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Research has been conducted on soil microbial communities. The effect of ammonium addition on these communities has been investigated, and the results demonstrate that ammonium addition has increased nitrification activity but did not affect ammonium oxidisers' community structure.

Research has been conducted on the nitrite reductase gene fragments from the denitrifying prokaryotes in marsh soil and forest upland. The genetic heterogeneity of these fragments has been investigated via the use of the molecular methods and the results demonstrate that the soil denitrifying communities contain various members.

Redox gradients in marine sediments probably arise from different metabolic activity of similar bacterial communities rather than from the development of different communities. These gradients occur in the top few millimeters to centimeters of soil.

Research has been conducted on the denitrifying bacteria genetic heterogeneity. The use of the single-copy genes that code for nitrite reductases as denitrifyng bacteria molecular markers is discussed.

A study reported the application of new primer systems for the nirK and nirS nitrite reductase genes through a system developed for the detection of denitrifying bacteria by the amplification of specific nitrite reductase gene fragments with polymerase chain reaction. Results suggested the suitability of the method for the qualitative discovery of denitrifying bacteria in environmental samples. This was exhibited by applying one generally amplifying primer combination for each nir gene developed.

An ARB-implemented tool, TRF-CUT, is developed to predict in silico the terminal restriction fragments of aligned small-subunit rRNA gene or functional gene sequences. This new tool is used to perform directed terminal restriction fragment length polymorphism analysis of pmoA products obtained from a forest soil and it has revealed that a novel cluster I methanotrophic bacteria is dominant.

A special variant of whole-cell hybridization termed recognition of individual genes-fluorescence in situ hybridization (RING-FISH) is used to understand the phylogeny of the organisms from which the nitrite reductase (nirK) gene originated. The results obtained from RING-FISH provide insight into the phylogenetic classification of nirK-type denitrifiers and the phylogeny and function of denitrifying microorganisms in the environment.

The influence of eight nonleguminous grassland plant species belonging to two functional groups on the composition of soil denitrifier communities is analyzed. The results have shown that individual species of nonleguminous plants have directly affected the composition of nitrifier communities in soil, but environmental conditions are shown to have additional significant effects.

Research has been conducted on nitric oxide reductase genes. The authors discuss the development of norB-specific primer sets used for detection of these genes, and the genetic diversity of nitric oxide reductase genes both in environmental samples and in pure culture.

Abstract: Rising atmospheric CO2 concentrations are expected to increase nitrous oxide (N2O) emissions from soils via changes in microbial nitrogen (N) transformations. Several studies have shown that N2O emission increases under elevated atmospheric CO2 (eCO2), but the underlying processes are not yet fully understood. Here, we present results showing changes in soil N transformation dynamics from the Giessen Free Air CO2 Enrichment (GiFACE): a permanent grassland that has been exposed to eCO2, +20% relative to ambient concentrations (aCO2), for 15 years. We applied in the field an ammonium‐nitrate fertilizer solution, in which either ammonium ( NH 4 +) or nitrate ( NO 3 −) was labelled with 15N. The simultaneous gross N transformation rates were analysed with a 15N tracing model and a solver method. The results confirmed that after 15 years of eCO2 the N2O emissions under eCO2 were still more than twofold higher than under aCO2. The tracing model results indicated that plant uptake of NH 4 + did not differ between treatments, but uptake of NO 3 − was significantly reduced under eCO2. However, the NH 4 + and NO 3 − availability increased slightly under eCO2. The N2O isotopic signature indicated that under eCO2 the sources of the additional emissions, 8,407 μg N2O–N/m2 during the first 58 days after labelling, were associated with NO 3 − reduction (+2.0%), NH 4 + oxidation (+11.1%) and organic N oxidation (+86.9%). We presume that increased plant growth and root exudation under eCO2 provided an additional source of bioavailable supply of energy that triggered as a priming effect the stimulation of microbial soil organic matter (SOM) mineralization and fostered the activity of the bacterial nitrite reductase. The resulting increase in incomplete denitrification and therefore an increased N2O:N2 emission ratio, explains the doubling of N2O emissions. If this occurs over a wide area of grasslands in the future, this positive feedback reaction may significantly accelerate climate change. [ABSTRACT FROM AUTHOR]

