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Biological nitrogen fixation is a fundamental process sustaining all life on earth. In the soil,Alphaproteobacteria, Betaproteobacteria, andCyanobacteriaare traditionally considered the major groups of nitrogen fixation population. This conventional knowledge has been accumulated by numerous PCR amplicon surveys for nitrogenase genes. However, this prevalent view appears to be inconsistent with results of recent PCR-free meta-omics investigations. Here, we show the global distribution and diversity of terrestrial diazotrophic microbiome, updated by fully leveraging the planetary collections of soil metagenomes along with recently expanded culture collections. After extensive analysis of 1,445 soil metagenomic samples, we proved that the previously-undervaluedAnaeromyxobacteraceaeandGeobacteraceaewithinDeltaproteobacteriaare ubiquitous and predominant groups of diazotrophic microbiome in the soils, spanning a broad spectrum of environments, with different geographic origins and land usage types, including aerobic (croplands, grasslands) and anaerobic ones (paddy soils, sediments). Our results delineate a revised scheme of soil nitrogen fixation, which is inclusive of both conventional diazotrophs and the so far undervaluedDeltaproteobacteria.

Crop diseases caused by soil-borne fungal pathogens are threatening worldwide biodiversity and food security, but the unavoidable chemical inputs used thus far for fungal pathogen control have led to environmental issues and the emergence of chemical resistance in pathogens. Here we show that native soil mesofauna can be used as a natural weapon against soil-borne fungal diseases. We found that the widespread soil mesofauna fungivores, represented by mites, naturally provide agricultural soils with resistance to fungal pathogens through fungal grazing. Furthermore, we found that such a preexisting resistance in soils can be artificially enhanced by modifying the belowground habitat of mites and thus exploited for the control of various soil-borne fungal diseases of crops. Our findings demonstrate that incorporating native mesofauna into the ‘environment dimension’ within the soil-borne ‘disease triangle’ and mesofauna grazing into ‘soil suppressiveness’ leads to a better understanding of the pathogenesis of soil-borne fungal diseases and opens a new direction for their control.

Three bacterial strains (Red232T, Red267T and Red630T) were isolated from paddy soils sampled in Japan. Cells of these strains were Gram-stain-negative, facultative anaerobic, long rod-shaped with monotrichous flagella or pilus-like structures for motility, and formed red colonies on agar plates. Phylogenetic trees based on 16S rRNA gene and multiple single-copy gene sequences showed that the three strains formed a cluster with the type strains of Anaeromyxobacter species, independent from any other strain genera. Similarity values of the 16S rRNA gene sequences and genomes among the three isolated strains and the type strain of Anaeromyxobacter , Anaeromyxobacter dehalogenans 2CP-1T, were 95.4–97.4% for 16S rRNA gene sequence, 75.3–79.5% for average nucleotide identity, 19.6–21.7% for digital DNA–DNA hybridization and 64.1–72.6% for average amino acid identity, all of which are below the species delineation thresholds. Nitrogenase genes were observed in the genomes of the three novel strains, but not in A. dehalogenans 2CP-1T. Moreover, multiple genomic, physiological and chemotaxonomic features supported the discrimination between these three strains. Based on the evidence in this study, the three isolates represent three novel independent species for which the following names are proposed: Anaeromyxobacter oryzae sp. nov., Anaeromyxobacter diazotrophicus sp. nov. and Anaeromyxobacter paludicola sp. nov. The type strains are Red232T (=NBRC 114074T=MCCC 1K03954T), Red267T (=NBRC 114075T=MCCC 1K04211T), and Red630T (=NBRC 114076T=MCCC 1K03957T), respectively.

