A study on the phylogeny and the ecology of ammonia-oxidizing bacteria using a new molecular marker based on the gene amoB

L'agricultura i la industrialització han causat un augment significatiu del nombre d'ambients rics en amoni. La presència de compostos nitrogenats redueix la qualitat de l'aigua, causant problemes de toxicitat, deteriorant el medi ambient i fins i tot afectant la salut humana. En conseqüència, la nitrificació s'ha convertit en un procés global que afecta al cicle del nitrogen a la biosfera. Els bacteris oxidadors d'amoni (AOB) són els responsables de l'oxidació de l'amoni a nitrit, i juguen un paper essencial en el cicle del nitrogen. Els primers oxidadors d'amoni foren aïllats a finals del segle XIX, però la lentitud del seu creixement i les dificultats per cultivar-los feren que fins als anys 80, amb els primers estudis emprant el gen 16SrDNA, no s'assolís un coneixement complert d'aquest grup bacterià. Actualment les bases de dades contenen multitud d'entrades amb seqüències corresponents a AOB. L'objectiu d'aquest treball era trobar, desenvolupar i avaluar eines útils i fiables per a l'estudi dels AOB en mostres ambientals. En aquest treball primer descrivim la utilització de la hibridació in situ amb fluorescència (FISH), mitjançant l'aplicació de sondes amb diana en el 16SrRNA dels AOB. La FISH ens va permetre detectar i recomptar aquest grup bacterià; no obstant, aquest mètode no permetia la detecció de noves seqüències, pel que es necessitava una nova eina. Amb aquesta intenció vam aplicar la seqüència de la sonda Nso1225 en una PCR. El fet d'amplificar específicament un fragment del 16SrDNA dels AOB va suposar el desenvolupament d'una nova eina molecular que permetia detectar la presència i diversitat d'aquests bacteris en ambients naturals. Malgrat tot, algunes seqüències pertanyents a bacteris no oxidadors d'amoni del subgrup β dels proteobacteris, eren també obtingudes amb aquesta tècnica. Així mateix, un dels inconvenients de l'ús del 16SrDNA com a marcador és la impossibilitat de detectar simultàniament els AOB que pertanyen als subgrups β i γ dels proteobacteris. El gen amoA, que codifica per la subunitat A de l'enzim amoni monooxigenasa (AMO), era aleshores àmpliament utilitzat com a marcador per a la detecció dels AOB. En aquest treball també descrivim la utilització d'aquest marcador en mostres procedents d'un reactor SBR. Aquest marcador ens va permetre identificar seqüències de AOB en la mostra, però la necessitat de detectar amoA mitjançant clonatge fa que l'ús d'aquest marcador requereixi massa temps per a la seva utilització com a eina en estudis d'ecologia microbiana amb moltes mostres. Per altra banda, alguns autors han assenyalat l'obtenció de seqüències de no AOB en utilitzar amoA en un protocol de PCR-DGGE. Amb la finalitat d'obtenir una eina ràpida i rigorosa per detectar i identificar els AOB, vam desenvolupar un joc nou d'oligonucleòtids amb diana en el gen amoB, que codifica per a la subunitat transmembrana de l'enzim AMO. Aquest gen ha demostrat ser un bon marcador molecular pels AOB, oferint, sense tenir en compte afiliacions filogenètiques, una elevada especificitat, sensibilitat i fiabilitat. En aquest treball també presentem una anàlisi de RT-PCR basada en la detecció del gen amoB per a la quantificació del gènere Nitrosococcus. El nou joc d'oligonucleòtids dissenyat permet una enumeració altament específica i sensible de tots els γ-Nitrosococcus coneguts. Finalment, vam realitzar un estudi poligènic, comparant i avaluant els marcadors amoA, amoB i 16SrDNA, i vàrem construir un arbre filogenètic combinat. Com a resultat concloem que amoB és un marcador adequat per a la detecció i identificació dels AOB en mostres ambientals, proporcionant alhora agrupacions consistents en fer inferències filogenètiques. Per altra banda, la seqüència sencera del gen 16S rDNA és indicada com a marcador en estudis amb finalitats taxonòmiques i filogenètiques en treballar amb cultius purs de AOB.

