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Paddy fields are a major source of atmospheric methane, a greenhouse gas produced by methanogens and consumed by methanotrophs in flooded soil. The inoculation of rice seeds with the bacterium Azoarcus sp. KH32C alters the rice root-associated soil bacterial community composition. The present study investigated the effects of KH32C-inoculated rice cultivation on soil methanogens and methanotrophs involved in methane emissions from a rice paddy field. KH32C-inoculated and non-inoculated rice (cv. Nipponbare) were cultivated in a Japanese rice paddy with and without nitrogen fertilizer. Measurements of methane emissions and soil solution chemical properties revealed increases in methane flux over the waterlogged period with elevations in the concentrations of dissolved methane, dissolved organic carbon, and ferrous iron, which is an indicator of soil reduction levels. Reverse transcription quantitative PCR and amplicon sequencing were used to assess the transcription of the methyl-coenzyme M reductase gene (mcrA) from methanogens and the particulate methane monooxygenase gene (pmoA) from methanotrophs in paddy soil. The results obtained showed not only the transcript copy numbers, but also the compositions of mcrA and pmoA transcripts were related to methane flux. KH32C-inoculated rice cultivation recruited soil methanogens and methanotrophs that suppressed high methane synthesis, increased methane consumption, and decreased methane emissions by 23.5 and 17.2% under non-fertilized and nitrogen-fertilized conditions, respectively, while maintaining rice grain yield. The present study demonstrated the mitigation of paddy field methane emissions arising from the use of KH32C in rice cultivation due to its influence on the compositions of soil methanogen and methanotroph populations.

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...

γ-Hexachlorocyclohexane (γ-HCH)-degrading strain, Sphingobium sp. TA15, was newly isolated from an experimental field soil from which the archetypal γ-HCH-degrading strain, S. japonicum UT26, was isolated previously. Comparison of the complete genome sequences of these 2 strains revealed that TA15 shares the same basic genome backbone with UT26, but also has the variable regions that are presumed to have changed either from UT26 or from a putative common ancestor. Organization and localization of lin genes of TA15 were different from those of UT26. It was inferred that transposition of IS6100 had played a crucial role in these genome rearrangements. The accumulation of toxic dead-end products in TA15 was lower than in UT26, suggesting that TA15 utilizes γ-HCH more effectively than UT26. These results suggested that genome evolution related to the γ-HCH metabolic function in the soil microbial population is ongoing.

Burial of the surface soil by volcanic ash deposition plays roles in organic matter accumulation. Assuming that decomposition of the buried humus is limited solely by labile substrate inputs, gluco...

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.

Excess nitrate (NO

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.

Excessive input of nitrogen fertilizer causes nitrogen pollution in aquatic environments. Utilizing microbial inoculants seems to be effective in decreasing the extent of nitrogen fertilize...

Denitrification in paddy soils is an environmentally important reaction, which reduces leaching or emission of nitrogen pollutants. This reaction has long been considered to be driven by typical denitrifiers mostly belonging to Alpha-, Beta-, and Gammaproteobacteria. Our recent metatranscriptomic analysis of rice paddy field soil suggested that paddy soil denitrification is a cooperative process of different nitrogen oxide reducers, i.e., NO2−, NO, and N2O reducers. However, it was not clear whether denitrification actually occurred in the soil samples examined, which was not easy to confirm under field conditions. Therefore, we carried out this study (1) to establish a soil microcosm with the steady activity of denitrification, and (2) to identify microbial communities, which drive each step of denitrification in the soil microcosm by metatranscriptomic analysis. As a result, a chemostat-type soil microcosm with steady denitrification activity was successfully established. Metatranscriptomic anal...

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 soil microbial community actively drives biogeochemical cycling even in the plant-dormant season of winter in temperate forests. The northern ecosystems are experiencing considerable winter climate change, which causes the snowpack to become thinner and the soil freeze-thaw cycles to occur more frequently in winter. These climatic and edaphic changes may affect the microbial community function. This study aimed to characterize the soil microbial community's response to winter climate change and its consequences in nitrogen (N) cycling. We conducted a large-scale snow removal experiment in a cool-temperate forest in northern Japan to simulate a winter climate change and assessed the abundance of total bacteria and fungi and ammonia oxidizers and the bacterial community composition throughout a year. This experiment indicated that snowpack decline prolonged the soil freeze-thaw period, which increased the carbon (C) availability to soil microbes in winter. The soil microbial community then sensitively responded by increasing the abundance and shifting the composition based on each taxon's absolute and relative abundances in the way that was phylogenetically patterned, which further activated microbial N cycling. However, the soil microbial community's high resilience driven by the C availability prevented the functional and compositional responses to winter climate change from persisting into the plant-growing season, which left no apparent cascading effect on the soil microbial community and N content during the plant-growing season. This study highlights the sensitive and phylogenetically patterned response of the soil microbial community to the change in soil nutrient availability and its high resilience under winter climate change in a forest.

