Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1007/s00248-019-01378-8

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier Ltd  

In southern China, high levels of atmospheric nitrogen (N) are being deposited in forests. Soil acidification and high rates of soil nitrification and subsequent NO3 − leaching have been observed in the N-saturated forests. We previously did not detect NH3-oxidizing bacteria in non-N-saturated or N-saturated forest soils. However, NH3-oxidizing archaea were present in both soils, more in the saturated ones. The purpose of this study was to investigate the roles of autotrophic NH3-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 (C2H2). We also reevaluated nitrification by NH3-oxidizing archaea by correlating the C2H2-inhibited gross nitrification rates with the abundance of the amoA transcripts of NH3-oxidizing archaea. We further measured the gross NH4 + production rates and analyzed the community composition of the NH3-oxidizing archaea. The results suggest that NH3-oxidizing archaea, rather than heterotrophic nitrifiers and NH3-oxidizing bacteria, are responsible for the nitrification in the N-saturated forest soils. NH3-oxidizing archaea in the soils could be acidophilic, having low amoA diversity, indicating their strong adaptation to the highly acidified soils. The gross NH4 + 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 NH3 oxidation activity of NH3-oxidizing archaea caused the high rates of nitrification and subsequent leaching of NO3 − in the N-saturated forest. This study suggests that acidophilic NH3-oxidizing archaea have a great impact on soil N cycling in N-saturated forests.

DOI： 10.1016/j.soilbio.2018.04.021

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Language：Japanese   Publishing type：Research paper (scientific journal)  

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Language：English   Publishing type：Research paper (scientific journal)  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SOC BIOSCIENCE BIOENGINEERING JAPAN  

The inhibitory effect of 20 substances of various chemical species on the anaerobic ammonia oxidation (anammox) activity of an enrichment culture, predominated by Candidatus Brocadia, was determined systematically by using a N-15 tracer technique. The initial anammox rate was determined during first 25 min with a small-scale anaerobic batch incubation supplemented with possible inhibitors. Although Cu2+ and Mn2+ did not inhibit anammox, the remaining 18 substances [Ni2+, Zn2+, Co2+, Moo(4)(2-), Fe2+, 4 amines, ethylenediaminetetraacetic acid (EDTA), ethylenediamine-N,N'-bis (2-hydroxyphenylacetic acid) (EDDHA), citric acid, nitrilotriacetic acid (NTA), N,N-dimethylacetamide (DMA), 1,4-dioxane, dimethyl sulfoxide (DMSO), N,N-dimethylformamide (DMF) and tetrahydrofuran (THF)] were inhibitory. Inhibitory effect of NTA, EDDHA, THF, DMF, DMA and amines on anammox was first determined in this study. Inhibitory effects of metals were re-evaluated because chelators, which may interfere inhibitory effect, have been used to dissolve metal salts into assay solution. The relative anammox activities as a function of concentration of each substance were described successfully (R-2 > 0.91) either with a linear inhibition model or with a Michaelis Menten-based inhibition model. IC50 values were estimated based on either model, and were compared. The IC50 values of the 4 chelators (0.06-2.7 mM) and 5 metal ions (0.02-1.09 mM) were significantly lower than those of the 4 amines (10.6-29.1 mM) and 5 organic solvents (3.5-82 mM). Although it did not show any inhibition within 25 min, 0.1 mM Cu2+ completely inhibited anammox activity in 240 min, suggesting that the inhibitory effect caused by Cu2+ is time-dependent. (C) 2017, The Society for Biotechnology, Japan. All rights reserved.

DOI： 10.1016/j.jbiosc.2017.04.010

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ACS Publications  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PERGAMON-ELSEVIER SCIENCE LTD  

The factors controlling the relative contributions of ammonia-(NH3) oxidizing archaea (AOA) and bacteria (AOB) to nitrification and nitrous oxide (N2O) production in soil remain unclear. A study was conducted to examine the contributions of AOA and AOB to nitrification, nitrite (NO2-) accumulation, and NO2--affected N2O production in three non-cropped Oregon soils. Nitrification potential rates in the three soils ranged seven-fold from 0.15 to 1.08 mu mol N g(-1) d(-1), with AOA contributing 64-71% of the total activity. AOA- and AOB-driven NO2- accumulation represented 8-100% of total NO2- + NO3- accumulation, persisted over 48 h, and was accompanied by acetylene-sensitive, ammonium-(NH4+) stimulated N2O production. Ammonium-and NOT-dependent N2O production occurred when both AOA and AOB, or AOA alone were active. By adding the NO2--oxidizing bacteria, Nitrobacter vulgaris, to soil slurries to increase NO2--oxidizing capacity, both NO2- accumulation and N2O production were prevented, while the overall rate of nitrification was unaffected. Yields of N2O-N amounted to 0.05 +/- 0.01% of total NO2- + NO3--N accumulation in the presence of supplemental NH4+, and 0.28 +/- 0.11% in the presence of both supplemental NH4+ + NO2-. Regression analysis of the N2O production against NO2- accumulation over 24 h revealed a positive, non-linear relationship for N2O production by both AOA plus AOB and by AOA alone. Values of V-max ranged 12-fold from 0.05 to 0.62 nmol N2O g(-1) d(-1), and predicted K-m values for NO2- ranged 15-fold from 0.02 to 0.30 smol NO2- g(-1) soil. These findings provide new insights into the impact of NO2- accumulation in soils on N2O production by both AOA and AOB, and show that NOT accumulation primarily drives N2O formation in these soils, and increases N2O yield by both AOA and AOB. (C) 2016 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.soilbio.2016.10.011

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：BIOMED CENTRAL LTD  

Nitrosospira briensis C-128 is an ammonia-oxidizing bacterium isolated from an acid agricultural soil. N. briensis C-128 was sequenced with PacBio RS technologies at the DOE-Joint Genome Institute through their Community Science Program (2010). The high-quality finished genome contains one chromosome of 3.21 Mb and no plasmids. We identified 3073 gene models, 3018 of which are protein coding. The two-way average nucleotide identity between the chromosomes of Nitrosospira multiformis ATCC 25196 and Nitrosospira briensis C-128 was found to be 77.2 %. Multiple copies of modules encoding chemolithotrophic metabolism were identified in their genomic context. The gene inventory supports chemolithotrophic metabolism with implications for function in soil environments.

DOI： 10.1186/s40793-016-0168-4

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCI LTD  

The impact of a sub-seabed CO2 leak from geological sequestration on the microbial process of ammonia oxidation was investigated in the field. Sediment samples were taken before, during and after a controlled sub-seabed CO2 leak at four zones differing in proximity to the CO2 source (epicentre, and 25 m, 75 m, and 450 m distant). The impact of CO2 release on benthic microbial ATP levels was compared to ammonia oxidation rates and the abundance of bacterial and archaeal ammonia amoA genes and transcripts, and also to the abundance of nitrite oxidizer (nirS) and anammox hydrazine oxidoreductase (hzo) genes and transcripts. The major factor influencing measurements was seasonal: only minor differences were detected at the zones impacted by CO2 (epicentre and 25 m distant). This included a small increase to ammonia oxidation after 37 days of CO2 release which was linked to an increase in ammonia availability as a result of mineral dissolution. A CO2 leak on the scale used within this study (<1 tonne day(-1)) would have very little impact to ammonia oxidation within coastal sediments. However, seawater containing 5% CO2 did reduce rates of ammonia oxidation. This was linked to the buffering capacity of the sediment, suggesting that the impact of a sub-seabed leak of stored CO2 on ammonia oxidation would be dependent on both the scale of the CO2 release and sediment type. (C) 2014 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.ijggc.2014.11.013