Splanchnic metabolism of nitrogenous compounds and urinary nitrogen excretion in steers fed alfalfa under conditions of increased absorption of ammonia and L-arginine supply across the portal-drained viscera

Effects of increased ammonia and/or arginine absorption across the portal-drained viscera (PDV) on net splanchnic (PDV and liver) metabolism of nitrogenous compounds and urinary N excretion were investigated in six cathetenzed Hereford x Angus steers (501 +/- 1 kg BW) fed a 75% alfalfa:25% (as-fed basis) corn-soybean meal diet (0.523 MJ of ME/[kg BW0.15.d]) every 2 h without (27.0 g of N/kg of dietary DM) and with 20 g of urea/kg of dietary DM (35.7 g of N/kg of dietary DM) in a split-plot design. Net splanchnic flux measurements were obtained immediately before beginning and ending a 72-h mesenteric vein infusion of L-arginine (15 mmol/h). For 3 d before and during arginine infusion, daily urine voided was measured and analyzed for N composition. Feeding urea increased PDV absorption (P < 0.01) and hepatic removal (P < 0.01) of ammonia N, accounting for 80% of increased hepatic urea N output (P < 0.01). Numerical increases in net hepatic removal of AA N could account for the remaining portion of increased hepatic urea N output. Arginine infusion increased hepatic arginine removal (P < 0.01) and hepatic urea N output (P < 0.03) and switched hepatic ornithine flux from net uptake to net output (P < 0.01), but numerical changes in net hepatic removal of ammonia and AA N could not account fully for the increase in hepatic urea N output. Increases in urine N excretion equaled quantities of N fed as urea or infused as arginine. Estimated salivary urea N excretion was not changed by either treatment. Urea cycle regulation occurs via a complex interaction of mechanisms and requires N sources other than ammonia, but the effect of increased ammonia absorption on hepatic catabolism of individual AA in the present study was not significant.

Splanchnic metabolism of nutrients and hormones in steers fed alfalfa under conditions of increased absorption of ammonia and L-arginine supply across the portal-drained viscera

Effects of increased ammonia and/or arginine absorption on net splanchnic (portal-drained viscera [PDV] plus liver) metabolism of nonnitrogenous nutrients and hormones in cattle were examined. Six Hereford x Angus steers (501 +/- 1 kg BW) prepared with vascular catheters for measurements of net flux across the splanchnic bed were fed a 75% alfalfa:25% (as-fed basis) corn and soybean meal diet (0.523 MJ of ME/[kg BW(0.75.)d]) every 2 h without (27.0 g of N/kg of DM) and. with 20 g of urea/kg of DM (35.7 g of N/kg of DM) in a split-plot design. Net flux measurements were made immediately before and after a 72-h mesenteric vein infusion Of L-arginine (15 mmol/h). There were no treatment effects on PDV or hepatic 02 consumption. Dietary urea had no effect on splanchnic metabolism of glucose or L-lactate, but arginine infusion decreased net hepatic removal Of L-lactate when urea was fed (P < 0.01). Net PDV appearance of n-butyrate was increased by arginine infusion (P < 0.07), and both dietary urea (P < 0.09) and arginine infusion (P < 0.05) increased net hepatic removal of n-butyrate. Dietary urea also increased total splanchnic acetate output (P < 0.06), tended to increase arterial glucagon concentration (P < 0.11), and decreased arterial ST concentration (P < 0.03). Arginine infusion increased arterial concentration (P < 0.07) and net PDV release (P < 0.10) and tended to increase hepatic removal (P < 0.11) of insulin, as well as arterial concentration (P < 0.01) and total splanchnic output (P < 0.01) of glucagon. Despite changes in splanchnic N metabolism, increased ammonia and arginine absorption had little measurable effect on splanchnic metabolism of glucose and other nonnitrogenous components of splanchnic energy metabolism.

