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Patterned ground is a characteristic landscape form in arid zones across the globe and is caused by the redistribution of runoff. The vegetation is concentrated in groves, which receive runoff water from the bare soil surface of the intergroves. Despite many soil chemical and physical investigations, biogeochemical cycles are not described for this landscape form. This study focuses on the distinct features of the nitrogen (N) and carbon (C) cycle in intergrove and grove areas of chenopod pattern-ground soils of the Australian rangelands. The N concentration of grove soils is low compared with the intergrove soil because of a close link between the N cycle in the topsoil and the plant primary production. In grove soils, denitrification including emission of [N.sub.2]O dominated the N cycle, whereas in intergrove soils, abiotic [N.sub.2]O uptake is the sole fate of atmospheric [N.sub.2]O. The intergrove soils appear to be generally poor in bacterial quantity and diversity, and lacking denitrification by bacteria, which has an impact on the C cycle as well. Production of C[O.sub.2] and consumption of C[H.sub.4] were substantially lower than grove soils. There was partitioning ofkcy biogeochemical processes between the intergrove and grove soils, which results in a spatially decoupled soil N and C cycle in arid chenopod, pattern-ground ecosystems. Received 24 July 2014, accepted 19 September 2014, published online 27 January 2015, Introduction Shrub-steppe covers 7.5% (451 000 [km.sup.2]) of Australia's arid and semi-arid rangelands, and is dominated by various annual and perennial species of the family Chenopodiaceae (Leigh 1972). These chenopod [...]

A set of equations governing oxygen diffusion and consumption in soils has been developed to include microbial and plant-root sinks. The dependent variable is the transformed oxygen concentration, which is the difference between the gaseous concentration and a scaled value of the aqueous oxygen concentration at the root-soil interface. The results show how, as the air-filled porosity decreases, the reduced oxygen flux causes the depth of extinction to decrease. The results also show how the depth of extinction at a particular value of soil water content decreases with increasing temperature, due to increased microbial respiration. The critical value of water content at which the oxygen concentration goes to extinction at a finite depth was compared with alternative calculations with only a microbial sink. By ignoring the feedback of oxygen concentration on root uptake, the alternative calculations yielded substantially higher critical values of water content at all temperatures. Two soil oxygen diffusion coefficient functions from the literature were compared and shown to give significantly different critical values of water content for fine-textured soils, one more realistic than the other. A single relationship between the extinction depth and the ratio of the water content to the critical value was shown to apply for all temperatures and soil textures. The oxygen profiles were used along with a function relating redox potential to oxygen concentration to generate redox potential profiles. This application of the model could be useful in explaining soil biochemical processes in soils. For one such process, denitrification, the depth at which a critical oxygen concentration is reached was calculated as a function of the air-filled porosity and temperature of the soil. The implications of the critical value of soil water content in terms of water-filled pore space and matric potential are discussed in relation to the diffusion coefficient functions and recent literature. Additional keywords: air-filled pore space, denitrification, diffusion coefficient function, oxygen transport, redox potential, soil respiration., Introduction The transport of oxygen into soil and its distribution within the profile are fundamental to the understanding of aeration, and biochemical and chemical reactions in soil. The oxygen status [...]

R. sphaeroides strain 2.4.3, when lacking the cbb3 oxidase, is unable to transition from aerobic respiration to denitrification using cellular respiration as a means of reducing oxygen levels. This is due to an inability to express nirK, the gene encoding nitrite reductase. Under certain photosynthetic conditions this strain can transition from aerobic to nitrate respiration, demonstrating that nirK expression can occur in the absence of a functional [cbb.sub.3] oxidase. If oxygen levels are reduced under non-photosynthetic conditions using low-oxygen gas mixes, nitrite reductase activity is detected at wild-type levels in the strain lacking the oxidase. In addition, co-culture experiments show that incubation of the [cbb.sub.3] deficient strain 2.4.3 with R. sphaeroides 2.4.1, which is nirK deficient but has the high-affinity [cbb.sub.3] oxidase, restores denitrification in sealed-vessel experiments. Taken together these results indicate that high end-point [O.sub.2] levels are the reason why the strain lacking the [cbb.sub.3] oxidase cannot transition from aerobic respiration to denitrification under certain conditions. The protein probably being affected by these [O.sub.2] levels is the transcriptional regulator NnrR. DOI 10.1099/mic.0.038703-0

