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Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to [N.sub.2] gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here, genomic analysis of single cells from the world's largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductases (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted ~40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. These results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth's most abundant organismal group., Alphaproteobacteria of the SAR11 clade form one of the most ecologically dominant organism groups on the planet, representing up to half of the total microbial community in the oxygen-rich surface [...]

We explored the microbial ecology of water draining through the soil (lysimeter samples) and in the shallow aquifers (bore samples) underlying sugarcane and banana fields near the Great Barrier Reef (GBR), Australia. Lysimeter and bore water samples were collected and analysed chemically and with DNA fingerprinting methods (PCR-DGGE and clone library sequencing) to characterise the structure of the bacterial community. Bacterial communities in soil water and bore water were distinct (P < 0.05), and a primary factor linked with bacterial community structure was water pH (P < 0.05), particularly in water sampled from lysimeters. Irrespective of treatment, >80% of all rRNA gene sequences originated from proteobacteria. However, groundwater communities differed from those in soil water by greater occurrence of Neisseriales and Comamonadaceae (P< 0.01). qPCR was used to measure copy numbers of the nirK and nirS genes encoding NO-forming nitrite reductases. Copy numbers of both genes were greater in soil water samples than groundwater (P = 0.05), with the difference in nirK being greater under sugarcane than banana. These differences in nirK-gene abundance show that there is greater potential for denitrification in soil water under sugarcane, leading to low concentrations of nitrate in the underlying groundwater. This knowledge can be used towards development of soil and land-use management practices promoting bacterial denitrification in groundwater to lessen the undesirable ecological consequences where groundwater discharges lower in the GBR catchment zones., Introduction The Great Barrier Reef (GBR), off the north-east coast of Australia, is the largest coral-reef ecosystem in the world. It is of immense ecological and economic significance, and is [...]

Analysis of the Rhodobacter sphaeroides 2.4.3 genome revealed four previously unidentified sequences similar to the binding site of the transcriptional regulator NnrR. Expression studies demonstrated that three of these sequences are within the promoters of genes, designated paz, norEF, and cdgA, in the NnrR regulon, while the status of the fourth sequence, within the tat operon promoter, remains uncertain, nnrV, under control of a previously identified NnrR site, was also identified, paz encodes a pseudoazurin that is a donor of electrons to nitrite reductase, paz inactivation did not decrease nitrite reductase activity, but loss of pseudoazurin and cytochrome [c.sub.2] together reduced nitrite reduction. Inactivation of norEF reduced nitrite and nitric oxide reductase activity and increased the sensitivity to nitrite in a taxis assay. This suggests that loss of norEF increases NO production as a result of decreased nitric oxide reductase activity. 2.4.3 is the only strain of R. sphaeroides with norEF, even though all four of the strains whose genomes have been sequenced have the norCBQD operon and nnrR. norEF was shown to provide resistance to nitrite when it was mobilized into R. sphaeroides strain 2.4.1 containing nirK. Inactivation of the other identified genes did not reveal any detectable denitrification-related phenotype. The distribution of members of the NnrR regulon in R. sphaeroides revealed patterns of coselection of structural genes with the ancillary genes identified here. The strong coselection of these genes indicates their functional importance under real-world conditions, even though inactivation of the majority of them does not impact denitrification under laboratory conditions. doi: 10.1128/JB.01026-09

Benthic foraminifers inhabit a wide range of aquatic environments including open marine, brackish, and freshwater environments. Here we show that several different and diverse foraminiferal groups (miliolids, rotaliids, textulariids) and Gromia, another taxon also belonging to Rhizaria, accumulate and respire nitrates through denitrification. The widespread occurrence among distantly related organisms suggests an ancient origin of the trait. The diverse metabolic capacity of these organisms, which enables them to respire with oxygen and nitrate and to sustain respiratory activity even when electron acceptors are absent from the environment, may be one of the reasons for their successful colonization of diverse marine sediment environments. The contribution of eukaryotes to the removal of fixed nitrogen by respiration may equal the importance of bacterial denitrification in ocean sediments. eukaryotic nitrate respiration | nitrogen cycle doi/10.1073/pnas.0908440107