Steinernema feltiae: ammonia triggers the emergence of their infective juveniles

Entomopathogenic nematodes complete their life cycles inside dead insects. The emergence of new infective juveniles from the cadaver has been attributed (but never demonstrated) to food depletion or to the accumulation of metabolites from the breakdown of the host's tissues. Here we give evidence that emergence is triggered by ammonia, a product of nematode defecation. We found that the emergence of Steinernema feltiae infective juveniles from Galleria mellonella cadavers was stimulated by a particular level of ammonia. Emergence was delayed when ammonia in the cadaver was decreased and was prompted when increased. These findings will further improve the understanding of the nematode life cycle. Here we speculate that production of infective juveniles can be mediated by ammonia and work in a manner analogous to that of the clatter recovery inhibiting factor (DRIF) in Caenorhabditis elegans. (C) 2008 Elsevier Inc. All rights reserved.

Effects of ammonia treatment and undegradable protein supplementation on nutrient digestion of sheep fed on wheat straw based diets.

A study was conducted to investigate the effects of wheat straw ammonisation and supplementation with a rumen undegradable protein (UDP) source on nutrient digestion and nitrogen balance by lambs while diets were supplemented with kibbled carob pods as energy source. Ammonisation increased the crude protein content of wheat straw by nearly 100% and decreased the contents of neutral detergent fibre and acid detergent fibre by 7% and 1.7% respectively. Treating the straw with ammonia resulted in significant (P<0.01) increase in nitrogen (N) intake and intakes of organic matter (OM) and dry matter (DM) tended toward significance (P<0.1). The UDP source had no effect (P>0.05) on DM and OM intakes but resulted in an increase (P<0.05) of N intakes. Both, ammonization and UDP supplementation increased (P<0.01) the DM, OM and N digestibility. In conclusion, the results of this study suggest that ammonisation and UDP supplementation is a practical dietary manipulation option to improve the nutritional status of ruminants fed on roughage-based diets.

Effluent quality and ammonia emissions from out-wintering pads in England, Wales and Ireland

Out-wintering pads offer a reduced cost system for wintering cattle, minimising damage to pasture, providing animal welfare and production benefits, and generate, potentially, a more manageable effluent and lower ammonia emissions. The objectives of the present study were (i) to contribute to improved understanding of the factors impacting on effluent quality, ammonia emissions and animal welfare via observations on four farm-based out-wintering pads (ComOWPs) in England, Wales and Ireland and more detailed studies undertaken on four experimental OWPs (ExpOWPs) constructed at Rothamsted Research North Wyke, Devon, England and (ii) to corroborate the effluent quality data from both the ComOWPs and the ExpOWPs, with findings in the literature. Woodchip size, feeding management and area allowance were the treatment factors applied on the ExpOWPs. These three factors were randomised across the four ExpOWPs, over four 6–7 week periods. Effluent quality from the ExpOWPs was sampled frequently in a flow proportional way and analysed for total N (TN); total P (TP); total solids (TS); ammonium-N (NH4+-N); nitrate-N (NO3−-N). Beef cattle were periodically weighed for determination of live weight gain (LWG). An approximate nitrogen balance was calculated as a means of understanding its partitioning and fate during and after the ExpOWPs use. Effluent quality from the ComOWPs was sampled frequently, also in a flow-proportional way, and analysed for TN, TP, TS, NH4+-N, NO3−-N, total K and COD. Effluent quality data from the ExpOWPs showed no significant differences (P > 0.05) between treatments, with average concentrations of 1095 mg l−1, and 806 mg l−1, for TN and NH4+-N, respectively. Average effluent concentrations from the ComOWPs were 356 mg l−1 TN and 124 mg l−1 NH4+-N. Ammonia emissions from the ExpOWPs showed no significant differences (P > 0.05) between the treatments, with average mean emission rates of 2.5 g m−2 d−1 NH3-N, respectively. A positive correlation was established between NH3-N emission rate and wind speed. Emission rates from the ComOWPs ranged from 0.7 to 1.6 g m−2 d−1 NH3-N. Average daily LWG on the ExpOWPs was 1.33 kg steer−1 d−1. The effluent from both the ComOWPs and ExpOWPs were more similar with dirty water and of consistently lower strength than beef cattle slurry, as supported by findings in the literature, and therefore, it is suggested to be subject to the regulatory requirements of dirty water rather than slurry.

