Submerged Paddy Soils Research Articles

Warming Shapes nirS- and nosZ-Type Denitrifier Communities and Stimulates N2O Emission in Acidic Paddy Soil.

Warming strongly stimulates soil nitrous oxide (N2O) emission, contributing to the global warming trend. Submerged paddy soils exhibit huge N2O emission potential; however, the N2O emission pathway and underlying mechanisms for warming are not clearly understood. We conducted an incubation experiment using 15N to investigate the dynamics of N2O emission at controlled temperatures (5, 15, 25, and 35°C) in 125% water-filled pore space. The community structures of nitrifiers and denitrifiers were determined via high-throughput sequencing of functional genes. Our results showed that elevated temperature sharply enhanced soil N2O emission from submerged paddy soil. Denitrification was the main contributor, accounting for more than 90% of total N2O emission at all treatment temperatures. N2O flux was coordinatively regulated by nirK-, nirS-, and nosZ-containing denitrifiers but not ammonia-oxidizing archaea or ammonia-oxidizing bacteria. The nirS-containing denitrifiers were more sensitive to temperature shifts, especially at a lower temperature range (5 to 25°C), and showed a stronger correlation with N2O flux than that of nirK-containing denitrifiers. In contrast, nosZ-containing denitrifiers exhibited substantial variation at higher temperatures (15 to 35°C), thereby playing an important role in N2O consumption. Certain taxa of nirS- and nosZ-containing denitrifiers regulated N2O flux, including nirS-containing denitrifiers affiliated with Rhodanobacter and Cupriavidus as well as nosZ-containing denitrifiers affiliated with Azoarcus and Azospirillum. Together, these findings suggest that elevated temperature can significantly increase N2O emission from denitrification in submerged paddy soils by shifting the overall community structures and enriching some indigenous taxa of nirS- and nosZ-containing denitrifiers. IMPORTANCE The interdependence between global warming and greenhouse gas N2O has always been the hot spot. However, information on factors contributing to N2O and temperature-dependent community structure changes is scarce. This study demonstrated high-temperature-induced N2O emission from submerged paddy soils, mainly via stimulating denitrification. Further, we speculate that key functional denitrifiers drive N2O emission. This study showed that denitrifiers were more sensitive to temperature rise than nitrifiers, and the temperature sensitivity differed among denitrifier communities. N2O-consuming denitrifiers (nosZ-containing denitrifiers) were more sensitive at a higher temperature range than N2O-producing denitrifiers (nirS-containing denitrifiers). This study's findings help predict N2O fluxes under different degrees of warming and develop strategies to mitigate N2O emissions from paddy fields based on microbial community regulation.

Effect of intermittent drainage in reduction of methane emission from paddy soils in Hokkaido, northern Japan

ABSTRACT Emission of methane (CH4), a major greenhouse gas, from submerged paddy soils is generally reduced by introducing intermittent drainage in summer, which is a common water management in Japan. However, such a practice is not widely conducted in Hokkaido, a northern region in Japan, to prevent a possible reduction in rice grain yield caused by cold weather. Therefore, the effects of intermittent drainage on CH4 emission and rice grain yield have not been investigated comprehensively in Hokkaido. In this study, we conducted a three-year field experiment in Hokkaido and measured CH4 and nitrous oxide (N2O) fluxes and rice grain yield to elucidate whether the reduction in CH4 emission can be achieved in Hokkaido as well as other regions in Japan. Four experimental treatments, namely, two soil types [soils of light clay (LiC) and heavy clay (HC) textures] and two water management [continuous flood irrigation (CF), and intermittent drainage (ID)], were used, and CH4 and N2O fluxes were measured throughout the rice cultivation periods from 2016 to 2018. Cumulative CH4 emissions in 2016 were markedly low, suggesting an initially low population of methanogens in the soils presumably due to no soil submergence or crop cultivation in the preceding years, which indicates a possible reduction in CH4 emission by introducing paddy-upland crop rotation. Cumulative CH4 emissions in the ID-LiC and ID-HC plots were 21–91% lower than those in the CF-LiC and CF-HC plots, respectively, whereas the cumulative N2O emissions did not significantly differ between the different water managements. The amount of CH4 emission reduction by the intermittent drainage was largest in 2018, with a comparatively long period of the first drainage for 12 days in summer. Rice grain yields did not significantly differ between the different water managements for the entire 3 years, although the percentage of well-formed rice grains was reduced by the intermittent drainage in 2018. These results suggest that CH4 emission from paddy fields can be reduced with no decrease in rice grain yield by the intermittent drainage in Hokkaido. In particular, the first drainage for a long period in summer is expected to reduce CH4 emission markedly.

