Jun Murase

Linking microbial community dynamics to rhizosphere carbon flow in a wetland rice soil

Photosynthesis by terrestrial vegetation is the driving force of carbon cycling between soil and the atmosphere. The soil microbiota, the decomposers of organic matter, is the second player carrying out carbon cycling. Numerous efforts have been made to quantify rhizodeposition and soil respiration to understand and predict the carbon cycling between the soil and atmosphere. However, there have been few attempts to link directly the soil microbial community to plant photosynthesis. We carried out a pulse-chase labeling experiment in a wetland rice system in which rice plants of various ages were labeled with (13)CO(2) for 6 h and the distribution of the assimilated (13)C to soil microorganisms was estimated by analyzing the (13)C profile of microbial phospholipid fatty acids (PLFAs). The results showed that total PLFA increased with plant growth, indicating an increase of microbial biomass. But the mono-unsaturated PLFAs increased faster than the branched chain fatty acids. The (13)C was incorporated into PLFAs immediately after the plant (13)CO(2) assimilation, proving the tight coupling of microbial activity to plant photosynthesis. In line with the finding of seasonal change in total PLFAs, more of (13)C was distributed to the straight chain fatty acids (16:0, 16:1omega7, 18:1omega7 and 18:1omega9) than to the branched chain fatty acids. The total plant carbon incorporation estimated from (13)C labeling roughly corresponded to the increase in total PLFAs over the growing season of plants. Our study suggests that microbial populations in rice soil differ greatly in their responses to plant photosynthate input.

Methane Production and Its Fate in Paddy Fields : I. Effects of Rice Straw Application and Percolation Rate on the Leaching of Methane and Other Soil Components into the Subsoil

Abstract Oxidation of methane and total water soluble organic carbon (TOC) in the subsoil, which percolated from the plow layer, was investigated in a column experiment. The amounts of both methane and TOC in the leachate decreased by percolation in the subsoil. Fe2+ percolated from the plow layer was nearly completely retained in the subsoil. The decomposition of methane and TOC in the subsoil was considered to result in the coupling with the formation of Fe2+. Methane was estimated to contribute ca. 19–21% to the total amount of Fe2+ formed in the subsoil by the organic materials in the leachate.

Impact of Protists on the Activity and Structure of the Bacterial Community in a Rice Field Soil

ABSTRACT Flooded rice fields have become a model system for the study of soil microbial ecology. In Italian rice fields, in particular, aspects from biogeochemistry to molecular ecology have been studied, but the impact of protistan grazing on the structure and function of the prokaryotic community has not been examined yet. We compared an untreated control soil with a γ-radiation-sterilized soil that had been reinoculated with a natural bacterial assemblage. In order to verify that the observed effects were due to protistan grazing and did not result from sterilization, we set up a third set of microcosms containing sterilized soil that had been reinoculated with natural assemblage bacteria plus protists. The spatial and temporal changes in the protistan and prokaryotic communities were examined by denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) analysis, respectively, both based on the small-subunit gene. Sequences retrieved from DGGE bands were preferentially affiliated with Cercozoa and other bacteriovorous flagellates. Without protists, the level of total DNA increased with incubation time, indicating that the level of the microbial biomass was elevated. Betaproteobacteria were preferentially preyed upon, while low-G+C-content gram-positive bacteria became more dominant under grazing pressure. The bacterial diversity detectable by T-RFLP analysis was greater in the presence of protists. The level of extractable NH4+ was lower and the level of extractable SO42− was higher without protists, indicating that nitrogen mineralization and SO42− reduction were stimulated by protists. Most of these effects were more obvious in the partially oxic surface layer (0 to 3 mm), but they could also be detected in the anoxic subsurface layer (10 to 13 mm). Our observations fit well into the overall framework developed for protistan grazing, but with some modifications pertinent to the wetland situation: O2 was a major control, and O2 availability may have limited directly and indirectly the development of protists. Although detectable in the lower anoxic layer, grazing effects were much more obvious in the partially oxic surface layer.

Selective grazing of methanotrophs by protozoa in a rice field soil

Biological methane oxidation is a key process in the methane cycle of wetland ecosystems. The methanotrophic biomass may be grazed by protozoa, thus linking the methane cycle to the soil microbial food web. In the present study, the edibility of different methanotrophs for soil protozoa was compared. The number of methanotroph-feeding protozoa in a rice field soil was estimated by determining the most-probable number (MPN) using methanotrophs as food bacteria; naked amoebae and flagellates were the dominant protozoa. Among ten methanotrophic strains examined as a food source, seven yielded a number of protozoa comparable with the yield with Escherichia coli [10(4) MPN (g soil dry weight)(-1)], and three out of four Methylocystis spp. yielded significantly fewer numbers [10(2)-10(3) MPN (g soil dry weight)(-1)]. The lower edibility of the Methylocystis spp. was not explained either by their growth phase or by harmful effects on protozoa. Incubation of the soil under methane resulted in a higher number of protozoa actively grazing on methanotrophs, especially on the less-edible group. Protozoa isolated from the soil demonstrated a grazing preference on the different methanotrophs consistent with the results of MPN counts. The results indicate that selective grazing by protozoa may be a biological factor affecting the methanotrophic community in a wetland soil.