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SOC GENERAL MICROBIOLOGY  

A moderately thermophilic, aerobic, stalked bacterium (strain MA2(T)) was isolated from marine sediments in Kagoshima Bay, Japan. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain MA2(T) was most closely related to the genera Rhodobium, Parvibaculum, and Rhodoligotrophos (92-93% similarity) within the class Alphaproteobacteria. Strain MA2(T) was a Gram-stain-negative and stalked dimorphic bacteria. The temperature range for growth was 16 48 degrees C (optimum growth at 42 degrees C). This strain required yeast extract and NaCI (>1%, w/v) for growth, tolerated up to 11% (w/v) NaCl, and was capable of utilizing various carbon sources. The major cellular fatty acid and major respiratory quinone were C-18:1 omega 7c and ubiquinone-10, respectively. The DNA G + C content was 60.7 mol%. Strain MA2(T) performed denitrification and produced N2O from nitrate under strictly microaerobic conditions. Strain MA2(T) possessed periplasmic nitrate reductase (Nap) genes but not membrane-bound nitrate reductase (Nar) genes. On the basis of this morphological, physiological, biochemical and genetic information a novel genus and species, Tepidicaulis marinus gen. nov., sp. nov., are proposed, with MA2(T) (=NBRC 109643(T)=DSM 27167(T)) as the type strain of the species.

DOI： 10.1099/ijs.0.000167

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PERGAMON-ELSEVIER SCIENCE LTD  

In temperate forest ecosystems, accelerated freeze-thaw cycles caused by winter climate change are expected to affect nitrogen (N) cycling in soils. Net N mineralization and nitrification rates were investigated via incubations of sieved soils transplanted from ten temperate forest ecosystems to two northern Japan sites with natural snowfall gradients. This was done to address: 1) how freeze-thaw cycles affect N mineralization and nitrification in temperate forest soils; 2) whether freeze-thaw cycles change the soil N transformation rates in the following growing season; and 3) which soil characteristics affect the response of the N transformation rates to freeze-thaw cycles. The effect of freeze-thaw cycles on inorganic N and dissolved organic carbon productions differed among soils, that is, some soils produced more inorganic N and dissolved organic carbon in the conditions imposed by freeze-thaw cycles than in the non-frozen treatment but the others did not. The response to the freeze(t)haw cycles was explained by soil microbial activity (gross N mineralization and nitrification rate) and soil fertility (inorganic N pools in the early spring and water soluble ions). Freeze-thaw cycles significantly increased N transformation rates in the following growing season, suggesting that winter climate change might also affect nutrient availability for vegetation and soil microbes in the growing season. The magnitude and frequency of freeze-thaw cycles were considered to be important indicators of N transformation rates during the growing season, suggesting that the higher intensity of freeze-thaw cycles in the original locations of soils changed the microbial communities and functions with high tolerance to freeze-thaw cycles; this resulted in greater N transformation rates in the following growing season. Microbial activity, soil fertility and climate patterns in the original locations of soils are believed to have an effect on the response to winter climate change and to cause large variability of soil response of N transformation rates to freeze-thaw cycles in both the dormant and growing seasons. (C) 2014 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.soilbio.2014.02.022

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER JAPAN KK  

We conducted a year-round measurement of gross N transformation rates using the N-15 dilution method, and analyzed seasonal changes and the mechanisms regulating gross N transformation in the Kiryu Experimental Forest in central Japan. While soil microbial biomass C (SMB-C) decreased from the dormant to growing seasons at the organic (O) horizon, no significant trend was observed in SMB-N. This resulted in SMB-C/N being high in the dormant season and low in the growing season, and suggests that the microbial composition changed seasonally. No clear seasonal trend was found in gross NH4 (+) production rates at either the O or surface mineral soil horizons. In contrast, the NH4 (+) consumption rate varied seasonally, with high values in January and April during the dormant season and low values in July and October during the growing season. There was no clear trend in seasonal fluctuation of net NH4 (+) production rates. Gross NH4 (+) production and gross NH4 (+) consumption rates were 10 times greater than the gross nitrification rate. Almost all of the produced NH4 (+) was immobilized, indicating that N tightly cycles at this study site. Considered together with results of the gross N transformation rates, the dominance of high SMB-C/N microbes might stimulate immobilization in the dormant season. At this study site, the change in microbial composition likely influences gross N transformation through immobilization efficiency.

DOI： 10.1007/s10310-013-0391-4

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SOC GENERAL MICROBIOLOGY  

A moderately thermophilic, methanol-oxidizing bacterium (strain Gela4(T)) was isolated from methane-utilizing mixed-culture originating from marine sediment near a hydrothermal vent. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain Gela4(T) was closely related to members of the genus `Methyloligella' (94.7% similarity) within the class Alphaproteobacteria. Strain Gela4(T) was a Gram-staining-negative and aerobic organism. Cells were rod-shaped and non-motile. The temperature range for growth of strain Gela4(T) was 19 43 degrees C (optimal growth at 35 degrees C). Strain Gela4(T) tolerated up to 9% NaCl with an optimum at 1 %. The organism was a facultative methylotroph that could utilize methanol, methylamine, trimethylamine and a variety of multi-carbon compounds. The major cellular fatty acid and major respiratory quinone were C-18:1 omega 7c and ubiquinone-10, respectively. The predominant phospholipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 63.9 mol%. On the basis of the morphological, physiological, biochemical and genetic information, a novel genus and species, Methyloceanibacter caenitepidi is proposed, with Gela4(T) (=NBRC 109540(T)=DSM 27242(T)) as the type strain.

DOI： 10.1099/ijs.0.053397-0

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

Anaerobic microbial activity has a major influence on the subsurface environment. We investigated the denitrification and methanogenesis in anoxic groundwater at a depth of 140m in two boreholes drilled in a sedimentary geological setting, where the redox potential fluctuated. The average maximum potential denitrification rates, measured under anaerobic conditions in the two boreholes using an N-15 tracer, were 0.060 and 0.085nmol (30)N(2)mL(-1)h(-1). The deduced NirS amino acid sequences obtained from in situ samples were similar to those of isolates belonging to the -, -, and -Proteobacteria, and the Firmicutes (72-100% similarity). Based on the nirS gene, the same operational taxonomic unit dominated incubated samples from each borehole. Methanogenesis candidates were detected by 16S rRNA gene analysis, but no sequence was detected using primers for the functional methanogenesis gene mcrA. Although the stable isotope signatures suggested that some of the dissolved methane was of biogenic origin, no potential for methane production was evident during the incubations. The groundwater at 140m depth did not contain oxygen, had an Eh ranging from -144 to 6.8 mV, and was found to be a potential field for denitrification.

DOI： 10.1111/1574-6941.12179

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Language：English   Publishing type：Research paper (scientific journal)  

Aims: To investigate community shifts of amoA-encoding archaea (AEA) and ammonia-oxidizing bacteria (AOB) in biofilter under nitrogen accumulation process. Methods and Results: A laboratory-scale rockwool biofilter with an irrigated water circulation system was operated for 436 days with ammonia loading rates of 49-63 NH3 g m-3 day-1. The AEA and AOB communities were investigated by denaturing gradient gel electrophoresis, sequencing and real-time PCR analysis based on amoA genes. The results indicated that changes in abundance and community compositions occurred in a different manner between archaeal and bacterial amoA during the operation. However, both microbial community structures mainly varied when free ammonia (FA) concentrations in circulation water were increasing, which caused a temporal decline in reactor performance. Dominant amoA sequences after this transition were related to Thaumarchaeotal Group I.1b, Nitrosomonas europaea lineages and one subcluster within Nitrosospira sp. cluster 3, for archaea and bacteria, respectively. Conclusions: The specific FA in circulation water seems to be the important factor, which relates to the AOB and AEA community shifts in the biofilter besides ammonium and pH. Significance and Impact of the Study: One of the key factors for regulating AEA and AOB communities was proposed that is useful for optimizing biofiltration technology. © 2013 The Society for Applied Microbiology.