Influence of winter crop residue and nitrogen form on greenhouse gas emissions from acidic paddy soil

We conducted an incubation experiment to explore the effect of different crop shoot residues (milk vetch, ryegrass, winter wheat and rape) and nitrogen forms (no fertilizer, CO(NH2)2, (NH4)2SO4 and KNO3) on greenhouse gas CO2, CH4 and N2O emissions from submerged paddy soils. Regardless of nitrogen form, cumulative CO2 and CH4 emissions were in the order of milk vetch > ryegrass > winter wheat > rape. (NH4)2SO4 and KNO3 application decreased CO2 emissions in comparison to treatments without N application. Compared with other N form fertilizer treatments, KNO3 application dramatically stimulated N2O emissions and inhibited CH4 emissions at all crop residue treatments. In the presence of KNO3, N2O emissions of milk vetch and ryegrass residue treatments were significantly higher than those of winter wheat and rape residue treatments. CO(NH2)2 application significantly lowered the N2O emissions from soils with rape residue amendment and increased that from soil with milk vetch residue amendment. We suspected that the differences among these treatments might due to differences of the speed of inorganic N immobilization and N release during crop residue decomposition. Milk vetch + (NH4)2SO4, rape + CO(NH2)2 and ryegrass + (NH4)2SO4 combinations got the relatively low global warming potential, which were recommended to reduce the global warming potentials in paddy soils.

Effects of Green Manures and Zinc Fertilizer Sources on DTPA-Extractable Zinc in Soil and Zinc Content in Basmati Rice Plants at Different Growth Stages

Rice is very sensitive to low zinc (Zn) supply in submerged paddy soils and Zn deficiency is one of the major limiting factors in determining rice production in India. A field experiment was conducted during the summer-rainy seasons of 2009 and 2010 at the research farm of the Indian Agricultural Research Institute, New Delhi, to determine the effects of summer green manure crops and Zn fertilizers on diethylenetriaminepentaacetic acid (DTPA)-extractable (available) Zn concentration in soil and total Zn content in Basmati rice cultivar Pusa Basmati 1 at periodic intervals. Summer green manure crops included Sesbania aculeata (Dhaincha), Crotalaria juncea (Sunhemp), and Vigna unguiculata (Cowpea) and the Zn fertilizers used were ethylenediaminetetraacetic acid (EDTA)-chelated Zn, ZnSO4·7H2O, ZnSO4·H2O, ZnO, and ZnSO4·7H2O + ZnO. Beneficial effects of summer green manure crops and Zn fertilizers on DTPA-extractable Zn concentration in soil and total Zn content in dry matter of Basmati rice at periodic intervals were observed, with significant increases in all the determined parameters, in comparison with those in the control (no Zn application or summer fallow). The rate of increase varied among summer green manure crops and Zn fertilizers during both years. Among the summer green manures, incorporation of S. aculeata led to a significant increase in mean Zn content in Basmati rice grain and straw when compared with C. juncea, V. unguiculata, and summer fallow treatments. Among the Zn fertilizers, significant increases in Zn content in Basmati rice dry matter and DTPA-extractable Zn concentration in soil during various growth stages of the plant were recorded with EDTA-chelated Zn application, followed by the application of ZnSO4·7H2O, ZnSO4·H2O, ZnSO4·7H2O + ZnO, ZnO, and no Zn. The highest mean Zn content in Basmati rice grain and straw was recorded with EDTA-chelated Zn application in 2009 and 2010, respectively. The application of ZnSO4·7H2O was the second best treatment after EDTA-chelated Zn; however, it was statistically inferior to EDTA-chelated Zn. The lowest values were recorded with the control (no Zn application) during both years of study. The amount of Zn concentration in soil was found to be significantly positively correlated with the Zn content in Basmati rice dry matter during both years. Significantly higher levels of residual fertility in soil after the harvest of Basmati rice were observed with application of EDTA-chelated Zn and incorporation of S. aculeata when compared with those of other Zn sources and summer green manures.

