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Laurent Philippot - One of the best experts on this subject based on the ideXlab platform.
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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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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.
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insights into the effect of soil ph on n2o and n2 emissions and denitrifier community size and activity
Applied and Environmental Microbiology, 2010Co-Authors: Jiři Cuhel, Miloslav Simek, R J Laughlin, D Cheneby, C J Watson, Laurent PhilippotAbstract:The objective of this study was to investigate how changes in soil pH affect the N2O and N2 emissions, denitrification activity, and size of a denitrifier community. We established a field experiment, situated in a grassland area, which consisted of three treatments which were repeatedly amended with a KOH solution (alkaline soil), an H2SO4 solution (acidic soil), or water (natural pH soil) over 10 months. At the site, we determined field N2O and N2 emissions using the 15N gas flux method and collected soil samples for the measurement of potential denitrification activity and quantification of the size of the denitrifying community by quantitative PCR of the narG, napA, nirS, nirK, and nosZ denitrification genes. Overall, our results indicate that soil pH is of importance in determining the nature of denitrification end products. Thus, we found that the N2O/(N2O + N2) ratio increased with decreasing pH due to changes in the total denitrification activity, while no changes in N2O production were observed. Denitrification activity and N2O emissions measured under laboratory conditions were correlated with N fluxes in situ and therefore reflected treatment differences in the field. The size of the denitrifying community was uncoupled from in situ N fluxes, but potential denitrification was correlated with the count of NirS denitrifiers. Significant relationships were observed between nirS, napA, and narG gene copy numbers and the N2O/(N2O + N2) ratio, which are difficult to explain. However, this highlights the need for further studies combining analysis of denitrifier ecology and quantification of denitrification end products for a comprehensive understanding of the regulation of N fluxes by denitrification.
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mapping field scale spatial patterns of size and activity of the denitrifier community
Environmental Microbiology, 2009Co-Authors: Jiři Cuhel, D Cheneby, Laurent Philippot, David Bru, Nicolas P A Saby, Alicia Chroňakova, Dominique ArrouaysAbstract:There is ample evidence that microbial processes can exhibit large variations in activity on a field scale. However, very little is known about the spatial distribution of the microbial communities mediating these processes. Here we used geostatistical modelling to explore spatial patterns of size and activity of the denitrifying community, a functional guild involved in N-cycling, in a grassland field subjected to different cattle grazing regimes. We observed a non-random distribution pattern of the size of the denitrifier community estimated by quantification of the denitrification genes copy numbers with a macro-scale spatial dependence (6-16 m) and mapped the distribution of this functional guild in the field. The spatial patterns of soil properties, which were strongly affected by presence of cattle, imposed significant control on potential denitrification activity, potential N(2)O production and relative abundance of some denitrification genes but not on the size of the denitrifier community. Absolute abundance of most denitrification genes was not correlated with the distribution patterns of potential denitrification activity or potential N(2)O production. However, the relative abundance of bacteria possessing the nosZ gene encoding the N(2)O reductase in the total bacterial community was a strong predictor of the N(2)O/(N(2) + N(2)O) ratio, which provides evidence for a relationship between bacterial community composition based on the relative abundance of denitrifiers in the total bacterial community and ecosystem processes. More generally, the presented geostatistical approach allows integrated mapping of microbial communities, and hence can facilitate our understanding of relationships between the ecology of microbial communities and microbial processes along environmental gradients.
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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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.
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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 microg 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 degrees 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.
Sara Hallin - One of the best experts on this subject based on the ideXlab platform.
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habitat partitioning of marine benthic denitrifier communities in response to oxygen availability
Environmental Microbiology Reports, 2016Co-Authors: Lea Wittorf, Christopher M. Jones, German Bonillarosso, Ola Backman, Stefan Hulth, Sara HallinAbstract:Summary Denitrification is of global significance for the marine nitrogen budget and the main process for nitrogen loss in coastal sediments. This facultative anaerobic respiratory pathway is modular in nature and the final step, the reduction of nitrous oxide (N2O), is performed by microorganisms with a complete denitrification pathway as well as those only capable of N2O reduction. Fluctuating oxygen availability is a significant driver of denitrification in sediments, but the effects on the overall N2O-reducing community that ultimately controls the emission of N2O from marine sediments is not well known. To investigate the effects of different oxygen regimes on N2O reducing communities, coastal marine surface sediment was incubated in microcosms under oxic, anoxic or oscillating oxygen conditions in the overlying water for 137 days. Quantification of the genetic potential for denitrification, anammox and respiratory ammonification indicated that denitrification supported nitrogen removal in these sediments. Furthermore, denitrifiers with a complete pathway were identified as the dominant community involved in N2O reduction, rather than organisms that are only N2O reducers. Specific lineages within each group were associated with different oxygen regimes suggesting that oxygen availability in the overlying water is associated with habitat partitioning of N2O reducers in coastal marine surface sediments.
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microbial functional diversity enhances predictive models linking environmental parameters to ecosystem properties
Ecology, 2015Co-Authors: Jeff R Powell, Allana Welsh, Sara HallinAbstract:Microorganisms drive biogeochemical processes, but linking these processes to real changes in microbial communities under field conditions is not trivial. Here, we present a model-based approach to estimate independent contributions of microbial community shifts to ecosystem properties. The approach was tested empirically, using denitrification potential as our model process, in a spatial survey of arable land encompassing a range of edaphic conditions and two agricultural production systems. Soil nitrate was the most important single predictor of denitrification potential (the change in Akaike's information criterion, corrected for sample size, ΔAICc = 20.29); however, the inclusion of biotic variables (particularly the evenness and size of denitrifier communities [ΔAICc = 12.02], and the abundance of one denitrifier genotype [ΔAICc = 18.04]) had a substantial effect on model precision, comparable to the inclusion of abiotic variables (biotic R2 = 0.28, abiotic R2 = 0.50, biotic + abiotic R2 = 0.76). Thi...
