Influence of maize mucilage on the diversity and activity of the denitrifying community

Pollution abatement reducing the river N2O emissions although it is partially offset by a warming climate: Insights from an urbanized watershed study

Global nitrogen (N) pollution has resulted in increased river nitrous oxide (N₂O) emissions, which contribute to climate change. However, little is known about how pollution abatement conversely reduces river N₂O production in a warming climate. Here, field observations and microcosmic experiments were conducted in a coastal urbanized watershed (S.E. China) to explore the interactive effect of changing nitrate and temperature on river sediment denitrification (DNF) and N₂O production. The results showed that urban river reaches (UR) with higher organic carbon content and denitrifying gene abundance in sediments have a greater DNF rate, nitrate removal efficiency (NRE), and N₂O concentration than agricultural river reaches (AR). Microcosmic incubation suggested that the DNF rate and associated N₂O production decreased under low nitrate addition, wherein the NRE increased. The scenario simulation illustrated a nonlinear response of N₂O production to nitrate removal (i.e., ΔN₂O/ΔNO₃-N) from both UR and AR sediments at a given temperature, and the DNF rate and N₂O production increased with increasing temperature. An increase in temperature by 1 degree Celsius would offset 18.75% of the N₂O reduction by nitrate removal via DNF. These findings implied that watershed pollution abatement undoubtedly contributes to the reduction in global river N₂O emissions although it is partially offset by extra N₂O production caused by global warming.

Soil characteristics and redox properties of infiltrating water are determinants of microbial communities at managed aquifer recharge sites

In this study, we conducted a meta-analysis of soil microbial communities at three, pilot-scale field sites simulating shallow infiltration for managed aquifer recharge (MAR). We evaluated shifts in microbial communities after infiltration across site location, through different soils, with and without carbon-rich amendments added to test plots. Our meta-analysis aims to enable more effective MAR basin design by identifying potentially important interactions between soil physical-geochemical parameters and microbial communities across several geographically separate MAR basins. We hypothesized infiltration and carbon amendments would lead to common changes in subsurface microbial communities at multiple field sites but instead found distinct differences. Sites with coarser (mainly sandy) soil had large changes in diversity and taxa abundance, while sites with finer soils had fewer significant changes in genera, despite having the greatest increase in nitrogen cycling. Below test plots amended with a carbon-rich permeable reactive barrier, we observed more nitrate removal and a decrease in genera capable of nitrification. Multivariate statistics determined that the soil texture (a proxy for numerous soil characteristics) was the main determinant of whether the microbial community composition changed because of infiltration. These results suggest that microbial communities in sandy soil with carbon-rich amendments are most impacted by infiltration. Soil composition is a critical parameter that links between microbial communities and nutrient cycling during infiltration and could influence the citing and operation of MAR to benefit water quality and supply.

Beneficial and pathogenic plant-microbe interactions during flooding stress

The number and intensity of flood events will likely increase in the future, raising the risk of flooding stress in terrestrial plants. Understanding flood effects on plant physiology and plant-associated microbes is key to alleviate flooding stress in sensitive species and ecosystems. Reduced oxygen supply is the main constrain to the plant and its associated microbiome. Hypoxic conditions hamper root aerobic respiration and, consequently, hydraulic conductance, nutrient uptake, and plant growth and development. Hypoxia favours the presence of anaerobic microbes in the rhizosphere and roots with potential negative effects to the plant due to their pathogenic behaviour or their soil denitrification ability. Moreover, plant physiological and metabolic changes induced by flooding stress may also cause dysbiotic changes in endosphere and rhizosphere microbial composition. The negative effects of flooding stress on the holobiont (i.e., the host plant and its associated microbiome) can be mitigated once the plant displays adaptive responses to increase oxygen uptake. Stress relief could also arise from the positive effect of certain beneficial microbes, such as mycorrhiza or dark septate endophytes. More research is needed to explore the spiralling, feedback flood responses of plant and microbes if we want to promote plant flood tolerance from a holobiont perspective.

A review of root exudates and rhizosphere microbiome for crop production

Increasing crop yields and ensuring food security is a major global challenge. In order to increase crop production, chemical fertilizers and pesticides are excessively used. However, the significance of root exudates is understudied. Beneficial interactions between plant and rhizosphere microbiome are critical for plant fitness and health. In this review, we discuss the application and progress of current research methods and technologies in terms of root exudates and rhizosphere microbiome. We summarize how root exudates promote plant access to nitrogen, phosphorus, and iron, and how root exudates strengthen plant immunity to cope with biotic stress by regulating the rhizosphere microbiome, and thereby reducing dependence on fertilizers and pesticides. Optimizing these interactions to increase plant nutrient uptake and resistance to biotic stresses offers one of the few untapped opportunities to confront sustainability issues in food security. To overcome the limitations of current research, combination of multi-omics, imaging technology together with synthetic communities has the potential to uncover the interaction mechanisms and to fill the knowledge gap for their applications in agriculture to achieve sustainable development.

A comparison of nitrate removal and denitrifying bacteria populations among three wetland plant communities

Reed canary grass (Phalaris arundinacea L.) is an invasive, cool-season grass commonly dominating wetlands with high nutrient loads. Its impact on nitrogen removal via denitrification in wetlands is unknown. Most studies of denitrification in treatment wetlands have focused on the effects of physical or chemical variables and not on the effects of plant roots on the soil environment. The purpose of this study was to measure effects of plant type on denitrification rates in typical wetland soils of the midwestern United States by comparing wet prairie mix, switchgrass-dominated, and reed canary grass plant communities. Nitrate (NO₃ ^- ) removal and other parameters were measured in miniature wetlands, or mesocosms, containing each plant community transplanted from a small agricultural treatment wetland in southern Minnesota. Quantitative polymerase chain reaction analysis was used to quantify the total bacteria population (measured with 16S rRNA genes) and denitrifying gene abundance (measured with nosZ genes) from the rhizosphere of each plant community. The wet prairie mix mesocosms on average removed the most NO₃ ^- in each test (p = .01 and .08). Whereas the wet prairie mix removed the most NO₃ ^- from the surface water (p < .01), reed canary grass removed more from the subsurface (p < .01). Ratios of denitrifying to total bacteria were higher in the wet prairie mix than in the other communities' root zones (p < .05). Results suggest that reed canary grass invasion could reduce denitrification in wetlands, especially during the spring and fall when it is growing but other plants are dormant.