DOI： 10.1111/jam.12091

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Language：Japanese   Publisher：THE JAPANESE FORESTRY SOCIETY  

DOI： 10.11519/jfsc.124.0.171.0

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：GENOMIC STAND CONSORT  

Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromosome with a total of 3,553 protein coding genes and 44 RNA genes was sequenced by the DOE-Joint Genome Institute Program CSP 2006.

DOI： 10.4056/sigs.3517166

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC MICROBIAL ECOLOGY, DEPT BIORESOURCE SCIENCE  

A model system developed to produce N2O emissions from degrading soybean nodules in the laboratory was used to clarify the mechanism of N2O emission from soybean fields. Soybean plants inoculated with nosZ-defective strains of Bradyrhizobium japonicum USDA110 (Delta nosZ, lacking N2O reductase) were grown in aseptic jars. After 30 days, shoot decapitation (D, to promote nodule degradation), soil addition (S, to supply soil microbes), or both (DS) were applied. N2O was emitted only with DS treatment. Thus, both soil microbes and nodule degradation are required for the emission of N2O from the soybean rhizosphere. The N2O flux peaked 15 days after DS treatment. Nitrate addition markedly enhanced N2O emission. A N-15 tracer experiment indicated that N2O was derived from N fixed in the nodules. To evaluate the contribution of bradyrhizobia, N2O emission was compared between a nirK mutant (Delta nirK Delta nosZ, lacking nitrite reductase) and Delta nosZ. The N2O flux from the Delta nirK Delta nosZ rhizosphere was significantly lower than that from Delta nosZ, but was still 40% to 60% of that of Delta nosZ, suggesting that N2O emission is due to both B. japonicum and other soil microorganisms. Only nosZ-competent B. japonicum (nosZ+ strain) could take up N2O. Therefore, during nodule degradation, both B. japonicum and other soil microorganisms release N2O from nodule N via their denitrification processes (N2O source), whereas nosZ-competent B. japonicum exclusively takes up N2O (N2O sink). Net N2O flux from soybean rhizosphere is likely determined by the balance of N2O source and sink.

DOI： 10.1264/jsme2.ME12100

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SOC BIOSCIENCE BIOENGINEERING JAPAN  

The anoxic ammonium oxidation (anammox) process has been regarded as an attractive alternative process to treat wastewater containing high ammonium concentrations. By the implementation of anammox process at moderately low temperatures (<25 degrees C), the anammox process will be applied to more various industrial wastewater treatments. In this study, we established enrichment cultures of anammox bacteria from freshwater sediments by using an up-flow column reactor equipped with porous polyester nonwoven fabric at moderately low temperatures. Their nitrogen conversion rates reached 0.07-0.26 kg-N/m(3)/d. Phylogenetic analysis based on 16S rRNA gene from enrichment cultures revealed the presence of various anammox bacteria affiliated with unknown anammox bacteria as well as known anammox candidates, i.e., Candidatus Kuenenia stuttgartiensis and Candidatus Brocadia fulgida, Candidatus Scalindua wagneri. Anammox bacterial populations were influenced by enrichment conditions, i.e., seed sediments and temperature. (C) 2012, The Society for Biotechnology, Japan. All rights reserved.

DOI： 10.1016/j.jbiosc.2012.05.003

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PERGAMON-ELSEVIER SCIENCE LTD  

Nitrite dynamics could he highly associated with forest N cycles. However, they have often been over-looked mainly because of the experimental difficulties that occur owing to chemical reactive nature of NO2-. We investigated NO2- dynamics in an N-saturated forest soil with a recently developed method using N-15. Soils were aerobically incubated for 145 h after (NO2-)-N-15 addition, and changes in N-14 and N-15 concentrations of NO2-, NO3-, NH4+, and dissolved organic N (DON) were monitored. Simultaneous production and consumption of NO2- were observed. The turnover rate of NO2- was even faster than that of NH4+ and NO3- calculated in other studies. Of the added (NO2-)-N-15, 28.5% was oxidized to NO3- and 17.8% was incorporated into the DON pool within 4 h. The remainder might be emitted as gas or fixed by insoluble soil organic matter. Our results suggested that rapid NO2- turnover could be a major driving force for N transformations in forest soil. (C) 2012 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.soilbio.2012.04.006

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC MICROBIAL ECOLOGY, DEPT BIORESOURCE SCIENCE  

An anammox assay involving a N-15 tracer and gas chromatography-mass spectrometry revealed that the potential anammox activity accounted for 1 to 5% of total N-2 production in a ravine paddy field, Japan. Among four 4-cm-deep layers, the top layer showed the highest activity. Clone libraries showed that the DNA in the top layer contained sequences related to those of Candidatus 'Brocadia fulgida', Ca. 'B. anammoxidans', and Ca. 'Kuenenia stuttgartiensis'. These results suggest that a specific population of anammox bacteria was present in paddy soils, although a small part of dinitrogen gas was emitted from the soil via anammox.

DOI： 10.1264/jsme2.ME11330

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：WILEY-BLACKWELL  

Nitrification has been believed to be performed only by autotrophic ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) until the recent discovery of ammonia-oxidizing archaea (AOA). Meanwhile, it has been questioned whether AOB are significantly responsible for NH3 oxidation in acidic forest soils. Here, we investigated nitrifying communities and their activity in highly acidified soils of three subtropical forests in southern China that had received chronic high atmospheric N deposition. Nitrifying communities were analyzed using PCR- and culture (most probable number)-based approaches. Nitrification activity was analyzed by measuring gross soil nitrification rates using a 15N isotope dilution technique. AOB were not detected in the three forest soils: neither via PCR of 16S rRNA and ammonia monooxygenase (amoA) genes nor via culture-based approaches. In contrast, an extraordinary abundance of the putative archaeal amoA was detected (3.2 x 1081.2 x 109 g soil-1). Moreover, this abundance was correlated with gross soil nitrification rates. This indicates that amoA-possessing archaea rather than bacteria were predominantly responsible for nitrification of the soils. Furthermore, sequences of the genus Nitrospira, a dominant group of soil NOB, were detected. Thus, nitrification of acidified subtropical forest soils in southern China could be performed by a combination of AOA and NOB.

DOI： 10.1111/j.1574-6941.2011.01294.x

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：TAYLOR & FRANCIS LTD  

Measurements of gross NH (4) (+) and NO (3) (-) production in forest soils were conducted using the N-15 pool dilution method. Mineral topsoils (0-10 cm depth) were collected from four forests from northern to southern Japan with a natural climate gradient to elucidate the mechanisms regulating gross nitrification rates in forest soils. Additionally, we attempted to evaluate the relative importance of heterotrophic nitrification in gross total nitrification using acetylene as a specific inhibitor of autotrophic nitrification. Distinct differences were found among sites in the gross rates of NH (4) (+) production (3.1-11.4 mg N kg(-1) day(-1)) and gross total nitrification (0.0-6.1 mg N kg(-1) day(-1)). The rates of gross heterotrophic nitrification were low in this study, indicating that heterotrophic nitrification is of minor importance in most forest mineral topsoils in Japan. Significant relations were found between gross autotrophic nitrification and gross NH (4) (+) production, soil N, and soil C concentrations, but none was found between gross autotrophic nitrification and soil pH. We determined the critical value of the gross NH (4) (+) production rates for gross autotrophic nitrification under which no gross autotrophic nitrification occurred, as well as the critical soil C/N ratio above which gross autotrophic nitrification ceased. Results show that tight coupling of production and consumption of NH (4) (+) prevents autotrophic nitrifiers from utilizing NH (4) (+) as long as NH (4) (+) availability is low.

