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Ralf Conrad - One of the best experts on this subject based on the ideXlab platform.
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methane production from Rice straw carbon in five different methanogenic Rice Soils rates quantities and microbial communities
Acta Geochimica, 2020Co-Authors: Xiaozhen Huang, Quan Yuan, Junpeng Rui, Shaojun Qiu, Ralf ConradAbstract:The input of organic substances (e.g., Rice straw) in Rice field Soils usually stimulates the production and emission of the greenhouse gas methane (CH4). However, the amount of CH4 derived from the applied Rice straw, as well as the response of bacterial and archaeal communities during the methanogenic phase, are poorly understood for different Rice field Soils. In this study, samples of five different Rice Soils were amended with 13C-labeled Rice straw (RS) under methanogenic conditions. Immediately after RS addition, the RS-derived CH4 production rates were higher in Soils (Uruguay, Fuyang) that possessed a stronger inherent CH4 production potential compared with other Soils with lower inherent potentials (Changsha, the Philippines, Vercelli). However, Soils with higher inherent potential did not necessarily produce higher amounts of CH4 from the RS applied, or vice versa. Quantitative PCR showed copy numbers of both bacteria and methanogens increased in straw-amended Soils. High-throughput sequencing of 16S rRNA genes showed distinct bacterial communities among the unamended soil samples, which also changed differently in response to RS addition. Nevertheless, RS addition generally resulted in all the Rice field Soils in a relative increase of primary fermenters belonging to Anaerolineaceae and Ruminococcaceae. Meanwhile, RS addition also generally resulted in a relative increase of Methanosarcinaceae and/or Methanocellaceae. Our results suggest that after RS addition the total amounts of RS-derived CH4 are distinct in different Rice field Soils under methanogenic conditions. Meanwhile, there are potential core bacterial populations that are often involved in primary fermentation of RS under methanogenic conditions.
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In Situ Stable Isotope Probing
2016Co-Authors: Of Methanogenic Archaea, In The Rice Rhizosphere, Ralf ConradAbstract:Microorganisms living in anoxic Rice Soils contribute 10 to 25 % of global meth-ane emissions. The most important carbon source for CH4 production is plant-derived carbon that enters soil as root exudates and debris. Pulse labeling of Rice plants with 13CO2 resulted in incorporation of 13C into the ribosomal RNA of Rice Cluster I Archaea in the soil, indicating that this archaeal group plays a key role in CH4 production from plant-derived carbon. This group of micro-organisms has not yet been isolated but appears to be of global environmental importance. The translocation of plant photosynthates below ground and their subsequent decom-position by rhizospheric microorganisms are key to the terrestrial ecosystem carbon budget (1). It has been shown that 30 to 60 % of net photosynthesized carbon is allocated to roots, and as much as 40 to 90 % of this fraction enters soil in the forms of root exudates, sloughed-off cells, and decaying roots (2). In wetland Soils and Rice paddies, the below-ground carbon flow provides a major carbon source for meth-ane production (3, 4). However, little is known about the microbiota that are involved in the rhizosphere carbon cycle, and the soil micro-biota is considered a Bblack box [ in studies of soil carbon dynamics (5). A combination of stable isotope probing (SIP) and biomarker-based fingerprinting can be a powerful approach to investigate micro-bial species and in situ activity (6, 7). Bio-markers that have been used with SIP include nucleic acids (7–11) and phospholipid fatty acids (6, 12–14). Nucleic acids are particularly useful because they provide specific taxonomic information (15). Here we report on the appli-cation of RNA SIP in an intact Rice-soil system to identify the active methane producers in the rhizosphere. Rice fields represent one of the most im-portant individual sources of the greenhouse gas CH 4 (16, 17). Below-ground carbon flo
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In situ stable isotope probing of methanogenic Archaea in the Rice rhizosphere
Science, 2005Co-Authors: Yahai Lu, Ralf ConradAbstract:Microorganisms living in anoxic Rice Soils contribute 10 to 25% of global methane emissions. The most important carbon source for CH 4 production is plant-derived carbon that enters soil as root exudates and debris. Pulse labeling of Rice plants with 13 CO 2 resulted in incorporation of 13 C into the ribosomal RNA of Rice Cluster I Archaea in the soil, indicating that this archaeal group plays a key role in CH 4 production from plant-derived carbon. This group of microorganisms has not yet been isolated but appears to be of global environmental importance.