The application of iron powder stimulated the growth of iron-reducing bacteria as a respiratory substrate and enhanced their nitrogen (N)-fixing activity in flooded paddy soils. High N fertilization (urea) in the flooded paddy soils has caused adverse environmental impacts such as ammonia (NH3) volatilization, nitrous oxide (N2O) emissions, and nitrate (NO3−) leaching. This study aims to investigate the effects of N fertilization rates in combination with an iron amendment on rice yields and N losses from flooded paddy fields. We performed a 2-year field plot experiment with traditional rice–wheat rotation in China’s Yangtze River Delta. The investigation consisted of seven treatments, including 100%, 80%, 60%, and 0% of the conventional N (urea and commercial organic manure) fertilization rate, and 80%, 60%, and 0% of the conventional N with the iron powder (≥99% purity) amendment. The rice yields decreased with a reduction in the conventional N fertilization rate, whereas they were comparable after the iron application under the 80% and 60% conventional N rate. The critical N losses, including NH3 volatilization, N2O emissions, and NO3− and NH4+ leaching, generally decreased with a reduction in the conventional N fertilization rate. These N losses were significantly greater after the iron amendment compared with the non-amended treatments under the 80% and 60% conventional N fertilization rate in the first rice-growing season. However, it was comparable between the iron-amended and the non-amended treatments in the second season. Furthermore, NO3− leaching was the most significant N loss throughout the two rice seasons, followed by NH3 volatilization. The iron amendment significantly increased soil Fe2+ content compared with the non-amended treatments irrespective of N fertilization, suggesting the reduction of amended iron by iron-reducing bacteria and their simultaneous N fixation. A combination of the iron application with 60–80% of the conventional N fertilization rate could maintain rice yields similar to the conventional N fertilization rate while reducing the critical N losses in the flooded paddy field tested in this study. Our study leads to the establishment of novel and practical rice cultivation, which is a step towards the development of green agriculture.

Anaeromyxobacter and Geobacter, iron-reducing bacteria belonging to Deltaproteobacteria, are newly discovered nitrogen-fixing bacteria predominant in paddy soils. We hypothesized that adding ferric...

Recent studies demonstrated that phylogenetically more diverse and abundant bacteria and fungi than previously considered are responsible for denitrification in terrestrial environments. We herein examined the effects of land-use types on the community composition of those denitrifying microbes based on their nitrite reductase gene (nirK and nirS) sequences. These genes can be phylogenetically grouped into several clusters. We used cluster-specific PCR primers to amplify nirK and nirS belonging to each cluster because the most widely used primers only amplify genes belonging to a single cluster. We found that the dominant taxa as well as overall community composition of denitrifying bacteria and fungi, regardless of the cluster they belonged to, differed according to the land-use type. We also identified distinguishing taxa based on individual land-use types, the distribution of which has not previously been characterized, such as denitrifying bacteria or fungi dominant in forest soils, Rhodanobacter having nirK, Penicillium having nirK, and Bradyrhizobium having nirS. These results suggest that land-use management affects the ecological constraints and consequences of denitrification in terrestrial environments through the assembly of distinct communities of denitrifiers.

Bacteria in the family Geobacteraceae have been proven to fill important niches in a diversity of anaerobic environments and global biogeochemical processes. Here, three bacterial strains in this family, designated Red875T, Red259T, and Red421T were isolated from river sediment and paddy soils in Japan. All of them are Gram-staining-negative, strictly anaerobic, motile, flagellum-harboring cells that form red colonies on agar plates and are capable of utilizing Fe(III)-NTA, Fe(III) citrate, ferrihydrite, MnO2, fumarate, and nitrate as electron acceptors with acetate, propionate, pyruvate, and glucose as electron donors. Phylogenetic analysis based on the 16S rRNA gene and 92 concatenated core proteins sequences revealed that strains Red259T and Red421T clustered with the type strains of Geomonas species, whereas strain Red875T formed an independent lineage within the family Geobacteraceae. Genome comparison based on average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values clearly distinguished these three strains from other Geobacteraceae members, with lower values than the thresholds for species delineation. Moreover, strain Red875T also shared low average amino acid identity (AAI) and percentage of conserved proteins (POCP) values with the type species of the family Geobacteraceae. Based on these physiological, chemotaxonomic, and phylogenetic distinctions, we propose that strain Red875T (=NBRC 114290T = MCCC 1K04407T) represents a novel genus in the family Geobacteraceae, namely, Geomesophilobacter sediminis gen. nov., sp. nov., and strains Red259T (=NBRC 114288T = MCCC 1K05016T) and Red421T (=NBRC 114289T = MCCC 1K06216T) represent two novel independent species in the genus Geomonas, namely, Geomonas propionica sp. nov. and Geomonas anaerohicana sp. nov., respectively.

