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Laurent Philippot - One of the best experts on this subject based on the ideXlab platform.
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relative contribution of nirk and nirs bacterial Denitrifiers as well as fungal Denitrifiers to nitrous oxide production from dairy manure compost
Environmental Science & Technology, 2017Co-Authors: Koki Maeda, Laurent Philippot, Sakae Toyoda, Shohei Hattori, Keiichi Nakajima, Yumi Ito, Naohiro YoshidaAbstract:The relative contribution of fungi, bacteria, and nirS and nirK denirifiers to nitrous oxide (N2O) emission with unknown isotopic signature from dairy manure compost was examined by selective inhibition techniques. Chloramphenicol (CHP), cycloheximide (CYH), and diethyl dithiocarbamate (DDTC) were used to suppress the activity of bacteria, fungi, and nirK-possessing Denitrifiers, respectively. Produced N2O were surveyed to isotopocule analysis, and its 15N site preference (SP) and δ18O values were compared. Bacteria, fungi, nirS, and nirK gene abundances were compared by qPCR. The results showed that N2O production was strongly inhibited by CHP addition in surface pile samples (82.2%) as well as in nitrite-amended core samples (98.4%), while CYH addition did not inhibit the N2O production. N2O with unknown isotopic signature (SP = 15.3–16.2‰), accompanied by δ18O (19.0–26.8‰) values which were close to bacterial denitrification, was also suppressed by CHP and DDTC addition (95.3%) indicating that nirK den...
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Loss in microbial diversity affects nitrogen cycling in soil
2013Co-Authors: Laurent Philippot, Christopher M. Jones, David Bru, Aymé Spor, Catherine Hénault, Pierre-alain MaronAbstract:Microbial communities have a central role in ecosystem processes by driving the Earth’s biogeochemical cycles. However, the importance of microbial diversity for ecosystem functioning is still debated. Here, we experimentally manipulated the soil microbial community using a dilution approach to analyze the functional consequences of diversity loss. A trait-centered approach was embraced using the Denitrifiers as model guild due to their role in nitrogen cycling, a major ecosystem service. How various diversity metrics related to richness, eveness and phylogenetic diversity of the soil denitrifier community were affected by the removal experiment was assessed by 454 sequencing. As expected, the diversity metrics indicated a decrease in diversity in the 1/103 and 1/105 dilution treatments compared with the undiluted one. However, the extent of dilution and the corresponding reduction in diversity were not commensurate, as a dilution of five orders of magnitude resulted in a 75% decrease in estimated richness. This reduction in denitrifier diversity resulted in a significantly lower potential denitrification activity in soil of up to 4-5 folds. Addition of wheat residues significantly increased differences in potential denitrification between diversity levels, indicating that the resource level can influence the shape of the microbial diversity-functioning relationship. This study shows that microbial diversity loss can alter terrestrial ecosystem processes, which suggests that the importance of functional redundancy in soil microbial communities has been overstated.
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soil environmental conditions rather than denitrifier abundance and diversity drive potential denitrification after changes in land uses
Global Change Biology, 2011Co-Authors: Eleonore Attard, Laurent Philippot, Sylvie Recous, Abad Chabbi, C De Berranger, Nadine Guillaumaud, J Labreuche, Bernhard Schmid, Le X RouxAbstract:Land-use practices aiming at increasing agro-ecosystem sustainability, e.g. no-till systems and use of temporary grasslands, have been developed in cropping areas, but their environmental benefits could be counterbalanced by increased N2O emissions produced, in particular during denitrification. Modelling denitrification in this context is thus of major importance. However, to what extent can changes in denitrification be predicted by representing the denitrifying community as a black box, i.e. without an adequate representation of the biological characteristics (abundance and composition) of this community, remains unclear. We analysed the effect of changes in land uses on Denitrifiers for two different agricultural systems: (i) crop/grassland conversion and (ii) cessation/application of tillage. We surveyed potential denitrification (PD), the abundance and genetic structure of Denitrifiers (nitrite reducers), and soil environmental conditions. N2O emissions were also measured during periods of several days on control plots. Time-integrated N2O emissions and PD were well correlated among all control plots. Changes in PD were partly due to changes in denitrifier abundance but were not related to changes in the structure of the denitrifier community. Using multiple regression analysis, we showed that changes in PD were more related to changes in soil environmental conditions than in denitrifier abundance. Soil organic carbon explained 81% of the variance observed for PD at the crop/temporary grassland site, whereas soil organic carbon, water-filled pore space and nitrate explained 92% of PD variance at the till/no-till site, without any residual effect of denitrifier abundance. Soil environmental conditions influenced PD by modifying the specific activity of Denitrifiers, and to a lesser extent by promoting a build-up of Denitrifiers. Our results show that an accurate simulation of carbon, oxygen and nitrate availability to Denitrifiers is more important than an accurate simulation of denitrifier abundance and community structure to adequately understand and predict changes in PD in response to land-use changes.