Predicting biodiversity effects on ecosystem functioning requires adequate evaluation of the mechanisms explaining why more diverse systems could perform better than less diverse ones. In this context, tackling functional diversity has become an important issue. Even though the aggregation of species into functional groups supposes niche differences among groups, the concept of niche has not been fully exploited in the context of the biodiversity--ecosystem functioning research. Here we report the results of microcosm experiments where we used bacteria as a model to explore whether niche differences among species provide a good estimation of community functioning. For that we used experimental communities of denitrifying bacterial species and investigated the effects of bacterial diversity on two community processes, denitrification and anaerobic C[O.sub.2]-production. We first measured the activities of 16 bacterial species grown individually on six different carbon sources. We then used the same set of species to assemble communities varying in both species richness and composition in microcosms containing a mixture of all six carbon sources. The performances of individual species on individual carbon sources were used to calculate, for each process measured, an a priori index called 'community niche' that accounted for the performances of the species present in a given community across the entire range of the six resources. We found that species richness had a positive but small effect on both community processes whereas community niche explained a much larger proportion of the variation. According to the results of a path analysis, community niche was the main driver for the corresponding community process, but species richness affected community niche and thus had an indirect effect on denitrification and C[O.sub.2] production. In addition to community niche, the presence of particular bacterial species also influenced community functioning, indicating that other effects than the capacity to use carbon sources played a, albeit minor, role in our experiment. Our study provides evidence for the importance of resource niches in shaping biodiversity--ecosystem functioning relationships of bacterial communities. Key words: anaerobic C[O.sub.2] production; bacterial diversity; biodiversity--ecosystem function relationships; carbon resource use; community niche; denitrification.

Nitrification, a key process in the global nitrogen cycle that generates nitrate through microbial activity, may enhance losses of fertilizer nitrogen by leaching and denitrification. Certain plants can suppress soil-nitrification by releasing inhibitors from roots, a phenomenon termed biological nitrification inhibition (BNI). Here, we report the discovery of an effective nitrification inhibitor in the root-exudates of the tropical forage grass Brachiaria humidicola (Rendle) Schweick. Named 'brachialactone,' this inhibitor is a recently discovered cyclic diterpene with a unique 5-8-5-membered ring system and a [gamma]-lactone ring. It contributed 60-90% of the inhibitory activity released from the roots of this tropical grass. Unlike nitrapyrin (a synthetic nitrification inhibitor), which affects only the ammonia mono-oxygenase (AMO) pathway, brachialactone appears to block both AMO and hydroxylamine oxidoreductase enzymatic pathways in Nitrosomonas. Release of this inhibitor is a regulated plant function, triggered and sustained by the availability of ammonium (N[H.sup.+ sub.4]) in the root environment. Brachialactone release is restricted to those roots that are directly exposed to N[H.sup.+ sub.4]. Within 3 years of establishment, Brachiaria pastures have suppressed soil nitrifier populations (determined as amoA genes; ammonia-oxidizing bacteria and ammonia-oxidizing archaea), along with nitrification and nitrous oxide emissions. These findings provide direct evidence for the existence and active regulation of a nitrification inhibitor (or inhibitors) release from tropical pasture root systems. Exploiting the BNI function could become a powerful strategy toward the development of low-nitrifying agronomic systems, benefiting both agriculture and the environment. global warming | nitrogen pollution | nitrous oxide emissions | root exudation | climate change doi/ 10.1073/pnas.0903694106

We measured denitrification rates using a field [sup.15]N-N[O.sup.-.sub.3] tracer-addition approach in a large, cross-site study of nitrate uptake in reference, agricultural, and suburban urban streams. We measured denitrification rates in 49 of 72 streams studied. Uptake length due to denitrification ([S.sub.Wden]) ranged from 89 m to 184 km (median of 9050 m) and there were no significant differences among regions or land-use categories, likely because of the wide range of conditions within each region and land use. [N.sub.2] production rates far exceeded [N.sub.2]O production rates in all streams. The fraction of total N[O.sup.-.sub.3] removal from water due to denitrification ranged from 0.5% to 100% among streams (median of 16%), and was related to N[H.sup.+.sub.4] concentration and ecosystem respiration rate (ER). Multivariate approaches showed that the most important factors controlling [S.sub.Wden] were specific discharge (discharge / width) and N[O.sup.-.sub.3] concentration (positive effects), and ER and transient storage zones (negative effects). The relationship between areal denitrification rate ([U.sub.den]) and N[O.sup.-.sub.3] concentration indicated a partial saturation effect. A power function with an exponent of 0.5 described this relationship better than a Michaelis--Menten equation. Although [U.sub.den] increased with increasing N[O.sup.-.sub.3] concentration, the efficiency of N[O.sup.-.sub.3] removal from water via denitrification declined, resulting in a smaller proportion of streamwater N[O.sup.-.sub.3] load removed over a given length of stream. Regional differences in stream denitrification rates were small relative to the proximate factors of N[O.sup.-.sub.3] concentration and ecosystem respiration rate. and land use was an important but indirect control on denitrification in streams, primarily via its effect on N[O.sup.-.sub.3] concentration.

