the exchangeable content by rice straw application before the incubation slightly lowered the content of weakly fixed . Air-drying after the incubation caused the fixation of exchangeable . Overall, the contents of exchangeable and weakly fixed were positively correlated (r = 0.58; p < 0.05), indicating that weakly fixed acted as a transitory pool between strongly fixed and exchangeable . The proposed sequential extraction method was effective to evaluate the interaction between exchangeable and fixed . Combining this method with an incubation experiment, it was demonstrated that fixed , especially weakly fixed , in the paddy soil can be released or retained in quantities sufficient to affect the dynamics of exchangeable .

Candidatus Methanoperedens-related archaea have recently been identified as anaerobic methane oxidizers in paddy soils. Fertilization practices, including the application of inorganic and organic fertilizers (e.g. chicken manure), may significantly influence their community dynamics and the associated methane cycling processes. However, the comparative effects of inorganic and chicken manure fertilization on these archaeal community in paddy fields remain unclear. This study aimed to examine the diversity, community composition, and abundance of Methanoperedens-related archaea at three representative soil layers of 0-10, 20-30, and 40-50cm under three fertilization treatments (no fertilizer, inorganic fertilizer, chicken manure fertilizer). High-throughput sequencing revealed significant differences in community composition among treatments, while overall diversity showed minimal changes. Quantitative Polymerase Chain Reaction indicated that archaeal abundance under inorganic (2.3×106 copies g-1) and chicken manure fertilization (2.2×106 copies g-1) treatments was significantly greater than that under no fertilization (1.8×106 copies g-1) in upper 30cm soils, with no significant difference at 40-50cm depth. Inorganic fertilization more strongly promoted archaeal abundance, whereas chicken manure had a greater effect on community structure. Soil ammonium, nitrate, and organic carbon contents were significantly correlated with archaeal community patterns. Both inorganic and organic fertilization can substantially influence the community structure and abundance of Methanoperedens-related archaea in paddy soils.

Microbial arsenite (As(III)) oxidation associated with nitrate (NO3-) reduction might be an important process in diminishing arsenic bioavailability and toxicity to rice when paddy soils are contaminated by arsenic. In a noncontaminated soil, however, the responses of bacterial communities and functional genes to As(III) under nitrate-reducing conditions are poorly understood. In this study, anaerobic paddy soil microcosms were established with As(III) and/or NO3- to investigate how the bacterial communities and their functional genes were stimulated during As(III) oxidation and nitrate reduction. Microbial oxidation of As(III) to As(V) was substantially accelerated by nitrate addition, while nitrate reduction was not affected by As(III) addition. Metagenomic analysis revealed that nitrate-reducing bacteria were principally affiliated with Pseudogulbenkiania, with narG, nirS, and norBC genes. Putative As(III)-oxidizing bacteria were dominated by an Azoarcus sp. with As(III) oxidase genes aioA and aioB detected in its draft genome, which also had complete sets of denitrification genes (mainly, napA, nirK, and nosZ). Quantitive PCR analysis confirmed that the abundance of Azoarcus spp., aioA, and nosZ genes was enhanced by As(III) addition. These findings suggest the importance of Azoarcus- and Pseudogulbenkiania-related spp., both of which showed various physio-ecological characteristics for arsenic and nitrogen biogeochemistry, in coupling As(III) oxidation and nitrate reduction in flooded paddy soil.

