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Sample records for ammonia-oxidizing nitrosomonas europaea

  1. Degradation of halogenated aliphatic compounds by the ammonia- oxidizing bacterium Nitrosomonas europaea.

    OpenAIRE

    Vannelli, T; Logan, M; Arciero, D M; Hooper, A B

    1990-01-01

    Suspensions of Nitrosomonas europaea catalyzed the ammonia-stimulated aerobic transformation of the halogenated aliphatic compounds dichloromethane, dibromomethane, trichloromethane (chloroform), bromoethane, 1,2-dibromoethane (ethylene dibromide), 1,1,2-trichloroethane, 1,1,1-trichloroethane, monochloroethylene (vinyl chloride), gem-dichloroethylene, cis- and trans-dichloroethylene, cis-dibromoethylene, trichloroethylene, and 1,2,3-trichloropropane, Tetrachloromethane (carbon tetrachloride),...

  2. Degradation of halogenated aliphatic compounds by the ammonia- oxidizing bacterium Nitrosomonas europaea.

    Science.gov (United States)

    Vannelli, T; Logan, M; Arciero, D M; Hooper, A B

    1990-01-01

    Suspensions of Nitrosomonas europaea catalyzed the ammonia-stimulated aerobic transformation of the halogenated aliphatic compounds dichloromethane, dibromomethane, trichloromethane (chloroform), bromoethane, 1,2-dibromoethane (ethylene dibromide), 1,1,2-trichloroethane, 1,1,1-trichloroethane, monochloroethylene (vinyl chloride), gem-dichloroethylene, cis- and trans-dichloroethylene, cis-dibromoethylene, trichloroethylene, and 1,2,3-trichloropropane, Tetrachloromethane (carbon tetrachloride), tetrachloroethylene (perchloroethylene), and trans-dibromoethylene were not degraded. PMID:2339874

  3. Nitrite as a stimulus for ammonia-starved Nitrosomonas europaea

    NARCIS (Netherlands)

    Laanbroek, H.J.; Bär-Gilissen, M.J.; Hoogveld, H.L.

    2002-01-01

    Ammonia-starved cells of Nitrosomonas europaea are able to preserve a high level of ammonia-oxidizing activity in the absence of ammonium. However, when the nitrite-oxidizing cells that form part of the natural nitrifying community do not keep pace with the ammonia-oxidizing cells, nitrite

  4. Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

    OpenAIRE

    Bollmann, A.; Sedlacek, C.J.; Norton, J.; Laanbroek, H.J.; Suwa, Y.; Stein, L.Y.; Klotz, M.G.; Arp, D.; Sayavedra-Soto, L.; Lu, M.; Bruce, D.; Detter, C.; Tapia, R.; Han, J.; Woyke, T.

    2013-01-01

    Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high interest because it is adapted to low ammonium and can be found in freshwater environments around the world. The 3,783,444-bp chromos...

  5. Impacts of ammonia on zinc oxide nanoparticle toxicity to Nitrosomonas europaea

    Science.gov (United States)

    Wu, Junkang; Chang, Yan; Gao, Huan; Yu, Ran

    2017-05-01

    A Although the toxicity effects of engineering nanoparticles (NPs) in biological wastewater nitrogen removal (BNR) system have been extensively attracted, the impacts of co-existing contaminants from wastewater on NP toxicity have been less addressed. In this study, the effects of ammonia on ZnO NP toxicity to typical ammonia oxidizing bacteria-Nitrosomonas europaea were investigated, as indicated by the cell density, membrane integrity, ammonia oxidation rate, and AMO activity. After 6-h’s exposure to 10 mg/L ZnO NPs, the cell density, membrane integrity, ammonia oxidation rate, and AMO activity was dramatically suppressed despite of the increasing ammonia loading. Ammonia at varying concentrations did not obviously affect ZnO NPs toxicity to cell density. The presence of ammonia at 100 or 200 mg/L significantly alleviated the antibacterial effects of ZnO NPs on cells. The reduction of the concentration of released Zn2+ might be responsible for the compromised ZnO NPs toxicity. However, the presence of extremely dosed ammonia at 200 mg/L imposed restrictions on further alleviation of ZnO NPs toxicities probably due to the production of free ammonia and acclamation of nitrite. All these findings would provide new insights for risk assessment of the combined effects of NPs with other co-existing contaminants in the BNR system.

  6. Global metabolomic responses of Nitrosomonas europaea 19718 to cold stress and altered ammonia feeding patterns.

    Science.gov (United States)

    Lu, Huijie; Ulanov, Alexander V; Nobu, Masaru; Liu, Wen-Tso

    2016-02-01

    The model ammonia-oxidizing bacterium Nitrosomonas europaea represents one of the environmentally and biotechnologically significant microorganisms. Genome-based studies over the last decade have led to many intriguing discoveries about its cellular biochemistry and physiology. However, knowledge regarding the regulation of overall metabolic routes in response to various environmental stresses is limited due to a lack of comprehensive, time-resolved metabolomic analyses. In this study, gas chromatography-mass spectrometry (GC-MS)-based metabolic profiling was performed to characterize the temporal variations of N. europaea 19718 intercellular metabolites in response to varied temperature (23 and 10 °C) and ammonia feeding patterns (shock loading and continuous feeding of 20 mg N/L). Approximately 87 metabolites were successfully identified and mapped to the existing pathways of N. europaea 19718, allowing interpretation of the influence of temperature and feeding pattern on metabolite levels. In general, varied temperature had a more profound influence on the overall metabolism than varied feeding patterns. Total extracellular metabolite concentrations (relative to internal standards and normalized to biomass weight) were lower under cold stress and shock loading conditions compared with the control (continuous feeding at 23 °C). Cold stress caused the widespread downregulation of metabolites involved in central carbon metabolism, amino acid, and lipid synthesis (e.g., malonic acid, succinic acid, putrescine, and phosphonolpyruvate). Metabolites that showed differences under varied feeding patterns were mainly involved in nucleotide acid, amino acid, and lipid metabolism (e.g., adenine, uracil, and spermidine). This study highlighted the roles of central carbon and nitrogen metabolism in countering cold stress and altered ammonia availability. In addition, transcriptomic, proteomic, and metabolomic data from three studies on N. europaea were compared to achieve a

  7. Global metabolomic responses of Nitrosomonas europaea 19718 to cold stress and altered ammonia feeding patterns

    KAUST Repository

    Lu, Huijie

    2015-11-05

    © 2015 Springer-Verlag Berlin Heidelberg The model ammonia-oxidizing bacterium Nitrosomonas europaea represents one of the environmentally and biotechnologically significant microorganisms. Genome-based studies over the last decade have led to many intriguing discoveries about its cellular biochemistry and physiology. However, knowledge regarding the regulation of overall metabolic routes in response to various environmental stresses is limited due to a lack of comprehensive, time-resolved metabolomic analyses. In this study, gas chromatography–mass spectrometry (GC-MS)-based metabolic profiling was performed to characterize the temporal variations of N. europaea 19718 intercellular metabolites in response to varied temperature (23 and 10 °C) and ammonia feeding patterns (shock loading and continuous feeding of 20 mg N/L). Approximately 87 metabolites were successfully identified and mapped to the existing pathways of N. europaea 19718, allowing interpretation of the influence of temperature and feeding pattern on metabolite levels. In general, varied temperature had a more profound influence on the overall metabolism than varied feeding patterns. Total extracellular metabolite concentrations (relative to internal standards and normalized to biomass weight) were lower under cold stress and shock loading conditions compared with the control (continuous feeding at 23 °C). Cold stress caused the widespread downregulation of metabolites involved in central carbon metabolism, amino acid, and lipid synthesis (e.g., malonic acid, succinic acid, putrescine, and phosphonolpyruvate). Metabolites that showed differences under varied feeding patterns were mainly involved in nucleotide acid, amino acid, and lipid metabolism (e.g., adenine, uracil, and spermidine). This study highlighted the roles of central carbon and nitrogen metabolism in countering cold stress and altered ammonia availability. In addition, transcriptomic, proteomic, and metabolomic data from three

  8. Gene expression profiles of Nitrosomonas europaea, an obligate chemolitotroph

    Energy Technology Data Exchange (ETDEWEB)

    Daniel J Arp

    2005-06-15

    Nitrosomonas europaea is an aerobic lithoautotrophic bacterium that uses ammonia (NH3) as its energy source. As a nitrifier, it is an important participant in the nitrogen cycle, which can also influence the carbon cycle. The focus of this work was to explore the genetic structure and mechanisms underlying the lithoautotrophic growth style of N. europaea. Whole genome gene expression. The gene expression profile of cells in exponential growth and during starvation was analyzed using microarrays. During growth, 98% of the genes increased in expression at least two fold compared to starvation conditions. In growing cells, approximately 30% of the genes were expressed eight fold higher, Approximately 10% were expressed more than 15 fold higher. Approximately 3% (91 genes) were expressed to more than 20 fold of their levels in starved cells. Carbon fixation gene expression. N. europaea fixes carbon via the Calvin-Benson-Bassham (CBB) cycle via a type I ribulose bisphosphate carboxylase/oxygenase (RubisCO). This study showed that transcription of cbb genes was up-regulated when the carbon source was limited, while amo, hao and other energy harvesting related genes were down-regulated. Iron related gene expression. Because N. europaea has a relatively high content of hemes, sufficient Fe must be available in the medium for it to grow. The genome revealed that approximately 5% of the coding genes in N. europaea are dedicated to Fe transport and assimilation. Nonetheless, with the exception of citrate biosynthesis genes, N. europaea lacks genes for siderophore production. The Fe requirements for growth and the expression of the putative membrane siderophore receptors were determined. The N. europaea genome has over 100 putative genes ({approx}5% of the coding genes) related to Fe uptake and its siderophore receptors could be grouped phylogenetically in four clusters. Fe related genes, such as a number of TonB-dependent Fe-siderophore receptors for ferrichrome and

  9. Gene expression profiles of Nitrosomonas europaea, an obligate chemolitotroph

    Energy Technology Data Exchange (ETDEWEB)

    Daniel J. Arp

    2005-05-25

    Nitrosomonas europaea is an aerobic lithoautotrophic bacterium that uses ammonia (NH3) as its energy source. As a nitrifier, it is an important participant in the nitrogen cycle, which can also influence the carbon cycle. The focus of this work was to explore the genetic structure and mechanisms underlying the lithoautotrophic growth style of N. europaea. Whole genome gene expression: The gene expression profile of cells in exponential growth and during starvation was analyzed using microarrays. During growth, 98% of the genes increased in expression at least two fold compared to starvation conditions. In growing cells, approximately 30% of the genes were expressed eight fold higher, Approximately 10% were expressed more than 15 fold higher. Approximately 3% (91 genes) were expressed to more than 20 fold of their levels in starved cells. Carbon fixation gene expression: N. europaea fixes carbon via the Calvin-Benson-Bassham (CBB) cycle via a type I ribulose bisphosphate carboxylase/oxygenase (RubisCO). This study showed that transcription of cbb genes was up-regulated when the carbon source was limited, while amo, hao and other energy harvesting related genes were down-regulated. Iron related gene expression: Because N. europaea has a relatively high content of hemes, sufficient Fe must be available in the medium for it to grow. The genome revealed that approximately 5% of the coding genes in N. europaea are dedicated to Fe transport and assimilation. Nonetheless, with the exception of citrate biosynthesis genes, N. europaea lacks genes for siderophore production. The Fe requirements for growth and the expression of the putative membrane siderophore receptors were determined. The N. europaea genome has over 100 putative genes ({approx}5% of the coding genes) related to Fe uptake and its siderophore receptors could be grouped phylogenetically in four clusters. Fe related genes, such as a number of TonB-dependent Fe-siderophore receptors for ferrichrome and

  10. Growth at low ammonium concentrations and starvation response as potential factors involved in niche differentiation among ammonia-oxidizing bacteria

    NARCIS (Netherlands)

    Bollmann, A.; Bär-Gilissen, M.J.; Laanbroek, H.J.

    2002-01-01

    In nature, ammonia-oxidizing bacteria have to compete with heterotrophic bacteria and plants for limiting amounts of ammonium. Previous laboratory experiments conducted with Nitrosomonas europaea suggested that ammonia-oxidizing bacteria are weak competitors for ammonium. To obtain a better

  11. Growth at low ammonium concentrations and starvation response as potential factors involved in niche differentiation among ammonia-oxidizing bacteria

    NARCIS (Netherlands)

    Bollmann, A.; Bär-Gilissen, M.J.; Laanbroek, H.J.

    2002-01-01

    In nature, ammonia-oxidizing bacteria have to compete with heterotrophic bacteria and plants for limiting amounts of ammonium. Previous laboratory experiments conducted with Nitrosomonas europaea suggested that ammonia-oxidizing bacteria are weak competitors for ammonium. To obtain a better insight

  12. Growth at low ammonium concentrations and starvation response as potential factors involved in niche differentiation among ammonia-oxidizing bacteria.

    Science.gov (United States)

    Bollmann, Annette; Bär-Gilissen, Marie-José; Laanbroek, Hendrikus J

    2002-10-01

    In nature, ammonia-oxidizing bacteria have to compete with heterotrophic bacteria and plants for limiting amounts of ammonium. Previous laboratory experiments conducted with Nitrosomonas europaea suggested that ammonia-oxidizing bacteria are weak competitors for ammonium. To obtain a better insight into possible methods of niche differentiation among ammonia-oxidizing bacteria, we carried out a growth experiment at low ammonium concentrations with N. europaea and the ammonia oxidizer G5-7, a close relative of Nitrosomonas oligotropha belonging to Nitrosomonas cluster 6a, enriched from a freshwater sediment. Additionally, we compared the starvation behavior of the newly enriched ammonia oxidizer G5-7 to that of N. europaea. The growth experiment at low ammonium concentrations showed that strain G5-7 was able to outcompete N. europaea at growth-limiting substrate concentrations of about 10 micro M ammonium, suggesting better growth abilities of the ammonia oxidizer G5-7 at low ammonium concentrations. However, N. europaea displayed a more favorable starvation response. After 1 to 10 weeks of ammonium deprivation, N. europaea became almost immediately active after the addition of fresh ammonium and converted the added ammonium within 48 to 96 h. In contrast, the regeneration time of the ammonia oxidizer G5-7 increased with increasing starvation time. Taken together, these results provide insight into possible mechanisms of niche differentiation for the ammonia-oxidizing bacteria studied. The Nitrosomonas cluster 6a member, G5-7, is able to grow at ammonium concentrations at which the growth of N. europaea, belonging to Nitrosomonas cluster 7, has already ceased, providing an advantage in habitats with continuously low ammonium concentrations. On the other hand, the ability of N. europaea to become active again after longer periods of starvation for ammonium may allow better exploitation of irregular pulses of ammonium in the environment.

  13. MeLiSSA third compartment: a kinetic and stoichiometric study for Nitrosomonas europaea and Nitrobacter winogradskyi axenic cultures

    Science.gov (United States)

    Creuly, Catherine; Poughon, Laurent; Dussap, Claude-Gilles; Farges, Berangere

    2012-07-01

    As a part of a natural biological N-cycle, nitrification is one of the steps included in the conception of artificial ecosystems designed for extraterrestrial life support systems (LSS). In MELiSSA loop, which is based on carbon and nitrogen recycling, the non-edible part of the higher plants and the waste produced by the crew are collected in the liquefying compartment that degrades the chemically complex wastes into simpler building blocks (organic acids and CO2). The organic acids are eliminated in the second photoheterotrophic compartment letting an organic free medium mostly containing minerals and N-NH+4 nitrogen. The third compartment is in charge to re-oxidize N-NH+4 in order to make nitrogen usable by the following compartments. In MELiSSA, the constraint is to perform axenic cultures in order to fully control the genetic status of the culture and a thorough modelling for developing a control strategy of the compartment and of the loop, knowing that the reliability of the production of oxidized forms of nitrogen NO3- directly impacts the behaviour of the following compartments. Nitrification in aerobic environments is carried out by two groups of bacteria in co-cultures in a two-step process. The ammonia-oxidizing bacteria (Nitrosomonas europaea) realize the oxidation of ammonia to nitrite and the nitrite-oxidizing bacteria (Nitrobacter winogradskyi) the oxidation of nitrite to nitrate. In both cases, the bacteria achieve the oxidations to obtain an energy and reductant source for their growth and maintenance. Both groups use CO2 predominantly as their carbon source. They are typically found together in ecosystems and, consequently, nitrite accumulation is rare. This study concerns kinetic and mass balances studies of axenic cultures of Ns. europaea and Nb. winogradskyi in autotrophic conditions. The daily follow-up of these cultures is done using a new protocol involving flow cytometry and ionic chromatography. Nitrogen substrates and products are

  14. Activity-Based Protein Profiling of Ammonia Monooxygenase in Nitrosomonas europaea

    Energy Technology Data Exchange (ETDEWEB)

    Bennett, Kristen; Sadler, Natalie C.; Wright, Aaron T.; Yeager, Chris; Hyman, Michael R.; Löffler, F. E.

    2016-01-29

    Nitrosomonas europaeais an aerobic nitrifying bacterium that oxidizes ammonia (NH3) to nitrite (NO2) through the sequential activities of ammonia monooxygenase (AMO) and hydroxylamine dehydrogenase (HAO). Many alkynes are mechanism-based inactivators of AMO, and here we describe an activity-based protein profiling method for this enzyme using 1,7-octadiyne (17OD) as a probe. Inactivation of NH4+-dependent O2uptake byN. europaeaby 17OD was time- and concentration-dependent. The effects of 17OD were specific for ammonia-oxidizing activity, andde novoprotein synthesis was required to reestablish this activity after cells were exposed to 17OD. Cells were reacted with Alexa Fluor 647 azide using a copper-catalyzed azide-alkyne cycloaddition (CuAAC) (click) reaction, solubilized, and analyzed by SDS-PAGE and infrared (IR) scanning. A fluorescent 28-kDa polypeptide was observed for cells previously exposed to 17OD but not for cells treated with either allylthiourea or acetylene prior to exposure to 17OD or for cells not previously exposed to 17OD. The fluorescent polypeptide was membrane associated and aggregated when heated with β-mercaptoethanol and SDS. The fluorescent polypeptide was also detected in cells pretreated with other diynes, but not in cells pretreated with structural homologs containing a single ethynyl functional group. The membrane fraction from 17OD-treated cells was conjugated with biotin-azide and solubilized in SDS. Streptavidin affinity-purified polypeptides were on-bead trypsin-digested, and amino acid sequences of the peptide fragments were determined by liquid chromatography-mass spectrometry (LC-MS) analysis. Peptide fragments from AmoA were the predominant peptides detected in 17OD-treated samples. In-gel digestion and

  15. Responses and recovery assessment of continuously cultured Nitrosomonas europaea under chronic ZnO nanoparticle stress: Effects of dissolved oxygen.

    Science.gov (United States)

    Wu, Junkang; Chang, Yan; Gao, Huan; Liang, Geyu; Yu, Ran; Ding, Zhen

    2018-03-01

    Although the antibacterial performances of emerging nanoparticles (NPs) have been extensively explored in the nitrifying systems, the impacts of dissolved oxygen (DO) levels on their bio-toxicities to the nitrifiers and the impaired cells' recovery potentials have seldom been addressed yet. In this study, the physiological and transcriptional responses of the typical ammonia oxidizers - Nitrosomonas europaea in a chemostat to the chronic ZnO NP exposure under different DO conditions were investigated. The results indicated that the cells in steady-growth state in the chemostat were more persevering than batch cultured ones to resist ZnO NP stress despite the dose-dependent NP inhibitory effects were observed. In addition, the occurred striking over-expressions of amoA and hao genes at the initial NP exposure stage suggested the cells' self-regulation potentials at the transcriptional level. The low DO (0.5 mg/L) cultured cells displayed higher sensitivity to NP stress than the high DO (2.0 mg/L) cultured ones, probably owning to the inefficient oxygen-dependent electron transfer from ammonia oxidation for energy conversion/production. The following 12-h NP-free batch recovery assays revealed that both high and low DO cultured cells possessed the physiological and metabolic activity recovery potentials, which were in negative correlation with the NP exposure time. The duration of NP stress and the resulting NP dissolution were critical for the cells' damage levels and their performance recoverability. The membrane preservation processes and the associated metabolism regulations were expected to actively participate in the cells' self-adaption to NP stress and thus be responsible for their metabolic activities recovery. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Short-term effects of TiO2, CeO2, and ZnO nanoparticles on metabolic activities and gene expression of Nitrosomonas europaea.

    Science.gov (United States)

    Yu, Ran; Fang, Xiaohua; Somasundaran, Ponisseril; Chandran, Kartik

    2015-06-01

    Nanosized TiO2 (n-TiO2), CeO2 (n-CeO2), and ZnO (n-ZnO) and bulk ZnO were chosen for a 4-h exposure study on a model ammonia oxidizing bacterium, Nitrosomonas europaea. n-ZnO displayed the most serious cytotoxicity while n-TiO2 was the least toxic one. The change of cell morphologies, the retardance of specific oxygen uptake rates and ammonia oxidation rates, and the depression of amoA gene expressions under NP stresses were generally observed when the cell densities and membrane integrities were not significantly impaired yet. The TEM imaging and the synchrotron X-ray fluorescence microscopy of the NPs impacted cells revealed the increase of the corresponding intracellular Ti, Ce or Zn contents and suggested the intracellular NP accumulation. The elevation of intracellular S contents accompanied with higher K contents implied the possible activation of thiol-containing glutathione and thioredoxin production for NP stress alleviation. The NP cytotoxicity was not always a function of NP concentration. The 200 mg L(-1) n-TiO2 or n-CeO2 impacted cells displayed the similar ammonia oxidation activities but higher amoA gene expression levels than the 20 mg L(-1) NPs impacted ones. Such phenomenon further indicated the possible establishment of an anti-toxicity mechanism in N. europaea at the genetic level to redeem the weakened AMO activities along with the NP aggregation effects. Copyright © 2015 Elsevier Ltd. All rights reserved.

  17. Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of Nitrosomonas europaea and Nitrobacter winogradskyi.

    Science.gov (United States)

    Mellbye, Brett L; Giguere, Andrew T; Murthy, Ganti S; Bottomley, Peter J; Sayavedra-Soto, Luis A; Chaplen, Frank W R

    2018-01-01

    Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, emits nitrogen (N) oxide gases (NO, NO 2 , and N 2 O), which are potentially hazardous compounds that contribute to global warming. To better understand the dynamics of nitrification-derived N oxide production, we conducted culturing experiments and used an integrative genome-scale, constraint-based approach to model N oxide gas sources and sinks during complete nitrification in an aerobic coculture of two model nitrifying bacteria, the ammonia-oxidizing bacterium Nitrosomonas europaea and the nitrite-oxidizing bacterium Nitrobacter winogradskyi . The model includes biotic genome-scale metabolic models (iFC578 and iFC579) for each nitrifier and abiotic N oxide reactions. Modeling suggested both biotic and abiotic reactions are important sources and sinks of N oxides, particularly under microaerobic conditions predicted to occur in coculture. In particular, integrative modeling suggested that previous models might have underestimated gross NO production during nitrification due to not taking into account its rapid oxidation in both aqueous and gas phases. The integrative model may be found at https://github.com/chaplenf/microBiome-v2.1. IMPORTANCE Modern agriculture is sustained by application of inorganic nitrogen (N) fertilizer in the form of ammonium (NH 4 + ). Up to 60% of NH 4 + -based fertilizer can be lost through leaching of nitrifier-derived nitrate (NO 3 - ), and through the emission of N oxide gases (i.e., nitric oxide [NO], N dioxide [NO 2 ], and nitrous oxide [N 2 O] gases), the latter being a potent greenhouse gas. Our approach to modeling of nitrification suggests that both biotic and abiotic mechanisms function as important sources and sinks of N oxides during microaerobic conditions and that previous models might have underestimated gross NO production during nitrification.

  18. AAU-Specific RNA Cleavage Mediated by MazF Toxin Endoribonuclease Conserved in Nitrosomonas europaea

    Directory of Open Access Journals (Sweden)

    Tatsuki Miyamoto

    2016-06-01

    Full Text Available Nitrosomonas europaea carries numerous toxin-antitoxin systems. However, despite the abundant representation in its chromosome, studies have not surveyed the underlying molecular functions in detail, and their biological roles remain enigmatic. In the present study, we found that a chromosomally-encoded MazF family member, predicted at the locus NE1181, is a functional toxin endoribonuclease, and constitutes a toxin-antitoxin system, together with its cognate antitoxin, MazE. Massive parallel sequencing provided strong evidence that this toxin endoribonuclease exhibits RNA cleavage activity, primarily against the AAU triplet. This sequence-specificity was supported by the results of fluorometric assays. Our results indicate that N. europaea alters the translation profile and regulates its growth using the MazF family of endoribonuclease under certain stressful conditions.

  19. MELiSSA third compartment: Nitrosomonas europaea and Nitrobacter winogradskyi axenic cultures in bioreactors

    Science.gov (United States)

    Cruvellier, Nelly; Lasseur, Christophe; Poughon, Laurent; Creuly, Catherine; Dussap, Gilles

    Nitrogen is a key element for the life and its balance on Earth is regulated by the nitrogen cycle. This loop includes several steps among which nitrification that permits the transformation of the ammonium into nitrate. The MELiSSA loop is an artificial ecosystem designed for life support systems (LSS). It is based on the carbon and nitrogen cycles and the recycling of the non-edible part of the higher plants and the waste produced by the crew. In this order, all the wastes are collected in the first compartment to degrade them into organic acids and CO2. These compounds are joining the second compartment which is a photoheterotrophic compartment where at the outlet an organic-free medium containing ammonium is produced. This solution will be the substrate of the third compartment where nitrification is done. This compartment has to oxidize the ammonium into nitrate, and this biological reaction needs two steps. In the MELiSSA loop, the nitrification is carried out by two bacteria: Nitrosomonas europaea ATCC® 19718™ which is oxidizing ammonia into nitrite and Nitrobacter winogradskyi ATCC® 25391™ which is producing nitrate from nitrite in the third compartment. These two bacteria are growing in axenic conditions on a fixed bed bioreactor filled with Biostyr® beads. The nitrogen compounds are controlled by Ionic Chromatography and colorimetric titration for each sample. The work presented here deals with the culture of both bacteria in pure cultures and mixed cultures in stirred and aerated bioreactors of different volumes. The first aim of our work is the characterization of the bacteria growth in bioreactors and in the nitrifying fixed-bed column. The experimental results confirm that the growth is slow; the maximal growth rate in suspended cultures is 0.054h-1 for Nitrosomonas europaea and 0.022h-1 for Nitrobacter winogradskyi. Mixed cultures are difficult to control and operate but one could be done for more than 500 hours. The characterization of the

  20. Effect of Low-Density Static Magnetic Field on the Oxidation of Ammonium by Nitrosomonas europaea and by Activated Sludge in Municipal Wastewater

    Science.gov (United States)

    Filipič, Jasmina; Kraigher, Barbara; Tepuš, Brigita; Kokol, Vanja

    2015-01-01

    Summary Ammonium removal is a key step in biological wastewater treatment and novel approaches that improve this process are in great demand. The aim of this study is to test the hypothesis that ammonium removal from wastewater can be stimulated by static magnetic fields. This was achieved by analysis of the effects of static magnetic field (SMF) on the growth and activity of Nitrosomonas europaea, a key ammonia-oxidising bacterium, where increased growth and increased ammonia oxidation rate were detected when bacteria were exposed to SMF at 17 mT. Additionally, the effect of SMF on mixed cultures of ammonia oxidisers in activated sludge, incubated in sequencing batch bioreactors simulating wastewater treatment process, was assessed. SMFs of 30 and 50 mT, but not of 10 mT, increased ammonium oxidation rate in municipal wastewater by up to 77% and stimulated ammonia oxidiser growth. The results demonstrate the potential for use of static magnetic fields in increasing ammonium removal rates in biological wastewater treatment plants. PMID:27904349

  1. Distribution of Nitrosomonas europaea and Nitrobacter winogradskyi in an autotrophic nitrifying biofilm reactor as depicted by molecular analyses and mathematical modelling.

    Science.gov (United States)

    Montràs, Anna; Pycke, Benny; Boon, Nico; Gòdia, Francesc; Mergeay, Max; Hendrickx, Larissa; Pérez, Julio

    2008-03-01

    The autotrophic two-species biofilm from the packed bed reactor of a life-support system, containing Nitrosomonas europaea ATCC 19718 and Nitrobacter winogradskyi ATCC 25391, was analysed after 4.8 years of continuous operation performing complete nitrification. Real-time quantitative polymerase chain reaction (Q-PCR) was used to quantify N. europaea and N. winogradskyi along the vertical axis of the reactor, revealing a spatial segregation of N. europaea and N. winogradskyi. The main parameters influencing the spatial segregation of both nitrifiers along the bed were assessed through a multi-species one-dimensional biofilm model generated with AQUASIM software. The factor that contributed the most to this distribution profile was a small deviation from the flow pattern of a perfectly mixed tank towards plug-flow. The results indicate that the model can estimate the impact of specific biofilm parameters and predict the nitrification efficiency and population dynamics of a multispecies biofilm.

  2. Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina -like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm

    DEFF Research Database (Denmark)

    Foesel, Bärbel U.; Gieseke, Armin; Schwermer, Carsten

    2008-01-01

    Zero-discharge marine aquaculture systems are an environmentally friendly alternative to conventional aquaculture. In these systems, water is purified and recycled via microbial biofilters. Here, quantitative data on nitrifier community structure of a trickling filter biofilm associated...... with a recirculating marine aquaculture system are presented. Repeated rounds of the full-cycle rRNA approach were necessary to optimize DNA extraction and the probe set for FISH to obtain a reliable and comprehensive picture of the ammonia-oxidizing community. Analysis of the ammonia monooxygenase gene (amo...

  3. Application of an integrated statistical design for optimization of culture condition for ammonium removal by Nitrosomonas europaea.

    Directory of Open Access Journals (Sweden)

    Yingling Bao

    Full Text Available Statistical methodology was applied to the optimization of the ammonium oxidation by Nitrosomonas europaea for biomass concentration (C(B, nitrite yield (Y(N and ammonium removal (R(A. Initial screening by Plackett-Burman design was performed to select major variables out of nineteen factors, among which NH4Cl concentration (C(N, trace element solution (TES, agitation speed (AS, and fermentation time (T were found to have significant effects. Path of steepest ascent and response surface methodology was applied to optimize the levels of the selected factors. Finally, multi-objective optimization was used to obtain optimal condition by compromise of the three desirable objectives through a combination of weighted coefficient method coupled with entropy measurement methodology. These models enabled us to identify the optimum operation conditions (C(N= 84.1 mM; TES = 0.74 ml; AS= 100 rpm and T = 78 h, under which C(B= 3.386×10(8 cells/ml; Y(N= 1.98 mg/mg and R(A = 97.76% were simultaneously obtained. The optimized conditions were shown to be feasible through verification tests.

  4. Expression and purification of recombinant proteins in Escherichia coli tagged with a small metal-binding protein from Nitrosomonas europaea.

    Science.gov (United States)

    Vargas-Cortez, Teresa; Morones-Ramirez, Jose Ruben; Balderas-Renteria, Isaias; Zarate, Xristo

    2016-02-01

    Escherichia coli is still the preferred organism for large-scale production of recombinant proteins. The use of fusion proteins has helped considerably in enhancing the solubility of heterologous proteins and their purification with affinity chromatography. Here, the use of a small metal-binding protein (SmbP) from Nitrosomonas europaea is described as a new fusion protein for protein expression and purification in E. coli. Fluorescent proteins tagged at the N-terminal with SmbP showed high levels of solubility, compared with those of maltose-binding protein and glutathione S-transferase, and low formation of inclusion bodies. Using commercially available IMAC resins charged with Ni(II), highly pure recombinant proteins were obtained after just one chromatography step. Proteins may be purified from the periplasm of E. coli if SmbP contains the signal sequence at the N-terminal. After removal of the SmbP tag from the protein of interest, high-yields are obtained since SmbP is a protein of just 9.9 kDa. The results here obtained suggest that SmbP is a good alternative as a fusion protein/affinity tag for the production of soluble recombinant proteins in E. coli. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Acetylene and oxygen as inhibitors of nitrous oxide production in Nitrosomonas europaea and Nitrosospira briensis: a cautionary tale

    NARCIS (Netherlands)

    Wrage, N.; Velthof, G.L.; Oenema, O.; Laanbroek, H.J.

    2004-01-01

    Autotrophic ammonia-oxidizing bacteria produce nitrous oxide (N2O) as a by-product of nitrification or as an intermediate of nitrifier denitrification. In soil incubations, acetylene (C2H2) and large partial pressures of oxygen (O-2) are used to distinguish between these sources. C2H2 inhibits

  6. Acetylene and oxygen as inhibitors of nitrous oxide production in Nitrosomonas europaea and Nitrosospira briensis: a cautionary tale

    NARCIS (Netherlands)

    Wrage, N.; Velthof, G.L.; Oenema, O.; Laanbroek, H.J.

    2004-01-01

    Autotrophic ammonia-oxidizing bacteria produce nitrous oxide (N2O) as a by-product of nitrification or as an intermediate of nitrifier denitrification. In soil incubations, acetylene (C2H2) and large partial pressures of oxygen (O2) are used to distinguish between these sources. C2H2 inhibits

  7. Activity and population dynamics of heterotrophic and ammonia-oxidizing microorganisms in soil surrounding sludge bands spiked with linear alkylbenzene sulfonate

    DEFF Research Database (Denmark)

    Brandt, K. K.; Sørensen, J.; Krogh, P. H.

    2003-01-01

    in a sandy soil surrounding well-defined sludge bands spiked with high but realistic LAS levels (7.1 or 31.3 g/kg). Surprisingly, LAS had no effect on heterotrophic respiration in the sludge compartment per se but stimulated activity and metabolic quotient (microbial activity per unit of biomass......Recent research has documented soil microorganisms to be rather sensitive to linear alkylbenzene sulfonates (LAS), which may enter the soil environment in considerable quantities following sewage sludge disposal. We here report field effects of LAS on selected microbial populations present......) in the surrounding soil. By contrast, autotrophic ammonia oxidation was initially inhibited in the LAS-spiked sludge. This led to dramatic transient increases of NH+4 availability in the sludge and surrounding soil, subsequently stimulating soil ammonia oxidizers. As judged from a Nitrosomonas europaea...

  8. The 1.3-A resolution structure of Nitrosomonas europaea Rh50 and mechanistic implications for NH3 transport by Rhesus family proteins.

    Science.gov (United States)

    Lupo, Domenico; Li, Xiao-Dan; Durand, Anne; Tomizaki, Takashi; Cherif-Zahar, Baya; Matassi, Giorgio; Merrick, Mike; Winkler, Fritz K

    2007-12-04

    The Rhesus (Rh) proteins are a family of integral membrane proteins found throughout the animal kingdom that also occur in a number of lower eukaryotes. The significance of Rh proteins derives from their presence in the human red blood cell membrane, where they constitute the second most important group of antigens used in transfusion medicine after the ABO group. Rh proteins are related to the ammonium transport (Amt) protein family and there is considerable evidence that, like Amt proteins, they function as ammonia channels. We have now solved the structure of a rare bacterial homologue (from Nitrosomonas europaea) of human Rh50 proteins at a resolution of 1.3 A. The protein is a trimer, and analysis of its subunit interface strongly argues that all Rh proteins are likely to be homotrimers and that the human erythrocyte proteins RhAG and RhCE/D are unlikely to form heterooligomers as previously proposed. When compared with structures of bacterial Amt proteins, NeRh50 shows several distinctive features of the substrate conduction pathway that support the concept that Rh proteins have much lower ammonium affinities than Amt proteins and might potentially function bidirectionally.

  9. Catalyst for Ammonia Oxidation

    DEFF Research Database (Denmark)

    2015-01-01

    The present invention relates to a bimetallic catalyst for ammonia oxidation, a method for producing a bimetallic catalyst for ammonia oxidation and a method for tuning the catalytic activity of a transition metal. By depositing an overlayer of less catalytic active metal onto a more catalytic...

  10. Seasonal variation in communities of ammonia-oxidizing bacteria based on polymerase chain reaction - denaturing gradient gel electrophoresis in a biofilm reactor for drinking water pretreatment.

    Science.gov (United States)

    Zhang, Xiao-Wen; Qin, Ying-Ying; Ren, Hong-Qiang; Li, Dao-Tang; Yang, Hong

    2008-05-01

    The diversity and variation of total and active ammonia-oxidizing bacteria in a full-scale aerated submerged biofilm reactor for drinking water pretreatment were characterized by clone libraries and denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA and its gene during a whole year. Sequences obtained from clone libraries affiliated with the Nitrosomonas oligotropha lineage and the Nitrosomonas communis lineage. An uncultured subgroup of Nitrosomonas communis lineage was also detected. Seasonal variations in both total and active ammonia-oxidizing bacteria communities were observed in the DGGE profiles, but an RNA-based analysis reflected more obvious dynamic changes in ammonia-oxidizer community than a DNA-based approach. Statistical study based on canonical correspondence analysis showed that a community shift of active ammonia oxidizers was significantly influenced by temperature and pH, but no significant correlation was found between environmental variables and total ammonia-oxidizer community shift.

  11. Ecophysiology and Comparative Genomics of Nitrosomonas mobilis Ms1 Isolated from Autotrophic Nitrifying Granules of Wastewater Treatment Bioreactor

    Directory of Open Access Journals (Sweden)

    SoeMyat Thandar

    2016-11-01

    Full Text Available Ammonia-oxidizing bacteria (AOB, which oxidize ammonia to nitrite in the first step of nitrification, play an important role in biological wastewater treatment systems. Nitrosomonas mobilis is an important and dominant AOB in various wastewater treatment systems. However, the detailed physiological and genomic properties of N. mobilis have not been thoroughly investigated because of limited success isolating pure cultures. This study investigated the key physiological characteristics of N. mobilis Ms1, which was previously isolated into pure culture from the nitrifying granules of wastewater treatment bioreactor. The pure culture of N. mobilis Ms1 was cultivated in liquid mineral medium with 30 mg-N L-1 (2.14 mM of ammonium at room temperature under dark conditions. The optimum growth of N. mobilis Ms1 occurred at 27°C and pH 8, with a maximum growth rate of 0.05–0.07 h-1, which corresponded to a generation time of 10–14 h. The half saturation constant for ammonium uptake rate and the maximum ammonium uptake rate of N. mobilis Ms1 were 30.70±0.51 μM NH4+ and 0.01±0.002 pmol NH4+ cells-1 h-1, respectively. N. mobilis Ms1 had higher ammonia oxidation activity than N. europaea in this study. The oxygen uptake activity kinetics of N. mobilis Ms1 were K_(m(O_2= 21.74±4.01 μM O2 and V_(max⁡(O_2= 0.06±0.02 pmol O2 cells-1 h-1. Ms1 grew well at ammonium and NaCl concentrations of up to 100 mM and 500 mM, respectively. The nitrite tolerance of N. mobilis Ms1 was extremely high (up to 300 mM compared to AOB previously isolated from activated sludge and wastewater treatment plants. The average nucleotide identity between the genomes of N. mobilis Ms1 and other Nitrosomonas species indicated that N. mobilis Ms1 was distantly related to other Nitrosomonas species. The organization of the genes encoding protein inventory involved in ammonia oxidation and nitrifier denitrification processes were different from other Nitrosomonas species. The

  12. Kinetic parameter estimation in N. europaea biofilms using a 2-D reactive transport model.

    Science.gov (United States)

    Lauchnor, Ellen G; Semprini, Lewis; Wood, Brian D

    2015-06-01

    Biofilms of the ammonia oxidizing bacterium Nitrosomonas europaea were cultivated to study microbial processes associated with ammonia oxidation in pure culture. We explored the hypothesis that the kinetic parameters of ammonia oxidation in N. europaea biofilms were in the range of those determined with batch suspended cells. Oxygen and pH microelectrodes were used to measure dissolved oxygen (DO) concentrations and pH above and inside biofilms and reactive transport modeling was performed to simulate the measured DO and pH profiles. A two dimensional (2-D) model was used to simulate advection parallel to the biofilm surface and diffusion through the overlying fluid while reaction and diffusion were simulated in the biofilm. Three experimental studies of microsensor measurements were performed with biofilms: i) NH3 concentrations near the Ksn value of 40 μM determined in suspended cell tests ii) Limited buffering capacity which resulted in a pH gradient within the biofilms and iii) NH3 concentrations well below the Ksn value. Very good fits to the DO concentration profiles both in the fluid above and in the biofilms were achieved using the 2-D model. The modeling study revealed that the half-saturation coefficient for NH3 in N. europaea biofilms was close to the value measured in suspended cells. However, the third study of biofilms with low availability of NH3 deviated from the model prediction. The model also predicted shifts in the DO profiles and the gradient in pH that resulted for the case of limited buffering capacity. The results illustrate the importance of incorporating both key transport and chemical processes in a biofilm reactive transport model. © 2014 Wiley Periodicals, Inc.

  13. Stable isotope probing and dynamic loading experiments provide insight into the ecophysiology of novel ammonia oxidizers in rapid gravity sand filters

    DEFF Research Database (Denmark)

    Fowler, Jane; Palomo, Alejandro; Gülay, Arda

    Nitrification is often the dominant microbial process in rapid gravity sand filters (RSF), used to treat aerated groundwater to produce drinking water. RSFs harbor diverse microbial communities including a range of ammonia oxidizing clades; Betaproteobacteria (Nitrosomonas, Nitrosospira), Archaea...... and oxygen limitation on ammonia oxidizers. Our observations indicate that the native conditions in the RSF used in this study foster the enrichment of comammox Nitrospira, which provides a preliminary step in the description of their ecophysiology....

  14. Anodic ammonia oxidation to nitrogen gas catalyzed by mixed biofilms in bioelectrochemical systems

    International Nuclear Information System (INIS)

    Zhan, Guoqiang; Zhang, Lixia; Tao, Yong; Wang, Yujian; Zhu, Xiaoyu; Li, Daping

    2014-01-01

    In this paper we report ammonia oxidation to nitrogen gas using microbes as biocatalyst on the anode, with polarized electrode (+600 mV vs. Ag/AgCl) as electron acceptor. In batch experiments, the maximal rate of ammonia-N oxidation by the mixed culture was ∼ 60 mg L −1 d −1 , and nitrogen gas was the main products in anode compartment. Cyclic voltammetry for testing the electroactivity of the anodic biofilms revealed that an oxidation peak appeared at +600 mV (vs. Ag/AgCl), whereas the electrode without biofilms didn’t appear oxidation peak, indicating that the bioanode had good electroactivities for ammonia oxidation. Microbial community analysis of 16S rRNA genes based on high throughput sequencing indicated that the combination of the dominant genera of Nitrosomonas, Comamonas and Paracocus could be important for the electron transfer from ammonia oxidation to anode

  15. Quantification of Aerobic Ammonia-Oxidizing Bacteria in Soil using Activity-Based Fluorescent Labeling of Ammonia Monooxygenase

    Science.gov (United States)

    Farnan, J.; Bennett, K.; Hyman, M. R.

    2016-12-01

    Nitrification is a key step in the biological nitrogen cycle and has a large effect on the fate of nitrogen species in both wastewater treatment systems and agricultural soils. Aerobic ammonia-oxidizing bacteria (AOB) initiate nitrification by converting ammonia (NH3) to nitrite (NO2-) and are therefore pivotal to the process. AOB are ubiquitous in the environment but are difficult to quantify as they grow poorly on solid media. Other quantification methods like iquid most-probable number techniques are slow and error-prone, while modern molecular approaches involving polymerase chain reaction amplification are faster and more accurate but do not differentiate between active and inactive AOB. In this study, we explored using activity-based fluorescent mechanisms for rapidly quantifying metabolically active forms of AOB in soils. Initial experiments using Nitrosomonas europaea aimed to establish a relationship between NH3-dependent nitrite production and bacterial cell numbers. Active AMO was treated cells with 1,7-octadiyne (17OD) to inactivate the enzyme and a subsequent copper-dependent "click" reaction attached a fluor. The labeled protein was quantified by SDS-PAGE and IR scanning. In future experiments, AOB will be stimulated in soil microcosms by adding NH4Cl. AMO will again be inactivated by adding 17OD, and total bacteria will be separated from the soil samples using gradient centrifugation. After "click" conjugation with AlexaFluor 647 azide, the abundance of AMO will be determined with SDS-PAGE and IR analysis while metabolically active AOB will be measured via fluorescence-activating cell sorting.

  16. Ammonia-Oxidizer Communities in an Agricultural Soil treated with Contrasting Nitrogen Sources.

    Directory of Open Access Journals (Sweden)

    Mussie Y. Habteselassie

    2013-11-01

    Full Text Available The community of ammonia-oxidizing prokaryotes was examined in an agricultural soil treated for 6 seasons with contrasting nitrogen (N sources. Molecular tools based on the gene encoding ammonia monooxygenase were used to characterize the ammonia oxidizer communities and their abundance. Soil DNA was extracted from soils sampled from silage corn plots that received no additional N (control, dairy waste compost (DC, liquid dairy waste (LW, and ammonium sulfate (AS treatments at approximately 100 and 200 kg available N ha-1 over 6 years. The N treatment affected the quantity of ammonia oxidizers based on estimates of amoA by real-time PCR. Ammonia oxidizing bacteria (AOB were higher in soils from the AS200, AS100, and LW200 treatments (2.5 x107, 2.5x107, and 2.1 x107 copies g-1 soil, respectively than in the control (8.1x106copies/g while the abundance of amoA encoding archaea (AOA was not significantly affected by treatment (3.8x107copies g-1 soil, average. The ratio of AOA/AOB was higher in the control and compost treated soils, both treatments have the majority of their ammonium supplied through mineralization of organic nitrogen. Clone libraries of partial amoA sequences indicated AOB related to Nitrosospira multiformis and AOA related to uncultured Nitrososphaera similar to those described by soil fosmid 54d9 were prevalent. Profiles of the amoC-amoA intergenic region indicated that both Nitrosospira- and Nitrosomonas-type AOB were present in all soils examined. In contrast to the intergenic amoC-amoA profile results, Nitrosomonas-like clones were recovered only in the LW200 treated soil-DNA. The impact of six years of contrasting nitrogen sources applications caused changes in ammonia oxidizer abundance while the community composition remained relatively stable for both AOB and AOA.

  17. Diversity of ammonia-oxidizing bacteria in relation to soil environment in Ebinur Lake Wetland

    Directory of Open Access Journals (Sweden)

    Wenge Hu

    2016-03-01

    Full Text Available Ammonia oxidation is the first and rate-limiting step of nitrification and is carried out by ammonia-oxidizing bacteria (AOB. Ebinur Lake Wetland, the most representative temperate arid zone wetland ecosystem in China, is the centre of oasis and desertification of the northern slope of Tianshan conjugate. Soil samples were collected from three sites (Tamarix ramosissima, Halocnemum strobilaceum and Phragmites australis and different soil layers (0–5, 5–15, 15–25 and 25–35 cm in this wetland in spring, summer and autumn and were used to characterize the diversity of AOB based on the ammonia monooxygenase (amoA gene. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE and bivariate correlation analysis were used to analyse the relationship between the diversity of AOB and soil environment factors. The PCR-DGGE indicated that the diversity of AOB was high in the entire sample and the Shannon diversity index varied from 1.369 to 2.471. The phylogenetic analysis showed that the amoA fragments were grouped into Nitrosospira sp. and Nitrosomonas sp. Most amoA gene sequences fell within the Nitrosospira sp. cluster, and only a few sequences were clustered with Nitrosomonas sp., indicating that Nitrosospira sp. may be more adaptable than Nitrosomonas sp. in this area. Bivariate correlation analysis showed that the diversity of AOB was significantly correlated with soil organic matter, conductivity, total phosphorus and nitrate in the Ebinur Lake Wetland in Xinjiang.

  18. Contribution of ammonia-oxidizing archaea and ammonia-oxidizing bacteria to ammonia oxidation in two nitrifying reactors.

    Science.gov (United States)

    Srithep, Papitchaya; Pornkulwat, Preeyaporn; Limpiyakorn, Tawan

    2018-03-01

    In this study, two laboratory nitrifying reactors (NRI and NRII), which were seeded by sludge from different sources and operated under different operating conditions, were found to possess distinct dominant ammonia-oxidizing microorganisms. Ammonia-oxidizing archaeal (AOA) amoA genes outnumbered ammonia-oxidizing bacterial (AOB) amoA genes in reactor NRI, while only AOB amoA genes were detectable in reactor NRII. The AOA amoA gene sequences retrieved from NRI were characterized within the Nitrososphaera sister cluster of the group 1.1b Thaumarchaeota. Two inhibitors for ammonia oxidation, allylthiourea (ATU) and 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), were applied individually and as a mixture to observe the ammonia-oxidizing activity of both microorganisms in the reactors' sludge. The results indicated that AOA and AOB jointly oxidized ammonia in NRI, while AOB played the main role in ammonia oxidation in NRII. DNA-stable isotope probing with labeled 13 C-HCO 3 - was performed on NRI sludge. Incorporation of 13 C into AOA and AOB implied that both microorganisms may perform autotrophy during ammonia oxidation. Taken together, the results from this study provide direct evidence demonstrating the contribution of AOA and AOB to ammonia oxidation in the nitrifying reactors.

  19. Vertical segregation and phylogenetic characterization of ammonia-oxidizing bacteria and archaea in the sediment of a freshwater aquaculture pond

    Directory of Open Access Journals (Sweden)

    Shimin eLu

    2016-01-01

    Full Text Available Pond aquaculture is the major freshwater aquaculture method in China. Ammonia-oxidizing communities inhabiting pond sediments play an important role in controlling culture water quality. However, the distribution and activities of ammonia-oxidizing microbial communities along sediment profiles are poorly understood in this specific environment. Vertical variations in the abundance, transcription, potential ammonia oxidizing rate, and community composition of ammonia-oxidizing bacteria (AOB and ammonia-oxidizing archaea (AOA in sediment samples (0–50 cm depth collected from a freshwater aquaculture pond were investigated. The concentrations of the AOA amoA gene were higher than those of the AOB by an order of magnitude, which suggested that AOA, as opposed to AOB, were the numerically predominant ammonia-oxidizing organisms in the surface sediment. This could be attributed to the fact that AOA are more resistant to low levels of dissolved oxygen. However, the concentrations of the AOB amoA mRNA were higher than those of the AOA by 2.5–39.9-fold in surface sediments (0–10 cm depth, which suggests that the oxidation of ammonia was mainly performed by AOB in the surface sediments, and by AOA in the deeper sediments, where only AOA could be detected. Clone libraries of AOA and AOB amoA sequences indicated that the diversity of AOA and AOB decreased with increasing depth. The AOB community consisted of two groups: the Nitrosospira and Nitrosomonas clusters, and Nitrosomonas were predominant in the freshwater pond sediment. All AOA amoA gene sequences in the 0–2 cm deep sediment were grouped into the Nitrososphaera cluster, while other AOA sequences in deeper sediments (10–15 and 20–25 cm depths were grouped into the Nitrosopumilus cluster.

  20. Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China

    Directory of Open Access Journals (Sweden)

    Qiufang eZhang

    2015-10-01

    Full Text Available Aerobic ammonia oxidation plays a key role in the nitrogen cycle, and the responsible microorganisms diversities are regulated by environmental factors. Abundance and composition of ammonia-oxidizing archaea (AOA and ammonia-oxidizing bacteria (AOB were investigated in the surface waters along an environmental gradient of Yong River in Ningbo, China. Water samples were collected from three zones: freshwaters in urban canals, brackish waters in the downstream Yong River, and coastal water of Hangzhou Bay. Shifts in activity and diversity of the ammonia oxidizers occurred with changes in salinity, ammonium and oxygen. The AOA abundance was always higher than that of AOB and related to the ammonia oxidation activity. The ratios of AOA/AOB in the brackish and marine waters were significantly higher than those found in freshwaters. Both AOA and AOB showed similar community compositions in brackish and marine waters, but only 31 and 35% similarity, respectively, between these waters and the urban inland freshwaters. Most of AOA-amoA sequences from freshwater were affiliated with sequences obtained from terrestrial environments and those collected from brackish and coastal areas were ubiquitous in marine, coastal, and terrestrial ecosystems. All AOB from freshwaters belonged to Nitrosomonas, and those from brackish and marine waters mainly belonged to Nitrosospira.

  1. Altitude ammonia-oxidizing bacteria and archaea in soils of Mount Everest.

    Science.gov (United States)

    Zhang, Li-Mei; Wang, Mu; Prosser, James I; Zheng, Yuan-Ming; He, Ji-Zheng

    2009-11-01

    To determine the abundance and distribution of bacterial and archaeal ammonia oxidizers in alpine and permafrost soils, 12 soils at altitudes of 4000-6550 m above sea level (m a.s.l.) were collected from the northern slope of the Mount Everest (Tibetan Plateau), where the permanent snow line is at 5800-6000 m a.s.l. Communities were characterized by real-time PCR and clone sequencing by targeting on amoA genes, which putatively encode ammonia monooxygenase subunit A. Archaeal amoA abundance was greater than bacterial amoA abundance in lower altitude soils (or=5700 m a.s.l.). Both archaeal and bacterial amoA abundance decreased abruptly in higher altitude soils. Communities shifted from a Nitrosospira amoA cluster 3a-dominated ammonia-oxidizing bacteria community in lower altitude soils to communities dominated by a newly designated Nitrosospira ME and cluster 2-related groups and Nitrosomonas cluster 6 in higher altitude soils. All archaeal amoA sequences fell within soil and sediment clusters, and the proportions of the major archaeal amoA clusters changed between the lower altitude and the higher altitude soils. These findings imply that the shift in the relative abundance and community structure of archaeal and bacterial ammonia oxidizers may result from selection of organisms adapted to altitude-dependent environmental factors in elevated soils.

  2. Quantitative analysis of ammonia-oxidizing bacteria in a combined system of MBR and worm reactors treating synthetic wastewater.

    Science.gov (United States)

    Liu, Jia; Tian, Yu; Wang, Dezhen; Lu, Yaobin; Zhang, Jun; Zuo, Wei

    2014-12-01

    The Static Sequencing Batch Worm Reactor (SSBWR) followed by the MBR (S-MBR) is one of the advanced excess sludge treatments. In this paper, the control MBR (C-MBR) and the SSBWR-MBR were operated in parallel to study the changes of NH3-N removal and ammonia oxidizing bacteria (AOB). The results showed that the capacity of NH3-N removal of the S-MBR was improved by the worm reactors along with the operation. The S-MBR was favorable because it selected for the higher activity of the ammonia oxidization and better cells appearance of the sludge. The five species (Nitrosomonas, Betaproteobacteria, Clostridium, Dechloromonas and Bacteria) were found to be significantly correlate with the ammonia oxidization functions and performance of NH3-N removal in the C-MBR and S-MBR. The Nitrosomonas, Betaproteobacteria and Dechloromonas remained and eventually enriched in the S-MBR played a primary role in the NH3-N removal of the S-MBR. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Community shift of ammonia-oxidizing bacteria along an anthropogenic pollution gradient from the Pearl River Delta to the South China Sea

    OpenAIRE

    Cao, Huiluo; Hong, Yiguo; Li, Meng; Gu, Ji-Dong

    2011-01-01

    The phylogenetic diversity and abundance of ammonia-oxidizing beta-proteobacteria (beta-AOB) was analyzed along an anthropogenic pollution gradient from the coastal Pearl River Delta to the South China Sea using the ammonia monooxygenase subunit A (amoA) gene. Along the gradient from coastal to the open ocean, the phylogenetic diversity of the dominant genus changed from Nitrosomonas to Nitrosospira, indicating the niche specificity by these two genera as both salinity and anthropogenic influ...

  4. [Ammonia oxidation kinetics of ammonia oxidizer mixed culture under the conditions of O2 and trace NO2 mixed gasses].

    Science.gov (United States)

    Zhang, Dai-Jun; Zu, Bo; Ren, Hong-Yang; Zhang, Ping; Cong, Li-Ying; Yan, Qing

    2008-01-01

    The kinetics of the NO2-dependent ammonia oxidation was developed for ammonia oxidizer mixed culture when there was no molecular oxygen in the batch tests. The kinetics parameters were determined, where the half saturate coefficient of NO2 was 0.821 micromol x L(-1), inhibition coefficient of NO2 concentration was 1.721 micromol x L(-1), and the maximum ammonia oxidation rate were 0.144 mg x (mg x h)(-1). After adding the volume fraction of O2 was 2% to trace NO2, the ammonia oxidation rates increased obviously. The maximum ammonia oxidation rate, 0.198 mg x (mg x h)(-1) occurred under the condition of the mixed gasses containing the volume fraction of O2 was 2% and 50 x 10(-6) NO2. Under the condition of mixed gasses containing the volume fraction of O2 was 21% to trace NO2, the ammonia oxidation rates further increased greatly. The maximum ammonia oxidation rate, 0.477 mg x (mg x h)(-1) occurred when the volume fraction of O2 was 21% and 100 x 10(-6) NO2 in the mixed gas, which is 3 times higher than the general aerobic ammonia oxidation rate. The function for NO2 apparently to enhance ammonia oxidation was suggested. The kinetics model of ammonia oxidation under the conditions of O2 and trace NO2 mixed gasses was developed. The model was validated by the results of ammonia oxidation experiments under the conditions of the mixed gasses containing 2% O2 and trace NO2. The mechanism for NO2 to enhance ammonia oxidation under the conditions of O2 and trace NO2 mixed gasses was discussed.

  5. Niche differentiation between ammonia-oxidizing bacteria in aquatic environments

    NARCIS (Netherlands)

    Coci, M.

    2007-01-01

    The aim of the studies presented in this thesis was the search for niche differentiation between the ammonia-oxidizing bacteria in aquatic environments. Ammonia-oxidizing bacteria are chemolitho-autotrophic microorganisms responsible for the first, mostly rate-limiting step of the nitrification

  6. Abundance and diversity of ammonia-oxidizing archaea and bacteria in the rhizosphere soil of three plants in the Ebinur Lake wetland.

    Science.gov (United States)

    He, Yuan; Hu, Wenge; Ma, Decao; Lan, Hongzhu; Yang, Yang; Gao, Yan

    2017-07-01

    Ammonia oxidation is carried out by ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). The Ebinur Lake wetland is the best example of a temperate arid zone wetland ecosystem in China. Soil samples were collected from rhizosphere and non-rhizosphere soil containing Halocnemum strobilaceum (samples H and H'), Phragmites australis (samples R and R'), and Karelinia caspia (samples K and K') to study the relationship between environmental factors and the community structure of AOB and AOA. Phylogenetic analysis showed that the AOA sequences belonged to the Nitrosopumilus and Nitrososphaera clusters. AOB were grouped into Nitrosospira sp. and Nitrosomonas sp. Quantitative polymerase chain reaction results showed that the AOA abundance ranged from 2.09 × 10 4 to 2.94 × 10 5 gene copies/g soil. The highest number of AOA was detected in sample K, followed by samples R and H. AOB abundance varied between 2.91 × 10 5 and 1.05 × 10 6 gene copies/g soil, which was higher than that of AOA. Redundancy analysis indicated that electrical conductivity, pH, and NH 4 + -N might influence the community structure of AOA and AOB. AOB might play a more crucial role than AOA in ammonia oxidation based on AOB's higher diversity and abundance in the Ebinur Lake wetland in Xinjiang.

  7. Modeling the low pH limit of Nitrosomonas eutropha in high-strength nitrogen wastewaters.

    Science.gov (United States)

    Fumasoli, Alexandra; Morgenroth, Eberhard; Udert, Kai M

    2015-10-15

    In wastewater treatment, the rate of ammonia oxidation decreases with pH and stops very often slightly below a pH of 6. Free ammonia (NH3) limitation, inhibition by nitrous acid (HNO2), limitation by inorganic carbon or direct effect of high proton concentrations have been proposed to cause the rate decrease with pH as well as the cessation of ammonia oxidation. In this study, we compare an exponential pH term common for food microbiology with conventionally applied rate laws based on Monod-type kinetics for NH3 limitation and non-competitive HNO2 inhibition as well as sigmoidal pH functions to model the low pH limit of ammonia oxidizing bacteria (AOB). For this purpose we conducted well controlled batch experiments which were then simulated with a computer model. The results showed that kinetics based on NH3 limitation and HNO2 inhibition can explain the rate decrease of ammonia oxidation between pH 7 and 6, but fail in predicting the pH limit of Nitrosomonas eutropha at pH 5.4 and rates close to that limit. This is where the exponential pH term becomes important: this term decreases the rate of ammonia oxidation to zero, as the pH limit approaches. Previously proposed sigmoidal pH functions that affect large pH regions, however, led to an overestimation of the pH effect and could therefore not be applied successfully. We show that the proposed exponential pH term can be explained quantitatively with thermodynamic principles: at low pH values, the energy available from the proton motive force is too small for the NADH production in Nitrosomonas eutropha and related AOB causing an energy limited state of the bacterial cell. Hence, energy limitation and not inhibition or limitation of enzymes is responsible for the cessation of the AOB activity at low pH values. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  8. Ammonia-Oxidizing Archaea and Bacteria Differentially Contribute to Ammonia Oxidation in Sediments from Adjacent Waters of Rushan Bay, China

    Directory of Open Access Journals (Sweden)

    Hui He

    2018-02-01

    Full Text Available Ammonia oxidation plays a significant role in the nitrogen cycle in marine sediments. Ammonia-oxidizing archaea (AOA and bacteria (AOB are the key contributors to ammonia oxidation, and their relative contribution to this process is one of the most important issues related to the nitrogen cycle in the ocean. In this study, the differential contributions of AOA and AOB to ammonia oxidation in surface sediments from adjacent waters of Rushan Bay were studied based on the ammonia monooxygenase (amoA gene. Molecular biology techniques were used to analyze ammonia oxidizers’ community characteristics, and potential nitrification incubation was applied to understand the ammonia oxidizers’ community activity. The objective was to determine the community structure and activity of AOA and AOB in surface sediments from adjacent waters of Rushan Bay and to discuss the different contributions of AOA and AOB to ammonia oxidation during summer and winter seasons in the studied area. Pyrosequencing analysis revealed that the diversity of AOA was higher than that of AOB. The majority of AOA and AOB clustered into Nitrosopumilus and Nitrosospira, respectively, indicating that the Nitrosopumilus group and Nitrosospira groups may be more adaptable in studied sediments. The AOA community was closely correlated to temperature, salinity and ammonium concentration, whereas the AOB community showed a stronger correlation with temperature, chlorophyll-a content (chla and nitrite concentration. qPCR results showed that both the abundance and the transcript abundance of AOA was consistently greater than that of AOB. AOA and AOB differentially contributed to ammonia oxidation in different seasons. AOB occupied the dominant position in mediating ammonia oxidation during summer, while AOA might play a dominant role in ammonia oxidation during winter.

  9. Growth of ammonia-oxidizing archaea and bacteria in cattle manure compost under various temperatures and ammonia concentrations.

    Science.gov (United States)

    Oishi, Ryu; Tada, Chika; Asano, Ryoki; Yamamoto, Nozomi; Suyama, Yoshihisa; Nakai, Yutaka

    2012-05-01

    A recent study showed that ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) coexist in the process of cattle manure composting. To investigate their physiological characteristics, liquid cultures seeded with fermenting cattle manure compost were incubated at various temperatures (37°C, 46°C, or 60°C) and ammonium concentrations (0.5, 1, 4, or 10 mM NH (4) (+) -N). The growth rates of the AOB and AOA were monitored using real-time polymerase chain reaction analysis targeting the bacterial and archaeal ammonia monooxygenase subunit A genes. AOB grew at 37°C and 4 or 10 mM NH (4) (+) -N, whereas AOA grew at 46°C and 10 mM NH (4) (+) -N. Incubation with allylthiourea indicated that the AOB and AOA grew by oxidizing ammonia. Denaturing gradient gel electrophoresis and subsequent sequencing analyses revealed that a bacterium related to Nitrosomonas halophila and an archaeon related to Candidatus Nitrososphaera gargensis were the predominant AOB and AOA, respectively, in the seed compost and in cultures after incubation. This is the first report to demonstrate that the predominant AOA in cattle manure compost can grow and can probably oxidize ammonia under moderately thermophilic conditions.

  10. Human settlement as driver of bacterial, but not of archaeal, ammonia oxidizers abundance and community structure in tropical stream sediments

    Directory of Open Access Journals (Sweden)

    Mariana De Paula Reis

    2015-08-01

    Full Text Available Ammonia-oxidizing archaea (AOA and bacteria (AOB are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human settlement on the AOA and AOB diversity and abundance have been assessed by phylogenetic and quantitative PCR analyses, using archaeal and bacterial amoA and 16S rRNA genes. Overall, each environment contained specific clades of amoA and 16S rRNA genes sequences, suggesting that selective pressures lead to AOA and AOB inhabiting distinct ecological niches. Human settlement activities, as derived from increased metal and mineral nitrogen contents, appear to cause a response among the AOB community, with Nitrosomonas taking advantage over Nitrosospira in impacted environments. We also observed a dominance of AOB over AOA in mining-impacted sediments, suggesting that AOB might be the primary drivers of ammonia oxidation in these sediments. In addition, ammonia concentrations demonstrated to be the driver for the abundance of AOA, with an inversely proportional correlation between them. Our findings also revealed the presence of novel ecotypes of Thaumarchaeota, such as those related to the obligate acidophilic Nitrosotalea devanaterra at ammonia-rich places of circumneutral pH. These data add significant new information regarding AOA and AOB from tropical freshwater sediments, albeit future studies would be required to provide additional insights into the niche differentiation among these microorganisms.

  11. Spatial distribution of ammonia-oxidizing archaea and bacteria across eight freshwater lakes in sediments from Jiangsu of China

    Directory of Open Access Journals (Sweden)

    Xu Sun

    2014-03-01

    Full Text Available Ammonia-oxidizingarchaea (AOA and ammonia-oxidizing bacteria (AOB play an important role innitrogen transformation in freshwater sediments. However, it is still unclear towhat extent the distribution patterns of these microorganisms are affected bythe freshwater sediment across a large geographical scale. This study wasdesigned to gain insight into the heterogeneity distribution of AOA and AOB in32 freshwater sediments from a wide range of ecologic types. Real-time quantitative polymerasechain reaction PCR(qPCR combined with the terminal restrictionfragment length polymorphism(T-RFLP were employed to characterize the abundance, diversity, and communitystructure of the AOA and AOB in 32 freshwater sediments. AOA and AOB wereubiquitous in all sediments, and archaeal amoA far outnumbered bacterial amoA inmost sediments with lower organic matters. The abundance of AOA and AOB did notvary with the freshwater ecological type (macrophyte dominated region and algaedominated region. Based on  the T-RFLP of an amoA gene, this research found that organicmatters in pore water rather than other factors affect the AOA communitystructure in sediments, while the AOB were not significantly different in thefreshwater sediments. Phylogenetic analysis showed that all archaeal amoAsequences fell within either the Crenarchaeotal Group (CG I.1b or the CGI.1asubgroup, and all AOB clustered with genus Nitrosomonas or Nitrosospira. The data obtained inthis study elucidates the role of ammonia-oxidizing archaea andammonia-oxidizing bacteria in the nitrogen cycle of freshwater ecosystems.

  12. Effect of chemical fertilization and green manure on the abundance and community structure of ammonia oxidizers in a paddy soil

    Directory of Open Access Journals (Sweden)

    Yu Fang

    2015-12-01

    Full Text Available Ammonia oxidization is a critical step in the soil N cycle and can be affected by the fertilization regimes. Chinese milk-vetch (Astragalus sinicus L., MV is a major green manure of rice (Oryza sativa L. fields in southern China, which is recommended as an important agronomic practice to improve soil fertility. Soil chemical properties, abundance and community structures of ammonia-oxidizing bacteria (AOB and ammonia-oxidizing archaea (AOA in a MV-rice rotation field under different fertilization regimes were investigated. The field experiment included six treatments: control, without MV and chemical fertilizer (CK; 100% chemical fertilizer (NPK; 18 000 kg MV ha-1 plus 100% chemical fertilizer (NPKM1; 18 000 kg MV ha-1 plus 40% chemical fertilizer (NPKM2; 18 000 kg MV ha-1 alone (MV; and 18 000 kg MV ha-1 plus 40% chemical fertilizer plus straw (NPKMS. Results showed that NPKMS treatment could improve the soil fertility greatly although the application of 60% chemical fertilizer. The abundance of AOB only in the MV treatment had significant difference with the control; AOA were more abundant than AOB in all corresponding treatments. The NPKMS treatment had the highest AOA abundance (1.19 x 10(8 amoA gene copies g-1 and the lowest abundance was recorded in the CK treatment (3.21 x 10(7 amoA gene copies g-1. The abundance of AOA was significantly positively related to total N, available N, NH4+-N, and NO3--N. The community structure of AOA exhibited little variation among different fertilization regimes, whereas the community structure of AOB was highly responsive. Phylogenetic analysis showed that all AOB sequences were affiliated with Nitrosospira or Nitrosomonas and all AOA denaturing gradient gel electrophoresis (DGGE bands belonged to the soil and sediment lineage. These findings could be fundamental to improve our understanding of AOB and AOA in the N cycle in the paddy soil.

  13. Ammonia biofiltration and community analysis of ammonia-oxidizing bacteria in biofilters.

    Science.gov (United States)

    Jun, Yin; Wenfeng, Xu

    2009-09-01

    Biological removal of ammonia was investigated using compost and sludge as packing materials in laboratory-scale biofilters. The aim of this study is to characterize the composition of ammonia-oxidizing bacteria (AOB) in two biofilters designed to remove ammonia. Experimental tests and measurements included analysis of removal efficiency and metabolic products. The inlet concentration of ammonia applied was 20-100 mg m(-3). Removal efficiencies of BFC and BFS were in the range of 97-99% and 95-99%, respectively. Periodic analysis of the biofilter packing materials showed ammonia was removed from air stream by nitrification and by the improved absorption of NH(3) in the resultant acidity. Nitrate was the dominant product of NH(3) transformation. Changes in the composition of AOB were examined by using nested PCR, denaturing gradient gel electrophoresis (DGGE) and sequencing of DGGE bands. DGGE analysis of biofilter samples revealed that shifts in the community structure of AOB were observed in the experiment; however, the idle phase did not cause the structural shift of AOB. Phylogenetic analysis revealed the population of AOB showed Nitrosospira sp. remains the predominant population in BFC, while Nitrosomonas sp. is the predominant population in BFS.