We measured the production of [N.sub.2] gas from anammox and denitrification simultaneously in intact sediment cores at six sites along a transect of the continental shelf (50 m) and deeper slope (2000 m) in the North Atlantic. Maximum rates of total [N.sub.2] production were measured on the shelf and were largely due to denitrification, with anammox contributing, on average, 33% of this production. On the continental slope, the production of [N.sub.2] gas decreased but the proportion due to anammox reached a maximum of 65%. This change in both amount and dominant pathway of [N.sub.2] production could be explained largely by the concentration of organic carbon at each site. With increasing carbon the total production of [N.sub.2] increased rapidly while the response of anammox was not significant. On the continental slope, total [N.sub.2] production fell below 2 [micro]mol N [m.sup.-2] [h.sup.-1] and anammox was strongly related (r = 0.95) to denitrification but the relative magnitude of anammox to denitrification (1.65:1) suggested that anammox could not be fuelled by N[O.sup.-.sub.2] from denitrification alone. On the shelf, however, where total [N.sub.2] production was predominantly greater than 2 [micro]mol N [m.sup.-2] [h.sup.-1], no relationship between anammox and denitrification was found and anammox remained constant at 1.4 [micro]mol N [m.sup.-2] [h.sup.-1]. Despite the constancy and greater availability of N[O.sup.-.sub.3] and lower temperatures on the continental slope, the significance of anammox to the total production of [N.sub.2] appears primarily controlled by the overall rate of [N.sub.2] production.

This article provides a synthesis of literature values to trace the fate of 150 Tg/yr anthropogenic nitrogen applied by humans to the Earth's land surface. Approximately 9 TgN/yr may be accumulating in the terrestrial biosphere in pools with residence times of ten to several hundred years. Enhanced fluvial transport of nitrogen in rivers and percolation to groundwater accounts for [approximately equal to] 35 and 15 TgN/yr, respectively. Greater denitrification in terrestrial soils and wetlands may account for the loss of [approximately equal to] 17 TgN/yr from the land surface, calculated by a compilation of data on the fraction of [N.sub.2]O emitted to the atmosphere and the current global rise of this gas in the atmosphere. A recent estimate of atmospheric transport of reactive nitrogen from land to sea (N[O.sub.x] and N[H.sub.x]) accounts for 48 TgN/yr. The total of these enhanced sinks, 124 TgN/yr, is less than the human-enhanced inputs to the land surface, indicating areas of needed additional attention to global nitrogen biogeochemistry. Policy makers should focus on increasing nitrogen-use efficiency in fertilization, reducing transport of reactive N to rivers and groundwater, and maximizing denitrification to its [N.sub.2] endproduct. biogeochemistry | denitrification |nitrogen cycle

One of the shallowest, most intense oxygen minimum zones (OMZs) is found in the eastern tropical South Pacific, off northern Chile and southern Peru. It has a strong oxygen gradient (upper oxycline) and high [N.sub.2]O accumulation. [N.sub.2]O cycling by heterotrophic denitrification along the upper oxycline was studied by measuring [N.sub.2]O production and consumption rates using an improved acetylene blockage method. Dissolved [N.sub.2]O and its isotope ([sup.15]N : [sup.14]N ratio in [N.sub.2]O or [[delta][sup.15]]N) and isotopomer composition (intramolecular distribution of [sup.15]N in the [N.sub.2]O or [[delta].sup.15]N[alpha] and [[delta].sup.15]N[beta]), dissolved [O.sub.2], nutrients, and other oceanographic variables were also measured. Strong [N.sub.2]O accumulation (up to 86 nmol [L.sup.-1]) was observed in the upper oxycline followed by a decline (around 812 nmol [l.sup.-1]) toward the OMZ core. [N.sub.2]O production rates by denitrification (N[O.sup.-.sub.2] reduction to [N.sub.2]O) were 2.2.5 to 50.0 nmol [L.sup.-1] [d.sup.-1], whereas [N.sub.2]O consumption rates ([N.sub.2]O reduction to [N.sub.2]) were 2.73 and 70.8 nmol [L.sup.-1] [d.sup.-1]. [[delta].sup.15]N in [N.sub.2]O increased from 8.57 [per thousand] in the middle oxycline (50-m depth) to 14.87 [per thousand] toward the OMZ core (100-m depth), indicating the progressive use of [N.sub.2]O as an electron acceptor by denitrifying organisms. Isotopomer signals of [N.sub.2]O ([[delta].sup.15]N[alpha] and [[delta].sup.15]N[beta]) showed an abrupt change at the middle oxycline, indicating different mechanisms of [N.sub.2]O production and consumption in this layer. Thus, partial denitrification along with aerobic ammonium oxidation appears to be responsible for [N.sub.2]O accumulation in the upper oxycline, where [O.sub.2] levels fluctuate widely; [N.sub.2]O reduction, on the other hand, is an important pathway for [N.sub.2] production. As a result, the proportion of [N.sub.2]O consumption relative to its production increased as [O.sub.2] decreased toward the OMZ core. A [N.sub.2]O mass balance in the subsurface layer indicates that only a small amount of the gas could be effluxed into the atmosphere (12.7-30.7 [micro]mol [m.sup.-2] [d.sup.-1]) and that most [N.sub.2]O is used as an electron acceptor during denitrification (107-468 [micro] mol [m.sup.-2] [d.sup.-1]).