DOI： 10.1007/s10310-011-0287-0

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER SOC MICROBIOLOGY  

Nitrosomonas sp. strain AL212 is an obligate chemolithotrophic ammonia-oxidizing bacterium (AOB) that was originally isolated in 1997 by Yuichi Suwa and colleagues. This organism belongs to Nitrosomonas cluster 6A, which is characterized by sensitivity to high ammonia concentrations, higher substrate affinity (lower Km), and lower maximum growth rates than strains in Nitrosomonas cluster 7, which includes Nitrosomonas europaea and Nitrosomonas eutropha. Genome-informed studies of this ammonia-sensitive cohort of AOB are needed, as these bacteria are found in freshwater environments, drinking water supplies, wastewater treatment systems, and soils worldwide.

DOI： 10.1128/JB.05521-11

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC MICROBIAL ECOLOGY, DEPT BIORESOURCE SCIENCE  

Twenty-five replicates of growth medium for anaerobic ammonium oxidation (anammox) containing (15)N-labeled ammonium and non-labeled nitrite were inoculated into an anammox enrichment culture at low density, and anaerobically incubated batchwise. In the headspace, (29)N(2) partial pressure linearly increased via anammox in 25 vials, confirming that anammox populations were viable in all subcultures. On prolonged incubation, exponential increases in (29)N(2) were not observed in all but 13 subcultures, suggesting that the anammox population may not proliferate unless all conditions for growth are satisfied. The estimated first-order rate coefficients in those 13 subcultures varied from 0.0029 to 0.0048 h(-1).

DOI： 10.1264/jsme2.ME10181

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC MICROBIAL ECOLOGY, DEPT BIORESOURCE SCIENCE  

Although the emission of N(2) via anaerobic ammonium oxidation (anammox) is a key process in the elimination of nitrogenous compounds from aquatic environments, little information is available regarding its significance and the relevant microorganisms (anammox bacteria) in eutrophic freshwater lakes. In the present study, the anammox bacteria in the sediment of a eutrophic lake in Japan, Lake Kitaura, were examined using a (15)N-tracer technique to measure their potential anammox activity. Potential anammox activity was localized to the northern region of the lake where a stable supply of both NH(4)(+) and NO(3)(-) existed in the sediment. These results suggest the contribution of anammox bacteria to the total emission of N(2) from sediment in this eutrophic lake to not be negligible. Moreover, selective PCR successfully amplified anammox bacteria-related (Brocadiales-related) 16S rRNA genes from sediment samples in which potential anammox activity was observed. The clone libraries consisted of diverse phylotypes except the genus "Scalindua"-lineages, and the lineages of genus "Brocadia" were dominantly recovered, followed by the genus "Kuenenia"-lineages. Most of them, however, were novel and phylogenetically distinguishable from known Brocadiales species. A unique population of anammox bacteria inhabits and potentially contributes to the emission of N(2) from Lake Kitaura.

DOI： 10.1264/jsme2.ME10184

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1264/jsme2.ME10184

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC MICROBIAL ECOLOGY, DEPT BIORESOURCE SCIENCE  

Mangrove forests are common in subtropical regions, and have received considerable attention as vegetative buffers against anthropogenic N-loading. In this study, we investigated anaerobic ammonium oxidation (anammox) as one of potentially important microbial N-removing pathways in mangrove and shrimp pond sediment in Haiphong, Vietnam. Measurements with (15)N-labeled compounds demonstrated the occurrence of anammox in sediment of mangrove forest and a water channel connecting shrimp ponds to the sea in both 2005 and 2007, and of a semi-intensive shrimp pond in 2005. The rate of potential anammox activity reached to 0.7 nmol-N(2) cm(-3) h(-1), although the contribution of anammox was less significant than denitrification. Anammox-type 16S rRNA gene fragments phylogenetically related to 'Scalindua' species were predominantly recovered from mangrove forest and water channel sediment in a PCR-clone library analysis targeting anammox bacteria. 'Kuenenia'-like gene fragments were also recovered from shrimp pond sediment as the major component. We demonstrated the occurrence of potential anammox activity, and suggested the possibility that diverse species of uncultured anammox bacteria contribute to the nitrogen cycle in subtropical mangrove-aquaculture ecosystems. Furthermore, this study provides new insight into the biogeography of anammox bacteria: 'Scalindua' and 'Kuenenia'-like species coexisted in the blackish sediment as in some temperate estuarine sediment.

DOI： 10.1264/jsme2.ME10150

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC MICROBIAL ECOLOGY, DEPT BIORESOURCE SCIENCE  

The measurement of N-15 concentrations in environmental samples requires sophisticated pretreatment devices and expensive isotope-ratio mass spectrometry (IRMS). This report describes the use of a gas chromatograph equipped with a quadrupole-type mass spectrometer (GC/MS) to measure N-15 concentrations of ammonium, nitrate, nitrite, and total dissolved nitrogen (TDN) in distilled water, a 2 M KCl solution and a 0.5 M K2SO4 solution. The system measures nitrous oxide (N2O) that is ultimately converted from the target N compound, requiring no special apparatus such as a purge-and-trap pretreatment device. It uses a denitrifier lacking N2O reductase, which produces N2O from nitrate. Persulfate oxidation was applied to convert TDN to nitrate, while additional pretreatment with ammonia diffusion was required for ammonium prior to the persulfate oxidation. Up to 100 samples can be measured daily using the system. We can generally run N-15 measurements with only 1-10 mL of sample for each chemical species of N, a volume 1/10-1/100 times smaller than the amount necessary for conventional methods. Our method is useful for measuring N-15 with GC/MS, offering greater convenience than IRMS.

DOI： 10.1264/jsme2.ME10159

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC MICROBIAL ECOLOGY, DEPT BIORESOURCE SCIENCE  

The measurement of N-15 concentrations in environmental samples requires sophisticated pretreatment devices and expensive isotope-ratio mass spectrometry (IRMS). This report describes the use of a gas chromatograph equipped with a quadrupole-type mass spectrometer (GC/MS) to measure N-15 concentrations of ammonium, nitrate, nitrite, and total dissolved nitrogen (TDN) in distilled water, a 2 M KCl solution and a 0.5 M K2SO4 solution. The system measures nitrous oxide (N2O) that is ultimately converted from the target N compound, requiring no special apparatus such as a purge-and-trap pretreatment device. It uses a denitrifier lacking N2O reductase, which produces N2O from nitrate. Persulfate oxidation was applied to convert TDN to nitrate, while additional pretreatment with ammonia diffusion was required for ammonium prior to the persulfate oxidation. Up to 100 samples can be measured daily using the system. We can generally run N-15 measurements with only 1-10 mL of sample for each chemical species of N, a volume 1/10-1/100 times smaller than the amount necessary for conventional methods. Our method is useful for measuring N-15 with GC/MS, offering greater convenience than IRMS.