  14. Wastewater treatment plant effluents change abundance and composition of ammonia-oxidizing microorganisms in mediterranean urban stream biofilms.

    Science.gov (United States)

    Merbt, Stephanie N; Auguet, Jean-Christophe; Blesa, Alba; Martí, Eugènia; Casamayor, Emilio O

    2015-01-01

    Streams affected by wastewater treatment plant (WWTP) effluents are hotspots of nitrification. We analyzed the influence of WWTP inputs on the abundance, distribution, and composition of epilithic ammonia-oxidizing (AO) assemblages in five Mediterranean urban streams by qPCR and amoA gene cloning and sequencing of both archaea (AOA) and bacteria (AOB). The effluents significantly modified stream chemical parameters, and changes in longitudinal profiles of both NH(4)(+) and NO(3)(-) indicated stimulated nitrification activity. WWTP effluents were an allocthonous source of both AOA, essentially from the Nitrosotalea cluster, and mostly of AOB, mainly Nitrosomonas oligotropha, Nitrosomonas communis, and Nitrosospira spp. changing the relative abundance and the natural composition of AO assemblages. Under natural conditions, Nitrososphaera and Nitrosopumilus AOA dominated AO assemblages, and AOB were barely detected. After the WWTP perturbation, epilithic AOB increased by orders of magnitude whereas AOA did not show quantitative changes but a shift in population composition to dominance of Nitrosotalea spp. The foraneous AOB successfully settled in downstream biofilms and probably carried out most of the nitrification activity. Nitrosotalea were only observed downstream and only in biofilms exposed to either darkness or low irradiance. In addition to other potential environmental limitations for AOA distribution, this result suggests in situ photosensitivity as previously reported for Nitrosotalea under laboratory conditions.

  15. [Effects of Corbicula fluminea bioturbation on the community composition and abundance of ammonia-oxidizing archaea and bacteria in surface sediments].

    Science.gov (United States)

    Wang, Xue; Zhao, Da-Yong; Zeng, Jin; Yu, Duo-Wei; Wu, Qing-Long

    2014-06-01

    To better understand the effects of Corbicula fluminea bioturbation on the ammonia-oxidizing microorganisms in the surface sediment, sediment-water microcosms with different densities of Corbicula fluminea were constructed. Clone libraries and real-time qPCR were applied to analyze the community composition and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the surface sediments. The results obtained indicated that the bioturbation of Corbicula fluminea accelerated the release of nitrogen from the surface sediment. In the amoA gene clone libraries, the identified AOA amoA gene sequences affiliated with the two known clusters (marine and soil clusters). The identified AOB amoA gene sequences mostly belonged to the Nitrosomonas of beta-Proteobacteria. The abundance of the bacterial amoA gene was higher than that of the archaeal amoA gene in all treatments. With increasing density of Corbicula fluminea, decreased abundances of the bacterial amoA gene were observed. At the same time, the diversity of AOA and AOB reduced in the Corbicula fluminea containing microcosms. In conclusion, the bioturbation of Corbicula fluminea could affected the community composition and abundance of ammonia-oxidizing microorganisms in surface sediments.

  16. Nitrogen metabolism and kinetics of ammonia-oxidizing archaea.

    Science.gov (United States)

    Martens-Habbena, Willm; Stahl, David A

    2011-01-01

    The discovery of ammonia-oxidizing mesophilic and thermophilic Group I archaea changed the century-old paradigm that aerobic ammonia oxidation is solely mediated by two small clades of Beta- and Gammaproteobacteria. Group I archaea are extremely diverse and ubiquitous in marine and terrestrial environments, accounting for 20-30% of the microbial plankton in the global oceans. Recent studies indicated that many of these organisms carry putative ammonia monooxygenase genes and are more abundant than ammonia-oxidizing bacteria in most natural environments suggesting a potentially significant role in the nitrogen cycle. The isolation of Nitrosopumilus maritimus strain SCM1 provided the first direct evidence that Group I archaea indeed gain energy from ammonia oxidation. To characterize the physiology of this archaeal nitrifier, we developed a respirometry setup particularly suited for activity measurements in dilute microbial cultures with extremely low oxygen uptake rates. Here, we describe the setup and review the kinetic experiments conducted with N. maritimus and other nitrifying microorganisms. These experiments demonstrated that N. maritimus is adapted to grow on ammonia concentrations found in oligotrophic open ocean environments, far below the survival threshold of ammonia-oxidizing bacteria. The described setup and experimental procedures should facilitate physiological studies on other nitrifying archaea and oligotrophic microorganisms in general. Copyright © 2011 Elsevier Inc. All rights reserved.

  17. Biokinetic characterization of the acceleration phase in autotrophic ammonia oxidation.

    Science.gov (United States)

    Chandran, Kartik; Smets, Barth F

    2008-08-01

    Batch autotrophic ammonia oxidation tracked through oxygen uptake measurements displays a preliminary acceleration phase. Failure to recognize the acceleration phase and fitting batch ammonia oxidation profiles with standard Monod-type mathematical models can result in meaningless kinetic parameter estimates. The objectives of this study were to examine the factors controlling the acceleration phase and to derive and test empirical and metabolic models for its description. Because of possible sustained reducing power limitation during batch ammonia oxidation, the extent of the acceleration phase (1) increased with increasing initial ammonia concentration, (2) did not systematically vary with initial biomass concentrations, and (3) increased in response to starvation. Concurrent hydroxylamine oxidation significantly reduced the acceleration phase potentially by relieving reducing power limitation. A nonlinear empirical model described the acceleration phase more accurately than a linear empirical model. The metabolic model also captured experimental trends exceedingly well, but required determination of additional parameters and variables.

  18. Habitat-associated phylogenetic community patterns of microbial ammonia oxidizers.

    Directory of Open Access Journals (Sweden)

    Antoni Fernàndez-Guerra

    Full Text Available Microorganisms mediating ammonia oxidation play a fundamental role in the connection between biological nitrogen fixation and anaerobic nitrogen losses. Bacteria and Archaea ammonia oxidizers (AOB and AOA, respectively have colonized similar habitats worldwide. Ammonia oxidation is the rate-limiting step in nitrification, and the ammonia monooxygenase (Amo is the key enzyme involved. The molecular ecology of this process has been extensively explored by surveying the gene of the subunit A of the Amo (amoA gene. In the present study, we explored the phylogenetic community ecology of AOB and AOA, analyzing 5776 amoA gene sequences from >300 isolation sources, and clustering habitats by environmental ontologies. As a whole, phylogenetic richness was larger in AOA than in AOB, and sediments contained the highest phylogenetic richness whereas marine plankton the lowest. We also observed that freshwater ammonia oxidizers were phylogenetically richer than their marine counterparts. AOA communities were more dissimilar to each other than those of AOB, and consistent monophyletic lineages were observed for sediments, soils, and marine plankton in AOA but not in AOB. The diversification patterns showed a more constant cladogenesis through time for AOB whereas AOA apparently experienced two fast diversification events separated by a long steady-state episode. The diversification rate (γ statistic for most of the habitats indicated γ(AOA > γ(AOB. Soil and sediment experienced earlier bursts of diversification whereas habitats usually eutrophic and rich in ammonium such as wastewater and sludge showed accelerated diversification rates towards the present. Overall, this work shows for the first time a global picture of the phylogenetic community structure of both AOB and AOA assemblages following the strictest analytical standards, and provides an ecological view on the differential evolutionary paths experienced by widespread ammonia-oxidizing

  19. Fauna Europaea

    DEFF Research Database (Denmark)

    Pape, Thomas; Beuk, Paul; Pont, Adrian Charles

    2015-01-01

    Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all extant multicellular European terrestrial and freshwater animals and their geographical distribution at the level of countries and major islands (east of the Urals and excluding...... density, and the more fertile habitats are extensively cultivated. This has undoubtedly increased the extinction risk for numerous species of brachyceran flies, yet with the recent re-discovery of Thyreophoracynophila (Panzer), there are no known cases of extinction at a European level. However, few...

  20. Macroecological patterns of archaeal ammonia oxidizers in the Atlantic Ocean

    NARCIS (Netherlands)

    Sintes, E.; Ouillon, N.; Herndl, G.J.

    2015-01-01

    Macroecological patterns are found in animals and plants, but also in micro-organisms.Macroecological and biogeographic distribution patterns in marine Archaea, however,have not been studied yet. Ammonia-oxidizing Archaea (AOA) show a bipolar distribution(i.e. similar communities in the northernmost

  1. Ammonia-oxidizing bacteria: A model for molecular microbial ecology

    NARCIS (Netherlands)

    Kowalchuk, G.A.; Stephen, J.R.

    2001-01-01

    The eutrophication of many ecosystems in recent decades has led to an increased interest in the ecology of nitrogen transformation. Chemolitho-autotrophic ammonia-oxidizing bacteria are responsible for the rate-limiting step of nitrification in a wide variety of environments, making them important

  2. A hydrophobic ammonia-oxidizing archaeon of the

    NARCIS (Netherlands)

    Jung, M.Y.; Kim, J.G.; Sinninghe Damsté, J.S.; Rijpstra, W.I.C.; Madsen, E.L.; Kim, S.J.; Hong, H.; Si, O.-J.; Kerou, M.; Schleper, C.; Rhee, S.K.

    2016-01-01

    A wide diversity of ammonia-oxidizing archaea (AOA)within the phylum Thaumarchaeota exists and playsa key role in the N cycle in a variety of habitats. In thisstudy, we isolated and characterized an ammoniaoxidizingarchaeon, strain MY3, from a coal tarcontaminatedsediment. Phylogenetically, strain

  3. Substrate and nutrient limitation of ammonia-oxidizing bacteria and archaea in temperate forest soil

    Science.gov (United States)

    J.S. Norman; J.E. Barrett

    2014-01-01

    Ammonia-oxidizing microbes control the rate-limiting step of nitrification, a critical ecosystem process, which affects retention and mobility of nitrogen in soil ecosystems. This study investigated substrate (NH4þ) and nutrient (K and P) limitation of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in temperate forest soils at Coweeta Hydrologic...

  4. Nitrosomonas

    African Journals Online (AJOL)

    Stolz, A. 2001. Basic and applied aspects in the microbial degradation of azo dyes. Appl. Microbiol. Biotechnol. 56:69-80. Tan, N.C.G., and J. A. Field.2000. Biodegradation of sulfonated aromatic compounds. In: Environmental Technologies to Treat. Sulfur Pollution: Principles and I. Engineering. Lens, P. and Hulshoff Pol, L.

  5. The effect of bacterial community members on the proteome of the ammonia-oxidizing bacterium Nitrosomonas sp. Is79

    NARCIS (Netherlands)

    Sedlacek, Christopher J.; Nielsen, Susanne; Greis, Kenneth D.; Haffey, Wendy D.; Revsbech, Niels Peter; Ticak, Tomislav; Laanbroek, Hendrikus J.; Bollmann, Annette

    2016-01-01

    Microorganisms in the environment do not exist as the often-studied pure cultures but as members of complex microbial communities. Characterizing the interactions within microbial communities is essential to understand their function in both natural and engineered environments. In this study we

  6. Comparison of Nitrogen Oxide Metabolism among Diverse Ammonia-Oxidizing Bacteria.

    Science.gov (United States)

    Kozlowski, Jessica A; Kits, K Dimitri; Stein, Lisa Y

    2016-01-01

    Ammonia-oxidizing bacteria (AOB) have well characterized genes that encode and express nitrite reductases (NIR) and nitric oxide reductases (NOR). However, the connection between presence or absence of these and other genes for nitrogen transformations with the physiological production of nitric oxide (NO) and nitrous oxide (N2O) has not been tested across AOB isolated from various trophic states, with diverse phylogeny, and with closed genomes. It is therefore unclear if genomic content for nitrogen oxide metabolism is predictive of net N2O production. Instantaneous microrespirometry experiments were utilized to measure NO and N2O emitted by AOB during active oxidation of ammonia (NH3) or hydroxylamine (NH2OH) and through a period of anoxia. This data was used in concert with genomic content and phylogeny to assess whether taxonomic factors were predictive of nitrogen oxide metabolism. Results showed that two oligotrophic AOB strains lacking annotated NOR-encoding genes released large quantities of NO and produced N2O abiologically at the onset of anoxia following NH3-oxidation. Furthermore, high concentrations of N2O were measured during active O2-dependent NH2OH oxidation by the two oligotrophic AOB in contrast to non-oligotrophic strains that only produced N2O at the onset of anoxia. Therefore, complete nitrifier denitrification did not occur in the two oligotrophic strains, but did occur in meso- and eutrophic strains, even in Nitrosomonas communis Nm2 that lacks an annotated NIR-encoding gene. Regardless of mechanism, all AOB strains produced measureable N2O under tested conditions. This work further confirms that AOB require NOR activity to enzymatically reduce NO to N2O in the nitrifier denitrification pathway, and also that abiotic reactions play an important role in N2O formation, in oligotrophic AOB lacking NOR activity.

  7. Differential responses of ammonia-oxidizing archaea and bacteria to long-term fertilization in a New England salt marsh

    Directory of Open Access Journals (Sweden)

    Xuefeng ePeng

    2013-01-01

    Full Text Available Since the discovery of ammonia-oxidizing archaea (AOA, new questions have arisen about population and community dynamics and potential interactions between AOA and ammonia-oxidizing Bacteria (AOB. We investigated the effects of long-term fertilization on AOA and AOB in the Great Sippewissett Marsh, Falmouth, MA, USA to address some of these questions. Sediment samples were collected from low and high marsh habitats in July 2009 from replicate plots that received low (LF, high (HF, and extra high (XF levels of a mixed NPK fertilizer biweekly during the growing season since 1974. Additional untreated plots were included as controls (C. Terminal restriction fragment length polymorphism analysis of the amoA genes revealed distinct shifts in AOB communities related to fertilization treatment, but the response patterns of AOA were less consistent. Four AOB operational taxonomic units (OTUs predictably and significantly responded to fertilization, but only one AOA OTU showed a significant pattern. Betaproteobacterial amoA gene sequences within the Nitrosospira-like cluster dominated at C and LF sites, while sequences related to Nitrosomonas spp. dominated at HF and XF sites. We identified some clusters of AOA sequences recovered primarily from high fertilization regimes, but other clusters consisted of sequences recovered from all fertilization treatments, suggesting greater physiological diversity. Surprisingly, fertilization appeared to have little impact on abundance of AOA or AOB. In summary, our data reveal striking patterns for AOA and AOB in response to long-term fertilization, and also suggest a missing link between community composition and abundance and nitrogen processing in the marsh.

  8. The Eponymous Cofactors in Cytochrome P460s from Ammonia-Oxidizing Bacteria Are Iron Porphyrinoids Whose Macrocycles Are Dibasic.

    Science.gov (United States)

    Smith, Meghan A; Lancaster, Kyle M

    2018-01-23

    The enzymes hydroxylamine oxidoreductase and cytochrome (cyt) P460 contain related unconventional "heme P460" cofactors. These cofactors are unusual in their inclusion of nonstandard cross-links between amino acid side chains and the heme macrocycle. Mutagenesis studies performed on the Nitrosomonas europaea cyt P460 that remove its lysine-heme cross-link show that the cross-link is key to defining the spectroscopic properties and kinetic competence of the enzyme. However, exactly how this cross-link confers these features remains unclear. Here we report the 1.45 Å crystal structure of cyt P460 from Nitrosomonas sp. AL212 and conclude that the cross-link does not lead to a change in hybridization of the heme carbon participating in the cross-link but rather enforces structural distortions to the macrocycle away from planarity. Time-dependent density functional theory coupled to experimental structural and spectroscopic analysis suggest that this geometric distortion is sufficient to define the spectroscopic properties of the heme P460 cofactor and provide clues toward establishing a relationship between heme P460 electronic structure and function.

  9. Diversity of Ammonia Oxidizing Archaea in Tropical Compost Systems

    OpenAIRE

    Vidya eDe Gannes; Gaius eEudoxie; David H Dyer; William James Hickey

    2012-01-01

    Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the p...

  10. Changes in community composition of ammonia-oxidizing betaproteobacteria from stands of Black mangrove (Avicennia germinans in response to ammonia enrichment and more oxic conditions

    Directory of Open Access Journals (Sweden)

    Hendrikus J. Laanbroek

    2013-11-01

    Full Text Available In flooded and non-flooded impounded forests of Black mangrove (Avicennia germinans, the community structure of the ammonia-oxidizing betaproteobacteria (β-AOB differed among distinct mangrove vegetation cover types and hydrological regimes. This had been explained by a differential response of lineages of β-AOB to the prevailing soil conditions that included increased levels of moisture and ammonium. To test this hypothesis, slurries of soils collected from a flooded and a non-flooded impoundment were subjected to enhanced levels of ammonium in the absence and presence of additional shaking. After a period of 6 days, the community composition of the β-AOB based on the 16S rRNA gene was determined and compared with the original community structures. Regardless of the incubation conditions and the origin of the samples, sequences belonging to the Nitrosomonas aestuarii lineage became increasingly dominant, whereas the number of sequences of the lineages of Nitrosospira (i.e. Cluster 1 and Nitrosomonas sp. Nm143 declined. Changes in community structure were related to changes in community sizes determined by quantitative PCR based on the amoA gene. The amoA gene copy numbers of β-AOB were compared to those of the ammonia-oxidizing archaea (AOA. Gene copy numbers of the bacteria increased irrespective of incubation conditions, but the numbers of archaea declined in the continuously shaken cultures. This observation is discussed in relation to the distribution of the β-AOB lineages in the impounded Black mangrove forests.

  11. Changes in community composition of ammonia-oxidizing betaproteobacteria from stands of Black mangrove (Avicennia germinans) in response to ammonia enrichment and more oxic conditions

    Science.gov (United States)

    Laanbroek, Hendrikus J.; Keijzer, Rosalinde M.; Verhoeven, Jos T. A.; Whigham, Dennis F.

    2013-01-01

    In flooded and non-flooded impounded forests of Black mangrove (Avicennia germinans), the community structure of the ammonia-oxidizing betaproteobacteria (β-AOB) differed among distinct mangrove vegetation cover types and hydrological regimes. This had been explained by a differential response of lineages of β-AOB to the prevailing soil conditions that included increased levels of moisture and ammonium. To test this hypothesis, slurries of soils collected from a flooded and a non-flooded impoundment were subjected to enhanced levels of ammonium in the absence and presence of additional shaking. After a period of 6 days, the community composition of the β-AOB based on the 16S rRNA gene was determined and compared with the original community structures. Regardless of the incubation conditions and the origin of the samples, sequences belonging to the Nitrosomonas aestuarii lineage became increasingly dominant, whereas the number of sequences of the lineages of Nitrosospira (i.e., Cluster 1) and Nitrosomonas sp. Nm143 declined. Changes in community structure were related to changes in community sizes determined by quantitative PCR based on the amoA gene. The amoA gene copy numbers of β-AOB were compared to those of the ammonia-oxidizing archaea (AOA). Gene copy numbers of the bacteria increased irrespective of incubation conditions, but the numbers of archaea declined in the continuously shaken cultures. This observation is discussed in relation to the distribution of the β-AOB lineages in the impounded Black mangrove forests. PMID:24312088

  12. Nitrogen and Oxygen Isotope Effects of Ammonia Oxidation by Thermophilic Thaumarchaeota from a Geothermal Water Stream.

    Science.gov (United States)

    Nishizawa, Manabu; Sakai, Sanae; Konno, Uta; Nakahara, Nozomi; Takaki, Yoshihiro; Saito, Yumi; Imachi, Hiroyuki; Tasumi, Eiji; Makabe, Akiko; Koba, Keisuke; Takai, Ken

    2016-08-01

    Ammonia oxidation regulates the balance of reduced and oxidized nitrogen pools in nature. Although ammonia-oxidizing archaea have been recently recognized to often outnumber ammonia-oxidizing bacteria in various environments, the contribution of ammonia-oxidizing archaea is still uncertain due to difficulties in the in situ quantification of ammonia oxidation activity. Nitrogen and oxygen isotope ratios of nitrite (δ(15)NNO2- and δ(18)ONO2-, respectively) are geochemical tracers for evaluating the sources and the in situ rate of nitrite turnover determined from the activities of nitrification and denitrification; however, the isotope ratios of nitrite from archaeal ammonia oxidation have been characterized only for a few marine species. We first report the isotope effects of ammonia oxidation at 70°C by thermophilic Thaumarchaeota populations composed almost entirely of "Candidatus Nitrosocaldus." The nitrogen isotope effect of ammonia oxidation varied with ambient pH (25‰ to 32‰) and strongly suggests the oxidation of ammonia, not ammonium. The δ(18)O value of nitrite produced from ammonia oxidation varied with the δ(18)O value of water in the medium but was lower than the isotopic equilibrium value in water. Because experiments have shown that the half-life of abiotic oxygen isotope exchange between nitrite and water is longer than 33 h at 70°C and pH ≥6.6, the rate of ammonia oxidation by thermophilic Thaumarchaeota could be estimated using δ(18)ONO2- in geothermal environments, where the biological nitrite turnover is likely faster than 33 h. This study extended the range of application of nitrite isotopes as a geochemical clock of the ammonia oxidation activity to high-temperature environments. Because ammonia oxidation is generally the rate-limiting step in nitrification that regulates the balance of reduced and oxidized nitrogen pools in nature, it is important to understand the biological and environmental factors underlying the regulation of

  13. Nitrogen and Oxygen Isotope Effects of Ammonia Oxidation by Thermophilic Thaumarchaeota from a Geothermal Water Stream

    Science.gov (United States)

    Sakai, Sanae; Konno, Uta; Nakahara, Nozomi; Takaki, Yoshihiro; Saito, Yumi; Imachi, Hiroyuki; Tasumi, Eiji; Makabe, Akiko; Koba, Keisuke; Takai, Ken

    2016-01-01

    ABSTRACT Ammonia oxidation regulates the balance of reduced and oxidized nitrogen pools in nature. Although ammonia-oxidizing archaea have been recently recognized to often outnumber ammonia-oxidizing bacteria in various environments, the contribution of ammonia-oxidizing archaea is still uncertain due to difficulties in the in situ quantification of ammonia oxidation activity. Nitrogen and oxygen isotope ratios of nitrite (δ15NNO2− and δ18ONO2−, respectively) are geochemical tracers for evaluating the sources and the in situ rate of nitrite turnover determined from the activities of nitrification and denitrification; however, the isotope ratios of nitrite from archaeal ammonia oxidation have been characterized only for a few marine species. We first report the isotope effects of ammonia oxidation at 70°C by thermophilic Thaumarchaeota populations composed almost entirely of “Candidatus Nitrosocaldus.” The nitrogen isotope effect of ammonia oxidation varied with ambient pH (25‰ to 32‰) and strongly suggests the oxidation of ammonia, not ammonium. The δ18O value of nitrite produced from ammonia oxidation varied with the δ18O value of water in the medium but was lower than the isotopic equilibrium value in water. Because experiments have shown that the half-life of abiotic oxygen isotope exchange between nitrite and water is longer than 33 h at 70°C and pH ≥6.6, the rate of ammonia oxidation by thermophilic Thaumarchaeota could be estimated using δ18ONO2− in geothermal environments, where the biological nitrite turnover is likely faster than 33 h. This study extended the range of application of nitrite isotopes as a geochemical clock of the ammonia oxidation activity to high-temperature environments. IMPORTANCE Because ammonia oxidation is generally the rate-limiting step in nitrification that regulates the balance of reduced and oxidized nitrogen pools in nature, it is important to understand the biological and environmental factors underlying

  14. Selective isolation of ammonia-oxidizing bacteria from autotrophic nitrifying granules by applying cell-sorting and sub-culturing of microcolonies

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    Hirotsugu eFujitani

    2015-10-01

    Full Text Available Nitrification is a key process in the biogeochemical nitrogen cycle and biological wastewater treatment that consists of two stepwise reactions, ammonia oxidation by ammonia-oxidizing bacteria (AOB or archaea followed by nitrite oxidation by nitrite-oxidizing bacteria. One of the representative of the AOB group is Nitrosomonas mobilis species. Although a few pure strains of this species have been isolated so far, approaches to their preservation in pure culture have not been established. Here, we report isolation of novel members of the N. mobilis species from autotrophic nitrifying granules used for ammonia-rich wastewater treatment. We developed an isolation method focusing on microcolonies formation of nitrifying bacteria. Two kinds of distinctive light scattering signatures in a cell-sorting system enabled to separate microcolonies from single cells and heterogeneous aggregates within granule samples. Inoculation of a pure microcolony into 96-well microtiter plates led to successful sub-culturing and increased probability of isolation. Obtained strain Ms1 is cultivated in the liquid culture with relatively high ammonia or nitrite concentration, not extremely slow growing. Considering environmental clones that were closely related to N. mobilis and detected in various environments, the availability of this novel strain would facilitate to reveal this member’s ecophysiology in a variety of habitats.

  15. Communities of sediment ammonia-oxidizing bacteria along a coastal pollution gradient in the East China Sea.

    Science.gov (United States)

    Hou, Manhua; Xiong, Jinbo; Wang, Kai; Ye, Xiansen; Ye, Ran; Wang, Qiong; Hu, Changju; Zhang, Demin

    2014-09-15

    Anthropogenic nitrogen (N) discharges has caused eutrophication in coastal zones. Ammonia-oxidizing bacteria (AOB) convert ammonia to nitrite and play important roles in N transformation. Here, we used pyrosequencing based on the amoA gene to investigate the response of the sediment AOB community to an N pollution gradient in the East China Sea. The results showed that AOB assemblages were primarily affiliated with Nitrosospira-like lineages, and only 0.4% of those belonged to Nitrosomonas-like lineage. The Nitrosospira-like lineage was separated into four clusters that were most similar to the sediment AOB communities detected in adjacent marine regions. Additionally, one clade was out grouped from the AOB lineages, which shared the high similarities with pmoA gene. The AOB community structures substantially changed along the pollution gradient, which were primarily shaped by NH4(+)-N, NO3(-)-N, SO4(2)(-)-S, TP and Eh. These results demonstrated that coastal pollution could dramatically influence AOB communities, which, in turn, may change ecosystem function. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Diversity of Ammonia Oxidizing Archaea in Tropical Compost Systems

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    Vidya eDe Gannes

    2012-07-01

    Full Text Available Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA has changed the paradigm of nitrification being initiated solely by ammonia oxidizing bacteria. In the present study, AOA abundance and diversity was examined in composts produced from combinations of plant waste materials common in tropical agriculture (rice straw, sugar cane bagasse, coffee hulls, which were mixed with either cow- or sheep-manure. The objective was to determine how AOA abundance and diversity varied as a function of compost system and time, the latter being a contrast between the start of the compost process (mesophilic phase and the finished product (mature phase. The results showed that AOA were relatively abundant in composts of tropical agricultural wastes, and significantly more so than were the ammonia-oxidizing bacteria. Furthermore, while the AOA communities in the composts were predominatly group I.1b, the communities were diverse and exhibited structures that diverged between compost types and phases. These patterns could be taken as indicators of the ecophysiological diversity in the soil AOA (groub I.1b, in that significantly different AOA communties developed when exposed to varying physico-chemical environments. Nitrification patterns and levels differed in the composts which, for the mature material, could have signifcant effects on its performanc as a plant growth medium. Thus, it will also be important to determine the association of AOA (and diversity in their communities with nitrification in these systems.

  17. Production of oceanic nitrous oxide by ammonia-oxidizing archaea

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    C. R. Löscher

    2012-07-01

    Full Text Available The recent finding that microbial ammonia oxidation in the ocean is performed by archaea to a greater extent than by bacteria has drastically changed the view on oceanic nitrification. The numerical dominance of archaeal ammonia-oxidizers (AOA over their bacterial counterparts (AOB in large parts of the ocean leads to the hypothesis that AOA rather than AOB could be the key organisms for the oceanic production of the strong greenhouse gas nitrous oxide (N2O that occurs as a by-product of nitrification. Very recently, enrichment cultures of marine ammonia-oxidizing archaea have been reported to produce N2O.

    Here, we demonstrate that archaeal ammonia monooxygenase genes (amoA were detectable throughout the water column of the eastern tropical North Atlantic (ETNA and eastern tropical South Pacific (ETSP Oceans. Particularly in the ETNA, comparable patterns of abundance and expression of archaeal amoA genes and N2O co-occurred in the oxygen minimum, whereas the abundances of bacterial amoA genes were negligible. Moreover, selective inhibition of archaea in seawater incubations from the ETNA decreased the N2O production significantly. In studies with the only cultivated marine archaeal ammonia-oxidizer Nitrosopumilus maritimus SCM1, we provide the first direct evidence for N2O production in a pure culture of AOA, excluding the involvement of other microorganisms as possibly present in enrichments. N. maritimus showed high N2O production rates under low oxygen concentrations comparable to concentrations existing in the oxycline of the ETNA, whereas the N2O production from two AOB cultures was comparably low under similar conditions. Based on our findings, we hypothesize that the production of N2O in tropical ocean areas results mainly from archaeal nitrification and will be affected by the predicted decrease in dissolved

  18. Ammonia oxidation kinetics and temperature sensitivity of a natural marine community dominated by Archaea

    Science.gov (United States)

    Horak, Rachel E A; Qin, Wei; Schauer, Andy J; Armbrust, E Virginia; Ingalls, Anitra E; Moffett, James W; Stahl, David A; Devol, Allan H

    2013-01-01

    Archaeal ammonia oxidizers (AOAs) are increasingly recognized as prominent members of natural microbial assemblages. Evidence that links the presence of AOA with in situ ammonia oxidation activity is limited, and the abiotic factors that regulate the distribution of AOA natural assemblages are not well defined. We used quantitative PCR to enumerate amoA (encodes α-subunit of ammonia monooxygenase) abundances; AOA amoA gene copies greatly outnumbered ammonia-oxidizing bacteria and amoA transcripts were derived primarily from AOA throughout the water column of Hood Canal, Puget Sound, WA, USA. We generated a Michaelis–Menten kinetics curve for ammonia oxidation by the natural community and found that the measured Km of 98±14 nmol l−1 was close to that for cultivated AOA representative Nitrosopumilus maritimus SCM1. Temperature did not have a significant effect on ammonia oxidation rates for incubation temperatures ranging from 8 to 20 °C, which is within the temperature range for depths of measurable ammonia oxidation at the site. This study provides substantial evidence, through both amoA gene copies and transcript abundances and the kinetics response, that AOA are the dominant active ammonia oxidizers in this marine environment. We propose that future ammonia oxidation experiments use a Km for the natural community to better constrain ammonia oxidation rates determined with the commonly used 15NH4+ dilution technique. PMID:23657360

  19. Community Structure of Ammonia-Oxidizing Archaea and Ammonia-Oxidizing Bacteria in Soil Treated with the Insecticide Imidacloprid

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    Mariusz Cycoń

    2015-01-01

    Full Text Available The purpose of this experiment was to assess the effect of imidacloprid on the community structure of ammonia-oxidizing archaea (AOA and ammonia-oxidizing bacteria (AOB in soil using the denaturing gradient gel electrophoresis (DGGE approach. Analysis showed that AOA and AOB community members were affected by the insecticide treatment. However, the calculation of the richness (S and the Shannon-Wiener index (H values for soil treated with the field rate (FR dosage of imidacloprid (1 mg/kg soil showed no changes in measured indices for the AOA and AOB community members. In turn, the 10*FR dosage of insecticide (10 mg/kg soil negatively affected the AOA community, which was confirmed by the decrease of the S and H values in comparison with the values obtained for the control soil. In the case of AOB community, an initial decline followed by the increase of the S and H values was obtained. Imidacloprid decreased the nitrification rate while the ammonification process was stimulated by the addition of imidacloprid. Changes in the community structure of AOA and AOB could be due to an increase in the concentration of N-NH4+, known as the most important factor which determines the contribution of these microorganisms to soil nitrification.

  20. Changing roles of ammonia-oxidizing bacteria and archaea in a continuously acidifying soil caused by over-fertilization with nitrogen.

    Science.gov (United States)

    Song, He; Che, Zhao; Cao, Wenchao; Huang, Ting; Wang, Jingguo; Dong, Zhaorong

    2016-06-01

    Nitrification coupled with nitrate leaching contributes to soil acidification. However, little is known about the effect of soil acidification on nitrification, especially on ammonia oxidation that is the rate-limiting step of nitrification and performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). Serious soil acidification occurs in Chinese greenhouses due to the overuse of N-fertilizer. In the present study, greenhouse soils with 1, 3, 5, 7, and 9 years of vegetable cultivation showed a consistent pH decline (i.e., 7.0, 6.3, 5.6, 4.9, and 4.3). Across the pH gradient, we analyzed the community structure and abundance of AOB and AOA by pyrosequencing and real-time PCR techniques, respectively. The recovered nitrification potential (RNP) method was used to determine relative contributions of AOA and AOB to nitrification potential. The results revealed that soil acidification shaped the community structures of AOA and AOB. In acidifying soil, soil pH, NH3 concentration, and DOC content were critical factors shaping ammonia oxidizer community structure. AOB abundance, but not AOA, was strongly influenced by soil acidification. When soil pH was below 5.0, AOA rather than AOB were responsible for almost all of the RNP. However, when soil pH ranged from 5.6 to 7.0, AOB were the major contributors to RNP. The group I.1a-associatied AOA had more relative abundance in low pH (pH<6.3), whereas group I.1b tended to prefer neutral pH. Clusters 2, 10, and 12 in AOB were more abundant in acidic soil (pH <5.6), while Nitrosomonas-like lineage and unclassified lineage 3 were prevailing in neutral soil and slightly acidic soil (pH, 6.0-6.5), respectively. These results suggested that soil acidification had a profound impact on ammonia oxidation and more specific lineages in AOB occupying different pH-associated niches required further investigation.

  1. Contributions of ammonia-oxidizing archaea and bacteria to nitrification in Oregon forest soils

    Science.gov (United States)

    Xinda Lu; Peter J. Bottomley; David D. Myrold

    2015-01-01

    Ammonia oxidation, the first step of nitrification, is mediated by both ammonia-oxidizing archaea (AOA) and bacteria (AOB); however, the relative contributions of AOA and AOB to soil nitrification are not well understood. In this study we used 1-octyne to discriminate between AOA-and AOB-supported nitrifi-cation determined both in soil-water slurries and in unsaturated...

  2. Interactions between archaeal ammonia oxidizers, Nitrospira and methanotrophs modulate autotrophic nitrification in volcanic grasslands soils

    NARCIS (Netherlands)

    Daebeler, A.; Bodelier, P.L.E.; Yan, Z; Hefting, Mariet|info:eu-repo/dai/nl/256197628; Laanbroek, Riks|info:eu-repo/dai/nl/070378282

    2014-01-01

    Ammonium/ammonia is the sole energy substrate of ammonia oxidizers, and is also an essential nitrogen source for other microorganisms. Ammonia oxidizers therefore must compete with other soil microorganisms such as methane-oxidizing bacteria (MOB) in terrestrial ecosystems when ammonium

  3. Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea

    NARCIS (Netherlands)

    Kim, J.G.; Park, S.J.; Sinninghe Damsté, J.S.; Schouten, S.; Rijpstra, W.I.C.; Jung, M.Y.; Kim, S.J.; Gwak, J.-H.; Hong, H.; Si, O.-J.; Lee, S.H.; Madsen, E.L.; Rhee, S.K.

    2016-01-01

    Ammonia-oxidizing archaea (AOA), that is, members of the Thaumarchaeotaphylum, occur ubiquitously in the environment and areof major significance for global nitrogen cycling. However, controls oncell growth and organic carbon assimilation by AOA are poorlyunderstood. We isolated an ammonia-oxidizing

  4. Drivers of archaeal ammonia-oxidizing communities in soil

    Directory of Open Access Journals (Sweden)

    Kateryna eZhalnina

    2012-06-01

    Full Text Available Soil ammonia-oxidizing archaea (AOA are highly abundant and play an important role in the nitrogen cycle. In addition, AOA have a significant impact on soil quality. AOA may cause nitrogen loss from soils, and the nitrate produced by AOA can lead to ground and surface water contamination, water eutrophication, and soil subsidence. The ammonia-oxidizing archaea discovered to date are classified in the phylum Thaumarchaeota. Only a few archaeal genomes are available in databases. As a result, AOA genes are not well annotated, and it is difficult to mine and identify archaeal genes within metagenomic libraries. Nevertheless, 16S rRNA and comparative analysis of ammonia monooxygenase sequences show that soils can vary greatly in the relative abundance of AOA. In some soils, AOA can comprise more than 10% of the total prokaryotic community. In other soils, AOA comprise less than 0.5% of the community. Many approaches have been used to measure the abundance and diversity of this group including DGGE, T-RFLP, q-PCR, and DNA sequencing. AOA have been studied across different soil types and various ecosystems from the Antarctic dry valleys to the tropical forests of South America to the soils near Mount Everest. Different studies have identified multiple soil factors that trigger the abundance of AOA. These factors include pH, concentration of available ammonia, organic matter content, moisture content, nitrogen content, clay content, as well as other triggers. Land use management appears to have a major effect on the abundance of AOA in soil, which may be the result of nitrogen fertilizer used in agricultural soils. This review summarizes the published results on this topic and suggests future work that will increase our understanding of how soil management and edaphoclimatic factors influence AOA.

  5. Molecular and biogeochemical evidence for ammonia oxidation by marine Crenarchaeota in the Gulf of California.

    Science.gov (United States)

    Beman, J Michael; Popp, Brian N; Francis, Christopher A

    2008-04-01

    Nitrification plays an important role in marine biogeochemistry, yet efforts to link this process to the microorganisms that mediate it are surprisingly limited. In particular, ammonia oxidation is the first and rate-limiting step of nitrification, yet ammonia oxidation rates and the abundance of ammonia-oxidizing bacteria (AOB) have rarely been measured in tandem. Ammonia oxidation rates have not been directly quantified in conjunction with ammonia-oxidizing archaea (AOA), although mounting evidence indicates that marine Crenarchaeota are capable of ammonia oxidation, and they are among the most abundant microbial groups in the ocean. Here, we have directly quantified ammonia oxidation rates by 15N labeling, and AOA and AOB abundances by quantitative PCR analysis of ammonia monooxygenase subunit A (amoA) genes, in the Gulf of California. Based on markedly different archaeal amoA sequence types in the upper water column (60 m) and oxygen minimum zone (OMZ; 450 m), novel amoA PCR primers were designed to specifically target and quantify 'shallow' (group A) and 'deep' (group B) clades. These primers recovered extensive variability with depth. Within the OMZ, AOA were most abundant where nitrification may be coupled to denitrification. In the upper water column, group A tracked variations in nitrogen biogeochemistry with depth and between basins, whereas AOB were present in relatively low numbers or undetectable. Overall, 15NH4+ oxidation rates were remarkably well correlated with AOA group A amoA gene copies (r2=0.90, Pmarine Crenarchaeota (r2=0.85, Pnitrification.

  6. Immobilization of ammonia-oxidizing bacteria by polyvinyl alcohol and sodium alginate.

    Science.gov (United States)

    Dong, Yuwei; Zhang, Yanqiu; Tu, Baojun

    Ammonia-oxidizing bacteria were immobilized by polyvinyl alcohol (PVA) and sodium alginate. The immobilization conditions and ammonia oxidation ability of the immobilized bacteria were investigated. The following immobilization conditions were observed to be optimal: PVA, 12%; sodium alginate, 1.1%; calcium chloride, 1.0%; inoculum concentration, 1.3 immobilized balls/mL of immobilized medium; pH, 10; and temperature, 30°C. The immobilized ammonia-oxidizing bacteria exhibited strong ammonia oxidation ability even after being recycled four times. The ammonia nitrogen removal rate of the immobilized ammonia-oxidizing bacteria reached 90.30% under the optimal immobilization conditions. When compared with ammonia-oxidizing bacteria immobilized by sodium alginate alone, the bacteria immobilized by PVA and sodium alginate were superior with respect to pH resistance, the number of reuses, material cost, heat resistance, and ammonia oxidation ability. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  7. Biogeochemical controls and isotopic signatures of nitrous oxide production by a marine ammonia-oxidizing bacterium

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    C. H. Frame

    2010-09-01

    Full Text Available Nitrous oxide (N2O is a trace gas that contributes to the greenhouse effect and stratospheric ozone depletion. The N2O yield from nitrification (moles N2O-N produced per mole ammonium-N consumed has been used to estimate marine N2O production rates from measured nitrification rates and global estimates of oceanic export production. However, the N2O yield from nitrification is not constant. Previous culture-based measurements indicate that N2O yield increases as oxygen (O2 concentration decreases and as nitrite (NO2 concentration increases. Here, we have measured yields of N2O from cultures of the marine β-proteobacterium Nitrosomonas marina C-113a as they grew on low-ammonium (50 μM media. These yields, which were typically between 4 × 10−4 and 7 × 10−4 for cultures with cell densities between 2 × 102 and 2.1 × 104 cells ml−1, were lower than previous reports for ammonia-oxidizing bacteria. The observed impact of O2 concentration on yield was also smaller than previously reported under all conditions except at high starting cell densities (1.5 × 106 cells ml−1, where 160-fold higher yields were observed at 0.5% O2 (5.1 μM dissolved O2 compared with 20% O2 (203 μM dissolved O2. At lower cell densities (2 × 102 and 2.1 × 104 cells ml−1, cultures grown under 0.5% O2 had yields that were only 1.25- to 1.73-fold higher than cultures grown under 20% O2. Thus, previously reported many-fold increases in N2O yield with dropping O2 could be reproduced only at cell densities that far exceeded those of ammonia oxidizers in the ocean. The presence of excess NO2 (up to 1 mM in the growth

  8. Molecular diversity of the ammonia-oxidizing bacteria community in disused tin-mining ponds located within Kampar, Perak, Malaysia.

    Science.gov (United States)

    Sow, S L S; Khoo, G; Chong, L K; Smith, T J; Harrison, P L; Ong, H K A

    2014-02-01

    Disused tin-mining ponds make up a significant amount of water bodies in Malaysia particularly at the Kinta Valley in the state of Perak where tin-mining activities were the most extensive, and these abundantly available water sources are widely used in the field of aquaculture and agriculture. However, the natural ecology and physicochemical conditions of these ponds, many of which have been altered due to secondary post-mining activities, remains to be explored. As ammonia-oxidizing bacteria (AOB) are directly related to the nutrient cycles of aquatic environments and are useful bioindicators of environmental variations, the focus of this study was to identify AOBs associated with disused tin-mining ponds that have a history of different secondary activities in comparison to ponds which were left untouched and remained as part of the landscape. The 16S rDNA gene was used to detect AOBs in the sediment and water sampled from the three types of disused mining ponds, namely ponds without secondary activity, ponds that were used for lotus cultivation and post-aquaculture ponds. When the varying pond types were compared with the sequence and phylogenetic analysis of the AOB clone libraries, both Nitrosomonas and Nitrosospira-like AOB were detected though Nitrosospira spp. was seen to be the most ubiquitous AOB as it was present in all ponds types. However, AOBs were not detected in the sediments of idle ponds. Based on rarefaction analysis and diversity indices, the disused mining pond with lotus culture indicated the highest richness of AOBs. Canonical correspondence analysis indicated that among the physicochemical properties of the pond sites, TAN and nitrite were shown to be the main factors that influenced the community structure of AOBs in these disused tin-mining ponds.

  9. Biogeography of anaerobic ammonia-oxidizing (anammox bacteria

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    Puntipar eSonthiphand

    2014-08-01

    Full Text Available Anaerobic ammonia-oxidizing (anammox bacteria are able to oxidize ammonia and reduce nitrite to produce N2 gas. After being discovered in a wastewater treatment plant (WWTP, anammox bacteria were subsequently characterized in natural environments, including marine, estuary, freshwater, and terrestrial habitats. Anammox bacteria play an important role in removing fixed N from both engineered and natural ecosystems, but broad scale anammox bacterial distributions, based on available data, have not yet been summarized. The objectives of this study were to explore global distributions and diversity of anammox bacteria and to identify factors that influence their biogeography. Over 6,000 anammox 16S rRNA gene sequences from the public database were analyzed in this current study. Data ordinations indicated that salinity was an important factor governing anammox bacterial distributions, with distinct populations inhabiting natural and engineered ecosystems. Gene phylogenies and rarefaction analysis demonstrated that freshwater environments and the marine water column harbored the highest and the lowest diversity of anammox bacteria, respectively. A co-occurrence network analysis indicated that Ca. Scalindua strongly correlated with other Ca. Scalindua taxa, whereas Ca. Brocadia co-occurred with taxa from both known and unknown anammox genera. Our survey provides a better understanding of ecological factors affecting anammox bacterial distributions and provides a comprehensive baseline for understanding the relationships among anammox communities in global environments.

  10. Bacterial domination over Archaea in ammonia oxidation in a monsoon-driven tropical estuary

    Digital Repository Service at National Institute of Oceanography (India)

    Vipindas, P.V.; Anas, A.; Jasmin, C.; Lallu, K.R.; Fausia, K.H.; Balachandran, K.K.; Muraleedharan, K.R.; Nair, S.

    Autotrophic ammonia oxidizing microorganisms,which are responsible for the rate-limiting step of nitrification in most aquatic systems, have not been studied in tropical estuaries. Cochin estuary (CE) is one of the largest, productive, and monsoon...

  11. Cultivation and genomic analysis of Candidatus Nitrosocaldus islandicus, a novel obligately thermophilic ammonia-oxidizing Thaumarchaeon

    OpenAIRE

    De La Torre, Jose; Kirkegaard, Rasmus; Daebeler, Anne; Sedlacek, Christopher; Wagner, Michael; Daims, Holger; Pjevac, Petra; Albersten, Mads; Vierheilig, Julia; Herbold, Craig

    2017-01-01

    Ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaea are the only known aerobic ammonia oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from the Nitrosocaldus clade, group 1.1b and group 1.1a Thaumarchaea in terrestrial high-temperature habitats, only one enrichment culture of an AOA thriving above 50 C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a nov...

  12. Distribution of ammonia oxidizers in relation to vegetation characteristics in the Qilian Mountains, northwestern China

    Science.gov (United States)

    Tai, X. S.; Mao, W. L.; Liu, G. X.; Chen, T.; Zhang, W.; Wu, X. K.; Long, H. Z.; Zhang, B. G.; Gao, T. P.

    2014-04-01

    Nitrogen is the major limiting nutrient in cold environments, and its availability is strongly dependent on nitrification. However, microbial communities driving this process remain largely uncharacterized in alpine meadow soils in northwestern China, namely those catalyzing the rate-limiting step of ammonia oxidation. In this study, ammonia-oxidizing communities in alpine meadow soils were characterized by real-time PCR and clone sequencing by targeting on amoA genes, which putatively encode ammonia monooxygenase subunit A. The results demonstrated that ammonia-oxidizing archaea (AOA) outnumbered ammonia-oxidizing bacteria (AOB) in the alpine meadow soils. Most of the AOA phylotypes detected in the study region fell within typical Group I.1b of Thaumarchaeota. Interestingly, a new ammonia-oxidizing archaeal group named "Kobresia meadow soil group" was found. Phylogenetic analysis of AOB communities exhibited a dominance of Nitrosospira-like sequences affiliated to beta-Proteobacteria. Compared with other alpine environments, Qilian Mountains had a great phylogenetic diversity of ammonia oxidizers. Principal Component Analysis (PCA) analysis showed that distinct AOA/AOB phylotype groups were attributed to different meadow types, reflecting an overall distribution of ammonia-oxidizing communities associated with meadow types. Redundancy Analysis (RDA) analysis showed that Axis 1 (90.9%) together with Axis 2 (9.1%) explained all the variables while Axis 1 exhibited a significant explanatory power. So that vegetation coverage mostly correlated to Axis 1 was the most powerful environmental factor in the study region. Characteristics of ammonia-oxidizing communities showed a close association with vegetation coverage.

  13. Transcriptional Response of the Archaeal Ammonia Oxidizer Nitrosopumilus maritimus to Low and Environmentally Relevant Ammonia Concentrations

    OpenAIRE

    Nakagawa, Tatsunori; Stahl, David A.

    2013-01-01

    The ability of chemoautotrophic ammonia-oxidizing archaea to compete for ammonia among marine microorganisms at low ambient concentrations has been in part attributed to their extremely high affinity for ammonia, but as yet there is no mechanistic understanding of supporting metabolism. We examined transcription of selected genes for anabolic functions (CO2 fixation, ammonia transport, and cell wall synthesis) and a central catabolic function (ammonia oxidation) in the thaumarchaeon Nitrosopu...

  14. Community structure analysis of soil ammonia oxidizers during vegetation restoration in southwest China.

    Science.gov (United States)

    Liang, Yueming; He, Xunyang; Liang, Shichu; Zhang, Wei; Chen, Xiangbi; Feng, Shuzheng; Su, Yirong

    2014-03-01

    Soil ammonia oxidizers play a critical role in nitrogen cycling and ecological restoration. The composition and structure of soil ammonia oxidizers and their impacting factors were studied in four typical ecosystem soils, tussock (T), shrub (S), secondary forest (SF), and primary forest (PF), during vegetation restoration in the Karst region of Southwest China. The composition and structure of the ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities were characterized by sequencing the amoA and arch-amoA genes, respectively. The diversity of soil ammonia oxidizers (except in S) and plant Shannon diversity index gradually increased with vegetation restoration, and the ammonia oxidizer communities differed significantly (p soils. AOB Nitrosospira cluster 3b only appeared in PF and SF soils, while Nitrosospira cluster 3a species were found in all soils. Changes in AOB paralleled the changes in soil ammonium content that occurred with vegetation restoration. Redundancy analysis showed that the distribution of dominant AOB species was linked to pH, soil urease activity, and soil C/N ratio, whereas the distribution of dominant AOA species was mainly influenced by litter nitrogen content and C/N ratio. These results suggested that the composition and structure of the AOB community were more sensitive to changes in vegetation and soil ammonium content, and may be an important indicator of nitrogen availability in Karst ecosystem soils. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Emergent macrophytes modify the abundance and community composition of ammonia oxidizers in their rhizosphere sediments.

    Science.gov (United States)

    Zhao, Dayong; He, Xiaowei; Huang, Rui; Yan, Wenming; Yu, Zhongbo

    2017-07-01

    Ammonia oxidation is a crucial process in global nitrogen cycling, which is catalyzed by the ammonia oxidizers. Emergent plants play important roles in the freshwater ecosystem. Therefore, it is meaningful to investigate the effects of emergent macrophytes on the abundance and community composition of ammonia oxidizers. In the present study, two commonly found emergent macrophytes (Zizania caduciflora and Phragmitas communis) were obtained from freshwater lakes and the abundance and community composition of the ammonia-oxidizing prokaryotes in the rhizosphere sediments of these emergent macrophytes were investigated. The abundance of the bacterial amoA gene was higher in the rhizosphere sediments of the emergent macrophytes than those of bulk sediments. Significant positive correlation was found between the potential nitrification rates (PNRs) and the abundance of bacterial amoA gene, suggesting that ammonia-oxidizing bacteria (AOB) might play an important role in the nitrification process of the rhizosphere sediments of emergent macrophytes. The Nitrosotalea cluster is the dominant ammonia-oxidizing archaea (AOA) group in all the sediment samples. Analysis of AOB group showed that the N. europaeal cluster dominated the rhizosphere sediments of Z. caduciflora and the bulk sediments, whereas the Nitrosospira cluster was the dominant AOB group in the rhizosphere sediments of P. communis. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Archaea produce lower yields of N2 O than bacteria during aerobic ammonia oxidation in soil.

    Science.gov (United States)

    Hink, Linda; Nicol, Graeme W; Prosser, James I

    2017-12-01

    Nitrogen fertilisation of agricultural soil contributes significantly to emissions of the potent greenhouse gas nitrous oxide (N 2 O), which is generated during denitrification and, in oxic soils, mainly by ammonia oxidisers. Although laboratory cultures of ammonia oxidising bacteria (AOB) and archaea (AOA) produce N 2 O, their relative activities in soil are unknown. This work tested the hypothesis that AOB dominate ammonia oxidation and N 2 O production under conditions of high inorganic ammonia (NH 3 ) input, but result mainly from the activity of AOA when NH 3 is derived from mineralisation. 1-octyne, a recently discovered inhibitor of AOB, was used to distinguish N 2 O production resulting from archaeal and bacterial ammonia oxidation in soil microcosms, and specifically inhibited AOB growth, activity and N 2 O production. In unamended soils, ammonia oxidation and N 2 O production were lower and resulted mainly from ammonia oxidation by AOA. The AOA N 2 O yield relative to nitrite produced was half that of AOB, likely due to additional enzymatic mechanisms in the latter, but ammonia oxidation and N 2 O production were directly linked in all treatments. Relative contributions of AOA and AOB to N 2 O production, therefore, reflect their respective contributions to ammonia oxidation. These results suggest potential mitigation strategies for N 2 O emissions from fertilised agricultural soils. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

  17. Ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium in two US Great Basin hot springs with abundant ammonia-oxidizing archaea.

    Science.gov (United States)

    Dodsworth, Jeremy A; Hungate, Bruce A; Hedlund, Brian P

    2011-08-01

    Many thermophiles catalyse free energy-yielding redox reactions involving nitrogenous compounds; however, little is known about these processes in natural thermal environments. Rates of ammonia oxidation, denitrification and dissimilatory nitrate reduction to ammonium (DNRA) were measured in source water and sediments of two ≈ 80°C springs in the US Great Basin. Ammonia oxidation and denitrification occurred mainly in sediments. Ammonia oxidation rates measured using (15)N-NO(3)(-) pool dilution ranged from 5.5 ± 0.8 to 8.6 ± 0.9 nmol N g(-1) h(-1) and were unaffected or only mildly stimulated by amendment with NH(4) Cl. Denitrification rates measured using acetylene block ranged from 15.8 ± 0.7 to 51 ± 12 nmol N g(-1) h(-1) and were stimulated by amendment with NO(3)(-) and complex organic compounds. The DNRA rate in one spring sediment measured using an (15)N-NO(3)(-) tracer was 315 ± 48 nmol N g(-1) h(-1). Both springs harboured distinct planktonic and sediment microbial communities. Close relatives of the autotrophic, ammonia-oxidizing archaeon 'Candidatus Nitrosocaldus yellowstonii' represented the most abundant OTU in both spring sediments by 16S rRNA gene pyrotag analysis. Quantitative PCR (qPCR) indicated that 'Ca. N. yellowstonii'amoA and 16S rRNA genes were present at 3.5-3.9 × 10(8) and 6.4-9.0 × 10(8) copies g(-1) sediment. Potential denitrifiers included members of the Aquificales and Thermales. Thermus spp. comprised springs and suggest that ammonia oxidation may be a major source of energy fuelling primary production. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

  18. Nitrification and the ammonia-oxidizing communities in the central Baltic Sea water column

    Science.gov (United States)

    Jäntti, Helena; Ward, Bess B.; Dippner, Joachim W.; Hietanen, Susanna

    2018-03-01

    The redoxclines that form between the oxic and anoxic water layers in the central Baltic Sea are sites of intensive nitrogen cycling. To gain better understanding of nitrification, we measured the biogeochemical properties along with potential nitrification rates and analyzed the assemblages of ammonia-oxidizing bacteria and archaea using functional gene microarrays. To estimate nitrification in the entire water column, we constructed a regression model for the nitrification rates and applied it to the conditions prevailing in the area in 2008-2012. The highest ammonia oxidation rates were found in a thin layer at the top of the redoxcline and the rates quickly decreased below detection limit when oxygen was exhausted. This is probably because extensive suboxic layers, which are known to harbor pelagic nitrification, are formed only for short periods after inflows in the Baltic Sea. The nitrification rates were some of the highest measured in the water columns, but the thickness of the layer where conditions were favorable for nitrification, was very small and it remained fairly stable between years. However, the depth of the nitrification layer varied substantially between years, particularly in the eastern Gotland Basin (EGB) due to turbulence in the water column. The ammonia oxidizer communities clustered differently between the eastern and western Gotland Basin (WGB) and the composition of ammonia-oxidizing assemblages correlated with the environmental variables. The ammonia oxidizer community composition was more even in the EGB, which may be related to physical instability of the redoxcline that does not allow predominance of a single archetype, whereas in the WGB, where the position of the redoxcline is more constant, the ammonia-oxidizing community was less even. Overall the ammonia-oxidizing communities in the Baltic Sea redoxclines were very evenly distributed compared to other marine environments where microarrays have been applied previously.

  19. The influence of trace NO(2) on the kinetics of ammonia oxidation and the characteristics of nitrogen removal from wastewater.

    Science.gov (United States)

    Zhang, Daijun; Cai, Qing; Zu, Bo; Bai, Cui; Zhang, Ping

    2010-01-01

    Ammonia oxidizing bacteria-enriched sludge was obtained in a sequencing batch reactor with synthetic wastewater. Batch tests of ammonia oxidation were carried out with the sludge, in the presence of only trace NO(2) and in the presence of O(2) and trace NO(2), respectively. The Andrews model is used to describe NO(2)-dependent ammonia oxidation. The maximum ammonia oxidation rate of 139.11 mg N.(g sludge COD h)(-1), occurred in the presence of 21% O(2) and 100 ppm NO(2), which was 3 times higher than the aerobic ammonia oxidation rate without NO(2). The kinetic model of ammonia oxidation in the presence of O(2) and trace NO(2) is developed, and the function of NO(2) apparently enhancing ammonia oxidation is suggested. The maximal nitrogen removel of 34.19% occurred at the 21% O(2) and 100 ppm NO(2) in the mixed gases. Nitrogen removal principally depended on the denitrification activity and NO(2)-dependent ammonia oxidation activity of ammonia-oxidizing bacteria (AOB).

  20. Ammonia oxidizers in a pilot-scale multilayer rapid infiltration system for domestic wastewater treatment.

    Directory of Open Access Journals (Sweden)

    Yingli Lian

    Full Text Available A pilot-scale multilayer rapid infiltration system (MRIS for domestic wastewater treatment was established and efficient removal of ammonia and chemical oxygen demand (COD was achieved in this study. The microbial community composition and abundance of ammonia oxidizers were investigated. Efficient biofilms of ammonia oxidizers in the stationary phase (packing material was formed successfully in the MRIS without special inoculation. DGGE and phylogenetic analyses revealed that proteobacteria dominated in the MRIS. Relative abundance of ammonia-oxidizing archaea (AOA and ammonia-oxidizing bacteria (AOB showed contrary tendency. In the flowing phase (water effluent, AOA diversity was significantly correlated with the concentration of dissolve oxygen (DO, NO3-N and NH3-N. AOB abundance was significantly correlated with the concentration of DO and chemical oxygen demand (COD. NH3-N and COD were identified as the key factors to shape AOB community structure, while no variable significantly correlated with that of AOA. AOA might play an important role in the MRIS. This study could reveal key environmental factors affecting the community composition and abundance of ammonia oxidizers in the MRIS.

  1. Transcriptional Response of the Archaeal Ammonia Oxidizer Nitrosopumilus maritimus to Low and Environmentally Relevant Ammonia Concentrations

    Science.gov (United States)

    Stahl, David A.

    2013-01-01

    The ability of chemoautotrophic ammonia-oxidizing archaea to compete for ammonia among marine microorganisms at low ambient concentrations has been in part attributed to their extremely high affinity for ammonia, but as yet there is no mechanistic understanding of supporting metabolism. We examined transcription of selected genes for anabolic functions (CO2 fixation, ammonia transport, and cell wall synthesis) and a central catabolic function (ammonia oxidation) in the thaumarchaeon Nitrosopumilus maritimus SCM1 growing at two ammonia concentrations, as measured by combined ammonia and ammonium, one well above the Km for ammonia oxidation (∼500 μM) and the other well below the Km (ammonia-replete to ammonia-limiting conditions. Transcript levels for ammonia oxidation, CO2 fixation, and one of the ammonia transport genes were approximately the same at high and low ammonia availability. Transcripts for all analyzed genes decreased with time in the complete absence of ammonia, but with various rates of decay. The new steady-state mRNA levels established are presumably more reflective of the natural physiological state of ammonia-oxidizing archaea and offer a reference for interpreting message abundance patterns in the natural environment. PMID:23995944

  2. Fauna Europaea - Orthopteroid orders.

    Science.gov (United States)

    Heller, Klaus-Gerhard; Bohn, Horst; Haas, Fabian; Willemse, Fer; de Jong, Yde

    2016-01-01

    Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all extant European terrestrial and freshwater animals, their geographical distribution at the level of countries and major islands (west of the Urals and excluding the Caucasus region), and some additional information. The Fauna Europaea project comprises about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. Fauna Europaea represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. The "Orthopteroid orders" is one of the 58 Fauna Europaea major taxonomic groups. It contains series of mostly well-known insect orders: Embiodea (webspinners), Dermaptera (earwigs), Phasmatodea (walking sticks), Orthoptera s.s. (grasshoppers, crickets, bush-crickets) and Dictyoptera with the suborders Mantodea (mantids), Blattaria (cockroaches) and Isoptera (termites). For the Orthopteroid orders, data from 35 families containing 1,371 species are included in this paper.

  3. Fauna Europaea: Mollusca - Bivalvia

    NARCIS (Netherlands)

    Araujo, R.; de Jong, Y.

    2015-01-01

    Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The

  4. Fauna Europaea - Orthopteroid orders

    NARCIS (Netherlands)

    Heller, K.-G.; Bohn, H.; Haas, F.; Willemse, F.; de Jong, Y.

    2016-01-01

    Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all extant European terrestrial and freshwater animals, their geographical distribution at the level of countries and major islands (west of the Urals and excluding the Caucasus region),

  5. Moisture and temperature controls on nitrification differ among ammonia oxidizer communities from three alpine soil habitats

    Science.gov (United States)

    Osborne, Brooke B.; Baron, Jill S.; Wallenstein, Matthew D.

    2016-01-01

    Climate change is altering the timing and magnitude of biogeochemical fluxes in many high elevation ecosystems. The consequent changes in alpine nitrification rates have the potential to influence ecosystem scale responses. In order to better understand how changing temperature and moisture conditions may influence ammonia oxidizers and nitrification activity, we conducted laboratory incubations on soils collected in a Colorado watershed from three alpine habitats (glacial outwash, talus, and meadow). We found that bacteria, not archaea, dominated all ammonia oxidizer communities. Nitrification increased with moisture in all soils and under all temperature treatments. However, temperature was not correlated with nitrification rates in all soils. Site-specific temperature trends suggest the development of generalist ammonia oxidizer communities in soils with greater in situ temperature fluctuations and specialists in soils with more steady temperature regimes. Rapidly increasing temperatures and changing soil moisture conditions could explain recent observations of increased nitrate production in some alpine soils.

  6. Nitrification of archaeal ammonia oxidizers in a high- temperature hot spring

    Science.gov (United States)

    Chen, Shun; Peng, Xiaotong; Xu, Hengchao; Ta, Kaiwen

    2016-04-01

    The oxidation of ammonia by microbes has been shown to occur in diverse natural environments. However, the link of in situ nitrification activity to taxonomic identities of ammonia oxidizers in high-temperature environments remains poorly understood. Here, we studied in situ ammonia oxidation rates and the diversity of ammonia-oxidizing Archaea (AOA) in surface and bottom sediments at 77 °C in the Gongxiaoshe hot spring, Tengchong, Yunnan, China. The in situ ammonia oxidation rates measured by the 15N-NO3- pool dilution technique in the surface and bottom sediments were 4.80 and 5.30 nmol N g-1 h-1, respectively. Real-time quantitative polymerase chain reaction (qPCR) indicated that the archaeal 16S rRNA genes and amoA genes were present in the range of 0.128 to 1.96 × 108 and 2.75 to 9.80 × 105 gene copies g-1 sediment, respectively, while bacterial amoA was not detected. Phylogenetic analysis of 16S rRNA genes showed high sequence similarity to thermophilic Candidatus Nitrosocaldus yellowstonii, which represented the most abundant operational taxonomic units (OTU) in both surface and bottom sediments. The archaeal predominance was further supported by fluorescence in situ hybridization (FISH) visualization. The cell-specific rate of ammonia oxidation was estimated to range from 0.410 to 0.790 fmol N archaeal cell-1 h-1, higher than those in the two US Great Basin hot springs. These results suggest the importance of archaeal rather than bacterial ammonia oxidation in driving the nitrogen cycle in terrestrial geothermal environments.

  7. Effect of potential electron acceptors on anoxic ammonia oxidation in the presence of organic carbon

    Energy Technology Data Exchange (ETDEWEB)

    Sabumon, P.C., E-mail: pcsabumon@yahoo.co.in [Environmental Engineering Division, School of Mechanical and Building Sciences, VIT University, Vellore 632 014 (India)

    2009-12-15

    A novel route of anoxic ammonia removal in the presence of organic carbon was identified recently from ecosystems contaminated with ammonia. Sequencing batch reactor (SBR) studies were carried out in anoxic condition at oxidation-reduction potential varied from -185 to -275 mV for anoxic ammonia oxidation with adapted biomass (mixed culture). SBR studies were carried out in absence and in the presence of externally added organic carbon and/or in the presence of inorganic electron acceptors like NO{sub 2}{sup -}, NO{sub 3}{sup -} and SO{sub 4}{sup 2-}. The results showed anoxic ammonia oxidation to nitrate (in contrast to reported anammox process) in the presence of organic carbon available through endogenous respiration whereas anoxic ammonia oxidation was effective in the presence of externally added organic compound for nitrogen removal. The presence of externally added inorganic electron acceptors like NO{sub 2}{sup -}, NO{sub 3}{sup -} and SO{sub 4}{sup 2-} was effective in anoxic ammonia oxidation, but failed to follow the reported anammox reaction's stoichiometry in nitrogen removal in the presence of organic carbon. However, the presence of NO{sub 2}{sup -} affected best in total nitrogen removal compared to other electron acceptors and maximum ammonia removal rate was 100 mg NH{sub 4}{sup +}/g MLVSS/d. Based on the results, it is possible to suggest that rate of anoxic ammonia oxidation depends up on the respiration activities of mixed culture involving organic carbon, NO{sub 2}{sup -}, NO{sub 3}{sup -} and SO{sub 4}{sup 2-}. The process shows possibilities of new pathways of ammonia oxidation in organic contaminated sediments and/or wastewater in anoxic conditions.

  8. Benthic Ammonia Oxidizers Differ in Community Structure and Biogeochemical Potential Across a Riverine Delta

    Directory of Open Access Journals (Sweden)

    Julian eDamashek

    2015-01-01

    Full Text Available Nitrogen pollution in coastal zones is a widespread issue, particularly in ecosystems with urban or agricultural watersheds. California’s Sacramento-San Joaquin Delta, at the landward reaches of San Francisco Bay, is highly impacted by both agricultural runoff and sewage effluent, leading to chronically high nutrient loadings. In particular, the massive discharge of ammonium into the Sacramento River has altered this ecosystem by increasing ammonium concentrations and thus changing the stoichiometry of inorganic nitrogen stocks, with potential effects throughout the food web. To date, however, there has been little research examining N biogeochemistry or N-cycling microbial communities in this system. We report the first data on benthic ammonia-oxidizing microbial communities and potential nitrification rates for the Sacramento-San Joaquin Delta, focusing on the functional gene amoA (encoding the α-subunit of ammonia monooxygenase. There were stark regional differences in ammonia-oxidizing communities, with ammonia-oxidizing bacteria (AOB outnumbering ammonia-oxidizing archaea (AOA only in the ammonium-rich Sacramento River. High potential nitrification rates in the Sacramento River suggested these communities may be capable of oxidizing significant amounts of ammonium, compared to the San Joaquin River and the upper reaches of San Francisco Bay. Gene diversity also showed regional patterns, as well as phylogenetically unique ammonia oxidizers in the Sacramento River. The community structure and biogeochemical function of benthic ammonia oxidizers appears related to nutrient loadings. Unraveling the microbial ecology and biogeochemistry of N cycling pathways is a critical step toward understanding how such ecosystems respond to the changing environmental conditions wrought by human development and climate change.

  9. Quantification of ammonia oxidation rates and the distribution of ammonia-oxidizing Archaea and Bacteria in marine sediment depth profiles from Catalina Island, California

    Directory of Open Access Journals (Sweden)

    J. Michael eBeman

    2012-07-01

    Full Text Available Microbial communities present in marine sediments play a central role in nitrogen biogeochemistry at local to global scales. Along the oxidation-reduction gradients present in sediment profiles, multiple nitrogen cycling processes (such as nitrification, denitrification, nitrogen fixation, and anaerobic ammonium oxidation are active and actively coupled to one another—yet the microbial communities responsible for these transformations and the rates at which they occur are still poorly understood. We report pore water geochemical (O2, NH4+, NO3- profiles, quantitative profiles of archaeal and bacterial amoA genes, and ammonia oxidation rate measurements, from bioturbated marine sediments of Catalina Island, California. Across triplicate sediment cores collected offshore at Bird Rock and within Catalina Harbor, oxygen penetration (0.24-0.5 cm depth and the abundance of amoA genes (up to 9.30 x 107 genes g-1 varied with depth and between cores. Bacterial amoA genes were consistently present at depths of up to 10 cm, and archaeal amoA was readily detected in Bird Rock cores, and Catalina Harbor cores from 2008, but not 2007. Although detection of DNA is not necessarily indicative of active growth and metabolism, ammonia oxidation rate measurements made in 2008 (using isotope tracer demonstrated the production of oxidized nitrogen at depths where amoA was present. Rates varied with depth and between cores, but indicate that active ammonia oxidation occurs at up to 10 cm depth in bioturbated Catalina Harbor sediments, where it may be carried out by either or both ammonia-oxidizing Archaea and Bacteria.

  10. Quantification of ammonia oxidation rates and the distribution of ammonia-oxidizing Archaea and Bacteria in marine sediment depth profiles from Catalina Island, California.