Annual replication is essential in evaluating the response of the soil microbiome to the genetic modification of maize in different biogeographical regions

The importance of geographic location and annual variation on the detection of differences in the rhizomicrobiome caused by the genetic modification of maize (Bt-maize, event MON810) was evaluated at experimental field sites across Europe including Sweden, Denmark, Slovakia and Spain. DNA of the rhizomicrobiome was collected at the maize flowering stage in three consecutive years and analyzed for the abundance and diversity of PCR-amplified structural genes of Bacteria, Archaea and Fungi, and functional genes for bacterial nitrite reductases (nirS, nirK). The nirK genes were always more abundant than nirS. Maize MON810 did not significantly alter the abundance of any microbial genetic marker, except for sporadically detected differences at individual sites and years. In contrast, annual variation between sites was often significant and variable depending on the targeted markers. Distinct, site-specific microbial communities were detected but the sites in Denmark and Sweden were similar to each other. A significant effect of the genetic modification of the plant on the community structure in the rhizosphere was detected among the nirK denitrifiers at the Slovakian site in only one year. However, most nirK sequences with opposite response were from the same or related source organisms suggesting that the transient differences in community structure did not translate to the functional level. Our results show a lack of effect of the genetic modification of maize on the rhizosphere microbiome that would be stable and consistent over multiple years. This demonstrates the importance of considering annual variability in assessing environmental effects of genetically modified crops.

Shifts in the Composition and Activities of Denitrifiers Dominate CO2 Stimulation of N2O Emissions

Elevated atmospheric CO₂ (eCO₂) often increases soil N₂O emissions, but the underlying mechanisms remain largely unknown. One hypothesis suggests that high N₂O emissions may stem from increased denitrification induced by CO₂ enhancement of plant carbon (C) allocation belowground. However, direct evidence illustrating linkages among N₂O emissions, plant C allocation, and denitrifying microbes under eCO₂ is still lacking. We examined the impact of eCO₂ on plant C allocation to roots and their associated arbuscular mycorrhizal fungi and its subsequent effects on N₂O emissions and denitrifying microbes in the presence of two distinct N sources, ammonium nitrogen (NH₄⁺-N) and nitrate nitrogen (NO₃^--N). Our results showed that the form of the N inputs dominated the effects of eCO₂ on N₂O emissions: eCO₂ significantly increased N₂O emissions with NO₃^--N inputs but had no effect with NH₄⁺-N inputs. eCO₂ increased plant biomass N more with NH₄⁺-N than with NO₃^--N inputs, likely reducing microbial access to available N under NH₄⁺-N inputs and/or contributing to higher N₂O emissions under NO₃^--N inputs. eCO₂ enhanced root and mycorrhizal N uptake and also increased N₂O emissions under NO₃^--N inputs. Further, eCO₂ enhancement of N₂O emissions under NO₃^--N inputs concurred with a shift in the soil denitrifier community composition in favor of N₂O-producing (nirK- and nirS-type) over N₂O-consuming (nosZ-type) denitrifiers. Together, these results indicate that eCO₂ stimulated N₂O emissions mainly through altering plant N preference in favor of NH₄⁺ over NO₃^- and thus stimulating soil denitrifiers and their activities. These findings suggest that effective management of N sources may mitigate N₂O emissions by negating the eCO₂ stimulation of soil denitrifying microbes and their activities.

Plant Nutrient Resource Use Strategies Shape Active Rhizosphere Microbiota Through Root Exudation

Plant strategies for soil nutrient uptake have the potential to strongly influence plant-microbiota interactions, due to the competition between plants and microorganisms for soil nutrient acquisition and/or conservation. In the present study, we investigate whether these plant strategies could influence rhizosphere microbial activities via root exudation, and contribute to the microbiota diversification of active bacterial communities colonizing the root-adhering soil (RAS) and inhabiting the root tissues. We applied a DNA-based stable isotope probing (DNA-SIP) approach to six grass species distributed along a gradient of plant nutrient resource strategies, from conservative species, characterized by low nitrogen (N) uptake, a long lifespans and low root exudation level, to exploitative species, characterized by high rates of photosynthesis, rapid rates of N uptake and high root exudation level. We analyzed their (i) associated microbiota composition involved in root exudate assimilation and soil organic matter (SOM) degradation by 16S-rRNA-based metabarcoding. (ii) We determine the impact of root exudation level on microbial activities (denitrification and respiration) by gas chromatography. Measurement of microbial activities revealed an increase in denitrification and respiration activities for microbial communities colonizing the RAS of exploitative species. This increase of microbial activities results probably from a higher exudation rate and more diverse metabolites by exploitative plant species. Furthermore, our results demonstrate that plant nutrient resource strategies have a role in shaping active microbiota. We present evidence demonstrating that plant nutrient use strategies shape active microbiota involved in root exudate assimilation and SOM degradation via root exudation.

Interacting effect of diclofop-methyl on the rice rhizosphere microbiome and denitrification

A better knowledge of the intertwined effects of herbicides on plant physiology and microbiome as well as nutrient biogeochemical cycles are needed for environmental management. Here we studied the influence of herbicide diclofop-methyl (DM) on the rice root microbiome and its relationship with N cycle. To do so, we exposed rice seedlings to 100 μg/L DM and studied rhizosphere microbiota using MiSeq-pyrosequencing, root exudation by GC-MS, and denitrification activity by ¹⁵N isotope-tracing and qRT-PCR. The richness and diversity of rhizosphere microorganisms, significantly increased after DM exposure combined with an increase in root exudation of amino acids, sugars, and fatty acids. Transcription of denitrification-related gene and denitrification rate increased significantly in the rice rhizosphere. Our results suggest that DM strongly influenced the root exudation of bacteria nutrients, which affected root microbiome community and potentially influenced N cycle in rice rhizosphere.

The effects of plant nutritional strategy on soil microbial denitrification activity through rhizosphere primary metabolites

The aim of this study was to determine (i) whether plant nutritional strategy affects the composition of primary metabolites exuded into the rhizosphere and (ii) the impact of exuded metabolites on denitrification activity in soil. We answered this question by analysing primary metabolite content extracted from the root-adhering soil (RAS) and the roots of three grasses representing different nutrient management strategies: conservative (Festuca paniculata), intermediate (Bromus erectus) and exploitative (Dactylis glomerata). We also investigated the impact of primary metabolites on soil microbial denitrification enzyme activity without carbon addition, comparing for each plant RAS and bulk soils. Our data show that plant nutritional strategy impacts on primary metabolite composition of root extracts or RAS. Further we show, for the first time, that RAS-extracted primary metabolites are probably better indicators to explain plant nutrient strategy than root-extracted ones. In addition, our results show that some primary metabolites present in the RAS were well correlated with soil microbial denitrification activity with positive relationships found between denitrification and the presence of some organic acids and negative ones with the presence of xylose. We demonstrated that the analysis of primary metabolites extracted from the RAS is probably more pertinent to evaluate the impact of plant on soil microbial community functioning.