Continuously rising atmospheric CO2 concentrations may lead to an increased transfer of organic C from plants to the soil through rhizodeposition and may affect the interaction between the C- and N-cycle. For instance, fumigation of soils with elevated CO2 (eCO2) concentrations (20% higher compared to current atmospheric concentrations) at the Giessen Free-Air Carbon Dioxide Enrichment (GiFACE) sites resulted in a more than 2-fold increase of long-term N2O emissions and an increase in dissimilatory reduction of nitrate compared to ambient CO2 (aCO2).We hypothesized that the observed differences in soil functioning were based on differences in the abundance and composition of microbial communities in general and especially of those which are responsible for N-transformations in soil. We also expected eCO2 effects on soil parameters, such as on nitrate as previously reported. To explore the impact of long-term eCO2 on soil microbial communities, we applied a molecular approach (qPCR, T-RFLP, and 454 pyrosequencing). Microbial groups were analyzed in soil of three sets of two FACE plots (three replicate samples from each plot), which were fumigated with eCO2 and aCO2, respectively. N-fixers, denitrifiers, archaeal and bacterial ammonia oxidizers, and dissimilatory nitrate reducers producing ammonia were targeted by analysis of functional marker genes, and the overall archaeal community by 16S rRNA genes. Remarkably, soil parameters as well as the abundance and composition of microbial communities in the top soil under eCO2 differed only slightly from soil under aCO2. Wherever differences in microbial community abundance and composition were detected, they were not linked to CO2 level but rather determined by differences in soil parameters (e.g., soil moisture content) due to the localization of the GiFACE sets in the experimental field. We concluded that +20% eCO2 had little to no effect on the overall microbial community involved in N-cycling in the soil but that spatial heterogeneity over extended periods had shaped microbial communities at particular sites in the field. Hence, microbial community composition and abundance alone cannot explain the functional differences leading to higher N2O emissions under eCO2 and future studies should aim at exploring the active members of the soil microbial community. [ABSTRACT FROM AUTHOR]

RATIONALE Fungi can contribute greatly to N2O production from denitrification. Therefore, it is important to quantify the isotopic signature of fungal N2O. The isotopic composition of N2O can be used to identify and analyze the processes of N2O production and N2O reduction. In contrast to bacteria, information about the oxygen exchange between denitrification intermediates and water during fungal denitrification is lacking, impeding the explanatory power of stable isotope methods. METHODS Six fungal species were anaerobically incubated with the electron acceptors nitrate or nitrite and 18O-labeled water to determine the oxygen exchange between denitrification intermediates and water. After seven days of incubation, gas samples were analyzed for N2O isotopologues by isotope ratio mass spectrometry. RESULTS All the fungal species produced N2O. N2O production was greater when nitrite was the sole electron acceptor (129 to 6558 nmol N2O g dw-1 h-1) than when nitrate was the electron acceptor (6 to 47 nmol N2O g dw-1 h-1). Oxygen exchange was complete with nitrate as electron acceptor in one of five fungi and with nitrite in two of six fungi. Oxygen exchange of the other fungi varied (41 to 89 % with nitrite and 11 to 61 % with nitrate). CONCLUSIONS This is the first report on oxygen exchange with water during fungal denitrification. The exchange appears to be within the range previously reported for bacterial denitrification. This adds to the difficulty of differentiating N2O producing processes based on the origin of N2O-O. However, the large oxygen exchange repeatedly observed for bacteria and now also fungi could lead to less variability in the δ18O values of N2O from soils, which could facilitate the assessment of the extent of N2O reduction. Copyright © 2013 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Denitrifying prokaryotes are phylogenetically and functionally diverse. Little is known about the relationship between soil denitrifier community composition and functional traits. We extracted bacterial cells from three cultivated peat soils with contrasting native pH by density gradient centrifugation and investigated their kinetics of oxygen depletion and [ABSTRACT FROM AUTHOR]

Microorganisms capable of denitrification are polyphyletic and exhibit distinct denitrification regulatory phenotypes ( DRP), and thus, denitrification in soils could be controlled by community composition. In a companion study (Dörsch et al., 2012) and preceding work, ex situ denitrification assays of three organic soils demonstrated profoundly different functional traits including N2O/ N2 ratios. Here, we explored the composition of the underlying denitrifier communities by analyzing the abundance and structure of denitrification genes ( nirK, nirS, and nosZ). The relative abundance of nosZ (vs. nirK + nirS) was similar for all communities, and hence, the low N2O reductase activity in one of the soils was not because of the lack of organisms with this gene. Similarity in community composition between the soils was generally low for nirK and nirS, but not for nosZ. The community with the most robust denitrification (consistently low N2O/ N2) had the highest diversity/richness of nosZ and nirK, but not of nirS. Contrary results found for a second soil agreed with impaired denitrification (low overall denitrification activity, high N2O/ N2). In conclusion, differences in community composition and in the absolute abundance of denitrification genes clearly reflected the functional differences observed in laboratory studies and may shed light on differences in in situ N2O emission of the soils. [ABSTRACT FROM AUTHOR]

To explore potential links between plant communities, soil denitrifiers and denitrifier function, the impact of presence, diversity (i.e. species richness) and plant combination on nirK-type denitrifier community composition and on denitrifier activity was studied in artificial grassland plant assemblages over two consecutive years. Mesocosms containing zero, four and eight species and different combinations of two species were set up. Differences in denitrifier community composition were analysed by canonical correspondence analyses following terminal restriction fragment length polymorphism analysis of PCR-amplified nirK gene fragments coding for the copper-containing nitrite reductase. As a measure of denitrifier function, denitrifier enzyme activity (DEA) was determined in the soil samples. The presence as well as the combination of plants and sampling time, but not plant diversity, affected the composition of the nirK-type denitrifier community and DEA. Denitrifier activity significantly increased in the presence of plants, especially when they were growing during summer and autumn. Overall, we found a strong and direct linkage of denitrifier community composition and functioning, but also that plants had additional effects on denitrifier function that could not be solely explained by their effects on nirK-type denitrifier community composition. [ABSTRACT FROM AUTHOR]

Discusses the effect of soil ammonium concentration on nitrous oxide release and on the community structure of ammonia oxidizers and denitrifiers. Soil samples; Experimental setup for nitrous oxide release; Molecular analysis; DNA extraction; Community analysis of bacteria and denitrifiers.