    Science.gov (United States)

    Beman, J M; Bertics, Victoria J; Braunschweiler, Thomas; Wilson, Jesse M

    2012-01-01

    Microbial communities present in marine sediments play a central role in nitrogen biogeochemistry at local to global scales. Along the oxidation-reduction gradients present in sediment profiles, multiple nitrogen cycling processes (such as nitrification, denitrification, nitrogen fixation, and anaerobic ammonium oxidation) are active and actively coupled to one another - yet the microbial communities responsible for these transformations and the rates at which they occur are still poorly understood. We report pore water geochemical (O(2), [Formula: see text], and [Formula: see text]) profiles, quantitative profiles of archaeal and bacterial amoA genes, and ammonia oxidation rate measurements, from bioturbated marine sediments of Catalina Island, California. Across triplicate sediment cores collected offshore at Bird Rock (BR) and within Catalina Harbor (CH), oxygen penetration (0.24-0.5 cm depth) and the abundance of amoA genes (up to 9.30 × 10(7) genes g(-) (1)) varied with depth and between cores. Bacterial amoA genes were consistently present at depths of up to 10 cm, and archaeal amoA was readily detected in BR cores, and CH cores from 2008, but not 2007. Although detection of DNA is not necessarily indicative of active growth and metabolism, ammonia oxidation rate measurements made in 2008 (using isotope tracer) demonstrated the production of oxidized nitrogen at depths where amoA was present. Rates varied with depth and between cores, but indicate that active ammonia oxidation occurs at up to 10 cm depth in bioturbated CH sediments, where it may be carried out by either or both ammonia-oxidizing archaea and bacteria.

  11. The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments

    NARCIS (Netherlands)

    Reis, Mariana De Paula; Ávila, Marcelo; Keijzer, Rosalinde Margriet; Barbosa, Francisco Antônio Rodrigues; Chartone-Souza, Edmar; Nascimento, Andréa; Laanbroek, (Riks) H.J.

    2015-01-01

    BACKGROUND: Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are a diverse and functionally important group in the nitrogen cycle. Nevertheless, AOA and AOB communities driving this process remain uncharacterized in tropical freshwater sediment. Here, the effect of human

  12. Nitrogen cycling and community structure of proteobacterial ß-subgroup ammonia-oxidizing bacteria within polluted marine fish farm sediments

    NARCIS (Netherlands)

    McCaig, A.E.; Phillips, C.B.; Stephen, J.R.; Kowalchuk, G.A.; Harvey, S.M.; Herbert, R.A.; Embley, T.M.; Prosser, J.I.

    1999-01-01

    A multidisciplinary approach was used to study the effects of pollution from a marine fish farm on nitrification rates and on the community structure of ammonia-oxidizing bacteria in the underlying sediment. Organic content, ammonium concentrations, nitrification rates, and ammonia oxidizer

  13. A hydrophobic ammonia-oxidizing archaeon of the Nitrosocosmicus clade isolated from coal tar-contaminated sediment

    NARCIS (Netherlands)

    Jung, Man-Young; Kim, Jong-Geol; Sinninghe Damsté, Jaap S; Rijpstra, W Irene C; Madsen, Eugene L; Kim, So-Jeong; Hong, Heeji; Si, Ok-Ja; Kerou, Melina; Schleper, Christa; Rhee, Sung-Keun

    2016-01-01

    A wide diversity of ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota exists and plays a key role in the N cycle in a variety of habitats. In this study, we isolated and characterized an ammonia-oxidizing archaeon, strain MY3, from a coal tar-contaminated sediment. Phylogenetically,

  14. Co-Mn-Al Mixed Oxides as Catalysts for Ammonia Oxidation to N2O.

    Czech Academy of Sciences Publication Activity Database

    Ludvíková, Jana; Jablońska, M.; Jirátová, Květa; Chmielarz, L.; Balabánová, Jana; Kovanda, F.; Obalová, L.

    2016-01-01

    Roč. 42, č. 3 (2016), s. 2669-2690 ISSN 0922-6168 R&D Projects: GA ČR GA14-13750S Institutional support: RVO:67985858 Keywords : Co-Mn-Al mixed oxides * catalytic ammonia oxidation * N2O production * mechanochemical production Subject RIV: CI - Industrial Chemistry, Chemical Engineering Impact factor: 1.369, year: 2016

  15. Changes in the community structure of ammonia-oxidizing bacteria during secondary succession of calcareous grasslands

    NARCIS (Netherlands)

    Kowalchuk, G.A.; Stienstra, A.W.; Heilig, G.H.J.; Stephen, J.R.; Woldendorp, J.W.

    2000-01-01

    The community structure of beta-subclass Proteobacteria ammonia-oxidizing bacteria was determined in semi-natural chalk grassland soils at different stages of secondary succession. Both culture-mediated (most probable number; MPN) and direct nucleic acid-based approaches targeting genes encoding 16S

  16. Continuous culture enrichments of ammonia-oxidizing bacteria at low ammonium concentrations

    NARCIS (Netherlands)

    Bollmann, A.; Laanbroek, H.J.

    2001-01-01

    Until now enrichments of ammonia-oxidizing bacteria from natural ammonium-limited environments have been performed mainly in the presence of much higher ammonia concentrations than those present in the natural environment and many have resulted in the enrichment and isolation of environmentally less

  17. Hydrogen peroxide detoxification is a key mechanism for growth of ammonia-oxidizing archaea

    NARCIS (Netherlands)

    Kim, Jong-Geol; Park, Soo-Je; Sinninghe Damsté, Jaap S.|info:eu-repo/dai/nl/07401370X; Schouten, Stefan|info:eu-repo/dai/nl/137124929; Rijpstra, W. Irene C.; Jung, Man-Young; Kim, So-Jeong; Gwak, Joo-Han; Hong, Heeji; Si, Ok-Ja; Lee, Sanghoon; Madsen, Eugene L.; Rhee, Sung-Keun

    2016-01-01

    Ammonia-oxidizing archaea (AOA), that is, members of the Thaumarchaeota phylum, occur ubiquitously in the environment and are of major significance for global nitrogen cycling. However, controls on cell growth and organic carbon assimilation by AOA are poorly understood. We isolated an

  18. Ammonia oxidizer populations vary with nitrogen cycling across a tropical montane mean annual temperature gradient

    Science.gov (United States)

    S. Pierre; I. Hewson; J. P. Sparks; C. M. Litton; C. Giardina; P. M. Groffman; T. J. Fahey

    2017-01-01

    Functional gene approaches have been used to better understand the roles of microbes in driving forest soil nitrogen (N) cycling rates and bioavailability. Ammonia oxidation is a rate limiting step in nitrification, and is a key area for understanding environmental constraints on N availability in forests. We studied how increasing temperature affects the role of...

  19. The distribution of ammonia-oxidizing betaproteobacteria in stands of Black mangroves (Avicennia germinans)

    NARCIS (Netherlands)

    Laanbroek, H.J.; Keijzer, R.M.; Verhoeven, J.T.A.; Whigham, D.F.

    2012-01-01

    The distribution of species of aerobic chemolitho-autotrophic microorganisms such as ammonia-oxidizing bacteria are governed by pH, salinity, and temperature as well as the availability of oxygen, ammonium, carbon dioxide, and other inorganic elements required for growth. Impounded mangrove forests

  20. Temporal and spatial stability of ammonia-oxidizing archaea and bacteria in aquarium biofilters.

    Directory of Open Access Journals (Sweden)

    Samik Bagchi

    Full Text Available Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA, as opposed to ammonia-oxidizing bacteria (AOB, were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4-5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥ 81-86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR for bacterial and thaumarchaeal ammonia monooxygenase (amoA genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS based on denaturing gradient gel electrophoresis (DGGE fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater

  1. Temporal and Spatial Stability of Ammonia-Oxidizing Archaea and Bacteria in Aquarium Biofilters

    KAUST Repository

    Bagchi, Samik

    2014-12-05

    Nitrifying biofilters are used in aquaria and aquaculture systems to prevent accumulation of ammonia by promoting rapid conversion to nitrate via nitrite. Ammonia-oxidizing archaea (AOA), as opposed to ammonia-oxidizing bacteria (AOB), were recently identified as the dominant ammonia oxidizers in most freshwater aquaria. This study investigated biofilms from fixed-bed aquarium biofilters to assess the temporal and spatial dynamics of AOA and AOB abundance and diversity. Over a period of four months, ammonia-oxidizing microorganisms from six freshwater and one marine aquarium were investigated at 4–5 time points. Nitrogen balances for three freshwater aquaria showed that active nitrification by aquarium biofilters accounted for ≥81–86% of total nitrogen conversion in the aquaria. Quantitative PCR (qPCR) for bacterial and thaumarchaeal ammonia monooxygenase (amoA) genes demonstrated that AOA were numerically dominant over AOB in all six freshwater aquaria tested, and contributed all detectable amoA genes in three aquarium biofilters. In the marine aquarium, however, AOB outnumbered AOA by three to five orders of magnitude based on amoA gene abundances. A comparison of AOA abundance in three carrier materials (fine sponge, rough sponge and sintered glass or ceramic rings) of two three-media freshwater biofilters revealed preferential growth of AOA on fine sponge. Denaturing gel gradient electrophoresis (DGGE) of thaumarchaeal 16S rRNA genes indicated that community composition within a given biofilter was stable across media types. In addition, DGGE of all aquarium biofilters revealed low AOA diversity, with few bands, which were stable over time. Nonmetric multidimensional scaling (NMDS) based on denaturing gradient gel electrophoresis (DGGE) fingerprints of thaumarchaeal 16S rRNA genes placed freshwater and marine aquaria communities in separate clusters. These results indicate that AOA are the dominant ammonia-oxidizing microorganisms in freshwater aquarium

  2. Ammonia-Oxidizing Archaea Show More Distinct Biogeographic Distribution Patterns than Ammonia-Oxidizing Bacteria across the Black Soil Zone of Northeast China

    Directory of Open Access Journals (Sweden)

    Junjie Liu

    2018-02-01

    Full Text Available Black soils (Mollisols of northeast China are highly productive and agriculturally important for food production. Ammonia-oxidizing microbes play an important role in N cycling in the black soils. However, the information related to the composition and distribution of ammonia-oxidizing microbes in the black soils has not yet been addressed. In this study, we used the amoA gene to quantify the abundance and community composition of ammonia-oxidizing archaea (AOA and ammonia-oxidizing bacteria (AOB across the black soil zone. The amoA abundance of AOA was remarkably larger than that of AOB, with ratios of AOA/AOB in the range from 3.1 to 91.0 across all soil samples. The abundance of AOA amoA was positively correlated with total soil C content (p < 0.001 but not with soil pH (p > 0.05. In contrast, the abundance of AOB amoA positively correlated with soil pH (p = 0.009 but not with total soil C. Alpha diversity of AOA did not correlate with any soil parameter, however, alpha diversity of AOB was affected by multiple soil factors, such as soil pH, total P, N, and C, available K content, and soil water content. Canonical correspondence analysis indicated that the AOA community was mainly affected by the sampling latitude, followed by soil pH, total P and C; while the AOB community was mainly determined by soil pH, as well as total P, C and N, water content, and sampling latitude, which highlighted that the AOA community was more geographically distributed in the black soil zone of northeast China than AOB community. In addition, the pairwise analyses showed that the potential nitrification rate (PNR was not correlated with alpha diversity but weakly positively with the abundance of the AOA community (p = 0.048, whereas PNR significantly correlated positively with the richness (p = 0.003, diversity (p = 0.001 and abundance (p < 0.001 of the AOB community, which suggested that AOB community might make a greater contribution to nitrification than AOA

  3. Fauna Europaea: Helminths (Animal Parasitic)

    Czech Academy of Sciences Publication Activity Database

    Gibson, D. I.; Bray, R. A.; Hunt, D.; Georgiev, B. B.; Scholz, Tomáš; Harris, P.D.; Bakke, T.A.; Pomajska, T.; Niewiadomska, K.; Kostadinova, Aneta; Tkach, V.; Bain, O.; Durette-Desset, M.-C.; Gibbons, L.; Moravec, František; Petter, A.; Dimitrova, Z.M.; Buchmann, K.; Valtonen, E. T.; de Jong, Y.

    -, č. 2 (2014), e1060 ISSN 1314-2828 Institutional support: RVO:60077344 Keywords : Acanthocephala * Biodiversity * Biodiversity Informatics * Cestoda * Fauna Europaea * Helminth * Monogenea * Nematoda * Parasite * Taxonomic indexing * Taxonomy * Trematoda * Zoology Subject RIV: EB - Genetics ; Molecular Biology

  4. Bacteria dominate ammonia oxidation in soils used for outdoor cattle overwintering

    Czech Academy of Sciences Publication Activity Database

    Radl, V.; Chroňáková, Alica; Čuhel, Jiří; Šimek, Miloslav; Elhottová, Dana; Welzl, G.; Schloter, M.

    2014-01-01

    Roč. 77, May (2014), s. 68-71 ISSN 0929-1393 R&D Projects: GA MŠk LC06066 Grant - others:Akademie věd ČR(CZ) D-CZ 45:05/06 Institutional support: RVO:60077344 Keywords : ammonia oxidation * bacteria * archaea * amoA diversity * urea * pasture Subject RIV: EH - Ecology, Behaviour Impact factor: 2.644, year: 2014

  5. Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome

    OpenAIRE

    Abby, Sophie S.; Melcher, Michael; Kerou, Melina; Krupovic, Mart; Stieglmeier, Michaela; Rossel, Claudia; Pfeifer, Kevin; Schleper, Christa

    2018-01-01

    Ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first enrichment of a thermophilic representative with a sequenced genome, which facilitates the search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota. Candidatus Nitrosocaldus cavascurensis has been enriched from a hot spring in Ischia, Italy. It grows optimally ...

  6. Kinetics of ammonia oxidation over Pt foil studied in a micro-structured quartz-reactor

    OpenAIRE

    Kraehnert, Ralf; Baerns, Manfred

    2008-01-01

    The kinetics of Pt-catalyzed ammonia oxidation on polycrystalline Pt were investigated at partial pressures of ammonia and oxygen up to 6 kPa and temperatures between 286 and 385 °C, applying a micro-structured reactor that ascertained temperature control of the exothermic reaction. Using literature-based mechanistic models, a micro-kinetic model was derived based on parameter optimization and a model discrimination procedure. The model described the rates of formation of all nitrogen-contain...

  7. Effects of drought on nitrogen turnover and abundances of ammonia-oxidizers in mountain grassland

    Science.gov (United States)

    Fuchslueger, L.; Kastl, E.-M.; Bauer, F.; Kienzl, S.; Hasibeder, R.; Ladreiter-Knauss, T.; Schmitt, M.; Bahn, M.; Schloter, M.; Richter, A.; Szukics, U.

    2014-11-01

    Future climate scenarios suggest an increased frequency of summer drought periods in the European Alpine Region. Drought can affect soil nitrogen (N) cycling, by altering N transformation rates, as well as the abundances of ammonia-oxidizing bacteria and archaea. However, the extent to which drought affects N cycling under in situ conditions is still controversial. The goal of this study was to analyse effects of drought on soil N turnover and ammonia-oxidizer abundances in soil without drought history. To this end we conducted rain-exclusion experiments at two differently managed mountain grassland sites, an annually mown and occasionally fertilized meadow and an abandoned grassland. Soils were sampled before, during and after drought and were analysed for potential gross rates of N mineralization, microbial uptake of inorganic N, nitrification, and the abundances of bacterial and archaeal ammonia-oxidizers based on gene copy numbers of the amoA gene (AOB and AOA, respectively). Drought induced different responses at the two studied sites. At the managed meadow drought increased NH4+ immobilization rates and NH4+ concentrations in the soil water solution, but led to a reduction of AOA abundance compared to controls. At the abandoned site gross nitrification and NO3- immobilization rates decreased during drought, while AOB and AOA abundances remained stable. Rewetting had only minor, short-term effects on the parameters that had been affected by drought. Seven weeks after the end of drought no differences to control plots could be detected. Thus, our findings demonstrated that in mountain grasslands drought had distinct transient effects on soil nitrogen cycling and ammonia-oxidizers, which could have been related to a niche differentiation of AOB and AOA with increasing NH4+ levels. However, the effect strength of drought was modulated by grassland management.

  8. Emergent Macrophytes Act Selectively on Ammonia-Oxidizing Bacteria and Archaea

    OpenAIRE

    Trias, Rosalia; Ruiz-Rueda, Olaya; García-Lledó, Arantzazu; Vilar-Sanz, Ariadna; López-Flores, Rocío; Quintana, Xavier D.; Hallin, Sara; Bañeras, Lluís

    2012-01-01

    Ammonia-oxidizing bacteria (AOB) and archaea (AOA) were quantified in the sediments and roots of dominant macrophytes in eight neutral to alkaline coastal wetlands. The AOA dominated in most samples, but the bacterial-to-archaeal amoA gene ratios increased with increasing ammonium levels and pH in the sediments. For all plant species, the ratios increased on the root surface relative to the adjacent bulk sediment. This suggests that root surfaces in these environments provide conditions favor...

  9. Diversity and abundance of ammonia oxidizing archaea in tropical compost systems

    OpenAIRE

    de Gannes, Vidya; Eudoxie, Gaius; Dyer, David H.; Hickey, William J.

    2012-01-01

    Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the p...

  10. Influence of tropical leaf litter on nitrogen mineralization and community structure of ammonia-oxidizing bacteria

    OpenAIRE

    Diallo, M. D.; Guisse, A.; Sall, S. N.; Dick, R. P.; Assigbetsé, Komi; Dieng, A. L.; Chotte, Jean-Luc

    2015-01-01

    Description of the subject. The present study concerns the relationships among leaf litter decomposition, substrate quality, ammonia-oxidizing bacteria (AOB) community composition and nitrogen (N) availability. Decomposition of organic matter affects the biogeochemical cycling of carbon (C) and N. Since the composition of the soil microbial community can alter the physiological capacity of the community, it is timely to study the litter quality effect on N dynamic in ecosystems. Objectives. T...

  11. Effect of communities of ammonia-oxidizing bacteria on degradation of 17-alpha-ethynylestradiol by nitrifying activated sludge

    Energy Technology Data Exchange (ETDEWEB)

    Limpiyakorn, T.; Sermwaraphan, P.; Kurisu, F.

    2009-07-01

    An endocrine disrupting compound, 17-alpha-ethynylestradiol (EE2), is a synthetic estrogen used as a key ingredient in oral contraceptives pill. this persistent organic pollutant, no biodegradable by most microorganisms, is discharged via municipal waste streams to natural receiving waters. Recently, it was found that ammonia-oxidizing bacteria (AOB) in nitrifying activated sludge (NAS) enriched with high ammonium loads can degrade EE2 via co-metabolism during ammonia oxidation. (Author)

  12. pH rather than nitrification and urease inhibitors determines the community of ammonia oxidizers in a vegetable soil.

    Science.gov (United States)

    Xi, Ruijiao; Long, Xi-En; Huang, Sha; Yao, Huaiying

    2017-12-01

    Nitrification inhibitors and urease inhibitors, such as nitrapyrin and N-(n-butyl) thiophosphoric triamide (NBPT), can improve the efficiencies of nitrogen fertilizers in cropland. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) across different soil pH levels are still unclear. In the present work, vegetable soils at four pH levels were tested to determine the impacts of nitrification and urease inhibitors on the nitrification activities, abundances and diversities of ammonia oxidizers at different pHs by real-time PCR, terminal restriction fragment length polymorphism (T-RFLP) and clone sequence analysis. The analyses of the abundance of ammonia oxidizers and net nitrification rate suggested that AOA was the dominate ammonia oxidizer and the key driver of nitrification in acidic soil. The relationships between pH and ammonia oxidizer abundance indicated that soil pH dominantly controlled the abundance of AOA but not that of AOB. The T-RFLP results suggested that soil pH could significantly affect the AOA and AOB community structure. Nitrapyrin decreased the net nitrification rate and inhibited the abundance of bacterial amoA genes in this vegetable soil, but exhibited no effect on that of the archaeal amoA genes. In contrast, NBPT just lagged the hydrolysis of urea and kept low NH 4 + -N levels in the soil at the early stage. It exhibited no or slight effects on the abundance and community structure of ammonia oxidizers. These results indicated that soil pH, rather than the application of urea, nitrapyrin and NBPT, was a critical factor influencing the abundance and community structure of AOA and AOB.

  13. Response of ammonia oxidizing archaea and bacteria to decabromodiphenyl ether and copper contamination in river sediments.

    Science.gov (United States)

    Wang, Linqiong; Li, Yi; Niu, Lihua; Zhang, Wenlong; Zhang, Huanjun; Wang, Longfei; Wang, Peifang

    2018-01-01

    Ammonia oxidation plays a fundamental role in river nitrogen cycling ecosystems, which is normally governed by both ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB). Co-contamination of typical emerging pollutant Polybrominated diphenyl ethers (PBDEs) and heavy metal on AOA and AOB communities in river sediments remains unknown. In this study, multiple analytical tools, including high-throughput pyrosequencing and real-time quantitative PCR (qPCR), were used to reveal the ammonia monooxygenase (AMO) activity, subunit alpha (amoA) gene abundance, and community structures of AOA and AOB in river sediments. It was found that the inhibition of AMO activities was increased with the increase of decabromodiphenyl ether (BDE 209, 1-100 mg kg -1 ) and copper (Cu, 50-500 mg kg -1 ) concentrations. Moreover, the synergic effects of BDE 209 and Cu resulted in a higher AMO activity reduction than the individual pollutant BDE 209. The AOA amoA copy number declined by 75.9% and 83.2% and AOB amoA gene abundance declined 82.8% and 90.0% at 20 and 100 mg kg -1 BDE 209 with a 100 mg kg -1 Cu co-contamination, respectively. The pyrosequencing results showed that both AOB and AOA community structures were altered, with a higher change of AOB than that of AOA. The results demonstrated that the AOB microbial community may be better adapted to BDE 209 and Cu pollution, while AOA might possess a greater capacity for stress resistance. Our study provides a better understanding of the ecotoxicological effects of heavy metal and micropollutant combined exposure on AOA and AOB in river sediments. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Geographic Distribution of Ammonia-Oxidizing Archaea along the Kuril Islands in the Western Subarctic Pacific

    Directory of Open Access Journals (Sweden)

    Hongmei Jing

    2017-06-01

    Full Text Available Community composition and abundance of ammonia-oxidizing archaea (AOA in the ocean were affected by different physicochemical conditions, but their responses to physical barriers (such as a chain of islands were largely unknown. In our study, geographic distribution of the AOA from the surface photic zone to the deep bathypelagic waters in the western subarctic Pacific adjacent to the Kuril Islands was investigated using pyrosequencing based on the ammonia monooxygenase subunit A (amoA gene. Genotypes of clusters A and B dominated in the upper euphotic zone and the deep waters, respectively. Quantitative PCR assays revealed that the occurrence and ammonia-oxidizing activity of ammonia-oxidizing archaea (AOA reached their maxima at the depth of 200 m, where a higher diversity and abundance of actively transcribed AOA was observed at the station located in the marginal sea exposed to more terrestrial input. Similar community composition of AOA observed at the two stations adjacent to the Kuril Islands maybe due to water exchange across the Bussol Strait. They distinct from the station located in the western subarctic gyre, where sub-cluster WCAII had a specific distribution in the surface water, and this sub-cluster seemed having a confined distribution in the western Pacific. Habitat-specific groupings of different WCB sub-clusters were observed reflecting the isolated microevolution existed in cluster WCB. The effect of the Kuril Islands on the phylogenetic composition of AOA between the Sea of Okhotsk and the western subarctic Pacific is not obvious, possibly because our sampling stations are near to the Bussol Strait, the main gateway through which water is exchanged between the Sea of Okhotsk and the Pacific. The vertical and horizontal distribution patterns of AOA communities among stations along the Kuril Islands were essentially determined by the in situ prevailing physicochemical gradients along the two dimensions.

  15. Diversity and abundance of ammonia oxidizing archaea in tropical compost systems.

    Science.gov (United States)

    de Gannes, Vidya; Eudoxie, Gaius; Dyer, David H; Hickey, William J

    2012-01-01

    Composting is widely used to transform waste materials into valuable agricultural products. In the tropics, large quantities of agricultural wastes could be potentially useful in agriculture after composting. However, while microbiological processes of composts in general are well established, relatively little is known about microbial communities that may be unique to these in tropical systems, particularly nitrifiers. The recent discovery of ammonia oxidizing archaea (AOA) has changed the paradigm of nitrification being initiated solely by ammonia oxidizing bacteria. In the present study, AOA abundance and diversity was examined in composts produced from combinations of plant waste materials common in tropical agriculture (rice straw, sugar cane bagasse, and coffee hulls), which were mixed with either cow- or sheep-manure. The objective was to determine how AOA abundance and diversity varied as a function of compost system and time, the latter being a contrast between the start of the compost process (mesophilic phase) and the finished product (mature phase). The results showed that AOA were relatively abundant in composts of tropical agricultural wastes, and significantly more so than were the ammonia-oxidizing bacteria. Furthermore, while the AOA communities in the composts were predominatly group I.1b, the communities were diverse and exhibited structures that diverged between compost types and phases. These patterns could be taken as indicators of the ecophysiological diversity in the soil AOA (group I.1b), in that significantly different AOA communties developed when exposed to varying physico-chemical environments. Nitrification patterns and levels differed in the composts which, for the mature material, could have significant effects on its performance as a plant growth medium. Thus, it will also be important to determine the association of AOA (and diversity in their communities) with nitrification in these systems.

  16. Ammonia oxidizing bacteria community dynamics in a pilot-scale wastewater treatment plant.

    Directory of Open Access Journals (Sweden)

    Xiaohui Wang

    Full Text Available BACKGROUND: Chemoautotrophic ammonia oxidizing bacteria (AOB have the metabolic ability to oxidize ammonia to nitrite aerobically. This metabolic feature has been widely used, in combination with denitrification, to remove nitrogen from wastewater in wastewater treatment plants (WWTPs. However, the relative influence of specific deterministic environmental factors to AOB community dynamics in WWTP is uncertain. The ecological principles underlying AOB community dynamics and nitrification stability and how they are related are also poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: The community dynamics of ammonia oxidizing bacteria (AOB in a pilot-scale WWTP were monitored over a one-year period by Terminal Restriction Fragment Length Polymorphism (T-RFLP. During the study period, the effluent ammonia concentrations were almost below 2 mg/L, except for the first 60 days, indicting stable nitrification. T-RFLP results showed that, during the test period with stable nitrification, the AOB community structures were not stable, and the average change rate (every 15 days of AOB community structures was 10% ± 8%. The correlations between T-RFLP profiles and 10 operational and environmental parameters were tested by Canonical Correlation Analysis (CCA and Mantel test. The results indicated that the dynamics of AOB community correlated most strongly with Dissolved Oxygen (DO, effluent ammonia, effluent Biochemical Oxygen Demand (BOD and temperature. CONCLUSIONS/SIGNIFICANCE: This study suggests that nitrification stability is not necessarily accompanied by a stable AOB community, and provides insight into parameters controlling the AOB community dynamics within bioreactors with stable nitrification.

  17. Ammonia-oxidizing activity and microbial community structure in acid tea (Camellia sinensis) orchard soil

    Science.gov (United States)

    Okamura, K.; Takanashi, A.; Yamada, T.; Hiraishi, A.

    2012-03-01

    The purpose of this study was to determine the ammonia-oxidizing activity and the phylogentic composition of microorganisms involved in acid tea (Camellia sinensis) orchard soil. All soil samples were collected from three sites located in Tahara and Toyohashi, Aichi Prefecture, Japan. The potential nitrification rate (PNR) was measured by the chlorate inhibition method. The soil pH of tea orchards studied ranged from 2.78 to 4.84, differing significantly from sample to sample, whereas that of meadow and unplanted fields ranged from 5.78 to 6.35. The PNR ranged from 0.050 to 0.193 μg NO2--Ng-1 h-1 and were positively correlated with the soil pH (r2 = 0.382, p<0.001). Bulk DNA was extracted from a tea orchard soil (pH 4.8; PNR, 0.078 μg NO2--Ng-1 h-1) and subjected to PCR-aided clone library analyses targeting archaeal and bacterial amoA genes. The detected archaeal clones separated from the cluster of the 'Soil clones' and tightly clustered with the clones originating from other acidic soil environments including the Chinese tea orchard soil. These results suggest that the specific archaeal populations dominate as the ammonia oxidizers in acid tea-orchard soils and possibly other acid soils, independent of geographic locations, which results from the adaptation to specific ecological niches.

  18. Ammonia-oxidizing activity and microbial community structure in acid tea (Camellia sinensis) orchard soil

    International Nuclear Information System (INIS)

    Okamura, K; Yamada, T; Hiraishi, A; Takanashi, A

    2012-01-01

    The purpose of this study was to determine the ammonia-oxidizing activity and the phylogentic composition of microorganisms involved in acid tea (Camellia sinensis) orchard soil. All soil samples were collected from three sites located in Tahara and Toyohashi, Aichi Prefecture, Japan. The potential nitrification rate (PNR) was measured by the chlorate inhibition method. The soil pH of tea orchards studied ranged from 2.78 to 4.84, differing significantly from sample to sample, whereas that of meadow and unplanted fields ranged from 5.78 to 6.35. The PNR ranged from 0.050 to 0.193 μg NO 2 - -Ng -1 h -1 and were positively correlated with the soil pH (r 2 0.382, p 2 - -Ng -1 h -1 ) and subjected to PCR-aided clone library analyses targeting archaeal and bacterial amoA genes. The detected archaeal clones separated from the cluster of the 'Soil clones' and tightly clustered with the clones originating from other acidic soil environments including the Chinese tea orchard soil. These results suggest that the specific archaeal populations dominate as the ammonia oxidizers in acid tea-orchard soils and possibly other acid soils, independent of geographic locations, which results from the adaptation to specific ecological niches.

  19. Simultaneous Fe(III) reduction and ammonia oxidation process in Anammox sludge.

    Science.gov (United States)

    Li, Xiang; Huang, Yong; Liu, Heng-Wei; Wu, Chuan; Bi, Wei; Yuan, Yi; Liu, Xin

    2018-02-01

    In recent years, there have been a number of reports on the phenomenon in which ferric iron (Fe(III)) is reduced to ferrous iron [Fe(II)] in anaerobic environments, accompanied by simultaneous oxidation of ammonia to NO 2 - , NO 3 - , or N 2. However, studies on the relevant reaction characteristics and mechanisms are rare. Recently, in research on the effect of Fe(III) on the activity of Anammox sludge, excess ammonia oxidization has also been found. Hence, in the present study, Fe(III) was used to serve as the electron acceptor instead of NO 2 - , and the feasibility and characteristics of Anammox coupled to Fe(III) reduction (termed Feammox) were investigated. After 160days of cultivation, the conversion rate of ammonia in the reactor was above 80%, accompanied by the production of a large amount of NO 3 - and a small amount of NO 2 - . The total nitrogen removal rate was up to 71.8%. Furthermore, quantities of Fe(II) were detected in the sludge fluorescence in situ hybridization (FISH) and denaturated gradient gel electrophoresis (DGGE) analyses further revealed that in the sludge, some Anammox bacteria were retained, and some microbes were enriched during the acclimatization process. We thus deduced that in Anammox sludge, Fe(III) reduction takes place together with ammonia oxidation to NO 2 - and NO 3 - along with the Anammox process. Copyright © 2017. Published by Elsevier B.V.

  20. Community size and composition of ammonia oxidizers and denitrifiers in an alluvial intertidal wetland ecosystem

    Directory of Open Access Journals (Sweden)

    Ziye eHu

    2014-07-01

    Full Text Available Global nitrogen cycling is mainly mediated by the activity of microorganisms. Nitrogen cycle processes are mediated by functional groups of microorganisms that are affected by constantly changing environmental conditions and substrate availability. In this study, we investigated the temporal and spatial patterns of nitrifier and denitrifier communities in an intertidal wetland. Soil samples were collected over four distinct seasons from three locations with different vegetative cover. Multiple environmental factors and process rates were measured and analyzed together with the community size and composition profiles. We observed that the community size and composition of the nitrifiers and denitrifiers are affected significantly by seasonal factors, while vegetative cover affected the community composition. The seasonal impacts on the community size of ammonia oxidizing archaea (AOA are much higher than that of ammonia oxidizing bacteria (AOB. The seasonal change was a more important indicator for AOA community composition patterns, while vegetation was more important for the AOB community patterns. The microbial process rates were correlated with both the community size and composition.

  1. Diversity of aerobic and anaerobic ammonia-oxidizing bacteria in marine sponges.

    Science.gov (United States)

    Mohamed, Naglaa M; Saito, Keiko; Tal, Yossi; Hill, Russell T

    2010-01-01

    Aerobic ammonia-oxidizing bacteria (AAOB) are known to have an important function in the marine nitrogen cycle. Anaerobic ammonium oxidation (anammox) carried out by some members of Planctomycetales is also an important process in marine ecosystems. Ammonia-monooxygenase gene (amoA) fragments were amplified to investigate the potential for nitrification and the diversity of the AAOB in two marine sponges Ircinia strobilina and Mycale laxissima. All of the AmoA sequences obtained from the two sponges clustered with the AmoA sequences of the Betaproteobacteria Nitrosospira spp. To investigate the anaerobic ammonia-oxidizing bacteria (AnAOB) in sponges, 16S rRNA gene fragments of Planctomycetales and anammox bacteria were also amplified with specific primers, and clone libraries were constructed. The Planctomycetales diversity detected in the two sponges was different. The Planctomycetales community in M. laxissima was affiliated with Pirellula, Planctomyces and anammox bacteria, while all of the I. strobilina Planctomycetales clones were solely affiliated with the candidate phylum 'Poribacteria'. Interestingly, sequences related to anammox genera were recovered only from M. laxissima. This is the first report of anammox bacteria in marine sponges. It is intriguing to find AAOB and AnAOB in M. laxissima, but the nature of their interaction with the sponge host and with each other remains unclear. This work further supports the potential of sponge-associated microorganisms for nitrification and sheds light on anammox as a new aspect of the nitrogen cycle in marine sponges.

  2. Interactive effects of multiple climate change factors on ammonia oxidizers and denitrifiers in a temperate steppe.

    Science.gov (United States)

    Zhang, Cui-Jing; Shen, Ju-Pei; Sun, Yi-Fei; Wang, Jun-Tao; Zhang, Li-Mei; Yang, Zhong-Ling; Han, Hong-Yan; Wan, Shi-Qiang; He, Ji-Zheng

    2017-04-01

    Global climate change could have profound effects on belowground microbial communities and subsequently affect soil biogeochemical processes. The interactive effects of multiple co-occurring climate change factors on microbially mediated processes are not well understood. A four-factorial field experiment with elevated CO2, watering, nitrogen (N) addition and night warming was conducted in a temperate steppe of northern China. Real-time polymerase chain reaction and terminal-restriction fragment length polymorphism, combined with clone library techniques, were applied to examine the effects of those climate change factors on N-related microbial abundance and community composition. Only the abundance of ammonia-oxidizing bacteria significantly increased by nitrogen addition and decreased by watering. The interactions of watering × warming on the bacterial amoA community and warming × nitrogen addition on the nosZ community were found. Redundancy analysis indicated that the ammonia-oxidizing archaeal community was affected by total N and total carbon, while the community of bacterial amoA and nosZ were significantly affected by soil pH. According to a structural equation modeling analysis, climate change influenced net primary production indirectly by altering microbial abundance and activities. These results indicated that microbial responses to the combination of chronic global change tend to be smaller than expected from single-factor global change manipulations. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. Do freshwater macrophytes influence the community structure of ammonia-oxidizing and denitrifying bacteria in the rhizospere?

    DEFF Research Database (Denmark)

    Herrmann, Martina; Schramm, Andreas

    2006-01-01

    DO FRESHWATER MACROPHYTES INFLUENCE THE COMMUNITY STRUCTURE OF AMMONIA-OXIDIZING AND DENITRIFYING BACTERIA IN THE RHIZOSPHERE? M. Herrmann, A. Schramm Department of Biological Sciences, Microbiology, University of Aarhus, Aarhus, Denmark Aquatic macrophytes such as Littorella uniflora and Lobelia...... to unvegetated sediment, especially with respect to the availability of oxygen, organic carbon, and inorganic nitrogen. We hypothesize that macrophyte species create specific niches for ammonia oxidizing and nitrate-reducing bacteria in their rhizosphere, leading to plant-dependant differences in abundance......-denitrification using the 15N isotope pairing technique. Ammonia-oxidizing and nitrate-reducing populations are analyzed based on the ammonia monooxygenase gene (amoA) and the nitrate reductase gene (narG) as functional markers. Preliminary data indicate that there in fact exist differences in the community composition...

  4. Physiological plasticity of the thermophilic ammonia oxidizing archaeon Nitrosocaldus yellowstonii in response to a changing environment

    Science.gov (United States)

    Jewell, T.; Johnson, A.; Gelsinger, D.; de la Torre, J. R.

    2012-12-01

    Our understanding of nitrogen biogeochemical cycling in high temperature environments underwent a dramatic revision with the discovery of ammonia oxidizing archaea (AOA). The importance of AOA to the global nitrogen cycle came to light when recent studies of marine AOA demonstrated the dominance of these organisms in the ocean microbiome and their role as producers of the greenhouse gas nitrous oxide (N2O). Understanding how AOA respond to fluctuating environments is crucial to fully comprehending their contribution to global biogeochemical cycling and climate change. In this study we use the thermophilic AOA Nitrosocaldus yellowstonii strain HL72 to explore the physiological plasticity of energy metabolism in these organisms. Previous studies have shown that HL72 grows autotrophically by aerobically oxidizing ammonia (NH3) to nitrite (NO2-). Unlike studies of marine AOA, we find that HL72 can grow over a wide ammonia concentration range (0.25 - 10 mM NH4Cl) with comparable generation times when in the presence of 0.25 to 4 mM NH4Cl. However, preliminary data indicate that amoA, the alpha subunit of ammonia monooxygenase (AMO), is upregulated at low ammonia concentrations (<50 μM) compared to growth at 1 mM. Although the ammonia oxidation pathway has not been fully elucidated, we have shown that nitric oxide (NO) appears to be a key intermediate: exponentially growing HL72 produces significant NO and the removal of NO using a scavenger reversibly inhibits growth. In addition to AMO, the HL72 genome also contains sequences for a urease encoded by subunits ureABC and an active urea transporter. Urea ((NH2)2CO) is an organic compound ubiquitous to aquatic and soil habitats that, when hydrolyzed, forms NH3 and CO2. We examined urea as an alternate source of ammonia for the ammonia oxidation pathway. HL72 grows over a wide range of urea concentrations (0.25 - 10 mM) at rates comparable to growth on ammonia. In a substrate competition experiment HL72 preferentially

  5. Fauna Europaea – Orthopteroid orders

    Science.gov (United States)

    Bohn, Horst; Haas, Fabian; Willemse, Fer

    2016-01-01

    Abstract Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms) of all extant European terrestrial and freshwater animals, their geographical distribution at the level of countries and major islands (west of the Urals and excluding the Caucasus region), and some additional information. The Fauna Europaea project comprises about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. Fauna Europaea represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. The “Orthopteroid orders“ is one of the 58 Fauna Europaea major taxonomic groups. It contains series of mostly well-known insect orders: Embiodea (webspinners), Dermaptera (earwigs), Phasmatodea (walking sticks), Orthoptera s.s. (grasshoppers, crickets, bush-crickets) and Dictyoptera with the suborders Mantodea (mantids), Blattaria (cockroaches) and Isoptera (termites). For the Orthopteroid orders, data from 35 families containing 1,371 species are included in this paper. PMID:27660531

  6. Growth of Nitrosococcus-Related Ammonia Oxidizing Bacteria Coincides with Extremely Low pH Values in Wastewater with High Ammonia Content

    NARCIS (Netherlands)

    Fumasoli, Alexandra; Bürgmann, Helmut; Weissbrodt, D.G.; Wells, G.N.; Beck, Karin; Mohn, Joachim; Morgenroth, Eberhard; Udert, Kai M.

    2017-01-01

    Ammonia oxidation decreases the pH in wastewaters where alkalinity is limited relative to total ammonia. The activity of ammonia oxidizing bacteria (AOB), however, typically decreases with pH and often ceases completely in slightly acidic wastewaters. Nevertheless, nitrification at low pH has

  7. Determination of Ammonia Oxidizing Bacteria and Nitrate Oxidizing Bacteria in Wastewater and Bioreactors

    Science.gov (United States)

    Francis, Somilez Asya

    2014-01-01

    The process of water purification has many different physical, chemical, and biological processes. One part of the biological process is the task of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB). Both play critical roles in the treatment of wastewater by oxidizing toxic compounds. The broad term is nitrification, a naturally occurring process that is carried out by AOB and NOB by using oxidation to convert ammonia to nitrite and nitrite to nitrate. To monitor this biological activity, bacterial staining was performed on wastewater contained in inoculum tanks and biofilm samples from bioreactors. Using microscopy and qPCR, the purpose of this experiment was to determine if the population of AOB and NOB in wastewater and membrane bioreactors changed depending on temperature and hibernation conditions to determine the optimal parameters for AOB/NOB culture to effectively clean wastewater.

  8. Ammonia-oxidizing Bacteria and Archaea in the Rhizosphere of Freshwater Macrophytes

    DEFF Research Database (Denmark)

    Herrmann, Martina; Schramm, Andreas

    2007-01-01

    AMMONIA-OXIDIZING ARCHAEA AND BACTERIA IN THE RHIZOSPHERE OF FRESHWATER MACROPHYTES Martina Herrmann and Andreas Schramm Department of Biological Sciences, Microbiology, University of Aarhus, Denmark Aquatic macrophytes such as Littorella uniflora and Lobelia dortmanna release oxygen from...... their roots and thereby stimulate nitrification and coupled nitrification-denitrification in their rhizosphere. However, oxygen release and inorganic nitrogen concentrations differ markedly between macrophyte species. We therefore propose (i) that the rhizosphere of freshwater macrophytes harbours a species......-specific microbial community distinct from that of unvegetated sediment and (ii) that aquatic macrophytes have an impact on abundance and activity of nitrifying and denitrifying bacteria in freshwater sediment. The goal of this study was to test these hypotheses for the key functional group for coupled nitrification-denitrification...

  9. Relative contributions of archaea and bacteria to microbial ammonia oxidation differ under different conditions during agricultural waste composting.

    Science.gov (United States)

    Zeng, Guangming; Zhang, Jiachao; Chen, Yaoning; Yu, Zhen; Yu, Man; Li, Hui; Liu, Zhifeng; Chen, Ming; Lu, Lunhui; Hu, Chunxiao

    2011-10-01

    The aim of this study was to compare the relative contribution of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to nitrification during agricultural waste composting. The AOA and AOB amoA gene abundance and composition were determined by quantitative PCR and denaturing gradient gel electrophoresis (DGGE), respectively. The results showed that the archaeal amoA gene was abundant throughout the composting process, while the bacterial amoA gene abundance decreased to undetectable level during the thermophilic and cooling stages. DGGE showed more diverse archaeal amoA gene composition when the potential ammonia oxidation (PAO) rate reached peak values. A significant positive relationship was observed between the PAO rate and the archaeal amoA gene abundance (R²=0.554; Parchaea dominated ammonia oxidation during the thermophilic and cooling stages. Bacteria were also related to ammonia oxidation activity (R²=0.503; P=0.03) especially during the mesophilic and maturation stages. Copyright © 2011 Elsevier Ltd. All rights reserved.

  10. Competitive interactions between methane- and ammonia-oxidizing bacteria modulate carbon and nitrogen cycling in paddy soil

    NARCIS (Netherlands)

    Zheng, Yan; Huang, Rong; Wang, B.; Bodelier, P.L.E.; Jia, Z.

    2014-01-01

    Pure culture studies have demonstrated that methanotrophs and ammonia oxidizers can both carry out the oxidation of methane and ammonia. However, the expected interactions resulting from these similarities are poorly understood, especially in complex, natural environments. Using DNA-based stable

  11. Archaeal ammonia oxidizers dominate in numbers, but bacteria drive gross nitrification in N-amended grassland soil

    Directory of Open Access Journals (Sweden)

    Anna E Sterngren

    2015-11-01

    Full Text Available Both ammonia-oxidizing archaea (AOA and ammonia-oxidizing bacteria (AOB play an important role in nitrification in terrestrial environments. Most often AOA outnumber AOB, but the relative contribution of AOA and AOB to nitrification rates remains unclear. The aim of this experiment was to test the hypotheses that high nitrogen availability would favor AOB and result in high gross nitrification rates, while high carbon availability would result in low nitrogen concentrations that favor the activity of AOA. The hypotheses were tested in a microcosm experiment where sugars, ammonium or amino acids were added regularly to a grassland soil for a period of 33 days. The abundance of amoA genes from AOB increased markedly in treatments that received nitrogen, suggesting that AOB were the main ammonia oxidizers here. However, AOB could not account for the entire ammonia oxidation activity observed in treatments where the soil was deficient in available nitrogen. The findings suggest that AOA are important drivers of nitrification under nitrogen-poor conditions, but that input of easily available nitrogen results in increased abundance, activity, and relative importance of AOB for gross nitrification in grassland soil.

  12. Influence of oxygen partial pressure and salinity on the community composition of ammonia-oxidizing bacteria in the Schelde estuary

    NARCIS (Netherlands)

    Bollmann, A.; Laanbroek, H.J.

    2002-01-01

    The influence of environmental factors on the community structure of ammonia-oxidizing bacteria (AOB) was investigated in the Schelde estuary. Simultaneously with the increase of oxygen and salinity, a shift of the dominant AOB was observed. Molecular analysis based on 16S rRNA genes showed that the

  13. Bottom-Up Design of a Copper-Ruthenium Nanoparticulate Catalyst for Low-Temperature Ammonia Oxidation

    DEFF Research Database (Denmark)

    Chakraborty, Debasish; Damsgaard, Christian Danvad; Silva, Hugo José Lopes

    2017-01-01

    A novel nanoparticulate catalyst of copper (Cu) and ruthenium (Ru) was designed for low-temperature ammonia oxidation at near-stoichiometric mixtures using a bottom-up approach. A synergistic effect of the two metals was found. An optimum CuRu catalyst presents a reaction rate threefold higher than...

  14. Potato cultivar type affects the structure of ammonia oxidizer communities in field soil under potato beyond the rhizosphere

    NARCIS (Netherlands)

    Cavalcante Franco Dias, A.; Hoogwout, E.F.; de Cassia Pereira e Silva, M.; Falcão Salles, J.; van Overbeek, L.S.; van Elsas, J.D.

    The effects of plants on the microbiota involved in the oxidation of ammonia in soils have been controversial. Here, we investigated the dynamics in the abundances and community structures of the bacterial and archaeal ammonia oxidizers (AOB and AOA, respectively) in two fields that were cropped

  15. Substrate availability drives spatial patterns in richness of ammonia-oxidizing bacteria and archaea in temperate forest soils

    Science.gov (United States)

    J.S. Norman; J.E. Barrett

    2016-01-01

    We sought to investigate the drivers of richness of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in temperate forest soils. We sampled soils across four experimental watersheds in the Coweeta Hydrologic Laboratory, North Carolina USA. These watersheds are geographically close, but vary in soil chemistry due to differences in land use history. While we...

  16. Aquarium nitrification revisited: Thaumarchaeota are the dominant ammonia oxidizers in freshwater aquarium biofilters.

    Directory of Open Access Journals (Sweden)

    Laura A Sauder

    Full Text Available Ammonia-oxidizing archaea (AOA outnumber ammonia-oxidizing bacteria (AOB in many terrestrial and aquatic environments. Although nitrification is the primary function of aquarium biofilters, very few studies have investigated the microorganisms responsible for this process in aquaria. This study used quantitative real-time PCR (qPCR to quantify the ammonia monooxygenase (amoA and 16S rRNA genes of Bacteria and Thaumarchaeota in freshwater aquarium biofilters, in addition to assessing the diversity of AOA amoA genes by denaturing gradient gel electrophoresis (DGGE and clone libraries. AOA were numerically dominant in 23 of 27 freshwater biofilters, and in 12 of these biofilters AOA contributed all detectable amoA genes. Eight saltwater aquaria and two commercial aquarium nitrifier supplements were included for comparison. Both thaumarchaeal and bacterial amoA genes were detected in all saltwater samples, with AOA genes outnumbering AOB genes in five of eight biofilters. Bacterial amoA genes were abundant in both supplements, but thaumarchaeal amoA and 16S rRNA genes could not be detected. For freshwater aquaria, the proportion of amoA genes from AOA relative to AOB was inversely correlated with ammonium concentration. DGGE of AOA amoA genes revealed variable diversity across samples, with nonmetric multidimensional scaling (NMDS indicating separation of freshwater and saltwater fingerprints. Composite clone libraries of AOA amoA genes revealed distinct freshwater and saltwater clusters, as well as mixed clusters containing both freshwater and saltwater amoA gene sequences. These results reveal insight into commonplace residential biofilters and suggest that aquarium biofilters may represent valuable biofilm microcosms for future studies of AOA ecology.

  17. Cultivation of autotrophic ammonia-oxidizing archaea from marine sediments in coculture with sulfur-oxidizing bacteria.

    Science.gov (United States)

    Park, Byoung-Joon; Park, Soo-Je; Yoon, Dae-No; Schouten, Stefan; Sinninghe Damsté, Jaap S; Rhee, Sung-Keun

    2010-11-01

    The role of ammonia-oxidizing archaea (AOA) in nitrogen cycling in marine sediments remains poorly characterized. In this study, we enriched and characterized AOA from marine sediments. Group I.1a crenarchaea closely related to those identified in marine sediments and "Candidatus Nitrosopumilus maritimus" (99.1 and 94.9% 16S rRNA and amoA gene sequence identities to the latter, respectively) were substantially enriched by coculture with sulfur-oxidizing bacteria (SOB). The selective enrichment of AOA over ammonia-oxidizing bacteria (AOB) is likely due to the reduced oxygen levels caused by the rapid initial growth of SOB. After biweekly transfers for ca. 20 months, archaeal cells became the dominant prokaryotes (>80%), based on quantitative PCR and fluorescence in situ hybridization analysis. The increase of archaeal 16S rRNA gene copy numbers was coincident with the amount of ammonia oxidized, and expression of the archaeal amoA gene was observed during ammonia oxidation. Bacterial amoA genes were not detected in the enrichment culture. The affinities of these AOA to oxygen and ammonia were substantially higher than those of AOB. [(13)C]bicarbonate incorporation and the presence and activation of genes of the 3-hydroxypropionate/4-hydroxybutyrate cycle indicated autotrophy during ammonia oxidation. In the enrichment culture, ammonium was oxidized to nitrite by the AOA and subsequently to nitrate by Nitrospina-like bacteria. Our experiments suggest that AOA may be important nitrifiers in low-oxygen environments, such as oxygen-minimum zones and marine sediments.

  18. Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system.

    Science.gov (United States)

    Sauder, Laura A; Albertsen, Mads; Engel, Katja; Schwarz, Jasmin; Nielsen, Per H; Wagner, Michael; Neufeld, Josh D

    2017-05-01

    Thaumarchaeota have been detected in several industrial and municipal wastewater treatment plants (WWTPs), despite the fact that ammonia-oxidizing archaea (AOA) are thought to be adapted to low ammonia environments. However, the activity, physiology and metabolism of WWTP-associated AOA remain poorly understood. We report the cultivation and complete genome sequence of Candidatus Nitrosocosmicus exaquare, a novel AOA representative from a municipal WWTP in Guelph, Ontario (Canada). In enrichment culture, Ca. N. exaquare oxidizes ammonia to nitrite stoichiometrically, is mesophilic, and tolerates at least 15 mm of ammonium chloride or sodium nitrite. Microautoradiography (MAR) for enrichment cultures demonstrates that Ca. N. exaquare assimilates bicarbonate in association with ammonia oxidation. However, despite using inorganic carbon, the ammonia-oxidizing activity of Ca. N. exaquare is greatly stimulated in enrichment culture by the addition of organic compounds, especially malate and succinate. Ca. N. exaquare cells are coccoid with a diameter of ~1-2 μm. Phylogenetically, Ca. N. exaquare belongs to the Nitrososphaera sister cluster within the Group I.1b Thaumarchaeota, a lineage which includes most other reported AOA sequences from municipal and industrial WWTPs. The 2.99 Mbp genome of Ca. N. exaquare encodes pathways for ammonia oxidation, bicarbonate fixation, and urea transport and breakdown. In addition, this genome encodes several key genes for dealing with oxidative stress, including peroxidase and catalase. Incubations of WWTP biofilm demonstrate partial inhibition of ammonia-oxidizing activity by 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO), suggesting that Ca. N. exaquare-like AOA may contribute to nitrification in situ. However, CARD-FISH-MAR showed no incorporation of bicarbonate by detected Thaumarchaeaota, suggesting that detected AOA may incorporate non-bicarbonate carbon sources or rely on an alternative and yet unknown

  19. Influence of tropical leaf litter on nitrogen mineralization and community structure of ammonia-oxidizing bacteria

    Directory of Open Access Journals (Sweden)

    Diallo, MD.

    2015-01-01

    Full Text Available Description of the subject. The present study concerns the relationships among leaf litter decomposition, substrate quality, ammonia-oxidizing bacteria (AOB community composition and nitrogen (N availability. Decomposition of organic matter affects the biogeochemical cycling of carbon (C and N. Since the composition of the soil microbial community can alter the physiological capacity of the community, it is timely to study the litter quality effect on N dynamic in ecosystems. Objectives. The aim of this study was to determine the influence of leaf litter decomposition on N mineralization. The specific objectives of this study were to evaluate the influence of the litter biochemistry of five plants species (Faidherbia albida A.Chev., Azadirachta indica A.Juss., Casuarina equisetifolia L., Andropogon gayanus Kunth and Eragrostis tremula Hochst. ex Steud. on N mineralization in a tropical ferrous soil (Lixisol, nitrification, and genetic diversity of ammonia-oxidizing bacteria. Denaturing gradient gel electrophoresis (DGGE of amplified fragments of genes coding for 16S rRNA was used to study the development of bacterial communities during decomposition of leaf litter in soils. Method. Community structure of AOB was determined at two time periods: day 0 and day 140. Ten strains were tested and each of these strains produced a single band. Thus, DGGE DNA band patterns were used to estimate bacterial diversity. Plant secondary compounds such as polyphenols are purported to influence nutrient cycling by affecting organic matter degradation, mineralization rates, N availability and humus formation. In a laboratory study, we investigated the influence of six phenolic acids (ferulic, gallic, vanillic, syringic, p-coumaric and p-HBA acids commonly found in the plant residues on N mineralization and NH4+ and NO3- production in soils. Results. The results showed that litter type did affect soil nitrification. Faidherbia albida litter was associated with

  20. OXIDATION OF METHYL FLUORIDE AND DIMETHYL ETHER BY AMMONIA MONOOXYGENASE IN NITROSOMONAS EUROPAEA. (R825689C009)

    Science.gov (United States)

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  1. Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome

    Directory of Open Access Journals (Sweden)

    Sophie S. Abby

    2018-01-01

    Full Text Available Ammonia oxidizing archaea (AOA of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first enrichment of a thermophilic representative with a sequenced genome, which facilitates the search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota. Candidatus Nitrosocaldus cavascurensis has been enriched from a hot spring in Ischia, Italy. It grows optimally at 68°C under chemolithoautotrophic conditions on ammonia or urea converting ammonia stoichiometrically into nitrite with a generation time of approximately 23 h. Phylogenetic analyses based on ribosomal proteins place the organism as a sister group to all known mesophilic AOA. The 1.58 Mb genome of Ca. N. cavascurensis harbors an amoAXCB gene cluster encoding ammonia monooxygenase and genes for a 3-hydroxypropionate/4-hydroxybutyrate pathway for autotrophic carbon fixation, but also genes that indicate potential alternative energy metabolisms. Although a bona fide gene for nitrite reductase is missing, the organism is sensitive to NO-scavenging, underlining the potential importance of this compound for AOA metabolism. Ca. N. cavascurensis is distinct from all other AOA in its gene repertoire for replication, cell division and repair. Its genome has an impressive array of mobile genetic elements and other recently acquired gene sets, including conjugative systems, a provirus, transposons and cell appendages. Some of these elements indicate recent exchange with the environment, whereas others seem to have been domesticated and might convey crucial metabolic traits.

  2. Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome.

    Science.gov (United States)

    Abby, Sophie S; Melcher, Michael; Kerou, Melina; Krupovic, Mart; Stieglmeier, Michaela; Rossel, Claudia; Pfeifer, Kevin; Schleper, Christa

    2018-01-01

    Ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first enrichment of a thermophilic representative with a sequenced genome, which facilitates the search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota. Candidatus Nitrosocaldus cavascurensis has been enriched from a hot spring in Ischia, Italy. It grows optimally at 68°C under chemolithoautotrophic conditions on ammonia or urea converting ammonia stoichiometrically into nitrite with a generation time of approximately 23 h. Phylogenetic analyses based on ribosomal proteins place the organism as a sister group to all known mesophilic AOA. The 1.58 Mb genome of Ca. N. cavascurensis harbors an amo AXCB gene cluster encoding ammonia monooxygenase and genes for a 3-hydroxypropionate/4-hydroxybutyrate pathway for autotrophic carbon fixation, but also genes that indicate potential alternative energy metabolisms. Although a bona fide gene for nitrite reductase is missing, the organism is sensitive to NO-scavenging, underlining the potential importance of this compound for AOA metabolism. Ca. N. cavascurensis is distinct from all other AOA in its gene repertoire for replication, cell division and repair. Its genome has an impressive array of mobile genetic elements and other recently acquired gene sets, including conjugative systems, a provirus, transposons and cell appendages. Some of these elements indicate recent exchange with the environment, whereas others seem to have been domesticated and might convey crucial metabolic traits.

  3. Candidatus Nitrosocaldus cavascurensis, an Ammonia Oxidizing, Extremely Thermophilic Archaeon with a Highly Mobile Genome

    Science.gov (United States)

    Abby, Sophie S.; Melcher, Michael; Kerou, Melina; Krupovic, Mart; Stieglmeier, Michaela; Rossel, Claudia; Pfeifer, Kevin; Schleper, Christa

    2018-01-01

    Ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first enrichment of a thermophilic representative with a sequenced genome, which facilitates the search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota. Candidatus Nitrosocaldus cavascurensis has been enriched from a hot spring in Ischia, Italy. It grows optimally at 68°C under chemolithoautotrophic conditions on ammonia or urea converting ammonia stoichiometrically into nitrite with a generation time of approximately 23 h. Phylogenetic analyses based on ribosomal proteins place the organism as a sister group to all known mesophilic AOA. The 1.58 Mb genome of Ca. N. cavascurensis harbors an amoAXCB gene cluster encoding ammonia monooxygenase and genes for a 3-hydroxypropionate/4-hydroxybutyrate pathway for autotrophic carbon fixation, but also genes that indicate potential alternative energy metabolisms. Although a bona fide gene for nitrite reductase is missing, the organism is sensitive to NO-scavenging, underlining the potential importance of this compound for AOA metabolism. Ca. N. cavascurensis is distinct from all other AOA in its gene repertoire for replication, cell division and repair. Its genome has an impressive array of mobile genetic elements and other recently acquired gene sets, including conjugative systems, a provirus, transposons and cell appendages. Some of these elements indicate recent exchange with the environment, whereas others seem to have been domesticated and might convey crucial metabolic traits. PMID:29434576

  4. Composition of ammonia-oxidizing archaea and their contribution to nitrification in a high-temperature hot spring

    Science.gov (United States)

    Chen, S.; Peng, X.-T.; Xu, H.-C.; Ta, K.-W.

    2015-10-01

    The oxidation of ammonia by microbes and associated organisms has been shown to occur in diverse natural environments. However, the contribution of ammonia-oxidizing archaea to nitrification in high-temperature environments remains unclear. Here, we studied in situ ammonia oxidation rates and the abundance of ammonia-oxidizing archaea (AOA) in surface and bottom sediments at 77 °C in the Gongxiaoshe hot spring, Tengchong, Yunnan, China. The in situ ammonia oxidation rates measured by the 15N-NO3- pool dilution technique in the surface sinter and bottom sediments were 4.8 and 5.3 nmol N g-1 h-1, respectively. Relative abundances of Crenarchaea in both samples were determined by fluorescence in situ hybridization (FISH). Phylogenetic analysis of 16S rRNA genes showed high sequence similarity to thermophilic "Candidatus Nitrosocaldus yellowstonii", which represented the most abundant operation taxonomic units (OTU) in both sediments. Furthermore, bacterial amoA was not detected in this study. Quantitative PCR (qPCR) indicated that AOA and 16S rRNA genes were present in the range of 2.75 to 9.80 × 105 and 0.128 to 1.96 × 108 gene copies g-1 sediment. The cell-specific nitrification rates were estimated to be in the range of 0.41 to 0.79 fmol N archaeal cell-1 h-1, which is consistent with earlier estimates in estuary environments. This study demonstrated that AOA were widely involved in nitrification in this hot spring. It further indicated the importance of archaea rather than bacteria in driving the nitrogen cycle in terrestrial geothermal environments.

  5. Effect of Real Wastewater on Biotransformation of 17α-ethynylestradiol by Ammonia-Oxidizing Bacteria in Nitrifying Activated Sludge

    OpenAIRE

    Natthawan Likitmongkonsakun; Tawan Limpiyakorn

    2013-01-01

    17α-ethynylestradiol (EE2) is a synthetic estrogen used as a key ingredient in an oral contraceptives pill. EE2 is an endocrine disrupting compound, high in estrogenic potency. Although EE2 exhibits low degree of biodegradability with common microorganisms in wastewater treatment plants (WWTPs), this compound can be biotransformed by ammonia-oxidizing bacteria (AOB) via a co-metabolism mechanism in WWTPs. This study aimed to investigate the effect of real wastewater on ...

  6. Comparison of the Effects of Phenylhydrazine Hydrochloride and Dicyandiamide on Ammonia-Oxidizing Bacteria and Archaea in Andosols

    Directory of Open Access Journals (Sweden)

    Wenjie Yang

    2017-11-01

    Full Text Available Dicyandiamide, a routinely used commercial nitrification inhibitor (NI, inhibits ammonia oxidation catalyzed by ammonia monooxygenase (AMO. Phenylhydrazine hydrochloride has shown considerable potential for the development of next-generation NIs targeting hydroxylamine dehydrogenase (HAO. The effects of the AMO inhibitor and the HAO inhibitor on ammonia-oxidizing bacteria (AOB and ammonia-oxidizing archaea (AOA present in agricultural soils have not been compared thus far. In the present study, the effects of the two inhibitors on soil nitrification and the abundance of AOA and AOB as well as their community structure were investigated in a soil microcosm using quantitative polymerase chain reaction and pyrosequencing. The net nitrification rates and the growth of AOA and AOB in this soil microcosm were inhibited by both NIs. Both NIs had limited effect on the community structure of AOB and no effect on that of AOA in this soil microcosm. The effects of phenylhydrazine hydrochloride were similar to those of dicyandiamide. These results indicated that organohydrazine-based NIs have potential for the development of next-generation NIs targeting HAO in the future.

  7. Fauna Europaea: Helminths (Animal Parasitic

    Directory of Open Access Journals (Sweden)

    David Gibson

    2014-09-01

    Full Text Available Fauna Europaea provides a public web-service with an index of scientific names (including important synonyms of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region, and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard reference suitable for many users in science, government, industry, nature conservation and education. Helminths parasitic in animals represent a large assemblage of worms, representing three phyla, with more than 200 families and almost 4,000 species of parasites from all major vertebrate and many invertebrate groups. A general introduction is given for each of the major groups of parasitic worms, i.e. the Acanthocephala, Monogenea, Trematoda (Aspidogastrea and Digenea, Cestoda and Nematoda. Basic information for each group includes its size, host-range, distribution, morphological features, life-cycle, classification, identification and recent key-works. Tabulations include a complete list of families dealt with, the number of species in each and the name of the specialist responsible for data acquisition, a list of additional specialists who helped with particular groups, and a list of higher taxa dealt with down to the family level. A compilation of useful references is appended.

  8. [Abundance and Community Composition of Ammonia-Oxidizing Archaea in Two Completely Autotrophic Nitrogen Removal over Nitrite Systems].

    Science.gov (United States)

    Gao, Jing-feng; Li, Ting; Zhang, Shu-jun; Fan, Xiao-yan; Pan, Kai-ling; Ma, Qian; Yuan, Ya-lin

    2015-08-01

    Ammonia oxidation is the first and rate-limiting step of nitrification, which was thought to be only performed by ammonia-oxidizing bacteria (AOB). In recent years, ammonia-oxidizing archaea (AOA) was also confirmed to take part in ammonia oxidation. The diversity and abundance of AOA have been investigated in various environments, however, little is known regarding the AOA in the completely autotrophic nitrogen removal over nitrite (CANON) wastewater treatment process. In this study, the abundance and diversity of AOA were investigated in the biofilm and flocculent activated sludge collected in a lab-scale (L) CANON system and a pilot-scale (P) CANON systems, respectively. The quantitative real time PCR (qPCR) was applied to investigate the abundance of AOA and the diversity of AOA was determined by polymerase chain reaction (PCR), cloning and sequencing. The qPCR results showed that the average abundance of AOA amoA gene of L and P was 2.42 x 10(6) copies x g(-1) dry sludge and 6.51 x 10(6) copies x g(-1) dry sludge, respectively. The abundance of AOA in biofilm was 10.1-14.1 times higher than that in flocculent activated sludge. For P system, the abundance of AOA in flocculent activated sludge was 1.8 times higher than that in biofilm. The results indicated that the abundance of AOA might be affected by different sludge morphology. The diversity of AOA in P system was extremely limited, only one OTU was observed, which was classified into Nitrosopumilus subcluster 5.2. The diversity of AOA in L system was higher, eight OTUs were observed, which were classified into five genera: Nitrososphaera subcluster 9, subcluster 8.1, subcluster 4.1, subcluster 1.1 and Nitrosopumilus subcluster 5.2. The diversity and abundance of AOA were different in CANON systems with different sludge morphology. AOA may play an important role in ammonia oxidation in CANON system.

  9. Ammonia-oxidizing archaea as main drivers of nitrification in cold-water sponges.

    Science.gov (United States)

    Radax, Regina; Hoffmann, Friederike; Rapp, Hans Tore; Leininger, Sven; Schleper, Christa

    2012-04-01

    The association of archaea with marine sponges was first described 15 years ago and their role in the nitrification process in Mediterranean and tropical sponges has been suggested. Here we explore the occurrence and abundance of potential ammonia-oxidizing archaea (AOA) in four morphologically different cold-water sponges (Phakellia ventilabrum, Geodia barretti, Antho dichotoma and Tentorium semisuberites) from the sublittoral and upper bathyal zone [Correction added on 30 December 2011, after first online publication on 19 December 2011: The term 'mesopelagic zone' has been replaced.] of the Norwegian coast, and relate them to nitrification rates determined in laboratory incubations. Net nitrification rates, calculated from the sum of nitrite and nitrate release during 24 h, were up to 1880 nmol N cm(-3) day(-1); i.e. comparable with those measured in Mediterranean sponges. Furthermore, a high abundance of archaeal cells was determined by fluorescence in situ hybridizations (CARD-FISH) and quantitative PCR, targeting archaeal amoA genes (encoding the alpha subunit of ammonia monooxygenase). AmoA genes as well as amoA transcripts were either exclusively detectable from archaea or were orders of magnitudes higher in abundance than their bacterial counterparts. Phylogenetic analyses of AOA and bacterial nitrite oxidizers (genus Nitrospira) confirmed the presence of specific populations of nitrifying microorganisms in the sponge mesohyl, which either were affiliated with groups detected earlier in marine sponges or were typical inhabitants of cold- and deep-water environments. Estimated cell-specific nitrification rates for P. ventilabrum were 0.6 to 6 fmol N archaeal cell(-1) day(-1), thus comparable with planktonic organisms. Our results identify AOA as the major drivers of nitrification in four cold-water sponges, and indicate that these archaea may be considered as a relevant factor in nitrogen cycling in ocean regions with high sponge biomass. © 2011 Society

  10. Ammonia-Oxidizing β-Proteobacteria from the Oxygen Minimum Zone off Northern Chile▿

    Science.gov (United States)

    Molina, Verónica; Ulloa, Osvaldo; Farías, Laura; Urrutia, Homero; Ramírez, Salvador; Junier, Pilar; Witzel, Karl-Paul

    2007-01-01

    The composition of ammonia-oxidizing bacteria from the β-Proteobacteria subclass (βAOB) was studied in the surface and upper-oxycline oxic waters (2- to 50-m depth, ∼200 to 44 μM O2) and within the oxygen minimum zone (OMZ) suboxic waters (50- to 400-m depth, ≤10 μM O2) of the eastern South Pacific off northern Chile. This study was carried out through cloning and sequencing of genes coding for 16S rRNA and the ammonia monooxygenase enzyme active subunit (amoA). Sequences affiliated with Nitrosospira-like cluster 1 dominated the 16S rRNA gene clone libraries constructed from both oxic and suboxic waters. Cluster 1 consists exclusively of yet-uncultivated βAOB from marine environments. However, a single clone, out of 224 obtained from the OMZ, was found to belong to Nitrosospira lineage cluster 0. To our knowledge, cluster 0 sequences have been derived from βAOB isolated only from sand, soil, and freshwater environments. Sequences in clone libraries of the amoA gene from the surface and upper oxycline could be grouped in a marine subcluster, also containing no cultured representatives. In contrast, all 74 amoA sequences originating from the OMZ were either closely affiliated with cultured Nitrosospira spp. from clusters 0 and 2 or with other yet-uncultured βAOB from soil and an aerated-anoxic Orbal process waste treatment plant. Our results reveal the presence of Nitrosospira-like βAOB in both oxic and suboxic waters associated with the OMZ but with a clear community shift at the functional level (amoA) along the strong oxygen gradient. PMID:17416686

  11. Spatiotemporal Dynamics of Ammonia-Oxidizing Thaumarchaeota in Distinct Arctic Water Masses

    Directory of Open Access Journals (Sweden)

    Oliver Müller

    2018-01-01

    Full Text Available One of the most abundant archaeal groups on Earth is the Thaumarchaeota. They are recognized as major contributors to marine ammonia oxidation, a crucial step in the biogeochemical cycling of nitrogen. Their universal success is attributed to a high genomic flexibility and niche adaptability. Based on differences in the gene coding for ammonia monooxygenase subunit A (amoA, two different ecotypes with distinct distribution patterns in the water column have been identified. We used high-throughput sequencing of 16S rRNA genes combined with archaeal amoA functional gene clone libraries to investigate which environmental factors are driving the distribution of Thaumarchaeota ecotypes in the Atlantic gateway to the Arctic Ocean through an annual cycle in 2014. We observed the characteristic vertical pattern of Thaumarchaeota abundance with high values in the mesopelagic (>200 m water throughout the entire year, but also in the epipelagic (<200 m water during the dark winter months (January, March and November. The Thaumarchaeota community was dominated by three OTUs which on average comprised 76% ± 11 and varied in relative abundance according to water mass characteristics and not to depth or ammonium concentration, as suggested in previous studies. The ratios of the abundance of the different OTU types were similar to that of the functional amoA water cluster types. Together, this suggests a strong selection of ecotypes within different water masses, supporting the general idea of water mass characteristics as an important factor in defining microbial community structure. If indeed, as suggested in this study, Thaumarchaeota population dynamics are controlled by a set of factors, described here as water mass characteristics and not just depth alone, then changes in water mass flow will inevitably affect the distribution of the different ecotypes.

