Yutaka Shiratori

Effectiveness of a subsurface drainage system in poorly drained paddy fields on reduction of methane emissions

Abstract Intensive field experiments were conducted from 1999 to 2001 to examine the effects of farmland improvement on methane (CH4) emission from two rice paddy fields in Niigata, Japan. Rice cultivation and field management were similar in both paddy fields; however, one field had a subsurface drainage system installed 0.6–0.8 m below the soil surface (drained paddy field) and the other had no such system (non-drained paddy field). Methane emissions from the drained paddy field during each rice-growing season were approximately 71% lower than those from the non-drained paddy field. The subsurface drainage system lowered the groundwater level and top of the gley soil layer to the drainage pipe level, enhanced soil permeability, and resulted in more oxidized soil conditions in the fallow season. The lower total and hot water extractable carbon in the plowed layer soil of the drained field versus the non-drained field strongly suggests that the organic substrate that gives rise to CH4 decomposed more quickly in the drained field. Ferrous iron concentrations in the fresh plowed layer soil, collected from before submergence up to mid-summer drainage, were also much lower in the drained field. This indicated that ferrous iron produced during the flooding seasons was quickly oxidized to ferric iron in the fallow season, which then acted as an electron accepter and inhibited CH4 production in the subsequent rice-growing season. In contrast, the continuous reductive conditions in the non-drained field (even in the fallow season) prevented most of the ferrous iron from being oxidized. Therefore, installing a subsurface drainage system greatly reduced CH4 emissions by improving aerobic conditions and reducing CH4 production potential. Methane emissions with a large inter-annual variation in the rice-growing season from the non-drained field were positively correlated with soil moisture in the plowed layer before submergence, which, in turn, greatly affected CH4 emission in the following rice-growing season.

Seasonal transition of active bacterial and archaeal communities in relation to water management in paddy soils

Paddy soils have an environment in which waterlogging and drainage occur during the rice growing season. Fingerprinting analysis based on soil RNA indicated that active microbial populations changed in response to water management conditions, although the fundamental microbial community was stable as assessed by DNA-based fingerprinting analysis. Comparative clone library analysis based on bacterial and archaeal 16S rRNAs (5,277 and 5,436 clones, respectively) revealed stable and variable members under waterlogged or drained conditions. Clones related to the class Deltaproteobacteria and phylum Euryarchaeota were most frequently obtained from the samples collected under both waterlogged and drained conditions. Clones related to syntrophic hydrogen-producing bacteria, hydrogenotrophic methanogenic archaea, rice cluster III, V, and IV, and uncultured crenarchaeotal group 1.2 appeared in greater proportion in the samples collected under waterlogged conditions than in those collected under drained conditions, while clones belonging to rice cluster VI related to ammonia-oxidizing archaea (AOA) appeared at higher frequency in the samples collected under drained conditions than in those collected under waterlogged conditions. These results suggested that hydrogenotrophic methanogenesis may become active under waterlogged conditions, whereas ammonia oxidation may progress by rice cluster VI becoming active under drained conditions in the paddy field.

Depression of methane production potential in paddy soils by subsurface drainage systems

Abstract Subsurface drainage systems (pipe/tile drain systems) in paddy fields have been used in Japan since the 1960s for appropriate water management to encourage rice growing. Water management using the drainage systems probably accelerates the aerobic decomposition of organic matter in the paddy soils, and the management using the systems also accelerates leaching of water-soluble fractions in the soils. To evaluate these side-effects of the drainage systems on methane (CH4) production potential in the soils, soil samples taken from four pairs of paddy fields with or without drainage systems (D-soils and ND-soils, respectively) were compared. In general, total C and N, hot-water-extractable hexose, ammonification and Fe2+ production were lower in D-soils than in ND-soils. Decomposition of buried rice straw during a fallow period was also accelerated in D-soils. Hence, both electron acceptors, such as reducible Fe, and electron donors, such as easily decomposable organic matter, in D-soils decreased on a short-term and long-term basis. To compare the effect of decreased electron acceptors and donors on the same criterion (mg Ceq kg−1 dry matter (d.m.)), the oxidative capacity (OxiC) and reductive capacity (RedC) in each soil were calculated from the soil chemical and biological properties. Both OxiC and RedC decreased in D-soils, but the rate of decrease in RedC was 2.7-fold higher than that of OxiC. As the soil conditions became relatively oxidative, CH4 production potential in D-soils decreased by approximately 40%. Thus, the installation of subsurface drainage systems under poorly drained paddy fields relatively decreased RedC in soil, and that CH4 production potential in the soil also decreased.