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.

The nutrition and flavor of cheese are generated by the microbial community. Thus, horse milk cheese with unique nutrition and flavor, an increasingly popular local cheese of the Xinjiang Uygur Autonomous Region of China, is considered to have diverse and specific bacterial community. To verify this hypothesis, horse, cow, and goat milk cheese samples produced under the same environmental conditions and manufacturing process were collected, and the 16S rRNA gene was targeted to determine the bacterial population size and community composition by real‐time quantitative PCR and high‐throughput sequencing. The bacterial community of horse milk cheese had a significantly larger bacterial population size, greater species richness, and a more diverse composition than those of cow and goat milk cheeses. Unlike the absolute dominance of Lactococcus and Streptococcus in cow and goat milk cheeses, Lactobacillus and Streptococcus dominated the bacterial community as the starter lactic acid bacteria in horse milk cheese. Additionally, horse milk cheese also contains a higher abundance of unclassified secondary bacteria and specific secondary bacteria (e.g., Psychrobacter, Sulfurisoma, Halomonas, and Brevibacterium) than cow and goat milk cheeses. These abundant, diverse, and specific starter lactic acid bacteria and secondary bacteria may generate unique nutrition and flavor of horse milk cheese., We collected horse, cow, and goat milk cheese samples produced via the same manufacturing process and under the same environmental conditions, and investigated the bacterial population size and community composition by real‐time quantitative PCR and high‐throughput sequencing. We found that the bacterial community of horse milk cheese had a significantly larger bacterial population size, greater species richness, and a more diverse composition than those of cow and goat milk cheeses. Horse milk cheese also had different starter lactic acid bacteria and secondary bacteria from cow and goat milk cheeses, this may be associated with the differences in the nutritional metabolism and flavor formation between horse milk cheese and cow and goat milk cheeses.

Purpose As a potential tool for the biodegradation of nitrogen contaminants, including nitrate, nitrite, and ammonium, in pickled foods with high salinity, the halophilic and denitrifying archaeal strain Halomicrobium sp. ZPS1 was isolated from edible salt particles. Methods Under anaerobic and static culture conditions, Halomicrobium sp. ZPS1 could simultaneously degrade nitrate, nitrite, and ammonium in liquid medium with 18% salinity and generate N2O. To gain insight into these physiological characteristics, the complete genome of Halomicrobium sp. ZPS1 was sequenced to reveal the mechanism of nitrogen metabolism associated with salt-tolerance. Result The complete genome sequencing revealed a genome size of 3,094,203 bp with a circular chromosome and a GC content of 65.64%. Based on gene annotation, 3191 CDSs, 6 rRNA genes, and 76 tRNA genes were identified. Moreover, 28 genes were annotated as related to salt tolerance, ammonium assimilation, and a truncated denitrification pathway. Conclusion The annotated functional genes indicate that Halomicrobium sp. ZPS1 could be a candidate strain for the simultaneous removal of nitrate, nitrite, and ammonia in extremely high salt environments.

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.

Introduction & objectives: Over ten thousand years, soils have been formed through events of volcanic ash deposition in Hokkaido, Japan. The soil organic matter (SOM) in the past surface layer has been buried in the deeper soil. The buried humic horizons serve as a large carbon (C) reservoir. The SOM in the deeper soil horizons is preserved due to lower microbial activities and limited inputs of fresh organic matters. However, when the buried humic horizons are exposed to the surface by deep plowing and bottom plow tillage, decomposition of the exposed SOM may be accelerated through priming effects, due to the increased supply of low-molecular-weight (LMW) substances from fresh plant litter inputs. To test this, we examined glucose concentration dependency of priming effect and the change of SOC balance through priming effect using 13C tracer incubation.Materials & methods: Soil samples were collected from the volcanic soil profiles in pasture site and adjacent forest sites in Hokkaido, Japan. The moist soils were sieved (< 4 mm) to eliminate plant debris and stones for the incubation study and the other analysis. A 13C-glucose solution (99 atom%; 0 – 3.9 mg glucose g-1) was added to moist soil (equivalent to 10 g oven-dried weight) and incubated at 20ºC in the dark for 30 days. The head space gas sample was periodically taken into the vial, and 13CO2 and 12CO2 concentrations were determined by GC-MS. Priming effect (PE) was calculated by subtraction between the amounts of 12CO2 with and without glucose. The head space gas in the bottle was flush out and replaced to CO2-free-air every sampling time. We also measured soil microbial biomass C (MBC) by chloroform fumigation method, bacterial and fungal biomass by 16S and 18S rRNA genes targeted real-time PCR, SOC concentrations, inorganic N concentrations (ammonium and nitrate) and the other physicochemical properties of the soil profiles.Results & discussion: Glucose addition induced the positive PEs in the buried humic soil samples of both sites, and the magnitudes of PEs (cumulative primed-CO2 amounts) in the buried humic soil samples were 0.4 to 1.5 times as those in the surface soils. However, the negative PEs were detected in the forest surface soil, probably because of low soil pH and relatively high inorganic N concentration. The magnitudes of PEs were dependent on added glucose concentrations for all the soils, and the threshold between negative and positive PEs corresponded to 3.5 % of glucose-C relative to MBC in the forest surface soil. The positive correlation between evolution rates of primed-CO2 significantly and bacterial or fungal biomass suggests both bacteria and fungi contributes to PE in the soils studied. Even if glucose addition induced PE, total SOC after incubation increased when glucose-C was added more than 0.5 mg C g-1 in the all soils. This implies that the optimized fresh litter input can control priming effects and C sequestration in volcanic soils.