Impact of plant domestication on rhizosphere microbiome assembly and functions

The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. Plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. Domestication of plant species has substantially contributed to human civilization, but also caused a strong decrease in the genetic diversity of modern crop cultivars that may have affected the ability of plants to establish beneficial associations with rhizosphere microbes. Here, we review how plants shape the rhizosphere microbiome and how domestication may have impacted rhizosphere microbiome assembly and functions via habitat expansion and via changes in crop management practices, root exudation, root architecture, and plant litter quality. We also propose a "back to the roots" framework that comprises the exploration of the microbiome of indigenous plants and their native habitats for the identification of plant and microbial traits with the ultimate goal to reinstate beneficial associations that may have been undermined during plant domestication.

Effects of cowpea (Vigna unguiculata) root mucilage on microbial community response and capacity for phenanthrene remediation

Biodegradation of polycyclic aromatic hydrocarbons (PAHs) is normally limited by their low solubility and poor bioavailability. Prior research suggests that biosurfactants are synthesized as intermediates during the production of mucilage at the root tip. To date the effects of mucilage on PAH degradation and microbial community response have not been directly examined. To address this question, our research compared 3 cowpea breeding lines (Vigna unguiculata) that differed in mucilage production for their effects on phenanthrene (PHE) degradation in soil. The High Performance Liquid Chromatography results indicated that the highest PHE degradation rate was achieved in soils planted with mucilage producing cowpea line C1, inoculated with Bradyrhizobium, leading to 91.6% PHE disappearance in 5 weeks. In root printing tests, strings treated with mucilage and bacteria produced larger clearing zones than those produced on mucilage treated strings with no bacteria or bacteria inoculated strings. Experiments with 14C-PHE and purified mucilage in soil slurry confirmed that the root mucilage significantly enhanced PHE mineralization (82.7%), which is 12% more than the control treatment without mucilage. The profiles of the PHE degraders generated by Denaturing gradient gel electrophoresis suggested that cowpea C1, producing a high amount of root mucilage, selectively enriched the PHE degrading bacteria population in rhizosphere. These findings indicate that root mucilage may play a significant role in enhancing PHE degradation and suggests that differences in mucilage production may be an important criterion for selection of the best plant species for use in phytoremediation of PAH contaminated soils.

Denitrifier community in the oxygen minimum zone of a subtropical deep reservoir

Denitrification is an important pathway for nitrogen removal from aquatic systems and this could benefit water quality. However, little is known about the denitrifier community composition and key steps of denitrification in the freshwater environments, and whether different bacteria have a role in multiple processes of denitrification reduction. In this study, quantitative PCR, quantitative RT-PCR, clone library and 454 pyrosequencing were used together to investigate the bacterial and denitrifier community in a subtropical deep reservoir during the strongly stratified period. Our results indicated that the narG gene recorded the highest abundance among the denitrifying genes (2.76×10⁹ copies L⁻¹ for DNA and 4.19×10⁸ copies L⁻¹ for RNA), and the lowest value was nosZ gene (7.56×10⁵ copies L⁻¹ for DNA and undetected for RNA). The RNA: DNA ratios indicated that narG gene was the most active denitrifying gene in the oxygen minimum zone of Dongzhen Reservoir. Further, α-, β- and γ- Proteobacteria were the overwhelmingly dominant classes of denitrifier communities. Each functional gene had its own dominant groups which were different at the genus level: the narG gene was dominated by Albidiferax, while nirS gene was dominated by Dechloromonas. The main OTU of nirK gene was Rhodopseudomonas palustris, but for norB and nosZ genes, they were Bacillus and Bradyrhizobium, respectively. These results contribute to the understanding of linkages between denitrifier community, function and how they work together to complete the denitrification process. Studies on denitrifier community and activity may be useful in managing stratified reservoirs for the ecosystem services and aiding in constructing nitrogen budgets.

Stimulation of nitrogen removal in the rhizosphere of aquatic duckweed by root exudate components

Plants can stimulate bacterial nitrogen (N) removal by secretion of root exudates that may serve as carbon sources as well as non-nutrient signals for denitrification. However, there is a lack of knowledge about the specific non-nutrient compounds involved in this stimulation. Here, we use a continuous root exudate-trapping system in two common aquatic duckweed species, Spirodela polyrrhiza (HZ1) and Lemna minor (WX3), under natural and aseptic conditions. An activity-guided bioassay using denitrifying bacterium Pseudomonas fluorescens showed that crude root exudates of the two species strongly enhanced the nitrogen-removal efficiency (NRE) of P. fluorescens (P < 0.05) under both conditions. Water-insoluble fractions (F) obtained under natural conditions stimulated NRE to a significant extent, promoting rates by about 30%. Among acidic, neutral and basic fractions, a pronounced stimulatory effect was also observed for the neutral fractions from HZ1 and WX3 under both conditions, whereas the acidic fractions from WX3 displayed an inhibitory effect. Analysis of the active fractions using gas chromatography/mass spectrometry (GC/MS) revealed that duckweed released fatty acid methyl esters and fatty acid amides, specifically: methyl hexadecanoate, methyl (Z)-7-hexadecenoate, methyl dodecanoate, methyl-12-hydroxystearate, oleamide, and erucamide. Methyl (Z)-7-hexadecenoate and erucamide emerged as the effective N-removal stimulants (maximum stimulation of 25.9 and 33.4%, respectively), while none of the other tested compounds showed stimulatory effects. These findings provide the first evidence for a function of fatty acid methyl esters and fatty acid amides in stimulating N removal of denitrifying bacteria, affording insight into the "crosstalk" between aquatic plants and bacteria in the rhizosphere.