The reaction between silylene and ammonia: some gas-phase kinetic and quantum chemical studies

Time-resolved kinetic studies of the reaction of silylene, SiH2, generated by 193 nm laser flash photolysis of silacyclopent-3-ene, have been carried out in the presence of ammonia, NH3. Second order kinetics were observed. The reaction was studied in the gas phase at 10 Torr total pressure in SF6 bath gas at each of the three temperatures, 299, 340 and 400 K. The second order rate constants (laser pulse energy of 60 mJ/pulse) fitted the Arrhenius equation: log(k/cm3 molecule-1 s-1) = (-10.37 ± 0.17) + (0.36 ± 1.12 kJ mol-1)/RTln10 Experiments at other pressures showed that these rate constants were unaffected by pressure in the range 10-100 Torr, but showed small decreases in value at 3 and 1 Torr. There was also a weak intensity dependence, with rate constants decreasing at laser pulse energies of 30 mJ/pulse. Ab initio calculations at the G3 level of theory, show that SiH2 + NH3 should form an initial adduct (donor-acceptor complex), but that energy barriers are too great for further reaction of the adduct. This implies that SiH2 + NH3 should be a pressure dependent association reaction. The experimental data are inconsistent with this and we conclude that SiH2 decays are better explained by reaction of SiH2 with the amino radical, NH2, formed by photodissociation of NH3 at 193 nm. The mechanism of this previously unstudied reaction is discussed.

Flow synthesis using gaseous ammonia in a Teflon AF-2400 tube-in-tube reactor: Paal–Knorr pyrrole formation and gas concentration measurement by inline flow titration

Using a simple and accessible Teflon AF-2400 based tube-intube reactor, a series of pyrroles were synthesised in flow using the Paal–Knorr reaction of 1,4-diketones with gaseous ammonia. An inline flow titration technique allowed measurement of the ammonia concentration and its relationship to residence time and temperature.

Continuous-flow processing of gaseous ammonia using a Teflon AF-2400 tube-in-tube reactor: synthesis of thioureas and in-line titrations

A simple tube-in-tube reactor based on the gas-permeable membrane Teflon AF-2400 was used in the continuous flow reaction of gaseous ammonia with isothiocyanates and one isocyanate. A colourimetric in-line titration technique is also reported as a simple method to quantify the amount of ammonia taken up by the solvent in the system.

Versatile microanalytical system with porous polypropylene capillary membrane for calibration gas generation and trace gaseous pollutants sampling applied to the analysis of formaldehyde, formic acid, acetic acid and ammonia in outdoor air

The analytical determination of atmospheric pollutants still presents challenges due to the low-level concentrations (frequently in the mu g m(-3) range) and their variations with sampling site and time In this work a capillary membrane diffusion scrubber (CMDS) was scaled down to match with capillary electrophoresis (CE) a quick separation technique that requires nothing more than some nanoliters of sample and when combined with capacitively coupled contactless conductometric detection (C(4)D) is particularly favorable for ionic species that do not absorb in the UV-vis region like the target analytes formaldehyde formic acid acetic acid and ammonium The CMDS was coaxially assembled inside a PTFE tube and fed with acceptor phase (deionized water for species with a high Henry s constant such as formaldehyde and carboxylic acids or acidic solution for ammonia sampling with equilibrium displacement to the non-volatile ammonium ion) at a low flow rate (8 3 nLs(-1)) while the sample was aspirated through the annular gap of the concentric tubes at 25 mLs(-1) A second unit in all similar to the CMDS was operated as a capillary membrane diffusion emitter (CMDE) generating a gas flow with know concentrations of ammonia for the evaluation of the CMDS The fluids of the system were driven with inexpensive aquarium air pumps and the collected samples were stored in vials cooled by a Peltier element Complete protocols were developed for the analysis in air of NH(3) CH(3)COOH HCOOH and with a derivatization setup CH(2)O by associating the CMDS collection with the determination by CE-C(4)D The ammonia concentrations obtained by electrophoresis were checked against the reference spectrophotometric method based on Berthelot s reaction Sensitivity enhancements of this reference method were achieved by using a modified Berthelot reaction solenoid micro-pumps for liquid propulsion and a long optical path cell based on a liquid core waveguide (LCW) All techniques and methods of this work are in line with the green analytical chemistry trends (C) 2010 Elsevier B V All rights reserved