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Influence of land-use intensity on the spatial distribution of N-cycling microorganisms in grassland soils
FEMS Microbiology Ecology, 2011Co-Authors: Daniel Keil, Laurent Philippot, Michael Schloter, Annabel Meyer, Doreen Berner, Christian Poll, André Schützenmeister, Hans-peter Piepho, Anna Vlqsenko, Ellen KandelerAbstract:A geostatistical approach using replicated grassland sites (10 m × 10 m) was applied to investigate the influence of grassland management, i.e. unfertilized pastures and fertilized mown meadows representing low and high land-use intensity (LUI), on soil biogeochemical properties and spatial distributions of ammonia-oxidizing and denitrifying microorganisms in soil. Spatial autocorrelations of the different N-cycling communities ranged between 1.4 and 7.6 m for ammonia oxidizers and from 0.3 m for nosZ-type Denitrifiers to scales >14 m for nirK-type Denitrifiers. The spatial heterogeneity of ammonia oxidizers and nirS-type Denitrifiers increased in high LUI, but decreased for biogeochemical properties, suggesting that biotic and/or abiotic factors other than those measured are driving the spatial distribution of these microorganisms at the plot scale. Furthermore, ammonia oxidizers (amoA ammonia-oxidizing archaea and amoA ammonia-oxidizing bacteria) and nitrate reducers (napA and narG) showed spatial coexistence, whereas niche partitioning was found between nirK- and nirS-type Denitrifiers. Together, our results indicate that spatial analysis is a useful tool to characterize the distribution of different functional microbial guilds with respect to soil biogeochemical properties and land-use management. In addition, spatial analyses allowed us to identify distinct distribution ranges indicating the coexistence or niche partitioning of N-cycling communities in grassland soil.
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Importance of Denitrifiers lacking the genes encoding the nitrous oxide reductase for N2O emissions from soil
Global Change Biology, 2010Co-Authors: Laurent Philippot, Janet Andert, Christopher M. Jones, Sara HallinAbstract:Analyses of the complete genomes of sequenced denitrifying bacteria revealed that approximately 1/3 have a truncated denitrification pathway, lacking the nosZ gene encoding the nitrous oxide reductase. We investigated whether the number of Denitrifiers lacking the genetic ability to synthesize the nitrous oxide reductase in soils is important for the proportion of N2O emitted by denitrification. Serial dilutions of the denitrifying strain Agrobacterium tumefaciens C58 lacking the nosZ gene were inoculated into three different soils to modify the proportion of Denitrifiers having the nitrous oxide reductase genes. The potential denitrification and N2O emissions increased when the size of inoculated C58 population in the soils was in the same range as the indigenous nosZ community. However, in two of the three soils, the increase in potential denitrification in inoculated microcosms compared with the noninoculated microcosms was higher than the increase in N2O emissions. This suggests that the indigenous denitrifier community was capable of acting as a sink for the N2O produced by A. tumefaciens. The relative amount of N2O emitted also increased in two soils with the number of inoculated C58 cells, establishing a direct causal link between the denitrifier community composition and potential N2O emissions by manipulating the proportion of Denitrifiers having the nosZ gene. However, the number of Denitrifiers which do not possess a nitrous oxide reductase might not be as important for N2O emissions in soils having a high N2O uptake capacity compared with those with lower. In conclusion, we provide a proof of principle that the inability of some Denitrifiers to synthesize the nitrous oxide reductase can influence the nature of the denitrification end products, indicating that the extent of the reduction of N2O to N2 by the denitrifying community can have a genetic basis.