  12. Fauna Europaea - all European animal species on the web

    DEFF Research Database (Denmark)

    de Jong, Yde; Verbeek, Melina; Michelsen, Verner

    2014-01-01

    Abstract Fauna Europaea is Europe's main zoological taxonomic index, making the scientific names and distributions of all living, currently known, multicellular, European land and freshwater animals species integrally available in one authoritative database. Fauna Europaea covers about 260...

  13. Cultivation and Genomic Analysis of “Candidatus Nitrosocaldus islandicus,” an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland

    Directory of Open Access Journals (Sweden)

    Anne Daebeler

    2018-02-01

    Full Text Available Ammonia-oxidizing archaea (AOA within the phylum Thaumarchaeota are the only known aerobic ammonia oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from the Nitrosocaldus clade, group 1.1b and group 1.1a Thaumarchaeota in terrestrial high-temperature habitats, only one§ enrichment culture of an AOA thriving above 50°C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a newly discovered thaumarchaeon from the deep-branching Nitrosocaldaceae family of which we have obtained a high (∼85% enrichment from biofilm of an Icelandic hot spring (73°C. This AOA, which we provisionally refer to as “Candidatus Nitrosocaldus islandicus,” is an obligately thermophilic, aerobic chemolithoautotrophic ammonia oxidizer, which stoichiometrically converts ammonia to nitrite at temperatures between 50 and 70°C. “Ca. N. islandicus” encodes the expected repertoire of enzymes proposed to be required for archaeal ammonia oxidation, but unexpectedly lacks a nirK gene and also possesses no identifiable other enzyme for nitric oxide (NO generation§. Nevertheless, ammonia oxidation by this AOA appears to be NO-dependent as “Ca. N. islandicus” is, like all other tested AOA, inhibited by the addition of an NO scavenger. Furthermore, comparative genomics revealed that “Ca. N. islandicus” has the potential for aromatic amino acid fermentation as its genome encodes an indolepyruvate oxidoreductase (iorAB as well as a type 3b hydrogenase, which are not present in any other sequenced AOA. A further surprising genomic feature of this thermophilic ammonia oxidizer is the absence of DNA polymerase D genes§ – one of the predominant replicative DNA polymerases in all other ammonia-oxidizing Thaumarchaeota. Collectively, our findings suggest that metabolic versatility and DNA replication might differ substantially between obligately

  14. Cultivation and Genomic Analysis of "Candidatus Nitrosocaldus islandicus," an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland.

    Science.gov (United States)

    Daebeler, Anne; Herbold, Craig W; Vierheilig, Julia; Sedlacek, Christopher J; Pjevac, Petra; Albertsen, Mads; Kirkegaard, Rasmus H; de la Torre, José R; Daims, Holger; Wagner, Michael

    2018-01-01

    Ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota are the only known aerobic ammonia oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from the Nitrosocaldus clade, group 1.1b and group 1.1a Thaumarchaeota in terrestrial high-temperature habitats, only one enrichment culture of an AOA thriving above 50°C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a newly discovered thaumarchaeon from the deep-branching Nitrosocaldaceae family of which we have obtained a high (∼85%) enrichment from biofilm of an Icelandic hot spring (73°C). This AOA, which we provisionally refer to as " Candidatus Nitrosocaldus islandicus," is an obligately thermophilic, aerobic chemolithoautotrophic ammonia oxidizer, which stoichiometrically converts ammonia to nitrite at temperatures between 50 and 70°C. " Ca. N. islandicus" encodes the expected repertoire of enzymes proposed to be required for archaeal ammonia oxidation, but unexpectedly lacks a nirK gene and also possesses no identifiable other enzyme for nitric oxide (NO) generation. Nevertheless, ammonia oxidation by this AOA appears to be NO-dependent as " Ca. N. islandicus" is, like all other tested AOA, inhibited by the addition of an NO scavenger. Furthermore, comparative genomics revealed that " Ca. N. islandicus" has the potential for aromatic amino acid fermentation as its genome encodes an indolepyruvate oxidoreductase ( iorAB ) as well as a type 3b hydrogenase, which are not present in any other sequenced AOA. A further surprising genomic feature of this thermophilic ammonia oxidizer is the absence of DNA polymerase D genes - one of the predominant replicative DNA polymerases in all other ammonia-oxidizing Thaumarchaeota. Collectively, our findings suggest that metabolic versatility and DNA replication might differ substantially between obligately thermophilic and other AOA.

  15. Cultivation and Genomic Analysis of “Candidatus Nitrosocaldus islandicus,” an Obligately Thermophilic, Ammonia-Oxidizing Thaumarchaeon from a Hot Spring Biofilm in Graendalur Valley, Iceland

    Science.gov (United States)

    Daebeler, Anne; Herbold, Craig W.; Vierheilig, Julia; Sedlacek, Christopher J.; Pjevac, Petra; Albertsen, Mads; Kirkegaard, Rasmus H.; de la Torre, José R.; Daims, Holger; Wagner, Michael

    2018-01-01

    Ammonia-oxidizing archaea (AOA) within the phylum Thaumarchaeota are the only known aerobic ammonia oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from the Nitrosocaldus clade, group 1.1b and group 1.1a Thaumarchaeota in terrestrial high-temperature habitats, only one§ enrichment culture of an AOA thriving above 50°C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a newly discovered thaumarchaeon from the deep-branching Nitrosocaldaceae family of which we have obtained a high (∼85%) enrichment from biofilm of an Icelandic hot spring (73°C). This AOA, which we provisionally refer to as “Candidatus Nitrosocaldus islandicus,” is an obligately thermophilic, aerobic chemolithoautotrophic ammonia oxidizer, which stoichiometrically converts ammonia to nitrite at temperatures between 50 and 70°C. “Ca. N. islandicus” encodes the expected repertoire of enzymes proposed to be required for archaeal ammonia oxidation, but unexpectedly lacks a nirK gene and also possesses no identifiable other enzyme for nitric oxide (NO) generation§. Nevertheless, ammonia oxidation by this AOA appears to be NO-dependent as “Ca. N. islandicus” is, like all other tested AOA, inhibited by the addition of an NO scavenger. Furthermore, comparative genomics revealed that “Ca. N. islandicus” has the potential for aromatic amino acid fermentation as its genome encodes an indolepyruvate oxidoreductase (iorAB) as well as a type 3b hydrogenase, which are not present in any other sequenced AOA. A further surprising genomic feature of this thermophilic ammonia oxidizer is the absence of DNA polymerase D genes§ – one of the predominant replicative DNA polymerases in all other ammonia-oxidizing Thaumarchaeota. Collectively, our findings suggest that metabolic versatility and DNA replication might differ substantially between obligately thermophilic and

  16. Effects of different fertilizers on the abundance and community structure of ammonia oxidizers in a yellow clay soil.

    Science.gov (United States)

    Yao, Huaiying; Huang, Sha; Qiu, Qiongfen; Li, Yaying; Wu, Lianghuan; Mi, Wenhai; Dai, Feng

    2016-08-01

    Yellow clay paddy soil (Oxisols) is a typical soil with low productivity in southern China. Nitrification inhibitors and slow release fertilizers have been used to improve nitrogen fertilizer utilization and reduce environmental impaction of the paddy soil. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in paddy soil have rarely been investigated. In the present work, we compared the influences of several slow release fertilizers and nitrification inhibitors on the community structure and activities of the ammonia oxidizers in yellow clay soil. The abundances and community compositions of AOA and AOB were determined with qPCR, terminal restriction fragment length polymorphism (T-RFLP), and clone library approaches. Our results indicated that the potential nitrification rate (PNR) of the soil was significantly related to the abundances of both AOA and AOB. Nitrogen fertilizer application stimulated the growth of AOA and AOB, and the combinations of nitrapyrin with urea (NPU) and urea-formaldehyde (UF) inhibited the growth of AOA and AOB, respectively. Compared with other treatments, the applications of NPU and UF also led to significant shifts in the community compositions of AOA and AOB, respectively. NPU showed an inhibitory effect on AOA T-RF 166 bp that belonged to Nitrosotalea. UF had a negative effect on AOB T-RF 62 bp that was assigned to Nitrosospira. These results suggested that NPU inhibited PNR and increased nitrogen use efficiency (NUE) by inhibiting the growth of AOA and altering AOA community. UF showed no effect on NUE but decreased AOB abundance and shifted AOB community.

  17. Diversity, abundance and niche differentiation of ammonia-oxidizing prokaryotes in mud deposits of the eastern China marginal seas

    Directory of Open Access Journals (Sweden)

    Shaolan eYu

    2016-02-01

    Full Text Available The eastern China marginal seas are prominent examples of river-dominated ocean margins, whose most characteristic feature is the existence of isolated mud patches on sandy sediments. Ammonia-oxidizing prokaryotes play a crucial role in the nitrogen cycles of many marine environments, including marginal seas. However, few studies have attempted to address the distribution patterns of ammonia-oxidizing prokaryotes in mud deposits of these seas. The horizontal and vertical community composition and abundance of ammonia-oxidizing archaea (AOA and bacteria (AOB were investigated in mud deposits of the South Yellow Sea (SYS and the East China Sea (ECS by using amoA clone libraries and quantitative PCR. The diversity of AOB was comparable or higher in the mud zone of SYS and lower in ECS when compared with AOA. Vertically, surface sediments had generally higher diversity of AOA and AOB than middle and bottom layers. Diversity of AOA and AOB showed significant correlation with latitude. Nitrosopumilus and Nitrosospira lineages dominated AOA and AOB communities, respectively. Both AOA and AOB assemblages exhibited greater variations across different sites than those among various depths at one site. The abundance of bacterial amoA was generally higher than that of archaeal amoA, and both of them decreased with depth. Niche differentiation, which was affected by dissolved oxygen, salinity, ammonia and silicate (SiO32-, was observed between AOA and AOB and among different groups of them. The spatial distribution of AOA and AOB was significantly correlated with δ15NTN and SiO32-, and nitrate and δ13C, respectively. Both archaeal and bacterial amoA abundance correlated strongly with SiO32-. This study improves our understanding of spatial distribution of AOA and AOB in ecosystems featuring oceanic mud deposits.

  18. Insights into high-temperature nitrogen cycling from studies of the thermophilic ammonia-oxidizing archaeon Nitrosocaldus yellowstonii. (Invited)

    Science.gov (United States)

    de la Torre, J. R.

    2010-12-01

    Our understanding of the nitrogen cycle has advanced significantly in recent years with the discovery of new metabolic processes and the recognition that key processes such as aerobic ammonia oxidation are more broadly distributed among extant organisms and habitat ranges. Nitrification, the oxidation of ammonia to nitrite and nitrate, is a key component of the nitrogen cycle and, until recently, was thought to be mediated exclusively by the ammonia-oxidizing bacteria (AOB). The discovery that mesophilic marine archaea, some of the most abundant microorganisms on the planet, are capable of oxidizing ammonia to nitrite fundamentally changed our perception of the global nitrogen cycle. Ammonia-oxidizing archaea (AOA) are now thought to be significant drivers of nitrification in many marine and terrestrial environments. Most studies, however, have focused on the contribution of AOA to nitrogen cycling in mesophilic environments. Our recent discovery of a thermophilic AOA, Nitrosocaldus yellowstonii, has expanded the role and habitat range of AOA to include high temperature environments. Numerous studies have shown that AOA are widely distributed in geothermal habitats with a wide range of temperature and pH. The availability of multiple AOA genome sequences, combined with metagenomic studies from mesophilic and thermophilic environments gives us a better understanding of the physiology, ecology and evolution of these organisms. Recent studies have proposed that the AOA represent the most deeply branching lineage within the Archaea, the Thaumarchaeota. Furthermore, genomic comparisons between AOA and AOB reveal significant differences in the proposed pathways for ammonia oxidation. These genetic differences likely explain fundamental physiological differences such as the resistance of N. yellowstonii and other AOA to the classical nitrification inhibitors allylthiourea and acetylene. Physiological studies suggest that the marine AOA are adapted to oligotrophic

  19. Contribution of crenarchaeal autotrophic ammonia oxidizers to the dark primary production in Tyrrhenian deep waters (Central Mediterranean Sea)

    OpenAIRE

    Yakimov, Michail M.; La Cono, Violetta; Smedile, Francesco; DeLuca, Thomas H.; Juarez, Silvia; Ciordia, Sergio; Fernandez, Marisol; Albar, Juan Pablo; Ferrer, Manuel; Golyshin, Peter N.; Giuliano, Laura

    2011-01-01

    Mesophilic Crenarchaeota have recently been thought to be significant contributors to nitrogen (N) and carbon (C) cycling. In this study, we examined the vertical distribution of ammonia-oxidizing Crenarchaeota at offshore site in Southern Tyrrhenian Sea. The median value of the crenachaeal cell to amoA gene ratio was close to one suggesting that virtually all deep-sea Crenarchaeota possess the capacity to oxidize ammonia. Crenarchaea-specific genes, nirK and ureC, for nitrite reductase and u...

  20. Responses of bacterial and archaeal ammonia oxidizers to soil organic and fertilizer amendments under long-term management

    Energy Technology Data Exchange (ETDEWEB)

    Wessen, E.; Nyberg, K.; Jansson, J.K.; Hallin, S.

    2010-05-01

    Ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) co-exist in soil, but their relative distribution may vary depending on the environmental conditions. Effects of changes in soil organic matter and nutrient content on the AOB and AOA are poorly understood. Our aim was to compare effects of long-term soil organic matter depletion and amendments with labile (straw) and more recalcitrant (peat) organic matter, with and without easily plant-available nitrogen, on the activities, abundances and community structures of AOB and AOA. Soil was sampled from a long-term field site in Sweden that was established in 1956. The potential ammonia oxidation rates, the AOB and AOA amoA gene abundances and the community structures of both groups based on T-RFLP of amoA genes were determined. Straw amendment during 50 years had not altered any of the measured soil parameters, while the addition of peat resulted in a significant increase of soil organic carbon as well as a decrease in pH. Nitrogen fertilization alone resulted in a small decrease in soil pH, organic carbon and total nitrogen, but an increase in primary production. Type and amount of organic matter had an impact on the AOB and AOA community structures and the AOA abundance. Our findings confirmed that AOA are abundant in soil, but showed that under certain conditions the AOB dominate, suggesting niche differentiation between the two groups at the field site. The large differences in potential rates between treatments correlated to the AOA community size, indicating that they were functionally more important in the nitrification process than the AOB. The AOA abundance was positively related to addition of labile organic carbon, which supports the idea that AOA could have alternative growth strategies using organic carbon. The AOB community size varied little in contrast to that of the AOA. This indicates that the bacterial ammonia oxidizers as a group have a greater ecophysiological diversity and

  1. Distribution and Abundance of Archaea in South China Sea Sponge Holoxea sp. and the Presence of Ammonia-Oxidizing Archaea in Sponge Cells

    Directory of Open Access Journals (Sweden)

    Fang Liu

    2011-01-01

    Full Text Available Compared with bacterial symbionts, little is known about archaea in sponges especially about their spatial distribution and abundance. Understanding the distribution and abundance of ammonia-oxidizing archaea will help greatly in elucidating the potential function of symbionts in nitrogen cycling in sponges. In this study, gene libraries of 16S rRNA gene and ammonia monooxygenase subunit A (amoA genes and quantitative real-time PCR were used to study the spatial distribution and abundance of archaea in the South China Sea sponge Holoxea sp. As a result, Holoxea sp. specific AOA, mainly group C1a (marine group I: Crenarchaeota were identified. The presence of ammonia-oxidizing crenarchaea was observed for the first time within sponge cells. This study suggested a close relationship between sponge host and its archaeal symbionts as well as the archaeal potential contribution to sponge host in the ammonia-oxidizing process of nitrification.

  2. The large-scale distribution of ammonia oxidizers in paddy soils is driven by soil pH, geographic distance and climatic factors

    Directory of Open Access Journals (Sweden)

    Hangwei eHu

    2015-09-01

    Full Text Available Paddy soils distribute widely from temperate to tropical regions, and are characterized by intensive nitrogen fertilization practices in China. Mounting evidence has confirmed the functional importance of ammonia-oxidizing archaea (AOA and bacteria (AOB in soil nitrification, but little is known about their biogeographic distribution patterns in paddy ecosystems. Here, we used barcoded pyrosequencing to characterize the effects of climatic, geochemical and spatial factors on the distribution of ammonia oxidizers from 11 representative rice-growing regions (75-1945 km apart of China. Potential nitrification rates varied greatly by more than three orders of magnitude, and were significantly correlated with the abundances of AOA and AOB. The community composition of ammonia oxidizer was affected by multiple factors, but changes in relative abundances of the major lineages could be best predicted by soil pH. The alpha diversity of AOA and AOB displayed contrasting trends over the gradients of latitude and atmospheric temperature, indicating a possible niche separation between AOA and AOB along the latitude. The Bray-Curtis dissimilarities in ammonia-oxidizing community structure significantly increased with increasing geographical distance, indicating that more geographically distant paddy fields tend to harbor more dissimilar ammonia oxidizers. Variation partitioning analysis revealed that spatial, geochemical and climatic factors could jointly explain majority of the data variation, and were important drivers defining the ecological niches of AOA and AOB. Our findings suggest that both AOA and AOB are of functional importance in paddy soil nitrification, and ammonia oxidizers in paddy ecosystems exhibit large-scale biogeographic patterns shaped by soil pH, geographic distance, and climatic factors.

  3. Archaeal dominated ammonia-oxidizing communities in Icelandic grassland soils are moderately affected by long-term N fertilization and geothermal heating

    Directory of Open Access Journals (Sweden)

    Anne eDaebeler

    2012-10-01

    Full Text Available The contribution of ammonia-oxidizing bacteria and archaea (AOB and AOA, respectively to the net oxidation of ammonia varies greatly between terrestrial environments. To better understand, predict and possibly manage terrestrial nitrogen turnover, we need to develop a conceptual understanding of ammonia oxidation as a function of environmental conditions including the ecophysiology of the associated organisms. We examined the discrete and combined effects of mineral nitrogen deposition and geothermal heating on ammonia-oxidizing communities by sampling soils from a long-term fertilisation site along a temperature gradient in Icelandic grasslands. Microarray, clone library and quantitative PCR analyses of the ammonia monooxygenase subunit A (amoA gene accompanied by physico-chemical measurements of the soil properties were conducted. In contrast to most other terrestrial environments, the ammonia-oxidizing communities consisted almost exclusively of archaea. Their bacterial counterparts proved to be undetectable by quantitative PCR suggesting AOB are only of minor relevance for ammonia oxidation in these soils. Our results show that fertilization and local, geothermal warming affected detectable ammonia-oxidizing communities, but not soil chemistry: only a subset of the detected AOA phylotypes was present in higher temperature soils and AOA abundance was increased in the fertilized soils, while the measured soil physico-chemical properties remained unchanged. Differences in distribution and structure of AOA communities were best explained by soil pH and clay content irrespective of temperature or fertilizer treatment in these grassland soils, suggesting that these factors have a greater potential for ecological niche-differentiation of AOA in soil than temperature and N fertilization.

  4. Temporal changes in abundance and composition of ammonia-oxidizing bacterial and archaeal communities in a drained peat soil in relation to N{sub 2}O emissions

    Energy Technology Data Exchange (ETDEWEB)

    Andert, Janet [Swedish Univ. of Agricultural Sciences, Uppsala (Sweden). Dept. of Microbiology; Max-Planck-Institute of Colloids and Interfaces, Potsdam (Germany); Wessen, Ella; Hallin, Sara [Swedish Univ. of Agricultural Sciences, Uppsala (Sweden). Dept. of Microbiology; Boerjesson, Gunnar [Swedish Univ. of Agricultural Sciences, Uppsala (Sweden). Dept. of Soil and Environment

    2011-12-15

    Boreal peat soils comprise about 3% of the terrestrial environments, and when drained, they become sources of the greenhouse gas nitrous oxide (N{sub 2}O). Ammonia oxidation can result in N{sub 2}O emissions, either directly or by fuelling denitrification, but we know little about the ecology of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in peat soils. Our aim was to determine temporal alterations in abundance and composition of these communities in a drained and forested peat soil in relation to N{sub 2}O emissions and ammonia oxidation activity. Materials and methods The peat was sampled at three different depths in the upper 0.5 m over a period of 9 months covering two summer and two winter samplings. Community composition and abundance were determined by T-RFLP and quantitative real-time PCR of the bacterial and archaeal amoA genes. Potential ammonia oxidation rates were measured using the chlorate inhibition technique, and in situ N{sub 2}O emission was determined using chambers. Results and discussion The soil parameters displayed little spatial and temporal heterogeneity, which probably explained why there were no depth-related effects on the abundance, composition, or activity of the ammonia oxidizers. In contrast to most terrestrial environments, the AOB dominated numerically over the AOA. Both groups changed in community composition between sampling occasions, although the AOB showed more significant seasonal signatures than the AOA. Temporal changes in abundance were only observed for the AOB, with a decrease in numbers from May to March. Such differences were not reflected by the activity or N{sub 2}O emissions. Conclusions The high ammonium concentrations in the peat soil likely favored the AOB over the AOA, and we hypothesize that they were more active than the AOA and therefore responded to climatic and environmental changes. However, other processes rather than ammonia oxidation were likely responsible for N{sub 2}O emissions at the site.

  5. Enrichment of Thermophilic Ammonia-Oxidizing Archaea from an Alkaline Hot Spring in the Great Basin, USA

    Science.gov (United States)

    Zhang, C.; Huang, Z.; Jiang, H.; Wiegel, J.; Li, W.; Dong, H.

    2010-12-01

    One of the major advances in the nitrogen cycle is the recent discovery of ammonia oxidation by archaea. While culture-independent studies have revealed occurrence of ammonia-oxidizing archaea (AOA) in nearly every surface niche on earth, most of these microorganisms have resisted isolation and so far only a few species have been identified. The Great Basin contains numerous hot springs, which are characterized by moderately high temperature (40-65 degree C) and circumneutral or alkaline pH. Unique thermophilic archaea have been identified based on molecular DNA and lipid biomarkers; some of which may be ammonia oxidizers. This study aims to isolate some of these archaea from a California hot spring that has pH around 9.0 and temperature around 42 degree C. Mat material was collected from the spring and transported on ice to the laboratory. A synthetic medium (SCM-5) was inoculated with the mat material and the culture was incubated under varying temperature (35-65 degree C) and pH (7.0-10.0) conditions using antibiotics to suppress bacterial growth. Growth of the culture was monitored by microscopy, decrease in ammonium and increase in nitrite, and increases in Crenarchaeota and AOA abundances over time. Clone libraries were constructed to compare archaeal community structures before and after the enrichment experiment. Temperature and pH profiles indicated that the culture grew optimally at pH 9.0 and temperature 45 degree C, which are consistent with the geochemical conditions of the natural environment. Phylogenetic analysis showed that the final OTU was distantly related to all known hyperthermophilic archaea. Analysis of the amoA genes showed two OTUs in the final culture; one of them was closely related to Candidatus Nitrososphaera gargensis. However, the enrichment culture always contained bacteria and attempts to separate them from archaea have failed. This highlights the difficulty in bringing AOA into pure culture and suggests that some of the AOA may

  6. Dynamics of nitrification and denitrification in root- oxygenated sediments and adaptation of ammonia-oxidizing bacteria to low-oxygen or anoxic habitats

    NARCIS (Netherlands)

    Bodelier, P.L.E.; Libochant, J.A.; Blom, C.W.P.M.; Laanbroek, H.J.

    1996-01-01

    Oxygen-releasing plants may provide aerobic niches in anoxic sediments and soils for ammonia-oxidizing bacteria. The oxygen-releasing, aerenchymatous emergent macrophyte Glyceria maxima had a strong positive effect on numbers and activities of the nitrifying bacteria in its root zone in spring and

  7. Dynamics of nitrification and denitrification in root- oxygenated sediments and adaptation of ammonia-oxidizing bacteria to low-oxygen or anoxic habitats

    NARCIS (Netherlands)

    Bodelier, P.L.E.; Libochant, J.A.; Blom, C.W.P.M.; Laanbroek, H.J.

    1996-01-01

    Oxygen-releasing plants may provide aerobic niches in anoxic sediments and soils for ammonia-oxidizing bacteria, The oxygen- releasing, aerenchymatous emergent macrophyte Glycerin maxima had a strong positive effect on numbers and activities of the nitrifying bacteria in its root zone in spring and

  8. Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats.

    Directory of Open Access Journals (Sweden)

    Elena V Lebedeva

    Full Text Available The discovery of ammonia-oxidizing archaea (AOA of the phylum Thaumarchaeota and the high abundance of archaeal ammonia monooxygenase subunit A encoding gene sequences in many environments have extended our perception of nitrifying microbial communities. Moreover, AOA are the only aerobic ammonia oxidizers known to be active in geothermal environments. Molecular data indicate that in many globally distributed terrestrial high-temperature habits a thaumarchaeotal lineage within the Nitrosopumilus cluster (also called "marine" group I.1a thrives, but these microbes have neither been isolated from these systems nor functionally characterized in situ yet. In this study, we report on the enrichment and genomic characterization of a representative of this lineage from a thermal spring in Kamchatka. This thaumarchaeote, provisionally classified as "Candidatus Nitrosotenuis uzonensis", is a moderately thermophilic, non-halophilic, chemolithoautotrophic ammonia oxidizer. The nearly complete genome sequence (assembled into a single scaffold of this AOA confirmed the presence of the typical thaumarchaeotal pathways for ammonia oxidation and carbon fixation, and indicated its ability to produce coenzyme F420 and to chemotactically react to its environment. Interestingly, like members of the genus Nitrosoarchaeum, "Candidatus N. uzonensis" also possesses a putative artubulin-encoding gene. Genome comparisons to related AOA with available genome sequences confirmed that the newly cultured AOA has an average nucleotide identity far below the species threshold and revealed a substantial degree of genomic plasticity with unique genomic regions in "Ca. N. uzonensis", which potentially include genetic determinants of ecological niche differentiation.

  9. Enrichment and genome sequence of the group I.1a ammonia-oxidizing Archaeon "Ca. Nitrosotenuis uzonensis" representing a clade globally distributed in thermal habitats.

    Science.gov (United States)

    Lebedeva, Elena V; Hatzenpichler, Roland; Pelletier, Eric; Schuster, Nathalie; Hauzmayer, Sandra; Bulaev, Aleksandr; Grigor'eva, Nadezhda V; Galushko, Alexander; Schmid, Markus; Palatinszky, Marton; Le Paslier, Denis; Daims, Holger; Wagner, Michael

    2013-01-01

    The discovery of ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota and the high abundance of archaeal ammonia monooxygenase subunit A encoding gene sequences in many environments have extended our perception of nitrifying microbial communities. Moreover, AOA are the only aerobic ammonia oxidizers known to be active in geothermal environments. Molecular data indicate that in many globally distributed terrestrial high-temperature habits a thaumarchaeotal lineage within the Nitrosopumilus cluster (also called "marine" group I.1a) thrives, but these microbes have neither been isolated from these systems nor functionally characterized in situ yet. In this study, we report on the enrichment and genomic characterization of a representative of this lineage from a thermal spring in Kamchatka. This thaumarchaeote, provisionally classified as "Candidatus Nitrosotenuis uzonensis", is a moderately thermophilic, non-halophilic, chemolithoautotrophic ammonia oxidizer. The nearly complete genome sequence (assembled into a single scaffold) of this AOA confirmed the presence of the typical thaumarchaeotal pathways for ammonia oxidation and carbon fixation, and indicated its ability to produce coenzyme F420 and to chemotactically react to its environment. Interestingly, like members of the genus Nitrosoarchaeum, "Candidatus N. uzonensis" also possesses a putative artubulin-encoding gene. Genome comparisons to related AOA with available genome sequences confirmed that the newly cultured AOA has an average nucleotide identity far below the species threshold and revealed a substantial degree of genomic plasticity with unique genomic regions in "Ca. N. uzonensis", which potentially include genetic determinants of ecological niche differentiation.

  10. Tide as steering factor in structuring archaeal and bacterial ammonia-oxidizing communities in mangrove forest soils dominated by Avicennia germinans and Rhizophora mangle

    NARCIS (Netherlands)

    Marcos, Magali S.; Barboza, A.D.H.; Keijzer, R.M.; Laanbroek, H.J.

    2018-01-01

    Mangrove species are adapted to grow at specific zones in a tidal gradient. Here we tested the hypothesis that the archaeal and bacterial ammonia-oxidizing microbial communities differ in soils dominated by the mangrove species Avicennia germinans and Rhizophora mangle. Two of the sampling locations

  11. Tide as steering factor in structuring archaeal and bacterial ammonia-oxidizing communities in mangrove forest soils dominated by Avicennia germinans and Rhizophora mangle

    NARCIS (Netherlands)

    Marcos, Magali S.; Barboza, A.D.H.; Keijzer, R.M.; Laanbroek, H.J.

    2017-01-01

    Mangrove species are adapted to grow at specific zones in a tidal gradient. Here we tested the hypothesis that the archaeal and bacterial ammonia-oxidizing microbial communities differ in soils dominated by the mangrove species Avicennia germinans and Rhizophora mangle. Two of the sampling locations

  12. Tide as Steering Factor in Structuring Archaeal and Bacterial Ammonia-Oxidizing Communities in Mangrove Forest Soils Dominated by Avicennia germinans and Rhizophora mangle.

    Science.gov (United States)

    Marcos, Magalí S; Barboza, Anthony D; Keijzer, Rosalinde M; Laanbroek, Hendrikus J

    2017-10-23

    Mangrove species are adapted to grow at specific zones in a tidal gradient. Here we tested the hypothesis that the archaeal and bacterial ammonia-oxidizing microbial communities differ in soils dominated by the mangrove species Avicennia germinans and Rhizophora mangle. Two of the sampling locations were tidal locations, while the other location was impounded. Differences in the community compositions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were analyzed by denaturing gradient gel electrophoresis (DGGE) of amoA genes and by MiSeq 16S rRNA gene-sequencing. The abundances of AOA and AOB were established by quantitative PCR of amoA genes. In addition, we analyzed the total microbial community composition based on 16S rRNA genes and explored the influence of soil physicochemical properties underneath Avicennia germinans and Rhizophora mangle on microbial communities. AOA were always more abundant than AOB, but the effect of mangrove species on total numbers of ammonia oxidizers was location-specific. The microbial communities including the ammonia oxidizers in soils associated with A. germinans and R. mangle differed only at the tidal locations. In conclusion, potential site-specific effects of mangrove species on soil microbial communities including those of the AOA and AOB are apparently overruled by the absence or presence of tide.

  13. Changes in community composition of ammonia-oxidizing betaproteobacteria from stands of Black mangrove (Avicennia germinans) in response to ammonia enrichment and more oxic conditions

    NARCIS (Netherlands)

    Laanbroek, H.J.; Keijzer, R.M.; Verhoeven, J.T.A.; Whigham, D.F.

    2013-01-01

    In flooded and non-flooded impounded forests of Black mangrove (Avicennia germinans), the community structure of the ammonia-oxidizing betaproteobacteria (β-AOB) differed among distinct mangrove vegetation cover types and hydrological regimes. This had been explained by a differential response of

  14. Spatial interaction of archaeal ammonia-oxidizers and nitrite-oxidizing bacteria in an unfertilized grassland soil

    Directory of Open Access Journals (Sweden)

    Barbara eStempfhuber

    2016-01-01

    Full Text Available Interrelated successive transformation steps of nitrification are performed by distinct microbial groups – the ammonia-oxidizers, comprising ammonia-oxidizing archaea (AOA and bacteria (AOB, and nitrite-oxidizers such as Nitrobacter and Nitrospira, which are the dominant genera in the investigated soils. Hence, not only their presence and activity in the investigated habitat is required for nitrification, but also their temporal and spatial interactions. To demonstrate the interdependence of both groups and to address factors promoting putative niche differentiation within each group, temporal and spatial changes in nitrifying organisms were monitored in an unfertilized grassland site over an entire vegetation period at the plot scale of 10 m². Nitrifying organisms were assessed by measuring the abundance of marker genes (amoA for AOA and AOB, nxrA for Nitrobacter, 16S rRNA gene for Nitrospira selected for the respective sub-processes. A positive correlation between numerically dominant AOA and Nitrospira, and their co-occurrence at the same spatial scale in August and October, suggests that the nitrification process is predominantly performed by these groups and is restricted to a limited timeframe. Amongst nitrite-oxidizers, niche differentiation was evident in observed seasonally varying patterns of co-occurrence and spatial separation. While their distributions were most likely driven by substrate concentrations, oxygen availability may also have played a role under substrate-limited conditions. Phylogenetic analysis revealed temporal shifts in Nitrospira community composition with an increasing relative abundance of OTU03 assigned to sublineage V from August onwards, indicating its important role in nitrite oxidation.

  15. Elevational diversity and distribution of ammonia-oxidizing archaea community in meadow soils on the Tibetan Plateau.

    Science.gov (United States)

    Zhao, Kang; Kong, Weidong; Khan, Ajmal; Liu, Jinbo; Guo, Guangxia; Muhanmmad, Said; Zhang, Xianzhou; Dong, Xiaobin

    2017-09-01

    Unraveling elevational diversity patterns of plants and animals has long been attracting scientific interests. However, whether soil microorganisms exhibit similar elevational patterns remains largely less explored, especially for functional microbial communities, such as ammonia oxidizers. Here, we investigated the diversity and distribution pattern of ammonia-oxidizing archaea (AOA) in meadow soils along an elevation gradient from 4400 m to the grassline at 5100 m on the Tibetan Plateau using terminal restriction fragment length polymorphism (T-RFLP) and sequencing methods by targeting amoA gene. Increasing elevations led to lower soil temperature and pH, but higher nutrients and water content. The results showed that AOA diversity and evenness monotonically increased with elevation, while richness was relatively stable. The increase of diversity and evenness was attributed to the growth inhibition of warm-adapted AOA phylotypes by lower temperature and the growth facilitation of cold-adapted AOA phylotypes by richer nutrients at higher elevations. Low temperature thus played an important role in the AOA growth and niche separation. The AOA community variation was explained by the combined effect of all soil properties (32.6%), and 8.1% of the total variation was individually explained by soil pH. The total AOA abundance decreased, whereas soil potential nitrification rate (PNR) increased with increasing elevations. Soil PNR positively correlated with the abundance of cold-adapted AOA phylotypes. Our findings suggest that low temperature plays an important role in AOA elevational diversity pattern and niche separation, rising the negative effects of warming on AOA diversity and soil nitrification process in the Tibetan region.

  16. Community Composition and Transcriptional Activity of Ammonia-Oxidizing Prokaryotes of Seagrass Thalassia hemprichii in Coral Reef Ecosystems

    Directory of Open Access Journals (Sweden)

    Juan Ling

    2018-01-01

    Full Text Available Seagrasses in coral reef ecosystems play important ecological roles by enhancing coral reef resilience under ocean acidification. However, seagrass primary productivity is typically constrained by limited nitrogen availability. Ammonia oxidation is an important process conducted by ammonia-oxidizing archaea (AOA and bacteria (AOB, yet little information is available concerning the community structure and potential activity of seagrass AOA and AOB. Therefore, this study investigated the variations in the abundance, diversity and transcriptional activity of AOA and AOB at the DNA and transcript level from four sample types: the leaf, root, rhizosphere sediment and bulk sediment of seagrass Thalassia hemprichii in three coral reef ecosystems. DNA and complementary DNA (cDNA were used to prepare clone libraries and DNA and cDNA quantitative PCR (qPCR assays, targeting the ammonia monooxygenase-subunit (amoA genes as biomarkers. Our results indicated that the closest relatives of the obtained archaeal and bacterial amoA gene sequences recovered from DNA and cDNA libraries mainly originated from the marine environment. Moreover, all the obtained AOB sequences belong to the Nitrosomonadales cluster. Nearly all the AOA communities exhibited higher diversity than the AOB communities at the DNA level, but the qPCR data demonstrated that the abundances of AOB communities were higher than that of AOA communities based on both DNA and RNA transcripts. Collectively, most of the samples shared greater community composition similarity with samples from the same location rather than sample type. Furthermore, the abundance of archaeal amoA gene in rhizosphere sediments showed significant relationships with the ammonium concentration of sediments and the nitrogen content of plant tissue (leaf and root at the DNA level (P < 0.05. Conversely, no such relationships were found for the AOB communities. This work provides new insight into the nitrogen cycle

  17. Dominant role of ammonia-oxidizing bacteria in nitrification due to ammonia accumulation in sediments of Danjiangkou reservoir, China.

    Science.gov (United States)

    Dang, Chenyuan; Liu, Wen; Lin, Yaxuan; Zheng, Maosheng; Jiang, Huan; Chen, Qian; Ni, Jinren

    2018-04-01

    Surface sediments are the inner source of contaminations in aquatic systems and usually maintain aerobic conditions. As the key participators of nitrification process, little is known about the activities and contributions of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in the surface sediments. In this study, we determined the net and potential nitrification rates and used 1-octyne as an AOB specific inhibitor to detect the contributions of AOA and AOB to nitrification in surface sediments of Danjiangkou reservoir, which is the water source area of the middle route of South-to-North Water Diversion Project in China. Quantitative PCR and Illumina high-throughput sequencing were used to evaluate the abundance and diversity of the amoA gene. The net and potential nitrification rates ranged from 0.42 to 1.93 and 2.06 to 8.79 mg N kg -1 dry sediments d -1 , respectively. AOB dominated in both net and potential nitrification, whose contribution accounted for 52.7-78.6% and 59.9-88.1%, respectively. The cell-specific ammonia oxidation rate calculation also revealed the cell-specific rates of AOB were higher than that of AOA. The Spearman's rank correlation analysis suggested that ammonia accumulation led to the AOB predominant role in net nitrification activity, and AOB abundance played the key role in potential nitrification activity. Furthermore, phylogenetic analysis suggested AOB were predominantly characterized by the Nitrosospira cluster, while AOA by the Nitrososphaera and Nitrososphaera sister clusters. This study will help us to better understand the contributions and characteristics of AOA and AOB in aquatic sediments and provide improved strategies for nitrogen control in large reservoirs.

  18. The response of ammonia-oxidizing microorganisms to trace metals and urine in two grassland soils in New Zealand.

    Science.gov (United States)

    Wang, Pengcheng; Di, Hong J; Cameron, Keith C; Tan, Qiling; Podolyan, Andriy; Zhao, Xiaohu; McLaren, Ron G; Hu, Chengxiao

    2017-01-01

    An incubation experiment was conducted to investigate the response of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and the nitrification rate to the contamination of Cu, Zn, and Cd in two New Zealand grassland soils. The soils spiked with different concentrations of Cu (20 and 50 mg kg -1 ), Zn (20 and 50 mg kg -1 ), and Cd (2 and 10 mg kg -1 ) were incubated for 14 days and then treated with 500 mg kg -1 urine-N before continuing incubation for a total of 115 days. Soils were sampled at intervals throughout the incubation. The nitrification rate in soils at each sampling period was determined, and the abundance of AOB and AOA was measured by real-time quantification polymerase chain reaction (qPCR) assay of the amoA gene copy numbers. The results revealed that moderate trace metal stress did not significantly affect the abundance of AOB and AOA in the two soils, probably due to the high organic matter content of the soils which would have reduced the toxic effect of the metals. Nitrification rates were much greater and the observable nitrification period was much shorter in the dairy farm (DF) soil, in which the AOB and AOA abundances were greater than those of the mixed cropping farm (MF) soil. AOB were shown to grow under high nitrogen conditions, whereas AOA were shown to grow under low N environments, with different metal concentrations. Therefore, nitrogen status rather than metal applications was the main determining factor for AOB and AOA growth in the two soils studied.

  19. Spatial distribution of archaeal and bacterial ammonia oxidizers in the littoral buffer zone of a nitrogen-rich lake.

    Science.gov (United States)

    Wang, Yu; Zhu, Guibing; Ye, Lei; Feng, Xiaojuan; Op den Camp, Huub J M; Yin, Chengqing

    2012-01-01

    The spatial distribution and diversity of archaeal and bacterial ammonia oxidizers (AOA and AOB) were evaluated targeting amoA genes in the gradient of a littoral buffer zone which has been identified as a hot spot for N cycling. Here we found high spatial heterogeneity in the nitrification rate and abundance of ammonia oxidizers in the five sampling sites. The bacterial amoA gene was numerically dominant in most of the surface soil but decreased dramatically in deep layers. Higher nitrification potentials were detected in two sites near the land/water interface at 4.4-6.1 microg NO(2-)-N/(g dry weight soil x hr), while only 1.0-1.7 microg NO(2-)-N/(g dry weight soil x hr) was measured at other sites. The potential nitrification rates were proportional to the amoA gene abundance for AOB, but with no significant correlation with AOA. The NH4+ concentration was the most determinative parameter for the abundance of AOB and potential nitrification rates in this study. Higher richness in the surface layer was found in the analysis of biodiversity. Phylogenetic analysis revealed that most of the bacterial amoA sequences in surface soil were affiliated with the genus of Nitrosopira while the archaeal sequences were almost equally affiliated with Candidatus 'Nitrososphaera gargensis' and Candidatus 'Nitrosocaldus yellowstonii'. The spatial distribution of AOA and AOB indicated that bacteria may play a more important role in nitrification in the littoral buffer zone of a N-rich lake.

  20. Diversity and Abundance of Ammonia-Oxidizing Archaeal Nitrite Reductase (nirK) Genes in Estuarine Sediments of San Francisco Bay

    Science.gov (United States)

    Reji, L.; Lee, J. A.; Damashek, J.; Francis, C. A.

    2013-12-01

    Nitrification, the microbially-mediated aerobic oxidation of ammonia to nitrate via nitrite, is an integral component of the global biogeochemical nitrogen cycle. The first and rate-limiting step of nitrification, ammonia oxidation, is carried out by two distinct microbial groups: ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Molecular ecological studies targeting the amoA gene have revealed the abundance and ubiquity of AOA in terrestrial as well as aquatic environments. In addition to the ammonia oxidation machinery that includes the amoA gene, AOA also encode a gene for copper-containing nitrite reductase (nirK). The distribution patterns and functional role of nirK in AOA remain mostly unknown; proposed functions include the indirect involvement in ammonia oxidation through the production of nitric oxide during nitrite reduction, and (2) nitrite detoxification. In the present study, the diversity and abundance of archaeal nirK genes in estuarine sediments were investigated using quantitative polymerase chain reaction, cloning and sequencing approaches. In sediment samples collected from the San Francisco Bay estuary, two archaeal nirK variants (AnirKa and AnirKb) were amplified using specific primer sets. Overall, AnirKa was observed to be significantly more abundant than AnirKb in the sediment samples, with variation in relative abundance spanning two to three orders of magnitude between sampling sites. Phylogenetic analysis revealed a number of unique archaeal nirK sequence types, as well as many that clustered with sequences from previous estuarine studies and cultured AOA isolates, such as Nitrosopumilus maritimus. This study yielded new insights into the diversity and abundance of archaeal nirK genes in estuarine sediments, and highlights the importance of further investigating the physiological role of this gene in AOA, as well as its suitability as a marker gene for studying AOA in the environment.

  1. Utilization of organic nitrogen by arbuscular mycorrhizal fungi-is there a specific role for protists and ammonia oxidizers?

    Science.gov (United States)

    Bukovská, Petra; Bonkowski, Michael; Konvalinková, Tereza; Beskid, Olena; Hujslová, Martina; Püschel, David; Řezáčová, Veronika; Gutiérrez-Núñez, María Semiramis; Gryndler, Milan; Jansa, Jan

    2018-04-01

    Arbuscular mycorrhizal (AM) fungi can significantly contribute to plant nitrogen (N) uptake from complex organic sources, most likely in concert with activity of soil saprotrophs and other microbes releasing and transforming the N bound in organic forms. Here, we tested whether AM fungus (Rhizophagus irregularis) extraradical hyphal networks showed any preferences towards certain forms of organic N (chitin of fungal or crustacean origin, DNA, clover biomass, or albumin) administered in spatially discrete patches, and how the presence of AM fungal hyphae affected other microbes. By direct 15 N labeling, we also quantified the flux of N to the plants (Andropogon gerardii) through the AM fungal hyphae from fungal chitin and from clover biomass. The AM fungal hyphae colonized patches supplemented with organic N sources significantly more than those receiving only mineral nutrients, organic carbon in form of cellulose, or nothing. Mycorrhizal plants grew 6.4-fold larger and accumulated, on average, 20.3-fold more 15 N originating from the labeled organic sources than their nonmycorrhizal counterparts. Whereas the abundance of microbes (bacteria, fungi, or Acanthamoeba sp.) in the different patches was primarily driven by patch quality, we noted a consistent suppression of the microbial abundances by the presence of AM fungal hyphae. This suppression was particularly strong for ammonia oxidizing bacteria. Our results indicate that AM fungi successfully competed with the other microbes for free ammonium ions and suggest an important role for the notoriously understudied soil protists to play in recycling organic N from soil to plants via AM fungal hyphae.

  2. The inhibitory effects of free ammonia on ammonia oxidizing bacteria and nitrite oxidizing bacteria under anaerobic condition.

    Science.gov (United States)

    Qian, Wenting; Peng, Yongzhen; Li, Xiyao; Zhang, Qiong; Ma, Bin

    2017-11-01

    The free ammonia (FA) inhibition on ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) under anaerobic condition was investigated in this study. The results indicated that NOB was more sensitive to the FA anaerobic treatment than AOB. The FA anaerobic inhibition on nitrifier gradually heightened with the increase of FA concentration. Accompanied with FA concentration increase from 0 to 16.82mgNH 3 -N·L -1 (the highest concentration adopted in this study), the activity of AOB reduced by 15.9%, while NOB decreased by 29.2%. After FA anaerobic treatment, nitrite was accumulated during nitrification. However, the nitrite accumulation disappeared on the sixth cycle of activity recovery tests with excessive aeration. Based on this result, a novel strategy for achieving nitritation is proposed, which involves recirculating a portion of the activated sludge through a side-line sludge treatment unit, where the sludge is subjected to treatment with FA under anaerobic condition. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Occurrence and elimination of antibiotics at four sewage treatment plants in Japan and their effects on bacterial ammonia oxidation.

    Science.gov (United States)

    Ghosh, Gopal Chandra; Okuda, Takashi; Yamashita, Naoyuki; Tanaka, Hiroaki

    2009-01-01

    The occurrence and elimination of seventeen antibiotics (three macrolides: azithromycin, clarithromycin and roxithromycin; five quinolones: ciprofloxacin, enrofloxacin, levofloxacin, nalidixic acid and norfloxacin; five sulfonamides: sulfadimethoxine, sulfadimizine, sulfamerazine, sulfamethoxazole and sulfamonomethoxine; and others: tetracycline, lincomycin, salinomycin and trimethoprim) were investigated at four full-scale sewage treatment plants in Japan. The highest concentration was recorded for clarithromycin (1,129 to 4,820 ng/L) in influent, followed by azithromycin (160 to 1,347 ng/L), levofloxacin (255 to 587 ng/L) and norfloxacin (155 to 486 ng/L). A vary inconsistence picture was obtained with negative to over 90% removal. Nalidixic acid (53 to 100%) exhibited higher removal efficiency followed by norfloxacin (75 to 95%), levofloxacin (40 to 90%), ciprofloxacin (60 to 83%) and enrofloxacin (38 to 74%). Among macrolides, clarithromycin (50 to 88%) and azithromycin (34 to 86%) showed relatively higher removal efficiency than roxithromycin (-32 to 59%). For most of the antibiotics removal efficiency was higher in A2O and AO based secondary treatment process than CAS process. The effect of the antibiotics on bacterial ammonia oxidation determined by oxygen uptake rate presented that there was no significant effect below 0.05 mg/L of each antibiotics. Even at the same concentration, antibiotics in mixed condition had higher inhibition effects than individuals.

  4. The Experiment Study of Anaerobic Ammonia Oxidation Start-up by Using the Upflow Double Layer Anaerobic Filter

    Directory of Open Access Journals (Sweden)

    YAO Li

    2018-02-01

    Full Text Available Anammox is an efficient nitrogen removal process, but it is difficult to start-up and operate, and ananammox reactor is the efficient way to resolve this problem. The start-up of anammox reactor by upflow anaerobic filter was studied. Denitrifying sludge, anaerobic sludge, and mixed sludge was inoculated on the packing materials, respectively and an autotrophic denitrification condition was provided by the simulated wastewater influent. Along with the gradual increase of matrix concentration and hydraulic load, the microflora was converted to the anaerobic ammonium oxidation(anammoxreaction. The results showed that the anammox reaction could be started by all the three sludge, and the time of start-up of denitrifying sludge, anaerobic sludge, mixed sludge was 42, 54 days and 45 days, respectively. The best result was that inoculated with denitrifying sludge with 82.2% of the total nitrogen removal rate, which started-up quickly and nitrogen was removed efficiently. Double packing effectively improved the stability of anammox process in the reactor, in which the suitable influent concentration loading for the anammox bacteria was 270 mg·L-1 and 360 mg·L-1 for ammonia nitrogen and nitrite nitrogen, respectively, and the COD concentration could not be more than 150 mg· L-1. Furthermore, there was a coexist-effect for anaerobic ammonia oxidation and methanation in this reactor system.

  5. Ammonia Oxidation by Abstraction of Three Hydrogen Atoms from a Mo–NH 3 Complex

    Energy Technology Data Exchange (ETDEWEB)

    Bhattacharya, Papri; Heiden, Zachariah M.; Wiedner, Eric S.; Raugei, Simone; Piro, Nicholas A.; Kassel, W. Scott; Bullock, R. Morris; Mock, Michael T.

    2017-02-15

    We report ammonia oxidation by homolytic cleavage of all three H atoms from a Mo-15NH3 complex using the 2,4,6-tri-tert-butylphenoxyl radical to afford a Mo-alkylimido (Mo=15NR) complex (R = 2,4,6-tri-t-butylcyclohexa-2,5-dien-1-one). Reductive cleavage of Mo=15NR generates a terminal Mo≡N nitride, and a [Mo-15NH]+ complex is formed by protonation. Computational analysis describes the energetic profile for the stepwise removal of three H atoms from the Mo-15NH3 complex and the formation of Mo=15NR. Acknowledgment. This work was supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Re-search Center funded by the U.S. Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences. EPR and mass spectrometry experiments were performed using EMSL, a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at PNNL. The authors thank Dr. Eric D. Walter and Dr. Rosalie Chu for assistance in performing EPR and mass spectroscopy analysis, respectively. Computational resources provided by the National Energy Re-search Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. Pacific North-west National Laboratory is operated by Battelle for the U.S. DOE.

  6. 3,4-Dimethylpyrazole phosphate (DMPP) reduces activity of ammonia oxidizers without adverse effects on non-target soil microorganisms and functions

    DEFF Research Database (Denmark)

    Kong, Xianwang; Duan, Yun-Feng (Kevin); Schramm, Andreas

    2016-01-01

    The nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) is widely used within agriculture to reduce nitrate leaching and improve nitrogen use efficiency of fertilizers, but few studies examined effects on non-target soil functions and microorganisms, i.e. other than the intended delay......, this study indicated that DMPP effectively inhibited nitrification activity without effects on ammonia oxidizer populations, as well as non-target soil microorganisms or functions....

  7. Diversity and abundance of ammonia-oxidizing prokaryotes in sediments from the coastal Pearl River estuary to the South China Sea

    OpenAIRE

    Cao, Huiluo; Hong, Yiguo; Li, Meng; Gu, Ji-Dong

    2011-01-01

    In the present study the diversity and abundance of nitrifying microbes including ammonia-oxidizing archaea (AOA) and betaproteobacteria (beta-AOB) were investigated, along with the physicochemical parameters potentially affecting them, in a transect of surface sediments from the coastal margin adjacent to the Pearl River estuary to the slope in the deep South China Sea. Nitrifying microbial diversity was determined by detecting the amoA (ammonia monooxygenase subunit A) gene. An obvious comm...

  8. Diversity of Ammonia Oxidation (amoA) and Nitrogen Fixation (nifH) Genes in Lava Caves of Terceira, Azores, Portugal.

    Science.gov (United States)

    Hathaway, Jennifer J Marshall; Sinsabaugh, Robert L; Dapkevicius, Maria De Lurdes N E; Northup, Diana E

    Lava caves are an understudied ecosystem in the subterranean world, particularly in regard to nitrogen cycling. The diversity of ammonia oxidation ( amoA ) and nitrogen fixation ( nifH ) genes in bacterial mats collected from lava cave walls on the island of Terceira (Azores, Portugal) was investigated using denaturing gradient gel electrophoresis (DGGE). A total of 55 samples were collected from 11 lava caves that were selected with regard to surface land use. Land use types above the lava caves were categorized into pasture, forested, and sea/urban, and used to determine if land use influenced the ammonia oxidizing and nitrogen fixing bacterial communities within the lava caves. The soil and water samples from each lava cave were analyzed for total organic carbon, inorganic carbon, total nitrogen, ammonium, nitrate, phosphate and sulfate, to determine if land use influences either the nutrient content entering the lava cave or the nitrogen cycling bacteria present within the cave. Nitrosospira -like sequences dominated the ammonia-oxidizing bacteria (AOB) community, and the majority of the diversity was found in lava caves under forested land. The nitrogen fixation community was dominated by Klebsiella pneumoniae -like sequences, and diversity was evenly distributed between pasture and forested land, but very little overlap in diversity was observed. The results suggest that land use is impacting both the AOB and the nitrogen fixing bacterial communities.

  9. Abundance and diversity of ammonia-oxidizing archaea and bacteria on biological activated carbon in a pilot-scale drinking water treatment plant with different treatment processes.

    Science.gov (United States)

    Kasuga, Ikuro; Nakagaki, Hirotaka; Kurisu, Futoshi; Furumai, Hiroaki

    2010-01-01

    The effects of different placements of rapid sand filtration on nitrification performance of BAC treatment in a pilot-scale plant were evaluated. In this plant, rapid sand filtration was placed after ozonation-BAC treatment in Process (A), while it preceded ozonation-BAC treatment in Process (B). Analysis of amoA genes of ammonia-oxidizing archaea (AOA) and bacteria (AOB) combined with nitrification potential test was conducted. BAC from Process (A) demonstrated slightly higher nitrification potential at every sampling occasion. This might be due to higher abundances of AOB on BAC from Process (A) than those on BAC from Process (B). However, AOA rather than AOB could be predominant ammonia-oxidizers in BAC treatment regardless of the position of rapid sand filtration. The highest nitrification potential was observed for BAC from both processes in February when the highest abundances of AOA-amoA and AOB-amoA genes were detected. Since rapid sand filtration was placed after BAC treatment in Process (A), residual aluminum concentration in BAC influent was higher in Process (A). However, adverse effects of aluminum on nitrification activity were not observed. These results suggest that factors other than aluminum concentration in different treatment processes could possibly have some influence on abundances of ammonia-oxidizing microorganisms on BAC.

  10. Abundance, composition and activity of ammonia oxidizer and denitrifier communities in metal polluted rice paddies from South China.

    Directory of Open Access Journals (Sweden)

    Yuan Liu

    Full Text Available While microbial nitrogen transformations in soils had been known to be affected by heavy metal pollution, changes in abundance and community structure of the mediating microbial populations had been not yet well characterized in polluted rice soils. Here, by using the prevailing molecular fingerprinting and enzyme activity assays and comparisons to adjacent non-polluted soils, we examined changes in the abundance and activity of ammonia oxidizing and denitrifying communities of rice paddies in two sites with different metal accumulation situation under long-term pollution from metal mining and smelter activities. Potential nitrifying activity was significantly reduced in polluted paddies in both sites while potential denitrifying activity reduced only in the soils with high Cu accumulation up to 1300 mg kg-1. Copy numbers of amoA (AOA and AOB genes were lower in both polluted paddies, following the trend with the enzyme assays, whereas that of nirK was not significantly affected. Analysis of the DGGE profiles revealed a shift in the community structure of AOA, and to a lesser extent, differences in the community structure of AOB and denitrifier between soils from the two sites with different pollution intensity and metal composition. All of the retrieved AOB sequences belonged to the genus Nitrosospira, among which species Cluster 4 appeared more sensitive to metal pollution. In contrast, nirK genes were widely distributed among different bacterial genera that were represented differentially between the polluted and unpolluted paddies. This could suggest either a possible non-specific target of the primers conventionally used in soil study or complex interactions between soil properties and metal contents on the observed community and activity changes, and thus on the N transformation in the polluted rice soils.

  11. Empowering a mesophilic inoculum for thermophilic nitrification: Growth mode and temperature pattern as critical proliferation factors for archaeal ammonia oxidizers.

    Science.gov (United States)

    Courtens, Emilie N P; Vandekerckhove, Tom; Prat, Delphine; Vilchez-Vargas, Ramiro; Vital, Marius; Pieper, Dietmar H; Meerbergen, Ken; Lievens, Bart; Boon, Nico; Vlaeminck, Siegfried E

    2016-04-01

    Cost-efficient biological treatment of warm nitrogenous wastewaters requires the development of thermophilic nitrogen removal processes. Only one thermophilic nitrifying bioreactor was described so far, achieving 200 mg N L(-1) d(-1) after more than 300 days of enrichment from compost samples. From the practical point of view in which existing plants would be upgraded, however, a more time-efficient development strategy based on mesophilic nitrifying sludge is preferred. This study evaluated the adaptive capacities of mesophilic nitrifying sludge for two linear temperature increase patterns (non-oscillating vs. oscillating), two different slopes (0.25 vs. 0.08 °C d(-1)) and two different reactor types (floc vs. biofilm growth). The oscillating temperature pattern (0.25 °C d(-1)) and the moving bed biofilm reactor (0.08 °C d(-1)) could not reach nitrification at temperatures higher than 46 °C. However, nitrification rates up to 800 mg N L(-1) d(-1) and 150 mg N g(-1) volatile suspended solids d(-1) were achieved at a temperature as high as 49 °C by imposing the slowest linear temperature increase to floccular sludge. Microbial community analysis revealed that this successful transition was related with a shift in ammonium oxidizing archaea dominating ammonia oxidizing bacteria, while for nitrite oxidation Nitrospira spp. was constantly more abundant than Nitrobacter spp.. This observation was accompanied with an increase in observed sludge yield and a shift in maximal optimum temperature, determined with ex-situ temperature sensitivity measurements, predicting an upcoming reactor failure at higher temperature. Overall, this study achieved nitrification at 49 °C within 150 days by gradual adaptation of mesophilic sludge, and showed that ex-situ temperature sensitivity screening can be used to monitor and steer the transition process. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Influence of silver nanoparticles and liberated silver ions on nitrifying sludge: ammonia oxidation inhibitory kinetics and mechanism.

    Science.gov (United States)

    Giao, Nguyen Thanh; Limpiyakorn, Tawan; Kunapongkiti, Pattaraporn; Thuptimdang, Pumis; Siripattanakul-Ratpukdi, Sumana

    2017-04-01

    Silver nanoparticles (AgNPs) are widely used in commercial products because of their excellent antimicrobial activity. Entrance of AgNPs and its released Ag ions (Ag + ) into wastewater treatment plants could harm ammonia oxidation (AO) process resulting in environmental problems. This study investigated inhibitory kinetics and mechanism of AO from nitrifying sludge influenced by AgNPs and Ag + . The findings demonstrated that AgNPs and Ag + adversely influenced on AO. Silver ions were more toxic to AO than AgNPs, which was indicated by the lower inhibitory constant (K i ) of 0.29 mg/L compared to that of AgNPs (K i of 73.5 mg/L). Over the experimental period of 60 h, AgNPs at 1, 10, and 100 mg/L released Ag + in the average concentrations of 0.059, 0.171, and 0.503 mg/L, respectively. Silver nanoparticles of 1-100 mg/L inhibited AO by 45-74%, whereas Ag + of 0.05-0.50 mg/L inhibited AO by 53-94%. This suggested that the AgNP toxicity mainly derived from the liberated Ag + . Scanning electron microscopy results revealed that AgNPs attached on microbial cell surfaces, and both AgNPs and Ag + induced cell morphological change from rod shape to shorter rod shape. Transmission electron microscopy showed that AgNPs and Ag + diminished the thickness of the outer layer and reduced the density of internal parts of the exposed microbial cells, which could be the reasons for the morphology change. Live/dead results also confirmed that AgNPs and Ag + damaged membrane integrity of cells in the nitrifying sludge. This study suggested that the primary mechanism for toxicity of AgNPs was the liberation of Ag + and then both of silver species caused cell death.

  13. Ammonia-Oxidizing Archaea Are More Resistant Than Denitrifiers to Seasonal Precipitation Changes in an Acidic Subtropical Forest Soil

    Directory of Open Access Journals (Sweden)

    Jie Chen

    2017-07-01

    Full Text Available Seasonal precipitation changes are increasingly severe in subtropical areas. However, the responses of soil nitrogen (N cycle and its associated functional microorganisms to such precipitation changes remain unclear. In this study, two projected precipitation patterns were manipulated: intensifying the dry-season drought (DD and extending the dry-season duration (ED but increasing the wet-season storms following the DD and ED treatment period. The effects of these two contrasting precipitation patterns on soil net N transformation rates and functional gene abundances were quantitatively assessed through a resistance index. Results showed that the resistance index of functional microbial abundance (-0.03 ± 0.08 was much lower than that of the net N transformation rate (0.55 ± 0.02 throughout the experiment, indicating that microbial abundance was more responsive to precipitation changes compared with the N transformation rate. Spring drought under the ED treatment significantly increased the abundances of both nitrifying (amoA and denitrifying genes (nirK, nirS, and nosZ, while changes in these gene abundances overlapped largely with control treatment during droughts in the dry season. Interestingly, the resistance index of the ammonia-oxidizing archaea (AOA amoA abundance was significantly higher than that of the denitrifying gene abundances, suggesting that AOA were more resistant to the precipitation changes. This was attributed to the stronger environmental adaptability and higher resource utilization efficiency of the AOA community, as indicated by the lack of correlations between AOA gene abundance and environmental factors [i.e., soil water content, ammonium (NH4+ and dissolved organic carbon concentrations] during the experiment.

  14. Community composition of ammonia-oxidizing archaea from surface and anoxic depths of oceanic oxygen minimum zones

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    Xuefeng ePeng

    2013-07-01

    Full Text Available Ammonia-oxidizing archaea (AOA have been reported at high abundance in much of the global ocean, even in environments, such as pelagic oxygen minimum zones (OMZs, where conditions seem unlikely to support aerobic ammonium oxidation. Due to the lack of information on any potential alternative metabolism of AOA, the AOA community composition might be expected to differ between oxic and anoxic environments, indicating some difference in ecology and/or physiology of the AOA assemblage. This hypothesis was tested by evaluating AOA community composition using a functional gene microarray that targets the ammonia monooxygenase gene subunit A (amoA. The relationship between environmental parameters and the biogeography of the Arabian Sea and the Eastern Tropical South Pacific (ETSP AOA assemblages was investigated using principal component analysis (PCA and redundancy analysis (RDA. In both the Arabian Sea and the ETSP, AOA communities within the core of the OMZ were not significantly different from those inhabiting the oxygenated surface waters above the OMZ. The AOA communities in the Arabian Sea were significantly different from those in the ETSP. In both oceans, the abundance of archaeal amoA gene in the core of the OMZ was higher than that in the surface waters. Our results indicate that AOA communities are distinguished by their geographic origin. RDA suggested that temperature was the main factor that correlated with the differences between the AOA communities from the Arabian Sea and those from the ETSP. Physicochemical properties that characterized the different environments of the OMZ and surface waters played a less important role, than did geography, in shaping the AOA community composition.

  15. Modeling of soil nitrification responses to temperature reveals thermodynamic differences between ammonia-oxidizing activity of archaea and bacteria.

    Science.gov (United States)

    Taylor, Anne E; Giguere, Andrew T; Zoebelein, Conor M; Myrold, David D; Bottomley, Peter J

    2017-04-01

    Soil nitrification potential (NP) activities of ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) were evaluated across a temperature gradient (4-42 °C) imposed upon eight soils from four different sites in Oregon and modeled with both the macromolecular rate theory and the square root growth models to quantify the thermodynamic responses. There were significant differences in response by the dominant AOA and AOB contributing to the NPs. The optimal temperatures (T opt ) for AOA- and AOB-supported NPs were significantly different (P12 °C greater than AOB. The change in heat capacity associated with the temperature dependence of nitrification (ΔC P ‡ ) was correlated with T opt across the eight soils, and the ΔC P ‡ of AOB activity was significantly more negative than that of AOA activity (Ptemperature (T min ) and different, albeit very similar, maximum temperature (T max ) values for AOB than for AOA activity. The results also suggested that there may be different forms of AOA AMO that are active over different temperature ranges with different T min , but no evidence of multiple T min values within the AOB. Fundamental differences in temperature-influenced properties of nitrification driven by AOA and AOB provides support for the idea that the biochemical processes associated with NH 3 oxidation in AOA and AOB differ thermodynamically from each other, and that also might account for the difficulties encountered in attempting to model the response of nitrification to temperature change in soil environments.

  16. Comparison of PCR-DGGE and Nested-PCR-DGGE Approach for Ammonia Oxidizers Monitoring in Membrane Bioreactors’ Activated Sludge

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    Ziembińska-Buczyńska Aleksandra

    2014-12-01

    Full Text Available Nitritation, the first stage of ammonia removal process is known to be limiting for total process performance. Ammonia oxidizing bacteria (AOB which perform this process are obligatory activated sludge habitants, a mixture consisting of Bacteria, Protozoa and Metazoa used for biological wastewater treatment. Due to this fact they are an interesting bacterial group, from both the technological and ecological point of view. AOB changeability and biodiversity analyses both in wastewater treatment plants and lab-scale reactors are performed on the basis of 16S rRNA gene sequences using PCR-DGGE (Polymerase Chain Reaction – Denaturing Gradient Gel Electrophoresis as a molecular biology tool. AOB researches are usually led with nested PCR. Because the application of nested PCR is laborious and time consuming, we have attempted to check the possibility of using only first PCR round to obtain DGGE fingerprinting of microbial communities. In this work we are comparing the nested and non-nested PCR-DGGE monitoring of an AOB community and presenting advantages and disadvantages of both methods used. The experiment revealed that PCR technique is a very sensitive tool for the amplification of even a minute amount of DNA sample. But in the case of nested-PCR, the sensitivity is higher and the template amount could be even smaller. The nested PCR-DGGE seems to be a better tool for AOB community monitoring and complexity research in activated sludge, despite shorter fragments of DNA amplification which seems to be a disadvantage in the case of bacteria identification. It is recommended that the sort of analysis approach should be chosen according to the aim of the study: nested-PCR-DGGE for community complexity analysis, while PCR-DGGE for identification of the dominant bacteria.

  17. Acetylene and oxygen as inhibitors of nitrous oxide production in Nitrosomonas euroepaea and Nitrosospir briensis: a cautionary tale

    NARCIS (Netherlands)

    Wrage, N.; Velthof, G.L.; Oenema, O.; Laanbroek, H.J.

    2004-01-01

    Autotrophic ammonia-oxidizing bacteria produce nitrous oxide (N2O) as a by-product of nitrification or as an intermediate of nitrifier denitrification. In soil incubations, acetylene (C2H2) and large partial pressures of oxygen (O2) are used to distinguish between these sources. C2H2 inhibits

  18. Somatic Embryogenesis in Olive (Olea europaea L. subsp. europaea var. sativa and var. sylvestris).

    Science.gov (United States)

    Rugini, Eddo; Silvestri, Cristian

    2016-01-01

    Protocols for olive somatic embryogenesis from zygotic embryos and mature tissues have been described for both Olea europaea sub. europaea var. sativa and var. sylvestris. Immature zygotic embryos (no more than 75 days old), used after fruit collection or stored at 12-14 °C for 2-3 months, are the best responsive explants and very slightly genotype dependent, and one single protocol can be effective for a wide range of genotypes. On the contrary, protocols for mature zygotic embryos and for mature tissue of cultivars are often genotype specific, so that they may require many adjustments according to genotypes. The use of thidiazuron and cefotaxime seems to be an important trigger for induction phase particularly for tissues derived from cultivars. Up to now, however, the application of this technique for large-scale propagation is hampered also by the low rate of embryo germination; it proves nonetheless very useful for genetic improvement.

  19. Effects of nitrogen application rate and a nitrification inhibitor dicyandiamide on ammonia oxidizers and N2O emissions in a grazed pasture soil.

    Science.gov (United States)

    Dai, Yu; Di, Hong J; Cameron, Keith C; He, Ji-Zheng

    2013-11-01

    Ammonia oxidizers, including ammonia oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) are important drivers of a key step of the nitrogen cycle - nitrification, which affects the production of the potent greenhouse gas, nitrous oxide (N2O). A field experiment was conducted to determine the effect of nitrogen application rates and the nitrification inhibitor dicyandiamide (DCD) on the abundance of AOB and AOA and on N2O emissions in a grazed pasture soil. Nitrogen (N) was applied at four different rates, with urea applied at 50 and 100 kg N ha(-1) and animal urine at 300 and 600 kg N ha(-1). DCD was applied to some of the N treatments at 10 kg ha(-1). The results showed that the AOB amoA gene copy numbers were greater than those of AOA. The highest ratio of the AOB to AOA amoA gene copy numbers was 106.6 which occurred in the urine-N 600 treatment. The AOB amoA gene copy numbers increased with increasing nitrogen application rates. DCD had a significant impact in reducing the AOB amoA gene copy numbers especially in the high nitrogen application rates. N2O emissions increased with the N application rates. DCD had the most significant effect in reducing the daily and total N2O emissions in the highest nitrogen application rate. The greatest reduction of total N2O emissions by DCD was 69% in the urine-N 600 treatment. The reduction in the N2O emission factor by DCD ranged from 58% to 83%. The N2O flux and NO3(-)-N concentrations were significantly correlated to the growth of AOB, rather than AOA. This study confirms the importance of AOB in nitrification and the effect of DCD in inhibiting AOB growth and in decreasing N2O emissions in grazed pasture soils under field conditions. Copyright © 2012 Elsevier B.V. All rights reserved.