Biochemical reduction of nitrous oxide (N2O) to dinitrogen (N2) by N2O reductase (N2OR) is the only known sink to consume N2O. Copper (Cu) and pH are two key factors determining the activity of the enzyme N2OR. We hypothesized that changes in the Cu level could enhance the reduction of N2O to N2 in denitrifier strains and decrease the N2O emissions from agricultural soils. To test this hypothesis, Cu-modified culture medium was applied to denitrifier strains, and Cu-modified organic fertilizer was applied to both soil microcosms and fields. Of 46 denitrifier strains, 25 showed higher denitrifying activities and 30N2/(46N2O + 30N2) after the addition of Cu under pure culture conditions. Among 10 genera, Azospirillum and Herbaspirillum were the most responsive to the Cu level changes. The N2O flux was significantly reduced 4 or 8 days onwards after the application of 130 mM CuSO4-modified organic fertilizer (vol:wt = 1:1) into Andosol or Fluvisol, respectively, under soil microcosm conditions. In addition, the cumulative N2O emissions were significantly reduced after the application of 130 mM CuSO4-modified organic fertilizer. They were moderately reduced after the application of 130 mM CuSO4-modified organic fertilizer (vol:wt = 1:1) into a Fluvisol field. They were significantly lower in Azospirillum sp. UNPF1-inoculated soils after the application of 130 mM CuSO4-modified organic fertilizer when compared with that in dual non-inoculated and unmodified soils. Soils inoculated with Herbaspirillum sp. UKPF54 showed results similar to non-inoculated Fluvisol fields. These results suggest that Cu may enhance N2O conversion to N2 in denitrifiers and that Cu-modified organic fertilizer may enhance N2O consumption or decrease N2O emissions in agricultural soils.

Nitrous oxide (N(2)O) is an important greenhouse gas and an ozone-depleting substance. Due to the long persistence of N(2)O in the atmosphere, the mitigation of anthropogenic N(2)O emissions, which are mainly derived from microbial N(2)O-producing processes, including nitrification and denitrification by bacteria, archaea, and fungi, in agricultural soils, is urgently necessary. Members of mesofauna affect microbial processes by consuming microbial biomass in soil. However, how microbial consumption affects N(2)O emissions is largely unknown. Here, we report the significant role of fungivorous mites, the major mesofaunal group in agricultural soils, in regulating N(2)O production by fungi, and the results can be applied to the mitigation of N(2)O emissions. We found that the application of coconut husks, which is the low-value part of coconut and is commonly employed as a soil conditioner in agriculture, to soil can supply a favorable habitat for fungivorous mites due to its porous structure and thereby increase the mite abundance in agricultural fields. Because mites rapidly consume fungal N(2)O producers in soil, the increase in mite abundance substantially decreases the N(2)O emissions from soil. Our findings might provide new insight into the mechanisms of soil N(2)O emissions and broaden the options for the mitigation of N(2)O emissions.