DOI： 10.1264/jsme2.ME10159

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ELSEVIER SCIENCE BV  

We modified and tuned a commercial model of a gas chromatography/mass spectrometry (GC/MS) instrument to develop a simple and rapid method for the simultaneous quantification of a variety of gas species. Using the developed method with the newly modified instrument, gas species such as H(2), N(2), O(2), CO, NO, CH(4), CO(2), and N(2)O, which are common components of microbial metabolism, were accurately identified based on their retention times and/or mass-to-charge ratios (m/z) in less than 2.5 min. By examining the sensitivities and dynamic ranges for the detection of H(2), N(2), O(2), CH(4), CO(2), and N(2)O, it was demonstrated that the method developed in this study was sufficient for accurately monitoring the production and the consumption of these gaseous species during microbial metabolism. The utility of the new method was demonstrated by a denitrification study with Pseudomonas aureofaciens ATCC 13985(T). This method will be suitable for a variety of applications requiring the identification of gaseous metabolites in microorganisms, microbial communities, and natural ecosystems. (C) 2010 Elsevier B.V. All rights reserved.

DOI： 10.1016/j.mimet.2010.10.009

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Language：Japanese   Publishing type：Research paper (scientific journal)  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：DESALINATION PUBL  

We are studying the nitrogen removal function of wetlands (rice paddy fields) The site of our investigation was polluted by nitrogen ground water from upland fields in which nitrogen fertilizer and animal manure were overused. We carried out an experiment with the aim of improving the purification capacity of these fields from 2006 to 2008 Two test plots were used Both had been non-vegetation plots since 1991 A temperature rise effect was higher in the tunnel plot than in the open-air plot. Temperatures were observed at 1-h intervals by automatic record thermometers The average temperatures were 18 9 degrees C for the tunnel plot and 16 6 degrees C for open-air plot. The average amount of nitrogen removal was 5574 kg ha(-1) y(-1) in the open-air plot and 661 8 kg ha(-1) y(-1) in the tunnel plot The amount of nitrogen removal in the tunnel plot reached a level 104 4 kg ha(-1) y(-1) larger than the open-air plot This means that the thermal effect of the tunnel plot was higher than in the open-air plot. The denitrification and ANAMMOX activity ratio in August was 5 1 in the open-air plot, but there was no ANAMMOX activity in the tunnel plot

DOI： 10.5004/dwt.2010.1907

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SPRINGER  

Although, there have been many published bacterial strains aerobically degrading the heterocyclic amine compounds, only one strain to date has been reported to degrade pyrrolidine under denitrifying conditions. In this study, denitrifying bacteria degrading pyrrolidine and piperidine were isolated from diverse geological and ecological origins through selective enrichment procedures. Based on the comparative sequence results of 16S rRNA genes, 30 heterocyclic amine-degrading isolates were grouped into ten distinct phylotypes belonging to the genera Thauera, Castellaniella, Rhizobium, or Paracoccus of the phylum Proteobacteria. The representative isolates of individual phylotypes were characterized by phylogenetic, phenotypic and chemotaxonomical traits, and dissimilatory nitrite reductase gene (nirK and nirS). All isolates completely degraded pyrrolidine and piperidine under both aerobic and anaerobic conditions. The anaerobic degradations were coupled to nitrate reduction. A metabolic pathway for the anaerobic degradation of pyrrolidine was proposed on the basis of enzyme activities implicated in pyrrolidine metabolism from three isolates. The three key pyrrolidine-metabolizing enzymes pyrrolidine dehydrogenase, gamma-aminobutyrate/alpha-ketoglutarate aminotransferase, and succinic semialdehyde dehydrogenase, were induced by heterocyclic amines under denitrifying conditions. They were also induced in cells grown aerobically on heterocyclic amines, suggesting that the anaerobic degradation of pyrrolidine shares the pathway with aerobic degradation.

DOI： 10.1007/s00203-008-0452-9

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Language：English   Publisher：JAPANESE SOC MICROBIAL ECOLOGY, DEPT BIORESOURCE SCIENCE  

DOI： 10.1264/jsme2.ME08541e

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J-GLOBAL

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Language：English   Publishing type：Research paper (scientific journal)  

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Language：English   Publishing type：Research paper (scientific journal)  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC MICROBIAL ECOLOGY, DEPT BIORESOURCE SCIENCE  

Denitrification activity and bacterial community constituents were investigated in both well-drained and poorly drained soils of a temperate forest in central Japan by N-15 tracer experiments and a cloning-sequencing approach. Denitrification activity was much higher in wet soil than in dry soil, based on (NN)-N-15-N-15 (N-30(2)) and (NNO)-N-15-N-15 ((N2O)-N-46) production. Labeled nitrate ((NO3-)-N-15) was immediately reduced to N-30(2) in wet soil, whereas it was only reduced to (N2O)-N-46 in dry soil. Thus, the wet soil at the lower end of the catchment is a functional site for the scavenging for NO3- and N2O. Nitrite reductase gene (nirK and nirS) fragments from these soils were PCR amplified, cloned, and sequenced. Both nirK and nirS fragments were detected in the wet soil, whereas only nirK fragments were detected in the dry soil. All the nirK and nirS clones showed less than 90% similarity to known clones. Numerous operational taxonomic units for nirK and nirS were found in the wet soil, Considerable diversification within the largest clade on the nirK phylogenetic tree, which contained no known sequence, was observed in wet soil. Thus, a wet soil environment can provide both the habitat and conditions for the expression of denitrification activity.

DOI： 10.1264/jsme2.ME08541

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC MICROBIAL ECOLOGY, DEPT BIORESOURCE SCIENCE  

A first assessment of anammox activity, which is a unique N-2 emission process, was conducted in samples of coastal marine sediment from Japan with a N-15 tracer. The occurrence and diversity of bacteria possibly responsible for the anammox process were also evaluated by selective PCR-amplification of the 16S rRNA gene for known anammox bacteria. Anammox activity, detected by measuring (NN)-N-14-N-15 gas production, was only found in samples collected at the intertidal sand bank located at the Yodo River estuary. In the Yodo River samples, 16S rRNA gene fragments affiliated with the known anammox bacterial lineage were also recovered, and the two major phylotypes were both "Candidatus Scalindua wagneri" relatives with 95% and 98% sequence similarity. Even from the other samples in which no recognizable anammox activity was detected, 16S rRNA gene fragments related to known anammox bacteria, but not to "Ca. S. wagneri", were detected. This is the first report of anammox-mediated N-2 emission in coastal marine environments in Japan. Notably, the PCR-based analysis allowed us to discover unexpected phylogenetic diversity of anammox bacteria-related 16S rRNA gene sequences. The selective PCR primer set developed in this study could be a powerful tool to unveil the ecology of anammox bacteria in natural environments.

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：独立行政法人産業技術総合研究所特許生物寄託センター  

CiNii Books

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PERGAMON-ELSEVIER SCIENCE LTD  

An anaerobic continuous-flow fixed-bed column reactor capable of degrading 3-chlorobenzoate (3-CBA) under denitrifying conditions was established, and its rate reached 2.26 mM d(-1). The denitrifying population completely degraded 3-CBA when supplied at 0.1-0.54 mM, but its activity was partly suppressed when 3-CBA was supplied at 0.89 mM. Nitrate was concomitantly consumed throughout the operation of the reactor, the amount of which was similar to or up to 35% higher than the theoretical stoichiometric value that was calculated by assuming that 3-CBA degradation is coupled with denitrification. Batch incubation experiments proved that nitrate is strictly required for 3-CBA degradation in the absence of molecular oxygen. The population also degraded 3-CBA aerobically. Benzoate and 4-CBA were degraded under denitrifying conditions as well as 3-CBA, but 2-CBA was not. Considering that the previously reported denitrifying 3-CBA-degrading cultures do not exhibit 4-CBA degradation under denitrifying conditions, nor aerobic 3-CBA degradation [FEMS Microbiol. Lett. 144 (1996) 213, Appl. Environ. Microbiol. 66 (2000) 3446], the microbial population developed in this experiment was physiologically versatile with respect to the utilization of both electron donors and electron acceptors. (C) 2003 Elsevier Ltd. All rights reserved.