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archaeal community structures in Rice Soils from different geographical regions before and after initiation of methane production
FEMS Microbiology Ecology, 2001Co-Authors: B Ramakrishnan, Ralf Conrad, Tillmann Lueders, Peter F Dunfield, Michael W FriedrichAbstract:The methane production potential of Rice Soils, which are situated in different geographical regions, shows inherent variations and is catalyzed by archaeal methanogens. We therefore investigated the archaeal community structure in 11 Rice field Soils which represent a range of climatic conditions (temperate to subtropical zones) and soil properties. Retrieval of environmental partial SSU rDNA sequences from the Rice Soils of Shenyang (China) and Gapan (The Philippines) showed that the communities were different from each other. However, despite the differences in soil properties and geographical region the sequences clustered in similar phylogenetic groups to those obtained earlier from Rice fields of Vercelli (Italy). The archaeal community structure in the other Rice field Soils was compared using terminal restriction fragment length polymorphism (T-RFLP) analysis targeting the SSU rRNA gene and the methyl-coenzyme M reductase α-subunit gene (mcrA). The relative abundance of each terminal restriction fragment (T-RF) was determined by fluorescence peak area integration. The 182-bp SSU rDNA T-RF (representing members of Methanosarcinaceae and Rice cluster (RC) VI) was dominant (40–80% contribution) in Chinese Soils (Zhenjiang, Changchun, Jurong, Beiyuan, Shenyang) and the Philippine soil of Gapan. The other Philippine Soils (Luisiana, Guangzhou, Pila) and the Italian Soils (Vercelli, Pavia) showed a dominant 389-bp T-RF (35–40% contribution), representing mainly the novel methanogenic RC-I. All the other T-RF (80, 88, 280, 375 and >800 bp) contributed <20%. Prolonged anoxic incubation (30–200 days) of the air-dried Soils resulted in the production of CH4, which was in some Soils preceded by a characteristic halt phase. T-RFLP analysis revealed that the Soils with a methanogenic halt phase also showed dramatic archaeal population dynamics which were related to the length of the halt phase. Our results show that the archaeal communities in Rice field Soils of different geographical origin are highly related, but nevertheless exhibit individual patterns and dynamics, thus providing evidence for the active participation of the community members in energy and carbon flow.
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effect of temperature on carbon and electron flow and on the archaeal community in methanogenic Rice field soil
Applied and Environmental Microbiology, 2000Co-Authors: Ralf ConradAbstract:Temperature is an important factor controlling CH4 production in anoxic Rice Soils. Soil slurries, prepared from Italian Rice field soil, were incubated anaerobically in the dark at six temperatures of between 10 to 37°C or in a temperature gradient block covering the same temperature range at intervals of 1°C. Methane production reached quasi-steady state after 60 to 90 days. Steady-state CH4 production rates increased with temperature, with an apparent activation energy of 61 kJ mol−1. Steady-state partial pressures of the methanogenic precursor H2 also increased with increasing temperature from <0.5 to 3.5 Pa, so that the Gibbs free energy change of H2 plus CO2-dependent methanogenesis was kept at −20 to −25 kJ mol of CH4−1 over the whole temperature range. Steady-state concentrations of the methanogenic precursor acetate, on the other hand, increased with decreasing temperature from <5 to 50 μM. Simultaneously, the relative contribution of H2 as methanogenic precursor decreased, as determined by the conversion of radioactive bicarbonate to 14CH4, so that the carbon and electron flow to CH4 was increasingly dominated by acetate, indicating that psychrotolerant homoacetogenesis was important. The relative composition of the archaeal community was determined by terminal restriction fragment length polymorphism (T-RFLP) analysis of the 16S rRNA genes (16S rDNA). T-RFLP analysis differentiated the archaeal Methanobacteriaceae, Methanomicrobiaceae, Methanosaetaceae, Methanosarcinaceae, and Rice clusters I, III, IV, V, and VI, which were all present in the Rice field soil incubated at different temperatures. The 16S rRNA genes of Rice cluster I and Methanosaetaceae were the most frequent methanogenic groups. The relative abundance of Rice cluster I decreased with temperature. The substrates used by this microbial cluster, and thus its function in the microbial community, are unknown. The relative abundance of acetoclastic methanogens, on the other hand, was consistent with their physiology and the acetate concentrations observed at the different temperatures, i.e., the high-acetate-requiring Methanosarcinaceae decreased and the more modest Methanosaetaceae increased with increasing temperature. Our results demonstrate that temperature not only affected the activity but also changed the structure and the function (carbon and electron flow) of a complex methanogenic system.