  20. Shifts in Abundance and Diversity of Soil Ammonia-Oxidizing Bacteria and Archaea Associated with Land Restoration in a Semi-Arid Ecosystem.

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    Zhu Chen

    Full Text Available The Grain to Green Project (GGP is an unprecedented land restoration action in China. The project converted large areas (ca 10 million ha of steep-sloped/degraded farmland and barren land into forest and grassland resulting in ecological benefits such as a reduction in severe soil erosion. It may also affect soil microorganisms involved in ammonia oxidization, which is a key step in the global nitrogen cycle. The methods for restoration that are typically adopted in semi-arid regions include abandoning farmland and growing drought tolerant grass (Lolium perenne L. or shrubs (Caragana korshinskii Kom.. In the present study, the effects of these methods on the abundance and diversity of ammonia-oxidizing bacteria (AOB and ammonia-oxidizing archaea (AOA were evaluated via quantitative real-time PCR, terminal restriction fragment length polymorphism and clone library analysis of amoA genes. Comparisons were made between soil samples from three restored lands and the adjacent farmland in Inner Mongolia. Both the abundance and community composition of AOB were significantly different between the restored lands and the adjacent control. Significantly lower nitrification activity was observed for the restored land. Clone library analysis revealed that all AOB amoA gene sequences were affiliated with Nitrosospira. Abundance of the populations that were associated with Nitrosospira sp. Nv6 which had possibly adapted to high concentrations of inorganic nitrogen, decreased on the restored land. Only a slight difference in the AOB communities was observed between the restored land with and without the shrub (Caragana korshinskii Kom.. A minor effect of land restoration on AOA was observed. In summary, land restoration negatively affected the abundance of AOB and soil nitrification activities, suggesting the potential role of GGP in the leaching of nitrates, and in the emission of N2O in related terrestrial ecosystems.

  1. Dominance of ammonia-oxidizing archaea community induced by land use change from Masson pine to eucalypt plantation in subtropical China.

    Science.gov (United States)

    Zhang, Fang-Qiu; Pan, Wen; Gu, Ji-Dong; Xu, Bin; Zhang, Wei-Hua; Zhu, Bao-Zhu; Wang, Yu-Xia; Wang, Yong-Feng

    2016-08-01

    A considerable proportion of Masson pine forests have been converted into eucalypt plantations in the last 30 years in Guangdong Province, subtropical China, for economic reasons, which may affect the ammonia-oxidizing archaea (AOA) community and the process of ammonia transformation. In order to determine the effects of forest conversion on AOA community, AOA communities in a Masson pine (Pinus massoniana) plantation and a eucalypt (Eucalyptus urophylla) plantation, which was converted from the Masson pine, were compared. Results showed that the land use change from the Masson pine to the eucalypt plantation decreased soil nutrient levels. A significant decrease of the potential nitrification rates (PNR) was also observed after the forest conversion (p < 5 %, n = 6). AOA were the only ammonia oxidizers in both plantations (no ammonia-oxidizing bacteria were detected). The detected AOA are affiliated with the genera Nitrosotalea and Nitrososphaera. A decrease of AOA abundance and an increase of the diversity were evident with the plantation conversion in the surface layer. AOA amoA gene diversity was negatively correlated with organic C and total N, respectively (p < 0.05, n = 12). AOA amoA gene abundance was negatively correlated with NH4 (+) and available P, respectively (p < 0.05, n = 12). However, AOA abundance was positively correlated with PNR, but not significantly (p < 0.05, n = 6), indicating AOA community change was only a partial reason for the decrease of PNR.

  2. Ammonia-oxidizing archaea are more resistant than denitrifiers to seasonal precipitation changes in an acidic subtropical forest soil

    Science.gov (United States)

    Chen, Jie

    2017-04-01

    More frequent droughts and storms will occur globally in the prediction of global climate change model, which will influence soil microorganisms and nutrient cycles. Understanding the resistance of soil functional microorganisms and the associated biogeochemical cycles to such climate changes is important in evaluating responses of ecosystem functioning. In order to clarify the responses of soil functional microorganisms involved in nitrogen (N) cycle to the predicted precipitation scenarios, two contrasting precipitation manipulation experiments were conducted in an acidic subtropical forest soil. One experiment manipulated drier dry-season and wetter wet-season (DD) by reducing dry-season rainfall and adding the equivalently reduced rainfall to wet-season. Another experiment manipulated extending dry-season and wetter wet-season (ED) by reducing spring-season rainfall and adding the equivalent rainfall in the late wet-season. The resistance index of ammonia-oxidizing archaea (AOA) amoA and denitrifying (nirK, nirS and nosZ) genes abundance, soil net N mineralization and nitrification rates were calculated during experiments to examine their responses to precipitation changes. As the results, the resistance index of functional microbial abundance (-0.03 ± 0.08) was much lower than that of net N transformation rates (0.55 ± 0.02), indicating more sensitive of functional microorganisms in response to precipitation changes than the related N processes. Extending dry-season showed greater effects on both AOA amoA and denitrifying genes abundance than drier dry-season, with significant increases of these microbial abundance after extending dry-season. This was mainly due to the interaction effects of soil water content (SWC), dissolve organic carbon (DOC) and NH4+ concentration during rainfall reduction in spring-season. Interestingly, the resistance index of AOA amoA abundance was significantly higher than that of denitrifying gene abundance, indicating more

  3. Fluctuations in ammonia oxidizing communities across agricultural soils are driven by soil structure and pH

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    Michele C ePereira e Silva

    2012-03-01

    Full Text Available The milieu in soil in which microorganisms dwell is never constant. Conditions such as temperature, water availability, pH and nutrients frequently change, impacting the overall functioning of the soil system. To understand the effects of such factors on soil functioning, proxies (indicators of soil function are needed that, in a sensitive manner, reveal normal amplitude of variation. Thus, the so-called normal operating range (NOR of soil can be defined. In this study we determined different components of nitrification by analyzing, in eight agricultural soils, how the community structures and sizes of ammonia oxidizing bacteria and archaea (AOB and AOA, respectively, and their activity, fluctuate over spatial and temporal scales. The results indicated that soil pH and soil type are the main factors that influence the size and structure of the AOA and AOB, as well as their function. The nitrification rates varied between 0.11 ± 0.03 µgN.h-1.gdw-1 and 1.68 ± 0.11 µgN.h-1.gdw-1, being higher in soils with higher clay content (1.09 ± 0.12 µgN.h-1.gdw-1 and lower in soils with lower clay percentages (0.27 ± 0.04 µgN.h-1.gdw-1. Nitrifying activity was driven by soil pH, mostly related to its effect on AOA but not on AOB abundance. Regarding the influence of soil parameters, clay content was the main soil factor shaping the structure of both the AOA and AOB communities. Overall, the potential nitrifying activities were higher and more variable over time in the clayey than in the sandy soils. Whereas the structure of AOB fluctuated more (62.7 ± 2.10% the structure of AOA communities showed lower amplitude of variation (53.65 ± 3.37%. Similar trends were observed for the sizes of these communities. The present work represents a first step towards defining a NOR for soil nitrification. Moreover, the clear effect of soil texture established here suggests that the NOR should be defined in a soil-type-specific manner.

  4. Distributions and activities of ammonia oxidizing bacteria and polyphosphate accumulating organisms in a pumped-flow biofilm reactor.

    Science.gov (United States)

    Wu, Guangxue; Nielsen, Michael; Sorensen, Ketil; Zhan, Xinmin; Rodgers, Michael

    2009-10-01

    The spatial distributions and activities of ammonia oxidizing bacteria (AOB) and polyphosphate accumulating organisms (PAOs) were investigated for a novel laboratory-scale sequencing batch pumped-flow biofilm reactor (PFBR) system that was operated for carbon, nitrogen and phosphorus removal. The PFBR comprised of two 16.5l tanks (Reactors 1 and 2), each with a biofilm module of 2m(2) surface area. To facilitate the growth of AOB and PAOs in the reactor biofilms, the influent wastewater was held in Reactor 1 under stagnant un-aerated conditions for 6 h after feeding, and was then pumped over and back between Reactors 1 and 2 for 12 h, creating aerobic conditions in the two reactors during this period; as a consequence, the biofilm in Reactor 2 was in an aerobic environment for almost all the 18.2 h operating cycle. A combination of micro-sensor measurements, molecular techniques, batch experiments and reactor studies were carried out to analyse the performance of the PFBR system. After 100 days operation at a filtered chemical oxygen demand (COD(f)) loading rate of 3.46 g/m(2) per day, the removal efficiencies were 95% COD(f), 87% TN(f) and 74% TP(f). While the PFBR microbial community structure and function were found to be highly diversified with substantial AOB and PAO populations, about 70% of the phosphorus release potential and almost 100% of the nitrification potential were located in Reactors 1 and 2, respectively. Co-enrichment of AOB and PAOs was realized in the Reactor 2 biofilm, where molecular analyses revealed unexpected microbial distributions at micro-scale, with population peaks of AOB in a 100-250 microm deep sub-surface zone and of PAOs in the 0-150 microm surface zone. The micro-distribution of AOB coincided with the position of the nitrification peak identified during micro-sensor analyses. The study demonstrates that enrichment of PAOs can be realized in a constant or near constant aerobic biofilm environment. Furthermore, the findings suggest

  5. Freshwater Ammonia-Oxidizing Archaea Retain amoA mRNA and 16S rRNA during Ammonia Starvation

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    Elizabeth French

    2015-05-01

    Full Text Available In their natural habitats, microorganisms are often exposed to periods of starvation if their substrates for energy generation or other nutrients are limiting. Many microorganisms have developed strategies to adapt to fluctuating nutrients and long-term starvation. In the environment, ammonia oxidizers have to compete with many different organisms for ammonium and are often exposed to long periods of ammonium starvation. We investigated the effect of ammonium starvation on ammonia-oxidizing archaea (AOA and bacteria (AOB enriched from freshwater lake sediments. Both AOA and AOB were able to recover even after almost two months of starvation; however, the recovery time differed. AOA and AOB retained their 16S rRNA (ribosomes throughout the complete starvation period. The AOA retained also a small portion of the mRNA of the ammonia monooxygenase subunit A (amoA for the complete starvation period. However, after 10 days, no amoA mRNA was detected anymore in the AOB. These results indicate that AOA and AOB are able to survive longer periods of starvation, but might utilize different strategies.

  6. Distribution and abundance of archaeal and bacterial ammonia oxidizers in the sediments of the Dongjiang River, a drinking water supply for Hong Kong.

    Science.gov (United States)

    Sun, Wei; Xia, Chunyu; Xu, Meiying; Guo, Jun; Wang, Aijie; Sun, Guoping

    2013-01-01

    Ammonia-oxidizing archaea (AOA) and bacteria (AOB) play important roles in nitrification. However, limited information about the characteristics of AOA and AOB in the river ecosystem is available. The distribution and abundance of AOA and AOB in the sediments of the Dongjiang River, a drinking water source for Hong Kong, were investigated by clone library analysis and quantitative real-time PCR. Phylogenetic analysis showed that Group 1.1b- and Group 1.1b-associated sequences of AOA predominated in sediments with comparatively high carbon and nitrogen contents (e.g. total carbon (TC) >13 g kg(-1) sediment, NH4(+)-N >144 mg kg(-1) sediment), while Group 1.1a- and Group 1.1a-associated sequences were dominant in sediments with opposite conditions (e.g. TC distribution of AOA and the sediment pH and TC, which suggested that AOA responded more sensitively than AOB to variations of environmental factors. These results extend our knowledge about the environmental responses of ammonia oxidizers in the river ecosystem.

  7. High abundances of potentially active ammonia-oxidizing bacteria and archaea in oligotrophic, high-altitude lakes of the Sierra Nevada, California, USA.

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    Curtis J Hayden

    Full Text Available Nitrification plays a central role in the nitrogen cycle by determining the oxidation state of nitrogen and its subsequent bioavailability and cycling. However, relatively little is known about the underlying ecology of the microbial communities that carry out nitrification in freshwater ecosystems--and particularly within high-altitude oligotrophic lakes, where nitrogen is frequently a limiting nutrient. We quantified ammonia-oxidizing archaea (AOA and bacteria (AOB in 9 high-altitude lakes (2289-3160 m in the Sierra Nevada, California, USA, in relation to spatial and biogeochemical data. Based on their ammonia monooxygenase (amoA genes, AOB and AOA were frequently detected. AOB were present in 88% of samples and were more abundant than AOA in all samples. Both groups showed >100 fold variation in abundance between different lakes, and were also variable through time within individual lakes. Nutrient concentrations (ammonium, nitrite, nitrate, and phosphate were generally low but also varied across and within lakes, suggestive of active internal nutrient cycling; AOB abundance was significantly correlated with phosphate (r(2 = 0.32, p<0.1, whereas AOA abundance was inversely correlated with lake elevation (r(2 = 0.43, p<0.05. We also measured low rates of ammonia oxidation--indicating that AOB, AOA, or both, may be biogeochemically active in these oligotrophic ecosystems. Our data indicate that dynamic populations of AOB and AOA are found in oligotrophic, high-altitude, freshwater lakes.

  8. Traditional Uses, Phytochemistry, and Pharmacology of Olea europaea (Olive

    Directory of Open Access Journals (Sweden)

    Muhammad Ali Hashmi

    2015-01-01

    Full Text Available Aim of the Review. To grasp the fragmented information available on the botany, traditional uses, phytochemistry, pharmacology, and toxicology of Olea europaea to explore its therapeutic potential and future research opportunities. Material and Methods. All the available information on O. europaea was collected via electronic search (using Pubmed, Scirus, Google Scholar, and Web of Science and a library search. Results. Ethnomedical uses of O. europaea are recorded throughout the world where it has been used to treat various ailments. Phytochemical research had led to the isolation of flavonoids, secoiridoids, iridoids, flavanones, biophenols, triterpenes, benzoic acid derivatives, isochromans, and other classes of secondary metabolites from O. europaea. The plant materials and isolated components have shown a wide spectrum of in vitro and in vivo pharmacological activities like antidiabetic, anticonvulsant, antioxidant, anti-inflammatory, immunomodulatory, analgesic, antimicrobial, antiviral, antihypertensive, anticancer, antihyperglycemic, antinociceptive, gastroprotective, and wound healing activities. Conclusions. O. europaea emerged as a good source of traditional medicine for the treatment of various ailments. The outcomes of phytochemical and pharmacological studies reported in this review will further expand its existing therapeutic potential and provide a convincing support to its future clinical use in modern medicine.

  9. Traditional Uses, Phytochemistry, and Pharmacology of Olea europaea (Olive)

    Science.gov (United States)

    Hashmi, Muhammad Ali; Khan, Afsar; Hanif, Muhammad; Farooq, Umar; Perveen, Shagufta

    2015-01-01

    Aim of the Review. To grasp the fragmented information available on the botany, traditional uses, phytochemistry, pharmacology, and toxicology of Olea europaea to explore its therapeutic potential and future research opportunities. Material and Methods. All the available information on O. europaea was collected via electronic search (using Pubmed, Scirus, Google Scholar, and Web of Science) and a library search. Results. Ethnomedical uses of O. europaea are recorded throughout the world where it has been used to treat various ailments. Phytochemical research had led to the isolation of flavonoids, secoiridoids, iridoids, flavanones, biophenols, triterpenes, benzoic acid derivatives, isochromans, and other classes of secondary metabolites from O. europaea. The plant materials and isolated components have shown a wide spectrum of in vitro and in vivo pharmacological activities like antidiabetic, anticonvulsant, antioxidant, anti-inflammatory, immunomodulatory, analgesic, antimicrobial, antiviral, antihypertensive, anticancer, antihyperglycemic, antinociceptive, gastroprotective, and wound healing activities. Conclusions. O. europaea emerged as a good source of traditional medicine for the treatment of various ailments. The outcomes of phytochemical and pharmacological studies reported in this review will further expand its existing therapeutic potential and provide a convincing support to its future clinical use in modern medicine. PMID:25802541

  10. Analysis of ammonia-oxidizing bacteria of the beta subdivision of the class Proteobacteria in coastal sand dunes by denaturing gradient gel electrophoresis and sequencing of PCR-amplified 16S ribosomal DNA fragments

    NARCIS (Netherlands)

    Kowalchuk, G.A.; Stephen, J.R.; De Boer, W.; Prosser, J.I.; Embley, T.M.; Woldendorp, J.W.

    1997-01-01

    Denaturing gradient gel electrophoresis (DGGE) is a powerful and convenient tool for analyzing the sequence diversity of complex natural microbial populations, DGGE was evaluated for the identification of ammonia oxidizers of the beta subdivision of the Proteobacteria based on the mobility of

  11. The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys

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    Catarina Maria Magalhães

    2014-09-01

    Full Text Available The McMurdo Dry Valleys of Antarctica are considered to be one of the most physically and chemically extreme terrestrial environments on the Earth. However, little is known about the organisms involved in nitrogen transformations in these environments. In this study, we investigated the diversity and abundance of ammonia-oxidizing archaea (AOA and bacteria (AOB in four McMurdo Dry Valleys with highly variable soil geochemical properties and climatic conditions: Miers Valley, Upper Wright Valley, Beacon Valley and Battleship Promontory. The bacterial communities of these four Dry Valleys have been examined previously, and the results suggested that the extremely localized bacterial diversities are likely driven by the disparate physicochemical conditions associated with these locations. Here we showed that AOB and AOA amoA gene diversity was generally low; only four AOA and three AOB operational taxonomic units (OTUs were identified from a total of 420 AOA and AOB amoA clones. Quantitative PCR analysis of amoA genes revealed clear differences in the relative abundances of AOA and AOB amoA genes among samples from the four Dry Valleys. Although AOB amoA gene dominated the ammonia-oxidizing community in soils from Miers Valley and Battleship Promontory, AOA amoA gene were more abundant in samples from Upper Wright and Beacon Valleys, where the environmental conditions are considerably harsher (e.g., extremely low soil C/N ratios and much higher soil electrical conductivity. Correlations between environmental variables and amoA genes copy numbers, as examined by redundancy analysis (RDA, revealed that higher AOA/AOB ratios were closely related to soils with high salts and Cu contents and low pH. Our findings hint at a dichotomized distribution of AOA and AOB within the Dry Valleys, potentially driven by environmental constraints.

  12. Land Spreading of Wastewaters from the Fruit-Packaging Industry and Potential Effects on Soil Microbes: Effects of the Antioxidant Ethoxyquin and Its Metabolites on Ammonia Oxidizers.

    Science.gov (United States)

    Papadopoulou, Evangelia S; Tsachidou, Bella; Sułowicz, Sławomir; Menkissoglu-Spiroudi, Urania; Karpouzas, Dimitrios G

    2016-01-15

    Thiabendazole (TBZ), imazalil (IMZ), ortho-phenylphenol (OPP), diphenylamine (DPA), and ethoxyquin (EQ) are used in fruit-packaging plants (FPP) with the stipulation that wastewaters produced by their application would be depurated on site. However, no such treatment systems are currently in place, leading FPP to dispose of their effluents in agricultural land. We investigated the dissipation of those pesticides and their impact on soil microbes known to have a key role on ecosystem functioning. OPP and DPA showed limited persistence (50% dissipation time [DT50], 0.6 and 1.3 days) compared to TBZ and IMZ (DT50, 47.0 and 150.8 days). EQ was rapidly transformed to the short-lived quinone imine (QI) (major metabolite) and the more persistent 2,4-dimethyl-6-ethoxyquinoline (EQNL) (minor metabolite). EQ and OPP exerted significant inhibition of potential nitrification, with the effect of the former being more persistent. This was not reflected in the abundance (determined by quantitative PCR [qPCR]) of the amoA gene of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Considering the above discrepancy and the metabolic pattern of EQ, we further investigated the hypothesis that its metabolites and not only EQ were toxic to ammonia oxidizers. Potential nitrification, amoA gene abundance, and amoA gene transcripts of AOB and AOA showed that QI was probably responsible for the inhibition of nitrification. Our findings have serious ecological and practical implications for soil productivity and N conservation in agriculturally impacted ecosystems and stress the need to include metabolites and RNA-based methods when the soil microbial toxicity of pesticides is assessed. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  13. Prevalence of Toxoplasma gondii in common moles (Talpa europaea)

    NARCIS (Netherlands)

    Krijger, I.M.; Cornelissen, J.B.W.J.; Wisselink, H.J.; Meerburg, B.G.

    2014-01-01

    Background The prevalence of Toxoplasma gondii in common moles, Talpa europaea, was investigated in order to determine whether moles can serve as an indicator species for T. gondii infections in livestock. Findings In total, 86 moles were caught from 25 different sites in the Netherlands. Five

  14. Fauna Europaea – all European animal species on the web

    Directory of Open Access Journals (Sweden)

    Yde de Jong

    2014-09-01

    Fauna Europaea provides a public web portal at faunaeur.org with links to other key biodiversity services, is installed as a taxonomic backbone in wide range of biodiversity services and actively contributes to biodiversity informatics innovations in various initiatives and EC programs.

  15. Olea europaea Linn (Oleaceae) Fruit Pulp Extract Exhibits Potent ...

    African Journals Online (AJOL)

    Olea europaea Linn (Oleaceae) Fruit Pulp Extract Exhibits Potent Antioxidant Activity and Attenuates Neuroinflammatory Responses in Lipopolysaccharide- Stimulated Microglial Cells. M-S Kim, S Koppula, S-H Jung, J-Y Kim, H-R Lee, S-R Lee, Y-D Park, K-A Lee, T-K Park, H Kang ...

  16. Olea europaea Linn (Oleaceae) Fruit Pulp Extract Suppresses Sterol ...

    African Journals Online (AJOL)

    Purpose: To investigate the molecular mechanisms underlying the role of Olea europaea Linn (Oleaceae) fruit pulp extract (OPF) in the prevention of high glucose-induced lipid accumulation in human HepG2 hepatocytes. Methods: HepG2 cells were pretreated with various concentration of OPF (0, 10, 20, 40 and 80 µg/ml) ...

  17. Genetic variation within the olive (Olea europaea L.) cultivar Oblica ...

    African Journals Online (AJOL)

    USER

    2010-05-17

    May 17, 2010 ... Genetic variation within the olive (Olea europaea L.) cultivar Oblica detected using amplified fragment length polymorphism (AFLP) markers. Frane Strikic1*, Dunja Bandelj Mavsar2, Slavko Perica1, Zlatko Cmelik3, Zlatko Satovic3 and. Branka Javornik4. 1Institute for Adriatic Crops and Karst Reclamation ...

  18. Spiders in Fauna Europaea: dual use of the database

    Directory of Open Access Journals (Sweden)

    Helsdingen, Peter J. van

    2012-07-01

    Full Text Available The history and current work of the project Fauna Europaea is outlined. The different sources used for building up the database and the efforts to keep it updated are described. Available models of national checklists are discussed and the ideal checklist is described. The double use of the database as a matrix behind the official site of Fauna Europaea – as well as a directly visible document on the website of the European Society of Arachnology – are indicated and the differences in transparency, links to literature sources, and facilities such as distribution maps and calculations of numbers of scores per species or of species per country are discussed. The future of the project is briefly outlined. The need for a European identification tool for spiders is stressed.

  19. Biological Significance of Seed Oil and Polyphenolic of Olea europaea

    OpenAIRE

    Mohammad Asif

    2013-01-01

    The olive tree Olea europaea have beneficial properties. Mainly used parts of the olive tree are fruits and seeds. Seeds oil of olive is used as a major component of the “diet.” Chief active components of olive oil include oleic acid, a monounsaturated fatty acid, polyphenolics and squalene. These main phenolic components are hydroxytyrosol, tyrosol, and oleuropein, which occur in highest amounts in virgin olive oil and have antioxidant properties. Olive oil has shown activity in against canc...

  20. Detection of Ammonia-Oxidizing Bacteria (AOB) Using a Porous Silicon Optical Biosensor Based on a Multilayered Double Bragg Mirror Structure.

    Science.gov (United States)

    Zhang, Hongyan; Lv, Jie; Jia, Zhenhong

    2018-01-01

    We successfully demonstrate a porous silicon (PS) double Bragg mirror by electrochemical etching at room temperature as a deoxyribonucleic acid (DNA) label-free biosensor for detecting ammonia-oxidizing bacteria (AOB). Compared to various other one-dimension photonic crystal configurations of PS, the double Bragg mirror structure is quite easy to prepare and exhibits interesting optical properties. The width of high reflectivity stop band of the PS double Bragg mirror is about 761 nm with a sharp and deep resonance peak at 1328 nm in the reflectance spectrum, which gives a high sensitivity and distinguishability for sensing performance. The detection sensitivity of such a double Bragg mirror structure is illustrated through the investigation of AOB DNA hybridization in the PS pores. The redshifts of the reflectance spectra show a good linear relationship with both complete complementary and partial complementary DNA. The lowest detection limit for complete complementary DNA is 27.1 nM and the detection limit of the biosensor for partial complementary DNA is 35.0 nM, which provides the feasibility and effectiveness for the detection of AOB in a real environment. The PS double Bragg mirror structure is attractive for widespread biosensing applications and provides great potential for the development of optical applications.

  1. Co-occurrence of nitrite-dependent anaerobic methane oxidizing and anaerobic ammonia oxidizing bacteria in two Qinghai-Tibetan saline lakes

    Science.gov (United States)

    Yang, Jian; Jiang, Hongchen; Wu, Geng; Hou, Weiguo; Sun, Yongjuan; Lai, Zhongping; Dong, Hailiang

    2012-12-01

    Nitrite-dependent anaerobic methane-oxidizing (n-damo) bacteria and anaerobic ammonia oxidizing (anammox) bacteria are two groups of microorganisms involved in global carbon and nitrogen cycling. In order to test whether the n-damo and anammox bacteria co-occur in natural saline environments, the DNA and cDNA samples obtained from the surficial sediments of two saline lakes (with salinity of 32 and 84 g/L, respectively) on the Tibetan Plateau were PCR-amplified with the use of anammox- and n-damo-specific primer sets, followed by clone library construction and phylogenetic analysis. DNA and cDNA-based clones affiliated with n-damo and anammox bacteria were successfully retrieved from the two samples, indicating that these two groups of bacteria can co-occur in natural saline environments with salinity as high as 84 g/L. Our finding has great implications for our understanding of the global carbon and nitrogen cycle in nature.

  2. Chemical treatment of contaminated sediment for phosphorus control and subsequent effects on ammonia-oxidizing and ammonia-denitrifying microorganisms and on submerged macrophyte revegetation.

    Science.gov (United States)

    Lin, Juan; Zhong, Yufang; Fan, Hua; Song, Chaofeng; Yu, Chao; Gao, Yue; Xiong, Xiong; Wu, Chenxi; Liu, Jiantong

    2017-01-01

    In this work, sediments were treated with calcium nitrate, aluminum sulfate, ferric sulfate, and Phoslock®, respectively. The impact of treatments on internal phosphorus release, the abundance of nitrogen cycle-related functional genes, and the growth of submerged macrophytes were investigated. All treatments reduced total phosphorus (TP) and soluble reactive phosphorus (SRP) in interstitial water, and aluminum sulfate was most efficient. Aluminum sulfate also decreased TP and SRP in overlying water. Treatments significantly changed P speciations in the sediment. Phoslock® transformed other P species into calcium-bound P. Calcium nitrate, ferric sulfate, and Phoslock® had negative influence on ammonia oxidizers, while four chemicals had positive influence on denitrifies, indicating that chemical treatment could inhibit nitrification but enhance denitrification. Aluminum sulfate had decreased chlorophyll content of the leaves of submerged macrophytes, while ferric sulfate and Phoslock® treatment would inhibit the growth of the root. Based on the results that we obtained, we emphasized that before application of chemical treatment, the effects on submerged macrophyte revegetation should be taken into consideration.

  3. Effects of sponge bleaching on ammonia-oxidizing Archaea: distribution and relative expression of ammonia monooxygenase genes associated with the barrel sponge Xestospongia muta.

    Science.gov (United States)

    López-Legentil, Susanna; Erwin, Patrick M; Pawlik, Joseph R; Song, Bongkeun

    2010-10-01

    Sponge-mediated nitrification is an important process in the nitrogen cycle, however, nothing is known about how nitrification and symbiotic Archaea may be affected by sponge disease and bleaching events. The giant barrel sponge Xestospongia muta is a prominent species on Caribbean reefs that contains cyanobacterial symbionts, the loss of which results in two types of bleaching: cyclic, a recoverable condition; and fatal, a condition associated with the disease-like sponge orange band (SOB) syndrome and sponge death. Terminal restriction fragment length polymorphism (TRFLP) analyses, clone libraries, and relative mRNA quantification of ammonia monooxygenase genes (amoA) were performed using a RNA transcript-based approach to characterize the active ammonia-oxidizing Archaea (AOA) community present in bleached, non-bleached, and SOB tissues of cyclically and fatally bleached sponges. We found that non-bleached and cyclically bleached tissues of X. muta harbored a unique Crenarchaeota community closely related to those reported for other sponges. In contrast, bleached tissue from the most degraded sponge contained a Crenarchaeota community that was more similar to those found in sediment and sand. Although there were no significant differences in amoA expression among the different tissues, amoA expression was higher in the most deteriorated tissues. Results suggest that a shift in the Crenarchaeota community precedes an increase in amoA gene expression in fatally bleached sponges, while cyclic bleaching did not alter the AOA community structure and its amoA gene expression.

  4. Genome sequence of the olive tree, Olea europaea.

    Science.gov (United States)

    Cruz, Fernando; Julca, Irene; Gómez-Garrido, Jèssica; Loska, Damian; Marcet-Houben, Marina; Cano, Emilio; Galán, Beatriz; Frias, Leonor; Ribeca, Paolo; Derdak, Sophia; Gut, Marta; Sánchez-Fernández, Manuel; García, Jose Luis; Gut, Ivo G; Vargas, Pablo; Alioto, Tyler S; Gabaldón, Toni

    2016-06-27

    The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive oil. The molecular bases underlying the phenotypic differences among domesticated cultivars, or between domesticated olive trees and their wild relatives, remain poorly understood. Both wild and cultivated olive trees have 46 chromosomes (2n). A total of 543 Gb of raw DNA sequence from whole genome shotgun sequencing, and a fosmid library containing 155,000 clones from a 1,000+ year-old olive tree (cv. Farga) were generated by Illumina sequencing using different combinations of mate-pair and pair-end libraries. Assembly gave a final genome with a scaffold N50 of 443 kb, and a total length of 1.31 Gb, which represents 95 % of the estimated genome length (1.38 Gb). In addition, the associated fungus Aureobasidium pullulans was partially sequenced. Genome annotation, assisted by RNA sequencing from leaf, root, and fruit tissues at various stages, resulted in 56,349 unique protein coding genes, suggesting recent genomic expansion. Genome completeness, as estimated using the CEGMA pipeline, reached 98.79 %. The assembled draft genome of O. europaea will provide a valuable resource for the study of the evolution and domestication processes of this important tree, and allow determination of the genetic bases of key phenotypic traits. Moreover, it will enhance breeding programs and the formation of new varieties.

  5. Nitrifying bacterial community structures and their nitrification performance under sufficient and limited inorganic carbon conditions.

    Science.gov (United States)

    Fukushima, Toshikazu; Whang, Liang-Ming; Chiang, Ting-Yu; Lin, Yi-Hsuan; Chevalier, Lizette R; Chen, Mei-Chun; Wu, Yi-Ju

    2013-07-01

    This study examined the hypothesis that different inorganic carbon (IC) conditions enrich different ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) populations by operating two laboratory-scale continuous-flow bioreactors fed with 15 and 100 mg IC/L, respectively. During this study, both bioreactors maintained satisfactory nitrification performance and stably oxidized 250 mg N/L of influent ammonium without nitrite accumulation. Based on results of cloning/sequencing and terminal restriction fragment length polymorphism targeting on the ammonia monooxygenase subunit A (amoA) gene, Nitrosomonas nitrosa lineage was identified as the dominant AOB population in the high-IC bioreactor, while Nitrosomonas europaea and Nitrosomonas nitrosa lineage AOB were dominant in the low-IC bioreactor. Results of real-time polymerase chain reactions for Nitrobacter and Nitrospira 16S rRNA genes indicated that Nitrospira was the predominant NOB population in the high-IC bioreactor, while Nitrobacter was the dominant NOB in the low-IC bioreactor. Furthermore, batch experiment results suggest that N. europaea and Nitrobacter populations are proliferated in the low-IC bioreactor due to their higher rates under low IC conditions despite the fact that these two populations have been identified as weak competitors, compared with N. nitrosa and Nitrospira, under low ammonium/nitrite environments. This study revealed that in addition to ammonium/nitrite concentrations, limited IC conditions may also be important in selecting dominant AOB/NOB communities of nitrifying bioreactors.

  6. Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea.

    Directory of Open Access Journals (Sweden)

    Kateryna V Zhalnina

    Full Text Available The activity of ammonia-oxidizing archaea (AOA leads to the loss of nitrogen from soil, pollution of water sources and elevated emissions of greenhouse gas. To date, eight AOA genomes are available in the public databases, seven are from the group I.1a of the Thaumarchaeota and only one is from the group I.1b, isolated from hot springs. Many soils are dominated by AOA from the group I.1b, but the genomes of soil representatives of this group have not been sequenced and functionally characterized. The lack of knowledge of metabolic pathways of soil AOA presents a critical gap in understanding their role in biogeochemical cycles. Here, we describe the first complete genome of soil archaeon Candidatus Nitrososphaera evergladensis, which has been reconstructed from metagenomic sequencing of a highly enriched culture obtained from an agricultural soil. The AOA enrichment was sequenced with the high throughput next generation sequencing platforms from Pacific Biosciences and Ion Torrent. The de novo assembly of sequences resulted in one 2.95 Mb contig. Annotation of the reconstructed genome revealed many similarities of the basic metabolism with the rest of sequenced AOA. Ca. N. evergladensis belongs to the group I.1b and shares only 40% of whole-genome homology with the closest sequenced relative Ca. N. gargensis. Detailed analysis of the genome revealed coding sequences that were completely absent from the group I.1a. These unique sequences code for proteins involved in control of DNA integrity, transporters, two-component systems and versatile CRISPR defense system. Notably, genomes from the group I.1b have more gene duplications compared to the genomes from the group I.1a. We suggest that the presence of these unique genes and gene duplications may be associated with the environmental versatility of this group.

  7. Differential Responses of Dinitrogen Fixation, Diazotrophic Cyanobacteria and Ammonia Oxidation Reveal a Potential Warming-Induced Imbalance of the N-Cycle in Biological Soil Crusts.

    Directory of Open Access Journals (Sweden)

    Xiaobing Zhou

    Full Text Available N2 fixation and ammonia oxidation (AO are the two most important processes in the nitrogen (N cycle of biological soil crusts (BSCs. We studied the short-term response of acetylene reduction assay (ARA rates, an indicator of potential N2 fixation, and AO rates to temperature (T, -5°C to 35°C in BSC of different successional stages along the BSC ecological succession and geographic origin (hot Chihuahuan and cooler Great Basin deserts. ARA in all BSCs increased with T until saturation occurred between 15 and 20°C, and declined at 30-35°C. Culture studies using cyanobacteria isolated from these crusts indicated that the saturating effect was traceable to their inability to grow well diazotrophically within the high temperature range. Below saturation, temperature response was exponential, with Q10 significantly different in the two areas (~ 5 for Great Basin BSCs; 2-3 for Chihuahuan BSCs, but similar between the two successional stages. However, in contrast to ARA, AO showed a steady increase to 30-35°C in Great Basin, and Chihuhuan BSCs showed no inhibition at any tested temperature. The T response of AO also differed significantly between Great Basin (Q10 of 4.5-4.8 and Chihuahuan (Q10 of 2.4-2.6 BSCs, but not between successional stages. Response of ARA rates to T did not differ from that of AO in either desert. Thus, while both processes scaled to T in unison until 20°C, they separated to an increasing degree at higher temperature. As future warming is likely to occur in the regions where BSCs are often the dominant living cover, this predicted decoupling is expected to result in higher proportion of nitrates in soil relative to ammonium. As nitrate is more easily lost as leachate or to be reduced to gaseous forms, this could mean a depletion of soil N over large landscapes globally.

  8. Abundance and diversity of ammonia-oxidizing archaea and bacteria on granular activated carbon and their fates during drinking water purification process.

    Science.gov (United States)

    Niu, Jia; Kasuga, Ikuro; Kurisu, Futoshi; Furumai, Hiroaki; Shigeeda, Takaaki; Takahashi, Kazuhiko

    2016-01-01

    Ammonia is a precursor to trichloramine, which causes an undesirable chlorinous odor. Granular activated carbon (GAC) filtration is used to biologically oxidize ammonia during drinking water purification; however, little information is available regarding the abundance and diversity of ammonia-oxidizing archaea (AOA) and bacteria (AOB) associated with GAC. In addition, their sources and fates in water purification process remain unknown. In this study, six GAC samples were collected from five full-scale drinking water purification plants in Tokyo during summer and winter, and the abundance and community structure of AOA and AOB associated with GAC were studied in these two seasons. In summer, archaeal and bacterial amoA genes on GACs were present at 3.7 × 10(5)-3.9 × 10(8) gene copies/g-dry and 4.5 × 10(6)-4.2 × 10(8) gene copies/g-dry, respectively. In winter, archaeal amoA genes remained at the same level, while bacterial amoA genes decreased significantly for all GACs. No differences were observed in the community diversity of AOA and AOB from summer to winter. Phylogenetic analysis revealed high AOA diversity in group I.1a and group I.1b in raw water. Terminal-restriction fragment length polymorphism analysis of processed water samples revealed that AOA diversity decreased dramatically to only two OTUs in group I.1a after ozonation, which were identical to those detected on GAC. It suggests that ozonation plays an important role in determining AOA diversity on GAC. Further study on the cell-specific activity of AOA and AOB is necessary to understand their contributions to in situ nitrification performance.

  9. Nonsterol Triterpenoids as Major Constituents of Olea europaea

    Science.gov (United States)

    Stiti, Naïm; Hartmann, Marie-Andrée

    2012-01-01

    Plant triterpenoids represent a large and structurally diverse class of natural products. A growing interest has been focused on triterpenoids over the past decade due to their beneficial effects on human health. We show here that these bioactive compounds are major constituents of several aerial parts (floral bud, leaf bud, stem, and leaf) of olive tree, a crop exploited so far almost exclusively for its fruit and oil. O. europaea callus cultures were analyzed as well. Twenty sterols and twenty-nine nonsteroidal tetra- and pentacyclic triterpenoids belonging to seven types of carbon skeletons (oleanane, ursane, lupane, taraxerane, taraxastane, euphane, and lanostane) were identified and quantified by GC and GC-MS as free and esterified compounds. The oleanane-type compounds, oleanolic acid and maslinic acid, were largely predominant in all the organs tested, whereas they are practically absent in olive oil. In floral buds, they represented as much as 2.7% of dry matter. In callus cultures, lanostane-type compounds were the most abundant triterpenoids. In all the tissues analyzed, free and esterified triterpene alcohols exhibited different distribution patterns of their carbon skeletons. Taken together, these data provide new insights into largely unknown triterpene secondary metabolism of Olea europaea. PMID:22523691

  10. Differential responses of dinitrogen fixation, diazotrophic cyanobacteria and ammonia oxidation reveal a potential warming-induced imbalance of the N-cycle in biological soil crusts

    Science.gov (United States)

    Zhou, Xiaobing; Smith, Hilda J.; Giraldo Silva, Ana; Belnap, Jayne; Garcia-Pichel, Ferran

    2017-01-01

    N2 fixation and ammonia oxidation (AO) are the two most important processes in the nitrogen (N) cycle of biological soil crusts (BSCs). We studied the short-term response of acetylene reduction assay (ARA) rates, an indicator of potential N2 fixation, and AO rates to temperature (T, -5°C to 35°C) in BSC of different successional stages along the BSC ecological succession and geographic origin (hot Chihuahuan and cooler Great Basin deserts). ARA in all BSCs increased with T until saturation occurred between 15 and 20°C, and declined at 30–35°C. Culture studies using cyanobacteria isolated from these crusts indicated that the saturating effect was traceable to their inability to grow well diazotrophically within the high temperature range. Below saturation, temperature response was exponential, with Q10 significantly different in the two areas (~ 5 for Great Basin BSCs; 2–3 for Chihuahuan BSCs), but similar between the two successional stages. However, in contrast to ARA, AO showed a steady increase to 30–35°C in Great Basin, and Chihuhuan BSCs showed no inhibition at any tested temperature. The T response of AO also differed significantly between Great Basin (Q10 of 4.5–4.8) and Chihuahuan (Q10 of 2.4–2.6) BSCs, but not between successional stages. Response of ARA rates to T did not differ from that of AO in either desert. Thus, while both processes scaled to T in unison until 20°C, they separated to an increasing degree at higher temperature. As future warming is likely to occur in the regions where BSCs are often the dominant living cover, this predicted decoupling is expected to result in higher proportion of nitrates in soil relative to ammonium. As nitrate is more easily lost as leachate or to be reduced to gaseous forms, this could mean a depletion of soil N over large landscapes globally.

  11. The effectiveness of the use of filter on the tilapia growth performance, number of Nitrosomonas sp., and water quality in aquaponics systems

    Directory of Open Access Journals (Sweden)

    Yuli Andriani

    2018-01-01

    Full Text Available ABSTRACT This study aims to determine the most effective type of living filter media for the bacteria Nitrosomonas sp. in order to improve water quality in aquaponics systems. The method used in this study was completely randomized design, consisting of five treatments and each was repeated three times. The treatments were: A (without addition of filter media, B (addition of palm fibers, silica sand, and activated carbon, C (addition of palm fibers, silica sand, gravel, and activated carbon, D (addition of palm fibers, silica sand, rocks, and activated carbon, and E (addition of palm fibers, silica sand, bioball, and activated carbon. Parameters measured were: 1 the number of Nitrosomonas bacteria, 2 water quality (ammonia, nitrate, and phosphate; and, 3 productivity of fish and Chinese spinach. Data were analyzed using a descriptive method. The findings show that the highest number of bacteria was found in treatment E, 9.29×105 CFU/mL on the bioball filter media and 4.43×105 CFU/mL in rearing tanks. The best water quality was in treatment B, with a concentration of ammonia of 0.17 mg/L, nitrate of 0.33 mg/L, and phosphate of 0.54 mg/L. Plant productivity was the best in treatment B in which the average length and weight reach 48.1 cm and 11.1 grams of plant/week, respectively. The best fish growth was seen in treatment C with an absolute growth rate of 4.4 grams and a specific growth rate of 1.9%/day. The recommended filter was made of Arenga pinnata fibers, silica sand, gravels, and active carbon of about 2 cm thick each.The results showed that the type of filter on the aquaponic system had an effect on the amount of Nitrosomonas sp. in water, water quality, and the productivity of Chinese spinach.Keywords: aquaponics, filter, water quality, Nitrosomonas sp.ABSTRAKPenelitian ini bertujuan untuk menentukan jenis filter yang paling efektif sebagai media hidup bakteri Nitrosomonas sp. sehingga menghasilkan kualitas air yang baik dalam sistem

  12. Abundance and diversity of bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants revealed by high-throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Zhu Wang

    Full Text Available Biological nitrification/denitrification is frequently used to remove nitrogen from tannery wastewater containing high concentrations of ammonia. However, information is limited about the bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants (WWTPs due to the low-throughput of the previously used methods. In this study, 454 pyrosequencing and Illumina high-throughput sequencing, combined with molecular methods, were used to comprehensively characterize structures and functions of nitrification and denitrification bacterial communities in aerobic and anaerobic sludge of two full-scale tannery WWTPs. Pyrosequencing of 16S rRNA genes showed that Proteobacteria and Synergistetes dominated in the aerobic and anaerobic sludge, respectively. Ammonia-oxidizing bacteria (AOB amoA gene cloning revealed that Nitrosomonas europaea dominated the ammonia-oxidizing community in the WWTPs. Metagenomic analysis showed that the denitrifiers mainly included the genera of Thauera, Paracoccus, Hyphomicrobium, Comamonas and Azoarcus, which may greatly contribute to the nitrogen removal in the two WWTPs. It is interesting that AOB and ammonia-oxidizing archaea had low abundance although both WWTPs demonstrated high ammonium removal efficiency. Good correlation between the qPCR and metagenomic analysis is observed for the quantification of functional genes amoA, nirK, nirS and nosZ, indicating that the metagenomic approach may be a promising method used to comprehensively investigate the abundance of functional genes of nitrifiers and denitrifiers in the environment.

  13. Nitrite Reductase (nirK) as an Alternative Molecular Marker for Ammonia-oxidizing Archaea: Quantification and Characterization of Thaumarchaeal nirK Genes in Estuarine Sediments from San Francisco Bay

    Science.gov (United States)

    Reji, L.; Lee, J. A.; Damashek, J.; Francis, C.

    2016-02-01

    Nitrification, the microbially-mediated oxidation of ammonia to nitrate via nitrite, is a key component of the biogeochemical nitrogen cycle. The first and rate-limiting step of nitrification is the aerobic oxidation of ammonia to nitrite. Recent molecular ecological studies targeting ammonia monooxygenase (amoA) genes have identified ammonia-oxidizing archaea (AOA) as key players in the process. In addition to the ammonia oxidation machinery that includes the amoA gene, AOA also possess a gene for copper-containing nitrite reductase (nirK). Despite the notably high abundance and expression of archaeal nirK in various environments, the distribution patterns and functional role of this gene in AOA remain mostly unknown. In the present study, the diversity and abundance of nirK genes in estuarine sediments were investigated using quantitative polymerase chain reaction, cloning and sequencing approaches. The abundance and phylogeny were compared with that of the conventional marker gene, amoA. Overall, nirK was observed to be significantly more abundant than amoA in the sediment samples, with variation in copy numbers spanning several orders of magnitude between sampling sites. The substantial difference in relative abundance suggests that the conventionally used amoA primers could be underestimating AOA diversity in marine/estuarine sediments. Phylogenetic analysis targeting archaeal nirK revealed a number of unique sequence types, as well as many that clustered with sequences from previous estuarine studies and cultured AOA isolates, including Nitrosopumilus maritimus and Nitrosoarchaeaum limnia. The nirK phylogeny was mostly congruent with that of archaeal amoA. Overall, this study provides new insights into the diversity and abundance of archaeal nirK genes in estuarine sediments, and highlights the importance of further investigating the physiological role of this gene in AOA, as well as its suitability as a marker gene for studying AOA in the environment.

  14. Photosynthetic characteristics of olive tree (Olea europaea) bark.

    Science.gov (United States)

    Filippou, Manolis; Fasseas, Costas; Karabourniotis, George

    2007-07-01

    Functional and structural characteristics of corticular photosynthesis of sun-exposed bark of olive tree (Olea europaea L.) were examined. Stomata are only sporadically present during stem primary growth. Light transmission through the phellem was age dependent, decreasing rapidly in stems older than five years of age. Light transmission was also low in pubescent 1-year-old stems. Light transmission was about 50% higher in wet phellem than in dry phellem. Photosynthetic capacity on a unit area basis (measured with an oxygen disc electrode at 27 degrees C and about 5% CO(2) on chlorophyllous tissue discs isolated from the stem) was higher in 1-, 20- and 30-year-old stems compared with 2-10-year-old stems. Low chlorophyll a/b ratio and light compensation points were recorded in olive stems with low phellem light transmission, in accordance with the shade acclimation hypothesis. The intrinsic photochemical efficiency of photosystem II of all stems, especially young stems, was less than that of the leaves. Our results show that olive tree bark possesses an efficient photosynthetic mechanism that may significantly contribute not only to the reduction in concentrations of CO(2) in the inner bark, but also to whole-tree carbon balance.

  15. Olive plants (Olea europaea L.) as a bioindicator for pollution.

    Science.gov (United States)

    Eliwa, Amal Mohamed; Kamel, Ehab Abdel-Razik

    2013-06-15

    In the present work, olive plant (Olea europaea L.) was used as a biological indicator for pollution in which, molecular and physiological parameters were studied. Olive plants were collected from polluted and non-polluted areas in Jeddah - Saudi Arabia, traffic area as an air polluted area, sewage treatment station as water polluted area, industrial area as solid waste polluted, costal area as marine polluted area and an area without a direct source of pollution far away from the city center, which was used as control. These changes conducted with nucleic acid content, minerals content, pigments and some growth parameters. Results showed significant reductions in DNA and RNA contents under all polluted sites. Mineral contents were varied widely depending on the different pollutants and locations of olive plant. Generally, micro-elements varied (increase/decrease) significantly within collected samples and the source of pollution. All growth parameters were decreased significantly within the studied samples of all pollutant areas except the relative water content was increased. The content of chlorophyll a has decreased highly significantly in all polluted leaves. While the content of chlorophyll b has increased significantly in all polluted leaves especially in air polluted leaves. The total content of carotenoid pigments has decreased highly significantly in all polluted leaves. It was concluded that olive plant can be used as a biological indicator to the environmental pollutants.

  16. Molecular studies in olive (Olea europaea L.): overview on DNA markers applications and recent advances in genome analysis.

    Science.gov (United States)

    Bracci, T; Busconi, M; Fogher, C; Sebastiani, L

    2011-04-01

    Olive (Olea europaea L.) is one of the oldest agricultural tree crops worldwide and is an important source of oil with beneficial properties for human health. This emblematic tree crop of the Mediterranean Basin, which has conserved a very wide germplasm estimated in more than 1,200 cultivars, is a diploid species (2n = 2x = 46) that is present in two forms, namely wild (Olea europaea subsp. europaea var. sylvestris) and cultivated (Olea europaea subsp. europaea var. europaea). In spite of its economic and nutritional importance, there are few data about the genetic of olive if compared with other fruit crops. Available molecular data are especially related to the application of molecular markers to the analysis of genetic variability in Olea europaea complex and to develop efficient molecular tools for the olive oil origin traceability. With regard to genomic research, in the last years efforts are made for the identification of expressed sequence tag, with particular interest in those sequences expressed during fruit development and in pollen allergens. Very recently the sequencing of chloroplast genome provided new information on the olive nucleotide sequence, opening the olive genomic era. In this article, we provide an overview of the most relevant results in olive molecular studies. A particular attention was given to DNA markers and their application that constitute the most part of published researches. The first important results in genome analysis were reported.

  17. ORF Alignment: NC_004757 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available MVPEMGDYYVPATQNNARILVRNENGIELLSNICRHRQATILEGRGSSRNIVCP 101 ... YVGHELMVPEMGDYYVPATQNNARILVRNENGIE...LLSNICRHRQATILEGRGSSRNIVCP Sbjct: 1 ... YVGHELMVPEMGDYYVPATQNNARILVRNENGIELLSNICRHRQATILEGRGSSRNIVCP 60 ... ...otein ... 2Fe-2S subunit [Nitrosomonas europaea ATCC 19718] ... Length = 99 ... Query: 42 ... YVGHEL

  18. ORF Alignment: NC_004757 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... [Nitrosomonas europaea ATCC 19718] ... Length = 75 ... Query: 1 ... MNHQARMRWRCRRGMLELDIVLQRFIDNHYEQLDEH...QLELFEMLLSLSDHDLWNIIIGNT 60 ... MNHQARMRWRCRRGMLELDIVLQRFIDNHYEQLDEHQLELFEM...LLSLSDHDLWNIIIGNT Sbjct: 1 ... MNHQARMRWRCRRGMLELDIVLQRFIDNHYEQLDEHQLELFEMLLSLSDHDLWNIIIGNT 60 ...

  19. ORF Alignment: NC_004757 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available ... [Nitrosomonas europaea ATCC 19718] ... Length = 96 ... Query: 3 ... YLIYGEDVPDSLAQRVASRPAHLARIRELQEQGRLLLAGPCPAIDS...IDPGPAGFTGSLIV 62 ... YLIYGEDVPDSLAQRVASRPAHLARIRELQEQGRLLLAGPCPAIDS...IDPGPAGFTGSLIV Sbjct: 1 ... YLIYGEDVPDSLAQRVASRPAHLARIRELQEQGRLLLAGPCPAIDSIDPGPAGFTGSLIV 60 ...

  20. Isolation and identification of radical scavengers in olive tree (Olea europaea) wood

    NARCIS (Netherlands)

    Pérez-Bonilla, M.; Salido, S.; Beek, van T.A.; Linares-Palomino, P.J.; Altarejos, J.; Nogueras, M.; Sánchez, A.

    2006-01-01

    Several extracts of Olea europaea wood (Picual olive cultivar) were obtained with solvents of different polarity and their antioxidant activities determined. The active compounds were detected in fractions of an ethyl acetate extract using HPLC with on-line radical scavenging detection. After

  1. Yeast functional screen to identify genes conferring salt stress tolerance in Salicornia europaea

    Directory of Open Access Journals (Sweden)

    Yoshiki eNakahara

    2015-10-01

    Full Text Available Salinity is a critical environmental factor that adversely affects crop productivity. Halophytes have evolved various mechanisms to adapt to saline environments. Salicornia europaea L. is one of the most salt-tolerant plant species. It does not have special salt-secreting structures like a salt gland or salt bladder, and is therefore a good model for studying the common mechanisms underlying plant salt tolerance. To identify candidate genes encoding key proteins in the mediation of salt tolerance in S. europaea, we performed a functional screen of a cDNA library in yeast. The library was screened for genes that allowed the yeast to grow in the presence of 1.3 M NaCl. We obtained three full-length S. europaea genes that confer salt tolerance. The genes are predicted to encode (1 a novel protein highly homologous to thaumatin-like proteins, (2 a novel coiled-coil protein of unknown function, and (3 a novel short peptide of 32 residues. Exogenous application of a synthetic peptide corresponding to the 32 residues improved salt tolerance of Arabidopsis. The approach described in this report provides a rapid assay system for large-scale screening of S. europaea genes involved in salt stress tolerance and supports the identification of genes responsible for such mechanisms. These genes may be useful candidates for improving crop salt tolerance by genetic transformation.

  2. Comparative proteomic analysis of differentially expressed proteins in shoots of Salicornia europaea under different salinity.

    Science.gov (United States)

    Wang, Xuchu; Fan, Pengxiang; Song, Hongmiao; Chen, Xianyang; Li, Xiaofang; Li, Yinxin

    2009-07-01

    Soil salinity is a major abiotic stress that limits agriculture productivity worldwide. Salicornia europaea is a succulent annual euhalophyte and one of the most salt tolerant plant species. The elucidation of its salt tolerance mechanism is of significance for generating salt-tolerant crops. In this study, we provided high resolution of proteome reference maps of S. europaea shoot and obtained evidence on the salt tolerance mechanism by analyzing the proteomic responses of this plant to high salinity. Our results demonstrated significant variations existed in 196 out of 1880 protein spots detected on CBB stained 2-DE gels. Of these, 111 proteins were identified by mass spectrometry. Among them, the majority was energy production and conversion related proteins, followed by photosynthesis and carbohydrate metabolism associated enzymes. Analysis of protein expression patters revealed that energy production and ion homeostasis associated proteins played important roles for this plant salt tolerance ability. Hierarchical clustering results revealed many proteins were involved in S. europaea salt tolerance mechanism as a dynamic network. Finally, based on our proteomic results, we brought forward a possible schematic representation of mechanism associated with the systematic salt tolerance phenotype in S. europaea.

  3. Yeast functional screen to identify genes conferring salt stress tolerance in Salicornia europaea.

    Science.gov (United States)

    Nakahara, Yoshiki; Sawabe, Shogo; Kainuma, Kenta; Katsuhara, Maki; Shibasaka, Mineo; Suzuki, Masanori; Yamamoto, Kosuke; Oguri, Suguru; Sakamoto, Hikaru

    2015-01-01

    Salinity is a critical environmental factor that adversely affects crop productivity. Halophytes have evolved various mechanisms to adapt to saline environments. Salicornia europaea L. is one of the most salt-tolerant plant species. It does not have special salt-secreting structures like a salt gland or salt bladder, and is therefore a good model for studying the common mechanisms underlying plant salt tolerance. To identify candidate genes encoding key proteins in the mediation of salt tolerance in S. europaea, we performed a functional screen of a cDNA library in yeast. The library was screened for genes that allowed the yeast to grow in the presence of 1.3 M NaCl. We obtained three full-length S. europaea genes that confer salt tolerance. The genes are predicted to encode (1) a novel protein highly homologous to thaumatin-like proteins, (2) a novel coiled-coil protein of unknown function, and (3) a novel short peptide of 32 residues. Exogenous application of a synthetic peptide corresponding to the 32 residues improved salt tolerance of Arabidopsis. The approach described in this report provides a rapid assay system for large-scale screening of S. europaea genes involved in salt stress tolerance and supports the identification of genes responsible for such mechanisms. These genes may be useful candidates for improving crop salt tolerance by genetic transformation.

  4. Abiotic factors influencing the occurrence of Salicornia europaea in West Estonia

    OpenAIRE

    Hulisz, Piotr; Elvisto, Tina; Karasiewicz, Mirosław T.; Piernik, Agnieszka

    2011-01-01

    The occurrence of Salicornia europaea in Western Estonia (Kassari and Topu bays) is the result of complex processes occurring in the Baltic coastal zone and conditioned by such abiotic factors as topography, lithology, hydrogeology and climate. This is reflected by very high salinity level of groundwater and soils.

  5. Headspace volatile composition of the flowers of Caralluma europaea N.E.Br. (Apocynaceae).

    Science.gov (United States)

    Formisano, Carmen; Senatore, Felice; Della Porta, Giovanna; Scognamiglio, Mariarosa; Bruno, Maurizio; Maggio, Antonella; Rosselli, Sergio; Zito, Pietro; Sajeva, Maurizio

    2009-11-11

    The volatile constituents of the flowers of Caralluma europaea (Guss.) N.E.Br (Apocynaceae) from Lampedusa Island were analyzed by a headspace GC method. The analyses allowed the identification and quantification of 41 compounds. The main components were, among the monoterpenoids, terpinolene (23.3%), alpha-terpinene (19.1%) and linalool (18.4%), whereas, among the carbonylic compounds the major constituents were heptanal (2.0%), octanoic acid (2.4%) and hexanoic acid (1.7%). The presence of a nitrogen containing compound, indole (0.8%) and of a sulphur containing compound, dimethylsulphide (t), noteworthy. The compounds found in the flowers of C. europaea have been compared with data available in the literature as regard to their odor, presence in other sapromyiophilous taxa, possible role as semiochemicals, and presence in decaying organic matter. 89.3% of total constituents have been described in other sapromyiophilous taxa. Some of the compounds are present in several types of decaying organic matter (excrements, decomposing bodies, and spoiled fish, etc). Several volatiles found in C. europaea flowers are used as semiochemicals by Hymenoptera, Coleoptera, Diptera, Lepidoptera and other insects. Sixteen volatiles, accounting for 32.4% of the total constituents, are described as attractants of some Diptera families, with a biology linked to decaying organic matter. Our data thus confirm that C. europaea floral bouquet falls within the sapromyiophilous pollination syndrome.

  6. ABILITY OF BACTERIAL CONSORTIUM: Bacillus coagulans, Bacilus licheniformis, Bacillus pumilus, Bacillus subtilis, Nitrosomonas sp. and Pseudomonas putida IN BIOREMEDIATION OF WASTE WATER IN CISIRUNG WASTE WATER TREATMENT PLANT

    Directory of Open Access Journals (Sweden)

    Ratu SAFITRI

    2015-10-01

    Full Text Available This study was conducted in order to determine the ability of bacterial consortium: Bacillus coagulans, Bacilus licheniformis, Bacillus pumilus, Bacillus subtilis, Nitrosomonas sp., and Pseudomonas putida in bioremediation of wastewater origin Cisirung WWTP. This study uses an experimental method completely randomized design (CRD, which consists of two treatment factors (8x8 factorial design. The first factor is a consortium of bacteria (K, consisting of 8 level factors (k1, k2, k3, k4, k5, k6, k7, and k8. The second factor is the time (T, consisting of a 7 level factors (t0, t1, t2, t3, t4, t5, t6, and t7. Test parameters consist of BOD (Biochemical Oxygen Demand, COD (Chemical Oxygen Demand, TSS (Total Suspended Solid, Ammonia and Population of Microbes during bioremediation. Data were analyzed by ANOVA, followed by Duncan test. The results of this study showed that the consortium of Bacillus pumilus, Bacillus subtilis, Bacillus coagulans, Nitrosomonas sp., and Pseudomonas putida with inoculum concentration of 5% (k6 is a consortium of the most effective in reducing BOD 71.93%, 64.30% COD, TSS 94.85%, and 88.58% of ammonia.

  7. Metabolomic Functional Analysis of Bacterial Genomes: Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Arp, Daniel J; Sayavedra-Soto, Luis A

    2008-01-01

    The availability of the complete DNA sequence of the bacterial genome of Nitrosomonas europaea offered the opportunity for unprecedented and detailed investigations of function. We studied the function of genes involved in carbohydrate and Fe metabolism. N. europaea has genes for the synthesis and degradation of glycogen and sucrose but cannot grow on substrates other than ammonia and CO2. Granules of glycogen were detected in whole cells by electron microscopy and quantified in cell-free extracts by enzymatic methods. The cellular glycogen and sucrose content varied depending on the composition of the growth medium and cellular growth stage. N. europaea also depends heavily on iron for metabolism of ammonia, is particularly interesting since it lacks genes for siderophore production, and has genes with only low similarity to known iron reductases, yet grows relatively well in medium containing low Fe. By comparing the transcriptomes of cells grown in iron-replete medium versus iron-limited medium, 247 genes were identified as differentially expressed. Mutant strains deficient in genes for sucrose, glycogen and iron metabolism were created and are being used to further our understanding of ammonia oxidizing bacteria.

  8. Polyphenols benefits of olive leaf (Olea europaea L) to human health.

    Science.gov (United States)

    Vogel, Patrícia; Kasper Machado, Isabel; Garavaglia, Juliano; Zani, Valdeni Terezinha; de Souza, Daiana; Morelo Dal Bosco, Simone

    2014-12-17

    The phenolic compounds present in olive leaves (Olea europaea L.) confer benefits to the human health. To review the scientific literature about the benefits of the polyphenols of olive leaves to human health. Literature review in the LILACS-BIREME, SciELO and MEDLINE databases for publications in English, Portuguese and Spanish with the descriptors "Olea europaea", "olive leaves", "olive leaf", "olive leaves extracts", "olive leaf extracts", "phenolic compounds", "polyphenols", "oleuropein", "chemical composition", and "health". There were identified 92 articles, but only 38 related to the objectives of the study and 9 articles cited in the works were included due to their relevance. The phenolic compounds present in olive leaves, especially the oleuropein, are associated to antioxidant, antihypertensive, hypoglycemic, hypocholesterolemic and cardioprotective activity. Furthermore, studies associate the oleuropein to an anti-inflammatory effect in trauma of the bone marrow and as a support in the treatment of obesity. Copyright AULA MEDICA EDICIONES 2014. Published by AULA MEDICA. All rights reserved.

  9. Characteristics, Phytochemical Analysis and Biological Activities of Extracts from Tunisian Chetoui Olea europaea Variety

    OpenAIRE

    Ines Khlif; Karim Jellali; Thomas Michel; Maria Halabalaki; Alexios Leandros Skaltsounis; Noureddine Allouche

    2015-01-01

    This study selected 10 extracts from Tunisian chetoui O. europaea variety for their total phenolics, flavonoids, and phytochemical analyses as well as for their antioxidant and antimicrobial activities determination. The in vitro antioxidant property was investigated using DPPH, ferric reducing antioxidant capacity (FRAP), oxygen reducing antioxidant capacity (ORAC), and β-carotene-linoleic acid bleaching assays while antimicrobial activity was evaluated using macrodilutions method. For all o...

  10. Fauna Europaea: Coleoptera 2 (excl. series Elateriformia, Scarabaeiformia, Staphyliniformia and superfamily Curculionoidea)

    Science.gov (United States)

    Alonso Zarazaga, Miguel-Angel; Slipinski, Adam; Nilsson, Anders; Jelínek, Josef; Taglianti, Augusto Vigna; Turco, Federica; Otero, Carlos; Canepari, Claudio; Kral, David; Liberti, Gianfranco; Sama, Gianfranco; Nardi, Gianluca; Löbl, Ivan; Horak, Jan; Kolibac, Jiri; Háva, Jirí; Sapiejewski, Maciej; Jäch, Manfred; Bologna, Marco Alberto; Biondi, Maurizio; Nikitsky, Nikolai B.; Mazzoldi, Paolo; Zahradnik, Petr; Wegrzynowicz, Piotr; Constantin, Robert; Gerstmeier, Roland; Zhantiev, Rustem; Fattorini, Simone; Tomaszewska, Wioletta; Rücker, Wolfgang H.; Vazquez-Albalate, Xavier; Cassola, Fabio; Angelini, Fernando; Johnson, Colin; Schawaller, Wolfgang; Regalin, Renato; Baviera, Cosimo; Rocchi, Saverio; Cianferoni, Fabio; Beenen, Ron; Schmitt, Michael; Sassi, David; Kippenberg, Horst; Zampetti, Marcello Franco; Trizzino, Marco; Chiari, Stefano; Carpaneto, Giuseppe Maria; Sabatelli, Simone

    2015-01-01

    Abstract Fauna Europaea provides a public web-service with an index of scientific names (including synonyms) of all living European land and freshwater animals, their geographical distribution at country level (up to the Urals, excluding the Caucasus region), and some additional information. The Fauna Europaea project covers about 230,000 taxonomic names, including 130,000 accepted species and 14,000 accepted subspecies, which is much more than the originally projected number of 100,000 species. This represents a huge effort by more than 400 contributing specialists throughout Europe and is a unique (standard) reference suitable for many users in science, government, industry, nature conservation and education. Coleoptera represent a huge assemblage of holometabolous insects, including as a whole more than 200 recognized families and some 400,000 described species worldwide. Basic information is summarized on their biology, ecology, economic relevance, and estimated number of undescribed species worldwide. Little less than 30,000 species are listed from Europe. The Coleoptera 2 section of the Fauna Europaea database (Archostemata, Myxophaga, Adephaga and Polyphaga excl. the series Elateriformia, Scarabaeiformia, Staphyliniformia and the superfamily Curculionoidea) encompasses 80 families (according to the previously accepted family-level systematic framework) and approximately 13,000 species. Tabulations included a complete list of the families dealt with, the number of species in each, the names of all involved specialists, and, when possible, an estimate of the gaps in terms of total number of species at an European level. A list of some recent useful references is appended. Most families included in the Coleoptera 2 Section have been updated in the most recent release of the Fauna Europaea index, or are ready to be updated as soon as the FaEu data management environment completes its migration from Zoological Museum Amsterdam to Berlin Museum für Naturkunde

  11. ORF Alignment: NC_004757 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004757 gi|30250333 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  12. ORF Alignment: NC_002488 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_002488 gi|15837680 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  13. ORF Alignment: NC_006369 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_006369 gi|54293610 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  14. ORF Alignment: NC_006085 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_006085 gi|50842381 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  15. ORF Alignment: NC_002946 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_002946 gi|59800726 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  16. ORF Alignment: NC_003919 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_003919 gi|21242823 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  17. ORF Alignment: NC_003112 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_003112 gi|15676600 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  18. ORF Alignment: NC_002977 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_002977 gi|53803220 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  19. ORF Alignment: NC_003902 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_003902 gi|21231567 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  20. ORF Alignment: NC_004551 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004551 gi|28572541 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  1. ORF Alignment: NC_004572 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004572 gi|28493349 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  2. ORF Alignment: NC_003869 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_003869 gi|20807422 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  3. ORF Alignment: NC_003116 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_003116 gi|15793872 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  4. ORF Alignment: NC_006368 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_006368 gi|54296649 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  5. ORF Alignment: NC_004556 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_004556 gi|28198275 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  6. ORF Alignment: NC_002942 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_002942 gi|52840863 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  7. ORF Alignment: NC_005966 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_005966 gi|50085709 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  8. ORF Alignment: NC_005085 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_005085 gi|34495926 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  9. ORF Alignment: NC_002516 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_002516 gi|15598180 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  10. ORF Alignment: NC_006513 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_006513 gi|56478742 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  11. ORF Alignment: NC_006834 [GENIUS II[Archive

    Lifescience Database Archive (English)

    Full Text Available NC_006834 gi|58581923 >2bc2A 10 205 522 711 9e-06 ... ref|NP_842403.1| DNA internalization...-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19718] emb|CAD86320.1| DNA ... internalizat...ion-related competence protein ComEC/Rec2 ... [Nitrosomonas europaea ATCC 19

  12. RESULTS OF INITIAL AMMONIA OXIDATION TESTING

    Energy Technology Data Exchange (ETDEWEB)

    Nash, C. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Fowley, M. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2016-12-30

    This memo presents an experimental survey of aqueous phase chemical processes to remove aqueous ammonia from waste process streams. Ammonia is generated in both the current Hanford waste flowsheet and in future waste processing. Much ammonia will be generated in the Low Activity Waste (LAW) melters.i Testing with simulants in glass melters at Catholic University has demonstrated the significant ammonia production.ii The primary reaction there is the reducing action of sugar on nitrate in the melter cold cap. Ammonia has been found to be a problem in secondary waste stabilization. Ammonia vapors are noxious and destruction of ammonia could reduce hazards to waste treatment process personnel. It is easily evolved especially when ammonia-bearing solutions are adjusted to high pH.