DOI： 10.1016/j.chemosphere.2003.10.022

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer  

Microbial consortia capable of degrading 3-chlorophenol (3-CP) were enriched in continuous up-flow column reactors under circum-denitrifying conditions. 3-CP degradation capability was developed and sustained when 3-CP was supplied at 16-21 μM, although suppression of the 3-CP degradation capability was observed when 3-CP was supplied at 42 μM. When 3-CP was stably degraded, the ratio of nitrate consumption to 3-CP degradation approached the theoretical stoichiometric value, which was calculated by assuming a 3-CP degradation-dependent nitrate reduction. Batchincubation experiments demonstrated that the microbial consortium that was enriched in the column reactors required either nitrate or oxygen for degrading 3-CP, while 3-CP was not degraded under sulfate-degrading conditions. Although many attempts were made to sustain the microbial 3-CP degradation capability under denitrifying conditions, mostly in batch cultures, none of them have been successful so far. Therefore, the results obtained in this study may be the first to demonstrate sustainable 3-CP degradation capability under circum-denitrifying conditions.

DOI： 10.1007/s00253-002-0974-z

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PubMed

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Society for General Microbiology  

Although chlorophenol (CP) degradation has been studied, no bacterium responsible for degradation of CP under denitrifying conditions has been isolated. Moreover, little substantial evidence for anaerobic degradation of CPs coupled with denitrification is available even for mixed cultures. Degradation of CP [2-CP, 3-CP, 4-CP, 2,4-dichlorophenol (DCP) or 2,6-DCP] under denitrifying conditions was examined in anaerobic batch culture inoculated with activated sludge. Although 3-CP, 4-CP, 2,4-DCP and 2,6-DCP were not stably degraded, 2-CP was degraded and its degradation capability was sustained in a subculture. However, the rate of 2-CP degradation was not significantly enhanced by subculturing. In 2-CP-degrading cultures, nitrate was consumed stoichiometrically and concomitantly during 2-CP degradation, and a dechlorination intermediate was not detected, suggesting that 2-CP degradation was coupled with nitrate reduction. A 2-CP-degrading enrichment culture degraded 2-CP in the presence of nitrate, but did not in the absence of nitrate or the presence of sulfate. This suggests that the enrichment culture strictly requires nitrate for degradation of 2-CP. The apparent specific growth rate of the 2-CP degrading species was 0.0139 d-1. Thus the apparent doubling time of the 2-CP-degrading population in the enrichment culture was greater than 50 d, which may explain difficulty in enrichment and isolation of micro-organisms responsible for CP degradation under denitrifying conditions.

DOI： 10.1099/00221287-148-1-221

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PubMed

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer  

Autotrophic ammonia-oxidizing bacteria use the essential enzyme ammonia monooxygenase (AMO) to transform ammonia to hydroxylamine. The amo operon consists of at least three genes, amoC, amoA, and amoB
amoA encodes the subunit containing the putative enzyme active site. The use of the amo genes as functional markers for ammonia-oxidizing bacteria in environmental applications requires knowledge of the diversity of the amo operon on several levels: (1) the copy number of the operon in the genome, (2) the arrangement of the three genes in an individual operon, and (3) the primary sequence of the individual genes. We present a database of amo gene sequences for pure cultures of ammonia-oxidizing bacteria representing both the β- and the γ-subdivision of Proteobacteria in the following genera: Nitrosospira (6 strains), Nitrosomonas (5 strains) and Nitrosococcus (2 strains). The amo operon was found in multiple (2-3) nearly identical copies in the β-subdivision representatives but in single copies in the γ-subdivision ammonia oxidizers. The analysis of the deduced amino acid sequence revealed strong conservation for all three Amo peptides in both primary and secondary structures. For the amoA gene within the β-subdivision, nucleotide identity values are approximately 85% within the Nitrosomonas or the Nitrosospira groups, but approximately 75% when comparing between these groups. Conserved regions in amoA and amoC were identified and used as primer sites for PCR amplification of amo genes from pure cultures, enrichments and the soil environment. The intergenic region between amoC and amoA is variable in length and may be used to profile the community of ammonia-oxidizing bacteria in environmental samples. Electronic supplementary material to this paper can be obtained by using the Springer LINK server located at http://dx.doi.org/10.1007/s00203-001-0369-z.

DOI： 10.1007/s00203-001-0369-z

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：国際水環境学会  

Attempts were made for removing ammonia from synthetic wastewater under the presence of phenol, which is inhibitory to nitrification, by using a single-stage activated sludge process with cross-flow filtration. Activated sludge biomass which had been acclimated with phenol for over 15 years was used for the inoculum, and synthetic wastewater was continuously supplied to the process retaining biomass at 8000mg VSSl-1. Phenol was completely removed, and ammonia was simultaneously nitrified to nitrate
nitrification rate reached 200mg Nl-1d-1 when phenol was removed at a rate up to 300mgl-1d-1. It was observed that 0-13% of the ammonia was removed via denitrification. Intermittent aeration enhanced the denitrification rate to 160mg Nl-1d-1 by utilizing phenol, and approximately 24% of the denitrified nitrogen was recovered as nitrous oxide. Methanol, which is the most commonly used electron donor in conventional nitrogen removal processes, did not enhance the denitrification rate of the phenol-acclimated activated sludge used in this study, however phenol did. The results suggest that this process potentially works as a space- and energy-saving nitrogen removal process by utilizing substances inhibitory to nitrifiers as electron donors for denitrification. Copyright © 2001 Elsevier Science Ltd.

DOI： 10.1016/S0043-1354(01)00032-X

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Microbiology Research Foundation  

DOI： 10.2323/jgam.46.317

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：AMER SOC MICROBIOLOGY  

Bacterial community structure and the predominant nitrifying activities and populations in each compartment of a three-compartment activated sludge system were determined, Each compartment was originally inoculated with the same activated sludge community entrapped in polyethylene glycol gel granules, and ammonium nitrogen was supplied to the system in an inorganic salts solution at a rate of 5.0 g of N liter of granular activated sludge(-1) day(-1). After 150 days of operation, the system was found to comprise a series of sequential nitrifying reactions (K, Note, T. Ogasawara, Y, Suwa, and T. Sumino, Water Res. 32:769-773, 1998), presumably mediated by different bacterial populations. Activity data showed that all NH4-N was completely oxidized in compartments one and two (approximately half in each), but no significant nitrite oxidation was observed in these compartments. In contrast, all available nitrite was oxidized to nitrate in compartment three. To study the microbial populations and communities in this system, total bacterial DNA isolated from each compartment was analyzed for community structure based on the G+C contents of the component populations. Compartment one showed dominant populations having 50 and 67% G+C contents. Compartment two was similar in structure to compartment one, The bacterial community in compartment three had dominant populations with 62 and 67% G+C contents and retained the 50% G+C content population only at a greatly diminished level, The 50% G+C content population from compartment one hybridized strongly with amo (ammonia monooxygenase) and hao (hydroxylamine oxidoreductase) gene probes from Nitrosomonas europaea. However, the 50% G+C content population from compartment two hybridized strongly with the hao probe but only weakly with the amo probe, suggesting that the predominant ammonia-oxidizing populations in compartments one and two might be different. Since different activities and populations come to dominate in each compartment from an identical inoculum, it appears that the nitrification processes may be somewhat incompatible, resulting in a series of sequential reactions and different communities in this three-compartment system.