Erratum to: pH shift-mediated dehydrogenation and hydrogen production are responsible for microbial iron(III) reduction in submerged paddy soils

Erratum to: pH shift-mediated dehydrogenation and hydrogen production are responsible for microbial iron(III) reduction in submerged paddy soils

PH shift-mediated dehydrogenation and hydrogen production are responsible for microbial iron(III) reduction in submerged paddy soils

pH shift-induced responses of iron(III) [Fe(III)] reduction and associated dehydrogenation and hydrogen (H2) production in submerged paddy soils were investigated to improve our understanding of the contribution of fermentative processes to microbial Fe(III) reduction. A 40-day anaerobic incubation experiment was conducted using two paddy soils from geographically distinct regions in northern (Hapli-Stagnic Anthosol, HSA; pH 8.14) and southern China (Fe-accumili-Stagnic Anthosol, FSA; pH 5.00), respectively. The initial soil pH was adjusted with aluminum sulfate or sodium carbonate to strongly acidic, acidic, neutral, alkaline, and strongly alkaline levels. During anaerobic incubation, as the initial soil pH shifts to acidic or lower levels, dehydrogenase activity (DHA) was greatly inhibited. However, increased acid-soluble Fe(III) level was accompanied by decreased maximum Fe(III) reduction potential (a) and prolonged time to maximum Fe(III) reduction rate (T Vmax ). Decreased pH led to a significantly lower peak partial pressure of H2 (ppH 2max ) in HSA and an increase in FSA. The initial shifts in pH to neutral and higher levels had no significant effect on DHA or acid-soluble Fe(III); however, ppH 2max declined in the neutral treatment of HSA, while T Vmax decreased slightly in the presence of a low ppH2 in the neutral to strongly alkaline FSA. DHA was correlated with Fe(II) accumulation in both paddy soils during the rapid Fe(III) reduction stage (p < 0.05). DHA is related to microbially mediated Fe(III) reduction in anaerobic paddy soils. pH shift-mediated enzymatic dehydrogenation and fermentative H2 production are responsible for microbial Fe(III) reduction in flooded rice fields, with initial pH as the main driving force.

Potential Utilization of Local Phosphate Rocks to Enhance Rice Production in Sub-Saharan Africa

It is known that phosphate rock (PR) deposits that account for most world′s PR production are found in African countries. However, the rate of phosphorus (P) fertilizer use in Africa is typically low, despite the high requirement for application of the same there. This applies particularly to sub-Saharan Africa (SSA), where P deficiency has been suggested as one of the key constraints to crop production, despite the many PR deposits. There have been many excellent reviews on PR utilization in SSA, but hardly any have focused on its effectiveness in lowland rice cultivation. Given this lack of information, we reviewed the potential of PRs produced in the SSA region, focusing particularly on the utilization of PRs for rice cultivation in this region. Our review indicates that PR direct application in lowland rice resulted in high performance, regardless of the PR reactivity and the location investigated. A Phosphate Rock Decision Support System can help disseminate information on PR utilization in SSA; however, there is room for further improvement in predicting agronomic efficiencies in lowland rice cultivation, with consideration of the unique changes in soil condition such as the reduced condition that occurs in submerged paddy soils. In conclusion, the local PRs produced in SSA can be effectively utilized for direct application on lowland rice cultivation, hence the need to elucidate the PRs solubilization mechanism and therefore clarify the condition that maximizes the effect of local PRs direct application in SSA.