The denitrification of human wastes by bacteria results into emission of nitrous oxide, which is a powerful pollutant. The denitrification rates are measured by nitrous oxide microprofiling in acetylene block core incubations and reactive transport modeling to measure the rate of denitrification at different depths in a macro tidal estuary.

Conventional agriculture has improved in crop yield but at large costs to the environment, particularly off-site pollution from mineral N fertilizers. In response to environmental concerns, organic agriculture has become an increasingly popular option. One component of organic agriculture that remains in question is whether it can reduce agricultural N losses to groundwater and the atmosphere relative to conventional agriculture. Here we report reduced N pollution from organic and integrated farming systems compared with a conventional farming system. We evaluated differences in denitrification potential and a suite of other soil biological and chemical properties in soil samples taken from organic, integrated, and conventional treatments in an experimental apple orchard. Organically farmed soils exhibited higher potential denitrification rates, greater denitrification efficiency, higher organic matter, and greater microbial activity than conventionally farmed soils. The observed differences in denitrifier function were then assessed under field conditions after fertilization. [N.sub.2]0 emissions were not significantly different among treatments; however, [N.sub.2] emissions were highest in organic plots. Annual nitrate leaching was 4.4-5.6 times higher in conventional plots than in organic plots, with the integrated plots in between. This study demonstrates that organic and integrated fertilization practices support more active and efficient denitrifier communities, shift the balance of [N.sub.2] emissions and nitrate losses, and reduce environmentally damaging nitrate losses. Although this study specifically examines a perennial orchard system, the ecological and biogeochemical processes we evaluated are present in all agroecosystems, and the reductions in nitrate loss in this study could also be achievable in other cropping systems. denitrification | nitrogen | organic agriculture | sustainable agriculture | integrated farming

Microbial N(sub 2)O release during the course of thawing of soil was investigated in model experiment focusing on denitrification, since freeze-thaw is shown to cause significant physical and biological changes in soil, including a surge of N(sub 2)O and CO(sub 2). The results support the view that the flush of N(sub 2)O and CO(sub 2) is a result of increased microbial activity during the dynamic event of freeze and thaw, instead of mere entrapment of gases due to the freeze barrier.

A study was conducted to examine the diversity and composition of denitrifying bacteria that vary across environmental gradients in both nitrate and salinity within an unconfined beach aquifer. The findings suggest that diversity in these enzymes results from adaptation to a particular environment rather than just random microheterogeneity alone.

The long-term effects of different organic and inorganic fertilizers on activity and composition of the denitrifying and total bacterial communities in arable soil are investigated. The results have shown that the addition of different fertilizers affects both the activity and the composition of the denitrifying communities in arable soil on a lorng-term basis.

The chromium addition has less influence on the denitrification bacteria than on the nitrification bacteria. Various measures to determine the removal efficiency of carbon and nitrogen substance using lab scale sequencing batch reactors (SBR) reactor fed with untreated tannery wastewater containing a relevant amount of chromium are discussed.

Research has been conducted on the (super)15 N isotope pairing technique. The principles of this technique and the application of the (super)15 N isotope pairing in sediments are discussed.

Research has been conducted on the monoterpenes with unsaturated hydrocarbon structure. Results indicate the presence of the monoterpene degradation pathway in Alcaligenes defragrans.

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.

Research has been conducted on the horizontal patchiness in microbial sediment communities. The examination of the horizontal heterogeneity for denitrifying bacteria in time and space is discussed.