Denitrification is a well-studied respiratory system that is also important in the biogeochemical nitrogen cycle. Environmental signals such as oxygen and N-oxides have been demonstrated to regulate denitrification, though how denitrification is regulated in a bacterial community remains obscure. Pseudomonas aeruginosa is a ubiquitous bacterium that controls numerous genes through cell-to-cell signals. The bacterium possesses at least two N-acyl-L-homoserine lactone (AHL) signals. In our previous study, these quorum-sensing signals controlled denitrification in P. aeruginosa. In addition to the AHL signals, a third cell-to-cell communication signal, 2-heptyl-3-hydroxy-4-quinolone, referred to as the Pseudomonas quinolone signal (PQS), has been characterized. In this study, we examined the effect of PQS on denitrification to obtain more insight into the respiratory regulation in a bacterial community. Denitrification in P. aeruginosa was repressed by PQS, which was partially mediated by PqsR and PqsE. Measuring the denitrifying enzyme activities indicated that nitrite reductase activity was increased by PQS, whereas PQS inhibited nitric oxide reductase and the nitrate-respiratory chain activities. This is the first report to demonstrate that PQS influences enzyme activities, suggesting this effect is not specific to P. aeruginosa. Furthermore, when iron was supplied to the PQS-added medium, denitrifying activity was almost restored, indicating that the iron chelating property of PQS affected denitrification. Thus, our data indicate that PQS regulates denitrification primarily through iron chelation. The PQS effect on denitrification was relevant in a condition where oxygen was limited and denitrification was induced, suggesting its role in controlling denitrification where oxygen is present.

Growth of Moraxella catarrhalis in a biofilm resulted in marked upregulation of two open reading frames (ORFs), aniA and norB, predicted to encode a nitrite reductase and a nitric oxide reductase, respectively (W. Wang, L. Reitzer, D. A. Rasko, M. M. Pearson, R. J. Blick, C. Laurence, and E. J. Hansen, Infect. Immun. 75:4959-4971, 2007). An ORF designated nsrR, which was located between aniA and norB, was shown to encode a predicted transcriptional regulator. Inactivation of nsrR resulted in increased expression of aniA and norB in three different M. catarrhalis strains, as measured by both DNA microarray analysis and quantitative reverse transcriptase PCR. Provision of a wild-type nsrR gene in trans in an nsrR mutant resulted in decreased expression of the AniA protein. DNA microarray analysis revealed that two other ORFs (MC ORF 683 and MC ORF 1550) were also consistently upregulated in an nsrR mutant. Consumption of both nitrite and nitric oxide occurred more rapidly with cells of an nsrR mutant than with wild-type cells. However, growth of nsrR mutants was completely inhibited by a low level of sodium nitrite. This inhibition of growth by nitrite was significantly reversed by introduction of an aniA mutation into the nsrR mutant and was completely reversed by the presence of a wild-type nsrR gene in trans. NsrR regulation of the expression of aniA was sensitive to nitrite, whereas NsrR regulation of norB was sensitive to nitric oxide.

Anaerobic growth of Pseudomonas aeruginosa PAO1 was affected by quorum sensing. Deletion of genes that produce N-acyl-L-homoserine lactone signals resulted in an increase in denitrification activity, which was repressed by exogenous signal molecules. The effect of the/as quorum-sensing system was dependent on the rhl quorum-sensing system in regulating denitrification.

A study to measure the denitrification rates in six different estuaries of the Northern Baltic Sea is conducted. The results demonstrate that the nitrogen load on the Baltic Sea cannot be satisfactorily reduced by the sediments of the fast-flowing rivers and the estuary areas with short residence times.

Dissimilatory nitrite reductase (NIR) is a key enzyme in denitrification, catalyzing the first step that leads to gaseous products (NO, [N.sub.2]O, and [N.sub.2]). We have determined the crystal structure of a Cu-containing NIR from a methylotrophic denitrifying bacterium, Hyphomicrobium denitrificans, at 2.2-[Angstrom] resolution. The overall structure of this H. denitrificans NIR reveals a trigonal prism-shaped molecule in which a monomer consisting of 447 residues and three Cu atoms is organized into a unique hexamer (i.e., a tightly associated dimer of trimers). Each monomer is composed of an N-terminal region containing a Greek key [beta]-barrel folding domain, cupredoxin domain I, and a C-terminal region containing cupredoxin domains II and III. Both cupredoxin domains I and II bind one type I Cu and are combined with a long loop comprising 31 amino acid residues. The type 2 Cu is ligated at the interface between domain II of one monomer and domain III of an adjacent monomer. Between the two trimeric C-terminal regions are three interfaces formed by an interaction between the domains I, and the type 1 Cu in the domain is required for dimerization of the trimer. The type 1 Cu in domain II functions as an electron acceptor from an electron donor protein and then transfers an electron to the type 2 Cu, binding the substrate to reduce nitrite to NO. The discussion of the intermolecular electron transfer process from cytochrome [c.sub.550] to the H. denitrificans NIR is based on x-ray crystallographic and kinetic results. denitrification | electron transfer | redox partner | intermolecular interaction | cupredoxin