  13. Global transcriptome profiling of Salicornia europaea L. shoots under NaCl treatment.

    Science.gov (United States)

    Ma, Jinbiao; Zhang, Meiru; Xiao, Xinlong; You, Jinjin; Wang, Junru; Wang, Tao; Yao, Yinan; Tian, Changyan

    2013-01-01

    Soil salinity is a major abiotic stress that limits agriculture productivity worldwide. Salicornia europaea is well adapted to extreme saline environments with more than 1,000 mM NaCl in the soil, so it could serve as an important model species for studying halophilic mechanisms in euhalophytes. To obtain insights into the molecular basis of salt tolerance, we present here the first extensive transcriptome analysis of this species using the Illumina HiSeq™ 2000. A total of 41 and 39 million clean reads from the salt-treated (Se200S) and salt-free (SeCKS) tissues of S. europaea shoots were obtained, and de novo assembly produced 97,865 and 101,751 unigenes, respectively. Upon further assembly with EST data from both Se200S and SeCKS, 109,712 high-quality non-redundant unigenes were generated with a mean unigene size of 639 bp. Additionally, a total of 3,979 differentially expressed genes (DEGs) were detected between the Se200S and SeCKS libraries, with 348 unigenes solely expressed in Se200S and 460 unigenes solely expressed in SeCKS. Furthermore, we identified a large number of genes that are involved in ion homeostasis and osmotic adjustment, including cation transporters and proteins for the synthesis of low-molecular compounds. All unigenes were functionally annotated within the COG, GO and KEGG pathways, and 10 genes were validated by qRT-PCR. Our data contains the extensive sequencing and gene-annotation analysis of S. europaea. This genetic knowledge will be very useful for future studies on the molecular adaptation to abiotic stress in euhalophytes and will facilitate the genetic manipulation of other economically important crops.

  14. Global transcriptome profiling of Salicornia europaea L. shoots under NaCl treatment.

    Directory of Open Access Journals (Sweden)

    Jinbiao Ma

    Full Text Available Soil salinity is a major abiotic stress that limits agriculture productivity worldwide. Salicornia europaea is well adapted to extreme saline environments with more than 1,000 mM NaCl in the soil, so it could serve as an important model species for studying halophilic mechanisms in euhalophytes. To obtain insights into the molecular basis of salt tolerance, we present here the first extensive transcriptome analysis of this species using the Illumina HiSeq™ 2000.A total of 41 and 39 million clean reads from the salt-treated (Se200S and salt-free (SeCKS tissues of S. europaea shoots were obtained, and de novo assembly produced 97,865 and 101,751 unigenes, respectively. Upon further assembly with EST data from both Se200S and SeCKS, 109,712 high-quality non-redundant unigenes were generated with a mean unigene size of 639 bp. Additionally, a total of 3,979 differentially expressed genes (DEGs were detected between the Se200S and SeCKS libraries, with 348 unigenes solely expressed in Se200S and 460 unigenes solely expressed in SeCKS. Furthermore, we identified a large number of genes that are involved in ion homeostasis and osmotic adjustment, including cation transporters and proteins for the synthesis of low-molecular compounds. All unigenes were functionally annotated within the COG, GO and KEGG pathways, and 10 genes were validated by qRT-PCR.Our data contains the extensive sequencing and gene-annotation analysis of S. europaea. This genetic knowledge will be very useful for future studies on the molecular adaptation to abiotic stress in euhalophytes and will facilitate the genetic manipulation of other economically important crops.

  15. [Study on the enrichment of oleuropein from Olea europaea leaves with macroporous resin D-101].

    Science.gov (United States)

    Dang, Jian-zhang; Zhang, Xing-sheng; Huang, Xiao-yu; Feng, Li-xiong

    2007-04-01

    To study the conditions and parameters of the enrichment of oleuropein with macroporous resin. Aqueous extract of Olea europaea leaves prepared through microwave extraction was adsorbed directly with macroporous resin D-101 and the impurities such sugar were washed out by water then oleuropein was eluted by 70% ethanol. HPLC was used to determine the content of oleuropein. The contents of oleuropein increased from 5% to 21.6% in the solid, with 88.6% of recovery rate. Macroporous resin D-101 fits in purification of water-soluble oleuropein. The process is simple and convenient and can be used for industrial production.

  16. Extraction and Characterization of Lipids from Salicornia virginica and Salicornia europaea

    Science.gov (United States)

    Kulis,Michael J.; Hepp, Aloysius F.; Pham, Phong X.; Ribita, Daniela; Bomani, Bilal M. M.; Duraj, Stan A.

    2010-01-01

    The lipid content from Salicornia virginica and Salicornia europaea is investigated. The plants are leafless halophytes with seeds contained in terminal nodes. The lipids, in the form of cell membranes and oil bodies that come directly from the node cells, are observed using fluorescence microscopy. Two extraction methods as well as the results of extracting from the seeds and from the entire nodes are described. Characterization of the fatty acid components of the lipids using Gas Chromatography in tandem with Mass Spectroscopy is also described. Comparisons are made between the two methods and between the two plant materials as lipid sources.

  17. High-throughput deep sequencing reveals that microRNAs play important roles in salt tolerance of euhalophyte Salicornia europaea.

    Science.gov (United States)

    Feng, Juanjuan; Wang, Jinhui; Fan, Pengxiang; Jia, Weitao; Nie, Lingling; Jiang, Ping; Chen, Xianyang; Lv, Sulian; Wan, Lichuan; Chang, Sandra; Li, Shizhong; Li, Yinxin

    2015-02-26

    microRNAs (miRNAs) are implicated in plant development processes and play pivotal roles in plant adaptation to environmental stresses. Salicornia europaea, a salt mash euhalophyte, is a suitable model plant to study salt adaptation mechanisms. S. europaea is also a vegetable, forage, and oilseed that can be used for saline land reclamation and biofuel precursor production on marginal lands. Despite its importance, no miRNA has been identified from S. europaea thus far. Deep sequencing was performed to investigate small RNA transcriptome of S. europaea. Two hundred and ten conserved miRNAs comprising 51 families and 31 novel miRNAs (including seven miRNA star sequences) belonging to 30 families were identified. About half (13 out of 31) of the novel miRNAs were only detected in salt-treated samples. The expression of 43 conserved and 13 novel miRNAs significantly changed in response to salinity. In addition, 53 conserved and 13 novel miRNAs were differentially expressed between the shoots and roots. Furthermore, 306 and 195 S. europaea unigenes were predicted to be targets of 41 conserved and 29 novel miRNA families, respectively. These targets encoded a wide range of proteins, and genes involved in transcription regulation constituted the largest category. Four of these genes encoding laccase, F-box family protein, SAC3/GANP family protein, and NADPH cytochrome P-450 reductase were validated using 5'-RACE. Our results indicate that specific miRNAs are tightly regulated by salinity in the shoots and/or roots of S. europaea, which may play important roles in salt tolerance of this euhalophyte. The S. europaea salt-responsive miRNAs and miRNAs that target transcription factors, nucleotide binding site-leucine-rich repeat proteins and enzymes involved in lignin biosynthesis as well as carbon and nitrogen metabolism may be applied in genetic engineering of crops with high stress tolerance, and genetic modification of biofuel crops with high biomass and regulatable

  18. Spencermartinsiella europaea gen. nov., sp. nov., a new member of the family Trichomonascaceae.

    Science.gov (United States)

    Péter, Gábor; Dlauchy, Dénes; Tornai-Lehoczki, Judit; Suzuki, Motofumi; Kurtzman, Cletus P

    2011-04-01

    Ten strains of a novel heterothallic yeast species were isolated from rotten wood collected at different locations in Hungary. Analysis of gene sequences for the D1/D2 domain of the large subunit rRNA, as well as analysis of concatenated gene sequences for the nearly complete nuclear large subunit rRNA, nuclear small subunit rRNA and translation elongation factor 1-α, placed the novel species in the family Trichomonascaceae, but showed that it was distinct from all currently recognized genera. The name Spencermartinsiella europaea gen. nov., sp. nov. is proposed to accommodate the new genus and novel species. The novel species could be distinguished from recognized species of neighbouring genera on the basis of standard phenotypic characteristics. The type and isotype strains of Spencermartinsiella europaea are NCAIM Y.01817(T) ( = NRRL Y-48265(T) =  CBS 11730(T)) and NCAIM Y.01819(I) ( = NRRL Y-48266(I) = CBS 11731(I)), respectively.

  19. Essential oil composition of stems and fruits of Caralluma europaea N.E.Br. (Apocynaceae).

    Science.gov (United States)

    Zito, Pietro; Sajeva, Maurizio; Bruno, Maurizio; Maggio, Antonella; Rosselli, Sergio; Formisano, Carmen; Senatore, Felice

    2010-01-27

    The essential oil of the stems and fruits of Caralluma europaea (Guss.) N.E.Br. (Apocynaceae) from Lampedusa Island has been obtained by hydrodistillation and its composition analyzed. The analyses allowed the identification and quantification of 74 volatile compounds, of which 16 were aromatic and 58 non-aromatic. Stems and fruits contained 1.4% and 2.7% of aromatic compounds respectively, while non-aromatic were 88.3% and 88.8%. Non-aromatic hydrocarbons were the most abundant compounds in both organs, followed by fatty acids. Data showed differences in the profiles between stems and fruits which shared only eighteen compounds; stems accounted for 38 compounds while fruits for 53. Fruits showed a higher diversity especially in aromatic compounds with twelve versus four in stems. Among the volatiles identified in stems and fruits of C. europaea 26 are present in other taxa of Apocynaceae, 52 are semiochemicals for many insects, and 21 have antimicrobial activity. The possible ecological role of the volatiles found is briefly discussed.

  20. Phenolic Compounds from Olea europaea L. Possess Antioxidant Activity and Inhibit Carbohydrate Metabolizing Enzymes In Vitro

    Directory of Open Access Journals (Sweden)

    Nadia Dekdouk

    2015-01-01

    Full Text Available Phenolic composition and biological activities of fruit extracts from Italian and Algerian Olea europaea L. cultivars were studied. Total phenolic and tannin contents were quantified in the extracts. Moreover 14 different phenolic compounds were identified, and their profiles showed remarkable quantitative differences among analysed extracts. Moreover antioxidant and enzymatic inhibition activities were studied. Three complementary assays were used to measure their antioxidant activities and consequently Relative Antioxidant Capacity Index (RACI was used to compare and easily describe obtained results. Results showed that Chemlal, between Algerian cultivars, and Coratina, among Italian ones, had the highest RACI values. On the other hand all extracts and the most abundant phenolics were tested for their efficiency to inhibit α-amylase and α-glucosidase enzymes. Leccino, among all analysed cultivars, and luteolin, among identified phenolic compounds, were found to be the best inhibitors of α-amylase and α-glucosidase enzymes. Results demonstrated that Olea europaea fruit extracts can represent an important natural source with high antioxidant potential and significant α-amylase and α-glucosidase inhibitory effects.

  1. Evaluation of the effects of Olea europaea L. subsp. africana (Mill.) P.S. Green (Oleaceae) leaf methanol extract against castor oil-induced diarrhoea in mice.

    Science.gov (United States)

    Amabeoku, George J; Bamuamba, Kapinga

    2010-03-01

    Olea europaea L. subsp. africana (Mill.) P.S. Green is widely used in South Africa by traditional medicine practitioners to treat diarrhoea. However, little is known scientifically about this South African species in the treatment of diarrhoea. The main aim of the study therefore was to investigate the antidiarrhoeal effect of the leaf methanol extract of the plant species in mice. The antidiarrhoeal activity of the leaf methanol extract of O. europaea subsp. africana was studied using a castor oil-induced diarrhoeal test. The antipropulsive activity of the plant extract was also investigated using the charcoal meal transit test. Standard methods were used to investigate the acute toxicity and effect of O. europaea subsp. africana on castor oil-induced intraluminal fluid accumulation. Leaf methanol extract of O. europaea subsp. africana and loperamide, a standard antidiarrhoeal drug, significantly reduced the number of diarrhoeal episodes induced by castor oil, significantly decreased the stool mass, significantly delayed the onset of the diarrhoea and protected the animals against castor oil-induced diarrhoea. Both O. europaea subsp. africana and loperamide significantly decreased the gastrointestinal transit of charcoal meal and castor oil-induced intraluminal fluid accumulation in mice. The LD50 value was found to be 3475 mg/kg (p.o.). The results obtained suggest that the leaf methanol extract of O. europaea subsp. africana has an antidiarrhoeal property and that, given orally, it may be non-toxic and/or safe in mice.

  2. Early performance of Olea europaea cv. Arbequina, Picual and Frantoio in the southern Atacama Desert

    Directory of Open Access Journals (Sweden)

    Freddy Mora

    2008-01-01

    Full Text Available The cultivars Arbequina, Picual and Frantoio of Olea europaea are cultivated in severalMediterranean countries. In 1999, these cultivars were planted at three locations in the region of Coquimbo,an arid, Mediterranean-like area in Chile. A generalized linear modeling approach was used in view of thenon-normal distribution of the agronomic data sets. Fruit yield (harvests of 2002-2003, precocity (2002 andtree survival (after four growing seasons differed significantly between the cultivars. Arbequina and Picualhad a positive effect on the yield. Picual was the earliest cultivar at two sites. The survival rate of Frantoio washigh at the three sites (90-100%, as opposed to Picual (56-83%. The approach of Generalized Linear Modelswas particularly useful where the assumption of normality was not satisfied. The selection of cultivars ispromising in this arid region of Chile, while the success will depend on the selection of well-adapted genotypesto a particular location.

  3. Olive tree (Olea europaea) leaves: potential beneficial effects on human health.

    Science.gov (United States)

    El, Sedef N; Karakaya, Sibel

    2009-11-01

    Olive tree (Olea europaea L.) leaves have been widely used in traditional remedies in European and Mediterranean countries such as Greece, Spain, Italy, France, Turkey, Israel, Morocco, and Tunisia. They have been used in the human diet as an extract, an herbal tea, and a powder, and they contain many potentially bioactive compounds that may have antioxidant, antihypertensive, antiatherogenic, anti-inflammatory, hypoglycemic, and hypocholesterolemic properties. One of these potentially bioactive compounds is the secoiridoid oleuropein, which can constitute up to 6-9% of dry matter in the leaves. Other bioactive components found in olive leaves include related secoiridoids, flavonoids, and triterpenes. The evidence supporting the potentially beneficial effects of olive leaves on human health are presented in this brief review.

  4. Genetic Markers Analyses and Bioinformatic Approaches to Distinguish Between Olive Tree (Olea europaea L.) Cultivars.

    Science.gov (United States)

    Ben Ayed, Rayda; Ben Hassen, Hanen; Ennouri, Karim; Rebai, Ahmed

    2016-12-01

    The genetic diversity of 22 olive tree cultivars (Olea europaea L.) sampled from different Mediterranean countries was assessed using 5 SNP markers (FAD2.1; FAD2.3; CALC; SOD and ANTHO3) located in four different genes. The genotyping analysis of the 22 cultivars with 5 SNP loci revealed 11 alleles (average 2.2 per allele). The dendrogram based on cultivar genotypes revealed three clusters consistent with the cultivars classification. Besides, the results obtained with the five SNPs were compared to those obtained with the SSR markers using bioinformatic analyses and by computing a cophenetic correlation coefficient, indicating the usefulness of the UPGMA method for clustering plant genotypes. Based on principal coordinate analysis using a similarity matrix, the first two coordinates, revealed 54.94 % of the total variance. This work provides a more comprehensive explanation of the diversity available in Tunisia olive cultivars, and an important contribution for olive breeding and olive oil authenticity.

  5. Polyploidy in the olive complex (Olea europaea): Evidence from flow cytometry and nuclear microsatellite analyses

    DEFF Research Database (Denmark)

    Besnard, G.; Garcia-Verdugo, C.; Rubio de Casas, R.

    2008-01-01

    Background: Phylogenetic and phylogeographic investigations have been previously performed to study the evolution of the olive tree complex (Olea europaea). A particularly high genomic diversity has been found in north-west Africa. However, to date no exhaustive study has been addressed to infer...... putative polyploidization events and their evolutionary significance in the diversification of the olive tree and its relatives. Methods: Representatives of the six olive subspecies were investigated using (a) flow cytometry to estimate genome content, and (b) six highly variable nuclear microsatellites....... Lastly, abnormalities in chromosomes inheritance leading to aneuploid formation were revealed using microsatellite analyses in the offspring from the controlled cross in subsp. maroccana. Conclusions: This study constitutes the first report for multiple polyploidy in olive tree relatives. Formation...

  6. Feeding and Development of Emerald Ash Borer (Coleoptera: Buprestidae) on Cultivated Olive, Olea europaea.

    Science.gov (United States)

    Cipollini, Don; Rigsby, Chad M; Peterson, Donnie L

    2017-08-01

    We examined the suitability of cultivated olive, Olea europaea L., as a host for emerald ash borer, Agrilus planipennis Fairmaire. In a bioassay using cut stems from a field-grown olive tree (cv. 'Manzanilla') we found that 45% of larvae that had emerged from eggs used to inoculate stems, were recovered alive, many as larvae or prepupae, during periodic debarking of a subset of stems. Three intact stems that 19 larvae successfully entered were exposed to a simulated overwintering treatment. Four live adults emerged afterwards, and an additional pupa and several prepupae were discovered after debarking these stems. Cultivated olive joins white fringetree as one of the two species outside of the genus Fraxinus capable of supporting the development of emerald ash borer from neonate to adult. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  7. Recent developments in olive (Olea europaea L.) genetics and genomics: applications in taxonomy, varietal identification, traceability and breeding.

    Science.gov (United States)

    Sebastiani, L; Busconi, M

    2017-09-01

    The latest results in DNA markers application and genomic studies in olive. Olive (Olea europaea L.) is among the most ancient tree crops worldwide and the source of oil beneficial for human health. Despite this, few data on olive genetics are available in comparison with other cultivated plant species. Molecular information is mainly linked to molecular markers and their application to the study of DNA variation in the Olea europaea complex. In terms of genomic research, efforts have been made in sequencing, heralding the era of olive genomic. The present paper represents an update of a previous review work published in this journal in 2011. The review is again mainly focused on DNA markers, whose application still constitutes a relevant percentage of the most recently published researches. Since the olive genomic era has recently started, the latest results in this field are also being discussed.

  8. Effects of UV-B radiation on Olea europaea: comparisons between a greenhouse and a field experiment

    Energy Technology Data Exchange (ETDEWEB)

    Liakoura, V.; Stavrianakou, S.; Liakopoulos, G.; Karabourniotis, G. [Athens Agricultural Univ. Dept. of Agricultural Biotechnology, Athens (Greece); Manetas, Y. [Patras Univ, Dept, of Biology, Patras (Greece)

    1999-11-01

    Olea europaea plants were grown in the field with or without supplemental ultraviolet B radiation equivalent to the increase at ground level resulting from a 15 per cent depletion in stratospheric ozone concentration. After one year, their morphology, anatomy and physiology were compared with that of plants grown in a greenhouse and exposed for four months to either zero UV-B radiation or UV-B radiation equivalent to that of supplemented outdoor treatment. Results showed an increase in adaxial epidermal thickness and reduced total protein concentration in plants grown in the field, in contrast to greenhouse-grown plants which under the influence of UV-B radiation showed significant increases in abaxial cutical thickness and trichome UV-B absorbing compounds. These observations suggest that Olea europaea plants have a high UV-B tolerance and are not affected by increase in UV-B radiation. 23 refs., 1 tab.

  9. Community structure variability of Uropodina mites (Acari: Mesostigmata) in nests of the common mole, Talpa europaea, in Central Europe

    OpenAIRE

    Napiera?a, Agnieszka; M?dra, Anna; Leszczy?ska-Deja, Kornelia; Gwiazdowicz, Dariusz J.; Go?dyn, Bart?omiej; B?oszyk, Jerzy

    2016-01-01

    Underground nests of Talpa europaea, known as the common mole, are very specific microhabitats, which are also quite often inhabited by various groups of arthropods. Mites from the suborder Uropodina (Acari: Mesostigmata) are only one of them. One could expect that mole nests that are closely located are inhabited by communities of arthropods with similar species composition and structure. However, results of empirical studies clearly show that even nests which are close to each other can be ...

  10. Encyclopaedia Europaea

    DEFF Research Database (Denmark)

    Sørensen, Gert

    depends on the conceptual or ideological constellation in which it takes part. This volume on one hand demonstrates the role of notions of identity in a variety of European contexts, and on the other hand highlights how there may be reasons to challenge the use of the term and corresponding social......, cultural, and political practices. Notions of national identity and national politics are challenged by European integration, as well as by increasing demographic heterogeneity due to migration, and migrants experience conflicts of identification stemming from clashes between cultural heritage...

  11. Encyclopaedia Europaea

    DEFF Research Database (Denmark)

    Sørensen, Gert

    Identity is a keyword in a number of academic fields as well as in public debate and in politics. During the last decades, references to identity have proliferated, yet there is no simple definition available that corresponds to the use of the notion in all contexts. The significance of the notio...... Christian Lammers, Saxo-Instituttet - Arkæologi, Etnologi, Historie og Græsk og Latin; Gert Sørensen, Institut for Engelsk, Germansk og Romansk ; Anne Ring Petersen, Institut for Kunst- og Kulturvidenskab...

  12. Aggiornamento sulla distribuzione di Talpa europaea in Umbria

    Directory of Open Access Journals (Sweden)

    A.M. Paci

    2003-10-01

    Full Text Available L?Umbria, in ragione della sua posizione centrale nella Penisola, appare particolarmente interessante dal punto di vista biogeografico. Per quanto riguarda le talpe, ad esempio, sono presenti tutti i taxa italiani ma, essendo ancora scarse e frammentarie le informazioni sulla loro distribuzione regionale, viene intanto aggiornato lo status di T. europaea con la sintesi di alcuni dati inediti raccolti nella provincia di Perugia: Zoccolanti, Città di Castello, 300 m as pa, 13-IV-2001; Monte Maggiore, Città di Castello, 605 m bc pa vu, 13-VI-2003; San Secondo, Città di Castello, 260 m ci pb vf, 3-VI-1995 / 9-V-2001; Lugnano, Città di Castello, 260 m ci pb vf, 25-XI-1992; Niccone, Umbertide, 250 m ce pb vf 14-VI-2003; Pietralunga, 505 m as pa, 19-IV-2002; Monte Cucco, Sigillo, 1050 m bc bm vu, 5-V-2003 Castiglione, Gubbio, 840 m bc pa, 30-V-1999; Schifanoia, Valfabbrica, 350 m bc pa, 30-V-2000; Oscano, Perugia, 470 m bc pa, 2002; Monte Melino, Magione, 225 m ci ps vt, 19-I-2001; Sant?Arcangelo, Magione; 260 m zu ps vt, IV-2002; Città della Pieve, 500 m as pa, 29-VI-2001 (bc bosco di caducifoglie, ce colture estensive, ci colture intensive, as area suburbana, zu zona umida, pa piano bioclimatico altocollinare, pb piano bioclimatico bassocollinare, bm piano bioclimatico bassomontano, ps piano bioclimatico collinare submediterraneo, vu variante umida, vf variante fredda, vt variante temperata. In letteratura la specie viene segnalata anche nel Comune di Assisi. In due località dell?Umbria nord-orientale ? Pietralunga e Monte Cucco - T. europaea è risultata in parapatria con T. caeca mentre, da recentissima bibliografia, entrerebbe in contatto con T. romana nella fascia centrale della regione. Contemporaneamente si è creduto opportuno riportare notizie relative ad individui marchigiani

  13. Molecular analysis of the interaction between Olea europaea and the biotrophic fungus Spilocaea oleagina.

    Science.gov (United States)

    Benitez, Yoselin; Botella, Miguel A; Trapero, Antonio; Alsalimiya, Mohammed; Caballero, Jose Luis; Dorado, Gabriel; Muñoz-Blanco, Juan

    2005-07-01

    SUMMARY The mitosporic fungus Spilocaea oleagina is an obligate biotroph of olive (Olea europaea) causing a scab disease associated with leaf fall and substantial losses in production. Using differential display we have identified 162 cDNA fragments corresponding to transcripts that show altered abundance during the defence response of a resistant olive cultivar to S. oleagina. Detailed analyses of 21 selected genes by real-time quantitative RT-PCR revealed different kinetics of induction. Genes involved in signalling, transcriptional control, oxidative stress, biotic and abiotic stress, and several genes with unknown function were found to be induced rapidly after infection. In contrast, genes involved in metabolism and cellular maintenance showed delayed induction. The induction of the selected genes in a susceptible cultivar was delayed and/or reduced during the response to S. oleagina. Interestingly, the basal expression of some genes in the uninfected resistant cultivar was higher than in the susceptible one, suggesting a constitutive activation of defence responses. Expression of these genes in response to salicylic acid, methyl jasmonate, a mixture of both, ethephon, hydrogen peroxide, menadione and wounding was also investigated. The results are discussed in relation to the molecular bases and signalling events involved in this biotrophic interaction.

  14. 454 Pyrosequencing of Olive (Olea europaea L. Transcriptome in Response to Salinity.

    Directory of Open Access Journals (Sweden)

    Christos Bazakos

    Full Text Available Olive (Olea europaea L. is one of the most important crops in the Mediterranean region. The expansion of cultivation in areas irrigated with low quality and saline water has negative effects on growth and productivity however the investigation of the molecular basis of salt tolerance in olive trees has been only recently initiated. To this end, we investigated the molecular response of cultivar Kalamon to salinity stress using next-generation sequencing technology to explore the transcriptome profile of olive leaves and roots and identify differentially expressed genes that are related to salt tolerance response. Out of 291,958 obtained trimmed reads, 28,270 unique transcripts were identified of which 35% are annotated, a percentage that is comparable to similar reports on non-model plants. Among the 1,624 clusters in roots that comprise more than one read, 24 were differentially expressed comprising 9 down- and 15 up-regulated genes. Respectively, inleaves, among the 2,642 clusters, 70 were identified as differentially expressed, with 14 down- and 56 up-regulated genes. Using next-generation sequencing technology we were able to identify salt-response-related transcripts. Furthermore we provide an annotated transcriptome of olive as well as expression data, which are both significant tools for further molecular studies in olive.

  15. In vitro propagation of olive (Olea europaea L.) by nodal segmentation of elongated shoots.

    Science.gov (United States)

    Lambardi, Maurizio; Ozudogru, Elif Aylin; Roncasaglia, Romano

    2013-01-01

    Olive (Olea europaea L.), long-living, ever-green fruit tree of the Old World, has been part of a traditional landscape in the Mediterranean area for centuries. Both the fruits consumed after processing and the oil extracted from the fruits are among the main components of the Mediterranean diet, widely used for salads and cooking, as well as for preserving other food. Documentations show that the ancient use of this beautiful tree also includes lamp fuel production, wool treatment, soap production, medicine, and cosmetics. However, unlike the majority of the fruit species, olive propagation is still a laborious practice. As regards traditional propagation, rooting of cuttings and grafting stem segments onto rootstocks are possible, former being achieved only when the cuttings are collected in specific periods (spring or beginning of autumn), and latter only when skilled grafters are available. In both the cases, performance of the cultivars varies considerably. The regeneration of whole plants from ovules, on the other hand, is used only occasionally. Micropropagation of olive is not easy mainly due to explant oxidation, difficulties in explant disinfection, and labor-oriented establishment of in vitro shoot cultures. However today, the progress in micropropagation technology has made available the complete protocols for several Mediterranean cultivars. This chapter describes a micropropagation protocol based on the segmentation of nodal segments obtained from elongated shoots.

  16. Production of triterpene acids by cell suspension cultures of Olea europaea.

    Science.gov (United States)

    Saimaru, Hiroshi; Orihara, Yutaka; Tansakul, Pimpimon; Kang, Young-Hwa; Shibuya, Masaaki; Ebizuka, Yutaka

    2007-05-01

    Olive (Olea europaea) contains large quantity of triterpene acids including oleanolic acid (6) as a major one. Varieties of biological activities exhibited by triterpene acids attracted our attentions, especially from pharmaceutical viewpoints. Cell culture of olive plant was induced and its triterpene constituents were studied. From the cell suspension cultures, six ursane type triterpene acids; ursolic acid (9), pomolic acid (10), rotundic acid (11), tormentic acid (12), 2alpha-hydroxyursolic acid (13) and 19alpha-hydroxyasiatic acid (14), and two oleanane type acids; oleanolic acid and maslinic acid (7), have been isolated. Quantity of ursane type triterpene acids produced by cell cultures was larger than that of oleanane type. Further, a multifunctional oxidosqualene cyclase (OSC) named OEA was cloned by homology based PCRs from the same cultured cells. Major product of OEA is alpha-amyrin (ursane skeleton), showing good accordance to higher content of ursane-type triterpene acids in the cultured cells, and strongly suggesting OEA to be a major contributor OSC for their production.

  17. Identification and Characterization of the Iridoid Synthase Involved in Oleuropein Biosynthesis in Olive (Olea europaea) Fruits*

    Science.gov (United States)

    Kries, Hajo; Panara, Francesco; Baldoni, Luciana; O'Connor, Sarah E.; Osbourn, Anne

    2016-01-01

    The secoiridoids are the main class of specialized metabolites present in olive (Olea europaea L.) fruit. In particular, the secoiridoid oleuropein strongly influences olive oil quality because of its bitterness, which is a desirable trait. In addition, oleuropein possesses a wide range of pharmacological properties, including antioxidant, anti-inflammatory, and anti-cancer activities. In accordance, obtaining high oleuropein varieties is a main goal of molecular breeding programs. Here we use a transcriptomic approach to identify candidate genes belonging to the secoiridoid pathway in olive. From these candidates, we have functionally characterized the olive homologue of iridoid synthase (OeISY), an unusual terpene cyclase that couples an NAD (P)H-dependent 1,4-reduction step with a subsequent cyclization, and we provide evidence that OeISY likely generates the monoterpene scaffold of oleuropein in olive fruits. OeISY, the first pathway gene characterized for this type of secoiridoid, is a potential target for breeding programs in a high value secoiridoid-accumulating species. PMID:26709230

  18. 454 Pyrosequencing of Olive (Olea europaea L.) Transcriptome in Response to Salinity.

    Science.gov (United States)

    Bazakos, Christos; Manioudaki, Maria E; Sarropoulou, Elena; Spano, Thodhoraq; Kalaitzis, Panagiotis

    2015-01-01

    Olive (Olea europaea L.) is one of the most important crops in the Mediterranean region. The expansion of cultivation in areas irrigated with low quality and saline water has negative effects on growth and productivity however the investigation of the molecular basis of salt tolerance in olive trees has been only recently initiated. To this end, we investigated the molecular response of cultivar Kalamon to salinity stress using next-generation sequencing technology to explore the transcriptome profile of olive leaves and roots and identify differentially expressed genes that are related to salt tolerance response. Out of 291,958 obtained trimmed reads, 28,270 unique transcripts were identified of which 35% are annotated, a percentage that is comparable to similar reports on non-model plants. Among the 1,624 clusters in roots that comprise more than one read, 24 were differentially expressed comprising 9 down- and 15 up-regulated genes. Respectively, inleaves, among the 2,642 clusters, 70 were identified as differentially expressed, with 14 down- and 56 up-regulated genes. Using next-generation sequencing technology we were able to identify salt-response-related transcripts. Furthermore we provide an annotated transcriptome of olive as well as expression data, which are both significant tools for further molecular studies in olive.

  19. Characterization of antioxidant enzymes and peroxisomes of olive (Olea europaea L.) fruits.

    Science.gov (United States)

    Lopez-Huertas, Eduardo; del Río, Luis A

    2014-10-15

    The presence of peroxisomes in olive (Olea europaea L.) fruits and different antioxidant enzymes occurring in this plant tissue is reported for the first time. Ultrastructural analysis showed that olive cells were characterized by the presence of large vacuoles and lipid drops. Plastids, mitochondria and peroxisomes were placed near the cell wall, showing some type of association with it. Olive fruit peroxisomes were purified by sucrose density-gradient centrifugation, and catalase, glutathione reductase and ascorbate peroxidase were found in peroxisomes. In olive fruit tissue the presence of a battery of antioxidant enzymes was demonstrated, including catalase, four superoxide dismutase isozymes (mainly an Fe-SOD plus 2 Cu,Zn-SOD and a Mn-SOD), all the enzymes of the ascorbate-glutathione cycle, reduced and oxidized glutathione, ascorbate, and four NADPH-recycling dehydrogenases. The knowledge of the full composition of antioxidants (enzymatic and non-enzymatic) in olive fruits is crucial to be able to understand the processes regulating the antioxidant composition of olive oil. Copyright © 2014 Elsevier GmbH. All rights reserved.

  20. Soil fluoride spiking effects on olive trees (Olea europaea L. cv. Chemlali).

    Science.gov (United States)

    Zouari, M; Ben Ahmed, C; Fourati, R; Delmail, D; Ben Rouina, B; Labrousse, P; Ben Abdallah, F

    2014-10-01

    A pot experiment under open air conditions was carried out to investigate the uptake, accumulation and toxicity effects of fluoride in olive trees (Olea europaea L.) grown in a soil spiked with inorganic sodium fluoride (NaF). Six different levels (0, 20, 40, 60, 80 and 100mM NaF) of soil spiking were applied through NaF to irrigation water. At the end of the experiment, total fluoride content in soil was 20 and 1770mgFkg(-1) soil in control and 100mM NaF treatments, respectively. The comparative distribution of fluoride partitioning among the different olive tree parts showed that the roots accumulated the most fluoride and olive fruits were minimally affected by soil NaF spiking as they had the lowest fluoride content. In fact, total fluoride concentration varied between 12 and 1070µgFg(-1) in roots, between 9 and 570µgFg(-1) in shoots, between 12 and 290µgFg(-1) in leaves, and between 10 and 29µgFg(-1) in fruits, respectively for control and 100mM NaF treatments. Indeed, the fluoride accumulation pattern showed the following distribution: roots>shoots>leaves>fruits. On the other hand, fluoride toxicity symptoms such as leaf necrosis and leaf drop appeared only in highly spiked soils (60, 80 and 100mM NaF). Copyright © 2014 Elsevier Inc. All rights reserved.

  1. Identification and Characterization of the Iridoid Synthase Involved in Oleuropein Biosynthesis in Olive (Olea europaea) Fruits.

    Science.gov (United States)

    Alagna, Fiammetta; Geu-Flores, Fernando; Kries, Hajo; Panara, Francesco; Baldoni, Luciana; O'Connor, Sarah E; Osbourn, Anne

    2016-03-11

    The secoiridoids are the main class of specialized metabolites present in olive (Olea europaea L.) fruit. In particular, the secoiridoid oleuropein strongly influences olive oil quality because of its bitterness, which is a desirable trait. In addition, oleuropein possesses a wide range of pharmacological properties, including antioxidant, anti-inflammatory, and anti-cancer activities. In accordance, obtaining high oleuropein varieties is a main goal of molecular breeding programs. Here we use a transcriptomic approach to identify candidate genes belonging to the secoiridoid pathway in olive. From these candidates, we have functionally characterized the olive homologue of iridoid synthase (OeISY), an unusual terpene cyclase that couples an NAD (P)H-dependent 1,4-reduction step with a subsequent cyclization, and we provide evidence that OeISY likely generates the monoterpene scaffold of oleuropein in olive fruits. OeISY, the first pathway gene characterized for this type of secoiridoid, is a potential target for breeding programs in a high value secoiridoid-accumulating species. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  2. Genetic improvement of olive (Olea europaea L.) by conventional and in vitro biotechnology methods.

    Science.gov (United States)

    Rugini, E; Cristofori, V; Silvestri, C

    2016-01-01

    In olive (Olea europaea L.) traditional methods of genetic improvement have up to now produced limited results. Intensification of olive growing requires appropriate new cultivars for fully mechanized groves, but among the large number of the traditional varieties very few are suitable. High-density and super high-density hedge row orchards require genotypes with reduced size, reduced apical dominance, a semi-erect growth habit, easy to propagate, resistant to abiotic and biotic stresses, with reliably high productivity and quality of both fruits and oil. Innovative strategies supported by molecular and biotechnological techniques are required to speed up novel hybridisation methods. Among traditional approaches the Gene Pool Method seems a reasonable option, but it requires availability of widely diverse germplasm from both cultivated and wild genotypes, supported by a detailed knowledge of their genetic relationships. The practice of "gene therapy" for the most important existing cultivars, combined with conventional methods, could accelerate achievement of the main goals, but efforts to overcome some technical and ideological obstacles are needed. The present review describes the benefits that olive and its products may obtain from genetic improvement using state of the art of conventional and unconventional methods, and includes progress made in the field of in vitro techniques. The uses of both traditional and modern technologies are discussed with recommendations. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Observation of eight ancient olive trees (Olea europaea L.) growing in the Garden of Gethsemane.

    Science.gov (United States)

    Petruccelli, Raffaella; Giordano, Cristiana; Salvatici, Maria Cristina; Capozzoli, Laura; Ciaccheri, Leonardo; Pazzini, Massimo; Lain, Orietta; Testolin, Raffaele; Cimato, Antonio

    2014-05-01

    For thousands of years, olive trees (Olea europaea L.) have been a significant presence and a symbol in the Garden of Gethsemane, a place located at the foot of the Mount of Olives, Jerusalem, remembered for the agony of Jesus Christ before his arrest. This investigation comprises the first morphological and genetic characterization of eight olive trees in the Garden of Gethsemane. Pomological traits, morphometric, and ultrastructural observations as well as SSR (Simple Sequence Repeat) analysis were performed to identify the olive trees. Statistical analyses were conducted to evaluate their morphological variability. The study revealed a low morphological variability and minimal dissimilarity among the olive trees. According to molecular analysis, these trees showed the same allelic profile at all microsatellite loci analyzed. Combining the results of the different analyses carried out in the frame of the present work, we could conclude that the eight olive trees of the Gethsemane Garden have been propagated from a single genotype. Copyright © 2014. Published by Elsevier SAS.

  4. The peculiar landscape of repetitive sequences in the olive (Olea europaea L.) genome.

    Science.gov (United States)

    Barghini, Elena; Natali, Lucia; Cossu, Rosa Maria; Giordani, Tommaso; Pindo, Massimo; Cattonaro, Federica; Scalabrin, Simone; Velasco, Riccardo; Morgante, Michele; Cavallini, Andrea

    2014-04-01

    Analyzing genome structure in different species allows to gain an insight into the evolution of plant genome size. Olive (Olea europaea L.) has a medium-sized haploid genome of 1.4 Gb, whose structure is largely uncharacterized, despite the growing importance of this tree as oil crop. Next-generation sequencing technologies and different computational procedures have been used to study the composition of the olive genome and its repetitive fraction. A total of 2.03 and 2.3 genome equivalents of Illumina and 454 reads from genomic DNA, respectively, were assembled following different procedures, which produced more than 200,000 differently redundant contigs, with mean length higher than 1,000 nt. Mapping Illumina reads onto the assembled sequences was used to estimate their redundancy. The genome data set was subdivided into highly and medium redundant and nonredundant contigs. By combining identification and mapping of repeated sequences, it was established that tandem repeats represent a very large portion of the olive genome (∼31% of the whole genome), consisting of six main families of different length, two of which were first discovered in these experiments. The other large redundant class in the olive genome is represented by transposable elements (especially long terminal repeat-retrotransposons). On the whole, the results of our analyses show the peculiar landscape of the olive genome, related to the massive amplification of tandem repeats, more than that reported for any other sequenced plant genome.

  5. Valuable nutrients and functional bioactives in different parts of olive (Olea europaea L.)-a review.

    Science.gov (United States)

    Ghanbari, Rahele; Anwar, Farooq; Alkharfy, Khalid M; Gilani, Anwarul-Hassan; Saari, Nazamid

    2012-01-01

    The Olive tree (Olea europaea L.), a native of the Mediterranean basin and parts of Asia, is now widely cultivated in many other parts of the world for production of olive oil and table olives. Olive is a rich source of valuable nutrients and bioactives of medicinal and therapeutic interest. Olive fruit contains appreciable concentration, 1-3% of fresh pulp weight, of hydrophilic (phenolic acids, phenolic alchohols, flavonoids and secoiridoids) and lipophilic (cresols) phenolic compounds that are known to possess multiple biological activities such as antioxidant, anticarcinogenic, antiinflammatory, antimicrobial, antihypertensive, antidyslipidemic, cardiotonic, laxative, and antiplatelet. Other important compounds present in olive fruit are pectin, organic acids, and pigments. Virgin olive oil (VOO), extracted mechanically from the fruit, is also very popular for its nutritive and health-promoting potential, especially against cardiovascular disorders due to the presence of high levels of monounsaturates and other valuable minor components such as phenolics, phytosterols, tocopherols, carotenoids, chlorophyll and squalene. The cultivar, area of production, harvest time, and the processing techniques employed are some of the factors shown to influence the composition of olive fruit and olive oil. This review focuses comprehensively on the nutrients and high-value bioactives profile as well as medicinal and functional aspects of different parts of olives and its byproducts. Various factors affecting the composition of this food commodity of medicinal value are also discussed.

  6. Nitrification by immobilized cells

    NARCIS (Netherlands)

    Wijffels, R.H.

    1994-01-01

    Nitrosomonas europaea and Nitrobacteragilis are nitrifying bacteria. Subsequently they oxidize ammonia to nitrite and nitrite to nitrate. Nitrification is a key process for the removal of nitrogen compounds from

  7. Competition for Ammonium between Plant-Roots and Nitrifying and Heterotrophic Bacteria and the Effects of Protozoan Grazing

    NARCIS (Netherlands)

    Verhagen, F.J.M.; Laanbroek, H.J.; Woldendorp, J.W.

    1995-01-01

    The competition for limiting amounts of ammonium between the chemolithotrophic ammonium-oxidizing species Nitrosomonas europaea, the heterotrophic species Arthrobacter globiformis and roots of Plantago lanceolata (Ribwort plantain) was studied in a series of model systems of increasing complexity,

  8. Proposal to support the 4th international conference on nitrification and related processes (ICoN4)

    Energy Technology Data Exchange (ETDEWEB)

    Klotz, Martin Gunter [Univ. of North Carolina, Charlotte, NC (United States)

    2016-11-04

    The 4th International Conference on Nitrification and Related Processes (ICoN4) commencing between June 27 and July 1, 2015, at the University of Alberta in Edmonton, Alberta, Canada brings together an international collection of academic, government, and private sector researchers of the global biogeochemical nitrogen cycle to share their scientific discoveries, innovations and pertinent societal impacts. The classical understanding of “nitrification” describes the two-step transformation of ammonium to nitrite and nitrite to nitrate; however, we now know from the analysis genome sequences, the application of ‘omics technologies, microbial ecology, biogeochemistry, and microbial physiology that the transformation of ammonium is not performed by a few particular groups of microorganisms nor is it confined to oxic environments. Past ICoN meetings have explored the interconnections between ammonium- and nitrite-consuming processes in all ecosystems, the emission of greenhouse gases by these processes and their control, and the intersection between intermediates of the nitrification process and other elemental cycles; this has generated tremendous progress in our understanding of the global nitrogen cycle and it has generated excitement in the next generation of N cycle researchers. Nitrification research has a long-standing connection to the Community Science Program of the DOE. Between 1999 and 2001, the JGI generated the first genome sequence of an ammonia-oxidizing bacterium, Nitrosomonas europaea ATCC 19718, and it has subsequently sequenced, or is in the process of sequencing over 50 additional genomes from ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and ammonia-oxidizing archaea. Autotrophic ammonia- and nitrite-transforming microorganisms play also a critical role in carbon cycling and sequestration in nearly all ecosystems. Not only do they control the concentration and speciation of biologically available N to plants and other

  9. Meloidogyne lusitanica n. sp. (Nematoda: Meloidogynidae), a Root-knot Nematode Parasitizing Olive Tree (Olea europaea L.)

    OpenAIRE

    de O. Abrantes, Isabel M.; de A. Santos, M. Susana N.

    1991-01-01

    A root-knot nematode from Portugal, Meloidogyne lusitanica n. sp., is described and illustrated from specimens obtained from olive trees (Olea europaea L.). Females of the new species have a characteristic perineal pattern with medium to high trapezoidal dorsal arch with distinct punctuations in the tail terminus area. The excretory pore is located posterior to the stylet, about 1.5-2.5 stylet lengths from the anterior end. The stylet is 17.1 μm long with pear-shaped knobs. Males have a round...

  10. Metabarcoding Analysis of Fungal Diversity in the Phyllosphere and Carposphere of Olive (Olea europaea).

    Science.gov (United States)

    Abdelfattah, Ahmed; Li Destri Nicosia, Maria Giulia; Cacciola, Santa Olga; Droby, Samir; Schena, Leonardo

    2015-01-01

    The fungal diversity associated with leaves, flowers and fruits of olive (Olea europaea) was investigated in different phenological stages (May, June, October and December) using an implemented metabarcoding approach. It consisted of the 454 pyrosequencing of the fungal ITS2 region and the subsequent phylogenetic analysis of relevant genera along with validated reference sequences. Most sequences were identified up to the species level or were associated with a restricted number of related taxa enabling supported speculations regarding their biological role. Analyses revealed a rich fungal community with 195 different OTUs. Ascomycota was the dominating phyla representing 93.6% of the total number of detected sequences followed by unidentified fungi (3.6%) and Basidiomycota (2.8%). A higher level of diversity was revealed for leaves compared to flowers and fruits. Among plant pathogens the genus Colletotrichum represented by three species (C. godetiae syn. C. clavatum, C. acutatum s.s and C. karstii) was the most abundant on ripe fruits but it was also detected in other organs. Pseudocercospora cladosporioides was detected with a high frequency in all leaf samples and to a less extent in ripe fruits. A much lower relative frequency was revealed for Spilocaea oleagina and for other putative pathogens including Fusarium spp., Neofusicoccum spp., and Alternaria spp. Among non-pathogen taxa, Aureobasidium pullulans, the species complex of Cladosporium cladosporioides and Devriesia spp. were the most represented. This study highlights the existence of a complex fungal consortium including both phytopathogenic and potentially antagonistic microorganisms that can have a significant impact on olive productions.

  11. Neurochemical and behavioral effects of Nigella sativa and Olea europaea oil in rats.

    Science.gov (United States)

    Cheema, M Atif Raza; Nawaz, Shazia; Gul, Sumera; Salman, Tabinda; Naqvi, Sabira; Dar, Ahsana; Haleem, Darakhshan J

    2018-04-01

    In the last few decades, therapeutic uses of medicinal compounds present in food as a normal constituent has risen substantially, largely because of their fewer side effects and adequate efficacy. This study is designed to investigate a role of brain serotonin (5-HT) and dopamine (DA) in the potential nootropic, anxiolytic, and other beneficial effects of Nigella sativa (NS) and Olea europaea (OE) oil in rat models. Animals were treated with NS and OE oil orally at doses of 0.1 ml/kg and 0.25 ml/kg for 5 weeks. Food intake and body weight change, anxiety-like effects in elevated plus maze and activity in a novel and familiar environment were monitored weekly. Effects on learning and memory after 5 weeks treatment were monitored using Morris water maze test. Neurochemical analysis was carried using HPLC-ECD method. NS and OE oil administration enhanced learning and memory in Morris water maze test and the effects were greater in NS than OE oil-treated animals. Low dose of OE oil increased exploration in an open field, higher dose of OE oil and both doses of NS oil produced no consistent effect on open field exploration. Effects of both oils on anxiety-like behavior, food and water intake, and activity in activity box were either not consistent or did not occur. The treatment increased homovanillic acid (HVA). 5-HT levels increased in high dose of NS oil and low dose of OE oil-treated groups. Low dose NS oil decreased 5-HT. The present study suggests that active components in NS and OE oil may prove useful in treating impaired cognition. OE oil may produce psychostimulant-like effect. Modulation of DA and serotonin neurotransmission seems important in the pharmacological effect of these oils.

  12. Identification and characterisation of Short Interspersed Nuclear Elements in the olive tree (Olea europaea L.) genome.

    Science.gov (United States)

    Barghini, Elena; Mascagni, Flavia; Natali, Lucia; Giordani, Tommaso; Cavallini, Andrea

    2017-02-01

    Short Interspersed Nuclear Elements (SINEs) are nonautonomous retrotransposons in the genome of most eukaryotic species. While SINEs have been intensively investigated in humans and other animal systems, SINE identification has been carried out only in a limited number of plant species. This lack of information is apparent especially in non-model plants whose genome has not been sequenced yet. The aim of this work was to produce a specific bioinformatics pipeline for analysing second generation sequence reads of a non-model species and identifying SINEs. We have identified, for the first time, 227 putative SINEs of the olive tree (Olea europaea), that constitute one of the few sets of such sequences in dicotyledonous species. The identified SINEs ranged from 140 to 362 bp in length and were characterised with regard to the occurrence of the tRNA domain in their sequence. The majority of identified elements resulted in single copy or very lowly repeated, often in association with genic sequences. Analysis of sequence similarity allowed us to identify two major groups of SINEs showing different abundances in the olive tree genome, the former with sequence similarity to SINEs of Scrophulariaceae and Solanaceae and the latter to SINEs of Salicaceae. A comparison of sequence conservation between olive SINEs and LTR retrotransposon families suggested that SINE expansion in the genome occurred especially in very ancient times, before LTR retrotransposon expansion, and presumably before the separation of the rosids (to which Oleaceae belong) from the Asterids. Besides providing data on olive SINEs, our results demonstrate the suitability of the pipeline employed for SINE identification. Applying this pipeline will favour further structural and functional analyses on these relatively unknown elements to be performed also in other plant species, even in the absence of a reference genome, and will allow establishing general evolutionary patterns for this kind of repeats in

  13. High-throughput sequencing of RNA silencing-associated small RNAs in olive (Olea europaea L..

    Directory of Open Access Journals (Sweden)

    Livia Donaire

    Full Text Available Small RNAs (sRNAs of 20 to 25 nucleotides (nt in length maintain genome integrity and control gene expression in a multitude of developmental and physiological processes. Despite RNA silencing has been primarily studied in model plants, the advent of high-throughput sequencing technologies has enabled profiling of the sRNA component of more than 40 plant species. Here, we used deep sequencing and molecular methods to report the first inventory of sRNAs in olive (Olea europaea L.. sRNA libraries prepared from juvenile and adult shoots revealed that the 24-nt class dominates the sRNA transcriptome and atypically accumulates to levels never seen in other plant species, suggesting an active role of heterochromatin silencing in the maintenance and integrity of its large genome. A total of 18 known miRNA families were identified in the libraries. Also, 5 other sRNAs derived from potential hairpin-like precursors remain as plausible miRNA candidates. RNA blots confirmed miRNA expression and suggested tissue- and/or developmental-specific expression patterns. Target mRNAs of conserved miRNAs were computationally predicted among the olive cDNA collection and experimentally validated through endonucleolytic cleavage assays. Finally, we use expression data to uncover genetic components of the miR156, miR172 and miR390/TAS3-derived trans-acting small interfering RNA (tasiRNA regulatory nodes, suggesting that these interactive networks controlling developmental transitions are fully operational in olive.

  14. The skeletal organic matrix from Mediterranean coral Balanophyllia europaea influences calcium carbonate precipitation.

    Directory of Open Access Journals (Sweden)

    Stefano Goffredo

    Full Text Available Scleractinian coral skeletons are made mainly of calcium carbonate in the form of aragonite. The mineral deposition occurs in a biological confined environment, but it is still a theme of discussion to what extent the calcification occurs under biological or environmental control. Hence, the shape, size and organization of skeletal crystals from the cellular level through the colony architecture, were attributed to factors as diverse as mineral supersaturation levels and organic mediation of crystal growth. The skeleton contains an intra-skeletal organic matrix (OM of which only the water soluble component was chemically and physically characterized. In this work that OM from the skeleton of the Balanophyllia europaea, a solitary scleractinian coral endemic to the Mediterranean Sea, is studied in vitro with the aim of understanding its role in the mineralization of calcium carbonate. Mineralization of calcium carbonate was conducted by overgrowth experiments on coral skeleton and in calcium chloride solutions containing different ratios of water soluble and/or insoluble OM and of magnesium ions. The precipitates were characterized by diffractometric, spectroscopic and microscopic techniques. The results showed that both soluble and insoluble OM components influence calcium carbonate precipitation and that the effect is enhanced by their co-presence. The role of magnesium ions is also affected by the presence of the OM components. Thus, in vitro, OM influences calcium carbonate crystal morphology, aggregation and polymorphism as a function of its composition and of the content of magnesium ions in the precipitation media. This research, although does not resolve the controversy between environmental or biological control on the deposition of calcium carbonate in corals, sheds a light on the role of OM, which appears mediated by the presence of magnesium ions.

  15. The skeletal organic matrix from Mediterranean coral Balanophyllia europaea influences calcium carbonate precipitation.

    Science.gov (United States)

    Goffredo, Stefano; Vergni, Patrizia; Reggi, Michela; Caroselli, Erik; Sparla, Francesca; Levy, Oren; Dubinsky, Zvy; Falini, Giuseppe

    2011-01-01

    Scleractinian coral skeletons are made mainly of calcium carbonate in the form of aragonite. The mineral deposition occurs in a biological confined environment, but it is still a theme of discussion to what extent the calcification occurs under biological or environmental control. Hence, the shape, size and organization of skeletal crystals from the cellular level through the colony architecture, were attributed to factors as diverse as mineral supersaturation levels and organic mediation of crystal growth. The skeleton contains an intra-skeletal organic matrix (OM) of which only the water soluble component was chemically and physically characterized. In this work that OM from the skeleton of the Balanophyllia europaea, a solitary scleractinian coral endemic to the Mediterranean Sea, is studied in vitro with the aim of understanding its role in the mineralization of calcium carbonate. Mineralization of calcium carbonate was conducted by overgrowth experiments on coral skeleton and in calcium chloride solutions containing different ratios of water soluble and/or insoluble OM and of magnesium ions. The precipitates were characterized by diffractometric, spectroscopic and microscopic techniques. The results showed that both soluble and insoluble OM components influence calcium carbonate precipitation and that the effect is enhanced by their co-presence. The role of magnesium ions is also affected by the presence of the OM components. Thus, in vitro, OM influences calcium carbonate crystal morphology, aggregation and polymorphism as a function of its composition and of the content of magnesium ions in the precipitation media. This research, although does not resolve the controversy between environmental or biological control on the deposition of calcium carbonate in corals, sheds a light on the role of OM, which appears mediated by the presence of magnesium ions.

  16. The Skeletal Organic Matrix from Mediterranean Coral Balanophyllia europaea Influences Calcium Carbonate Precipitation

    Science.gov (United States)

    Goffredo, Stefano; Vergni, Patrizia; Reggi, Michela; Caroselli, Erik; Sparla, Francesca; Levy, Oren; Dubinsky, Zvy; Falini, Giuseppe

    2011-01-01

    Scleractinian coral skeletons are made mainly of calcium carbonate in the form of aragonite. The mineral deposition occurs in a biological confined environment, but it is still a theme of discussion to what extent the calcification occurs under biological or environmental control. Hence, the shape, size and organization of skeletal crystals from the cellular level through the colony architecture, were attributed to factors as diverse as mineral supersaturation levels and organic mediation of crystal growth. The skeleton contains an intra-skeletal organic matrix (OM) of which only the water soluble component was chemically and physically characterized. In this work that OM from the skeleton of the Balanophyllia europaea, a solitary scleractinian coral endemic to the Mediterranean Sea, is studied in vitro with the aim of understanding its role in the mineralization of calcium carbonate. Mineralization of calcium carbonate was conducted by overgrowth experiments on coral skeleton and in calcium chloride solutions containing different ratios of water soluble and/or insoluble OM and of magnesium ions. The precipitates were characterized by diffractometric, spectroscopic and microscopic techniques. The results showed that both soluble and insoluble OM components influence calcium carbonate precipitation and that the effect is enhanced by their co-presence. The role of magnesium ions is also affected by the presence of the OM components. Thus, in vitro, OM influences calcium carbonate crystal morphology, aggregation and polymorphism as a function of its composition and of the content of magnesium ions in the precipitation media. This research, although does not resolve the controversy between environmental or biological control on the deposition of calcium carbonate in corals, sheds a light on the role of OM, which appears mediated by the presence of magnesium ions. PMID:21799830

  17. Metabarcoding Analysis of Fungal Diversity in the Phyllosphere and Carposphere of Olive (Olea europaea.

    Directory of Open Access Journals (Sweden)

    Ahmed Abdelfattah

    Full Text Available The fungal diversity associated with leaves, flowers and fruits of olive (Olea europaea was investigated in different phenological stages (May, June, October and December using an implemented metabarcoding approach. It consisted of the 454 pyrosequencing of the fungal ITS2 region and the subsequent phylogenetic analysis of relevant genera along with validated reference sequences. Most sequences were identified up to the species level or were associated with a restricted number of related taxa enabling supported speculations regarding their biological role. Analyses revealed a rich fungal community with 195 different OTUs. Ascomycota was the dominating phyla representing 93.6% of the total number of detected sequences followed by unidentified fungi (3.6% and Basidiomycota (2.8%. A higher level of diversity was revealed for leaves compared to flowers and fruits. Among plant pathogens the genus Colletotrichum represented by three species (C. godetiae syn. C. clavatum, C. acutatum s.s and C. karstii was the most abundant on ripe fruits but it was also detected in other organs. Pseudocercospora cladosporioides was detected with a high frequency in all leaf samples and to a less extent in ripe fruits. A much lower relative frequency was revealed for Spilocaea oleagina and for other putative pathogens including Fusarium spp., Neofusicoccum spp., and Alternaria spp. Among non-pathogen taxa, Aureobasidium pullulans, the species complex of Cladosporium cladosporioides and Devriesia spp. were the most represented. This study highlights the existence of a complex fungal consortium including both phytopathogenic and potentially antagonistic microorganisms that can have a significant impact on olive productions.

  18. High-Throughput Sequencing of RNA Silencing-Associated Small RNAs in Olive (Olea europaea L.)

    Science.gov (United States)

    Donaire, Livia; Pedrola, Laia; de la Rosa, Raúl; Llave, César

    2011-01-01

    Small RNAs (sRNAs) of 20 to 25 nucleotides (nt) in length maintain genome integrity and control gene expression in a multitude of developmental and physiological processes. Despite RNA silencing has been primarily studied in model plants, the advent of high-throughput sequencing technologies has enabled profiling of the sRNA component of more than 40 plant species. Here, we used deep sequencing and molecular methods to report the first inventory of sRNAs in olive (Olea europaea L.). sRNA libraries prepared from juvenile and adult shoots revealed that the 24-nt class dominates the sRNA transcriptome and atypically accumulates to levels never seen in other plant species, suggesting an active role of heterochromatin silencing in the maintenance and integrity of its large genome. A total of 18 known miRNA families were identified in the libraries. Also, 5 other sRNAs derived from potential hairpin-like precursors remain as plausible miRNA candidates. RNA blots confirmed miRNA expression and suggested tissue- and/or developmental-specific expression patterns. Target mRNAs of conserved miRNAs were computationally predicted among the olive cDNA collection and experimentally validated through endonucleolytic cleavage assays. Finally, we use expression data to uncover genetic components of the miR156, miR172 and miR390/TAS3-derived trans-acting small interfering RNA (tasiRNA) regulatory nodes, suggesting that these interactive networks controlling developmental transitions are fully operational in olive. PMID:22140484

  19. Metabarcoding Analysis of Fungal Diversity in the Phyllosphere and Carposphere of Olive (Olea europaea)

    Science.gov (United States)

    Abdelfattah, Ahmed; Li Destri Nicosia, Maria Giulia; Cacciola, Santa Olga; Droby, Samir; Schena, Leonardo

    2015-01-01

    The fungal diversity associated with leaves, flowers and fruits of olive (Olea europaea) was investigated in different phenological stages (May, June, October and December) using an implemented metabarcoding approach. It consisted of the 454 pyrosequencing of the fungal ITS2 region and the subsequent phylogenetic analysis of relevant genera along with validated reference sequences. Most sequences were identified up to the species level or were associated with a restricted number of related taxa enabling supported speculations regarding their biological role. Analyses revealed a rich fungal community with 195 different OTUs. Ascomycota was the dominating phyla representing 93.6% of the total number of detected sequences followed by unidentified fungi (3.6%) and Basidiomycota (2.8%). A higher level of diversity was revealed for leaves compared to flowers and fruits. Among plant pathogens the genus Colletotrichum represented by three species (C. godetiae syn. C. clavatum, C. acutatum s.s and C. karstii) was the most abundant on ripe fruits but it was also detected in other organs. Pseudocercospora cladosporioides was detected with a high frequency in all leaf samples and to a less extent in ripe fruits. A much lower relative frequency was revealed for Spilocaea oleagina and for other putative pathogens including Fusarium spp., Neofusicoccum spp., and Alternaria spp. Among non-pathogen taxa, Aureobasidium pullulans, the species complex of Cladosporium cladosporioides and Devriesia spp. were the most represented. This study highlights the existence of a complex fungal consortium including both phytopathogenic and potentially antagonistic microorganisms that can have a significant impact on olive productions. PMID:26132745

  20. Human absorption and metabolism of oleuropein and hydroxytyrosol ingested as olive (Olea europaea L.) leaf extract.

    Science.gov (United States)

    de Bock, Martin; Thorstensen, Eric B; Derraik, José G B; Henderson, Harold V; Hofman, Paul L; Cutfield, Wayne S

    2013-11-01

    Phenolic compounds derived from the olive plant (Olea europaea L.), particularly hydroxytyrosol and oleuropein, have many beneficial effects in vitro. Olive leaves are the richest source of olive phenolic compounds, and olive leaf extract (OLE) is now a popular nutraceutical taken either as liquid or capsules. To quantify the bioavailability and metabolism of oleuropein and hydroxytyrosol when taken as OLE, nine volunteers (five males) aged 42.8 ± 7.4 years were randomized to receive either capsulated or liquid OLE as a single lower (51.1 mg oleuropein, 9.7 mg hydroxytyrosol) or higher (76.6 mg oleuropein, 14.5 mg hydroxytyrosol) dose, and then the opposite strength (but same formulation) a week later. Plasma and urine samples were collected at fixed intervals for 24 h post-ingestion. Phenolic content was analyzed by LC-ESI-MS/MS. Conjugated metabolites of hydroxytyrosol were the primary metabolites recovered in plasma and urine after OLE ingestion. Peak oleuropein concentrations in plasma were greater following ingestion of liquid than capsule preparations (0.47 versus 2.74 ng/mL; p = 0.004), but no such effect was observed for peak concentrations of conjugated (sulfated and glucuronidated) hydroxytyrosol (p = 0.94). However, the latter peak was reached earlier with liquid preparation (93 versus 64 min; p = 0.031). There was a gender effect on the bioavailability of phenolic compounds, with males displaying greater plasma area under the curve for conjugated hydroxytyrosol (11,600 versus 2550 ng/mL; p = 0.048). All conjugated hydroxytyrosol metabolites were recovered in the urine within 8 h. There was wide inter-individual variation. OLE effectively delivers oleuropein and hydroxytrosol metabolites to plasma in humans. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Profiling and functional classification of esterases in olive (Olea europaea) pollen during germination.

    Science.gov (United States)

    Rejón, Juan D; Zienkiewicz, Agnieszka; Rodríguez-García, María Isabel; Castro, Antonio J

    2012-10-01

    A pollen grain contains a number of esterases, many of which are released upon contact with the stigma surface. However, the identity and function of most of these esterases remain unknown. In this work, esterases from olive pollen during its germination were identifided and functionally characterized. The esterolytic capacity of olive (Olea europaea) pollen was examined using in vitro and in-gel enzymatic assays with different enzyme substrates. The functional analysis of pollen esterases was achieved by inhibition assays by using specific inhibitors. The cellular localization of esterase activities was performed using histochemical methods. Olive pollen showed high levels of non-specific esterase activity, which remained steady after hydration and germination. Up to 20 esterolytic bands were identified on polyacrylamide gels. All the inhibitors decreased pollen germinability, but only diisopropyl fluorophosphate (DIFP) hampered pollen tube growth. Non-specific esterase activity is localized on the surface of oil bodies (OBs) and small vesicles, in the pollen intine and in the callose layer of the pollen tube wall. Acetylcholinesterase (AChE) activity was mostly observed in the apertures, exine and pollen coat, and attached to the pollen tube wall surface and to small cytoplasmic vesicles. In this work, for the first time a systematic functional characterization of esterase enzymes in pollen from a plant species with wet stigma has been carried out. Olive pollen esterases belong to four different functional groups: carboxylesterases, acetylesterases, AChEs and lipases. The cellular localization of esterase activity indicates that the intine is a putative storage site for esterolytic enzymes in olive pollen. Based on inhibition assays and cellular localization of enzymatic activities, it can be concluded that these enzymes are likely to be involved in pollen germination, and pollen tube growth and penetration of the stigma.

  2. Dental morphology of Talpa europaea and Talpa occidentalis (Mammalia: Insectivora) with a discussion of fossil Talpa in the Pleistocene of Europe

    NARCIS (Netherlands)

    Cleef-Roders, van J.T.; Hoek Ostende, van den L.W.

    2001-01-01

    A description is given of the last premolar and molars of T. europaea from The Netherlands and T. occidentalis of Spain. The metrical and morphological differences between the dentitions of the two species are small. A review is given of the literature of fossil Talpa in the Pleistocene of Europe.

  3. Isolation of antioxidative secoiridoids from olive wood (Olea europaea L.) guided by on-line HPLC-DAD-radical scavenging detection

    NARCIS (Netherlands)

    Pérez-Bonilla, M.; Salido, S.; Beek, van T.A.; Waard, de P.; Linares-Palomino, P.J.; Sánchez, A.; Altarejos, J.

    2011-01-01

    The woody portion of olive tree pruning is a source of natural antioxidants of potential interest for the food industry. This work deals with the isolation and identification of further antioxidants present in an ethyl acetate extract of olive (Olea europaea L.) wood. Thus, a new secoiridoid,

  4. Salt stress induces differential regulation of the phenylpropanoid pathway in Olea europaea cultivars Frantoio (salt-tolerant) and Leccino (salt-sensitive)

    NARCIS (Netherlands)

    Rossi, Lorenzo; Borghi, Monica; Francini, Alessandra; Lin, Xiuli; Xie, De Yu; Sebastiani, Luca

    2016-01-01

    Olive tree (Olea europaea L.) is an important crop in the Mediterranean Basin where drought and salinity are two of the main factors affecting plant productivity. Despite several studies have reported different responses of various olive tree cultivars to salt stress, the mechanisms that convey

  5. Simultaneous separation and purification of flavonoids and oleuropein from Olea europaea L. (olive) leaves using macroporous resin.

    Science.gov (United States)

    Li, Chen; Zheng, Yuanyuan; Wang, Xiaofei; Feng, Shilan; Di, Duolong

    2011-12-01

    This study developed a feasible process to simultaneously separate and purify polyphenols, including flavonoids and oleuropein, from the leaves of Olea europaea L. Macroporous resins were used as the separation and purification materials. The performance and separation capabilities of eight resins (D101, DM130, HPD450, LSA-21, LSA-40, 07C, LSD001 and HPD600) were systematically evaluated. The contents of target polyphenols in different extracts were determined using ultraviolet (for flavonoids) and high-performance liquid chromatographic (for oleuropein) methods. The static adsorption and desorption results showed that resin LSA-21 had better adsorption properties among the eight resins. Influential factors such as extraction method, pH value of feeding solution, desorption solution, adsorption kinetics and adsorption isotherm, etc. to the extraction and purification of these polyphenols were successively investigated on resin LSA-21. The target flavonoids and oleuropein were selectively purified using resin LSA-21. Compared with the contents in raw leaves, the contents of total flavonoids and oleuropein in the final purified products were increased 13.2-fold (from 16 to 211 g kg(-1) ) and 7.5-fold (from 120 to 902 g kg(-1) ) with recovery yields of 87.9% and 85.6%, respectively. This extraction and purification method could be used in the large-scale enrichment or purification of flavonoids, oleuropein and other polyphenols from O. europaea L. leaves or other herbal materials in industrial, food processing and medical manufacture. Copyright © 2011 Society of Chemical Industry.

  6. H(+) -pyrophosphatase from Salicornia europaea confers tolerance to simultaneously occurring salt stress and nitrogen deficiency in Arabidopsis and wheat.

    Science.gov (United States)

    Lv, Sulian; Jiang, Ping; Nie, Lingling; Chen, Xianyang; Tai, Fang; Wang, Duoliya; Fan, Pengxiang; Feng, Juanjuan; Bao, Hexigeduleng; Wang, Jinhui; Li, Yinxin

    2015-11-01

    High salinity and nitrogen (N) deficiency in soil are two key factors limiting crop productivity, and they usually occur simultaneously. Here we firstly found that H(+) -PPase is involved in salt-stimulated NO3 (-) uptake in the euhalophyte Salicornia europaea. Then, two genes (named SeVP1 and SeVP2) encoding H(+) -PPase from S. europaea were characterized. The expression of SeVP1 and SeVP2 was induced by salt stress and N starvation. Both SeVP1 or SeVP2 transgenic Arabidopsis and wheat plants outperformed the wild types (WTs) when high salt and low N occur simultaneously. The transgenic Arabidopsis plants maintained higher K(+) /Na(+) ratio in leaves and exhibited increased NO3 (-) uptake, inorganic pyrophosphate-dependent vacuolar nitrate efflux and assimilation capacity under this double stresses. Furthermore, they had more soluble sugars in shoots and roots and less starch accumulation in shoots than WT. These performances can be explained by the up-regulated expression of ion, nitrate and sugar transporter genes in transgenic plants. Taken together, our results suggest that up-regulation of H(+) -PPase favours the transport of photosynthates to root, which could promote root growth and integrate N and carbon metabolism in plant. This work provides potential strategies for improving crop yields challenged by increasing soil salinization and shrinking farmland. © 2015 John Wiley & Sons Ltd.

  7. Comparative and evaluation of anti-leech (Limnatis Nilotica effect of Olive (Olea Europaea L. with Levamisol and Tiabendazole

    Directory of Open Access Journals (Sweden)

    Majid Gholami-Ahangaran

    2012-05-01

    Full Text Available Objective: Until now, there is no registered drug for treatment of complications with leech in the world. According to the available scientific evidence, Olive is an effective anti-parasitic plant. Hence, in the present experiment we studied the inhibitory and killing effect of Olive methanolic extract on Limnatis nilotica. Methods: In this study, 100 leeches (Limnatis nilotica were collected from some wells in western area of Iran (south region in Ilam province and evaluated the antileech effects of Olive methanolic extract (Olea europaea L. in comparison with levamisole and tinidazole. Results: The results indicated no effect of tinidasole and distilled water on killing or mortality rate of the leeches but Olea europaea L. plant and levamisole have more effect on the L. nilotica. The mean death time of leech for levamisole and Olive determined 10依0.98 and 210依 24.1 minutes, respectively. Conclusions: The results showed that treatments of Olive methanolic extract and levamisole have the most effects on leeches and could be used as natural anti-L. nilotica. However it is necessary to achieve further studies for confirm of this subject.