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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.
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Ecological and evolutionary factors underlying global and local assembly of denitrifier communities
The ISME Journal, 2010Co-Authors: Christopher M. Jones, Sara HallinAbstract:The conversion of nitrite to nitric oxide in the denitrification pathway is catalyzed by at least two structurally dissimilar nitrite reductases, NirS and NirK. Although they are functionally equivalent, a genome with genes encoding both reductases has yet to be found. This exclusivity raises questions about the ecological equivalency of denitrifiers with either nirS or nirK , and how different ecological and evolutionary factors influence community assembly of nirS and nirK denitrifiers. Using phylogeny-based methods for analyzing community structure, we analyzed nirS and nirK data sets compiled from sequence repositories. Global patterns of phylogenetic community structure were determined using Unifrac, whereas community assembly processes were inferred using different community relatedness metrics. Similarities between globally distributed communities for both genes corresponded to similarities in habitat salinity. The majority of communities for both genes were phylogenetically clustered; however, nirK marine communities were more phylogenetically overdispersed than nirK soil communities or nirS communities. A more in-depth analysis was performed using three case studies in which a comparison of nirS and nirK community relatedness within the sites could be examined along environmental gradients. From these studies we observed that nirS communities respond differently to environmental gradients than nirK communities. Although it is difficult to attribute nonrandom patterns of phylogenetic diversity to specific niche-based or neutral assembly processes, our results indicate that coexisting nirS and nirK denitrifier communities are not under the same community assembly rules in different environments.
Tim J Daniell - One of the best experts on this subject based on the ideXlab platform.
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effect of model root exudate on denitrifier community dynamics and activity at different water filled pore space levels in a fertilised soil
Soil Biology & Biochemistry, 2018Co-Authors: Adrian Langaricafuentes, Marta Manrubia, Susan Mitchell, Madeline Giles, Tim J DaniellAbstract:Although a “rhizosphere effect” on denitrification rates has been established, a clear understanding of the effects of exudate addition on denitrifier community dynamics remains elusive. A microcosm experiment was designed to explore the interaction between exudate addition and soil moisture on community dynamics and denitrification rates. Artificial root exudate at 5 different carbon concentrations was added daily to soil microcosms at contrasting target WFPS (50, 70 and 90%). After a 7-day period, total denitrification and N2O emission rates were measured and community dynamics assessed using molecular methods. The response of denitrifier genes to exudate addition was different, with nirS and nosZ-I showing a stronger effect than nirK and nosZ-II. Distinct community structures were observed for nirS and nosZ-I at 90% target WFPS when compared to 50% and 70%. NirS denitrifier population size showed a ca. 5-fold increase in gene copy number at 90% WFPS when exudate was added at the highest C input. Significant total denitrification and N2O emission rates were observed only at 90% WFPS, which increased with C input. Our study improves the understanding of the complex interaction between microbial communities, the abiotic environment and process rates which can inform management practices aimed at increasing complete denitrification and controlling greenhouse gas production from agriculture.
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variable response of nirk and nirs containing denitrifier communities to long term ph manipulation and cultivation
Fems Microbiology Letters, 2018Co-Authors: Miriam B Herold, Madeline Giles, Colin J Alexander, Tim J Daniell, Elizabeth M BaggsAbstract:Denitrification is a key process responsible for the majority of soil nitrous oxide (N2O) emissions but the influences of pH and cultivation on the soil denitrifier community remain poorly understood. We hypothesised that the abundance and community structure of the total bacterial community and bacterial denitrifiers would be pH sensitive and that nirK and nirS containing denitrifiers would differ in their responses to change in pH and cultivation. We investigated the effect of long-term pH adjusted soils (ranging from pH 4.2 to pH 6.6) under different lengths of grass cultivation (one, two and three years of ley grass) on the general bacterial and denitrifier functional communities using 16S rRNA, nirK and nirS genes as markers. Denitrifier abundance increased with pH, and at pH below 4.7 there was a greater loss in nirS abundance per unit drop in pH than soils above this threshold pH. All community structures responded to changes in soil pH whilst cultivation only influenced the community structure of nirK. These differences in denitrifier responses highlight the importance of considering both nirK and nirS gene markers for estimating denitrifier activity. Identifying such thresholds in response of the microbial community to changes in pH is essential to understanding impacts of management or environmental change.
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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isolation of oligotrophic denitrifiers carrying previously uncharacterized functional gene sequences
Applied and Environmental Microbiology, 2011Co-Authors: Satoshi Ishii, Shigeto Otsuka, Naoaki Ashida, Keishi SenooAbstract:Oligotrophic denitrifying bacteria, including those belonging to the genera Herbaspirillum, Azospirillum, and Bradyrhizobium, were obtained using a single-cell isolation technique. The taxonomic composition of the denitrifier population was similar to those assessed by previous culture-independent studies. The sequencing of nitrite reductase and N2O reductase genes of these strains revealed previously unknown links between 16S rRNA and the denitrification-functional gene phylogenies. In particular, we identified Bradyrhizobium strains that harbor nirS sequences previously detected only in culture-independent studies.