Rising atmospheric CO 2 concentrations are expected to increase nitrous oxide (N 2 O) emissions from soils via changes in microbial nitrogen (N) transformations. Several studies have shown that N 2 O emission increases under elevated atmospheric CO 2 (eCO 2 ), but the underlying processes are not yet fully understood. Here, we present results showing changes in soil N transformation dynamics from the Giessen Free Air CO 2 Enrichment (GiFACE): a permanent grassland that has been exposed to eCO 2 , +20% relative to ambient concentrations (aCO 2 ), for 15 years. We applied in the field an ammonium-nitrate fertilizer solution, in which either ammonium ( NH 4 + ) or nitrate ( NO 3 - ) was labelled with 15 N. The simultaneous gross N transformation rates were analysed with a 15 N tracing model and a solver method. The results confirmed that after 15 years of eCO 2 the N 2 O emissions under eCO 2 were still more than twofold higher than under aCO 2 . The tracing model results indicated that plant uptake of NH 4 + did not differ between treatments, but uptake of NO 3 - was significantly reduced under eCO 2 . However, the NH 4 + and NO 3 - availability increased slightly under eCO 2 . The N 2 O isotopic signature indicated that under eCO 2 the sources of the additional emissions, 8,407 μg N 2 O-N/m 2 during the first 58 days after labelling, were associated with NO 3 - reduction (+2.0%), NH 4 + oxidation (+11.1%) and organic N oxidation (+86.9%). We presume that increased plant growth and root exudation under eCO 2 provided an additional source of bioavailable supply of energy that triggered as a priming effect the stimulation of microbial soil organic matter (SOM) mineralization and fostered the activity of the bacterial nitrite reductase. The resulting increase in incomplete denitrification and therefore an increased N 2 O:N 2 emission ratio, explains the doubling of N 2 O emissions. If this occurs over a wide area of grasslands in the future, this positive feedback reaction may significantly accelerate climate change., (© 2018 John Wiley & Sons Ltd.)

Continuously rising atmospheric CO 2 concentrations may lead to an increased transfer of organic C from plants to the soil through rhizodeposition and may affect the interaction between the C- and N-cycle. For instance, fumigation of soils with elevated CO 2 ( e CO 2 ) concentrations (20% higher compared to current atmospheric concentrations) at the Giessen Free-Air Carbon Dioxide Enrichment (GiFACE) sites resulted in a more than 2-fold increase of long-term N 2 O emissions and an increase in dissimilatory reduction of nitrate compared to ambient CO 2 ( a CO 2 ). We hypothesized that the observed differences in soil functioning were based on differences in the abundance and composition of microbial communities in general and especially of those which are responsible for N-transformations in soil. We also expected e CO 2 effects on soil parameters, such as on nitrate as previously reported. To explore the impact of long-term e CO 2 on soil microbial communities, we applied a molecular approach (qPCR, T-RFLP, and 454 pyrosequencing). Microbial groups were analyzed in soil of three sets of two FACE plots (three replicate samples from each plot), which were fumigated with e CO 2 and a CO 2 , respectively. N-fixers, denitrifiers, archaeal and bacterial ammonia oxidizers, and dissimilatory nitrate reducers producing ammonia were targeted by analysis of functional marker genes, and the overall archaeal community by 16S rRNA genes. Remarkably, soil parameters as well as the abundance and composition of microbial communities in the top soil under e CO 2 differed only slightly from soil under a CO 2 . Wherever differences in microbial community abundance and composition were detected, they were not linked to CO 2 level but rather determined by differences in soil parameters (e.g., soil moisture content) due to the localization of the GiFACE sets in the experimental field. We concluded that +20% e CO 2 had little to no effect on the overall microbial community involved in N-cycling in the soil but that spatial heterogeneity over extended periods had shaped microbial communities at particular sites in the field. Hence, microbial community composition and abundance alone cannot explain the functional differences leading to higher N 2 O emissions under e CO 2 and future studies should aim at exploring the active members of the soil microbial community.

We studied the propensity of the tank bromeliad Werauhia gladioliflora to emit the greenhouse gas nitrous oxide (N 2 O) at current and at increased N deposition levels in the range of predicted future scenarios. Potential production rates and net accumulation of N 2 O from tank substrate corresponded to N availability. N 2 O was produced in excess at all N levels due to a low level of N 2 O reductase activity which agreed well with a low abundance of N 2 O reducers compared to nitrite reducers. Transcriptional activation, however, indicated that expression of denitrification genes may be enhanced with increasing N supply eventually leading to more efficient N 2 O turnover with potential for adaptation of denitrifier communities to higher N levels. Our findings indicate that tank bromeliads may constitute a novel source of N 2 O in Neotropical forest canopies but further studies are required to understand the size and significance of in situ N 2 O fluxes from tank bromeliads to the environment.