Research has been conducted on the nirS gene for Paracoccus pantotrophus cytochrome cd (sub)1 nitrite reductase. The determination of the gene transcription start site and the length of nirS promoter transcripts are discussed.

The activity of denitrifying bacteria in the gut of Lumbricus rubellus and Ostoclasium lacteum was analyzed to determine the role of earthworms in the synthesis of VH or N2O in terrestrial ecosystems. Denitrifying activity was exhibited by 3% to 10% of the microbes isolated from earthworm gut material. The anaerobic gut homogenates also catalyzed the synthesis of N2O and N2 from nitrate after prolonged incubation. Furthermore, N2O production by earthworms was also mediated by nitrification, assimilatory nitrate reduction and dissimilatory reduction of nitrate to ammonium.

A study of nitrogen isotopes at three sites in the Arabian Sea indicates changes in the 15N/14N values due to climatic variations, as confirmed by the agreement of the variations with Milankovitch cycle values. This implies that subsurface nitrate level and denitrification vary with climate. These factors may have serious implications on the changes in marine biogeochemical cycles.

Sensitive mass spectrometry and denitrification bioassay studies compute (15)N abundance in nanogram pools of NO2- and NO3-, that are reduced to N2O gas by Pseudomonas aeruginosa. Samples containing low N2O gas levels are spiked with a reference N2O-containing gas of natural (15)N abundance to calculate (15)N abundance. The reduced contamination risk during N2O studies is used in isotopic analysis of inorganic N conversions by denitrifying and nitrifying bacteria.

Oxygen concentrations in overlying waters affect nitrification and denitrification, and their regulatory processes in fresh water sediment microcosms. High oxygen concentrations shift nitrification to the lower section of the oxic zone and decrease denitrification due to increased NO(sub 3) diffusion to the denitrifying regions of the anoxic sediment.

Hydrogen-oxidizing denitrifying bacterial strains isolated from nitrate-contaminated gravel and sand aquifer play a significant role in the bioremediation of nitrate-contamination in ground water. All the strains grow autotrophically on hydrogen, produce innocuous end products and are sequentially manipulated for oxygen and nitrate consumption.

The fnrA gene supports anaerobic development of nitrate-determined fnr deletion mutant of Escherichia coli. The gene possesses a 0.85 kb single transcript. Insertional mutagenesis results in mutations in fnrA, followed by gene replacement. Arginine deiminase presence and lack of fnrA transcript indicate gene replacement. The same bacterium may also contain another fnr homolog, as implied by anaerobic activation of the promoter-probe vector for transcription involving fnr.

The chemistry of azoalkanes and bicyclopentanes is stimulated by photosensitized electron transfer (PET). The intricate working of the process is determined by intramolecular trapping experiments. Derivatives such as cyclopentadienes are generated due to the possible intermediary role of the allyl cation -H+. The participation of diazenyl radical cations is examined. Rare radical cation chemistry is revealed by the 2,3-diazabicyclo(2.2.1)hept-2-ene products due to PET. 1,3-diyl radical cations use the azoalkanes as precursors in a complex manner.

The role of the nnR gene product in the response of Rhodobacter sphaeroides 2.4.1 to exogenous nitric oxide was analyzed. The nnR gene was subcloned and sequenced from the fragments taken from the pool of plasmids. Results of the study revealed that R. sphaeroides 2.4.1. carries nnR, the nor operon and the nnrS which are used for the denitrification of the bacterium. This indicate that products of nnrR and the genes flanking it are utilized when 2.4.1 is growing in the occurrence of denitrification.

The spatial heterogeneity in the distribution of denitrifying enzyme activity (DEA) was 3.5 times more in artificial denitrification activity zones than in bulk soil and the denitrifier biomass was 1-4 times more in activity zones. The potential heterogeneous distribution of denitrifying bacteria should be considered while measuring the denitrifying specific activity.