Predominant but Previously-overlooked Prokaryotic Drivers of Reductive Nitrogen Transformation in Paddy Soils, Revealed by Metatranscriptomics

Waterlogged paddy soils possess anoxic zones in which microbes actively induce reductive nitrogen transformation (RNT). In the present study, a shotgun RNA sequencing analysis (metatranscriptomics) of paddy soil samples revealed that most RNT gene transcripts in paddy soils were derived from Deltaproteobacteria, particularly the genera Anaeromyxobacter and Geobacter. Despite the frequent detection of the rRNA of these microbes in paddy soils, their RNT-associated genes have rarely been identified in previous PCR-based studies. This metatranscriptomic analysis provides novel insights into the diversity of RNT microbes present in paddy soils and the ecological function of Deltaproteobacteria predominating in these soils.

Nitrous oxide (N 2 O)-reducing denitrifier-inoculated organic fertilizer mitigates N 2 O emissions from agricultural soils

The only known sink for nitrous oxide (N2O) is biochemical reduction to dinitrogen (N2) by N2O reductase (N2OR). We hypothesized that the application of N2O-reducing denitrifier-inoculated organic fertilizer could enhance soil N2O consumption while the disruption of nosZ genes could result in inactivation of N2O consumption. To test such hypotheses, a denitrifier-inoculated granular organic fertilizer was applied to both soil microcosms and fields. Of 41 denitrifier strains, 38 generated 30N2 in the end products of denitrification (30N2 and 46N2O) after the addition of Na15NO3 in culture condition, indicating their high N2O reductase activities. Of these 41 strains, 18 were screened in soil microcosms after their inoculation into the organic fertilizer, most of which were affiliated with Azospirillum and Herbaspirillum. These 18 strains were nutritionally starved to improve their survival in soil, and 14 starved and/or non-starved strains significantly decreased N2O emissions in soil microcosms. However, the N2O emission had not been decreased in soil microcosms after inoculating with a nosZ gene-disruptive strain, suggesting that N2O reductase activity might be essential for N2O consumption. Although the decrease of N2O was not significant at field scales, the application of organic fertilizer inoculated with Azospirillum sp. TSH100 and Herbaspirillum sp. UKPF54 had decreased the N2O emissions by 36.7% in Fluvisol and 23.4% in Andosol in 2014, but by 21.6% in Andosol in 2015 (H. sp. UKPF54 only). These results suggest that the application of N2O-reducing denitrifier-inoculated organic fertilizer may enhance N2O consumption or decrease N2O emissions in agricultural soils.

Silicon elution from three types of steel slag fertilizers in a paddy field analyzed by electron probe micro-analyzer (EPMA)

Abstract Elution of silicon (Si) from three types of slag fertilizers was tested in a paddy field. They were made from granulated blast furnace slag, dephosphorization slag and decarburization slag, respectively. Each fertilizer, embedded in epoxy resin to expose the cross section, was analyzed to get initial two-dimensional distribution images of Si, calcium (Ca), oxygen (O), magnesium (Mg), aluminum (Al), manganese (Mn) and iron (Fe) by electron probe micro-analyzer (EPMA). These resin specimens were set in a paddy field for 75 d. Then the second two-dimensional distribution images of Si, Ca, O, Mg, Al, Mn and Fe at the same site were analyzed again by EPMA. A comparison of the two-dimensional distribution images before and after setting in paddy field elucidated the following results: (1) Si eluted clearly from dephosphorization slag and decarburization slag; (2) Si, Ca, Mg and Al distributed homogeneously in granulated blast furnace slag. X-ray diffraction (XRD) clarified that granulated blast furnace slag was amorphous. The content of plant-available Si in each slag fertilizer was evaluated by the cation exchange resin extraction method. It was the highest in dephosphorization slag fertilizer. This result corresponded to Si elution from dephosphorization slag observed by EPMA. The content of plant-available Si was low in granulated blast furnace slag but high in air-cooled blast furnace slag. Although the content of plant-available Si in decarburization slag was low, the efficacy of Si elution was the highest in decarburization slag. From X-ray diffraction analyses, calcium silicate or larnite (Ca2SiO4) was considered to be the causative substance for efficient Si elution from decarburization slag and dephosphorization slag. Because of the high content of plant-available Si, dephosphorization slag and air-cooled blast furnace slag are recommended as silicate fertilizers in paddy fields.