  8. Antimicrobial activity of Olea europaea Linné extracts and their applicability as natural food preservative agents.

    Science.gov (United States)

    Thielmann, J; Kohnen, S; Hauser, C

    2017-06-19

    The antimicrobial activity of phenolic compounds from Olea (O.) europaea Linné (L.) is part of the scientific discussion regarding the use of natural plant extracts as alternative food preservative agents. Although, the basic knowledge on the antimicrobial potential of certain molecules such as oleuropein, hydroxytyrosol or elenolic acid derivatives is given, there is still little information regarding their applicability for food preservation. This might be primarily due to the lack of information regarding the full antimicrobial spectrum of the compounds, their synergisms in natural or artificial combinations and their interaction with food ingredients. The present review accumulates available literature from the past 40 years, investigating the antimicrobial activity of O. europaea L. derived extracts and compounds in vitro and in food matrices, in order to evaluate their food applicability. In summary, defined extracts from olive fruit or leaves, containing the strongest antimicrobial compounds hydroxytyrosol, oleacein or oleacanthal in considerable concentrations, appear to be suitable for food preservation. Nonetheless there is still need for consequent research on the compounds activity in food matrices, their effect on the natural microbiota of certain foods and their influence on the sensorial properties of the targeted products. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Oil, protein, antioxidants and free radical scavenging activity of stone from wild olive trees (Olea europaea L.).

    Science.gov (United States)

    Hannachi, Hédia; Elfalleh, Walid; Marzouk, Sizaiem

    2013-05-01

    The wild olive trees or oleaster (var. sylvestris) and the cultivated olive trees (var. europaea) constitute the two botanical varieties of Olea europaea L. from Mediterranean. In this study, a partial chemical profile was conducted including the total lipids, the fatty acid profiles, soluble proteins, polyphenols, flavanoids contents and antioxidants activities of stone from six oleaster trees. The comparison was made by two olive cultivars cultivated in the same region. The oleaster and cultivar stones were richer in oil content having an average of 8.99 and 7.38 % dry weight basis (DW), respectively. Qualitatively, all studied oils have the same fatty acids profile with the oleic acid C18:1n-9 as the major fatty acid. The oleaster stone oils were richer in monounsaturated fatty acids having an average of 64.87%. They, also, richer in protein content with an average of 198.86 mg/g DW.The globulin is the major fraction, followed by the albumin, the prolamin and the glutemin fractions. The oleaster stone extracts contain polyphenols, flavonoids with an average of 151.14 and 11.91 mg gallic acid equivalent/100g of DW, respectively. The studied extracts showed antioxidant activity using the free radical scavenging activity determined by DPPH and ABTS. The unexploited oleaster stone seems to be a source of oil with good fatty acids balance, in protein and antioxidants metabolites and would be useful for the formulation of supplements and/or pharmaceutical ingredients.

  10. Plant-parasitic nematodes associated with olive tree (Olea europaea L.) with a focus on the Mediterranean Basin: a review.

    Science.gov (United States)

    Ali, Nadine; Chapuis, Elodie; Tavoillot, Johannes; Mateille, Thierry

    2014-01-01

    The olive tree (Olea europaea ssp. europaea.) is one of the most ancient cultivated trees. It is an emblematic species owing to its ecological, economic and cultural importance, especially in the Mediterranean Basin. Plant-parasitic nematodes are major damaging pests on olive trees, mainly in nurseries. They significantly contribute to economic losses in the top-ten olive-producing countries in the world. However, the damages they induce in orchards and nurseries are specifically documented only in a few countries. This review aims to update knowledge about the olive-nematode pathosystem by: (1) updating the list of plant-parasitic nematodes associated with olive trees; (2) analysing their diversity (taxonomic level, trophic groups, dominance of taxa), which allowed us (i) to assess the richness observed in each country, and (ii) to exhibit and describe the most important taxa able to induce damages on olive trees such as: Meloidogyne, Pratylenchus, Helicotylenchus, Xiphinema, Tylenchulus, Rotylenchulus, Heterodera (distribution especially in the Mediterranean Basin, pathogenicity and reactions of olive trees); (3) describing some management strategies focusing on alternative control methods; (4) suggesting new approaches for controlling plant-parasitic nematodes based on the management of the diversity of their communities, which are structured by several environmental factors such as olive diversity (due to domestication of wild olive in the past, and to breeding now), cropping systems (from traditional to high-density orchards), irrigation, and terroirs. Copyright © 2014 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  11. Partial nitrification using aerobic granules in continuous-flow reactor: rapid startup.

    Science.gov (United States)

    Wan, Chunli; Sun, Supu; Lee, Duu-Jong; Liu, Xiang; Wang, Li; Yang, Xue; Pan, Xiangliang

    2013-08-01

    This study applied a novel strategy to rapid startup of partial nitrification in continuous-flow reactor using aerobic granules. Mature aerobic granules were first cultivated in a sequencing batch reactor at high chemical oxygen demand in 16 days. The strains including the Pseudoxanthomonas mexicana strain were enriched in cultivated granules to enhance their structural stability. Then the cultivated granules were incubated in a continuous-flow reactor with influent chemical oxygen deamnad being stepped decreased from 1,500 ± 100 (0-19 days) to 750 ± 50 (20-30 days), and then to 350 ± 50 mg l(-1) (31-50 days); while in the final stage 350 mg l(-1) bicarbonate was also supplied. Using this strategy the ammonia-oxidizing bacterium, Nitrosomonas europaea, was enriched in the incubated granules to achieve partial nitrification efficiency of 85-90% since 36 days and onwards. The partial nitrification granules were successfully harvested after 52 days, a period much shorter than those reported in literature. Copyright © 2013 Elsevier Ltd. All rights reserved.

  12. UV-B radiation modulates physiology and lipophilic metabolite profile in Olea europaea.

    Science.gov (United States)

    Celeste Dias, Maria; Pinto, Diana C G A; Correia, Carlos; Moutinho-Pereira, José; Oliveira, Helena; Freitas, Helena; Silva, Artur M S; Santos, Conceição

    2018-03-01

    Ultraviolet-B (UV-B) radiation plays an important role in plant photomorphogenesis. Whilst the morpho-functional disorders induced by excessive UV irradiation are well-known, it remains unclear how this irradiation modulates the metabolome, and which metabolic shifts improve plants' tolerance to UV-B. In this study, we use an important Mediterranean crop, Olea europaea, to decipher the impacts of enhanced UV-B radiation on the physiological performance and lipophilic metabolite profile. Young olive plants (cv. 'Galega Vulgar') were exposed for five days to UV-B biologically effective doses of 6.5 kJ m -2  d -1 and 12.4 kJ m -2 d -1 . Cell cycle/ploidy, photosynthesis and oxidative stress, as well as GC-MS metabolites were assessed. Both UV-B treatments impaired net CO 2 assimilation rate, transpiration rate, photosynthetic pigments, and RuBisCO activity, but 12.4 kJ m -2  d -1 also decreased the photochemical quenching (qP) and the effective efficiency of PSII (Φ PSII ). UV-B treatments promoted mono/triperpene pathways, while only 12.4 kJ m -2  d -1 increased fatty acids and alkanes, and decreased geranylgeranyl-diphosphate. The interplay between physiology and metabolomics suggests some innate ability of these plants to tolerate moderate UV-B doses (6.5 kJ m -2  d -1 ). Also their tolerance to higher doses (12.4 kJ m -2  d -1 ) relies on plants' metabolic adjustments, where the accumulation of specific compounds such as long-chain alkanes, palmitic acid, oleic acid and particularly oleamide (which is described for the first time in olive leaves) play an important protective role. This is the first study demonstrating photosynthetic changes and lipophilic metabolite adjustments in olive leaves under moderate and high UV-B doses. Copyright © 2018 Elsevier GmbH. All rights reserved.

  13. Role of carbohydrate reserves in yield production of intensively cultivated oil olive (Olea europaea L.) trees.

    Science.gov (United States)

    Bustan, Amnon; Avni, Avishai; Lavee, Shimon; Zipori, Isaac; Yeselson, Yelena; Schaffer, Arthur A; Riov, Joseph; Dag, Arnon

    2011-05-01

    Olive (Olea europaea) has a very high tendency for year-to-year deviation in yield (alternate bearing), which has a negative economic impact on the olive oil industry. Among possible reasons for alternate bearing, depletion of stored carbohydrates (CHO) during the On-year (high yield) has often been mentioned. The objective of the present study was to verify the role of CHO reserves, as a cause or effect, in the alternate bearing of intensively cultivated olives. A monthly survey of soluble sugar and starch concentrations in the leaves, branches, bark and roots of On- and Off-trees (cv. Barnea) was carried out during a complete reproductive cycle from November 2005 to October 2006. Carbohydrate concentration in the sapwood was determined in January, as well as an estimate of whole-tree biomass. The trunk and limbs possess the largest portion of CHO reserves. The influence of reduced fruit load on CHO reserves was also investigated. Starch, mannitol and sucrose concentrations increased from December to March in all tissues, and then declined along with fruit development. Leaves, branches and bark have a significant role in CHO storage, whereas roots accumulated the lowest CHO concentrations. However, fluctuations in reserve content suggested considerable involvement of roots in the CHO budget. Nevertheless, there were no meaningful differences in the annual pattern of CHO concentration between On- and Off-trees. Even a 75-100% reduction in fruit number brought about only a minor, sluggish increase in CHO content, though this was more pronounced in the roots. Carbohydrate reserves were not depleted, even under maximum demands for fruit and oil production. It is concluded that in olives, the status of CHO reserves is not a yield determinant. However, they may play a significant role in the olive's survival strategy, ensuring tree recovery in the unpredictable semiarid Mediterranean environment. This suggests that CHO reserves in olive act like an active sink

  14. EFFET HYPOUPIDEMIANT DE L'HUILE D'OLIVIER SAIWAGEOLEA EUROPAEA OLÉASTRE OU OLEA SYLVESTRIS.

    OpenAIRE

    BENDIMERAD, SORAYA

    2014-01-01

    L'Olivier sauvage (Olea europaea oléastre/sylvestris) est une espèce végétale ancêtre de l'olivier cultivé bordant le pourtourméditerranéen. L'extraction par un procédé triphasique de fruit de cet arbre donne une huile sacrée par ses multiples usages. La détermination des indices physico- chimiques a révélé que l'huile est vierge, nonsiccative, constituée de chaines moyenne d'acides gras. La composition en acides gras montre une instauration prépondérante due à la teneur élevée...

  15. Phenol metabolism in the leaves of the olive tree (Olea europaea L.) cv. Picual, Verdial, Arbequina, and Frantoio during ripening.

    Science.gov (United States)

    Ortega-García, Francisca; Peragón, Juan

    2010-12-08

    The kinetic behavior and protein-expression level of phenylalanine ammonia-lyase (PAL) and polyphenol oxidase (PPO) have been determined in the leaves of the olive tree (Olea europaea L.) of cv. Picual, Verdial, Arbequina, and Frantoio during fruit ripening. Moreover, the concentration of total phenolic compounds, oleuropein, hydroxytyrosol, and tyrosol has been also determined. This study was carried out in 20-year-old olive trees grown in Jaén (Spain). The concentration of total and specific phenols showed a specific pattern in each cultivar. Frantoio showed the highest phenol concentration followed by Arbequina, Picual, and Verdial. A coordinated response between PAL, PPO, and the concentration of total phenols in the four cultivars was found. Also, specific changes were shown over the course of ripening, indicating a regulation of PAL, PPO, and phenol concentration in the olive-tree leaves during fruit ripening.

  16. Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events.

    Science.gov (United States)

    Julca, Irene; Marcet-Houben, Marina; Vargas, Pablo; Gabaldón, Toni

    2018-01-25

    Polyploidization is one of the major evolutionary processes that shape eukaryotic genomes, being particularly common in plants. Polyploids can arise through direct genome doubling within a species (autopolyploidization) or through the merging of genomes from distinct species after hybridization (allopolyploidization). The relative contribution of both mechanisms in plant evolution is debated. Here we used phylogenomics to dissect the tempo and mode of duplications in the genome of the olive tree (Olea europaea), one of the first domesticated Mediterranean fruit trees. Our results depict a complex scenario involving at least three past polyploidization events, of which two-at the bases of the family Oleaceae and the tribe Oleeae, respectively-are likely to be the result of ancient allopolyploidization. A more recent polyploidization involves specifically the olive tree and relatives. Our results show the power of phylogenomics to distinguish between allo- and auto polyploidization events and clarify the contributions of duplications in the evolutionary history of the olive tree.

  17. Dynamique de la conductance hydraulique chez l'olivier de table (Olea europaea L., cv Meski

    Directory of Open Access Journals (Sweden)

    Hechmi, C.

    2007-01-01

    Full Text Available Hydraulic Conductance Dynamic in Olive Table Tree (Olea europaea L. cv Meski. Cette étude expose les effets de l'aménagement des pâturages par la digue filtrante sur la dynamique de la végétation. Dans les régions sahéliennes, de nombreuses techniques sont appliquées sur les sols pour la restauration des parcours dégradés. La digue filtrante s'intéresse particulièrement aux axes de drainage ou bas-fonds en dégradation. La méthode d'étude a consisté à évaluer l'impact des digues filtrantes par l'inventaire de la végétation, la mesure de la biomasse produite, et l'analyse chimique d'échantillons de fourrage et de sol. Ces observations ont été faites à la fois sur l'espace aménagé et sur un espace témoin représentatif en deux fois durant cinq ans. Les observations sur l'espace aménagé (stations d'observation d'un ha ont été faites en fonction du gradient par rapport à la digue filtrante tandis que sur le témoin (station d'observation d'un ha, les mesures ont été homogénéisées sur l'ensemble de la parcelle. Les résultats obtenus des inventaires de végétation montrent un effet positif de l'aménagement sur la dynamique de la végétation qui se maintient après cinq années. Les effets concernent la composition floristique pour laquelle certaines espèces connaissent une amélioration. Il s'agit de Panicum laetum (+ 5,9% en 1999 et + 1,9% en 2003, Setaria pallide fusca (+ 2,4 à + 8,6%, Cassia obtusifolia (+ 13,6% à + 9,3% et Zornia glochidiata (- 2,9% à + 1,7 %. Les espèces en régression sont surtout composées de Schoenefeldia gracilis (+ 1,7% à - 12% et Microchloa indica (- 28,9% à - 12,1% entre 1999 et 2003. L'écart de recouvrement du sol entre la parcelle aménagée et le témoin a été de -0,4% en 1999 contre + 14,6% en 2003. La biomasse produite et la capacité de charge ont connu une expansion allant de 3,14 à 4,5 fois par rapport à l'espace non aménagé. Cependant, des suivis doivent

  18. Composition, quality and oxidative stability of virgin olive oils from some selected wild olives (Olea europaea L. subsp. oleaster)

    OpenAIRE

    Zarrouk, Mokhtar; Daoud, Douja; Krichene, Douha; Nouairi, Issam; Guerfel, Mokhtar; Baccouri, Olfa; Zarrouk, Wissem; Baccouri, Bechir

    2008-01-01

    A study on the characterization of virgin olive oils from wild olives (Olea europaea L. subsp. oleaster) was conducted in order to define new cultivars which are welladapted to the Tunisian environment and yield high quality oils. The study was done during the crop years 2003/04, 2004/05 and 2005/06. The main analytical parameters of the oils were evaluated: fatty acid compositions, chlorophylls, carotenoids, tocopherols and phenolic compounds as well as their relationship with oxidative stab...

  19. Isolation of Endophytic Plant Growth-Promoting Bacteria Associated with the Halophyte Salicornia europaea and Evaluation of their Promoting Activity Under Salt Stress.

    Science.gov (United States)

    Zhao, Shuai; Zhou, Na; Zhao, Zheng-Yong; Zhang, Ke; Wu, Guo-Hua; Tian, Chang-Yan

    2016-10-01

    Several reports have highlighted that many plant growth-promoting endophytic bacteria (PGPE) can assist their host plants in coping with various biotic and abiotic stresses. However, information about the PGPE colonizing in the halophytes is still scarce. This study was designed to isolate and characterize PGPE from salt-accumulating halophyte Salicornia europaea grown under extreme salinity and to evaluate in vitro the bacterial mechanisms related to plant growth promotion. A total of 105 isolates were obtained from the surface-sterilized roots, stems, and assimilation twigs of S. europaea. Thirty-two isolates were initially selected for their ability to produce 1-aminocyclopropane-1-carboxylate deaminase as well as other properties such as production of indole-3-acetic acid and phosphate-solubilizing activities. The 16S rRNA gene-sequencing analysis revealed that these isolates belong to 13 different genera and 19 bacterial species. For these 32 strains, seed germination and seedling growth in axenically grown S. europaea seedlings at different NaCl concentrations (50-500 mM) were quantified. Five isolates possessing significant stimulation of the host plant growth were obtained. The five isolates were identified as Bacillus endophyticus, Bacillus tequilensis, Planococcus rifietoensis, Variovorax paradoxus, and Arthrobacter agilis. All the five strains could colonize and can be reisolated from the host plant interior tissues. These results demonstrate that habitat-adapted PGPE isolated from halophyte could enhance plant growth under saline stress conditions.

  20. Research Article Special Issue

    African Journals Online (AJOL)

    pc

    2017-11-10

    Nov 10, 2017 ... CULTURE. Kasmuri1,*, R. W. Lovitt2 and M. Omar3 gineering, UniversitiTeknologi MARA, Shah Alam, Selangor, Malaysia eering, Swansea ... performed by Nitrosomonas species and Nitrobacter species. ... other types of nitrifying bacteria in the fish effluent, i.e. ammonia oxidizing organisms which.

  1. Anaerobic ammonia oxidation in a fertilized paddy soil

    DEFF Research Database (Denmark)

    Zhu, Guibing; Wang, Shanyun; Wang, Yu

    2011-01-01

    Evidence for anaerobic ammonium oxidation in a paddy field was obtained in Southern China using an isotope-pairing technique, quantitative PCR assays and 16S rRNA gene clone libraries, along with nutrient profiles of soil cores. A paddy field with a high load of slurry manure as fertilizer was se...

  2. Ammonia oxidation at high pressure and intermediate temperatures

    DEFF Research Database (Denmark)

    Song, Yu; Hashemi, Hamid; Christensen, Jakob Munkholt

    2016-01-01

    oxidizing conditions the onset temperature for reaction was 850–875 K at 30 bar, while at 100 bar it was about 800 K, with complete consumption of NH3 at 875 K. The products of reaction were N2 and N2O, while NO and NO2 concentrations were below the detection limit even under oxidizing conditions. The data...... was satisfactory. The main oxidation path for NH3 at high pressure under oxidizing conditions is NH3⟶+OH NH2⟶+HO2,NO2 H2NO⟶+O2 HNO⟶+O2 NO ⟶+NH2 N2. The modeling predictions are most sensitive to the reactions NH2 + NO = NNH + OH and NH2 + HO2 = H2NO + OH, which promote the ammonia consumption by forming OH...

  3. Community structure variability of Uropodina mites (Acari: Mesostigmata) in nests of the common mole, Talpa europaea, in Central Europe.

    Science.gov (United States)

    Napierała, Agnieszka; Mądra, Anna; Leszczyńska-Deja, Kornelia; Gwiazdowicz, Dariusz J; Gołdyn, Bartłomiej; Błoszyk, Jerzy

    2016-04-01

    Underground nests of Talpa europaea, known as the common mole, are very specific microhabitats, which are also quite often inhabited by various groups of arthropods. Mites from the suborder Uropodina (Acari: Mesostigmata) are only one of them. One could expect that mole nests that are closely located are inhabited by communities of arthropods with similar species composition and structure. However, results of empirical studies clearly show that even nests which are close to each other can be different both in terms of the species composition and abundance of Uropodina communities. So far, little is known about the factors that can cause these differences. The major aim of this study was to identify factors determining species composition, abundance, and community structure of Uropodina communities in mole nests. The study is based on material collected during a long-term investigation conducted in western parts of Poland. The results indicate that the two most important factors influencing species composition and abundance of Uropodina communities in mole nests are nest-building material and depth at which nests are located. Composition of Uropodina communities in nests of moles was also compared with that of other microhabitats (e.g. rotten wood, forest litter, soil) based on data from 4421 samples collected in Poland. Communities of this habitat prove most similar to these of open areas, especially meadows, as well as some forest types.

  4. High-Throughput Sequencing Analysis of the Endophytic Bacterial Diversity and Dynamics in Roots of the Halophyte Salicornia europaea.

    Science.gov (United States)

    Zhao, Shuai; Zhou, Na; Zhao, Zheng-Yong; Zhang, Ke; Tian, Chang-Yan

    2016-05-01

    Endophytic bacterial communities of halophyte Salicornia europaea roots were analyzed by 16S rRNA gene pyrosequencing. A total of 20,151 partial 16S rRNA gene sequences were obtained. These sequences revealed huge amounts of operational taxonomic units (OTUs), that is, 747-1405 OTUs in a root sample, at 3 % cut-off level. Root endophytes mainly comprised four phyla, among which Proteobacteria was the most represented, followed by Bacteroidetes, Actinobacteria, and Firmicutes. Gammaproteobacteria was the most abundant class of Proteobacteria, followed by Betaproteobacteria and Alphaproteobacteria. Genera Pantoea, Halomonas, Azomonas, Serpens, and Pseudomonas were shared by all growth periods. A marked difference in endophytic bacterial communities was evident in roots from different host life-history stages. Gammaproteobacteria increased during the five periods, while Betaproteobacteria decreased. The richest endophytic bacteria diversity was detected in the seedling stage. Endophytic bacteria diversity was reduced during the flowering stage and fruiting stage. The five libraries contained 2321 different OTUs with 41 OTUs in common. As a whole, this study first surveys communities of endophytic bacteria by tracing crucial stages in the process of halophyte growth using high-throughput sequencing methods.

  5. Sustainability, Innovation, and Green Chemistry in the Production and Valorization of Phenolic Extracts from Olea europaea L.

    Directory of Open Access Journals (Sweden)

    Annalisa Romani

    2016-10-01

    Full Text Available This paper describes a circular economy process based on environmentally and economically sustainable procedures which was applied to the sector of olive oil processing on an industrial scale. Olea europaea L. tissues and by-products represent a renewable and low-cost source of polyphenols, in particular hydroxytyrosol (HTyr, a naturally occurring compound well known for its biological properties. Specifically, green leaves (GL, dried leaves (DL, and pitted olive pulp were treated with water in a pneumatic extractor to obtain the corresponding polyphenolic extracts. Three standardized fractions, named Soft Extract Olea GL, Soft Extract Olea DL, and Soft Extract Olea HTyr resulted after the following two steps: a separation process carried out by membrane technology, and a concentration step performed under reduced pressure and low temperature. The polyphenolic fractions showed antiradical activity and have potential industrial applications in the food, nutraceutical, pharmaceutical, feed, and agronomic fields. Novel functionalized extracts containing hydroxytyrosol methyl carbonate (HTyr-MC were obtained from Soft Extract Olea HTyr through an innovative approach based on green chemistry procedures, which appear to be a promising tool to increase the applications of the polyphenolic extracts.

  6. Characterization of polyphenol oxidase from the Manzanilla cultivar (Olea europaea pomiformis) and prevention of browning reactions in bruised olive fruits.

    Science.gov (United States)

    Segovia-Bravo, Kharla A; Jarén-Galan, Manuel; García-García, Pedro; Garrido-Fernandez, Antonio

    2007-08-08

    The crude extract of the polyphenol oxidase (PPO) enzyme from the Manzanilla cultivar (Olea europaea pomiformis) was obtained, and its properties were characterized. The browning reaction followed a zero-order kinetic model. Its maximum activity was at pH 6.0. This activity was completely inhibited at a pH below 3.0 regardless of temperature; however, in alkaline conditions, pH inhibition depended on temperature and was observed at values above 9.0 and 11.0 at 8 and 25 degrees C, respectively. The thermodynamic parameters of substrate oxidation depended on pH within the range in which activity was observed. The reaction occurred according to an isokinetic system because pH affected the enzymatic reaction rate but not the energy required to carry out the reaction. In the alkaline pH region, browning was due to a combination of enzymatic and nonenzymatic reactions that occurred in parallel. These results correlated well with the browning behavior observed in intentionally bruised fruits at different temperatures and in different storage solutions. The use of a low temperature ( approximately 8 degrees C) was very effective for preventing browning regardless of the cover solution used.

  7. Caracterización histoquimica de la etapa temprana del desarrollo del fruto del olivo (Olea europaea L.

    Directory of Open Access Journals (Sweden)

    Corrêa Maria José Pinheiro

    2002-01-01

    Full Text Available Se estudia el desarrollo a nivel histoquimico de la etapa temprana del fruto del olivo (Olea europaea L. variedad Picual, vigorosa y elevado rendimiento graso. Para ello, se utilizaron flores de olivo recién fecundadas y también com tres, siete y diez días tras la fecundación. Hemos utilizado tinción com "Sudan Black", para hacer un seguimiento de los lípidos en las diferentes etapas de desarrollo del fruto del olivo. Como resultado se puede decir que en la etapa temprana del desarrollo del fruto, el exocarpo se presenta rico en lípidos en todas las etapas de estudio. El mesocarpo y el embrión presentan tinción no homogénea, o sea, hay algunas regiones de ellos que presentan lipidos, mientras que la zona vascular del mesocarpo y el endocarpo se presentan libre de tinción y la zona vascular del embrión se mantiene rica en lipidos.

  8. Effet du sucre sur l'embryogenèse somatique de l'olivier (Olea europaea L. cv. 'Picholine marocaine'

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    Abousalim A.

    2008-01-01

    Full Text Available Effect of sugar on somatic embryogenesis of olive tree (Olea europaea L. cv ' Moroccan Picholine '. The somatic embryogenesis of the olive tree cv ' Moroccan Picholine ' has been until now very little studied, in spite of its importance for Morocco.Thus, our work aimed to study the effects of type and concentrations of sugar on the induction and the development of somatic embryos of this variety. Regeneration of olive plants via somatic embryogenesis has been achieved from cotyledon fragments. Embryogenic, nodular and compact calli have been induced on media supplemented with 0.5 mg.l-1 zeatin and 2 mg.l-1 NAA and different types of sugar as mannitol, saccharose and sorbitol and different saccharose concentrations (20, 30, 60 and 90 g.l-1. The highest percentage of callus induction (P < 0.001 was observed with mannitol (90.6%. Up to 37% somatic embryogenesis was obtained in the case of saccharose (P < 0.001. The best callus induction was obtained in presence of 30 g.l-1 saccharose. This concentration was the best for olive plantlets regeneration. No morphogenesis was obtained with sorbitol. Somatic embryogenesis seems to be able to constitute an interesting source of micropropagation of olive tree in Morocco.

  9. An in vitro nutritive evaluation of olive tree (Olea europaea) pruning residues as affected by cutting regimen.

    Science.gov (United States)

    Al-Masri, M R

    2012-01-01

    Nutritive values of the branches from Olea europaea trees cut at 25, 50, 75 or 100 cm distance from the tip were evaluated by determination of the in vitro digestible organic matter (IVDOM), metabolizable energy (ME), net energy lactation (NEL), and presence nutritional and anti-nutritional components. The values of nutritive components, nitrogen forms, IVDOM, ME and NEL declined and concentrations of crude fiber and cell wall constituents increased with the increase in cutting length. Total phenols, hydrolysable tannins and condensed tannins amounted to 70, 17 and 0.6 g/kg DM, respectively. The addition of polyethylene glycol (PEG, 6000) to the plant samples incubated with rumen fluid at a ratio of (2:1 PEG:substrate) increased the values of IVDOM, ME and NEL by 40 g/kg DM, 0.59 MJ/kg DM and 0.42 MJ/kg DM, respectively. IVDOM, ME and NEL were negatively correlated with crude fiber and cell wall constituents but positively correlated with nitrogen forms and non-fiber carbohydrates. Olive pruning branches in diameter<3 mm could be used as sources of feeds for small ruminants. Copyright © 2011 Elsevier Ltd. All rights reserved.

  10. Histochemical location of key enzyme activities involved in receptivity and self-incompatibility in the olive tree (Olea europaea L.).

    Science.gov (United States)

    Serrano, Irene; Olmedilla, Adela

    2012-12-01

    Stigma-surface and style enzymes are important for pollen reception, selection and germination. This report deals with the histochemical location of the activity of four basic types of enzyme involved in these processes in the olive (Olea europaea L.). The detection of peroxidase, esterase and acid-phosphatase activities at the surface of the stigma provided evidence of early receptivity in olive pistils. The stigma maintained its receptivity until the arrival of pollen. Acid-phosphatase activity appeared in the style at the moment of anthesis and continued until the fertilization of the ovule. RNase activity was detected in the extracellular matrix of the styles of flowers just before pollination and became especially evident in pistils after self-pollination. This activity gradually decreased until it practically disappeared in more advanced stages. RNase activity was also detected in pollen tubes growing in pollinated pistils and appeared after in vitro germination in the presence of self-incompatible pistils. These findings suggest that RNases may well be involved in intraspecific pollen rejection in olive flowers. To the best of our knowledge this is the first time that evidence of enzyme activity in stigma receptivity and pollen selection has been described in this species. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  11. Nutrition metabolism plays an important role in the alternate bearing of the olive tree (Olea europaea L..

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    Mine Turktas

    Full Text Available The olive tree (Olea europaea L. is widely known for its strong tendency for alternate bearing, which severely affects the fruit yield from year to year. Microarray based gene expression analysis using RNA from olive samples (on-off years leaves and ripe-unripe fruits are particularly useful to understand the molecular mechanisms influencing the periodicity in the olive tree. Thus, we carried out genome wide transcriptome analyses involving different organs and temporal stages of the olive tree using the NimbleGen Array containing 136,628 oligonucleotide probe sets. Cluster analyses of the genes showed that cDNAs originated from different organs could be sorted into separate groups. The nutritional control had a particularly remarkable impact on the alternate bearing of olive, as shown by the differential expression of transcripts under different temporal phases and organs. Additionally, hormonal control and flowering processes also played important roles in this phenomenon. Our analyses provide further insights into the transcript changes between "on year" and "off year" leaves along with the changes from unrpipe to ripe fruits, which shed light on the molecular mechanisms underlying the olive tree alternate bearing. These findings have important implications for the breeding and agriculture of the olive tree and other crops showing periodicity. To our knowledge, this is the first study reporting the development and use of an olive array to document the gene expression profiling associated with the alternate bearing in olive tree.

  12. De Novo Transcriptome Sequencing of Olea europaea L. to Identify Genes Involved in the Development of the Pollen Tube

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    Domenico Iaria

    2016-01-01

    Full Text Available In olive (Olea europaea L., the processes controlling self-incompatibility are still unclear and the molecular basis underlying this process are still not fully characterized. In order to determine compatibility relationships, using next-generation sequencing techniques and a de novo transcriptome assembly strategy, we show that pollen tubes from different olive plants, grown in vitro in a medium containing its own pistil and in combination pollen/pistil from self-sterile and self-fertile cultivars, have a distinct gene expression profile and many of the differentially expressed sequences between the samples fall within gene families involved in the development of the pollen tube, such as lipase, carboxylesterase, pectinesterase, pectin methylesterase, and callose synthase. Moreover, different genes involved in signal transduction, transcription, and growth are overrepresented. The analysis also allowed us to identify members in actin and actin depolymerization factor and fibrin gene family and member of the Ca2+ binding gene family related to the development and polarization of pollen apical tip. The whole transcriptomic analysis, through the identification of the differentially expressed transcripts set and an extended functional annotation analysis, will lead to a better understanding of the mechanisms of pollen germination and pollen tube growth in the olive.

  13. Salicornia europaea L. Na⁺/H⁺ antiporter gene improves salt tolerance in transgenic alfalfa (Medicago sativa L.).

    Science.gov (United States)

    Zhang, L Q; Niu, Y D; Huridu, H; Hao, J F; Qi, Z; Hasi, A

    2014-07-24

    In order to obtain a salt-tolerant perennial alfalfa (Medicago sativa L.), we transferred the halophyte Salicornia europaea L. Na(+)/H(+) antiporter gene, SeNHX1, to alfalfa by using the Agrobacterium-mediated transformation method. The transformants were confirmed by both PCR and RT-PCR analyses. Of 197 plants that were obtained after transformation, 36 were positive by PCR analysis using 2 primer pairs for the CaMV35S-SeNHX1 and SeNHX1-Nos fragments; 6 plants survived in a greenhouse. RT-PCR analysis revealed that SeNHX1 was expressed in 5 plants. The resultant transgenic alfalfa had better salt tolerance. After stress treatment for 21 days with 0.6% NaCl, the chlorophyll and MDA contents in transgenic plants were lower, but proline content and SOD, POD, and CAT activities were higher than those in wild-type plants. These results suggest that the salt tolerance of transgenic alfalfa was improved by the overexpression of the SeNHX1 gene.

  14. Nutrition metabolism plays an important role in the alternate bearing of the olive tree (Olea europaea L.).

    Science.gov (United States)

    Turktas, Mine; Inal, Behcet; Okay, Sezer; Erkilic, Emine Gulden; Dundar, Ekrem; Hernandez, Pilar; Dorado, Gabriel; Unver, Turgay

    2013-01-01

    The olive tree (Olea europaea L.) is widely known for its strong tendency for alternate bearing, which severely affects the fruit yield from year to year. Microarray based gene expression analysis using RNA from olive samples (on-off years leaves and ripe-unripe fruits) are particularly useful to understand the molecular mechanisms influencing the periodicity in the olive tree. Thus, we carried out genome wide transcriptome analyses involving different organs and temporal stages of the olive tree using the NimbleGen Array containing 136,628 oligonucleotide probe sets. Cluster analyses of the genes showed that cDNAs originated from different organs could be sorted into separate groups. The nutritional control had a particularly remarkable impact on the alternate bearing of olive, as shown by the differential expression of transcripts under different temporal phases and organs. Additionally, hormonal control and flowering processes also played important roles in this phenomenon. Our analyses provide further insights into the transcript changes between "on year" and "off year" leaves along with the changes from unrpipe to ripe fruits, which shed light on the molecular mechanisms underlying the olive tree alternate bearing. These findings have important implications for the breeding and agriculture of the olive tree and other crops showing periodicity. To our knowledge, this is the first study reporting the development and use of an olive array to document the gene expression profiling associated with the alternate bearing in olive tree.

  15. Valuable Nutrients and Functional Bioactives in Different Parts of Olive (Olea europaea L.)—A Review

    Science.gov (United States)

    Ghanbari, Rahele; Anwar, Farooq; Alkharfy, Khalid M.; Gilani, Anwarul-Hassan; Saari, Nazamid

    2012-01-01

    The Olive tree (Olea europaea L.), a native of the Mediterranean basin and parts of Asia, is now widely cultivated in many other parts of the world for production of olive oil and table olives. Olive is a rich source of valuable nutrients and bioactives of medicinal and therapeutic interest. Olive fruit contains appreciable concentration, 1–3% of fresh pulp weight, of hydrophilic (phenolic acids, phenolic alchohols, flavonoids and secoiridoids) and lipophilic (cresols) phenolic compounds that are known to possess multiple biological activities such as antioxidant, anticarcinogenic, antiinflammatory, antimicrobial, antihypertensive, antidyslipidemic, cardiotonic, laxative, and antiplatelet. Other important compounds present in olive fruit are pectin, organic acids, and pigments. Virgin olive oil (VOO), extracted mechanically from the fruit, is also very popular for its nutritive and health-promoting potential, especially against cardiovascular disorders due to the presence of high levels of monounsaturates and other valuable minor components such as phenolics, phytosterols, tocopherols, carotenoids, chlorophyll and squalene. The cultivar, area of production, harvest time, and the processing techniques employed are some of the factors shown to influence the composition of olive fruit and olive oil. This review focuses comprehensively on the nutrients and high-value bioactives profile as well as medicinal and functional aspects of different parts of olives and its byproducts. Various factors affecting the composition of this food commodity of medicinal value are also discussed. PMID:22489153

  16. Influence of high concentrations of mineral salts on production process and NaCl accumulation by Salicornia europaea plants as a constituent of the LSS phototroph link

    Science.gov (United States)

    Tikhomirova, N. A.; Ushakova, S. A.; Kovaleva, N. P.; Gribovskaya, I. V.; Tikhomirov, A. A.

    Use of halophytes (salt-tolerant vegetation), in a particular vegetable Salicornia europaea plants which are capable of utilizing NaCl in rather high concentrations, is one of possible means of NaCl incorporation into mass exchange of bioregenerative life support systems. In preliminary experiments it was shown that S. europaea plants, basically, could grow on urine pretreated with physicochemical processing and urease-enzyme decomposing of urea with the subsequent ammonia distillation. But at the same time inhibition of the growth process of the plants was observed. The purpose of the given work was to find out the influence of excessive quantities of some mineral elements contained in products of physicochemical processing of urine on the production process and NaCl accumulation by S. europaea plants. As the content of mineral salts in the human liquid wastes (urine) changed within certain limits, two variants of experimental solutions were examined. In the first variant, the concentration of mineral salts was equivalent to the minimum salt content in the urine and was: K - 1.5 g/l, P - 0.5 g/l, S - 0.5 g/l, Mg - 0.07 g/l, Ca - 0.2 g/l. In the second experimental variant, the content of mineral salts corresponded to the maximum salt content in urine and was the following: K - 3.0 g/l, P - 0.7 g/l, S - 1.2 g/l, Mg - 0.2 g/l, Ca - 0.97 g/l. As the control, the Tokarev nutrient solution containing nitrogen in the form of a urea, and the Knop nutrient solution with nitrogen in the nitrate form were used. N quantity in all four variants made up 177 mg/l. Air temperature was 24 °C, illumination was continuous. Light intensity was 690 μmol/m 2s of photosynthetically active radiation. NaCl concentration in solutions was 1%. Our researches showed that the dry aboveground biomass of an average plant of the first variant practically did not differ from the control and totaled 11 g. In the second variant, S. europaea productivity decreased and the dry aboveground biomass

  17. The first cytogenetic description of Euleptes europaea (Gené, 1839 from Northern Sardinia reveals the highest diploid chromosome number among sphaerodactylid geckos (Sphaerodactylidae, Squamata

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    Ekaterina Gornung

    2013-06-01

    Full Text Available The karyotype of a sphaerodactylid gecko Euleptes europaea (Gené, 1839 was assembled for the first time in this species. It is made of 2n = 42 gradually decreasing in size chromosomes, the highest chromosome number so far acknowledged in the family Sphaerodactylidae. The second chromosome pair of the karyotype appears slightly heteromorphic in the male individual. Accordingly, FISH with a telomeric probe revealed an uneven distribution of telomeric repeats on the two homologues of this pair, which may be indicative of an XY sex-determination system in the species, to be further investigated.

  18. Effect of NaCl Concentration on Productivity and Mineral Composition of Salicrnia europaea as a Plausible Representative of LSS Photosynthesizing Component

    Science.gov (United States)

    Ushakova, S.; Kovaleva, N.; Gribovskaya, I.; Dolgushev, V.; Tikhomirova, N.

    In man-made ecosystems the problem of deadlock wastes generated among other reasons by accumulation of NaCl-containing human liquid wastes has no efficient solution, yet. This retards development of man-made highly closed biological ecosystems where the deadlock wastes must be minimized. A possible solution of the problem is to select plant species capable of utilizing NaCl with sufficiently high concentrations, being edible by humans and featuring high productivity. So far the higher plants used in life support systems were either sensitive to salination (wheat, many bean species, carrots, potatoes, corn) or relatively salt-resistant (barley, beet roots, spinach). Salicornia europaea whose overground part is fully edible for humans is one of most acceptable for this purpose. By the literature evidence this plant is capable of accumulating up to 50% NaCl in terms of dry matter. In addition, excessive accumulation of sodium ions should bring forth increase of carry-out of potassium ions and other biogenous elements. The aim of this work is to study the feasibility of using S. europaea species in growth chambers to involve NaCl into matter turnover. Plants were grown in vegetation chambers under the irradiance of 100 W/m 2 PAR and the temperature of air 24?? by two methods. The first method was to cultivate on a substrate which was peat: without salination (1 version) and with addition of 3.5% (2 version) or 7% NaCl (3 version) in terms of dry peat mass. The second method was to cultivate on an aqueous solution with addition of a complete set of nutrients and, depending on the version, containing ? NaCl at the concentration of 0%, 1% or 2%. The study showed that addition of NaCl to the substrate or to the solution resulted in formation of more succulent plants which considerably increased their biomass. The amount of NaCl uptake was the highest in the plants grown in aqueous cultu e, its part in the dry matter was not less than 30%.r As the sodium uptake increased

  19. Hepatoprotective and antioxidant properties of the aqueous extract of Olea europaea leaves against Diclofenac-induced liver damages in mice.

    Science.gov (United States)

    Soussi, Rawya; Hfaiedh, Najla; Guesmi, Fatma; Sakly, Mohsen; Ben Rhouma, Khémais

    2018-04-20

    Historically, olive tree "Olea europaea" is one of the most important fruit trees in Mediterranean countries. Several studies suggest that olive leaf is a significant source of bioactive phenolic compounds compared to olive oil and fruits. This study was undertaken to investigate, the protective effect of the aqueous extract of « Chemlali » olive leaves against diclofenac-induced damages in liver and haematological alterations in swiss albinos mice. For this, twenty-eight mice were divided into four groups: a control group, a diclofenac-treated group (2.37 mg/kg) for 5 consecutive days, a group orally gavaged with aqueous extract of olive leaves, (3.3g/kg) during 28 days, and a group pre-treated with aqueous extract of olive leaves during 23 days then injected with diclofenac for 5 days. Results obtained from this study revealed that administration of diclofenac alone led to disturbance of some haematological parameters including red and white blood cells (RBC), (WBC) haemoglobin (Hb) and platelets content (PLT). However, diclofenac-treated mice group showed a increasing in the levels of cholesterol, triglyceride, glucose, creatinine, urea, aspartate aminotransferase (ASAT), and alanine aminotransferase (ALAT). Additionally we noted a state of oxidative stress in hepatic tissue indicated by the increasing of lipid peroxidation level (TBARS) and decreasing of superoxide dismutase (SOD), catalase (CAT) and glutathione peroxidase (GPX). Interstingly, pre-treatment with olive leaves extract improved the haematological parameters and minimised the adverse effect on the hepatic function markers induced by diclofenac. The beneficial effect of olive leaves could be attributed to its antioxidant components as confirmed by phytochemical analysis.

  20. Identification of new polymorphic regions and differentiation of cultivated olives (Olea europaea L. through plastome sequence comparison

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    Baldoni Luciana

    2010-09-01

    Full Text Available Abstract Background The cultivated olive (Olea europaea L. is the most agriculturally important species of the Oleaceae family. Although many studies have been performed on plastid polymorphisms to evaluate taxonomy, phylogeny and phylogeography of Olea subspecies, only few polymorphic regions discriminating among the agronomically and economically important olive cultivars have been identified. The objective of this study was to sequence the entire plastome of olive and analyze many potential polymorphic regions to develop new inter-cultivar genetic markers. Results The complete plastid genome of the olive cultivar Frantoio was determined by direct sequence analysis using universal and novel PCR primers designed to amplify all overlapping regions. The chloroplast genome of the olive has an organisation and gene order that is conserved among numerous Angiosperm species and do not contain any of the inversions, gene duplications, insertions, inverted repeat expansions and gene/intron losses that have been found in the chloroplast genomes of the genera Jasminum and Menodora, from the same family as Olea. The annotated sequence was used to evaluate the content of coding genes, the extent, and distribution of repeated and long dispersed sequences and the nucleotide composition pattern. These analyses provided essential information for structural, functional and comparative genomic studies in olive plastids. Furthermore, the alignment of the olive plastome sequence to those of other varieties and species identified 30 new organellar polymorphisms within the cultivated olive. Conclusions In addition to identifying mutations that may play a functional role in modifying the metabolism and adaptation of olive cultivars, the new chloroplast markers represent a valuable tool to assess the level of olive intercultivar plastome variation for use in population genetic analysis, phylogenesis, cultivar characterisation and DNA food tracking.

  1. Thriving at the limit: Differential reproductive performance in range-edge populations of a Mediterranean sclerophyll (Olea europaea)

    Science.gov (United States)

    Granado-Yela, Carlos; Balaguer, Luis; García-Verdugo, Carlos; Carrillo, Katty; Méndez, Marcos

    2013-10-01

    Peripheral populations are often lumped together on the assumption of thriving in marginal habitats where reproductive performance is compromised. We have tested this hypothesis in peripheral populations of wild olive tree (Olea europaea L.) presumably limited by different factors at the westernmost limit of the species range. Additionally, we hypothesized that differences in reproductive outcome among populations are better explained by site-specific environmental conditions (PAR, soil water, soil nutrients, air humidity and air temperature) than by differences in phenotypic traits (tree size and leaf traits). To test these hypotheses, we assessed the number of flowering trees, the flowering intensity, fruit set and seed viability in eight populations for three consecutive years. Our findings provided sufficient evidence to reject the first hypothesis. Peripheral populations that occur under oceanic conditions, resembling the Tertiary subtropical climate, consistently presented higher values for all components of reproductive performance than those at the thermal and rainfall tolerance limits. In support of our second hypothesis, the variation in reproductive performance among populations was primarily accounted for by local environmental conditions. Leaf traits, however, also explained reproductive variation but to a lesser extent. Finally, we found that small changes in tree size may cause large differences in reproductive performance. This close relationship between tree size and reproductive performance suggests that any impact on population size structure would likely jeopardize persistence and expansion at the range edge. Our results suggest that reproductive performance of wild olive trees was not shaped by the population geographic position within the species range, but by the interaction between local environment, as the main driver, and individual phenotypic traits.

  2. Construction of Core Collections Suitable for Association Mapping to Optimize Use of Mediterranean Olive (Olea europaea L.) Genetic Resources

    Science.gov (United States)

    El Bakkali, Ahmed; Haouane, Hicham; Moukhli, Abdelmajid; Costes, Evelyne; Van Damme, Patrick; Khadari, Bouchaib

    2013-01-01

    Phenotypic characterisation of germplasm collections is a decisive step towards association mapping analyses, but it is particularly expensive and tedious for woody perennial plant species. Characterisation could be more efficient if focused on a reasonably sized subset of accessions, or so-called core collection (CC), reflecting the geographic origin and variability of the germplasm. The questions that arise concern the sample size to use and genetic parameters that should be optimized in a core collection to make it suitable for association mapping. Here we investigated these questions in olive (Olea europaea L.), a perennial fruit species. By testing different sampling methods and sizes in a worldwide olive germplasm bank (OWGB Marrakech, Morocco) containing 502 unique genotypes characterized by nuclear and plastid loci, a two-step sampling method was proposed. The Shannon-Weaver diversity index was found to be the best criterion to be maximized in the first step using the Core Hunter program. A primary core collection of 50 entries (CC50) was defined that captured more than 80% of the diversity. This latter was subsequently used as a kernel with the Mstrat program to capture the remaining diversity. 200 core collections of 94 entries (CC94) were thus built for flexibility in the choice of varieties to be studied. Most entries of both core collections (CC50 and CC94) were revealed to be unrelated due to the low kinship coefficient, whereas a genetic structure spanning the eastern and western/central Mediterranean regions was noted. Linkage disequilibrium was observed in CC94 which was mainly explained by a genetic structure effect as noted for OWGB Marrakech. Since they reflect the geographic origin and diversity of olive germplasm and are of reasonable size, both core collections will be of major interest to develop long-term association studies and thus enhance genomic selection in olive species. PMID:23667437

  3. Immunoproteomic tools are used to identify masked allergens: Ole e 12, an allergenic isoflavone reductase from olive (Olea europaea) pollen.

    Science.gov (United States)

    Castro, Lourdes; Crespo, Jesús F; Rodríguez, Julia; Rodríguez, Rosalía; Villalba, Mayte

    2015-12-01

    Proteins performing important biochemical activities in the olive tree (Olea europaea) pollen have been identified as allergens. One novel 37-kDa protein seems to be associated to the IgE-binding profile of a group of patients suffering allergy to peach and olive pollen. Three previously described olive pollen allergens exhibit very similar molecular mass. Our objective was to identify this allergen by using immunoproteomic approaches. After 2D-electrophoresis and mass spectrometry, peptide sequences from several IgE-binding spots, allowed identifying this new allergen, as well as cloning and DNA sequencing of the corresponding gene. The allergen, named Ole e 12, is a polymorphic isoflavone reductase-like protein of 308 amino acids showing 80% and 74% identity with birch and pear allergens, Bet v 6 and Pyr c 5, respectively. A prevalence of 33% in the selected population is in contrast to 4%-10% in groups of subjects suffering from pollinosis. Recombinant allergen was produced in Escherichia coli, and deeply characterised. Immunoblotting and ELISA detection as well as inhibition experiments were performed with polyclonal antisera and allergic patients' sera. The recombinant allergen retains the IgE reactivity of its natural counterpart. Close structural and immunological relationships between members of this protein family were supported by their IgG recognition in vegetable species. In summary, Ole e 12 is a minor olive pollen allergen, which gains relevance in patients allergic to peach with olive pollinosis. Proteomic approaches used to analyse this allergen provide useful tools to identify hidden allergens, relevant for several allergic populations and thus complete allergenic panels. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Comparing the historic olive trees (Olea europaea L.) of Santa Cruz with contemporaneous trees in the Santa Barbara, CA area: a case study of diversity and structure in an introduced agricultural species conserved in situ

    Science.gov (United States)

    Historic populations of crop species outside their centers of origin and diversity, like the domestic olive (Olea europaea L.) in North America, are genetic resources for contemporary agriculture, including genotypes that could be adapted to, local conditions. The primary goal of this study was to d...

  5. Biochemistry of Ammonia Monoxygenase from Nitrosomonas

    Energy Technology Data Exchange (ETDEWEB)

    Alan Hooper

    2009-07-15

    Major results. 1. CytochromecM552, a protein in the electron transfer chain to ammonia monooxygenase. Purification, modeling of protein structure based on primary structure, characterization of 4 hemes by magnetic spectroscopy, potentiometry, ligand binding and turnover. Kim, H. J., ,Zatsman, et al. 2008). 2. Characterization of proteins which thought to be involved in the AMO reaction or to protect AMO from toxic nitrogenous intermediates such as NO. Nitrosocyanin is a protein present only in bacteria which catalyze the ammonia monoxygenase reaction (1). Cytochrome c P460 beta and cytochrome c’ beta.

  6. Partial Root-Zone Drying of Olive (Olea europaea var. 'Chetoui') Induces Reduced Yield under Field Conditions.

    Science.gov (United States)

    Dbara, Soumaya; Haworth, Matthew; Emiliani, Giovani; Ben Mimoun, Mehdi; Gómez-Cadenas, Aurelio; Centritto, Mauro

    2016-01-01

    The productivity of olive trees in arid and semi-arid environments is closely linked to irrigation. It is necessary to improve the efficiency of irrigation techniques to optimise the amount of olive fruit produced in relation to the volume of water used. Partial root-zone drying (PRD) is a water saving irrigation technique that theoretically allows the production of a root-to-shoot signal that modifies the physiology of the above-ground parts of the plant; specifically reducing stomatal conductance (gs) and improving water use efficiency (WUE). Partial root-zone drying has been successfully applied under field conditions to woody and non-woody crops; yet the few previous trials with olive trees have produced contrasting results. Thirty year-old olive trees (Olea europaea 'var. Chetoui') in a Tunisian grove were exposed to four treatments from May to October for three-years: 'control' plants received 100% of the potential evapotranspirative demand (ETc) applied to the whole root-zone; 'PRD100' were supplied with an identical volume of water to the control plants alternated between halves of the root-zone every ten-days; 'PRD50' were given 50% of ETc to half of the root-system, and; 'rain-fed' plants received no supplementary irrigation. Allowing part of the root-zone to dry resulted in reduced vegetative growth and lower yield: PRD100 decreased yield by ~47% during productive years. During the less productive years of the alternate bearing cycle, irrigation had no effect on yield; this suggests that withholding of water during 'off-years' may enhance the effectiveness of irrigation over a two-year cycle. The amount and quality of oil within the olive fruit was unaffected by the irrigation treatment. Photosynthesis declined in the PRD50 and rain-fed trees due to greater diffusive limitations and reduced biochemical uptake of CO2. Stomatal conductance and the foliar concentration of abscisic acid (ABA) were not altered by PRD100 irrigation, which may indicate the

  7. Partial Root-Zone Drying of Olive (Olea europaea var. 'Chetoui' Induces Reduced Yield under Field Conditions.

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    Soumaya Dbara

    Full Text Available The productivity of olive trees in arid and semi-arid environments is closely linked to irrigation. It is necessary to improve the efficiency of irrigation techniques to optimise the amount of olive fruit produced in relation to the volume of water used. Partial root-zone drying (PRD is a water saving irrigation technique that theoretically allows the production of a root-to-shoot signal that modifies the physiology of the above-ground parts of the plant; specifically reducing stomatal conductance (gs and improving water use efficiency (WUE. Partial root-zone drying has been successfully applied under field conditions to woody and non-woody crops; yet the few previous trials with olive trees have produced contrasting results. Thirty year-old olive trees (Olea europaea 'var. Chetoui' in a Tunisian grove were exposed to four treatments from May to October for three-years: 'control' plants received 100% of the potential evapotranspirative demand (ETc applied to the whole root-zone; 'PRD100' were supplied with an identical volume of water to the control plants alternated between halves of the root-zone every ten-days; 'PRD50' were given 50% of ETc to half of the root-system, and; 'rain-fed' plants received no supplementary irrigation. Allowing part of the root-zone to dry resulted in reduced vegetative growth and lower yield: PRD100 decreased yield by ~47% during productive years. During the less productive years of the alternate bearing cycle, irrigation had no effect on yield; this suggests that withholding of water during 'off-years' may enhance the effectiveness of irrigation over a two-year cycle. The amount and quality of oil within the olive fruit was unaffected by the irrigation treatment. Photosynthesis declined in the PRD50 and rain-fed trees due to greater diffusive limitations and reduced biochemical uptake of CO2. Stomatal conductance and the foliar concentration of abscisic acid (ABA were not altered by PRD100 irrigation, which may

  8. Genome-wide identification of alternate bearing-associated microRNAs (miRNAs in olive (Olea europaea L.

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    Yanik Huriye

    2013-01-01

    Full Text Available Abstract Background Alternate bearing is a widespread phenomenon among crop plants, defined as the tendency of certain fruit trees to produce a high-yield crop one year ("on-year", followed by a low-yield or even no crop the following year ("off-year". Several factors may affect the balance between such developmental phase-transition processes. Among them are the microRNA (miRNA, being gene-expression regulators that have been found to be involved as key determinants in several physiological processes. Results Six olive (Olea europaea L. cv. Ayvalik variety small RNA libraries were constructed from fruits (ripe and unripe and leaves (”on year” and ”off year” leaves in July and in November, respectively and sequenced by high-throughput Illumina sequencing. The RNA was retrotranscribed and sequenced using the high-throughput Illumina platform. Bioinformatics analyses of 93,526,915 reads identified 135 conserved miRNA, belonging to 22 miRNA families in the olive. In addition, 38 putative novel miRNAs were discovered in the datasets. Expression of olive tree miRNAs varied greatly among the six libraries, indicating the contribution of diverse miRNA in balancing between reproductive and vegetative phases. Predicted targets of miRNA were categorized into 108 process ontology groups with significance abundance. Among those, potential alternate bearing-associated processes were found, such as development, hormone-mediated signaling and organ morphogenesis. The KEGG analyses revealed that the miRNA-targeted genes are involved in seven main pathways, belonging to carbohydrate metabolism and hormone signal-transduction pathways. Conclusion A comprehensive study on olive miRNA related to alternate bearing was performed. Regulation of miRNA under different developmental phases and tissues indicated that control of nutrition and hormone, together with flowering processes had a noteworthy impact on the olive tree alternate bearing. Our results also

  9. Genome-wide identification of alternate bearing-associated microRNAs (miRNAs) in olive (Olea europaea L.).

    Science.gov (United States)

    Yanik, Huriye; Turktas, Mine; Dundar, Ekrem; Hernandez, Pilar; Dorado, Gabriel; Unver, Turgay

    2013-01-15

    Alternate bearing is a widespread phenomenon among crop plants, defined as the tendency of certain fruit trees to produce a high-yield crop one year ("on-year"), followed by a low-yield or even no crop the following year ("off-year"). Several factors may affect the balance between such developmental phase-transition processes. Among them are the microRNA (miRNA), being gene-expression regulators that have been found to be involved as key determinants in several physiological processes. Six olive (Olea europaea L. cv. Ayvalik variety) small RNA libraries were constructed from fruits (ripe and unripe) and leaves ("on year" and "off year" leaves in July and in November, respectively) and sequenced by high-throughput Illumina sequencing. The RNA was retrotranscribed and sequenced using the high-throughput Illumina platform. Bioinformatics analyses of 93,526,915 reads identified 135 conserved miRNA, belonging to 22 miRNA families in the olive. In addition, 38 putative novel miRNAs were discovered in the datasets. Expression of olive tree miRNAs varied greatly among the six libraries, indicating the contribution of diverse miRNA in balancing between reproductive and vegetative phases. Predicted targets of miRNA were categorized into 108 process ontology groups with significance abundance. Among those, potential alternate bearing-associated processes were found, such as development, hormone-mediated signaling and organ morphogenesis. The KEGG analyses revealed that the miRNA-targeted genes are involved in seven main pathways, belonging to carbohydrate metabolism and hormone signal-transduction pathways. A comprehensive study on olive miRNA related to alternate bearing was performed. Regulation of miRNA under different developmental phases and tissues indicated that control of nutrition and hormone, together with flowering processes had a noteworthy impact on the olive tree alternate bearing. Our results also provide significant data on the miRNA-fruit development

  10. Niche partitioning within genus Nitrospira is affected by environmental copper concentration

    DEFF Research Database (Denmark)

    Fowler, Jane; Dechesne, Arnaud; Wagner, Florian Benedikt

    of nitrifying bacteria; Betaproteobacterial ammonia oxidizers (Nitrosomonas, Nitrosospira; AOB), ammonia oxidizing archaea (AOA), diverse heterotrophs potentially capable of ammonia and/or nitrite oxidation and a large fraction of Nitrospira spp., recently shown to comprise both nitrite oxidizers and comammox....... The reasons for the loss of Clade B comammox are currently unclear. Higher sensitivity to copper toxicity in Clade B relative to Clade A and nitrite-oxidizing Nitrospira seems unlikely due to the extremely low copper concentrations applied. An overall stimulation of the growth of nitrifying bacteria occurred...

  11. Density and distribution of nitrifying guilds in rapid sand filters for drinking water production: Dominance of Nitrospira spp

    DEFF Research Database (Denmark)

    Tatari, Karolina; Musovic, Sanin; Gülay, Arda

    2017-01-01

    distribution of these guilds, filter material was sampled at four drinking water treatment plants (DWTPs) in parallel filters of the pre- and after-filtration stages at different locations and depths. The target guilds were quantified by qPCR targeting 16S rRNA and amoA genes. Total bacterial densities......We investigated the density and distribution of total bacteria, canonical Ammonia Oxidizing Bacteria (AOB) (Nitrosomonas plus Nitrosospira), Ammonia Oxidizing Archaea (AOA), as well as Nitrobacter and Nitrospira in rapid sand filters used for groundwater treatment. To investigate the spatial...

  12. De l’olivier à l’oléastre : origine et domestication de l’Olea europaea L. dans le Bassin méditerranéen

    OpenAIRE

    Breton, Catherine; Médail, Frédéric; Pinatel, Christian; Berville, Andre

    2006-01-01

    De l’olivier à l’oléastre : origine et domestication de l’Olea europaea L. dans le Bassin méditerranéen Keywords : VEGETAL PRODUCTIONS, NATURAL RESOURCES AND ENVIRONMENTRésumé : L’olivier occupe la 24 e place des 35 espèces les plus cultivées dans le monde. La diversité phénologique des cultivars est remarquable et l’intérêt économique de l’espèce est majeur. Pourtant peu d’études ont porté sur la domestication de l’olivier et sur les relations entre l’olivier et sa forme sauvage, l’oléastre....

  13. Effect of NaCl concentration on productivity and mineral composition of Salicornia europaea as a potential crop for utilization NaCl in LSS

    Science.gov (United States)

    Ushakova, S. A.; Kovaleva, N. P.; Gribovskaya, I. V.; Dolgushev, V. A.; Tikhomirova, N. A.

    The accumulation of solid and liquid wastes in manmade ecosystems presents a problem that has not been efficiently solved yet. Urine, containing NaCl, are part of these products. This is an obstacle to the creation of biological systems with a largely closed material cycling, because the amount of solid and liquid wastes in them must be reduced to a minimum. A possible solution to the problem is to select plant species capable of utilizing sufficiently high concentrations of NaCl, edible for humans, and featuring high productivity. Until recently, the life support systems have included the higher plants that were either sensitive to salinization (wheat, many of the legumes, carrot, potato, maize) or relatively salt-resistant (barley, sugar beet, spinach). Salicomia europaea, whose above-ground part is fully edible for humans, is one of the most promising candidates to be included in life support systems. It is reported in the literature that this plant is capable of accumulating up to 50% NaCl (dry basis). Besides, excessive accumulation of sodium ions should bring forth a decrease in the uptake of potassium ions and other biogenic elements. The aim of this work is to study the feasibility of using S. europaea plants in growth chambers to involve NaCl into material cycling. Plants were grown in vegetation chambers at the irradiance of 100 or 150 W/m 2 PAR (photosynthetically active radiation) and the air temperature 24 °C, by two methods. The first method was to grow the plants on substrate - peat. The peat was supplemented with either 3% NaCl (Variant 1) or 6% NaCl (Variant 2) of the oven-dry mass of the peat. The second method was to grow the plants in water culture, using the solution with a full complement of nutrients, which contained 0.0005% of NaCl, 1% or 2%. The study showed that the addition of NaCl to the substrate or to the solution resulted in the formation of more succulent plants, which considerably increased their biomass. The amount of NaCl uptake

  14. Transcriptional Analysis of Stearoyl-Acyl Carrier Protein Desaturase Genes from Olive (Olea europaea) in Relation to the Oleic Acid Content of the Virgin Olive Oil.

    Science.gov (United States)

    Parvini, Farshid; Sicardo, M Dolores; Hosseini-Mazinani, Mehdi; Martinez-Rivas, Jose M; Hernandez, M Luisa

    2016-10-02

    The specific contribution of different stearoyl-ACP desaturase (SAD) genes to the oleic acid content in olive (Olea europaea) fruit has been studied. Towards that end, we isolated three distinct cDNA clones encoding three SAD isoforms from olive (cv. Picual), as revealed by sequence analysis. The expression levels of olive SAD genes were determined in different tissues from Picual and Arbequina cultivars, including developing mesocarp and seed, together with the unsaturated fatty acid content. Lipid and gene expression analysis indicate that OeSAD2 seems to be the main gene contributing to the oleic acid content of the olive fruit and, therefore, of the virgin olive oil. This conclusion was confirmed when the study was extended to Hojiblanca, Picudo and Manzanilla cultivars. Furthermore, our data indicate that the olive microsomal oleate desaturase gene OeFAD2-2, but not OeSAD2, is responsible for the linoleic acid content in the virgin olive oil.

  15. The efficacy of kaolin particle film on oil quality indices of olive trees (Olea europaea L.) cv 'Zard' grown under warm and semi-arid region of Iran.

    Science.gov (United States)

    Khaleghi, Esmaeil; Arzani, Kazem; Moallemi, Norollah; Barzegar, Mohsen

    2015-01-01

    Kaolin particle film (0%, 3% and 6%; w/v), as an antitranspirant treatment, was applied to mature 'Zard' olive trees (Olea europaea L.). Olive oil was extracted from harvested fruit and fatty acid composition and other oil quality indices of the fruit assessed over crop seasons. Kaolin increased chlorophyll and carotenoid contents, but decreased peroxide and iodine values, and UV absorbance extinction coefficients, of the oil. The highest palmitic acid was observed in the oil obtained from untreated trees (17%). Kaolin increased oleic acid up to 65% and 64% in the first and second crop seasons, respectively, but decreased linoleic and linolenic acid contents. Monounsaturated acids (65%) and oleic acid/linoleic acid ratios (4) were higher in oil obtained from kaolin treated than untreated trees. Therefore it can be expected that extracted olive oil from kaolin treated trees has a higher oxidative stability and shelf life than untreated trees. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Olive tree (Olea europaea L.) leaf as a waste by-product of table olive and olive oil industry: a review.

    Science.gov (United States)

    Şahin, Selin; Bilgin, Mehmet

    2018-03-01

    Research into finding new uses for by-products of table olive and olive oil industry are of great value not only to the economy but also to the environment where olives are grown and to the human health. Since leaves represent around 10% of the total weight of olives arriving at the mill, it is worth obtaining high added-value compounds from those materials for the preparation of dietary supplements, nutraceuticals, functional food ingredients or cosmeceuticals. In this review article, olive tree (Olea europaea L.) leaf is reviewed as being a potential inexpensive, renewable and abundant source of biophenols. The importance of this agricultural and industrial waste is emphasised by means of describing its availability, nutritional and therapeutic effects and studies conducted on this field. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  17. Composition, quality and oxidative stability of virgin olive oils from some selected wild olives (Olea europaea L. subsp. oleaster

    Directory of Open Access Journals (Sweden)

    Zarrouk, Mokhtar

    2008-12-01

    Full Text Available A study on the characterization of virgin olive oils from wild olives (Olea europaea L. subsp. oleaster was conducted in order to define new cultivars which are welladapted to the Tunisian environment and yield high quality oils. The study was done during the crop years 2003/04, 2004/05 and 2005/06. The main analytical parameters of the oils were evaluated: fatty acid compositions, chlorophylls, carotenoids, tocopherols and phenolic compounds as well as their relationship with oxidative stability. The fatty acid composition of all the wild olive trees tested produced virgin olive oil which complies with commercial standards, as well as for their appreciable amounts of tocopherols and phenolic compounds. Tocopherol analysis by HPLC revealed the presence of α, β, γ and δ tocopherols in all the studied olive oils. Total tocopherol content was significantly influenced by the varietal factor. It ranged from 310 (SB12 to 780 mg/kg (H3. As for total tocopherols, the amount of each tocopherol varied according to genotype. α tocopherol is the most prominent, whereas β, γ and δ tocopherols are less represented. Results showed a clear influence of total phenols and o-diphenols on virgin olive oil stability (R = 0.905, 0.963 P En este trabajo se han caracterizado los aceites obtenidos a partir de siete acebuches previamente seleccionados entre varias poblaciones de Olea europea L. Subsp. oleaster. El estudio se llevó a cabo durante las campañas de producción 2003/04, 2004/05 y 2005/06.Varios parámetros analíticos fueron evaluados: composiciones en ácidos grasos, pigmentos, tocoferoles, fenoles; así mismo, se investigó la relación de estos parámetros con la estabilidad de los aceites. Los resultados obtenidos mostraron que todas las muestras de frutos de acebuche produjeron aceites cuya composición de ácidos grasos, tocoferoles y compuestos fenólicos cumplió las normas comerciales para aceite de oliva virgen del Comit

  18. Polen atmosférico de Olea europaea L. en Madrid (Ciudad Universitaria y Aranjuez durante los años 1994-1997

    Directory of Open Access Journals (Sweden)

    Sáenz Laín, Concepción

    1999-12-01

    Full Text Available The results of four years of study (1994-1997 of the atmospheric levéis of pollen from Olea europaea L. in Madrid and Aranjuez are presented. The principal pollination period (PPP for each year and each season were calculated, using the mean daily concentrations, and fell between weeks 16 and 26, with maximum daily valúes registered between 3rd May and 7th June. The presence of olive pollen was greater in Aranjuez than in Madrid (mean 3,307 grains of pollen/year and 2,123 grains/year, respectively. The pollen season was similar in each locality. A preliminary comparison of pollen data with temperature and precipitation seems to indicates that accumulated pre-season temperatures, but not rainfall, can have decisive influence on the initiation of pollination. His nuclear what influence rainfall has on the account of pollen collected.Presentamos los resultados obtenidos durante cuatro años de estudio (1994-1997 del contenido atmosférico de polen de Olea europaea L. en Madrid (Ciudad Universitaria y en Aranjuez. A partir de las concentraciones medias diarias, hemos calculado el Período de Polinización Principal (PPP para cada año y cada estación, que se ha producido siempre entre las semanas 16 y 26, con valores máximos diarios registrados entre el 3 de mayo y el 7 de junio. La presencia del polen de olivo ha sido mayor en Aranjuez que en Madrid (media del período, 3.307 granos de polen/año y 2.123, respectivamente. Las estación polínica transcurre de forma similar en ambas localidades. De una primera comparación de los datos polínicos con los datos de temperatura y precipitación, parece deducirse que las temperaturas acumuladas durante el período preestacional pueden tener una influencia decisiva en el inicio de la polinización, no así las precipitaciones. Tampoco parece clara su influencia sobre el total anual de polen recogido.