Methane emission from plots with differences in fertilizer application in thai paddy fields

Abstract Methane emission rates from plots with differences in fertilizer application (no fertilizer: NF-, chemical fertilizer: CF-, and organic materials: OM-) in 3 typical Thai paddy fields (fresh water alluvial, acid sulfate, and low humic gley paddy fields) were measured every week throughout the rice-growing period. The CH4 emission rates from the NF- and CF-plots in the paddy field with acid sulfate soil were much lower than the CH4 emission rates from similar plots in other countries, while those from the paddy field with low humic gley soil were much higher. The CH4 emission rates from these plots in the paddy field with fresh water alluvial soil corresponded to the lower reported values. The CH4 emission rates from the OM-plots in Thailand were within the ranges of reported values or higher. Methane was mainly emitted in the first half of the growth period in Thailand irrespective of the plots, in contrast to reports stating that CH4 emission was higher in the second half of the growth period in ...

Methane production and its fate in paddy fields II. Oxidation of methane and its coupled ferric oxide reduction in subsoil

Oxidation of methane and total water soluble organic carbon (TOC) in the subsoil, which percolated from the plow layer, was investigated in a column experiment. The amounts of both methane and TOC in the leachate decreased by percolation in the subsoil. Fe2+ percolated from the plow layer was nearly completely retained in the subsoil. The decomposition of methane and TOC in the subsoil was considered to result in the coupling with the formation of Fe2+. Methane was estimated to contribute ca. 19–21% to the total amount of Fe2+ formed in the subsoil by the organic materials in the leachate.

Dynamics of methane in mesotrophic Lake Biwa, Japan

As a part of a core project of IGBP (International Geosphere-Biosphere Programme), distribution, production, oxidation and transport processes of methane in bottom sediments and lake water in a mesotrophic lake (Lake Biwa) have been studied with special reference to the spatial heterogeneity of each process. In this study, we attempted to synthesize previously reported results with newly obtained ones to depict the methane dynamics in the entire lake. The pelagic water column exhibited subsurface maxima of dissolved methane during a stratified period. Transect observation at the littoral zone suggested that horizontal transportation may be a reason for the high methane concentration in epilimnion and thermocline at the offshore area. Tributary rivers and littoral sediments were suggested to be the source. Observations also showed that the internal wave caused resuspension of the bottom sediment and release of methane from the sediment into the lake water. The impact of the internal waves was pronounced in the late stage of a stratified period. The littoral sediment showed much higher methanogenic activity than the profundal sediments, and the bottom water of the littoral sediments had little methanotrophic activity. In the profundal sediment, most of the methane that diffused up from the deeper part was oxidized when it passed through the oxic layer. Active methane oxidation was also observed in the hypolimnetic water, while the lake water in the epilimnion and thermocline showed very low methane oxidation, probably due to the inhibitory effect of light. These results mean a longer residence time for methane in the epilimnion than in the hypolimnion. Horizontal inflow of dissolved methane from the river and/or littoral sediment, together with the longer residence time in the surface water, may cause the subsurface maxima, which have also been observed in other lakes and in the ocean.

Anaerobic reoxidation of Mn2+, Fe2+, S0 and S2– in submerged paddy soils

Abstract 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.

Suppression of methane fluxes from flooded paddy soil with rice plants by foliar spray of nitrogen fertilizers

Abstract A pot experiment was conducted to evaluate the effects of the kind of ammonium fertilizers (ammonium sulfate, ammonium chloride, and urea) and method of topdressing (broadcasting and foliar spray) on the methane fluxes from paddy fields. Among the broadcasted plots, the methane flux from the ammonium sulfate plot to the atmosphere was the lowest, followed by the ammonium chloride and urea plots, in this order. Topdressing by foliar spray reduced the methane fluxes in each fertilizer plot compared with the respective broadcasted plots, with a reduction of 45, 60, and 20% in the ammonium sulfate plot, the ammonium chloride plot, and the urea plot, respectively. Topdressing by foliar spray decreased the grain yield. Among the three kinds of nitrogen fertilizers, the methane flux rate for the production of a unit weight grain was the lowest in the (NH4)2SO4 plot in both methods of topdressing. Topdressing of (NH4)2SO4 fertilizer by broadcasting was the most appropriate method in this experiment, when...

Low Nitrogen Fertilization Adapts Rice Root Microbiome to Low Nutrient Environment by Changing Biogeochemical Functions

Reduced fertilizer usage is one of the objectives of field management in the pursuit of sustainable agriculture. Here, we report on shifts of bacterial communities in paddy rice ecosystems with low (LN), standard (SN), and high (HN) levels of N fertilizer application (0, 30, and 300 kg N ha−1, respectively). The LN field had received no N fertilizer for 5 years prior to the experiment. The LN and HN plants showed a 50% decrease and a 60% increase in biomass compared with the SN plant biomass, respectively. Analyses of 16S rRNA genes suggested shifts of bacterial communities between the LN and SN root microbiomes, which were statistically confirmed by metagenome analyses. The relative abundances of Burkholderia, Bradyrhizobium and Methylosinus were significantly increased in root microbiome of the LN field relative to the SN field. Conversely, the abundance of methanogenic archaea was reduced in the LN field relative to the SN field. The functional genes for methane oxidation (pmo and mmo) and plant association (acdS and iaaMH) were significantly abundant in the LN root microbiome. Quantitative PCR of pmoA/mcrA genes and a 13C methane experiment provided evidence of more active methane oxidation in the rice roots of the LN field. In addition, functional genes for the metabolism of N, S, Fe, and aromatic compounds were more abundant in the LN root microbiome. These results suggest that low-N-fertilizer management is an important factor in shaping the microbial community structure containing key microbes for plant associations and biogeochemical processes in paddy rice ecosystems.