Land use in the Lake Taupo catchment is under scrutiny, as early signs of deteriorating water quality in Lake Taupo have been observed. Although the fate of contaminants in soil and groundwater are comparatively well studied, the transformations in the lower vadose zone, i.e. the zone between the soil and the groundwater, are less well understood. The capacity for [NO.sub.3]-N removal via biological denitrification, based on utilising the resident C substrate, in the vadose zone of the Lake Taupo catchment is quantified in this work. Complete vadose zone profiles were sampled at 3 sites (Rangiatea, Waihora, and Kinloch), from the soil surface down to the watertable in approximately 0.5-m depth increments. Texture, allophane content, pH, and concentrations of extractable [NO.sub.3]-N, [NH.sub.4]-N, and dissolved organic carbon were determined. Incubations were undertaken to determine the denitrification capacity of the vadose zone materials amended with [NO.sub.3][sup.-15N], but no added carbon substrate, and maintained under anaerobic conditions at 28°C. Gas samples were taken from the headspace after 48 h and analysed for [N.sub.2] and [N.sub.2]O. In soil depths down to about 1.2 m, the denitrification capacity ranged from 0.03 to 9.18 kgN/ha.day, and below this depth it ranged from Additional keywords: nitrate, groundwater, land-use impacts., Greg Barkle (A), Tim Clough (B), and Roland Stenger (c) (A)Corresponding author. Aqualinc Research Ltd, PO Box 14-041, Hamilton, New Zealand. Email: G.Barkle@Aqualinc.co.nz (B) Agriculture & Life Sciences Division, PO [...]

When grown anaerobically on a succinate + nitrate (SN) medium, Paracoccus denitrificans forms the membrane-bound, cytoplasmically oriented, chlorate-reducing nitrate reductase Nar, while the periplasmic enzyme Nap is expressed during aerobic growth on butyrate +oxygen (BO) medium. Preincubation of SN cells with chlorate produced a concentration-dependent decrease in nitrate utilization, which could be ascribed to Nar inactivation. Toluenization rendered Nar less sensitive to chlorate, but more sensitive to chlorite, suggesting that the latter compound may be the true inactivator. The Nap enzyme of BO cells was inactivated by both chlorate and chlorite at concentrations that were at least two orders of magnitude lower than those shown to affect Nar. Partial purification of Nap resulted in insensitivity to chlorate and diminished sensitivity to chlorite. Azide was specific for SN cells in protecting nitrate reductase against chlorate attack, the protective effect of nitrate being more pronounced in BO cells. The results are discussed in terms of different metabolic activation of chlorine oxoanions in both types of cells, and limited permeation of chlorite across the cell membrane. DOI 10.1099/mic.0.29276-0

Abstract: This paper describes a laboratory investigation that simulates in situ treatment of leachate representative of that generated by a municipal solid waste (MSW) landfill. The objective of the investigation [...]

Copper-containing nitrite reductases catalyze the reduction of nitrite to nitric oxide (NO), a key step in denitrification that results in the loss of terrestrial nitrogen to the atmosphere. They are found in a wide variety of denitrifying bacteria and fungi of different physiology from a range of soil and aquatic ecosystems. Structural analysis of potential intermediates in the catalytic cycle is an important goal in understanding enzyme mechanism. Using 'crystal harvesting' and substrate-soaking techniques, we have determined atomic resolution structures of four forms of the green Cu-nitrite reductase, from the soil bacterium Achromobacter cycloclastes. These structures are the resting state of the enzyme at 0.9 [Angstrom], two species exhibiting different conformations of nitrite bound at the catalytic type 2 Cu, one of which is stable and also has NO present, at 1.10 [Angstrom], and 1.15 A, and a stable form with the product NO bound side-on to the catalytic type 2 Cu, at 1.12 [Angstrom] resolution. These structures provide incisive insights into the initial binding of substrate, its repositioning before catalysis, bond breakage (O-NO), and the formation of a stable NO adduct. catalysis | denitrification | enzyme mechanism | nitrite and nitric oxide binding | crystal structures