Different land use intensities in grassland ecosystems drive ecology of microbial communities involved in nitrogen turnover in soil

Understanding factors driving the ecology of N cycling microbial communities is of central importance for sustainable land use. In this study we report changes of abundance of denitrifiers, nitrifiers and nitrogen-fixing microorganisms (based on qPCR data for selected functional genes) in response to different land use intensity levels and the consequences for potential turnover rates. We investigated selected grassland sites being comparable with respect to soil type and climatic conditions, which have been continuously treated for many years as intensely used meadows (IM), intensely used mown pastures (IP) and extensively used pastures (EP), respectively. The obtained data were linked to above ground biodiversity pattern as well as water extractable fractions of nitrogen and carbon in soil. Shifts in land use intensity changed plant community composition from systems dominated by s-strategists in extensive managed grasslands to c-strategist dominated communities in intensive managed grasslands. Along the different types of land use intensity, the availability of inorganic nitrogen regulated the abundance of bacterial and archaeal ammonia oxidizers. In contrast, the amount of dissolved organic nitrogen determined the abundance of denitrifiers (nirS and nirK). The high abundance of nifH carrying bacteria at intensive managed sites gave evidence that the amounts of substrates as energy source outcompete the high availability of inorganic nitrogen in these sites. Overall, we revealed that abundance and function of microorganisms involved in key processes of inorganic N cycling (nitrification, denitrification and N fixation) might be independently regulated by different abiotic and biotic factors in response to land use intensity.

Soil functional operating range linked to microbial biodiversity and community composition using denitrifiers as model guild

Soil microorganisms are key players in biogeochemical cycles. Yet, there is no consistent view on the significance of microbial biodiversity for soil ecosystem functioning. According to the insurance hypothesis, declines in ecosystem functioning due to reduced biodiversity are more likely to occur under fluctuating, extreme or rapidly changing environmental conditions. Here, we compare the functional operating range, a new concept defined as the complete range of environmental conditions under which soil microbial communities are able to maintain their functions, between four naturally assembled soil communities from a long-term fertilization experiment. A functional trait approach was adopted with denitrifiers involved in nitrogen cycling as our model soil community. Using short-term temperature and salt gradients, we show that the functional operating range was broader and process rates were higher when the soil community was phylogenetically more diverse. However, key bacterial genotypes played an important role for maintaining denitrification as an ecosystem functioning under certain conditions.

Soil nitrate reducing processes - drivers, mechanisms for spatial variation, and significance for nitrous oxide production

The microbial processes of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two important nitrate reducing mechanisms in soil, which are responsible for the loss of nitrate ([Formula: see text]) and production of the potent greenhouse gas, nitrous oxide (N(2)O). A number of factors are known to control these processes, including O(2) concentrations and moisture content, N, C, pH, and the size and community structure of nitrate reducing organisms responsible for the processes. There is an increasing understanding associated with many of these controls on flux through the nitrogen cycle in soil systems. However, there remains uncertainty about how the nitrate reducing communities are linked to environmental variables and the flux of products from these processes. The high spatial variability of environmental controls and microbial communities across small sub centimeter areas of soil may prove to be critical in determining why an understanding of the links between biotic and abiotic controls has proved elusive. This spatial effect is often overlooked as a driver of nitrate reducing processes. An increased knowledge of the effects of spatial heterogeneity in soil on nitrate reduction processes will be fundamental in understanding the drivers, location, and potential for N(2)O production from soils.

Relationships between nitrogen transformation rates and gene abundance in a riparian buffer soil

Denitrification is a critical biogeochemical process that results in the conversion of nitrate to volatile products, and thus is a major route of nitrogen loss from terrestrial environments. Riparian buffers are an important management tool that is widely utilized to protect water from non-point source pollution. However, riparian buffers vary in their nitrate removal effectiveness, and thus there is a need for mechanistic studies to explore nitrate dynamics in buffer soils. The objectives of this study were to examine the influence of specific types of soluble organic matter on nitrate loss and nitrous oxide production rates, and to elucidate the relationships between these rates and the abundances of functional genes in a riparian buffer soil. Continuous-flow soil column experiments were performed to investigate the effect of three types of soluble organic matter (citric acid, alginic acid, and Suwannee River dissolved organic carbon) on rates of nitrate loss and nitrous oxide production. We found that nitrate loss rates increased as citric acid concentrations increased; however, rates of nitrate loss were weakly affected or not affected by the addition of the other types of organic matter. In all experiments, rates of nitrous oxide production mirrored nitrate loss rates. In addition, quantitative polymerase chain reaction (qPCR) was utilized to quantify the number of genes known to encode enzymes that catalyze nitrite reduction (i.e., nirS and nirK) in soil that was collected at the conclusion of column experiments. Nitrate loss and nitrous oxide production rates trended with copy numbers of both nir and 16s rDNA genes. The results suggest that low-molecular mass organic species are more effective at promoting nitrogen transformations than large biopolymers or humic substances, and also help to link genetic potential to chemical reactivity.

Effects of elevated CO2 on communities of denitrifying bacteria and methanogens in a temperate marsh microcosm

The effects of elevated CO(2) on soil bacterial community with upland vegetation have been widely studied, but limited information is available regarding responses of denitrifier and methanogen communities to elevated CO(2) in wetland ecosystems. Using restriction fragment length polymorphism (RFLP), terminal RFLP analysis, and real-time quantitative PCR, we compared communities of denitrifiers and methanogens in a laboratory-scale wetland system planted with one of three macrophytes, Typha latifolia, Scirpus lacustris, or Juncus effusus, after 110 days of incubation. Our study showed that elevated CO(2) could affect community structures of both denitrifiers and methanogens, each of which had a unique response pattern. In particular, elevated CO(2) shifted nirS-containing community with a unique structure irrespective of vegetation type. mcrA-containing community appeared to shift to community with unique types of hydrogenotrophs under elevated CO(2) conditions. The change of dissolved organic carbon driven by elevated CO(2) appeared to be related with the shift of both denitrifiers and methanogens. Overall, this study indicates that elevated CO(2) could change the community structure of denitrifiers and methanogens temporarily. These results also suggest a presence of stable dominant populations that were not substantially affected by changes in CO(2) concentration.

Influence of fertilisation regimes on a nosZ-containing denitrifying community in a rice paddy soil

BACKGROUND

Denitrification is a microbial process that has received considerable attention during the past decade since it can result in losses of added nitrogen fertilisers from agricultural soils. Paddy soil has been known to have strong denitrifying activity, but the denitrifying microorganisms responsible for fertilisers in paddy soil are not well known. The objective of this study was to explore the impacts of 17-year application of inorganic and organic fertiliser (rice straw) on the abundance and composition of a nosZ-denitrifier community in paddy soil. Soil samples were collected from CK plots (no fertiliser), N (nitrogen fertiliser), NPK (nitrogen, phosphorus and potassium fertilisers) and NPK + OM (NPK plus organic matter). The nitrous oxide reductase gene (nosZ) community composition was analysed using terminal restriction fragment length polymorphism, and the abundance was determined by quantitative PCR.