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：国際水環境学会  

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：土壌微生物学会  

DOI： 10.18946/jssm.52.0_41

CiNii Books

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：日本微生物生態学会  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：工業技術院資源環境技術総合研究所  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：工業技術院資源環境技術総合研究所  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Microbiology Research Foundation  

DOI： 10.2323/jgam.43.373

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：ヨーロッパ微生物学会連合  

DOI： 10.1016/0168-6496(95)00074-7

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：アメリカ微生物学会  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：アメリカ微生物学会  

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：工業技術院資源環境技術総合研究所  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PERGAMON-ELSEVIER SCIENCE LTD  

Activated sludges were acclimated to p-nitrophenol (PNP) in two operational modes, a batch and a continuous. The operational mode of the PNP acclimation of activated sludges strongly affected the physiological characteristics of predominant microorganisms responsible for PNP degradation. Predominant PNP degraders in the sludge in batch mode (Sludge B) had lower PNP affinity and were relatively insensitive to PNP concentration. Those of the sludge in continuous mode (Sludge C), on the other hand, had very high PNP affinity and were sensitive to PNP. MPN enumeration of PNP degraders in sludge B and C using media with different PNP concentrations (0.05, 0.2, 0.5 and 2.0 mM) supported the above results. Medium with 0.2 mM of PNP did not recover PNP degraders in sludge C well, while it recovered PNP degraders in sludge B as well as the medium with 0.05 mM did. When switching from one operational mode to the other, the predominant population in sludge B shifted to the sensitive group, but that of sludge C did not shift at the given loading of PNP, showing relative resistance to inhibitive concentration.

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：国際水環境学会  

Ammonia oxidizers were enumerated in 34 activated sludges, including sludges which were from sewage treatment plants (S-sludge), nightsoil treatment plants (N-sludge) and activated sludges cultivated with organic (O-sludge) or inorganic (I-sludge) artificial wastewaters in the laboratory. Two media were used for enumeration, one containing 0.76 mM (AL medium) and the other 37.9 mM (AH medium) of (NH4)2SO4. The MPN estimated with AL medium were higher than those with AH medium in S-sludges, N-sludges and O-sludges, while both media gave almost the same MPN for I-sludges. Ten ammonia oxidizers, all identified as Nitrosomonas spp, were isolated from sludge samples. Isolates obtained as predominants in S- and O-sludges were sensitive to (NH4)2SO4
they grew in medium containing 0.71 mM of (NH4)2SO4 but not in medium containing 35.7 mM of (NH4)2SO4. On the other hand, those obtained as predominants in an I-sludge, as well as ATCC strains grew in both media. The Monod equation described the relationship between (NH4)2SO4 concentration and nitrite production rates for (NH4)2SO4-insensitive strains but not for sensitive strains, which exhibited a relationship closer to the Haldane equation describing substrate inhibition kinetics. Among isolates obtained from S-sludge sample, Km and Vmax values of an (NH4)2SO4-sensitive strain were much lower than those of an insensitive strain. Similarly, among laboratory sludge isolates, Km and Km values of an (NH4)2SO4-sensitive strain from an O-sludge were lower than those of an insensitive strain from an I-sludge. These results suggest that (NH4)2SO4-sensitive strains had a growth advantage in lower (NH4)2SO4 concentrations, while insensitive strains had an advantage in higher (NH4)2SO4 concentrations. © 1994.

DOI： 10.1016/0043-1354(94)90218-6

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier  

Surface sediments collected from 40 stations in Ise Bay, which is one of the most polluted bays in Japan, were subjected to phospholipid ester-linked fatty acid (PLFA) analysis. Thirty-five fatty acids were identified in the sediments
they included saturated, unsaturated and branched fatty acids. The major fatty acids included the even-numbered straight chain fatty acid 16:0 (20%), branched chain fatty acids i15:0 (8%) and a15:0 (11%),and monounsaturated fatty acids 16:1d9c (11%) and 18:1d11 (10%). Fatty acids which are common in bacterial membranes were found, and low amounts of longer chain fatty acids were detected in relatively constant amounts in the bay. One of the characteristic features of the PLFA analysis in Ise Bay is the virtual absence of polyunsaturated fatty acids in the sediments, except for 18:2. The PLFA profiles indicate that the microbial community structure is characterized by the absence of polyunsaturated fatty acids typical of microeukaryotes and high proportions of fatty acid biomarkers of prokaryotes in sediments. A wide distribution of aerobic bacteria. Gram-positive bacteria, anaerobic bacteria and sulfate-reducing bacteria in the microbial community structure was indicated by the presence of biomarker fatty acids. Similarity analysis of the PLFA profiles in sediments of all the stations showed that they were similar at the 90% level. The results of Tukey's test showed that a majority of the fatty acids in sediments were not significantly enriched in the bay. The absence of significant variation in the PLFA profiles in sediments revealed that the microbial community structure is similar throughout the bay, and this uniformity was attributed to the reported pollution and eutrophication in Ise Bay. Further, the significant PLFA patterns, with a high proportion of prokaryotic biomarker fatty acids and an absence of microeukaryotic biomarkers, indicate that PLFA analysis could be used as a measure of pollution in sediments. © 1993.

DOI： 10.1016/0304-4203(93)90248-M

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：PERGAMON-ELSEVIER SCIENCE LTD  

We examined what kind and how much of the specific inhibitor is effective for the estimation availabilities of substrates for methanogens in anaerobic sludges. The chloroform (0.1%, v/v) inhibited 90% of the methanogenesis in an anaerobic sludge (LD), which was cultivated with glucose, and was more effective than 2-bromoethanesulfonic acid (BES, 0-200 mM). Hydrogen, acetate and propionate were linearly accumulated when the methanogenesis was inhibited by 0.1% of chloroform. The propionate accumulation rate in the presence of chloroform was identical with that in the presence of high partial pressure of hydrogen (H-2:CO2 = 20:80) which inhibits syntrophic H-2-producing fatty-acids-oxidizing bacteria. This shows that the methanogens utilized hydrogen and acetate converted by syntrophic hydrogen-producing propionate-oxidizing bacteria through interspecies hydrogen transfer. Using chloroform (0.1%) as the specific inhibitor, in the LD sludge 49% of methane was estimated to be derived from propionate. The H-2 + CO2 and acetate from the other pathway (NS), contributed 2 and 34% of the methanogenesis, respectively. This method was also applied to a municipal sewage digester sludge (MD). In the MD sludge, methanogenesis from propionate, H-2 + CO2 and acetate via the NS pathway were 16, 2 and 78%, respectively. Major substrates for methanogenesis, therefore, could be estimated in anaerobic sludges.