H U Neue - One of the best experts on this subject based on the ideXlab platform.
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a rapid chloroform fumigation extraction method for measuring soil microbial biomass carbon and nitrogen in flooded Rice Soils
Biology and Fertility of Soils, 2000Co-Authors: C Witt, J L Gaunt, C C Galicia, J C G Ottow, H U NeueAbstract:A chloroform-fumigation extraction method with fumigation at atmospheric pressure (CFAP, without vacuum) was developed for measuring microbial biomass C (CBIO) and N (NBIO) in water-saturated Rice Soils. The method was tested in a series of laboratory experiments and compared with the standard chloroform-fumigation extraction (CFE, with vacuum). For both methods, there was little interference from living Rice roots or changing soil water content (0.44–0.55 kg kg–1 wet soil). A comparison of the two techniques showed a highly significant correlation for both CBIO and NBIO (P<0.001) suggesting that the simple and rapid CFAP is a reliable alternative to the CFE. It appeared, however, that a small and relatively constant fraction of well-protected microbial biomass may only be lysed during fumigation under vacuum. Determinations of microbial C and N were highly reproducible for both methods, but neither fumigation technique generated NBIO values which were positively correlated with CBIO. The range of observed microbial C:N ratios of 4–15 was unexpectedly wide for anaerobic soil conditions. Evidence that this was related to inconsistencies in the release, degradation, and extractability of NBIO rather than CBIO came from the observation that increasing the fumigation time from 4 h to 48 h significantly increased NBIO but not CBIO. The release pattern of CBIO indicated that the standard fumigation time of 24 h is applicable to water-saturated Rice Soils. To correct for the incomplete recovery of CBIO, we suggest applying the k C factor of 2.64, commonly used for aerobic Soils (Vance et al. 1987), but caution is required when correcting NBIO data. Until differences in fumigation efficiencies among CFE and CFAP are confirmed for a wider range of Rice Soils, we suggest applying the same correction factor for both methods.
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effect of soil characteristics on sequential reduction and methane production in sixteen Rice paddy Soils from china the philippines and italy
Biogeochemistry, 1999Co-Authors: H Yao, Ralf Conrad, Reiner Wassmann, H U NeueAbstract:The potentials for sequential reduction of inorganic electron acceptors and production of methane have been examined in sixteen Rice Soils obtained from China, the Philippines, and Italy. Methane, CO2, Fe(II), NO 3 − , SO 4 2− , pH, Eh, H2 and acetate were monitored during anaerobic incubation at 30 °C for 120 days. Based on the accumulation patterns of CO2 and CH4, the reduction process was divided into three distinct phases: (1) an initial reduction phase during which most of the inorganic electron acceptors were depleted and CO2 production was at its maximum, (2) a methanogenic phase during which CH4 production was initiated and reached its highest rate, and (3) a steady state phase with constant production rates of CH4. and CO2. The reduction phases lasted for 19 to 75 days with maximum CO2 production of 2.3 to 10.9μmol d−1 g−1 dry soil. Methane production started after 2 to 87 days and became constant after about 38–68 days (one soil >120 days). The maximum CH4 production rates ranged between 0.01 and 3.08μmol d−1 g−1. During steady state the constant CH4 and CO2 production rates varied from 0.07 to 0.30μmol d−1 g−1 and 0.02 and 0.28μmol d−1 g−1, respectively. Within the 120 d of anaerobic incubation only 6–17% of the total soil organic carbon was released into the gas phase. The gaseous carbon released consisted of 61–100% CO2, <0.1–35% CH4, and <5% nonmethane hydrocarbons. Associated with the reduction of available Fe(III) most of the CO2 was produced during the reduction phase. The electron transfer was balanced between total CO2 produced and both CH4 formed and Fe(III), sulfate and nitrate reduced. Maximum CH4 production rate (r=0.891) and total CH4 produced (r =0.775) correlated best with the ratio of soil nitrogen to electron acceptors. Total nitrogen content was a better indicator for “available” organic substrates than the total organic carbon content. The redox potential was not a good predictor of potential CH4 production. These observations indicate that the availability of degradable organic substrates mainly controls the CH4 production in the absence of inorganic electron acceptors.