Denitrification of nitrate in static cultures of Paracoccus denitrificans was examined. Nitrate was reduced to a gaseous state without the aggregation of nitrite due to parallel and balanced functioning of nitrate and nitrite reductase in nutrient broth. Results proved that the manner of denitrification in Paracoccus denitrificans was not stable. This process is also dependent on the nutritional constitution of the culture medium.

The regulation of denitrification is examined in the model organism Paracoccus denitrificans during transition to anoxia both at pH 7 and when challenged with pHs ranging from 6 0t 7.5. The studies have shown that the inhibition has occurred during protein synthesis/assembly rather than transcription and have helped in understanding the regulation of the [N.sub.2]O redustase and the important role of pH in [N.sub.2]O emission.

The Methylomicrobium album ATCC 33003 and Methylocystis sp. strain ATCC 49242 in cultures with high nitrite levels and high ammonium levels were explored to study the effects of nitrite and ammonium on cultivated methanotrophic bacteria. M. album pure cultures and cocultures which consumed nitrite and produced nitrous oxide indicated the association between denitrification and nitrite tolerance.

The microbial community present in the produced waters from the Enermark field during nitrate injection is determined by denaturing gradient gel electrophoresis (DGGE) and the fate of the injected nitrate is determined by monitoring ammonium concentration in produced and injection waters. The results have shown that nitrate injected into an oil field to oxidize sulfide is reduced by denitrifying bacteria and that perhaps counterintuitively, nitrate injection has led to decreasing ammonium concentrations in produced waters.

Denitrification and artificial wastewater media was used to monitor denitrification activity of strain TR2 isolated from the aerobic denitrifying bacterium Pseudomonas stutzeri. The results demonstrated that some of the bacterial species such as strain TR2 has adopted a strategy for survival by preferring denitrification to oxygen respiration and the bacterium is also found to contain the potential to reduce [N.sub.2]O emissions when applied to sewage disposal fields.

A comparative study was conducted to understand the relationship between soil and vegetation factors and microbial community structure and function in restored and reference wetlands within a mitigation bank. Microbial functions was found to be influenced by composition of bacterial communities and soil fertility and the denitrifying populations could potential use for the development of predictive models for restoration of biogeochemical transformations and improve the success of wetland restoration efforts.

Isolation of five species of denitrifying bacteria from three phyla from subsurface sediments exposed to metal radionuclide and nitrate contamination as part of the U.S. Department of Energy's Oak Ridge Integrated Field Research Challenge (OR-IFRC) is described. The results demonstrated that a combination of cultivation and genomic and metagenomic data is essential to the in situ characterization of denitrifiers and that current PCR-based approaches are not suitable for deep coverage of denitrifiers.

Geostatistical modeling to map spatial patterns were used to explore the distribution of the community structure, size, and activity of one functional group in N cycling, the denitrifiers, in relation to 23 soil parameters over a 44-ha farm divided into one organic and one integrated crop production system. The different community patterns along with the spatial distribution of the nirS/nirK abundance ratio suggested habitat selection on the nirS- and nirK-type denitrifiers and constituted a first step in identifying positions for denitrifiers at scales relevant to land management.

An rRNA-derived eukaryote clone library was constructed to identify the active protozoan phylotypes present in activated sludge and RNA-SIP was used to track carbon from bicarbonate and acetate into protozoa under ammonia-oxidizing and denitrifying conditions. The results from RNA-SIP analysis indicated that the peritrich ciliate Epistylis galea dominated the acquisition of carbon from bacteria with access to C[O.sub.2] under ammonia-oxidizing conditions, while no evidence was found for the specific grazing on acetate consumers under denitrifying conditions.

A study was conducted to determine the effects of red clover, soybean, and barley plant residues and of glucose on denitrifier abundance, denitrification gene mRNA levels, nitrous oxide ([N.sub.2]O) emissions, and denitrification rate quantified in anoxic soil microcosms for 72 h. Denitrification and respiration was found to increase in soil amended with organic carbon, including plant residues, compared to unamended soil.