RESULTS

Both the largest abundance of nosZ-denitrifier and the highest potential denitrifying activity (PDA) occurred in the NPK + OM treatment with about four times higher than that in the CK and two times higher than that in the N and NPK treatments (no significant difference). Denitrifying community composition differed significantly among fertilisation treatments except for the comparison between CK and N treatments. Of the measured abiotic factors, total organic carbon was significantly correlated with the observed differences in community composition and abundance (P < 0.01 by Monte Carlo permutation).

CONCLUSION

This study shows that the addition of different fertilisers affects the size and composition of the nosZ-denitrifier community in paddy soil.

Assessment of denitrifying bacterial composition in activated sludge

The abundance and structure of denitrifying bacterial community in different activated sludge samples were assessed, where the abundance of denitrifying functional genes showed nirS in the range of 10(4)-10(5), nosZ with 10(4)-10(6) and 16S rRNA gene in the range 10(9)-10(10) copy number per ml of sludge. The culturable approach revealed Pseudomonas sp. and Alcaligenes sp. to be numerically high, whereas culture independent method showed betaproteobacteria to dominate the sludge samples. Comamonas sp. and Pseudomonas fluorescens isolates showed efficient denitrification, while Pseudomonas mendocina, Pseudomonas stutzeri and Brevundimonas diminuta accumulated nitrite during denitrification. Numerically dominant RFLP OTUs of the nosZ gene from the fertilizer factory sludge samples clustered with the known isolates of betaproteobacteria. The data also suggests the presence of different truncated denitrifiers with high numbers in sludge habitat.

Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops

Widespread adaptation of biomass production for bioenergy may influence important biogeochemical functions in the landscape, which are mainly carried out by soil microbes. Here we explore the impact of four potential bioenergy feedstock crops (maize, switchgrass, Miscanthus X giganteus, and mixed tallgrass prairie) on nitrogen cycling microorganisms in the soil by monitoring the changes in the quantity (real-time PCR) and diversity (barcoded pyrosequencing) of key functional genes (nifH, bacterial/archaeal amoA and nosZ) and 16S rRNA genes over two years after bioenergy crop establishment. The quantities of these N-cycling genes were relatively stable in all four crops, except maize (the only fertilized crop), in which the population size of AOB doubled in less than 3 months. The nitrification rate was significantly correlated with the quantity of ammonia-oxidizing archaea (AOA) not bacteria (AOB), indicating that archaea were the major ammonia oxidizers. Deep sequencing revealed high diversity of nifH, archaeal amoA, bacterial amoA, nosZ and 16S rRNA genes, with 229, 309, 330, 331 and 8989 OTUs observed, respectively. Rarefaction analysis revealed the diversity of archaeal amoA in maize markedly decreased in the second year. Ordination analysis of T-RFLP and pyrosequencing results showed that the N-transforming microbial community structures in the soil under these crops gradually differentiated. Thus far, our two-year study has shown that specific N-transforming microbial communities develop in the soil in response to planting different bioenergy crops, and each functional group responded in a different way. Our results also suggest that cultivation of maize with N-fertilization increases the abundance of AOB and denitrifiers, reduces the diversity of AOA, and results in significant changes in the structure of denitrification community.

Towards food, feed and energy crops mitigating climate change

Agriculture is an important source of anthropogenic emissions of the greenhouse gases (GHG), methane (CH(4)) and nitrous oxide (N(2)O), and crops can affect the microbial processes controlling these emissions in many ways. Here, we summarize the current knowledge of plant-microbe interactions in relation to the CH(4) and N(2)O budgets and show how this is promoting new generations of crop cultivars that have the potential to mitigate GHG emissions for future agricultural use. The possibility of breeding low GHG-emitting cultivars is a paradigm shift towards sustainable agriculture that balances climate change and food and bioenergy security.

Identification and isolation of active N2O reducers in rice paddy soil

Dissolved N(2)O is occasionally detected in surface and ground water in rice paddy fields, whereas little or no N(2)O is emitted to the atmosphere above these fields. This indicates the occurrence of N(2)O reduction in rice paddy fields; however, identity of the N(2)O reducers is largely unknown. In this study, we employed both culture-dependent and culture-independent approaches to identify N(2)O reducers in rice paddy soil. In a soil microcosm, N(2)O and succinate were added as the electron acceptor and donor, respectively, for N(2)O reduction. For the stable isotope probing (SIP) experiment, (13)C-labeled succinate was used to identify succinate-assimilating microbes under N(2)O-reducing conditions. DNA was extracted 24  h after incubation, and heavy and light DNA fractions were separated by density gradient ultracentrifugation. Denaturing gradient gel electrophoresis and clone library analysis targeting the 16S rRNA and the N(2)O reductase gene were performed. For culture-dependent analysis, the microbes that elongated under N(2)O-reducing conditions in the presence of cell-division inhibitors were individually captured by a micromanipulator and transferred to a low-nutrient medium. The N(2)O-reducing ability of these strains was examined by gas chromatography/mass spectrometry. Results of the SIP analysis suggested that Burkholderiales and Rhodospirillales bacteria dominated the population under N(2)O-reducing conditions, in contrast to the control sample (soil incubated with only (13)C-succinate). Results of the single-cell isolation technique also indicated that the majority of the N(2)O-reducing strains belonged to the genera Herbaspirillum (Burkholderiales) and Azospirillum (Rhodospirillales). In addition, Herbaspirillum strains reduced N(2)O faster than Azospirillum strains. These results suggest that Herbaspirillum spp. may have an important role in N(2)O reduction in rice paddy soils.