Gesche Braker - One of the best experts on this subject based on the ideXlab platform.
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ph driven shifts in overall and transcriptionally active Denitrifiers control gaseous product stoichiometry in growth experiments with extracted bacteria from soil
Frontiers in Microbiology, 2015Co-Authors: Kristof Brenzinger, Gesche Braker, Peter DorschAbstract:Soil pH is a strong regulator for activity as well as for size and composition of denitrifier communities. Low pH not only lowers overall denitrification rates but also influences denitrification kinetics and gaseous product stoichiometry. N2O reductase is particularly sensitive to low pH which seems to impair its activity post-transcriptionally, leading to higher net N2O production. Little is known about how complex soil denitrifier communities respond to pH change and whether their ability to maintain denitrification over a wider pH range relies on phenotypic redundancy. In the present study, we followed the abundance and composition of an overall and transcriptionally active denitrifier community extracted from a farmed organic soil in Sweden (pHH2O = 7.1) when exposed to pH 5.4 and drifting back to pH 6.6. The soil was previously shown to retain much of its functioning (low N2O/N2 ratios) over a wide pH range, suggesting a high functional versatility of the underlying community. We found that denitrifier community composition, abundance and transcription changed throughout incubation concomitant with pH change in the medium, allowing for complete reduction of nitrate to N2 with little accumulation of intermediates. When exposed to pH 5.4, the denitrifier community was able to grow but reduced N2O to N2 only when near-neutral pH was reestablished by the alkalizing metabolic activity of an acid-tolerant part of the community. The genotypes proliferating under these conditions differed from those dominant in the control experiment run at neutral pH. Denitrifiers of the nirS-type appeared to be severely suppressed by low pH and nirK-type and nosZ-containing Denitrifiers showed strongly reduced transcriptional activity and growth, even after restoration of neutral pH. Our study suggests that low pH episodes alter transcriptionally active populations which shape denitrifier communities and determine their gas kinetics.
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Diversity and activity of Denitrifiers of chilean arid soil ecosystems.
Frontiers in microbiology, 2012Co-Authors: Julieta Orlando, Margarita Carú, Bianca Pommerenke, Gesche BrakerAbstract:The Chilean sclerophyllous matorral is a Mediterranean semiarid ecosystem affected by erosion, with low soil fertility and limited by nitrogen. However, limitation of resources is even more severe for desert soils such as from the Atacama Desert, one of the most extreme arid deserts on Earth. Topsoil organic matter, nitrogen and moisture content were significantly higher in the semiarid soil compared to the desert soil. Although the most significant loss of biologically preferred nitrogen from terrestrial ecosystems occurs via denitrification, virtually nothing is known on the activity and composition of denitrifier communities thriving in arid soils. In this study, we explored denitrifier communities from two soils with profoundly distinct edaphic factors. While denitrification activity in the desert soil was below detection limit, the semiarid soil sustained denitrification activity. To elucidate the genetic potential of the soils to sustain denitrification processes we performed community analysis of Denitrifiers based on nitrite reductase (nirK and nirS) genes as functional marker genes for this physiological group. Presence of nirK-type Denitrifiers in both soils was demonstrated but failure to amplify nirS from the desert soil suggests very low abundance of nirS-type Denitrifiers shedding light on the lack of denitrification activity. Phylogenetic analysis showed a very low diversity of nirK with only three distinct genotypes in the desert soil which conditions presumably exert a high selection pressure. While nirK diversity was also limited to only few, albeit distinct genotypes, the semiarid matorral soil showed a surprisingly broad genetic variability of the nirS gene. The Chilean matorral is a shrub land plant community which form vegetational patches stabilizing the soil and increasing its nitrogen and carbon content. These islands of fertility may sustain the development and activity of the overall microbial community and of Denitrifiers in particular.