The various effects of the changes taking place in the soil pH on the [N.sub.2]O and [N.sub.2] emissions and the activity of the denitrifier community are discussed. The nature of the denitification end products is shown to be completely determined by the pH of the soil.

The denitrifier community of an nitrous oxide ([N.sub.2]O)-emitting fen (pH 4.7 to 5.2) is examined. The studies have shown that the regional fen has harbored novel, highly diverse, acid-tolerant denitrifier communities that are capable of complete denitrification and consumption of atmospheric [N.sub.2]O at in situ pH.

The portion of the nirK denitrifying community that is active and has contributed to denitrification under conditions in a potato crop field is studied. The results have shown that the soil denitrifier populations bearing nirK genes are not all contributing to denitrification and that the denitrifying populations that are active are abundant and ubiquitous nirK-bearing denitrifiers.

A comparative 16S rRNA gene analysis is conducted to explain the response of the microbial populations to denitrification, including the different conditions observed in the rice paddy soil. The various potential key players involved in the nitrate respiration and denitrification processes are also identified.

The development of a stable isopropyl-[beta]-D-thiogalactopyranoside (IPTG)-inducible-expression plasmid, pIND4 which permitted graduated levels of protein expression in the alphaproteobacteria Rhodobacter sphaeroides and Paracoccus denitrificans is described. The plasmid pIND4 showed kanamycin resistance and combined the stable replicon of pMG160 with the [lacI.sup.q] gene from pYanni3 and the lac promoter, [P.sub.A1/04/03] from pJBA24.

The criteria for standardizing operational taxonomic units (OUT) assignment of environmental narG and nosZ sequences is resolved and the impact of horizontal gene transfer on narG is examined. The studies have shown that genus-level tree topologies of narG and nosZ are similar to those of the corresponding 16S rRNA genes.

The denitrifying properties of Ochrobactrum anthropi are examined, where the strain YD50.2 has denitrified high levels of N[O.sub.2.sup.-] to dinitrogen under anaerobic conditions. The results have shown that Ochrobactrum anthropi YD50.2 has mechanisms that have produced tolerance to reactive nitrogen species (RNS).

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.

A study is conducted to examine the factors such as environmental conditions, nutrient availability and levels of pollutants on denitrifying microbial community composition and denitrification enzyme activities (DEA) at a California salt marsh with high nutrient loading. The community composition and DEA are found to be highly variable within the dynamic salt marsh system, but each is strongly affected by elevation and carbon content as well as by selected metals.

A research study is conducted to measure nitric oxide reductase (cnorB) gene expression in Pseudomonas mandelii and [N.sub.2]O emissions from denitrification with and without a nitrate substrate. The results demonstrated that P. mandelii cnorB gene expression is induced when nitrate is present in the medium and accumulation of [N.sub.2]O has indicated the production of cNorB enzyme.

The physiological, genetic, and biochemical experiments are performed to detect genes encoding monooxygenase and dioxygenase enzymes potentially involved in benzene degradation in strain BC. The results revealed that oxygen formed during the dismutation of chlorite might be used as terminal electron acceptor in strain BC as well as to attack molecules by means of oxygenases.

Study is conducted to reveal the denitrification ability of candidate accumulibacter phosphates organism. The results of this study material can be adapted to other uncultured bacteria.

The inhibitory effects of acetylene, methanol and allyithiourea (ATU) on anammox and denitrification activities in marine sediments re examined. No marked effects on the rates of anammox and denitrification were found in ATU.

An evolutionary algorithm is applied to study the complex interactions between medium parameters and their effects on the isolation of denitrifying bacteria, both in number and in diversity. One hundred ninety-nine denitrifiers are isolated, the majority of which belonged to the Betaproteobacteria (50.4%) and the Alphaproteobacteria (36.8%).