Denitrification and arginine fermentation are central metabolic processes performed by the opportunistic pathogen Pseudomonas aeruginosa during biofilm formation and infection of lungs of patients with cystic fibrosis. Genome-wide searches for additional components of the anaerobic metabolism identified potential genes for pyruvate-metabolizing NADH-dependent lactate dehydrogenase (ldhA), phosphotransacetylase (pta), and acetate kinase (ackA). While pyruvate fermentation alone does not sustain significant anaerobic growth of P. aeruginosa, it provides the bacterium with the metabolic capacity for long-term survival of up to 18 days. Detected conversion of pyruvate to lactate and acetate is dependent on the presence of intact ldhA and ackA-pta loci, respectively. DNA microarray studies in combination with reporter gene fusion analysis and enzyme activity measurements demonstrated the anr- and ihfA-dependent anaerobic induction of the ackA-pta promoter. Potential Anr and integration host factor binding sites were localized. Pyruvate-dependent anaerobic long-term survival was found to be significantly reduced in anr and ihfA mutants. No obvious IdhA regulation by oxygen tension was observed. Pyruvate fermentation is pH dependent. Nitrate respiration abolished pyruvate fermentation, while arginine fermentation occurs independently of pyruvate utilization.

In littoral sediments, microphytobenthic (MPB) nitrogen assimilation often exceeds nitrogen removal by denitrification, partly because MPB activity suppresses denitrification. Little is known about the balance between these two processes at sublittoral depths. Benthic pigment composition, light and dark oxygen, and nutrient fluxes (N[O.sub.3.sup.-], N[H.sub.4.sup.+], dissolved organic nitrogen (DON), P[O.sup.3-.sub.4], Si([(OH).sub.4]), as well as denitrification were measured between 1 and 15 m in depth in Gullmar Fjord (Skagerrak) in spring and autumn. The hypothesis was that the assimilation/ denitrification ratio would decrease with depth, along with decreasing MPB activity caused by light limitation. MPB photosynthesis occurred along the entire depth gradient, although sediments were net autotrophic only above 5 m. Inorganic nitrogen (DIN) (and silica) flux changed along the depth gradient, the general pattern being sediment uptake at [less than or equal to] 5 m and efflux at [greater than or equal] 10 m depth. DON flux (~50% of total dissolved nitrogen flux) showed a less clear pattern. Two trends regarding DIN fluxes and denitrification--significant light effects and negative correlations with gross primary productivity--showed that MPB activity influenced nitrogen (N) turnover. Although denitrification increased with depth, rates remained low (

Abstract We examined the fate of [N.sub.2]O following the addition of labelled nitrate and subsequent irrigation. Repacked silt loam soil columns, 1 m deep, were wetted up and instrumented with [...]

Three strains of heterotrophic denitrifying bacteria were cultured in artificial seawater medium under trace metal clean conditions to investigate their physiological response to changes in copper concentration. Decreasing the copper concentration in cultures of Pseudomonas stutzeri and Paracoccus denitrificans resulted in accumulation of nitrous oxide ([N.sub.2]O) gas compared to copper-replete cultures and cessation of growth before complete denitrification to dinitrogen. Correspondingly, the activity of the copper enzyme nitrous oxide reductase, measured for P. denitrificans cultures, was high in copper-replete cultures and was below detection in copper-deficient cultures. Addition of copper to copper-deficient cultures following the accumulation of [N.sub.2]O resulted in resumption of growth and complete consumption of [N.sub.2]O in solution. Growth of the third strain, WLB20, in copper-deficient medium caused a marked accumulation of nitrite, suggesting that WLB20 has the copper form of nitrite reductase. These observations suggest a role for trace metals in regulating redox cycling of nitrogen and trace gas production in the ocean.

A groundwater plume enriched in [sup.15]N[O.sup.-.sub.3] was created upgradient of a mesohaline salt marsh. By measuring the changes in concentration and isotopic enrichment of N[O.sup.-.sub.3], [N.sub.2]O, N[H.sup.+.sub.4], and particulate organic nitrogen (PON) during plume transport through the marsh, in situ rates of dissimilatory nitrate reduction to ammonium (DNRA) and denitrification (DNF) were estimated, as well as N storage in the reduced N pools. For groundwater discharge within the top 10 cm of marsh, N[O.sup.-.sub.3] removal was 90% complete within the 50 cm of marsh nearest the upland border. The peak N[O.sup.-.sub.3] loss rate from the plume ranged from 208 to 645 [micro]M [d.sup.-1]. Rates of DNRA (180 [micro]M [d.sup.-1]) and DNF (387-465 [micro]M [d.sup.-1]) processed 30% and 70% of the N[O.sup.-.sub.3] load, respectively. Terminal [N.sub.2]O production was approximately equal to [N.sub.2] production rates during DNE Comparison of [sup.15]N lost from the [sup.15]N[O.sup. -.sub.3] pool and [sup.15]N gained in each of the reduced products accounted for only 22% of the reduced [sup.15]N, thus indicating N export from the system. Despite high rates of DNRA, the N[H.sup.+.sub.4] produced was not a long-term repository for the groundwater-derived N but was instead rapidly immobilized into marsh PON and retained on longer timescales. The small inventory of [sup.15]N in the [N.sub.2]O and [N.sub.2] pools relative to DNF rates, coincident with an undersaturation of dissolved argon, indicated that denitrified N was exported to the atmosphere on short timescales. The relative magnitudes of DNF and DNRA in conjunction with the immobilization of N[H.sup.+.sub.4] and evasion of N gases dictated the extent of export versus retention of the groundwater N[O.sup.-.sub.3] load.