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impact of plant functional group plant species and sampling time on the composition of nirk type denitrifier communities in soil
Applied and Environmental Microbiology, 2007Co-Authors: Christina Bremer, Gesche Braker, Diethart Matthies, Andreas Reuter, Christof Engels, Ralf ConradAbstract:We studied the influence of eight nonleguminous grassland plant species belonging to two functional groups (grasses and forbs) on the composition of soil denitrifier communities in experimental microcosms over two consecutive years. Denitrifier community composition was analyzed by terminal restriction fragment length polymorphism (T-RFLP) of PCR-amplified nirK gene fragments coding for the copper-containing nitrite reductase. The impact of experimental factors (plant functional group, plant species, sampling time, and interactions between them) on the structure of soil denitrifier communities (i.e., T-RFLP patterns) was analyzed by canonical correspondence analysis. While the functional group of a plant did not affect nirK-type denitrifier communities, plant species identity did influence their composition. This effect changed with sampling time, indicating community changes due to seasonal conditions and a development of the plants in the microcosms. Differences in total soil nitrogen and carbon, soil pH, and root biomass were observed at the end of the experiment. However, statistical analysis revealed that the plants affected the nirK-type denitrifier community composition directly, e.g., through root exudates. Assignment of abundant T-RFs to cloned nirK sequences from the soil and subsequent phylogenetic analysis indicated a dominance of yet-unknown nirK genotypes and of genes related to nirK from Denitrifiers of the order Rhizobiales. In conclusion, individual species of nonleguminous plants directly influenced the composition of denitrifier communities in soil, but environmental conditions had additional significant effects.
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communities of nirs type Denitrifiers in the water column of the oxygen minimum zone in the eastern south pacific
Environmental Microbiology, 2005Co-Authors: Maribeb Castrogonzalez, Gesche Braker, Laura Farias, Osvaldo UlloaAbstract:Summary The major sites of water column denitrification in the ocean are oxygen minimum zones (OMZ), such as one in the eastern South Pacific (ESP). To understand the structure of denitrifying communities in the OMZ off Chile, denitrifier communities at two sites in the Chil- ean OMZ (Antofagasta and Iquique) and at different water depths were explored by terminal restriction fragment length polymorphism analysis and cloning of polymerase chain reaction (PCR)-amplified nirS genes. NirS is a functional marker gene for denitrifi- cation encoding cytochrome cd 1 -containing nitrite reductase, which catalyses the reduction of nitrite to nitric oxide, the key step in denitrification. Major dif- ferences were found between communities from the two geographic locations. Shifts in community struc- ture occurred along a biogeochemical gradient at Antofagasta. Canonical correspondence analysis indicated that O 2 , NO 3 - , NO 2 - and depth were impor- tant environmental factors governing these communi- ties along the biogeochemical gradient in the water column. Phylogenetic analysis grouped the majority of clones from the ESP in distinct clusters of genes from presumably novel and yet uncultivated denitri- fers. These nirS clusters were distantly related to those found in the water column of the Arabian Sea but the phylogenetic distance was even higher com- pared with environmental sequences from marine sediments or any other habitat. This finding suggests similar environmental conditions trigger the develop- ment of Denitrifiers with related nirS genotypes despite large geographic distances.
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effect of soil ammonium concentration on n2o release and on the community structure of ammonia oxidizers and Denitrifiers
Applied and Environmental Microbiology, 2002Co-Authors: Sharon Avrahami, Ralf Conrad, Gesche BrakerAbstract:The effect of ammonium addition (6.5, 58, and 395 μg of NH4+-N g [dry weight] of soil−1) on soil microbial communities was explored. For medium and high ammonium concentrations, increased N2O release rates and a shift toward a higher contribution of nitrification to N2O release occurred after incubation for 5 days at 4°C. Communities of ammonia oxidizers were assayed after 4 weeks of incubation by denaturant gradient gel electrophoresis (DGGE) of the amoA gene coding for the small subunit of ammonia monooxygenase. The DGGE fingerprints were invariably the same whether the soil was untreated or incubated with low, medium, or high ammonium concentrations. Phylogenetic analysis of cloned PCR products from excised DGGE bands detected amoA sequences which probably belonged to Nitrosospira 16S rRNA clusters 3 and 4. Additional clones clustered with Nitrosospira sp. strains Ka3 and Ka4 and within an amoA cluster from unknown species. A Nitrosomonas-like amoA gene was detected in only one clone. In agreement with the amoA results, community profiles of total bacteria analyzed by terminal restriction fragment length polymorphism (T-RFLP) showed only minor differences. However, a community shift occurred for denitrifier populations based on T-RFLP analysis of nirK genes encoding copper-containing nitrite reductase with incubation at medium and high ammonia concentrations. Major terminal restriction fragments observed in environmental samples were further described by correspondence to cloned nirK genes from the same soil. Phylogenetic analysis grouped these clones into clusters of soil nirK genes. However, some clones were also closely related to genes from known Denitrifiers. The shift in the denitrifier community was probably the consequence of the increased supply of oxidized nitrogen through nitrification. Nitrification activity increased upon addition of ammonium, but the community structure of ammonium oxidizers did not change.