Stress in pacu exposed to ammonia in water

The present study evaluated stress indicators in pacu exposed to ammonia in water under the following conditions: without NH4Cl (0.00 g/L); with 0.0078 g NH4Cl/L; and with 0.078 g NH4Cl/L (pH 8.3 and 27 ºC). After the salt dilution the water flow was interrupted and reestablished in 24 hours. Sampling occurred prior to the addition of NH4Cl (control) and after 12, 24 and 48 hours. Glycaemia increased only in fish with the highest salt concentration when compared with group control, regardless of time, and at 24 hours, regardless of treatment. Plasma ammonia, highest in fish exposed to the highest NH4Cl concentration, decreased progressively up to 48 hours. Plasma chloride only decreased in fish not exposed to salt when compared with control and osmolality increased after 24 hours. Hematocrit (Ht), number and volume of erythrocytes and hemoglobin did not change when NH4Cl was added; Ht decrease was reported after 12 hours, but it was not followed by the other blood parameters. The results show tolerance of the pacu to ammonia in the environment.

Ontogenetic Variation in Ammonia Excretion during the Early Life Stages of the Amazon River Prawn, Macrobrachium amazonicum

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Phenylalanine ammonia-lyase activity in soybean roots extract measured by reverse-phase high performance liquid chromatography

The high performance liquid chromatography (HPLC) technique was applied to measure phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) activity in soybean (Glycine max L. Merril cv. BR16) roots. t-Cinnamate, the catalytic product of the PAL reaction was quantified at 275 nm by isocratic elution with methanol:water through an ODS(M) column. Comparative experiments were carried out with 1.0 mM ferulic acid, an inducer of PAL activity. The results suggest that liquid chromatography is a rapid and sensitive method to analyze PAL activity in non-purified extract.

Peroxidase and phenylalanine ammonia-lyase activities, phenolic acid contents, and allelochemicals-inhibited root growth of soybean

The influence of the allelochemicals ferulic (FA) and vanillic (VA) acids on peroxidase (POD, EC 1.11.1.7) and phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) activities and their relationships with phenolic acid (PhAs) contents and root growth of soybean (Glycine max (L.) Merr.) were examined. Three-day-old seedlings were cultivated in nutrient solution containing FA or VA (0.1 to 1 mM) for 48 h. Both compounds (at 0.5 and 1 mM) decreased root length (RL), fresh weight (FW) and dry weight (DW) and increased PhAs contents. At 0.5 and 1 mM, FA increased soluble POD activity (18% and 47%, respectively) and cell wall (CW)-bound POD activity (61% and 34%), while VA increased soluble POD activity (33% and 17%) but did not affect CW-bound POD activity. At I mM, FA increased (82%) while VA reduced (32%) PAL activities. The results are discussed on the basis of the role of these compounds on phenylpropanoid metabolism and root growth and suggest that the effects caused on POD and PAL activities are some of the many mechanisms by which allelochemicals influence plant growth.

Simultaneous effects of ferulic and vanillic acids on peroxidase and phenylalanine ammonia-lyase in soybean (Glycine max) roots

Simultaneous effects of ferulic (FA) and vanillic (VA) acids on peroxidase (POD, EC 1.11.1.7) and phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) activities on soybean (Glycine max (L.) MERR.) root growth were analyzed. Three-day-old seedlings were cultivated in nutrient solution containing FA or VA (0.5 mM; 1.0 mM or equimolar mixtures) for 48 h. Acting alone, both compounds (at 0.5 or 1.0 mM) decreased root length (RL), fresh weight (FW), dry weight (DW) and increased soluble POD and cell wall (CW)-bound POD activities. At 1.0 mM, FA increased (but VA decreased) the PAL activity. Acting simultaneously, the effects of the allelochemical interaction were lower than the sum of the effects of each compound tested separately, suggesting antagonism.