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.

The soil microbial community plays essential roles in bioavailable nitrogen (N) cycling, and microbial dynamics during the plant dormant season could affect N cycling in the subsequent growing season. Despite frequent observations of seasonal shifts in microbial community composition in forests, the biogeochemical consequences for bioavailable N cycling have not been well characterized. Here we examine the relationship between microbial community dynamics and bioavailable N dynamics throughout a year in a cool-temperate deciduous forest, with a focus on the dormant season. Specifically, we analyzed temporal changes in abundances of N-cycling microbial populations and N concentrations and transformations in soils. We also assessed temporal changes in bacterial community composition by deep sequencing of 16S rRNA genes. Even though the bacterial community composition was stable throughout the year, we found a drastic increase in abundances of total bacterial and fungal populations in the mid-winter, followed by a subsequent decrease during the snowmelt period in the early spring. We also found a temporary increase in abundances of NH3-oxidizing bacterial population in the mid-winter and of denitrifying bacterial and fungal populations during the snowmelt period. Correspondingly, soil NH4+, NO3−, and dissolved organic N concentrations sequentially peaked in the winter and early spring. These results suggest that successive growth of litter degraders, ammonifiers, nitrifiers, and denitrifiers in the dormant season drives the subsequent bioavailable N transformations. High microbial N metabolic activities during the dormant season could also support plant growth during the growing season and increase the efficiency of annual N cycling in the forest via the seasonal partitioning of N between plants and microbial communities.

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.

In southern China, high levels of atmospheric nitrogen (N) are being deposited in forests. Soil acidification and high rates of soil nitrification and subsequent NO 3 − leaching have been observed in the N-saturated forests. We previously did not detect NH 3 -oxidizing bacteria in non-N-saturated or N-saturated forest soils. However, NH 3 -oxidizing archaea were present in both soils, more in the saturated ones. The purpose of this study was to investigate the roles of autotrophic NH 3 -oxidizing archaea and heterotrophic nitrifiers in soil N transformations in N-saturated and non-N-saturated forests in southern China. We investigated the contribution of heterotrophic nitrifiers in the soils by determining the gross nitrification rates with and without an inhibitor of autotrophic nitrification, acetylene (C 2 H 2 ). We also reevaluated nitrification by NH 3 -oxidizing archaea by correlating the C 2 H 2 -inhibited gross nitrification rates with the abundance of the amoA transcripts of NH 3 -oxidizing archaea. We further measured the gross NH 4 + production rates and analyzed the community composition of the NH 3 -oxidizing archaea. The results suggest that NH 3 -oxidizing archaea, rather than heterotrophic nitrifiers and NH 3 -oxidizing bacteria, are responsible for the nitrification in the N-saturated forest soils. NH 3 -oxidizing archaea in the soils could be acidophilic, having low amoA diversity, indicating their strong adaptation to the highly acidified soils. The gross NH 4 + production rate did not differ between N-saturated and non-N-saturated forests; however, the gross nitrification rate was higher in N-saturated forests. Consequently, the high abundance and NH 3 oxidation activity of NH 3 -oxidizing archaea caused the high rates of nitrification and subsequent leaching of NO 3 − in the N-saturated forest. This study suggests that acidophilic NH 3 -oxidizing archaea have a great impact on soil N cycling in N-saturated forests.

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...