Satoshi Ishii - One of the best experts on this subject based on the ideXlab platform.
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isolation and characterization of Denitrifiers from woodchip bioreactors for bioaugmentation application
Journal of Applied Microbiology, 2020Co-Authors: Emily L Anderson, Jeonghwan Jang, Rodney T Venterea, Gary W Feyereisen, Satoshi IshiiAbstract:AIMS This study was done to obtain Denitrifiers that could be used for bioaugmentation in woodchip bioreactors to remove nitrate from agricultural subsurface drainage water. METHODS AND RESULTS We isolated Denitrifiers from four different bioreactors in Minnesota, and characterized the strains by measuring their denitrification rates and analysing their whole genomes. A total of 206 bacteria were isolated from woodchips and thick biofilms (bioslimes) that formed in the bioreactors, 76 of which were able to reduce nitrate at 15°C. Among those, nine potential denitrifying strains were identified, all of which were isolated from the woodchip samples. Although many nitrate-reducing strains were isolated from the bioslime samples, none were categorized as Denitrifiers but instead as carrying out dissimilatory nitrate reduction to ammonium. CONCLUSIONS Among the Denitrifiers confirmed by 15 N stable isotope analysis and genome analysis, Cellulomonas cellasea strain WB94 and Microvirgula aerodenitrificans strain BE2.4 appear to be promising for bioreactor bioaugmentation due to their potential for both aerobic and anaerobic denitrification, and the ability of strain WB94 to degrade cellulose. SIGNIFICANCE AND IMPACT OF THE STUDY Denitrifiers isolated in this study could be useful for bioaugmentation application to enhance nitrate removal in woodchip bioreactors.
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Data_Sheet_1_Denitrifying Bacteria Active in Woodchip Bioreactors at Low-Temperature Conditions.PDF
2019Co-Authors: Jeonghwan Jang, Emily L Anderson, Rodney T Venterea, Michael J Sadowsky, Carl J Rosen, Gary W Feyereisen, Satoshi IshiiAbstract:Woodchip bioreactor technology removes nitrate from agricultural subsurface drainage by using denitrifying microorganisms. Although woodchip bioreactors have demonstrated success in many field locations, low water temperature can significantly limit bioreactor efficiency and performance. To improve bioreactor performance, it is important to identify the microbes responsible for nitrate removal at low temperature conditions. Therefore, in this study, we identified and characterized Denitrifiers active at low-temperature conditions by using culture-independent and -dependent approaches. By comparative 16S rRNA (gene) analysis and culture isolation technique, Pseudomonas spp., Polaromonas spp., and Cellulomonas spp. were identified as being important bacteria responsible for denitrification in woodchip bioreactor microcosms at relatively low temperature conditions (15°C). Genome analysis of Cellulomonas sp. strain WB94 confirmed the presence of nitrite reductase gene nirK. Transcription levels of this nirK were significantly higher in the denitrifying microcosms than in the non-denitrifying microcosms. Strain WB94 was also capable of degrading cellulose and other complex polysaccharides. Taken together, our results suggest that Cellulomonas sp. Denitrifiers could degrade woodchips to provide carbon source and electron donors to themselves and other Denitrifiers in woodchip bioreactors at low-temperature conditions. By inoculating these Denitrifiers (i.e., bioaugmentation), it might be possible to increase the nitrate removal rate of woodchip bioreactors at low-temperature conditions.