The nitrogen (N) requirement for paddy rice cultivated in Bangladesh amounts to approximately 80 kg N ha −1 . Lack of knowledge on N mineralization from soil organic matter leads farmers to meet this N requirement exclusively by costly mineral fertilizers, which have typically an efficiency of less than 40%. We assessed to what extent routinely analysed soil properties (N and carbon (C), texture, pH, extractable iron (Fe), aluminium (Al) and manganese (Mn), soil mineralogy and length of the annual inundation period) are able to predict net aerobic and anaerobic N mineralization in paddy soils. Both soil N and C correlated positively with the aerobic but not with the anaerobic N mineralization rate. Instead, relative anaerobic N mineralization showed a significant negative correlation with soil N content. We observed no significant influence of clay mineralogy on soil N mineralization. Aerobic but not anaerobic N mineralization increased with length of the annual inundation period while the proportion of the soil N that was mineralized during 120 days decreased. The large clay content of fields that are inundated for 9–10 months annually explains the co‐occurrence of large soil N contents and relatively small N mineralization rates in these fields. However, variation in texture did not explain variation in N mineralization of soils with inundation periods of 3–8 months. Instead, the anaerobic N mineralization correlated positively with Na pyrophosphate‐extractable Fe and negatively with pH (both at P &lt; 0.01). Thus, pH and Fe content, rather than soil N content, clay mineralogy or texture, explained the substantial variation in anaerobic N mineralization of paddy soils in Bangladesh inundated for 3–8 months. It is not known if these relationships between net evolution of ammonium in soil and pH and Fe content are causal or indirect. Elucidation of these mechanisms would greatly further our comprehension of the biochemistry of the young ‘floodplain soils' with relatively low content of pedogenic oxides throughout southeast Asia.

An incubation experiment under aseptic and septic conditions using 15N-labelled NH4+-N and NO3–-N, was carried out to study the effect of N transformations after flooding on NH4+ fixation in a paddy soil from China. After flooding ammonification was favoured, providing NH4+ for fixation by clay minerals. NH4+ fixation was more pronounced under low redox potential (Eh) conditions. Close correlations existed between exchangeable NH4+, Eh, and non-exchangeable NH4+. Therefore, two major conditions for NH4+ fixation induced by flooding in paddy soil were found, namely flooding promoted net production of NH4+ due to the deamination of organic N and, in addition, decreased the Eh of the soil. A lower Eh was caused by reduction and dissolution of Fe oxide coating on the clay minerals' surfaces, eliminating the obstacles for NH4+ diffusing into or out of the interlayers of clay minerals. A higher concentration of exchangeable NH4+ from deamination of organic N would drive NH4+ diffusing from the soil solution into the interlayers of clay minerals. 15N-labelled NO3– incorporated into the flooded soil was not reduced to NH3. The addition of NO3– retarded the decrease in the soil Eh and, therefore, NH4+ fixation.

To evaluate whether the capacity of interlayer sites affects the dynamics of fixed ammonium (NH4+) in a paddy soil, a combination of potassium (K)–saturation treatment and stepwise extraction of nonexchangeable K with 0.01 mol L−1 hydrochloric acid was applied to a soil incubated anaerobically up to 70 days. The capacity of interlayer sites increased with an increase of weakly fixed NH4+ during the initial 28 days (r = 0.78, P < 0.01), and remained stable thereafter. On the other hand, the concentration of exchangeable NH4+ increased curvilinearly during the whole incubation period, which was correlated with an increase of weakly fixed NH4+ (r = 0.85, P < 0.01). These results suggested that the dynamics of weakly fixed NH4+ in a paddy soil is regulated not only by the chemical equilibrium between exchangeable and weakly fixed NH4+ but also by the capacity of interlayer sites within a few weeks after flooding.