Condensed tannins are a class of plant secondary metabolites which are formed by the condensation of flavanols, and play an important role in plant-soil-microbes interactions by influencing the colonisation of arbuscular mycorrhizal (AM) fungi. The aim of this study was to determine the influence of AM fungi on condensed tannins concentrations in roots, stems and leaves of birdsfoot trefoil (Lotus japonicus L.). The concentrations of condensed tannins in roots, stems and leaves of the Lotus japonicus plants were measured using histochemical staining and spectrophotometry. The extent of AM fungal colonisation in roots was also quantified. Soluble and insoluble condensed tannins concentrations in roots were lower in plants inoculated with AM fungi but higher in stems and leaves compared to plants not inoculated with AM fungi. The higher concentration of condensed tannins in the stems and leaves were associated with AM fungi colonisation of roots. This had increased animal feed value and also could be influenced by the plant-soil-microbes feedback processes.

Nitrite reductase is a key enzyme for denitrification. There are two types of nitrite reductases: copper-containing NirK and cytochrome cd1-containing NirS. Most denitrifiers possess either nirK or nirS, although a few strains been reported to possess both genes. We herein report the presence of nirK and nirS in the soil-denitrifying bacterium Bradyrhizobium sp. strain TSA1T. Both nirK and nirS were identified and actively transcribed under denitrification conditions. Based on physiological, chemotaxonomic, and genomic properties, strain TSA1T (=JCM 18858T=KCTC 62391T) represents a novel species within the genus Bradyrhizobium, for which we propose the name Bradyrhizobium nitroreducens sp. nov.

Elucidating the soil phosphorus cycle driven by soil microbes is a vital question in soil microbial ecology. The Japanese arable Andisols, occupying half of the Japanese cropland, are known for their high phosphorus sorption capacity. However, limited information is currently available on microbially driven phosphorus mineralization in arable Andisols. We herein report that the phosphorus-mineralizing community in the Japanese arable Andisols showed characteristic distribution and composition patterns, from those in other types of soils. We performed a chemical analysis and microbial community analysis of 43 amble Andisols along the Japanese archipelago. Soil phosphomonoesterase activities measured at pH 11 were approximately 70% of those at pH 6.5, which indicates that alkaline phosphatase contributes to phosphorus cycling, although most soil samples were acidic. Functional gene predictions based on 16S rRNA gene sequencing indicated that the alkaline phosphatase gene phoD was more abundant than other alkaline phosphatase genes and, thus, plays major roles. Hence, amplicon sequencing targeting phoD was performed and the results obtained showed that alphaproteobacterial phoD was dominant. This is in contrast to previously reported phoD compositions in other soils and may be attributed to the nutrient conditions in arable Andisols, which favor copiotrophic Alphaproteobacteria. Furthermore, the composition of phoD correlated with soil pH and bioavailable phosphorus concentrations rather than carbon or nitrogen concentrations. These results were partly different from previous findings, varying in the soil types and geographic ranges of sampling sites. Collectively, the present results indicate that the phosphorus-mineralizing community in the Japanese arable Andisols is regulated differently from those in other soil types., Article, MICROBES AND ENVIRONMENTS. 33(3):282-289 (2018)

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.

Azospirillum sp. strains TSA2S and TSH100 are plant growth-promoting rhizobacteria with the capacity to mitigate N2O from agricultural soil. They were isolated from the rhizosphere of paddy soil in Tokyo, Japan. Here, we present the genome sequences of these two strains.

Azospirillum sp. strains TSA2S and TSH100 are plant growth-promoting rhizobacteria with the capacity to mitigate N 2 O from agricultural soil. They were isolated from the rhizosphere of paddy soil in Tokyo, Japan. Here, we present the genome sequences of these two strains.

We tested the ecosystem functions of microbial diversity with a focus on ammonification (involving diverse microbial taxa) and nitrification (involving only specialized microbial taxa) in forest nitrogen cycling. This study was conducted on a forest slope, in which the soil environment and plant growth gradually changed. We measured the gross and net rates of ammonification and nitrification, the abundance of predicted ammonifiers and nitrifiers, and their community compositions in the soils. The abundance of predicted ammonifiers did not change along the soil environmental gradient, leading to no significant change in the gross ammonification rate. On the other hand, the abundance of nitrifiers and the gross nitrification rate gradually changed. These accordingly determined the spatial distribution of net accumulation of ammonium and nitrate available to plants. The community composition of predicted ammonifiers gradually changed along the slope, implying that diverse ammonifiers were more likely to include taxa that were acclimated to the soil environment and performed ammonification at different slope locations than specialized nitrifiers. Our findings suggest that the abundance of ammonifiers and nitrifiers directly affects the corresponding nitrogen transformation rates, and that their diversity affects the stability of the rates against environmental changes. This study highlights the role of microbial diversity in biogeochemical processes under changing environments and plant growth.