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automated chamber measurements of methane and nitrous oxide flux in a flooded Rice soil ii fallow period emissions
Soil Science Society of America Journal, 1997Co-Authors: K F Bronson, H U Neue, E B Abao, Upendra SinghAbstract:Methane and N 2 O are radiatively important gases that are emitted from waterlogged Soils. Automated chamber measurements of CH 4 and N 2 O fluxes were carried out at the International Rice Research Institute in the Philippines in flooded Rice (Oryza sativa L.) and fallow Rice fields 24 h a day between December 1992 and April 1994. This period included three 5- to 11-wk rainfed fallow periods. During the first two fallows, the soil was generally aerobic, and moderate amounts of NO 3 accumulated (7-20 kg NO 3 -N ha -1 ). Moderately high, continuous N 2 O fluxes were evident during these two fallow periods. This N 2 O was apparently emitted during nitrification of mineralized organic N in the topsoil and possibly from denitrification in the wet subsoil. Nitrous oxide fluxes were highest (up to 80 mg N 2 O-N m -2 d -1 ) immediately after rainfalls >20 mm, and following the establishment of flooding for Rice at the end of the fallows. Acetylene inhibition in intact cores at these times showed that more N 2 was produced than N 2 O. Denitrification of accumulated NO 3 was therefore occurring after the wetting events. Methane emissions were generally absent during the fallow periods. Two exceptions were immediately after Rice harvest and 1 to 2 wk after the establishment of the permanent flood. Following flooding and green manure (GM; Sesbania rostrata L.) incorporation, CH 4 fluxes appeared within 7 d. During the third fallow period, which was unusually wet, no NO 3 accumulated in the soil. Nitrous oxide emissions were not significant, and low levels of CH4 fluxes persisted throughout this fallow period. This study demonstrates that Rice Soils in the fallow periods can be significant sources of N 2 O, and during wet fallow seasons, important sources of CH 4 as well.
Sanjay Kumar - One of the best experts on this subject based on the ideXlab platform.
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Influence of long-term fertilisation and crop rotation on changes in fungal and bacterial residues in a tropical Rice-field soil
Biology and Fertility of Soils, 2013Co-Authors: Rajasekaran Murugan, Sanjay KumarAbstract:Amino sugars, as a microbial residue biomarker, are highly involved in microbial-mediated soil organic matter formation. However, accumulation of microbial biomass and responses of bacterial and fungal residues to the management practices are different and poorly characterized in Rice Soils. The objectives of this study were to evaluate the effects of mineral fertiliser (MIN), farmyard manure (FYM) and groundnut oil cake (GOC) on crop yield and co-accumulation of microbial residues and microbial biomass under Rice-monoculture (RRR) and Rice–legume–Rice (RLR) systems. In the organic fertiliser treatments and RLR, Rice grain yield and stocks of soil and microbial nutrients were significantly higher than those of the MIN treatment and RRR, respectively. The increased presence of saprotrophic fungi in the organic fertiliser treatments and RRR was indicated by significantly increased ergosterol/C_mic ratio and extractable sulphur. In both crop rotation systems, the long-term application of FYM and GOC led to increased bacterial residues as indicated by greater accumulation of muramic acid. In contrast, the higher fungal C/bacterial C ratio and lower ergosterol/C_mic ratio in the MIN treatment, is likely caused by a shift within the fungal community structure towards ergosterol-free arbuscular mycorrhizal fungi (AMF). The organic fertiliser treatments contributed 22 % more microbial residual C to soil organic C compared to the MIN treatment. Our results suggest that the negative relationship between the ratios ergosterol/C_mic and fungal C/bacterial C encourages studying responses of both saprotrophic fungi and AMF when assessing management effects on the soil microbial community.
Yahai Lu - One of the best experts on this subject based on the ideXlab platform.
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In situ stable isotope probing of methanogenic Archaea in the Rice rhizosphere
Science, 2005Co-Authors: Yahai Lu, Ralf ConradAbstract:Microorganisms living in anoxic Rice Soils contribute 10 to 25% of global methane emissions. The most important carbon source for CH 4 production is plant-derived carbon that enters soil as root exudates and debris. Pulse labeling of Rice plants with 13 CO 2 resulted in incorporation of 13 C into the ribosomal RNA of Rice Cluster I Archaea in the soil, indicating that this archaeal group plays a key role in CH 4 production from plant-derived carbon. This group of microorganisms has not yet been isolated but appears to be of global environmental importance.