Fate of a branched nonylphenol isomer in submerged paddy soils amended with nitrate

Using a 14C-labelled branched isomer of NP, the fate of NP was studied in two flooded typical paddy soils under anoxic conditions. Biodegradation of NP occurred under anoxic conditions and was accompanied by the production of polar metabolites and bound residues in alkaline soil extract and humin. The addition of nitrate (20 mM) increased the degradation of NP in both soils, especially in soil derived from silt loam deposit, which contained high amounts of organic matter. Less than 1% NP mineralization was detected as free CO 2 in both soils, whereas up to 30, 21, 31% of NP residues comprised at least two polar metabolites, those extractable from humic substances and from the humin fraction, respectively. The denaturing gradient gel electrophoresis (DGGE) analysis of DNA extract of the soil microorganisms hinted differences of microbial community between soils with different degradation rates of NP. The present study provides for the first time information about the fate of a branched nonylphenol isomer in submerged soils amended with nitrate. The production of high amounts of polar metabolites under anoxic conditions suggests the necessity of also considering the fate and possible effects of the degradation products of NP in anoxic environment such as in waterlogged soil.

Aging activity of DDE in dissimilar rice soils in a greenhouse experiment

A green-house study was conducted in late 2005 to investigate the aging behavior of p, p′-DDE in two types of soil, Hydragric Anthrosols (An) and Hydragric Acrisols (Ac), according to the World Reference Base (WRB) [FAO/ISRIC/ISSS. 1998. World reference base for soil resources. World soil resources reports, Rome. p. 87]. Paddy rice and dry rice were grown in submerged paddy soils and non-submerged upland soils, respectively. The concentration of extractable p, p′-DDE in fresh DDE-spiked soils was 746.2 ng g −1. During the first few weeks of the experiment, the extractability of p, p′-DDE became increasingly low as the aging period prolonged. However, certain amount of p, p′-DDE that had been captured by soil minerals and organic matter (OM) could be released and became extractable in the later period. The extractability of p, p′-DDE in submerged soils was significantly lower than that in non-submerged soil, because flooding could increase the binding of pollutants to soil particles. The plantation of both dry rice and paddy rice slowed down the aging process of p, p′-DDE. After one month’s growth of rice, p, p′-DDE bound to soil particles was released and became extractable. The OM and silt content of An are higher than that of Ac, resulting in more bound residues and relative lower extractability of p, p′-DDE in An. In addition, the extractability of p, p′-DDE could be reduced by the addition of rice straw to soils.

Bioavailability to grains of rice of aged and fresh DDD and DDE in soils

DDT had been widely used around the world before 1980s and is still under production and use for non-agricultural purposes in China. Because of their special physicochemical properties, p,p'-DDT and its main metabolites, p,p'-DDD and p,p'-DDE, accumulated and persisted in the environment, presenting potential menace on biota. A green-house study was conducted to determine the bioavailability of p,p'-DDD and p,p'-DDE to grains of rice and the influences of traditional Chinese farming practices on their bioaccumulation. Paddy rice and dry rice were grown in submerged paddy soils and non-submerged upland soils, respectively. Two types of soil, Hydragric Anthrosols (An) and Hydragric Acrisols (Ac), were employed. Bioaccumulation factors (BAFs) of DDE ranged from 0.67 for rice grown in non-submerged An to 0.84 in submerged An in the control group, whilst BAFs were all below 0.04 in experimental groups. BAFs of DDD varied from 1.39 for submerged An to 2.26 for submerged Ac in original soils. In contrast, BAFs were between 0.05 for non-submerged Ac and 0.08 for submerged An in DDD-contaminated soils. Flooding seemed to have two contradictory effects on the DDE/DDD accumulation by rice: on one hand, it made the pollutants more mobile and bioavailable; while on the other hand, it enhanced the degradation and binding of POPs. Adding rice straw to the soils protected DDE from being taken up yet promoted DDD accumulation by rice. Furthermore, the distinct inorganic component of the soils might also play an important role in the environmental activities of POPs.