Effect of earthworm feeding guilds on ingested dissimilatory nitrate reducers and denitrifiers in the alimentary canal of the earthworm

The earthworm gut is an anoxic nitrous oxide (N(2)O)-emitting microzone in aerated soils. In situ conditions of the gut might stimulate ingested nitrate-reducing soil bacteria linked to this emission. The objective of this study was to determine if dissimilatory nitrate reducers and denitrifiers in the alimentary canal were affected by feeding guilds (epigeic [Lumbricus rubellus], anecic [Lumbricus terrestris], and endogeic [Aporrectodea caliginosa]). Genes and gene transcripts of narG (encodes a subunit of nitrate reductase and targets both dissimilatory nitrate reducers and denitrifiers) and nosZ (encodes a subunit of N(2)O reductase and targets denitrifiers) were detected in guts and soils. Gut-derived sequences were similar to those of cultured and uncultured soil bacteria and to soil-derived sequences obtained in this study. Gut-derived narG sequences and narG terminal restriction fragments (TRFs) were affiliated mainly with Gram-positive organisms (Actinobacteria). The majority of gut- and uppermost-soil-derived narG transcripts were affiliated with Mycobacterium (Actinobacteria). In contrast, narG sequences indicative of Gram-negative organisms (Proteobacteria) were dominant in mineral soil. Most nosZ sequences and nosZ TRFs were affiliated with Bradyrhizobium (Alphaproteobacteria) and uncultured soil bacteria. TRF profiles indicated that nosZ transcripts were more affected by earthworm feeding guilds than were nosZ genes, whereas narG transcripts were less affected by earthworm feeding guilds than were narG genes. narG and nosZ transcripts were different and less diverse in the earthworm gut than in mineral soil. The collective results indicate that dissimilatory nitrate reducers and denitrifiers in the earthworm gut are soil derived and that ingested narG- and nosZ-containing taxa were not uniformly stimulated in the guts of worms from different feeding guilds.

Identification and quantification of a novel nitrate-reducing community in sediments of Suquía River basin along a nitrate gradient

We evaluated the molecular diversity of narG gene from Suquía River sediments to assess the impact of the nitrate concentration and water quality on the composition and structure of the nitrate-reducing bacterial community. To this aim, a library of one of the six monitoring stations corresponding to the highest nitrate concentration was constructed and 118 narG clones were screened. Nucleotide sequences were associated to narG gene from alpha-, beta-, delta-, gammaproteobacteria and Thermus thermophilus. Remarkably, 18% of clones contained narG genes with less than 69% similarity to narG sequences available in databases. Thus, indicating the presence of nitrate-reducing bacteria with novel narG genes, which were quantified by real-time PCR. Results show a variable number of narG copies, ranging from less than 1.0 x 10(2) to 5.0 x 10(4) copies per ng of DNA, which were associated with a decreased water quality index monitored along the basin at different times.

Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE

We re-evaluated PCR primers targeting nirS, nirK and nosZ genes for denaturing gradient gel electrophoresis as a tool to survey denitrifying community composition in environmental samples. New primers for both nirS and nosZ were combined with existing primers, while for nirK the previously published F1aCu:R3Cu set was chosen for denaturing electrophoresis. All three sets yielded amplicons smaller than 500 bp and amplified the correct fragment in all environmental samples. The denaturing gradient gel electrophoresis worked satisfactorily for nirK and nosZ, but not for nirS. This was probably due to the multiple melting domains in this particular nirS fragment. From the excised and sequenced bands, only sequences related to the target genes were detected and tree analysis showed that the selected primers acted as broad range primers for each of the three genes. By use of the new nirS primers it was demonstrated that agricultural soil harbours a substantial diversity of nirS denitrifiers.

Genome-derived criteria for assigning environmental narG and nosZ sequences to operational taxonomic units of nitrate reducers

Ninety percent of cultured bacterial nitrate reducers with a 16S rRNA gene similarity of > or =97% had a narG or nosZ similarity of > or =67% or > or =80%, respectively, suggesting that 67% and 80% could be used as standardized, conservative threshold similarity values for narG and nosZ, respectively (i.e., any two sequences that are less similar than the threshold similarity value have a very high probability of belonging to different species), for estimating species-level operational taxonomic units. Genus-level tree topologies of narG and nosZ were generally similar to those of the corresponding 16S rRNA genes. Although some genomes contained multiple copies of narG, recent horizontal gene transfer of narG was not apparent.

Microbial community composition and denitrifying enzyme activities in salt marsh sediments

Denitrifying microbial communities and denitrification in salt marsh sediments may be affected by many factors, including environmental conditions, nutrient availability, and levels of pollutants. The objective of this study was to examine how microbial community composition and denitrification enzyme activities (DEA) at a California salt marsh with high nutrient loading vary with such factors. Sediments were sampled from three elevations, each with different inundation and vegetation patterns, across 12 stations representing various salinity and nutrient conditions. Analyses included determination of cell abundance, total and denitrifier community compositions (by terminal restriction fragment length polymorphism), DEA, nutrients, and eluted metals. Total bacterial (16S rRNA) and denitrifier (nirS) community compositions and DEA were analyzed for their relationships to environmental variables and metal concentrations via multivariate direct gradient and regression analyses, respectively. Community composition and DEA were highly variable within the dynamic salt marsh system, but each was strongly affected by elevation (i.e., degree of inundation) and carbon content as well as by selected metals. Carbon content was highly related to elevation, and the relationships between DEA and carbon content were found to be elevation specific when evaluated across the entire marsh. There were also lateral gradients in the marsh, as evidenced by an even stronger association between community composition and elevation for a marsh subsystem. Lastly, though correlated with similar environmental factors and selected metals, denitrifier community composition and function appeared uncoupled in the marsh.

A review of stable isotope techniques for N2O source partitioning in soils: recent progress, remaining challenges and future considerations

Nitrous oxide is produced in soil during several processes, which may occur simultaneously within different micro-sites of the same soil. Stable isotope techniques have a crucial role to play in the attribution of N(2)O emissions to different microbial processes, through estimation (natural abundance, site preference) or quantification (enrichment) of processes based on the (15)N and (18)O signatures of N(2)O determined by isotope ratio mass spectrometry. These approaches have the potential to become even more powerful when linked with recent developments in secondary isotope mass spectrometry, with microbial ecology, and with modelling approaches, enabling sources of N(2)O to be considered at a wide range of scales and related to the underlying microbiology. Such source partitioning of N(2)O is inherently challenging, but is vital to close the N(2)O budget and to better understand controls on the different processes, with a view to developing appropriate management practices for mitigation of N(2)O. In this respect, it is essential that as many of the contributing processes as possible are considered in any study aimed at source attribution, as mitigation strategies for one process may not be appropriate for another. To aid such an approach, here the current state of the art is critically examined, remaining challenges are highlighted, and recommendations are made for future direction.