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：国際水環境学会  

Nitrogen removal by a single-stage, single-sludge activated sludge process with cross-flow filtration was qualitatively studied. Artificial wastewater had a BOD/TKN ratio from 1.8 to 24.5. The BOD loading to the process ranged from 0.33 to 1.66 g l-1 d-1, the TKN loading from 0.032 to 0.268 g l-1 d-1 and the sludge retention time (SRT) was quite long (54-4200 d). In each experiment, more than 97% of organic carbon was removed. The sludge biomass concentration (MLVSS) was high at a high volumetric BOD loading. Total Kjeldahl nitrogen (TKN) was successfully nitrified and higher than 29% of the TKN which was loaded to the reactor was removed in many of the experimental runs. The nitrogen balance of each unit was calculated. Denitrification was estimated to be responsible for 39-86% of the removed nitrogen in an aeration vessel. Although denitrification was not observed up to 0.438 g l-1 d-1 of BOD loading, the denitrification rate increased as the BOD loading increased. The percentage of nitrogen removal was a function of the BOD/TKN ratio of the influent. Lower DO concentration did not increase the denitrification rate, but intermittent aeration-BOD loading did increase it
TKN was completely removed up to 0.21 TKN g l-1 d-1, and the denitrification rate reached 0.0074 gN VSS-1 d-1. © 1992.

DOI： 10.1016/0043-1354(92)90174-3

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier  

Phospholipid ester-linked fatty acid (PLFA) composition in sediments were determined in order to understand the microbial community structure in a polluted bay. The PLFA pattern in sediments revealed the presence of aerobic and anaerobic bacteria, the composition of which differed among the stations. The community structure in sediments, as characterized by the composition of PLFA showed an absence of polyunsaturated fatty acids, except 18:2, signature fatty acids of microeukaryotes and a greater proportion of bacterial biomarker fatty acids. The results of Tukey's honestly significant difference test showed distinctive differences in the PLFA among the stations and also shifts in the microbial community structure in the bay. The significant patterns of PLFA in sediments with the virtual absence of lipid biomarkers for microeukaryotes and the relatively high proportions of bacterial biomarkers indicate the prokaryotic consortium responsive to organic contamination. © 1992.

DOI： 10.1016/0025-326X(92)90591-S

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：水質汚濁研究協会  

Nitrification of total Kjeldahl nitrogen (TKN) by an activated sludge process with cross-flow filtration was examined by using an artificial organic wastewater. To determine the maximum nitrification rate of the reactor, the TKN loading was increased by adding ammonium sulfate to the influent. The step increase rate of the TKN loading was smaller than that had been in a similar experiment with the same influent BOD concentration in the previous work. The nitrification rate reached 0.59gTKN·l^-1·d^-1, which was twice higher than the maximum value obtained in the previous work. The result indicates that a smaller rate of the step increase of the TKN loading is required to make the nitrification rate of the reactor higher, especially when the nitrification rate of the reactor is higher.

DOI： 10.2965/jswe1978.14.261

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：醗酵工学会  

Oxidation of inorganic ammonium (NH_4^+) was done by an activated sludge process with cross-flow filtration. The reactor was operated by a complete mixing and continuous feeding method. Activated sludge was seldom drawn off to retain slow growing nitrifiers in the reactor well. Although no organic substances were supplied to the reactor, the sludge concentration increased up to 6,600-8,700 mgVSS/l. No ammonim nitrogen was detected in the effluent, with the reactor was operated with ammonium loading up to 0.79-1.18 g NH_4-N・l^<-1>・d^<-1>. The ammonium oxidation rate reached 1.90 NH_4-N・l^<-1>・d^<-1>; this value is six-fold higher than the maximum nitrification rate when Kjeldahl nitrogen and organic substance were treated by this activated sludge process at the same time.

CiNii Books

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Other Link： http://dl.ndl.go.jp/info:ndljp/pid/10545486

Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：水質汚濁研究協会  

DOI： 10.2965/jswe1978.13.93

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：工業技術院公害資源研究所  

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：工業技術院公害資源研究所  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：SOC FERMENTATION BIOENGINEERING, JAPAN  

Web of Science

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：工業技術院公害資源研究所  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：工業技術院公害資源研究所  

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Language：Japanese   Publishing type：Research paper (scientific journal)   Publisher：東北大学農学研究所  

CiNii Books

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：日本土壌肥料学会  

DOI： 10.1080/00380768.1987.10557598

Scopus

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：日本土壌肥料学会  

Bacteria in paddy soil were cultured at 10-, 100-, 10, 000-fold dilutions of the conventional nutrient broth (NB/10, NB/100, NB/10, 000). After about 3 weeks of incubation, the organisms which grew on the full strength nutrient broth (NB) (NB organisms) became predominant in the NB/10 culture. On the other hand, those which grew on the NB/100 medium but not on the NB medium (DNB organisms) became predominant in the NB/10, 000 culture. In the NB/100 culture, the number of NB and DNB organisms was similar. In order to compare predominance of microorganisms growing at different dilutions of nutrient broth, the cell morphology and fatty acid composition was studied in 49 to 68 isolates obtained from each culture. It was observed that the organisms which predominated in the NB/10 culture were markedly different from those in the NB/10, 000 culture. Based on growth responses of NB and DNB organisms to the media at various concentrations, the former were considered to be zymogenous organisms and the latter autochthonous organisms. Such a marked difference in the populations was neither recognized between the NB/10 and NB/100 cultures, nor between the NB/100 and NB/10, 000 cultures. © Taylor &amp
Francis Group, LLC.

DOI： 10.1080/00380768.1987.10557569

Scopus

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：日本土壌肥料学会  

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：応用微生物学研究奨励会  

The cellular fatty acids of 88 bacterial isolates were analyzed, including 46 strains which did not grow on full-strength nutrient broth (NB) but grew on its 100-fold dilution (DNB organisms) and 42 strains which grew on both NB and its 100-fold dilution (NB organisms). All strains were grouped into 14 clusters according to their fatty acid composition, using average linkage cluster analysis and similarity values based on correlation coefficients. Among these 14 clusters, five comprised only DNB organisms and six comprised NB organisms. In the remaining three clusters, DNB organisms and NB organisms were not segregated with respect to similarity values based on their fatty acid composition, but were distinguished on the basis of other bacteriological characteristics such as quinone systems, cell morphology, or other physiological characteristics. © 1986, Applied Microbiology, Molecular and Cellular Biosciences Research Foundation. All rights reserved.

DOI： 10.2323/jgam.32.451

Scopus

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC SOIL SCIENCE PLANT NUTRITION  

Web of Science

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：JAPANESE SOC SOIL SCIENCE PLANT NUTRITION  

Web of Science

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J-GLOBAL

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Language：Japanese   Publisher：日本微生物生態学会  

CiNii Books

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Language：Japanese   Publisher：一般社団法人日本土壌肥料学会  

CiNii Books

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Language：Japanese  

CiNii Books

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J-GLOBAL

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J-GLOBAL

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J-GLOBAL

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J-GLOBAL

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J-GLOBAL

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J-GLOBAL

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Language：Japanese   Publisher：日本土壌微生物学会  

DOI： 10.18946/jssm.64.2_138_1

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J-GLOBAL

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J-GLOBAL

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Language：English  

CiNii Books

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Language：Japanese   Publisher：一般社団法人日本土壌肥料学会  

CiNii Books

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Language：Japanese   Publishing type：Article, review, commentary, editorial, etc. (other)   Publisher：日本農芸化学会  

DOI： 10.1271/kagakutoseibutsu.47.82

CiNii Books

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Other Link： https://jlc.jst.go.jp/DN/JALC/00326503834?from=CiNii

J-GLOBAL

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Language：English   Publishing type：Article, review, commentary, editorial, etc. (other)   Publisher：In Microbial Diversity and Genetics of Biodegradation. Horikoshi, K. , Fukuda, M. and Kudo, T. ( eds. ), Japan Sci, Soc. Press, Tokyo.  

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