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denitrifying bacteria active in woodchip bioreactors at low temperature conditions
Frontiers in Microbiology, 2019Co-Authors: Jeonghwan Jang, Emily L Anderson, Rodney T Venterea, Michael J Sadowsky, Carl J Rosen, Gary W Feyereisen, Satoshi IshiiAbstract:Woodchip bioreactor technology removes nitrate from agricultural subsurface drainage by using denitrifying microorganisms. Although woodchip bioreactors have demonstrated success in many field locations, low water temperature can significantly limit bioreactor efficiency and performance. To improve bioreactor performance, it is important to identify the microbes responsible for nitrate removal at low temperature conditions. Therefore, in this study, we identified and characterized Denitrifiers active at low-temperature conditions by using culture-independent and -dependent approaches. By comparative 16S rRNA (gene) analysis and culture isolation technique, Pseudomonas spp., Polaromonas spp., and Cellulomonas spp. were identified as being important bacteria responsible for denitrification in woodchip bioreactor microcosms at relatively low temperature conditions (15°C). Genome analysis of Cellulomonas sp. strain WB94 confirmed the presence of nitrite reductase gene nirK. Transcription levels of this nirK were significantly higher in the denitrifying microcosms than in the non-denitrifying microcosms. Strain WB94 was also capable of degrading cellulose and other complex polysaccharides. Taken together, our results suggest that Cellulomonas sp. Denitrifiers could degrade woodchips to provide carbon source and electron donors to themselves and other Denitrifiers in woodchip bioreactors at low-temperature conditions. By inoculating these Denitrifiers (i.e., bioaugmentation), it might be possible to increase the nitrate removal rate of woodchip bioreactors at low-temperature conditions.
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phylogenetic and functional diversity of denitrifying bacteria isolated from various rice paddy and rice soybean rotation fields
Microbes and Environments, 2011Co-Authors: Kanako Tago, Tomoyasu Nishizawa, Shigeto Otsuka, Satoshi Ishii, Keishi SenooAbstract:Denitrifiers can produce and consume nitrous oxide (N2O). While little N2O is emitted from rice paddy soil, the same soil produces N2O when the land is drained and used for upland crop cultivation. In this study, we collected soils from two types of fields each at three locations in Japan; one type of field had been used for continuous cultivation of rice and the other for rotational cultivation of rice and soybean. Active Denitrifiers were isolated from these soils using a functional single-cell isolation method, and their taxonomy and denitrifying properties were examined. A total of 110 Denitrifiers were obtained, including those previously detected by a culture-independent analysis. Strains belonging to the genus Pseudogulbenkiania were dominant at all locations, suggesting that Pseudogulbenkiania Denitrifiers are ubiquitous in various rice paddy soils. Potential denitrifying activity was similar among the strains, regardless of the differences in taxonomic position and soil of origin. However, relative amounts of N2 in denitrification end products varied among strains isolated from different locations. Our results also showed that crop rotation had minimal impact on the functional diversity of the denitrifying strains. These results indicate that soil and other environmental factors, excluding cropping systems, could select for N2-producing Denitrifiers.
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isolation of functional single cells from environments using a micromanipulator application to study denitrifying bacteria
Applied Microbiology and Biotechnology, 2010Co-Authors: Naoaki Ashida, Shigeto Otsuka, Kanako Tago, Satoshi Ishii, Sadakazu Hayano, Takashi Tsuji, Yoshitaka Yoshimura, Keishi SenooAbstract:We developed a novel method to isolate functionally active single cells from environmental samples and named it the functional single-cell (FSC) isolation method. This method is based on a combination of substrate-responsive direct viable counts, live-cell staining with 5-carboxyfluorescein diacetate acetoxymethyl ester, and micromanipulation followed by cultivation in a medium. To evaluate this method, we applied it to study a denitrifying community in rice paddy soil. Similar denitrifier counts were obtained by the conventional most probable number analysis and our FSC isolation method. Using the FSC isolation method, 37 denitrifying bacteria were isolated, some of which harbored copper-containing nitrite reductase gene (nirK). The 16S rRNA gene analysis showed that members belonging to the genera Azospirillum and Ochrobactrum may be the major Denitrifiers in the rice paddy soil. These results indicate that the FSC isolation method is a useful tool to obtain functionally active single cells from environmental samples.