Researchers have discovered that a strain of Rhodococcus can completely degrade nitroglycerin, removing all three nitrogen atoms. Pseudomonas putida, Arthrobacter sp., and Klebsiella sp. were also able to use nitroglycerin as their sole nitrogen source, but only Rhodococcus could remove all three nitrogen atoms.

Researchers estimated denitrification and nitrogen fixation rates in sediments from a Texas sea grass bed using an isotope-pairing technique and a membrane inlet mass spectrometer. Denitrification rates were an average of 20 microgram-atoms of N per square meter per hour, and nitrogen fixation rates were an average of 60 microgram-atoms of N per square meter per hour.

It may not be necessary to recycle sludge between anaerobic and aerobic zones when using Paracoccus denitrificans as the polyphosphate-accumulating organism. This bacterium is capable of removing phosphate and nitrate without the need for alternating anaerobic/aerobic switches.`

Results points out to the involvement of cobK and cobJ genes in the anaerobic synthesis of cobalamin in Paracoccus denitrificans. This unusual anerobic behavior is mediated by the cobalamin-dependent ribonucleotide reductase.

Research was conducted to examine the occurrence of anaerobic processes in aerated activated sludge using a combination of various techniques. Microsensor calculations were taken for the different parameters in 250 individual activated sludge flocs. Results indicate that the respiration capacity of activated sludge is simply not sufficient to create anoxia under air saturation. A likely explanation for the absence of anoxia may be that oxygen transport is not only diffusional but enhanced by advection.

Denitrifying bacteria in the gut of earthworms are responsible for the emission of nitrous oxide by the earthworm. This emission accounts for about one-third of the nitrous oxide emitted by garden soil.

Chloramphenicol should not be used in denitrifying enzyme activity (DEA) assays in concentrations greater than 0.1 g/liter. The antibiotic is used in these assays to inhibit the synthesis of new denitrifying enzymes, but it inhibits existing enzymes as well.

Researchers report five denitrifying strains of bacteria that can degrade compounds with a quaternary carbon atom in the absence of oxygen. Two strains belong to the alpha-Proteobacteria and three belong to the beta-Proteobacteria.

Research was conducted to show the requirement of periplasmic nitrate reductase in the first step of denitrification in Pseudomonas sp. strain G-179 using both biochemical and genetic proof. It was proposed that two systems are responsible for dissimilatory nitrate reduction in denitrifiers. Results demonstrate that the periplasmic nitrate reductase provides one of the significant mechanisms for aerobic nitrate reduction. Also, aerobic nitrate reduction and aerobic denitrification may have potential applications in water and industrial water treatment.

The diversity of nitrous oxide reductase (nosZ) genes in sediments obtained from the Atlantic Ocean and Pacific Ocean continental shelves has been investigated using the polymerase chain reaction assaying technique. An estimated 1,100 bp of the nosZ gene were amplified using nosZ gene-specific primers, with 37 copies characterized. The conservation of important structural motifs was confirmed by alignment of the derived amino acid sequences. In addition, three major clusters of nosZ genes have been identified by phylogenetic analysis, with little overlap between culture-based and environmental groups.

Two sets of PCR primers have been designed to amplify fragments of the gene coding for nitric reductase, a key enzyme involved in bacterial denitrification. Consensus regions in gene sequences encoding the two forms of nitrite reductase, cd(sub 1)-nir and Cu-nir were used in the preparation of the primers. Results show that the primers were able to amplify the correct gene, although they failed to amplify genes of nondenitrifying strains.

Research was conducted to examine the kinetics of nirS expression (cytochrome cd1 nitrite reductase) in Pseudomonas stutzeri during the transition from aerobic respiration to denitrification. The signal and regulator requirements for the transcriptional activation of nirS, norCB and nosZ were examined after a shifting of the respiratory metabolism from oxygen to nitrate or nitrite. Results provide evidence that a nitrate- and nitrite-responsive regulatory circuit independent of NarXL is required for the activation of denitrification genes.

Research was conducted to examine the potential of an oxygen-limited autotrophic nitrification-denitrification (OLAND) system with a nitrifying sludge as the biocatalyst. Results demonstrated that with low oxygen concentrations, nitrite oxidizers were strongly inhibited. Findings indicated that autotrophic conversion of NH4+-N to N2 in the OLAND system may be influenced largely by ammonium oxidizers and not by nitrite oxidizers.