Ferrous iron (Fe(II)) oxidation and nitrate (NO3 −) reduction are commonly observed in environments with denitrifying bacteria. The intermediate nitrite (NO2 −) from denitrification can chemically oxidize Fe(II). However, it is difficult to distinguish how chemical and biological reactions are involved. Pseudomonas stutzeri LS-2, a denitrifying bacterium isolated from paddy soil in southern China, was used in this study to investigate the chemical and biological reactions contributing to Fe(II) oxidation and NO3 − reduction under denitrifying conditions. Concentrations of dissolved Fe(II), NO3 −, NO2 −, and nitrous oxide (N2O) over time were quantified to investigate the kinetics of Fe(II) oxidation and NO3 −/NO2 − reduction in different treatments (i.e., microbial treatments: Cell + NO3 − and Cell + NO2 −, chemical treatment: Fe(II) + NO2 −, and combined treatments: LS-2 + Fe(II) + NO3 − and LS-2 + Fe(II) + NO2 −). Stable isotope fractionations of δ15N-N2O in different treatments were also determined over time. Fe(III) minerals and cell-mineral precipitates formed due to Fe(II) oxidation after 6 days of incubation were characterized using X-ray diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). P. stutzeri LS-2 could completely reduce NO3 − or NO2 − within 2 days in the microbial treatment of Cell + NO3 − or Cell + NO2 −. The presence of Fe(II) resulted in a decrease of NO3 − or NO2 − reduction rates and an increase in the amount of nitrous oxide (N2O) production in the combined treatments of Cell + Fe(II) + NO3 − and Cell + Fe(II) + NO2 −. Fe(II) oxidation was only observed in the two combined treatments and the chemical treatment of Fe(II) + NO2 −. Lepidocrocite was formed due to Fe(II) oxidation after 6 days of incubation, which fully covered the bacterial cell surfaces in both combined treatments. Encrustation occurred in the periplasm and on the cell surface. The δ15N-N2O were 7.8 to − 10‰ in both microbial treatments during incubation, while those were − 23 to − 15‰ in the Fe(II) + NO2 − and Cell + Fe(II) + NO2 − treatments. In the Cell + Fe(II) + NO3 − treatment, however, the δ15N in N2O were − 37 to − 25‰, which were different from the microbial and chemical treatments. This difference is probably due to the accelerated reaction between Fe(II) and NO3 −/NO2 − by lepidocrocite. Our results indicate that once NO3 − was reduced to NO2 − by the denitrifying bacterium P. stutzeri LS-2, the NO2 − chemically reacted with Fe(II), and the concomitant Fe(III) oxide formation and cell encrustation led to an inhibition to denitrification. The stable isotope fractionation technique in combination with the transformation kinetics analyses is useful to distinguish the chemical and biological reactions involved in Fe(II) oxidation and nitrate reduction by denitrifying bacteria.

The denitrification process is the main process of the soil nitrogen (N) cycle in paddy fields, which leads to the production of large amounts of nitrous oxide (N2O) and increases N loss in paddy soil. Plant-derived bio denitrification inhibitor procyanidins are thought to inhibit soil denitrification, thereby reducing N2O emissions and soil N loss. However, the denitrification inhibition effect of procyanidins in paddy soils with high organic matter content remains unclear, and their high price is not conducive to practical application. Therefore, this study conducted a 21-day incubation experiment using low-cost proanthocyanidins (containing procyanidins) and paddy soil with high organic matter content in Northeast China to explore the effects of proanthocyanidins on N2O emissions and related microorganisms in paddy soil. The results of the incubation experiment showed that the application of proanthocyanidins in paddy soil in Northeast China could promote the production of N2O in the first three days but inhibited the production of N2O thereafter. Throughout the incubation period, proanthocyanidins inhibited the enzyme nitrate reductase (NaR) activity and the abundance of nirS and nirk denitrifying bacteria, with a significant dose-response relationship. Although the application of proanthocyanidins also reduced the soil nitrate nitrogen (NO3−-N) content, the soil NO3−-N content increased significantly with increasing incubation time. In addition, the application of proanthocyanidins increased soil microbial respiration, ammonia-oxidizing archaea (AOA) amoA gene abundance, and soil ammonium nitrogen (NH4+-N) content. Therefore, the application of proanthocyanidins to paddy soil in Northeast China can effectively regulate denitrification. However, in future studies, it is necessary to explore the impact of proanthocyanidins on the nitrification process and use them in combination with urease inhibitors and/or nitrification inhibitors to better regulate soil N transformation and reduce N2O emissions in paddy soil.