Three bacterial strains, designated Red330T, Red736T and Red745T, were isolated from forest and paddy soils in Japan. Strains Red330T, Red736T and Red745T are flagella-harbouring and strictly anaerobic bacteria forming red colonies. A 16S rRNA gene sequence-based phylogenetic tree showed that all three strains were located in a cluster, including the type strains of Geomonas species, which were recently separated from the genus Geobacter within the family Geobacteraceae . Similarities of the 16S rRNA gene sequences among the three strains and Geomonas oryzae S43T, the type species of the genus Geomonas , were 96.3–98.5 %. The genome-related indexes, average nucleotide identity, digital DNA–DNA hybridization, and average amino acid identity, among the three strains and G. oryza e S43T were 74.7–86.8 %, 21.2–33.3 % and 70.4–89.8 %, respectively, which were lower than the species delineation thresholds. Regarding the phylogenetic relationships based on genome sequences, the three strains clustered with the type strains of Geomonas species, which were independent from the type strains of Geobacter species. The distinguishableness of the three isolated strains was supported by physiological and chemotaxonomic properties, with the profile of availability of electron donors and cellular fatty acids composition being particularly different among them. Based on genetic, phylogenetic and phenotypic properties, the three isolates represent three novel independent species in the genus Geomonas , for which the names Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov. are proposed. The type strains are Red330T (=NBRC 114028T=MCCC 1K03949T), Red736T (=NBRC 114029T=MCCC 1K03950T) and Red745T (=NBRC 114030T=MCCC 1K03951T), respectively.

The area of Kanto-Koushinetsu occupies 16% (63,041 km2) of the land area of Japan. This region includes the Tokyo metropolis and the prefectures of Ibaraki, Tochigi, Gunma, Saitama, Chiba, Kanagawa, Yamanashi, Nagano, Niigata. Significant depletion in agricultural land has been progressed from 1972 to 2011 due to the population concentration in the urban area of Tokyo metropolis and the prefectures of Saitama, Chiba, Kanagawa. The area around the population concentration zone plays an important role in supplying vegetables, and the national share of items is 33.8% for vegetables and 25.6% for a flowering plant, and these values are the top of the Japan. In the Kanto region, the plain area occupies a large area, and agricultural activities are being developed under good water use and the existence of a populated area. The characteristics of geology, topography, climatic conditions and soil characteristics and the effects of volcanic ash soil in this area are described. The relationship between the recent agricultural production of Kanto-Koshinetsu area and the soil characteristics of each area was clarified. On the other hand, anthropogenic soils are increasing in Tokyo metropolis and problems in current soil classification system emerged from these soils has been pointed out. As a topic, an action on restoration of habitat for the reintroduction of the crested ibis in Sado Island (Sado City, Niigata Prefecture) for selected as Globally Important Agricultural Heritage System (GIAHS) was introduced. Furthermore, examples of agricultural production and soil environment conservation were introduced.

Biological nitrogen fixation is an essential reaction in a major pathway for supplying nitrogen to terrestrial environments. Previous culture-independent analyses based on soil DNA/RNA/protein sequencing could globally detect the nitrogenase genes/proteins of Anaeromyxobacter (in the class Deltaproteobacteria), commonly distributed in soil environments and predominant in paddy soils; this suggests the importance of Anaeromyxobacter in nitrogen fixation in soil environments. However, direct experimental evidence is lacking; there has been no research on the genetic background and ability of Anaeromyxobacter to fix nitrogen. Therefore, we verified the diazotrophy of Anaeromyxobacter based on both genomic and culture-dependent analyses using Anaeromyxobacter sp. strains PSR-1 and Red267 isolated from soils. Based on the comparison of nif gene clusters, strains PSR-1 and Red267 as well as strains Fw109-5, K, and diazotrophic Geobacter and Pelobacter in the class Deltaproteobacteria contain the minimum set of genes for nitrogenase (nifBHDKEN). These results imply that Anaeromyxobacter species have the ability to fix nitrogen. In fact, Anaeromyxobacter PSR-1 and Red267 exhibited N2-dependent growth and acetylene reduction activity (ARA) in vitro. Transcriptional activity of the nif gene was also detected when both strains were cultured with N2 gas as a sole nitrogen source, indicating that Anaeromyxobacter can fix and assimilate N2 gas by nitrogenase. In addition, PSR-1- or Red267-inoculated soil showed ARA activity and the growth of the inoculated strains on the basis of RNA-based analysis, demonstrating that Anaeromyxobacter can fix nitrogen in the paddy soil environment. Our study provides novel insights into the pivotal environmental function, i.e., nitrogen fixation, of Anaeromyxobacter, which is a common soil bacterium. IMPORTANCEAnaeromyxobacter is globally distributed in soil environments, especially predominant in paddy soils. Current studies based on environmental DNA/RNA analyses frequently detect gene fragments encoding nitrogenase of Anaeromyxobacter from various soil environments. Although the importance of Anaeromyxobacter as a diazotroph in nature has been suggested by culture-independent studies, there has been no solid evidence and validation from genomic and culture-based analyses that Anaeromyxobacter fixes nitrogen. This study demonstrates that Anaeromyxobacter harboring nitrogenase genes exhibits diazotrophic ability; moreover, N2-dependent growth was demonstrated in vitro and in the soil environment. Our findings indicate that nitrogen fixation is important for Anaeromyxobacter to survive under nitrogen-deficient environments and provide a novel insight into the environmental function of Anaeromyxobacter, which is a common bacterium in soils.