Intercontinental comparison of greenhouse gas emissions from irrigated rice fields under feasible water management practices: Brazil and Japan

ABSTRACT Flooded rice fields are a significant anthropogenic source of methane (CH4) and nitrous oxide (N2O) from agriculture in Asia, Latin America, and the Caribbean regions. In this work, we comparatively assessed the potential of intermittent irrigation and continuous rice flooding for reducing soil CH4 and N2O emissions, partial global warming potential (pGWP), and its yield-scaled version (YpGWP) in northwestern Japan and southern Brazil. Seasonal CH4 emissions under continuous flooded soils were slight higher in Japan (738 ± 87 kg ha−1) than in Brazil (623 ± 197 kg ha−1), and they were probably related to the higher level of soil organic C and the longer period under flooding in the seedling transplanting system in the Japanese site. Intermittent irrigation had similar efficiency in decreasing soil CH4 emissions in both study areas, with the maximum mitigation potential of 71% in northwestern Japan and of 62% in southern Brazil. No significant difference in seasonal soil N2O emissions (−0.17 ± 0.05 to −0.24 ± 0.06 kg N2O ha−1 in Japan and 0.32 ± 0.08–1.16 ± 0.40 kg ha−1 in Brazil) or rice yield (7328–8064 kg ha−1 in Japan and 9391–10,231 kg ha−1 in Brazil) between irrigation systems was observed in either area. The potential of intermittent irrigation for reducing pGWP was around three times higher than that of continuous flooding in both sites. Thus, a reduction by 47–63% and 62–80% in yield-scaled pGWP was observed in southern Brazil and northwestern Japan, respectively. Like the well-established labor-intensive rice transplanting systems used in Asia, the introduction of feasible irrigation suppression systems in mechanized direct seeding rice fields in southern Brazil and other countries of Latin America and the Caribbean region is an effective choice for reducing greenhouse gas emissions with no adverse impact on rice yield.

Metatranscriptomic insights into microbial consortia driving methane metabolism in paddy soils

ABSTRACT Flooded paddy soils are global sources of the greenhouse gas methane. Net methane fluxes from paddy fields reflect the sum of methane generation in the anoxic zone and methane consumption in the oxic zone, which are driven by methanogenic archaea and methanotrophic bacteria, respectively. Furthermore, methanogenic archaea produce methane utilizing hydrogen or acetate generated by hydrogen-producing bacteria or acetogenic bacteria, respectively. Therefore, methane emissions are regulated and orchestrated by hydrogen production, acetogenesis, methanogenesis, and methane oxidation. However, a comprehensive understanding of the microbial consortia that regulate methane emissions has yet to be achieved owing to the lack of simultaneous assessments of microbial drivers involved in these four processes, especially the production of hydrogen and acetate, which are primary substrates for methanogenesis. In this study, the transcriptional profiles of genes encoding the enzymes that catalyze each process were comprehensively investigated by shotgun RNA sequencing analysis (metatranscriptomics). Seasonal and spatial transitions in soil redox potentials and the transcriptional activities of methanogens indicated active methane metabolism in paddy soils 5 weeks after waterlogging, when the soil redox conditions of the surface (0–1 cm depth; S layer) and subsurface (5–7 cm depth; D layer) were the most divergent. Deep metatranscriptomics focusing on such soils suggested that: (1) in the anoxic D layer, rather than in the oxic S layer, Deltaproteobacteria, Acidobacteria, and Planctomycetes actively generate hydrogen; (2) Deltaproteobacteria, Betaproteobacteria, Acidobacteria, and Alphaproteobacteria generate acetate; (3) utilizing these products as substrates for methanogenesis, the archaea Methanocella, Methanoregula, and Methanosaeta actively produce methane; (4) concurrently, in the oxic S layer, methanotrophs related to Methylocystis and Methylogaea oxidize methane. The present study represents the first comprehensive report of the community structure and dynamics of the microbial consortia underpinning the methane emissions from paddy fields.