Microbiota responsible for the decomposition of rice straw in a submerged paddy soil estimated from phospholipid fatty acid composition

To identify the microbiota responsible for rice straw decomposition in submerged paddy soils, phospholipid fatty acids (PLFAs) in decomposing rice straw (RS) under submerged incubation conditions with changes in the incubation temperature (22 and 30°C) and nitrogen status (without N amendment, and with ammonium sulfate or urea amendment) were determined. Straight, saturated PLFAs, especially 16 : 0 PLFA, predominated in the RS before decomposition in soil, and they accounted for 65% of the total PLFAs in RS, followed by straight, mono-unsaturated PLFAs (27%). The percentages of straight, saturated PLFAs and straight, mono-unsaturated PLFAs in RS decreased with the decomposition to the levels of 36 to 44% for the straight, saturated PLFAs and of 12 to 16% for the straight, mono-unsaturated PLFAs, while the percentages of branched-chain PLFAs increased markedly from 2% to the level of 40 to 46%, irrespective of the incubation temperature and nitrogen status, which indicated that Gram-positive bacteria were mainly responsible for the RS decomposition in the submerged paddy soil. Microbial succession in the decomposition process of RS was inferred based on cluster analysis and principal component analysis. The stress factor estimated from the trans/cis ratio of 16 : 1ω7 PLFA in the RS undergoing decomposition ranged from 0.21 to 0.40 at 22°C, and from 0.27 to 0.58 at 30°C irrespective of the nitrogen status, indicating that decomposing RS was a highly stressed environment for the microorganisms inhabiting within RS.

Effect of Long-Term Management of Groundwater Level during Fallow Season on Methane Emission from Submerged Paddy Soils in Lysimeter

Effect of Long-Term Management of Groundwater Level during Fallow Season on Methane Emission from Submerged Paddy Soils in Lysimeter

Anaerobic reoxidation of Mn 2+ , Fe 2+ , S 0 and S 2- in submerged paddy soils

Anaerobic reoxidation of reduced products in paddy soils was investigated. Ferrous iron (Fe2+) and monosulfide ion (S2–) added to the soil chemically reduced MnO2 to Mn2+, and MnO2 and Fe(OH)3 to Mn2+ and Fe2+, respectively, where Fe2+ and S2– were considered to be oxidized to Fe3+ and S0. Elemental sulfur was oxidized to sulfate by anaerobic incubation with NO3– MnO2 and Fe(OH)3. A new conceptual model for the reduction processes in submerged paddy soil including the reoxidation processes of reduced products, in which soil heterogeneity in paddy fields was taken into consideration, was proposed based on the results.

Bacterial numbers and biomass in leachate and in subsoil of a submerged paddy field

By a leaching experiment with glass columns packed with submerged paddy soils, the relationships among numbers of total bacteria, total Gram-positive bacteria, culturare aerobic bacteria and a amount of bacterial biomass both in the leachate, and in the subsoil after leaching incubation were studied. The leachate from soil columns was collected every 3 d during the 30-d incubation period. The soil columns were packed with plow layer soil samples with and without rice straw (RS) amendment, and the subsoil column was connected to the plow layer soil column without RS. Numbers of total bacteria, culturable aerobic bacteria, and a amount of bacterial biomass in the leachate decreased with the incubation time. There was no correlation between the number of total bacteria in the leachate and the concentration of total organic carbon in the leachate. Bacteria less than 0.1 µsm3 in size predominated in the leachate, especially in that from the plow layer soil column with RS. Percentages of the number of Gram-positive bacteria in the leachate were very low (less than 7% of the total bacterial number), while the percentage in the subsoil after the leaching experiment was in the range of 21–82%. The sum of the number of bacteria percolated from the plow layer soil column with RS during the 30-d period of incubation and the sum of the amount of biomass C were 39 and 77% less than the corresponding values for the bacteria percolated from the plow layer soil column without RS. Percentages of culturable aerobic bacteria among the total bacteria ranged between 2.8 and 37% in the leachate, while less than 0.6% in the subsoil after the leaching experiment.

Estimation of the increase in CH4 emission from paddy soils by rice straw application

The relationship between the amount of CH4 emission to the atmosphere from submerged paddy soils with rice plants and the application level (0–8 g kg-1) of rice straw (RS) in soil was investigated in a pot experiment. Amounts of CH4 emitted from pots with respective RS levels differed between a clayey yellow soil and a silty gray lowland soil. However, the increase in cumulative amounts of CH4 emission with the increase in the application level of RS was similar in pattern between the two soils, and the increase (Y) was formulated with a logistic curve: x, application level of RS; k, a coefficient for relative CH4 emission.