Bacteria of the family Geobacteraceae are particularly common and deeply involved in many biogeochemical processes in terrestrial and freshwater environments. As part of a study to understand biogeochemical cycling in freshwater sediments, three iron-reducing isolates, designated as Red96T, Red100T, and Red88T, were isolated from the soils of two paddy fields and pond sediment located in Japan. The cells were Gram-negative, strictly anaerobic, rod-shaped, motile, and red-pigmented on agar plates. Growth of these three strains was coupled to the reduction of Fe(III)-NTA, Fe(III) citrate, and ferrihydrite with malate, methanol, pyruvate, and various organic acids and sugars serving as alternate electron donors. Phylogenetic analysis based on the housekeeping genes (16S rRNA gene, gyrB, rpoB, nifD, fusA, and recA) and 92 concatenated core genes indicated that all the isolates constituted a coherent cluster within the family Geobacteraceae. Genomic analyses, including average nucleotide identity and DNA&ndash, DNA hybridization, clearly differentiated the strains Red96T, Red100T, and Red88T from other species in the family Geobacteraceae, with values below the thresholds for species delineation. Along with the genomic comparison, the chemotaxonomic features further helped distinguish the three isolates from each other. In addition, the lower values of average amino acid identity and percentage of conserved protein, as well as biochemical differences with their relatives, indicated that the three strains represented a novel genus in the family Geobacteraceae. Hence, we concluded that strains Red96T, Red100T, and Red88T represented three novel species of a novel genus in the family Geobacteraceae, for which the names Oryzomonas japonicum gen. nov., sp. nov., Oryzomonas sagensis sp. nov., and Oryzomonas ruber sp. nov. are proposed, with type strains Red96T (= NBRC 114286T = MCCC 1K04376T), Red100T (= NBRC 114287T = MCCC 1K04377T), and Red88T (= MCCC 1K03694T = JCM 33033T), respectively.

Novoherbaspirillum sp. strain UKPF54, a plant growth-promoting rhizobacterium with the ability to mitigate nitrous oxide emission from agriculture soils, has been successfully isolated from paddy soil in Kumamoto, Japan. Here, we report the whole-genome sequence of this strain.

Arthrobacter sp. strain UKPF54-2, a plant growth-promoting rhizobacterium having the potential ability to control fungal and bacterial pathogens, was isolated from paddy soil in Kumamoto, Japan. We report here the whole-genome sequence of this strain.

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 wer...

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 ...

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.

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.