Metaproteomics: a new approach for studying functional microbial ecology

In the postgenomic era, there is a clear recognition of the limitations of nucleic acid-based methods for getting information on functions expressed by microbial communities in situ. In this context, the large-scale study of proteins expressed by indigenous microbial communities (metaproteome) should provide information to gain insights into the functioning of the microbial component in ecosystems. Characterization of the metaproteome is expected to provide data linking genetic and functional diversity of microbial communities. Studies on the metaproteome together with those on the metagenome and the metatranscriptome will contribute to progress in our knowledge of microbial communities and their contribution in ecosystem functioning. Effectiveness of the metaproteomic approach will be improved as increasing metagenomic information is made available thanks to the environmental sequencing projects currently running. More specifically, analysis of metaproteome in contrasted environmental situations should allow (1) tracking new functional genes and metabolic pathways and (2) identifying proteins preferentially associated with specific stresses. These proteins considered as functional bioindicators should contribute, in the future, to help policy makers in defining strategies for sustainable management of our environment.

Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments

Estuarine systems are the major conduits for the transfer of nitrate from agricultural and other terrestrial-anthropogenic sources into marine ecosystems. Within estuarine sediments some microbially driven processes (denitrification and anammox) result in the net removal of nitrogen from the environment, while others (dissimilatory nitrate reduction to ammonium) do not. In this study, molecular approaches have been used to investigate the diversity, abundance, and activity of the nitrate-reducing communities in sediments from the hypernutrified Colne estuary, United Kingdom, via analysis of nitrate and nitrite reductase genes and transcripts. Sequence analysis of cloned PCR-amplified narG, napA, and nrfA gene sequences showed the indigenous nitrate-reducing communities to be both phylogenetically diverse and also divergent from previously characterized nitrate reduction sequences in soils and offshore marine sediments and from cultured nitrate reducers. In both the narG and nrfA libraries, the majority of clones (48% and 50%, respectively) were related to corresponding sequences from delta-proteobacteria. A suite of quantitative PCR primers and TaqMan probes was then developed to quantify phylotype-specific nitrate (narG and napA) and nitrite reductase (nirS and nrfA) gene and transcript numbers in sediments from three sites along the estuarine nitrate gradient. In general, both nitrate and nitrite reductase gene copy numbers were found to decline significantly (P < 0.05) from the estuary head towards the estuary mouth. The development and application, for the first time, of quantitative reverse transcription-PCR assays to quantify mRNA sequences in sediments revealed that transcript numbers for three of the five phylotypes quantified were greatest at the estuary head.

Microbial succession of nitrate-reducing bacteria in the rhizosphere of Poa alpina across a glacier foreland in the Central Alps

Changes in community structure and activity of the dissimilatory nitrate-reducing community were investigated across a glacier foreland in the Central Alps to gain insight into the successional pattern of this functional group and the driving environmental factors. Bulk soil and rhizosphere soil of Poa alpina was sampled in five replicates in August during the flowering stage and in September after the first snowfalls along a gradient from 25 to 129 years after deglaciation and at a reference site outside the glacier foreland (>2000 years deglaciated). In a laboratory-based assay, nitrate reductase activity was determined colorimetrically after 24 h of anaerobic incubation. In selected rhizosphere soil samples, the community structure of nitrate-reducing microorganisms was analysed by restriction fragment length polymorphism (RFLP) analysis using degenerate primers for the narG gene encoding the active site of the membrane-bound nitrate reductase. Clone libraries of the early (25 years) and late (129 years) succession were constructed and representative clones sequenced. The activity of the nitrate-reducing community increased significantly with age mainly due to higher carbon and nitrate availability in the late succession. The community structure, however, only showed a small shift over the 100 years of soil formation with pH explaining a major part (19%) of the observed variance. Clone library analysis of the early and late succession pointed to a trend of declining diversity with progressing age. Presumably, the pressure of competition on the nitrate reducers was relatively low in the early successional stage due to minor densities of microorganisms compared with the late stage; hence, a higher diversity could persist in this sparse environment. These results suggest that the nitrate reductase activity is regulated by environmental factors other than those shaping the genetic structure of the nitrate-reducing community.

Perception and modification of plant flavonoid signals by rhizosphere microorganisms

Flavonoids are a diverse class of polyphenolic compounds that are produced as a result of plant secondary metabolism. They are known to play a multifunctional role in rhizospheric plant-microbe and plant-plant communication. Most familiar is their function as a signal in initiation of the legume-rhizobia symbiosis, but, flavonoids may also be signals in the establishment of arbuscular mycorrhizal symbiosis and are known agents in plant defence and in allelopathic interactions. Flavonoid perception by, and impact on, their microbial targets (e.g. rhizobia, plant pathogens) is relatively well characterized. However, potential impacts on 'non-target' rhizosphere inhabitants ('non-target' is used to distinguish those microorganisms not conventionally known as targets) have not been thoroughly investigated. Thus, this review first summarizes the conventional roles of flavonoids as nod gene inducers, phytoalexins and allelochemicals before exploring questions concerning 'non-target' impacts. We hypothesize that flavonoids act to shape rhizosphere microbial community structure because they represent a potential source of carbon and toxicity and that they impact on rhizosphere function, for example, by accelerating the biodegradation of xenobiotics. We also examine the reverse question, 'how do rhizosphere microbial communities impact on flavonoid signals?' The presence of microorganisms undoubtedly influences the quality and quantity of flavonoids present in the rhizosphere, both through modification of root exudation patterns and microbial catabolism of exudates. Microbial alteration and attenuation of flavonoid signals may have ecological consequences for below-ground plant-microbe and plant-plant interaction. We have a lack of knowledge concerning the composition, concentration and bioavailability of flavonoids actually experienced by microbes in an intact rhizosphere, but this may be addressed through advances in microspectroscopic and biosensor techniques. Through the use of plant mutants defective in flavonoid biosynthesis, we may also start to address the question of the significance of flavonoids in shaping rhizosphere community structure and function.

Quantitative detection of the nosZ gene, encoding nitrous oxide reductase, and comparison of the abundances of 16S rRNA, narG, nirK, and nosZ genes in soils

Nitrous oxide (N2O) is an important greenhouse gas in the troposphere controlling ozone concentration in the stratosphere through nitric oxide production. In order to quantify bacteria capable of N2O reduction, we developed a SYBR green quantitative real-time PCR assay targeting the nosZ gene encoding the catalytic subunit of the nitrous oxide reductase. Two independent sets of nosZ primers flanking the nosZ fragment previously used in diversity studies were designed and tested (K. Kloos, A. Mergel, C. Rösch, and H. Bothe, Aust. J. Plant Physiol. 28:991-998, 2001). The utility of these real-time PCR assays was demonstrated by quantifying the nosZ gene present in six different soils. Detection limits were between 10(1) and 10(2) target molecules per reaction for all assays. Sequence analysis of 128 cloned quantitative PCR products confirmed the specificity of the designed primers. The abundance of nosZ genes ranged from 10(5) to 10(7) target copies g(-1) of dry soil, whereas genes for 16S rRNA were found at 10(8) to 10(9) target copies g(-1) of dry soil. The abundance of narG and nirK genes was within the upper and lower limits of the 16S rRNA and nosZ gene copy numbers. The two sets of nosZ primers gave similar gene copy numbers for all tested soils. The maximum abundance of nosZ and nirK relative to 16S rRNA was 5 to 6%, confirming the low proportion of denitrifiers to total bacteria in soils.