Variations in the Process of Nitrification and Nitrate Reduction in Submerged Paddy Soils as Measured by15N Isotope Dilution Technique

Temporal variations in the process of nitrification and nitrate reduction in paddy fields after flooding were investigated by applying the 15N isotope dilution technique in laboratory model experiments using wet or air-dried soil. When the sample of wet paddy soil from the Hokuriku National Agricultural Experiment Station was submerged and kept at 25°C, an oxidative surface layer (1 cm thick) and an underlying reductive layer were differentiated after 20 days. Nitrifying activity in the oxidative surface layer increased from 100 ng-atoms N per g dry soil per day to 250 for 30 days, and declined later. Nitrate reducing activity was hardly detected. In the underlying reductive layer, the nitrifying activity did not vary appreciably after submergence but the nitrate reducing activity increased after 30 days and attained a level of 250 ng-atoms per g dry soil per day after 60 days. When the air dried soil was submerged, the two layers were distinguished within 5 days. The thickness of the oxidative surface layer was only 1 mm or less. Nitrifying activity in the surface layer (0–1 cm) which could not be detected during the first 15 days. increased up to 50 ng-atoms per g dry soil per day subsequently. Nitrate reducing activity in the surface layer increased almost linearly with time and attained a level of 200 ng-atoms N per g drY soil per day after 60 days.

Nitrogen Dynamics in the Uppermost Part of Submerged Paddy Soils in Temperate and Tropical Regions

The segregation of fine particles in the uppermost part of Thai (Surin) and Japanese (Katagiri) sandy paddy soils was studied under field and laboratory conditions. Under laboratory conditions, the soil was puddled under shallow (1 cm) or deep (12 cm) surface water. There was a pronounced segregation of clay and silt in the uppermost part of the Surin soil when the soil was puddled under deep surface water, the extent of which was similar to that under field conditions. Remarkable segregation of these fine particles also occurred in the Katagiri soil when the soil was puddled under deep surface water, to a much larger extent than under field conditions. This difference in the sorting effect in the Katagiri soil between field and laboratory conditions may be ascribed to a higher rate of water percolation under the former condition, while in the rainfed Surin soil no water percolation took place under field conditions compared with laboratory conditions. Puddling under deep surface water promoted the segreg...

Nitrogen dynamics in the uppermost part of submerged paddy soils in temperate and tropical regions

Nitrogen dynamics in the uppermost part of submerged paddy soils in temperate and tropical regions

Influence of hexachlorocyclohexane on the nitrogenase activity of rice rhizosphere soil

The influence of application of hexachlorocyclohexane (HCH=gamma BHC), to a submerged tropical field soil at rates equivalent to recommended field rates (1–2.5kg a.i./ha) and twice this level, upon the rhizosphere soil nitrogenase, nitrogen fixers, and soil redox potential (Eh) was investigated. The rhizosphere soil from HCH-treated field exhibited significantly higher nitrogenase activity than that from untreated fields. HCH retarded the drop in redox potential of the field soil upto 80 days after transplantation under submerged conditions. Populations of nitrogen-fixingAzospirillum sp. and Azotobacter, to a greater extent, and anaerobic organisms, to a lesser extent, were stimulated in HCH-treated soils. Results indicate the stimulation of heterotrophic nitrogen-fixing bacteria by HCH in submerged paddy soils.

Organic debris as micro-site for nitrogen fixation

Abstract The importance of non-symbiotic N2 fixation in the reduced layers of submerged paddy soils was stressed in previous papers by field surveys (1, 2) and model experiments in the laboratory (2, 3). In these investigations, the activity of the non-symbiotic N2 fixation in the manured plots was found to be higher than that in the non-manured plots. Now, it is rather well established that fairly large part of soil organic matter exists in the form of organic debris in paddy soils (4), that the amount of organic debris is larger in manured plots than in non-manured plots (5) and that soil microbial activities are high on and around the organic debris (6). The organic debris might be the active micro-sites for non-symbiotic N2 fixation. The experiment conducted on this assumption will be described in the present paper.