The use of N fertilizers for agricultural production acts as a sources of atmospheric $$\hbox {N}_2\hbox {O}$$ . Fertilizer induced $$\hbox {N}_2\hbox {O}$$ emission considerably varies in accordance with environmental factors. We conducted a $$\hbox {N}_2\hbox {O}$$ flux measurement campaign across 10 different experimental sites with various soil types throughout Japan and investigated the fertilizer induced $$\hbox {N}_2\hbox {O}$$ emission factors (FIEFs) of synthetic fertilizers (mainly urea) in multiple growing periods at each experimental site. FIEFs considerably varied among the 10 sites, and measurement periods ranged from 0.00 to 7.13 % in 40 total observations. Soil profile information divided the experimental sites into two major groups through cluster analysis, which are volcanic or non-volcanic soils. According to this classification, FIEFs were clearly differentiated into high and low FIEF groups (mean values: 2.67 and 0.59 %, respectively). Regression trees selected total soil carbon, the depth to the Fe mottling horizon, and mean air temperature as the key parameters to determine the strength of FIEFs out of 10 explanatory variables (e.g., N fertilizer application rates, fertilizer application times, clay content, total precipitation during measurement periods, pH, total soil carbon, and total soil nitrogen). The existence of shallow Fe mottling layer (up to 42.5 cm) induced high FIEFs in this model, suggesting that upward $$\hbox {N}_2\hbox {O}$$ emissions derived from the intermediate Fe mottling layers presumably contributed high $$\hbox {N}_2\hbox {O}$$ emissions in such soils. Our results suggest that the soil profile information associated with the water regime is an important index for synthetic fertilizer induced $$\hbox {N}_2\hbox {O}$$ emissions.

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 ...

Fungal denitrification in soils is receiving considerable attention as one of the dominant N 2 O production processes. However, because of the lack of a methodology to detect fungal denitrification-related genes, the diversity and ecological behavior of denitrifying fungi in soil remains unknown. Thus, we designed a primer set to detect the fungal nitrite reductase gene ( nirK ) and validated its sensitivity and specificity. Through clone library analyses, we identified congruence between phylogenies of the 18S rRNA gene and nirK of denitrifying fungal isolates obtained from the surface-fertilized cropland soil and showed that fungi belonging to Eurotiales, Hypocreales, and Sordariales were primarily responsible for N 2 O emissions in the soil.

Agricultural fields are one of the largest anthropogenic sources of atmospheric nitrous oxide (N2O). Fungi have been suggested to contribute substantially to N2O emission in terrestrial environments; however, the extent of the fungal contribution and the phylogenetic and physiologic nature of related fungal communities in agricultural fields are largely unknown. This study focused on the large N2O emission from cropland soil that occurs after granular organic fertilizers were applied to the surface. The granular organic fertilizers applied were evidently covered by fungal mycelia. An experiment using a soil microcosm was established to imitate the field observations. N2O emissions following surface organic fertilization were suppressed by 84 and 20% after the addition of cycloheximide (a fungal inhibitor) and streptomycin (a bacterial inhibitor), respectively, suggesting that fungi provide the main contribution to the observed N2O emission. The population density and community composition of fungi in the surface-fertilized and non-fertilized soils in the field were determined using colony counting, denaturing gradient gel electrophoresis and subsequent phylogenetic analyses. Thirty-four fungal strains were isolated from the soils, and their N2O producing activities were analyzed. Fungal population density in the surface-fertilized soil (2.6 × 106 CFU/g) was much higher than that in the non-fertilized soil (1.0 × 105 CFU/g). In addition, the fungal community compositions of the soils differed. Actinomucor elegans, Bionectria ochroleuca, Fusarium avenaceum, Fusarium equiseti, Fusarium oxysporum, Fusarium solani and Nectria sp. dominated the surface-fertilized soil, and their activity in producing N2O was confirmed. These results suggested that N2O emission after the surface application of granular organic fertilizers in the cropland field mainly resulted from fungal denitrification.

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.