Research was conducted to examine the vertical and temporal distribution of NO3- in diatom-covered sediment during light-dark cycles using a novel microscale NO3- biosensor characterized by absence of interference from chemical species other than NO2- and N2O. Vertical distribution of NO3- assimilation, nitrification and denitrification was measured from the calculated steady-state NO3- profiles by diffusion reaction models. Results show that the stimulatory effect on nitrification by illumination was caused by algal production of O2.NH4+.

Acetylene blockage method was used to examine impact of nitrate concentration on the denitrification rate and N2O production in intact sediment cores from a river continuum. An increase in denitrification rate was observed after the addition of nitrate in the overlying water. A Michaelis-Menten-type curve was shown and a strong response to nitrate addition was observed in the denitrification rate of intact sediment.

The isolation and identification of three new phenol-degrading denitrifying microorganisms of the genera Azoarcus from sediments of various geographical locations are described. The strains have the ability to use phenol as a source of carbon and energy under denitrifying conditions. The strains are short gram-negative rods and, although a polar flagellum is present in the exponential phase, motility is lost in older cultures. Moreover, the isolates are only able to degrade phenol under denitrifying states and not in aerobic conditions.

Photoinhibition of nitrite reduction caused light-mediated nitrite accumulation of Pseudomonas sp. strain JR12. This was gleaned in an examination of the effect of light on the denitrifying capacity of this nonphotosynthetic denitrifier. Inhibition of nitrite reduction in cells illuminated with green light was the highest, as against inhibition upon exposure to blue and red light. Exposure of the cells to light caused a photooxidation of cytochrome c, affirming that light exposure prevents electron flow from cytochrome c to nitrite reductase.

Cleavage of chromosomal DNA from Pseudomonas aeruginosa PAO by SpeI and DpnI were employed to determine the map location of certain primary denitrification genes. These are narGH, nirS, nirE, norCB, nosZ and nosA. Genes related to anaerobic or microaerophilic metabolism were also examined. These are napA, ccoN, hemN, an fnr-like regulatory gene, and azu and fdxA. A homologue of nosA encoding a putative portion of the Cu-processing mechanism for nitrous-oxide reductase was identified. There is an indication of a linkage of anr with hemN and ccoN, and the presence of a napA gene in both P. aeruginosa and P. stutzeri.

The effect of several monoterpenes on methane oxidation by pure cultures of the methanotrophs Methylosinus trichosporium OB3b and Methylobacter luteus, denitrification by six environmental isolates and aerobic metabolism by heterotrophic laboratory cultures were investigated. Inhibition occurred to various extents and was transient. Complete inhibition of methane oxidation by Methylosinus trichosporium OB3b with 1.1 nM (-)-alpha-pinene lasted for more than two days. Inhibition was greater in conditions under which particulate methane monooxygenase was expressed.

A study was conducted on the expression and in situ activity of the membrane-bound and periplasmic nitrate reductases in carbon-limited continuous cultures of Paracoccus denitrificans Pd1222. The findings indicate that the nature of the carbon substrate and oxygen concentration can affect the expression of the periplasmic and membrane-bound nitrate reductases.

A study was conducted on the isolation of two species of Pseudomonas from nitroglycerin (NG)-contaminated soils using enrichment culture. One species uses NG as a sole source of nitrogen while the other tolerates high concentrations of NG in the growth medium. The results indicate that the two flavoenzymes exhibit different selectivities for removal of the first nitro group from NG. Moreover, the selectivity of each enzyme is partially maintained during removal of the second nitro group from the dinitroglycerol isomers.

A study was conducted on the structural genes of nitric oxide reductases in Alcaligenes eutrophus H16. The results indicate that inactivation of both norB and norZ was lethal to the cells under anaerobic living conditions and that anaerobic growth was restored through the introduction of either norB or norZ on a broad-host-range plasmid. Thus, the norB and norZ gene products are instrumental and isofunctional in denitrification.

A study was conducted on the variation of nitrifying and denitrifying bacteria culture aeration in relation to NO and N2O emissions. NO and N2O production were examined in the denitrifiers Pseudomonas stutzeri and Alcaligenes eutrophus and the nitrifier Nitrosomonas europaea cultured at different aeration levels. Results reveal that nitrifiers can only dominate soil NO and N2O emissions when nitrite is present.

A study was conducted on the blue copper protein azurin and cytochrome c(sub 551) to determine their role in the dissimilatory nitrate reduction of Pseudomonas aeruginosa. Results have shown through an in vivo approach that cytochrome c(sub 551) rather than azurin has a physiological role in denitrification in Pseudomonas aeruginosa. Moreover, a Western Blotting analysis show that azu expression is regulated by RpoS and ANR.