Analysis of denitrification genes and comparison of nosZ, cnorB and 16S rDNA from culturable denitrifying bacteria in potato cropping systems

Bacterial denitrification in agricultural soils is a major source of nitrous oxide, a potent greenhouse gas. This study examined the culturable bacterial population of denitrifiers in arable field soils in potato (Solanum tuberosum L.) production and denitrification genes (nir, nor and nos) and 16S rDNA in those isolates. Enrichments for culturable denitrifiers yielded 31 diverse isolates that were then analysed for denitrification genes. The nitrous oxide reductase (nosZ) gene was found in all isolates. The majority of isolates ( approximately 90%) contained the cnorB nitric oxide reductase gene, with the remainder containing the qnorB gene. Nitrite reductase genes (nirS and nirK) were amplifiable from most of the isolates, and were segregated between species similar to previously isolated denitrifiers. Isolated strains were preliminarily identified using fatty acid methyl ester analysis and further identified using 16S rDNA sequencing. The majority of isolates (21) were classified as Pseudomonas sp., with smaller groups of isolates being most similar to Bosea spp. (4), Achromobacter spp. (4) and two isolates closely related to Sinorhizobium/Ensifer spp. Phylogenetic trees were compared among nosZ, cnorB and 16S rDNA genes for a subset of Pseudomonas strains. The trees were mostly congruent, but some Pseudomonas sp. isolates grouped differently depending on the gene analysed, indicating potential horizontal gene transfer of denitrification genes. Although Bosea spp. are known denitrifiers, to the best of our knowledge this is the first report of isolation and sequencing of denitrification genes from this bacterial genus.

Nitrous oxide reductase genes (nosZ) of denitrifying microbial populations in soil and the earthworm gut are phylogenetically similar

Earthworms emit nitrous oxide (N2O) and dinitrogen (N2). It has been hypothesized that the in situ conditions of the earthworm gut activates ingested soil denitrifiers during gut passage and leads to these in vivo emissions (M. A. Horn, A. Schramm, and H. L. Drake, Appl. Environ. Microbiol. 69:1662-1669, 2003). This hypothesis implies that the denitrifiers in the earthworm gut are not endemic to the gut but rather are regular members of the soil denitrifier population. To test this hypothesis, the denitrifier populations of gut and soil from three different sites were comparatively assessed by sequence analysis of nosZ, the gene for the terminal enzyme in denitrification, N2O reductase. A total of 182 and 180 nosZ sequences were retrieved from gut and soil, respectively; coverage of gene libraries was 79 to 100%. Many of the nosZ sequences were heretofore unknown, clustered with known soil-derived sequences, or were related to N2O reductases of the genera Bradyrhizobium, Brucella, Dechloromonas, Flavobacterium, Pseudomonas, Ralstonia, and Sinorhizobium. Although the numbers of estimators for genotype richness of sequence data from the gut were higher than those of soil, only one gut-derived nosZ sequence did not group phylogenetically with any of the soil-derived nosZ sequences. Thus, the phylogenies of nosZ from gut and soil were not dissimilar, indicating that gut denitrifiers are soil derived.

Structure and activity of the denitrifying community in a maize-cropped field fertilized with composted pig manure or ammonium nitrate

One alternative to mineral fertilization is to use organic fertilizers. Our aim was to compare the impacts of 7-year applications of composted pig manure and ammonium nitrate on the structure and activity of the denitrifying community. Mineralization and organization of N, denitrification rates and N2O/N2 ratio were also investigated. Fourteen months after the last application, the potential denitrifying activity (+319%), N mineralization (+110%) and organization (+112%) were higher under pig compost than under ammonium nitrate fertilization. On the other hand, the N2O/(N2O+N2) ratio was lower (P<0.05, n=5) under organic fertilization. These effects of organic fertilization were in accordance with its higher total carbon content and microbial biomass. Fingerprints and clone library analyses showed that the structure of the denitrifying community was affected by the fertilization regime. Our results reveal that organic or mineral fertilizer applications could affect both structure and activity of the denitrifying community, with a possible influence on in situ N2O fluxes. These effects of the fertilization regime persisted for at least 14 months after the last application.

Activity and composition of the denitrifying bacterial community respond differently to long-term fertilization

The objective of this study was to explore the long-term effects of different organic and inorganic fertilizers on activity and composition of the denitrifying and total bacterial communities in arable soil. Soil from the following six treatments was analyzed in an experimental field site established in 1956: cattle manure, sewage sludge, Ca(NO3)2, (NH4)2SO4, and unfertilized and unfertilized bare fallow. All plots but the fallow were planted with corn. The activity was measured in terms of potential denitrification rate and basal soil respiration. The nosZ and narG genes were used as functional markers of the denitrifying community, and the composition was analyzed using denaturing gradient gel electrophoresis of nosZ and restriction fragment length polymorphism of narG, together with cloning and sequencing. A fingerprint of the total bacterial community was assessed by ribosomal intergenic spacer region analysis (RISA). The potential denitrification rates were higher in plots treated with organic fertilizer than in those with only mineral fertilizer. The basal soil respiration rates were positively correlated to soil carbon content, and the highest rates were found in the plots with the addition of sewage sludge. Fingerprints of the nosZ and narG genes, as well as the RISA, showed significant differences in the corresponding communities in the plots treated with (NH4)2SO4 and sewage sludge, which exhibited the lowest pH. In contrast, similar patterns were observed among the other four treatments, unfertilized plots with and without crops and the plots treated with Ca(NO3)2 or with manure. This study shows that the addition of different fertilizers affects both the activity and the composition of the denitrifying communities in arable soil on a long-term basis. However, the treatments in which the denitrifying and bacterial community composition differed the most did not correspond to treatments with the most different activities, showing that potential activity was uncoupled to community composition.