Keishi Senoo - One of the best experts on this subject based on the ideXlab platform.
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effects of copper on nitrous oxide n2o reduction in Denitrifiers and n2o emissions from agricultural soils
Biology and Fertility of Soils, 2020Co-Authors: Weishou Shen, Toru Fujiwara, Kazuo Isobe, Huaiwen Xue, Nan Gao, Yutaka Shiratori, Takehiro Kamiya, Keishi SenooAbstract: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.
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inoculation with nitrous oxide n2o reducing denitrifier strains simultaneously mitigates n2o emission from pasture soil and promotes growth of pasture plants
Soil Biology & Biochemistry, 2016Co-Authors: Weishou Shen, Hiroko Kakuta, Noriko Takaya, Tomoyasu Nishizawa, Shigeto Otsuka, Tadashi Nagamine, Toru Fujiwara, Kazuo Isobe, Nobuhiro Tanaka, Keishi SenooAbstract:Abstract The aim of this study was to screen nitrous oxide (N 2 O)-reducing denitrifier strains showing both N 2 O mitigation and plant growth-promoting (PGP) effects in soil systems, and the effects of selected strains were monitored in soil and plant, analyzed, and comparatively evaluated. Forty denitrifier strains affiliated with Azospirillum and Herbaspirillum , previously isolated from three different paddy soils, were evaluated. Of these, 11 produced indole-3-acetic acid (>5 μg mL −1 ), 9 promoted the growth of red clover ( Trifolium pratense L. var. Medium) or timothy ( Phleum pratense L. var. Horizon) on agar plates, and 7 were inoculated into two different soils for cultivating red clover and timothy in a greenhouse. Compared with non-inoculated control, N 2 O flux from red clover soil and from timothy soil were significantly lower 8 and 14 days and 9 days onwards, respectively, after inoculation with these seven strains. Cumulative N 2 O emissions from red clover soil were significantly lowered through inoculation with these seven strains. The growth parameters, including plant height, leaf area, fresh weight or dry weight, of the two pasture plants were significantly greater in soils inoculated with most of these seven strains than in non-inoculated soils. The uptake of C and N by the two pasture plants was significantly greater in soils inoculated with most of these seven strains than in non-inoculated soils. In conclusion, inoculating N 2 O-reducing Denitrifiers to pasture soil could mitigate N 2 O emissions and simultaneously promote the growth of pasture plants in a greenhouse. These strains will be invaluable microbiological resources for developing novel biofertilizers.
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phylogenetic and functional diversity of denitrifying bacteria isolated from various rice paddy and rice soybean rotation fields
Microbes and Environments, 2011Co-Authors: Kanako Tago, Tomoyasu Nishizawa, Shigeto Otsuka, Satoshi Ishii, Keishi SenooAbstract:Denitrifiers can produce and consume nitrous oxide (N2O). While little N2O is emitted from rice paddy soil, the same soil produces N2O when the land is drained and used for upland crop cultivation. In this study, we collected soils from two types of fields each at three locations in Japan; one type of field had been used for continuous cultivation of rice and the other for rotational cultivation of rice and soybean. Active Denitrifiers were isolated from these soils using a functional single-cell isolation method, and their taxonomy and denitrifying properties were examined. A total of 110 Denitrifiers were obtained, including those previously detected by a culture-independent analysis. Strains belonging to the genus Pseudogulbenkiania were dominant at all locations, suggesting that Pseudogulbenkiania Denitrifiers are ubiquitous in various rice paddy soils. Potential denitrifying activity was similar among the strains, regardless of the differences in taxonomic position and soil of origin. However, relative amounts of N2 in denitrification end products varied among strains isolated from different locations. Our results also showed that crop rotation had minimal impact on the functional diversity of the denitrifying strains. These results indicate that soil and other environmental factors, excluding cropping systems, could select for N2-producing Denitrifiers.