In order to analyze the mitigation of methane (CH 4 ) emissions and the global warming potentials (GWPs) of CH 4 and nitrous oxide (N 2 O) emissions from paddy fields by modifying the adopted water-management technique, we conducted field experiments to measure the CH 4 and N 2 O fluxes at nine sites across Japan. Over 2 years, we tested different water-management strategies such as prolonged midseason drainage (MD) in each site. The CH 4 emission rates at each site varied considerably; the rates were dependent on the ratio of reductive and oxidative capacities of the fields. Seasonal CH 4 emission was effectively reduced at most sites by prolonging MD beyond its conventional duration, especially at sites where organic matter was added to the soil before the cultivation. We attribute this result to the effective suppression of the CH 4 emission peak that occurs early in the cultivation period. Despite the large variation in seasonal CH 4 emissions among the sites, the rate of CH 4 emission resulting from alternative water-management strategies relative to that resulting from conventional water-management strategies is highly dependent on the degree of drainage during the MD period. N 2 O emission at most sites, in terms of GWP-based CO 2 -equivalent, was much smaller than that of CH 4 emission. Compared to conventional water-management strategies, the seasonal CH 4 emissions and the net 100-year GWPs (CH 4 + N 2 O) can be suppressed to 69.5 ± 3.4 (SE)% and 72.0 ± 3.1% while maintaining grain yields as high as 96.2 ± 2.0% by prolonging MD on average by employing the selected alternative water-management strategies that satisfied the following conditions: the percent of CH 4 emission of alternative water-management strategies was less than 90% and the grain yield was greater than 85% relative to conventional water-management strategies.

The authors have constructed a simultaneous multi-point illuminance measurement system to measure illuminance. The functions of this system include environment measurement, signal transmission via wired and wireless networks, and data analysis. The system contains a control PC and a control module. The control module is made up of the voltage supply, the communication part, and the measuring module, which includes the illuminance meters. Measured values are converted from analogue to digital signals, and they are transmitted to the control PC through both the wired and wireless LAN systems. The operating system of the control PC is Wmdows 2000 and the controlling software is Visual Basic 6.0. The authors will discuss the measurement results (which are now applicable) of the following illuminances: continuing long time and maximum and simultaneous multi-points.

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 (nondrained 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.

Denitrification is an important process in the global nitrogen cycle. The genes encoding NirK and NirS (nirK and nirS), which catalyze the reduction of nitrite to nitric oxide, have been used as marker genes to study the ecological behavior of denitrifiers in environments. However, conventional polymerase chain reaction (PCR) primers can only detect a limited range of the phylogenetically diverse nirK and nirS. Thus, we developed new PCR primers covering the diverse nirK and nirS. Clone library and qPCR analysis using the primers showed that nirK and nirS in terrestrial environments are more phylogenetically diverse and 2–6 times more abundant than those revealed with the conventional primers. RNA- and culture-based analyses using a cropland soil also suggested that microorganisms with previously unconsidered nirK or nirS are responsible for denitrification in the soil. PCR techniques still have a greater capacity for the deep analysis of target genes than PCR-independent methods including metagenome analysis, although efforts are needed to minimize the PCR biases. The methodology and the insights obtained here should allow us to achieve a more precise understanding of the ecological behavior of denitrifiers and facilitate more precise estimate of denitrification in environments.

A new interstellar carbon chain molecule, C4Si, has been detected in the envelope of the evolved star IRC + 10216. This molecule is the carrier of six unidentified lines which had been detected during the molecular line survey at Nobeyama Radio Observatory. The identification was made through astronomical detections followed by quantum chemical calculations and laboratory spectroscopic experiments. The rotational constant and the centrifugal distortion constant were B(0) = 1533.77206(146) MHz and D(0) = 0.00005827(35) MHz, respectively, where the numbers in parentheses represent one standard deviation in units of the last significant digits. The rotation temperature and the column density were 15 + or - 2 K and (7 + or - 1) x 10 to the 12th/sq cm, respectively, assuming a source size of 25 arcsec.