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carbon cycling in Rice field ecosystems in the context of input decomposition and translocation of organic materials and the fates of their end products co2 and ch4
Soil Biology & Biochemistry, 2004Co-Authors: Makoto Kimura, Jun Murase, Yahai LuAbstract:Abstract Rice fields are intensively managed, unique agroecosystems, where soil flooding is general performance for Rice cultivation. Flooding the field results in reductive soil conditions, under which decomposition of organic materials proceeds during the period of Rice cultivation. A large variety of organic materials are incorporated into Rice Soils according to field management. In this review, the kind and abundance of organic materials entering carbon cycling in the Rice field ecosystem are evaluated first. Then, decomposition of plant residues and soil organic matter in Rice fields is reviewed quantitatively. Decomposition of plant residues is shown to be the active process in carbon cycling in Rice fields. Rice releases photosynthates into the rhizosphere (rhizodeposition), and they follow a different avenue of decomposition in soil from that of plant residues. Incorporation of rhizodeposition into microbial biomass and soil organic matter during the period of Rice cultivation, and their fates after harvesting are evaluated quantitatively from 13C pulse labeled experiments. Percolating water transports inorganic and organic carbon from the plow layer to the subsoil layer. The amounts of their transport and accumulation in the subsoil layer are evaluated in relation to the amounts of soil organic C in the plow layer. Not only CO2 but also CH4 are produced in the decomposition process of organic materials in flooded Rice fields. CH4 evolution from Rice fields is of global concern from the viewpoint of global warming. Origins of CH4 evolved from Rice fields are estimated first, followed by the fates of CH4 in Rice field ecosystems. Rhizodeposition is shown to be the main origin of CH4 evolved from Rice fields. Evolution to the atmosphere is not the sole pathway of CH4 produced in Rice fields. The amounts of CH4 retained in soil, percolated to the subsoil layer and decomposed in soil are evaluated in the context of the amounts of CH4 efflux. Thus, this review focuses on carbon cycling in the Rice field ecosystem from the viewpoints of input, decomposition, and translocation of organic materials and the fates of their end products (CO2 and CH4).
Jiafang Wang - One of the best experts on this subject based on the ideXlab platform.
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abundance composition and activity of ammonia oxidizer and denitrifier communities in metal polluted Rice paddies from south china
PLOS ONE, 2014Co-Authors: Yuan Liu, Genxing Pan, Yongzhuo Liu, Yuanjun Ding, Jinwei Zheng, Tong Zhou, David E Crowley, Jufeng Zheng, Xuhui Zhang, Jiafang WangAbstract:While microbial nitrogen transformations in Soils had been known to be affected by heavy metal pollution, changes in abundance and community structure of the mediating microbial populations had been not yet well characterized in polluted Rice Soils. Here, by using the prevailing molecular fingerprinting and enzyme activity assays and comparisons to adjacent non-polluted Soils, we examined changes in the abundance and activity of ammonia oxidizing and denitrifying communities of Rice paddies in two sites with different metal accumulation situation under long-term pollution from metal mining and smelter activities. Potential nitrifying activity was significantly reduced in polluted paddies in both sites while potential denitrifying activity reduced only in the Soils with high Cu accumulation up to 1300 mg kg−1. Copy numbers of amoA (AOA and AOB genes) were lower in both polluted paddies, following the trend with the enzyme assays, whereas that of nirK was not significantly affected. Analysis of the DGGE profiles revealed a shift in the community structure of AOA, and to a lesser extent, differences in the community structure of AOB and denitrifier between Soils from the two sites with different pollution intensity and metal composition. All of the retrieved AOB sequences belonged to the genus Nitrosospira, among which species Cluster 4 appeared more sensitive to metal pollution. In contrast, nirK genes were widely distributed among different bacterial genera that were represented differentially between the polluted and unpolluted paddies. This could suggest either a possible non-specific target of the primers conventionally used in soil study or complex interactions between soil properties and metal contents on the observed community and activity changes, and thus on the N transformation in the polluted Rice Soils.