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isolation of functional single cells from environments using a micromanipulator application to study denitrifying bacteria
Applied Microbiology and Biotechnology, 2010Co-Authors: Naoaki Ashida, Shigeto Otsuka, Kanako Tago, Satoshi Ishii, Sadakazu Hayano, Takashi Tsuji, Yoshitaka Yoshimura, Keishi SenooAbstract:We developed a novel method to isolate functionally active single cells from environmental samples and named it the functional single-cell (FSC) isolation method. This method is based on a combination of substrate-responsive direct viable counts, live-cell staining with 5-carboxyfluorescein diacetate acetoxymethyl ester, and micromanipulation followed by cultivation in a medium. To evaluate this method, we applied it to study a denitrifying community in rice paddy soil. Similar denitrifier counts were obtained by the conventional most probable number analysis and our FSC isolation method. Using the FSC isolation method, 37 denitrifying bacteria were isolated, some of which harbored copper-containing nitrite reductase gene (nirK). The 16S rRNA gene analysis showed that members belonging to the genera Azospirillum and Ochrobactrum may be the major Denitrifiers in the rice paddy soil. These results indicate that the FSC isolation method is a useful tool to obtain functionally active single cells from environmental samples.
Duujong Lee - One of the best experts on this subject based on the ideXlab platform.
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facultative autotrophic Denitrifiers in denitrifying sulfide removal granules
Bioresource Technology, 2013Co-Authors: Duujong Lee, Xiangliang Pan, Aijie WangAbstract:The denitrifying sulfide removal (DSR) process applied autotrophic and heterotrophic denitrification pathways to achieve simultaneous conversion of nitrate to N, sulfide to elementary sulfur, and organic substances to CO. However, autotrophic Denitrifiers and heterotrophic Denitrifiers have to grow at comparable rates so the long-term DSR stability can be maintained. This work assessed the autotrophic and heterotrophic denitrification activities by 16 isolates from anaerobic granules collected from a DSR-expanded granular sludge bed reactor. A group of strains with closest relatives as Pseudomonas sp. (89.9-98.3% similarity), Agrobacterium sp. (94.6% similarity) and Acinetobacter sp. (96.6% similarity) were identified with both autotrophic and heterotrophic denitrification capabilities. These facultative autotrophic Denitrifiers can be applied as potential strains for lifting the limitation by balanced growth of two distinct bacterial groups in the DSR reactor.
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aerobic denitrification by novel isolated strain using no n as nitrogen source
Bioresource Technology, 2011Co-Authors: Chunli Wan, Xue Yang, Duujong Lee, Fang Wan, Chuan ChenAbstract:Biological denitrification reaction can be achieved under aerobic environment. Few aerobic Denitrifiers using nitrite as sole nitrogen source were identified. Using nitrite as the sole nitrogen source, this work assessed the denitrification activity of yy7, an aerobic heterotrophic denitrifier identified as Pseudomonas sp. (94% similarity) by 16S rRNA sequencing analysis. The logistic equation describes the cell growth curve, yielding a generation time of 2.9h at an initial 18 mg l(-1)NO(-)₂-N. Reduction of NO(-)₂-N was primarily achieved during its logarithmic growth phase, and was accompanied by an increase in suspension pH and near complete consumption of dissolved oxygen. Three genes relating to nirK, norB, and nosZ were noted to involve in isolate strain. Isolate yy7 can survive and remove up to 40 mg l(-1)NO(-)₂-N and, hence, can be applied as an effective aerobic denitrifier during simultaneous nitrification and denitrification via nitrite processes.
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enhanced performance of denitrifying sulfide removal process under micro aerobic condition
Journal of Hazardous Materials, 2010Co-Authors: Chuan Chen, Duujong Lee, Nanqi Ren, Aijie Wang, Lihong LiuAbstract:The denitrifying sulfide removal (DSR) process with bio-granules comprising both heterotrophic and autotrophic Denitrifiers can simultaneously convert nitrate, sulfide and acetate into di-nitrogen gas, elementary sulfur and carbon dioxide, respectively, at high loading rates. This study determines the reaction rate of sulfide oxidized into sulfur, as well as the reduction of nitrate to nitrite, would be enhanced under a micro-aerobic condition. The presence of limited oxygen mitigated the inhibition effects of sulfide on denitrifier activities, and enhanced the performance of DSR granules. The advantages and disadvantages of applying the micro-aerobic condition to the DSR process are discussed.