  19. Influence of inorganic and organic amendments in the soil properties and the growth and survival of Olea Europaea var. Sylvestris in the semiarid Mediterranean area

    Science.gov (United States)

    Ortega, Raúl; Miralles, Isabel; Anguita-Maeso, Manuel; Domene, Miguel; Soriano, Miguel

    2017-04-01

    Selecting the most appropriate types of plants adapted to the harsh climatic conditions of restoring drylands is essential to success in landscape restoration. Besides improving soil quality is a key factor to consider when designing the restoration procedures. The use of organic and inorganic amendments can help with this task. On this study, we evaluated the influence of different mineral (clays) and organic (compost and poultry) amendments on the properties of a bare soil and how this influenced on the growth and survival of the Olea europaea var. sylvestrys, a perennial bush plant adapted to the Mediterranean semi-arid zone. Tests were designed and carried out in a greenhouse at the "Experimental Station of Cajamar foundation "Las Palmerillas" in El Ejido (Almería, Spain). Plants were grown in 250L pots and their substrate was bare soil and mineral and/or organic amendments. The experimental design consisted of three replicas for five treatments: 1. compost, 2. "ZeoPro", a cliptonolite commercial clay, 3. mordenite clay from local quarries plus compost, 4. cliptonolite clay from Turkey plus compost, 5. cliptonolite from Turquey plus poultry; with four levels each one: 5%, 10%, 20%, 30% volume of amendment. Including three control samples without amendment total plants accounted for 63. Climatic sensors inside and outside the greenhouse permitted to establish the same meteorological conditions for the plants and only emergency watering was supplied when necessary for the survival of the plants when arid conditions were extreme. The physico-chemical soil properties of each treatment and level were analyzed before planting and the biovolume and the survival rates of the plants were measured regularly along eleven months. Statistically the best treatment for the growing of the plants was number 3 (mordenite and compost) with no deaths recorded. According to the growing rates the best level was soil with 20% of amendment. Besides we analyzed the evolution of the

  20. AcEST: DK944957 [AcEST

    Lifescience Database Archive (English)

    Full Text Available ant alignments: (bits) Value sp|Q82Y15|ORN_NITEU Oligoribonuclease OS=Nitrosomonas europaea G... 31 1.7 sp|Q9JLC8|SACS_MOUSE Sacsi...LVVTDAQLNTLAEAPVLVVHQPDDI 54 >sp|Q9JLC8|SACS_MOUSE Sacsin OS=Mus musculus GN=Sacs PE=1 SV=2 Length = 4582 Sc

  1. Variability of virgin olive oil phenolic compounds in a segregating progeny from a single cross in Olea europaea L. and sensory and nutritional quality implications.

    Directory of Open Access Journals (Sweden)

    Ana G Pérez

    Full Text Available Virgin olive oil phenolic compounds are responsible for its nutritional and sensory quality. The synthesis of phenolic compounds occurs when enzymes and substrates meet as olive fruit is crushed during the industrial process to obtain the oil. The genetic variability of the major phenolic compounds of virgin olive oil was studied in a progeny of the cross of Picual x Arbequina olive cultivars (Olea europaea L.. They belong to four different groups: compounds that included tyrosol or hydroxytyrosol in their molecules, lignans, flavonoids, and phenolic acids. Data of phenolics in the oils showed that the progeny displayed a large degree of variability, widely transgressing the genitor levels. This high variability can be of interest on breeding programs. Thus, multivariate analysis allowed to identify genotypes within the progeny particularly interesting in terms of phenolic composition and deduced organoleptic and nutritional quality. The present study has demonstrated that it is possible to obtain enough degree of variability with a single cross of olive cultivars for compounds related to the nutritional and organoleptic properties of virgin olive oil.

  2. The influence of field margins on the presence and spatial distribution of the European mole Talpa europaea L. within the agricultural landscape of northern Poland

    Directory of Open Access Journals (Sweden)

    Zurawska-Seta Ewa

    2012-01-01

    Full Text Available European moles are widespread in both cultivated and uncultivated areas in Poland. Their occurrence and distribution in relation to the physical and chemical characteristics of soil has been already studied in previous research. However, there is still an open question about the impact of the structure of anthropogenic habitats produced by agriculture on moles. The main aim of this study is to assess the influence of different kinds of field margins on the presence and spatial distribution of the European mole Talpa europaea L. in farmlands. Methods included the monitoring of six investigative sites in northern Poland. Observations were made during three six-month periods in 2005-2008 of the presence or absence of moles as recognized by recent molehills and surface tunnels. There was a very clear tendency by moles to occupy areas within arable fields close to field boundaries with wide verges containing ruderal and woodland communities with a spacious zone of ecotones. Narrow boundary strips were avoided by moles. In conclusion, the conducted research confirms that field margins have an impact on the presence and spatial distribution of moles within ploughed lands. Our results may be helpful in improving the relation between agricultural development and biodiversity conservation, and the rational use of nature by humankind.

  3. Spatial genetic structure in the Laperrine's olive (Olea europaea subsp. laperrinei), a long-living tree from the central Saharan mountains.

    Science.gov (United States)

    Besnard, G; Christin, P A; Baali-Cherif, D; Bouguedoura, N; Anthelme, F

    2007-12-01

    The Laperrine's olive (Olea europaea subsp. laperrinei) is an emblematic species of the Sahelo-Saharan Mountains. Populations of this tree are locally threatened by extinction due to climatic vicissitudes and human activities, particularly in Niger and Algeria. In order to study the spatial genetic structure and the dynamics of O. e. laperrinei populations, we sampled trees in four isolated mountain ranges (Tassili n'Ajjer and Hoggar (Algeria), Tamgak and Bagzane (Niger)). A total of 237 genets were identified using nuclear microsatellites. Phylogenetic reconstruction based on plastid DNA data supported a maternal origin of O. e. laperrinei populations in South Algeria, where a higher allelic richness was observed. Based on nuclear microsatellite data, two levels of structure were revealed: first, individuals from Niger and Algeria were separated in two distinct groups; second, four less differentiated clusters corresponded to the four studied mountain ranges. These results give support to the fact that desert barriers have greatly limited long distance gene flow. Within populations, pairwise kinship coefficients were significantly correlated to geographical distance for Niger populations but not for Algerian mountains. Historical factors and habitat heterogeneity may explain the differences observed. We conclude that the Hoggar acts as an important genetic reservoir that has to be taken into account in future conservation programmes. Moreover, very isolated endangered populations (for example, Bagzane) displaying evident genetic particularities have to be urgently considered for their endemism.

  4. Identification of leaf volatiles from olive (Olea europaea) and their possible role in the ovipositional preferences of olive fly, Bactrocera oleae (Rossi) (Diptera: Tephritidae).

    Science.gov (United States)

    Malheiro, Ricardo; Casal, Susana; Cunha, Sara C; Baptista, Paula; Pereira, José Alberto

    2016-01-01

    The olive fly, Bactrocera oleae (Rossi), is a monophagous pest that displays an oviposition preference among cultivars of olive (Olea europaea L.). To clarify the oviposition preference, the olive leaf volatiles of three olive cultivars (Cobrançosa, Madural and Verdeal Transmontana) were assessed by headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC/MS) at six different periods of olive fruit maturation and degrees of infestation. A total of 39 volatiles were identified, mainly esters and alcohols, with a minor percentage of aldehydes, ketones and terpenic compounds, including sesquiterpenes. At sampling dates with higher degrees of infestation, cv. Cobrançosa had, simultaneously, significantly lower infestation degrees and higher volatile amounts than the other two cultivars, with a probable deterrent effect for oviposition. The green leaf volatiles (GLVs) (Z)-3-hexen-1-ol and (Z)-3-hexen-1-ol acetate) were the main compounds identified in all cultivars, together with toluene. The abundance of GLVs decreased significantly throughout maturation, without significant differences among cultivars, while toluene showed a general increase and positive correlation with olive fly infestation levels. The results obtained could broaden our understanding of the roles of various types and amounts of olive volatiles in the environment, especially in olive fly host selection and cultivar preference. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Changes in olive oil volatile organic compounds induced by water status and light environment in canopies of Olea europaea L. trees.

    Science.gov (United States)

    Benelli, Giovanni; Caruso, Giovanni; Giunti, Giulia; Cuzzola, Angela; Saba, Alessandro; Raffaelli, Andrea; Gucci, Riccardo

    2015-09-01

    Light and water are major factors in fruit development and quality. In this study, the effect of water and light in Olea europaea trees on volatile organic compounds (VOCs) in olive oil was studied over 2 years. Mature fruits were harvested from three zones of the canopy with different light exposure (64%, 42% and 30% of incident light) of trees subjected to full, deficit or complementary irrigation. VOCs were determined by SPME GC-MS and analysed by principal component analysis followed by discriminant analysis to partition treatment effects. Fruit fresh weight and mesocarp oil content decreased in zones where intercepted light was less. Low light levels significantly slowed down fruit maturation, whereas conditions of water deficit accelerated the maturation process. The presence of cyclosativene and α-muurulene was associated with water deficit, nonanal, valencene with full irrigation; α-muurulene, (E)-2-hexanal were related to low light conditions, while trans-β-ocimene, α-copaene, (Z)-2-penten-1-ol, hexanal and nonanal to well exposed zones. The year strongly affected the VOC profile of olive oil. This is the first report on qualitative changes in VOCs induced by light environment and/or water status. This information is valuable to better understand the role of environmental factors on the sensory quality of virgin olive oil. © 2014 Society of Chemical Industry.

  6. Colonization of olive trees (Olea europaea L.) with the arbuscular mycorrhizal fungus Glomus sp. modified the glycolipids biosynthesis and resulted in accumulation of unsaturated fatty acids.

    Science.gov (United States)

    Mechri, Beligh; Attia, Faouzi; Tekaya, Meriem; Cheheb, Hechmi; Hammami, Mohamed

    2014-09-01

    The influence of arbuscular mycorrhizal (AM) fungi colonization on photosynthesis, mineral nutrition, the amount of phospholipids and glycolipids in the leaves of olive (Olea europaea L.) trees was investigated. After six months of growth, the rate of photosynthesis, carboxylation efficiency, transpiration and stomatal conductance in mycorrhizal (M) plants was significantly higher than that of non-mycorrhizal (NM) plants. The inoculation treatment increased the foliar P and Mg but not N. The amount of glycolipids in the leaves of M plants was significantly higher than that of NM plants. However, the amount of phospholipids in the leaves of M plants was not significantly different to that in the leaves of NM plants. Also, we observed a significant increase in the level of α-linolenic acid (C18:3ω3) in glycolipids of M plants. This work supports the view that increased glycolipids level in the leaves of M plants could be involved, at least in part, in the beneficial effects of mycorrhizal colonization on photosynthesis performance of olive trees. To our knowledge, this is the first report on the effect of AM fungi on the amount of glycolipids in the leaves of mycorrhizal plants. Copyright © 2014 Elsevier GmbH. All rights reserved.

  7. Variability of virgin olive oil phenolic compounds in a segregating progeny from a single cross in Olea europaea L. and sensory and nutritional quality implications.

    Science.gov (United States)

    Pérez, Ana G; León, Lorenzo; Pascual, Mar; Romero-Segura, Carmen; Sánchez-Ortiz, Araceli; de la Rosa, Raúl; Sanz, Carlos

    2014-01-01

    Virgin olive oil phenolic compounds are responsible for its nutritional and sensory quality. The synthesis of phenolic compounds occurs when enzymes and substrates meet as olive fruit is crushed during the industrial process to obtain the oil. The genetic variability of the major phenolic compounds of virgin olive oil was studied in a progeny of the cross of Picual x Arbequina olive cultivars (Olea europaea L.). They belong to four different groups: compounds that included tyrosol or hydroxytyrosol in their molecules, lignans, flavonoids, and phenolic acids. Data of phenolics in the oils showed that the progeny displayed a large degree of variability, widely transgressing the genitor levels. This high variability can be of interest on breeding programs. Thus, multivariate analysis allowed to identify genotypes within the progeny particularly interesting in terms of phenolic composition and deduced organoleptic and nutritional quality. The present study has demonstrated that it is possible to obtain enough degree of variability with a single cross of olive cultivars for compounds related to the nutritional and organoleptic properties of virgin olive oil.

  8. Thermal stability of oils added with avocado (Persea americana cv. Hass) or olive (Olea europaea cv. Arbequina) leaf extracts during the French potatoes frying.

    Science.gov (United States)

    Jiménez, Paula; García, Paula; Bustamante, Andrés; Barriga, Andrés; Robert, Paz

    2017-04-15

    Effect of the addition of avocado (Persea americana cv. Hass) or olive (Olea europaea cv. Arbequina) hydroalcoholic leaf extracts (AHE and OHE, respectively) on thermal stability of canola oil (CO) and high oleic sunflower oil (HOSO) during French potatoes frying at 180°C was studied. The extracts were characterized by the total phenolic content, phenol chromatographic profiles and antioxidant activity. B-type trimer procyanidins were the major phenolic compounds identified in AHE. OHE showed higher phenol content, antioxidant activity regarding AHE. CO+OHE and HOSO+OHE decreased the formation of polar compounds and showed an anti-polymeric effect with respect to oils without extracts, whereas AHE extract showed a prooxidant effect on HOSO. Therefore, OHE showed an antioxidant effect on HOSO and CO under the studied conditions. In addition, all systems (CO+AHE, HOSO+AHE, CO+OHE and HOSO+OHE) increased the retention of tocopherols. These results demonstrate the potential utility of OHE as natural antioxidant for oils. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. A possible role for flowering locus T-encoding genes in interpreting environmental and internal cues affecting olive (Olea europaea L.) flower induction.

    Science.gov (United States)

    Haberman, Amnon; Bakhshian, Ortal; Cerezo-Medina, Sergio; Paltiel, Judith; Adler, Chen; Ben-Ari, Giora; Mercado, Jose Angel; Pliego-Alfaro, Fernando; Lavee, Shimon; Samach, Alon

    2017-08-01

    Olive (Olea europaea L.) inflorescences, formed in lateral buds, flower in spring. However, there is some debate regarding time of flower induction and inflorescence initiation. Olive juvenility and seasonality of flowering were altered by overexpressing genes encoding flowering locus T (FT). OeFT1 and OeFT2 caused early flowering under short days when expressed in Arabidopsis. Expression of OeFT1/2 in olive leaves and OeFT2 in buds increased in winter, while initiation of inflorescences occurred i n late winter. Trees exposed to an artificial warm winter expressed low levels of OeFT1/2 in leaves and did not flower. Olive flower induction thus seems to be mediated by an increase in FT levels in response to cold winters. Olive flowering is dependent on additional internal factors. It was severely reduced in trees that carried a heavy fruit load the previous season (harvested in November) and in trees without fruit to which cold temperatures were artificially applied in summer. Expression analysis suggested that these internal factors work either by reducing the increase in OeFT1/2 expression or through putative flowering repressors such as TFL1. With expected warmer winters, future consumption of olive oil, as part of a healthy Mediterranean diet, should benefit from better understanding these factors. © 2017 John Wiley & Sons Ltd.

  10. Endophytic colonization and biocontrol performance of Pseudomonas fluorescens PICF7 in olive (Olea europaea L.) are determined neither by pyoverdine production nor swimming motility.

    Science.gov (United States)

    Maldonado-González, M Mercedes; Schilirò, Elisabetta; Prieto, Pilar; Mercado-Blanco, Jesús

    2015-09-01

    Pseudomonas fluorescens PICF7 is an indigenous inhabitant of olive (Olea europaea L.) rhizosphere, able to display endophytic lifestyle in roots, to induce a wide range of defence responses upon colonization of this organ and to exert effective biological control against Verticillium wilt of olive (VWO) (Verticillium dahliae). We aimed to evaluate the involvement of specific PICF7 phenotypes in olive root colonization and VWO biocontrol effectiveness by generating mutants impaired in swimming motility (fliI) or siderophore pyoverdine production (pvdI). Besides, the performance of mutants with diminished in vitro growth in potato dextrose agar medium (gltA) and cysteine (Cys) auxotrophy was also assessed. Results showed that olive root colonization and VWO biocontrol ability of the fliI, pvdI and gltA mutants did not significantly differ from that displayed by the parental strain PICF7. Consequently, altered in vitro growth, swimming motility and pyoverdine production contribute neither to PICF7 VWO suppressive effect nor to its colonization ability. In contrast, the Cys auxotroph mutant showed reduced olive root colonization capacity and lost full biocontrol efficacy. Moreover, confocal laser scanning microscopy revealed that all mutants tested were able to endophytically colonize root tissue to the same extent as wild-type PICF7, discarding these traits as relevant for its endophytic lifestyle. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  11. A de novo transcriptomic approach to identify flavonoids and anthocyanins switch-off in olive (Olea europaea L. drupes at different stages of maturation

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    Domenico eIaria

    2016-01-01

    Full Text Available During ripening, the fruits of the olive tree (Olea europaea L. undergo a progressive chromatic change characterized by the formation of a red-brown spot which gradually extends on the epidermis and in the innermost part of the mesocarp. This event finds an exception in the Leucocarpa cultivar, in which we observe a destabilized equilibrium between the metabolisms of chlorophyll and other pigments, particularly the anthocyanins whose switch-off during maturation promotes the white coloration of fruits. Despite its importance, genomic information on the olive tree is still lacking. Different RNA-seq libraries were generated from drupes of ‘Leucocarpa’ and ‘Cassanese’ olive genotypes, sampled at 100 and 130 days after flowering (DAF, and were used in order to identify transcripts involved in the main phenotypic changes of fruits during maturation and their corresponding expression patterns. A total of 103,359 transcripts were obtained and 3792 and 3064 were differentially expressed in ‘Leucocarpa’ and ‘Cassanese’ genotypes, respectively, during 100-130 DAF transition. Among them flavonoid and anthocyanin related transcripts such as phenylalanine ammonia lyase (PAL, cinnamate 4-hydroxylase (C4H, 4-coumarate-CoA ligase (4CL, chalcone synthase (CHS, chalcone isomerase (CHI, flavanone 3-hydroxylase (F3H, flavonol 3’-hydrogenase (F3'H, flavonol 3’5’-hydrogenase (F3'5'H, flavonol synthase (FLS, dihydroflavonol 4-reductase (DFR, anthocyanidin synthase (ANS, UDP-glucose:anthocianidin:flavonoid glucosyltransferase (UFGT were identified.These results contribute to reducing the current gap in information regarding metabolic processes, including those linked to fruit pigmentation in the olive.

  12. Biogenic synthesis of copper oxide nanoparticles using olea europaea leaf extract and evaluation of their toxicity activities: An in vivo and in vitro study.

    Science.gov (United States)

    Sulaiman, Ghassan M; Tawfeeq, Amer T; Jaaffer, Marwa D

    2018-01-01

    Copper oxide nanoparticles (CUNPs) were synthesized using Olea europaea leaf extract as reducing and protecting agent. The formation of nanoparticles was observed through a color change from yellowish to brownish black. The CUNPs were confirmed with UV-Vis spectrophotometer, which revealed a peak absorbance at 289 nm. The synthesized CUNPs were characterized by XRD, FTIR, SEM, and TEM. The XRD pattern revealed that CUNPs were crystalline in nature with a diameter around 20 nm. FTIR spectral analysis showed that CUNPs were capped with plant constituents. From SEM and TEM analyses, the CUNPs were generally found to be spherical in shape, and the size range was 20-50 nm. Free radical scavenging potential of CUNPs against DPPH was confirmed by its stable antioxidant effects. In addition, the toxicity of CUNPs in mice was also assessed by body weight and weights of liver, kidneys, spleen, and thymus. The immune response in mice was signaled through an obvious change in spleen and thymus index, with a decrease of ADA enzyme activity in serum, spleen, and thymus after CUNPs treatment. The CUNPs were found to exert cell growth arrest against AMJ-13 and SKOV-3 cancer cells in a dose-dependent manner and induce cell death by apoptosis. Less significant cytotoxic effect was observed in normal dermal fibroblast cells. These findings suggest that CUNPs may have the potential to be anticancer agents. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:218-230, 2018. © 2017 American Institute of Chemical Engineers.

  13. Olive (Olea europaea) leaf methanolic extract prevents HCl/ethanol-induced gastritis in rats by attenuating inflammation and augmenting antioxidant enzyme activities.

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    Al-Quraishy, Saleh; Othman, Mohamed S; Dkhil, Mohamed A; Abdel Moneim, Ahmed Esmat

    2017-07-01

    Gastritis is preponderantly characterized by inflammation of the lining epithelial layer and the chronic gastritis is considered as a pre-cancer lesion. For many centuries olive (Olea europaea) leaf has been used for its putative health potential, nonetheless, to date, the gastroprotective effects of olive leaves have not been studied yet. Hence, in this study we investigated whether olive leaf extract (OLE) could protect gastric mucosa against HCl/ethanol-induced gastric mucosal damage in rats. Hcl/ethanol administration caused significant damage to the gastric mucosa, as confirmed by gastric ulcer index and histological evaluation. However, this damage was largely prevented by pre-administering 20mg/kg omeprazole or 100mg/kg OLE. Interestingly, the damage was completely prevented by pre-administering 200 and 300mg/kg OLE. Moreover, OLE attenuated the inflammatory response by decreasing nuclear factor-κB (NF-κB), cycloxygenase-2 (COX-2) and tumor necrosis factor-α (TNF-α) expressions, and down-regulating inducible nitric oxide synthase (iNOS) and interleukin-1β (IL-1β) in gastric mucosa. The gastroprotective mechanism of OLE involved the promotion of enzymatic and nonenzymatic molecules (superoxide dismutase, catalase, glutathione peroxidase, glutathione reductase and glutathione reduced form), promoting nuclear factor erythroid 2-related factor 2 (Nrf2) mRNA expression, halting lipid peroxidation and preventing the overproduction of nitric oxide. Together, our findings clearly demonstrated that OLE could prevent HCl/ethanol-induced gastritis by attenuating inflammation and oxidant/antioxidant imbalance. Indeed, OLE could potentially be useful as a natural therapy for gastritis. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  14. Spatiotemporal variation of arbuscular mycorrhizal fungal colonization in olive (Olea europaea L.) roots across a broad mesic-xeric climatic gradient in North Africa.

    Science.gov (United States)

    Meddad-Hamza, Amel; Hamza, Nabila; Neffar, Souad; Beddiar, Arifa; Gianinazzi, Silvio; Chenchouni, Haroun

    2017-04-01

    This study aims to determine the spatiotemporal dynamics of root colonization and spore density of arbuscular mycorrhizal fungi (AMF) in the rhizosphere of olive trees (Olea europaea) with different plantation ages and under different climatic areas in Algeria. Soil and root samples were seasonally collected from three olive plantations of different ages. Other samples were carried out in productive olive orchards cultivated under a climatic gradient (desertic, semi-arid, subhumid, and humid). The olive varieties analysed in this study were Blanquette, Rougette, Chemlel and the wild-olive. Spore density, mycorrhization intensity (M%), spore diversity and the most probable number (MPN) were determined. Both the intensity of mycorrhizal colonization and spore density increased with the increase of seasonal precipitation and decreased with the increase of air temperature regardless of the climatic region or olive variety. The variety Rougette had the highest mycorrhizal levels in all plantation ages and climates. Spore community was composed of the genera Rhizophagus, Funneliformis, Glomus, Septoglomus, Gigaspora, Scutellospora and Entrophospora. The genus Glomus, with four species, predominated in all climate regions. Spores of Gigaspora sp. and Scutellospora sp. were the most abundant in desertic plantations. Statistical models indicated a positive relationship between spore density and M% during spring and winter in young seedlings and old plantations. A significant positive relationship was found between MPN and spore density under different climates. For a mycotrophic species, the rhizosphere of olive trees proved to be poor in mycorrhiza in terms of mycorrhizal colonization and numbers of the infective AMF propagules. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. RP-HPLC-DAD-ESI-QTOF-MS based metabolic profiling of the potential Olea europaea by-product "wood" and its comparison with leaf counterpart.

    Science.gov (United States)

    Ammar, Sonda; Contreras, Maria Del Mar; Gargouri, Boutheina; Segura-Carretero, Antonio; Bouaziz, Mohamed

    2017-05-01

    Olea europaea L. organs such as leaves, stems and roots have been associated with numerous in vivo and in vitro biological activities and used for traditional medicinal purposes. However, tree wood is an untapped resource with little information about their chemical composition. That is why, the objective of this study is to increase the knowledge about phytochemicals from 'Chemlali' olive wood by means of mass spectrometry-based analyses. Its comparison with by-products derived from leaves was also studied. Hydromethanol extracts from wood and leaves with stems of 'Chemlali' olive cultivar were analysed using reversed-phase (RP) high-performance liquid chromatography (HPLC) coupled to two detection systems: diode-array detection (DAD) and quadrupole time-of-flight (QTOF) mass spectrometry (MS) in negative ion mode. Tandem MS experiments were performed to establish the chemical structure of olive phytochemicals. A total of 85 compounds were characterised in the studied olive parts and classified as: sugars (3), organic acids (5), one phenolic aldehyde, simple phenolic acids (6), simple phenylethanoids (5), flavonoids (14), coumarins (3), caffeoyl phenylethanoid derivatives (6), iridoids (5), secoiridoids (32), and lignans (5). To our knowledge, the major part of these metabolites was not previously reported in olive tree wood, and 10 olive chemical constituents were identified for the first time in the Oleaceae family. The results presented here demonstrated the usefulness of the methodology proposed, based on RP-HPLC-DAD-ESI-QTOF-MS and MS/MS, to develop an exhaustive metabolic profiling and to recover new biologically active compounds in olive wood with pharmacologic and cosmetic potential. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  16. On the use of leaf spectral indices to assess water status and photosynthetic limitations in Olea europaea L. during water-stress and recovery.

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    Pengsen Sun

    Full Text Available Diffusional limitations to photosynthesis, relative water content (RWC, pigment concentrations and their association with reflectance indices were studied in olive (Olea europaea saplings subjected to water-stress and re-watering. RWC decreased sharply as drought progressed. Following rewatering, RWC gradually increased to pre-stress values. Photosynthesis (A, stomatal conductance (gs, mesophyll conductance (gm, total conductance (gt, photochemical reflectance index (PRI, water index (WI and relative depth index (RDI closely followed RWC. In contrast, carotenoid concentration, the carotenoid to chlorophyll ratio, water content reflectance index (WCRI and structural independent pigment index (SIPI showed an opposite trend to that of RWC. Photosynthesis scaled linearly with leaf conductance to CO2; however, A measured under non-photorespiratory conditions (A1%O2 was approximately two times greater than A measured at 21% [O2], indicating that photorespiration likely increased in response to drought. A1%O2 also significantly correlated with leaf conductance parameters. These relationships were apparent in saturation type curves, indicating that under non-photorespiratory conditions, CO2 conductance was not the major limitations to A. PRI was significant correlated with RWC. PRI was also very sensitive to pigment concentrations and photosynthesis, and significantly tracked all CO2 conductance parameters. WI, RDI and WCRI were all significantly correlated with RWC, and most notably to leaf transpiration. Overall, PRI correlated more closely with carotenoid concentration than SIPI; whereas WI tracked leaf transpiration more effectively than RDI and WCRI. This study clearly demonstrates that PRI and WI can be used for the fast detection of physiological traits of olive trees subjected to water-stress.

  17. Assessing Animal Welfare Impacts in the Management of European Rabbits (Oryctolagus cuniculus), European Moles (Talpa europaea) and Carrion Crows (Corvus corone)

    Science.gov (United States)

    Baker, Sandra E.; Sharp, Trudy M.; Macdonald, David W.

    2016-01-01

    Human-wildlife conflict is a global issue. Attempts to manage this conflict impact upon wild animal welfare, an issue receiving little attention until relatively recently. Where human activities harm animal welfare these effects should be minimised where possible. However, little is known about the welfare impacts of different wildlife management interventions, and opinions on impacts vary widely. Welfare impacts therefore need to be assessed objectively. Our objectives were to: 1) establish whether an existing welfare assessment model could differentiate and rank the impacts of different wildlife management interventions (for decision-making purposes); 2) identify and evaluate any additional benefits of making formal welfare assessments; and 3) illustrate issues raised by application of the model. We applied the welfare assessment model to interventions commonly used with rabbits (Oryctolagus cuniculus), moles (Talpa europaea) and crows (Corvus corone) in the UK. The model ranked interventions for rabbits (least impact first: fencing, head shot, chest shot) and crows (shooting, scaring, live trapping with cervical dislocation). For moles, managing molehills and tunnels scored least impact. Both spring trapping, and live trapping followed by translocation, scored greater impacts, but these could not be compared directly as they scored on different axes of the model. Some rankings appeared counter-intuitive, highlighting the need for objective formal welfare assessments. As well as ranking the humaneness of interventions, the model highlighted future research needs and how Standard Operating Procedures might be improved. The model is a milestone in assessing wildlife management welfare impacts, but our research revealed some limitations of the model and we discuss likely challenges in resolving these. In future, the model might be developed to improve its utility, e.g. by refining the time-scales. It might also be used to reach consensus among stakeholders about

  18. Assessing Animal Welfare Impacts in the Management of European Rabbits (Oryctolagus cuniculus, European Moles (Talpa europaea and Carrion Crows (Corvus corone.

    Directory of Open Access Journals (Sweden)

    Sandra E Baker

    Full Text Available Human-wildlife conflict is a global issue. Attempts to manage this conflict impact upon wild animal welfare, an issue receiving little attention until relatively recently. Where human activities harm animal welfare these effects should be minimised where possible. However, little is known about the welfare impacts of different wildlife management interventions, and opinions on impacts vary widely. Welfare impacts therefore need to be assessed objectively. Our objectives were to: 1 establish whether an existing welfare assessment model could differentiate and rank the impacts of different wildlife management interventions (for decision-making purposes; 2 identify and evaluate any additional benefits of making formal welfare assessments; and 3 illustrate issues raised by application of the model. We applied the welfare assessment model to interventions commonly used with rabbits (Oryctolagus cuniculus, moles (Talpa europaea and crows (Corvus corone in the UK. The model ranked interventions for rabbits (least impact first: fencing, head shot, chest shot and crows (shooting, scaring, live trapping with cervical dislocation. For moles, managing molehills and tunnels scored least impact. Both spring trapping, and live trapping followed by translocation, scored greater impacts, but these could not be compared directly as they scored on different axes of the model. Some rankings appeared counter-intuitive, highlighting the need for objective formal welfare assessments. As well as ranking the humaneness of interventions, the model highlighted future research needs and how Standard Operating Procedures might be improved. The model is a milestone in assessing wildlife management welfare impacts, but our research revealed some limitations of the model and we discuss likely challenges in resolving these. In future, the model might be developed to improve its utility, e.g. by refining the time-scales. It might also be used to reach consensus among

  19. Neuroprotection by Combined Administration with Maslinic Acid, a Natural Product from Olea europaea, and MK-801 in the Cerebral Ischemia Model

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    Yisong Qian

    2016-08-01

    Full Text Available Glutamate-mediated excitotoxicity is a major cause of ischemic brain damage. MK-801 confers neuroprotection by attenuating the activation of the N-methyl-d-aspartate (NMDA receptor, but it failed in clinical use due to the short therapeutic window. Here we aim to investigate the effects of maslinic acid, a natural product from Olea europaea, on the therapeutic time window and dose range for the neuroprotection of MK-801. Rats were administered with maslinic acid intracerebroventricularly and cerebral ischemia was induced by middle cerebral artery occlusion (MCAO followed by reperfusion. MK-801 was administered at 1 h, 2 h, 3 h and 4 h after ischemia, respectively. The cerebral infarct volume was determined by 2,3,5-Triphenyltetrazolium chloride (TTC staining, neuronal damage was assessed by Haematoxylin Eosin (H&E staining, and the expression of glial glutamate transporters and glial fibrillary acidic protein (GFAP was evaluated by immunohistochemistry and Western blot post-ischemia. Results showed that the presence of maslinic acid extended the therapeutic time window for MK-801 from 1 h to 3 h. Co-treatment of maslinic acid and MK-801 at a subthreshold dosage obviously induced neuroprotection after ischemia. The combination of these two compounds improved the outcome in ischemic rats. Moreover, maslinic acid treatment promoted the expression of GLT-1 and GFAP post-ischemia. These data suggest that the synergistic effect of maslinic acid on neurological protection might be associated with the improvement of glial function, especially with the increased expression of GLT-1. The combination therapy of maslinic acid and MK-801 may prove to be a potential strategy for treating acute ischemic stroke.

  20. Differential Contribution of Endoplasmic Reticulum and Chloroplast ω-3 Fatty Acid Desaturase Genes to the Linolenic Acid Content of Olive (Olea europaea) Fruit.

    Science.gov (United States)

    Hernández, M Luisa; Sicardo, M Dolores; Martínez-Rivas, José M

    2016-01-01

    Linolenic acid is a polyunsaturated fatty acid present in plant lipids, which plays key roles in plant metabolism as a structural component of storage and membrane lipids, and as a precursor of signaling molecules. The synthesis of linolenic acid is catalyzed by two different ω-3 fatty acid desaturases, which correspond to microsomal- (FAD3) and chloroplast- (FAD7 and FAD8) localized enzymes. We have investigated the specific contribution of each enzyme to the linolenic acid content in olive fruit. With that aim, we isolated two different cDNA clones encoding two ω-3 fatty acid desaturases from olive (Olea europaea cv. Picual). Sequence analysis indicates that they code for microsomal (OepFAD3B) and chloroplast (OepFAD7-2) ω-3 fatty acid desaturase enzymes, different from the previously characterized OekFAD3A and OekFAD7-1 genes. Functional expression in yeast of the corresponding OepFAD3A and OepFAD3B cDNAs confirmed that they encode microsomal ω-3 fatty acid desaturases. The linolenic acid content and transcript levels of olive FAD3 and FAD7 genes were measured in different tissues of Picual and Arbequina cultivars, including mesocarp and seed during development and ripening of olive fruit. Gene expression and lipid analysis indicate that FAD3A is the gene mainly responsible for the linolenic acid present in the seed, while FAD7-1 and FAD7-2 contribute mostly to the linolenic acid present in the mesocarp and, therefore, in the olive oil. These results also indicate the relevance of lipid trafficking between the endoplasmic reticulum and chloroplast in determining the linolenic acid content of membrane and storage lipids in oil-accumulating photosynthetic tissues. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  1. The influence of light, temperature and feeding on the growth of the Coras cladocora caespitosa and Balanophyllia europaea; L'influenza di luce, temperatura e alimentazione sulla crescita dei coralli mediterranei Cladocora caespitosa e Balanophyllia europaea. Risultati preliminari di una sperimentazione in ambiente controllato

    Energy Technology Data Exchange (ETDEWEB)

    Rodolfo-Metalpa, R.; Abbate, M.; Peirano, A. [ENEA, Divisione Ambiente Globale e Mediterraneo, Centro Ricerche S. Teresa, La Spezia (Italy)

    2001-07-01

    In the course of the environmental studies, carried out by ENEA-CRAM Center of S. Teresa near La Spezia, research has been performed about bioconstructional organisms in the Mediterranean Sea. To understand how these organisms respond to environmental parameters an experiment has been carried out in aquaria. Specimens of the Mediterranean coral Cladocora caespitosa and Balanophyllia europaea has been maintained in 80 independent aquaria for four months. Growth rates, pigments concentration and asexual reproduction of the corals were compared in experimental procedures with controlled conditions of light, temperature and food. Environmental parameters have been set out to simulate natural (winter and summer) ambient in the Ligurian Sea. Heterotrophic and autotrophic abilities of the corals have been compared. Results show different growth rates between the two species but similar heterotrophic growth patterns. Summer temperature largely influences growth rates and asexual reproduction of the species while light influence is small. [Italian] Nell'ambito delle ricerche svolte dall'ENEA sullo studio degli organismi biocostruttori nell'ambiente marino, e' stata svolta una sperimentazione al fine di valutare l'influenza di alcuni parametri ambientali (luce, temperatura e alimentazione), impostati in modo da simulare la naturale stagionalita' (inverno ed estate), sulla crescita e sulla riproduzione asessuale dei coralli mediterranei Cladocora caespitosa e Balanophyllia europaea. Queste sperimentazioni sono state condotte, per un periodo di circa quattro mesi, in ottanta acquari indipendenti caratterizzati da differenti livelli di luce, temperatura e alimentazione. Le valutazioni degli incrementi di peso e della crescita lineare sono state eseguite utilizzando differenti metodiche note in letteratura. Soprattutto la tecnica del Peso Galleggiante (Buoyant Weight) si e' dimostrata molto sensibile ed efficace. La capacita' (eterotrofia

  2. Physiological Response of Common Glasswort (Salicornia europaea L. to Potassium Nano-Particles Grown in Saline Soils around the Lake Urmia

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    Alireza Pirzad

    2016-06-01

    Full Text Available To evaluate the effects of spraying potassium nano-particles on the osmolytes, photosynthetic pigments, total carotenoids and nutrients of aerial parts of common glasswort (Salicornia europaea L., a factorial experiment based on randomized complete block design with three replications was conducted at the marginal lands of Lake Urmia in 2012. The treatments consisted of application of potassium nano-particle concentrations at five levels (0, 1, 2, 3 and 4 g/l of K nano-particles applied, once, twice and three times. Results of analysis of variance (ANOVA showed that there were significant interaction between the levels and concentrations of potassium nano-particles sprayings on aerial parts with respect to their contents proline, total soluble carbohydrates, total chlorophyll, chlorophyll a and b, total carotenoids (xanthophyll and carotene and nutrients (nitrogen, phosphorus, potassium, calcium and sodium. The highest levels of proline (1.84 mg/g dry weight at one time spraying 4 g/l of K, total soluble carbohydrates (66.9 mg/g dry weight at three times spraying 4 g/l, total chlorophyll (26.23 mg/g fresh weight and chlorophyll b (22.85 mg/g fresh weight at two times of water spraying, and chlorophyll a (9.93 mg/g fresh weight at three times of 4g/l of potassium nano-particles sprayings were obtained. The highest nitrogen (0.95 % of aerial parts and phosphorus (2.99 g/kg dry weight of aerial parts contents were obtained from three times water spraying. However, the highest amounts of aerial plant part of potassium (65.08 g/kg dry weight and sodium (403 g/kg dry weight belonged to the two times, and calcium (29.23 g/kg dry weight to the three times spraying of 4 g/l nano-potassium. Despite of the high concentration of osmolytes by potassium spraying, the nutrient accumulations levels were not significantly different from each other.

  3. Validation of reference genes for gene expression analysis in olive (Olea europaea) mesocarp tissue by quantitative real-time RT-PCR.

    Science.gov (United States)

    Ray, Debashree L; Johnson, Joshua C

    2014-05-18

    Gene expression analysis using quantitative reverse transcription PCR (qRT-PCR) is a robust method wherein the expression levels of target genes are normalised using internal control genes, known as reference genes, to derive changes in gene expression levels. Although reference genes have recently been suggested for olive tissues, combined/independent analysis on different cultivars has not yet been tested. Therefore, an assessment of reference genes was required to validate the recent findings and select stably expressed genes across different olive cultivars. A total of eight candidate reference genes [glyceraldehyde 3-phosphate dehydrogenase (GAPDH), serine/threonine-protein phosphatase catalytic subunit (PP2A), elongation factor 1 alpha (EF1-alpha), polyubiquitin (OUB2), aquaporin tonoplast intrinsic protein (TIP2), tubulin alpha (TUBA), 60S ribosomal protein L18-3 (60S RBP L18-3) and polypyrimidine tract-binding protein homolog 3 (PTB)] were chosen based on their stability in olive tissues as well as in other plants. Expression stability was examined by qRT-PCR across 12 biological samples, representing mesocarp tissues at various developmental stages in three different olive cultivars, Barnea, Frantoio and Picual, independently and together during the 2009 season with two software programs, GeNorm and BestKeeper. Both software packages identified GAPDH, EF1-alpha and PP2A as the three most stable reference genes across the three cultivars and in the cultivar, Barnea. GAPDH, EF1-alpha and 60S RBP L18-3 were found to be most stable reference genes in the cultivar Frantoio while 60S RBP L18-3, OUB2 and PP2A were found to be most stable reference genes in the cultivar Picual. The analyses of expression stability of reference genes using qRT-PCR revealed that GAPDH, EF1-alpha, PP2A, 60S RBP L18-3 and OUB2 are suitable reference genes for expression analysis in developing Olea europaea mesocarp tissues, displaying the highest level of expression stability across

  4. Quantificação dos níveis endógenos de auxinas e da actividade enzimática das polifenoloxidases em oliveira (Olea europaea L. Quantification of endogenous auxin levels and polyphenoloxidase enzymatic activity in olive (Olea europaea L.

    Directory of Open Access Journals (Sweden)

    C. Serra

    2007-01-01

    Full Text Available A actividade enzimática de polifenoloxidases foi avaliada em folhas e na zona apical, média e basal de ramos de duas cultivares de oliveira (Olea europaea L., comuns no Alentejo (‘Galega vulgar’ e ‘Cobrançosa’, mostrando que a actividade enzimática nas folhas foi muito superior à encontrada em tecidos de ramos do ano. Maior actividade enzimática foi também detectada na variedade ‘Cobrançosa’ versus ‘Galega vulgar’. As condições óptimas para a determinação da actividade enzimática foram: pH= 5.5 e T= 40 ºC, com 20 mM de 4-metilcatecol em tampão acetato. Nestas condições o KM determinado foi: 2,60 e 3,48 mM com o método de Michaelis-Menten e Lineweaver-Burk, respectivamente. A melhor recuperação das auxinas AIA (ácido indol-3-acético e AIB (ácido indolbutírico em material vegetal foi conseguida através da extracção das amostras com acetona. A separação, identificação e quantificação do AIA e AIB em padrões, material vegetal dopado (tecidos de oliveira dopados com uma concentração conhecida de padrão e não dopado, foi efectuada por técnicas cromatográficas (HPLC-DAD e LCMS, mostrando os resultados taxas de recuperação superiores a 40% para o AIA e 60% para o AIB.The poliphenoloxidase enzymatic activity was evaluated in two olive cultivars (Olea europaea L. widespread in Alentejo (‘Galega vulgar and ‘Cobrançosa. Leaves and apical, medium and basal regions of the year stems were used as sample material. When compared with the different regions of the year stem, the results have shown that enzymatic activity was significantly higher in the leaves of both cultivars. Between cultivars, it was observed that ‘Cobrançosa’ presented higher enzymatic activity than ‘Galega vulgar’. The pH at 5.5 and 40 ºC temperature, using 20 mM of 4methylcatecol in acetate buffer were the optimized conditions for the enzymatic analysis. Under these conditions, the measured KM was 2,60 and 3,48 m

  5. Preliminary Evaluation of 29 Olive (Olea europaea L. Cultivars for Production and Alternate Bearing, in the Huasco Valley, Northern Chile Evaluación Preliminar de la Produción y Añerismo en 29 Variedades de Olivo (Olea europaea L. en el Valle del Huasco, Norte de Chile

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    Francisco Tapia C

    2009-09-01

    Full Text Available There is increasing interest in the development of intensively managed olive orchards (Olea europaea L. in northern Chile. The selection of specific varieties that perform well on a particular site is considered crucial to maximizing productivity. The present study was undertaken to evaluate the productive performance of 29 varieties of olive in the Huasco Valley (28°34' S, 70°47' W, Northern Chile.The traits evaluated were: mean olive production per tree considering a longitudinal (PML analysis over a period of five years, 2003 to 2007, total olive production in the same period (PA03-07 and alternate bearing index (ABI. The effect of variety was highly significant (p En el norte de Chile existe un creciente interés en el desarrollo de huertos de olivo (Olea europaea L. manejados intensivamente. La selección de variedades específicas que han respondido bien en un sitio en particular es considerada clave para la maximización de la productividad. El presente estudio fue realizado para evaluar el desempeño de algunas características agronómicas en 29 variedades de olivo, en el Valle del Huasco (28°34' S, 70°47' O, norte de Chile. Las características analizadas correspondieron a producción de frutos promedio por árbol (PML en un análisis longitudinal durante un período de 5 años, 2003 a 2007, producción acumulada del mismo período (PA03-07 y el índice de alternancia de producción (ABI. El efecto debido a la variedad fue altamente significativo (p < 0,01 para las tres características. El ABI fue moderado (0,52, con una PML de 37,37 kg árbol-1 y PA03-07 de 186 kg árbol-1. Correlaciones de Spearman entre los ranking de cada característica fueron positivas y significativamente diferentes de cero (p < 0,05. ‘Leccino’ tuvo la mejor respuesta considerando únicamente la producción de frutos. ‘Arbequina’, ‘Picholine’, ‘Manzanilla Racimo’, ‘Picual’, ‘Manzanilla de Sevilla’, ‘Frantoio’ y

  6. Influência do número de nós em estacas semilenhosas de oliveira (Olea europaea L. no enraizamento sob câmara de nebulização Influence the number of nodes on semi-woody cuttings of olive tree (Olea europaea L. on the rooting in misty room

    Directory of Open Access Journals (Sweden)

    Adelson Francisco de Oliveira

    2003-04-01

    Full Text Available Com o objetivo de avaliar o enraizamento de estacas semilenhosas de oliveira (Olea europaea L. com diferentes números de nós, foi conduzido no Centro de Investigación y Formación Agraria - CIFA "Alameda del Obispo" de Córdoba - Espanha, experimento sob condições de câmara de nebulização intermitente. As estacas foram tratadas com ácido indolbutítico (AIB na concentração de 3.000 mg.L-1, antes da instalação do ensaio, submergindo durante cinco segundos as suas bases, aproximadamente 2,5 centímetros, em solução contendo o produto. Utilizaram-se estacas medianas, que foram coletadas de plantas em desenvolvimento vegetativo contínuo. O delineamento experimental utilizado foi o de blocos casualizados em fatorial 2 x 5, sendo respectivamente duas variedades, Picual e Arbequina, e cinco tamanhos de estacas: dois nós com duas folhas, três nós com duas folhas, três nós com quatro folhas, quatro nós com quatro folhas e cinco nós com quatro folhas. Utilizaram-se quatro repetições com parcelas experimentais constituídas por trinta estacas plantadas em substrato de perlita, em mesas suspensas, com aquecimento controlado. Avaliaram-se aos 75 dias porcentagem de estacas enraizadas, mortas e número e comprimento médio de raízes. Observou-se que, entre estacas de quatro nós e cinco nós, com quatro folhas, não houve diferença nos parâmetros considerados; estacas com três nós, com duas e quatro folhas também não diferenciaram. Estacas com dois nós e duas folhas, de ambas as variedades, apresentaram maior mortalidade.With the objective of assessing the rooting efficiency of semi-woody cuttings of olive tree (Olea europaea L., with different nodes, an experiment under intermittent misty room conditions and with the use of IBA at the concentration of 3000 mg L-1 was run at the Centro de Investigación y Formación Agraria 'Alameda del Obispo' in Cordoba, Spain. The cuttings were treated before the establishment of the trial

  7. Separation and identification of phenolic compounds of extra virgin olive oil from Olea europaea L. by HPLC-DAD-SPE-NMR/MS. Identification of a new diastereoisomer of the aldehydic form of oleuropein aglycone.

    Science.gov (United States)

    Pérez-Trujillo, Míriam; Gómez-Caravaca, Ana María; Segura-Carretero, Antonio; Fernández-Gutiérrez, Alberto; Parella, Teodor

    2010-08-25

    The phenolic fraction of a monovarietal extra virgin olive oil (EVOO) from Olea europaea L. var. Cornezuelo was studied by the hyphenated HPLC-DAD-SPE-NMR/MS techniques. This survey led to the identification of 25 main compounds. One was identified as a new diastereoisomer of the aldehydic form of oleuropein aglycone (AOA) and characterized by 1D and 2D NMR techniques. The relative configuration of this new AOA was determined as 5R*,8S*,9S* on the basis of the results obtained from the combination of NOE experiments and Monte Carlo conformational search calculations. Assuming, as for the described diastereoisomers, that the new AOA comes from the natural oleuropein aglycone (OA), the absolute configuration was proposed as 5S,8R,9R.

  8. Oxygen Distribution and Potential Ammonia Oxidation in Floating, Liquid Manure Crusts

    DEFF Research Database (Denmark)

    Nielsen, Daniel Aagren; Nielsen, Lars Peter; Schramm, Andreas

    2010-01-01

     availability. In old natural crusts total potential NH3 oxidation rates were similar to reported fluxes of NH3 from slurry without surface crust. These results indicate that old, natural surface crusts may develop into a porous matrix with high O2 availability that harbors an active population of aerobic...

  9. Organic nitrogen-driven stimulation of arbuscular mycorrhizal fungal hyphae correlates with abundance of ammonia oxidizers

    Directory of Open Access Journals (Sweden)

    Petra eBukovská

    2016-05-01

    Full Text Available Large fraction of mineral nutrients in natural soil environments is recycled from complex and heterogeneously distributed organic sources. These sources are explored by both roots and associated mycorrhizal fungi. However, the mechanisms behind the responses of arbuscular mycorrhizal (AM hyphal networks to soil organic patches of different qualities remain little understood. Therefore, we conducted a multiple-choice experiment examining hyphal responses to different soil patches within the root-free zone by two AM fungal species (Rhizophagus irregularis and Claroideoglomus claroideum associated with Medicago truncatula, a legume forming nitrogen-fixing root nodules. Hyphal colonization of the patches was assessed microscopically and by quantitative real-time PCR (qPCR using AM taxon-specific markers, and the prokaryotic and fungal communities in the patches (pooled per organic amendment treatment were profiled by 454-amplicon sequencing. Specific qPCR markers were then designed and used to quantify the abundance of prokaryotic taxa showing the strongest correlation with the pattern of AM hyphal proliferation in the organic patches as per the 454-sequencing. The hyphal density of both AM fungi increased due to nitrogen (N-containing organic amendments (i.e., chitin, DNA, albumin, and clover biomass, while no responses as compared to the non-amended soil patch were recorded for cellulose, phytate, or inorganic phosphate amendments. Abundances of several prokaryotes, including Nitrosospira sp. (an ammonium oxidizer and an unknown prokaryote with affiliation to Acanthamoeba endosymbiont, which were frequently recorded in the 454-sequencing profiles, correlated positively with the hyphal responses of R. irregularis to the soil amendments. Strong correlation between abundance of these two prokaryotes and the hyphal responses to organic soil amendments by both AM fungi was then confirmed by qPCR analyses using all individual replicate patch samples. Further research is warranted to ascertain the causality of these correlations and particularly which direct roles (if any do these prokaryotes play in the observed AM hyphal responses to organic N amendment, organic N utilization by the AM fungus and its (N-unlimited host plant. Further, possible trophic dependencies between the different players in the AM hyphosphere needs to be elucidated upon decomposing the organic N sources.

  10. Traveling interface modulations and anisotropic front propagation in ammonia oxidation over Rh(110)

    Energy Technology Data Exchange (ETDEWEB)

    Rafti, Matías [Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Fac. Cs. Exactas, Universidad Nacional de La Plata, 64 y Diag. 113 (1900), La Plata (Argentina); Institut für Physikalische Chemie und Elektrochemie, Leibniz-Universität Hannover, Callinstr. 3-3a, D-30167 Hannover (Germany); Borkenhagen, Benjamin; Lilienkamp, Gerhard [Institut für Energieforschung und Physikalische Technologien, Technische Universität Clausthal, Leibnizstr. 4, 38678 Clausthal-Zellerfeld (Germany); Lovis, Florian; Smolinsky, Tim; Imbihl, Ronald, E-mail: imbihl@pci.uni-hannvover.de [Institut für Physikalische Chemie und Elektrochemie, Leibniz-Universität Hannover, Callinstr. 3-3a, D-30167 Hannover (Germany)

    2015-11-14

    The bistable NH{sub 3} + O{sub 2} reaction over a Rh(110) surface was explored in the pressure range 10{sup −6}–10{sup −3} mbar and in the temperature range 300–900 K using photoemission electron microscopy and low energy electron microscopy as spatially resolving methods. We observed a history dependent anisotropy in front propagation, traveling interface modulations, transitions with secondary reaction fronts, and stationary island structures.

  11. Nitrogen removal performance of anaerobic ammonia oxidation (ANAMMOX) in presence of organic matter.

    Science.gov (United States)

    Zhu, Weiqiang; Zhang, Peiyu; Yu, Deshuang; Dong, Huiyu; Li, Jin

    2017-06-01

    A sequencing batch reactor (SBR) was used to test the nitrogen removal performance of anaerobic ammonium oxidation (ANAMMOX) in presence of organic matter. Mesophilic operation (30 ± 0.5 °C) was performed with influent pH 7.5. The results showed, independent of organic matter species, ANAMMOX reaction was promoted when COD was lower than 80 mg/L. However, specific ANAMMOX activity decreased with increasing organic matter content. Ammonium removal efficiency decreased to 80% when COD of sodium succinate, sodium potassium tartrate, peptone and lactose were 192.5, 210, 225 and 325 mg/L, respectively. The stoichiometry ratio resulting from different OM differed largely and R 1 could be as an indicator for OM inhibition. When COD concentration was 240 mg/L, the loss of SAA resulting from lactose, peptone, sodium potassium tartrate and sodium succinate were 28, 36, 50 and 55%, respectively. Sodium succinate had the highest inhibitory effect on SAA. When ANAMMOX process was used to treat wastewater containing OM, the modified Logistic model could be employed to predict the NRE max .

  12. Metagenomic analysis of ammonia oxidizing archaea affiliated with the soil group

    Directory of Open Access Journals (Sweden)

    Christa eSchleper

    2012-06-01

    Full Text Available Ammonia-oxidising archaea (AOA have recently been recognized as a significant component of many microbial communities and represent one of the most abundant prokaryotic groups in the biosphere. However, only few AOA have been successfully cultivated so far and information on the physiology and genomic content remains scarce. We have performed a metagenomic analysis to extend the knowledge of the AOA affiliated with groupI.1b that is widespread in terrestrial habitats and of which no genome sequences has been described yet. A fosmid library was generated from samples of a radioactive thermal cave (46°C in the Austrian Central Alps in which AOA had been found as a major part of the microbial community. Out of sixteen fosmids that possessed either an amoA or 16S rRNA gene affiliating with AOA, five were fully sequenced, four of which grouped with the soil/I.1b (Nitrososphaera- lineage and one with marine/I.1a (Nitrosopumilus- lineage. Phylogenetic analyses of amoBC and an associated conserved gene were congruent with earlier analyses based on amoA and 16S rRNA genes and supported the separation of the soil and marine group. Several putative genes that did not have homologues in currently available marine thaumarchaeota genomes indicated that AOA of the soil group contain specific genes that are distinct from their marine relatives. Potential cis-regulatory elements around conserved promoter motifs found upstream of the amo genes in sequenced (meta- genomes differed in marine and soil group AOA. On one fosmid, a group of genes including amoA and amoB were flanked by identical transposable insertion sequences, indicating that amoAB could potentially be co-mobilized in the form of a composite transposon. This might be one of the mechanisms that caused the greater variation in gene order compared to genomes in the marine counterparts. Our findings highlight the genetic diversity within the two major and widespread lineages of thaumarchaeota.

  13. Intact polar lipids of ammonia-oxidizing Archaea: structural diversity application in molecular ecology

    NARCIS (Netherlands)

    Pitcher, A.M.

    2011-01-01

    Non-extremophilic Crenarchaeota are ubiquitous, and comprise a major component of the microbial assemblages in many modern-day systems. Several studies have analyzed glycerol dialkyl glycerol tetraether (GDGT) membrane lipids synthesized by non-extremophilic Crenarchaeota to interpret the presence,

  14. Organic Nitrogen-Driven Stimulation of Arbuscular Mycorrhizal Fungal Hyphae Correlates with Abundance of Ammonia Oxidizers

    Czech Academy of Sciences Publication Activity Database

    Bukovská, Petra; Gryndler, Milan; Gryndlerová, Hana; Püschel, David; Jansa, Jan

    2016-01-01

    Roč. 4, MAY 12 (2016), s. 711 ISSN 1664-302X R&D Projects: GA ČR GAP504/12/1665; GA MŠk(CZ) LK11224 Institutional support: RVO:61388971 Keywords : soil heterogeneity * organic amendments * arbuscular mycorrhizal (AM) fungi Subject RIV: EE - Microbiology, Virology Impact factor: 4.076, year: 2016

  15. Ammonia Oxidation and Nitrite Reduction in the Verrucomicrobial Methanotroph Methylacidiphilum fumariolicum SolV

    Directory of Open Access Journals (Sweden)

    Sepehr S. Mohammadi

    2017-09-01

    Full Text Available The Solfatara volcano near Naples (Italy, the origin of the recently discovered verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV was shown to contain ammonium (NH4+ at concentrations ranging from 1 to 28 mM. Ammonia (NH3 can be converted to toxic hydroxylamine (NH2OH by the particulate methane monooxygenase (pMMO, the first enzyme of the methane (CH4 oxidation pathway. Methanotrophs rapidly detoxify the intermediate NH2OH. Here, we show that strain SolV performs ammonium oxidation to nitrite at a rate of 48.2 nmol NO2-.h−1.mg DW−1 under O2 limitation in a continuous culture grown on hydrogen (H2 as an electron donor. In addition, strain SolV carries out nitrite reduction at a rate of 74.4 nmol NO2-.h−1.mg DW−1 under anoxic condition at pH 5–6. This range of pH was selected to minimize the chemical conversion of nitrite (NO2- potentially occurring at more acidic pH values. Furthermore, at pH 6, we showed that the affinity constants (Ks of the cells for NH3 vary from 5 to 270 μM in the batch incubations with 0.5–8% (v/v CH4, respectively. Detailed kinetic analysis showed competitive substrate inhibition between CH4 and NH3. Using transcriptome analysis, we showed up-regulation of the gene encoding hydroxylamine dehydrogenase (haoA cells grown on H2/NH4+ compared to the cells grown on CH4/NO3- which do not have to cope with reactive N-compounds. The denitrifying genes nirk and norC showed high expression in H2/NH4+ and CH4/NO3- grown cells compared to cells growing at μmax (with no limitation while the norB gene showed downregulation in CH4/NO3- grown cells. These cells showed a strong upregulation of the genes in nitrate/nitrite assimilation. Our results demonstrate that strain SolV can perform ammonium oxidation producing nitrite. At high concentrations of ammonium this may results in toxic effects. However, at low oxygen concentrations strain SolV is able to reduce nitrite to N2O to cope with this toxicity.

  16. Autotrophic ammonia-oxidizing bacteria contribute minimally to nitrification in a nitrogen-impacted forested ecosystem

    Science.gov (United States)

    Fiona L. Jordan; J. Jason L. Cantera; Mark E. Fenn; Lisa Y. Stein

    2005-01-01

    Deposition rates of atmospheric nitrogenous pollutants to forests in the San Bernardino Mountains range east of Los Angeles, California, are the highest reported in North America. Acidic soils from the west end of the range are N-saturated and have elevated rates of N-mineralization, nitrification, and nitrate leaching. We assessed the impact of this heavy nitrogen...

  17. Comammox Nitrospira are abundant ammonia oxidizers in diverse groundwater‐fed rapid sand filter communities

    DEFF Research Database (Denmark)

    Fowler, Susan Jane; Palomo, Alejandro; Dechesne, Arnaud

    2017-01-01

    The recent discovery of completely nitrifying Nitrospira demands a re‐examination of nitrifying environments to evaluate their contribution to nitrogen cycling. To approach this challenge, tools are needed to detect and quantify comammox Nitrospira. We present primers for the simultaneous quantif...

  18. The Complete Genome Sequence of the Marine, Chemolithoautotrophic, Ammonia-Oxidizing Bacterium Nitrosococcus oceani ATCC19707

    Energy Technology Data Exchange (ETDEWEB)

    Klotz, M G; Arp, D J; Chain, P S; El-Sheikh, A F; Hauser, L J; Hommes, N G; Larimer, F W; Malfatti, S A; Norton, J M; Poret-Peterson, A T; Vergez, L M; Ward, B B

    2006-08-03

    The Gammaproteobacterium, Nitrosococcus oceani (ATCC 19707), is a Gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. Sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; 50.4% G+C) and a plasmid (40,420 bp) that contain 3052 and 41 candidate protein-encoding genes, respectively. The genes encoding proteins necessary for the function of known modes of lithotrophy and autotrophy were identified. In contrast to betaproteobacterial nitrifier genomes, the N. oceani genome contained two complete rrn operons. In contrast, only one copy of the genes needed to synthesize functional ammonia monooxygenase and hydroxylamine oxidoreductase, as well as the proteins that relay the extracted electrons to a terminal electron acceptor were identified. The N. oceani genome contained genes for 13 complete two-component systems. The genome also contained all the genes needed to reconstruct complete central pathways, the tricarboxylic acid cycle and the Embden-Meyerhof-Parnass and pentose phosphate pathways. The N. oceani genome contains the genes required to store and utilize energy from glycogen inclusion bodies and sucrose. Polyphosphate and pyrophosphate appear to be integrated in this bacterium's energy metabolism, stress tolerance and the ability to assimilate carbon via gluconeogenesis. One set of genes for type I RuBisCO was identified, while genes necessary for methanotrophy and for carboxysome formation were not identified. The N. oceani genome contains two copies each of the genes or operons necessary to assemble functional complexes I and IV as well as ATP synthase (one H{sup +}-dependent F{sub 0}F{sub 1}-type, one Na{sup +}-dependent V-type).

  19. QPCR quantification of ammonia oxidizing bacteria: What should the target be?

    DEFF Research Database (Denmark)

    Musovic, Sanin; Palomo, Alejandro; Diwan, Vaibhav

    be carried out by targeting either the 16S rRNA gene or amoA, for which standard primer sets are widely used. Using these two approaches to quantify AOB abundance across three Danish rapid sand filters (RSFs) revealed a significant discrepancy: in two RSFs, the amoA-based qPCR consistently yielded estimate...

  20. Influence of Biological Macromolecules and Aquatic Chemistries on the Inhibition of Nitrifying Bacteria by Silver Nanoparticles

    Science.gov (United States)

    Radniecki, T. S.; Anderson, J. W.; Schneider, M. C.; Stankus, D. P.; Nason, J. A.; Semprini, L.

    2010-12-01

    The use of silver nanoparticles (Ag-NP) as a broad spectrum biocide in a wide range of consumer goods has grown exponentially since 2006 (1), which may result in an increased release of Ag-NP into wastewater streams and ultimately the receiving bodies of water. Ammonia oxidizing bacteria (AOB) play a critical role in the global nitrogen cycle through the oxidation of ammonia (NH3) to nitrite (NO2-) and are widely considered to be the most sensitive microbial fauna in the environment being readily inhibited by contaminants, including Ag-NP (2). This research used physiological techniques in combination with physical/chemical assays to characterize the inhibition of Nitrosomonas europaea, the model AOB, by silver ions (Ag+), 3-5 nm Ag-NP, 20 nm Ag-NP and 80 nm Ag-NP under a variety of aqueous chemistries. In addition, the stability of Ag-NP suspensions was examined under a variety of aqueous chemistries including in the presences of divalent cations, chloride anions, natural organic matter (NOM), proteins (BSA) and lipopolysaccharides (alginate). Using the stable Ag-NP/test media suspensions, N. europaea was found to be extremely sensitive to Ag+, 3-5 nm Ag-NP, 20 nm Ag-NP and 80 nm Ag-NP with concentrations of 0.1, 0.12, 0.5 and 1.5 ppm, respectively, resulting in a 50% decrease in nitrification rates. The inhibition was correlated with the amount of Ag+ released into solution. It is suspected that the inhibition observed from Ag-NP exposure is caused by the liberated Ag+. The aquatic chemistry of the test media was found to have a profound influence on the stability of Ag-NP suspensions. The presence of Ag ligands (e.g. EDTA and Cl-) reduced toxicity of Ag-NP through the formation of Ag-ligand complexes with the liberated Ag+. The presence of divalent cations (e.g. Ca2+ or Mg2+) resulted in the rapid aggregation of Ag-NP leading to a decrease in Ag+ liberation and thus a decrease in N. europaea inhibition. The presence of 5 ppm NOM resulted in a highly stable Ag

  1. Fauna Europaea: Mollusca – Bivalvia

    Directory of Open Access Journals (Sweden)

    Rafael Araujo

    2015-07-01

    European freshwater bivalves belong to the Orders Unionoida and Cardiida. All the European unionoids are included in the superfamily Unionoidea, the freshwater mussels or naiads. The European cardiids belong to the following three superfamilies: Cardioidea, Cyrenoidea and Dreissenoidea. Among the Unionoidea there are the most imperilled animal groups on the planet while the Cardioidea includes the cosmopolitan genus Pisidium, the Cyrenoidea the Asiatic clam (Corbicula fluminea and the Dreissenoidea the famous invasive zebra mussel (Dreissena polymorpha. Basic information is summarized on their taxonomy and biology. Tabulations include a complete list of the current estimated families, genera and species.

  2. Efecto vasodilatador e inhibidor de vasoconstricción del extracto hidroalcohólico de hojas de Olea europaea (olivo sobre anillos aórticos de ratas

    Directory of Open Access Journals (Sweden)

    Job Nexar-QH

    2013-10-01

    Full Text Available Objetivos: Evaluar el efecto vasodilatador, la inhibición de la vasoconstricción, así como el mecanismo responsable, del extracto hidroalcohólico de hojas de Olea europaea (olivo, sobre anillos aórticos en ratas. Diseño: Experimental. Lugar: Centro de Investigación y Desarrollo Científico, Facultad de Medicina, Universidad Nacional de San Agustín, Arequipa, Perú. Material biológico: Hojas de Olea europea y anillos aórticos de Rattus norvegicus, variedad albina swiss. Intervenciones: Se obtuvo un extracto hidroalcohólico de las hojas de Olea europaea. Se usó anillos aórticos de rata en cámara de órganos aislados y se registró la actividad vasomotora con un transductor de tensión isométrica. Se produjo contracción basal máxima con CaCl2 6 mM y se determinó el efecto vasodilatador con dosis de 25, 50 y 100 mg/mL de extracto hidroalcohólico de las hojas de Olea europaea. Se usó 1H-[1,2,4] oxadiazolo [4,3 alquinoxalin-1-one] (ODQ y nifedipino para determinar el mecanismo de acción. Se comparó la inhibición de la vasoconstricción tras la incubación durante 30 minutos con extracto 100 mg/mL y con captopril 10 µM. Principales medidas de resultados: Porcentaje de vasodilatación y de vasoconstricción. Resultados: Se obtuvo una vasodilatación de 7,20 ± 1,49%, 9,84 ± 1,42% y 12,31 ± 1,16% para las dosis de 25, 50 y 100 mg/mL, respectivamente, siendo significativa con la dosis de 100 mg/mL. La vasodilatación se incrementó tras la administración de ODQ 100 mM. La vasodilatación se inhibió tras la incubación con ODQ 100 mM más nifedipino 5 µM. No se encontró diferencia significativa entre la inhibición de la vasoconstricción con captopril 10µM y extracto a 100 mg/mL. Conclusiones: El extracto hidroalcohólico de hojas de Olea europea, a una dosis de 100 mg/mL, tiene efecto vasodilatador sobre anillos aórticos de ratas, mediado por el bloqueo de canales de calcio; además, posee efecto inhibidor de la

  3. Essais de prolifération et d'enracinement de matériel issu de rajeunissement par bouturage d'oliviers adultes (Olea europaea L. et de germination in vitro : effets de cytokinine et d'auxines

    Directory of Open Access Journals (Sweden)

    Walali Loudiyi D

    2005-01-01

    Full Text Available Proliferation and rooting of juvenile and adult olive explants (Olea europaea L.: effects of cytokinin and auxins. The micropropagation trials conducted concerned juvenile and adult material from the ‘Moroccan Picholine’ olive cultivar. Zeatin, added to the proliferation medium, was tested at 0, 1, 5, 10 et 20 mg/l. Root induction was performed on media contaning IAA, IBA or NAA tested at 0, 0.5, 1, 2 et 4 mg/l. A significant (P<0.001 interaction exists between the explant type and the cytokinine concentration on one hand and the type and concentration of auxin on the other hand. The highest bud sprouting and shoot development were obtained on medium supplemented with 5 mg/l zeatin. For economical reasons, satisfying results can be obtained with only 1 mg/l. Rooting of microcuttings reached 100% when NAA, which proved to be the best auxin for root induction, was used at 1 mg/l. No rooting was observed in the case of adult plant material. Further investigations are being undertaken to improve the reactivity of this recalcitrant type of material.

  4. Twelve-month consumption of a polyphenol extract from olive (Olea europaea) in a double blind, randomized trial increases serum total osteocalcin levels and improves serum lipid profiles in postmenopausal women with osteopenia.

    Science.gov (United States)

    Filip, R; Possemiers, S; Heyerick, A; Pinheiro, I; Raszewski, G; Davicco, M-J; Coxam, V

    2015-01-01

    Osteoporosis is a skeletal disorder characterized by impaired bone turnover and compromised bone strength, thereby predisposing to increased risk of fracture. Preclinical research has shown that compounds produced by the olive tree (Olea europaea), may protect from bone loss, by increasing osteoblast activity at the expense of adipocyte formation. The aim of this exploratory study was to obtain a first insight on the effect of intake of an olive extract on bone turnover in postmenopausal women with decreased bone mass (osteopenia). For that, a double blind, placebo-controlled study was performed in which participants were randomly allocated to either treatment or placebo groups. 64 osteopenic patients, with a mean bone mineral density (BMD) T-score between -1.5 and -2.5 in the lumbar spine (L2-L4) were included in the study. PARTICIPANTS received for 12 months daily either 250 mg/day of olive extract and 1000 mg Ca (treatment) or 1000 mg Ca alone (placebo). Primary endpoints consisted of evaluation of bone turnover markers. Secondary endpoints included BMD measurements and blood lipid profiles. After 12 months, the levels of the pro-osteoblastic marker osteocalcin were found to significantly increase in the treatment group as compared to placebo. Simultaneously, BMD decreased in the placebo group, while remaining stable in the treatment group. In addition, improved lipid profiles were observed, with significant decrease in total- and LDL-cholesterol in the treatment group. This exploratory study supports preclinical observations and warrants further research by showing that a specific olive polyphenol extract (Bonolive®) affects serum osteocalcin levels and may stabilize lumbar spine BMD. Moreover, the improved blood lipid profiles suggest additional health benefits associated to the intake of the olive polyphenol extract.

  5. Evidence of novel plant-species specific ammonia oxidizing bacterial clades in acidic South African fynbos soils

    CSIR Research Space (South Africa)

    Ramond, JB

    2015-02-01

    Full Text Available identified in a wide range of natural (e.g. soils, sediments, estuarine, and freshwaters) and man created or impacted habitats (e.g. wastewater treatment plants and agricultural soils). However, little is known on the plant-species association of AOBs...

  6. Fluctuations in ammonia oxidizing communities across agricultural soils are driven by soil structure and pH

    NARCIS (Netherlands)

    de Cassia Pereira e Silva, M.; Poly, F.; Guillaumaud, N.; van Elsas, J.D.; Falcao Salles, J.

    2012-01-01

    The milieu in soil in which microorganisms dwell is never constant. Conditions such as temperature, water availability, pH and nutrients frequently change, impacting the overall functioning of the soil system. To understand the effects of such factors on soil functioning, proxies (indicators) of

  7. Utilization of organic nitrogen by arbuscular mycorrhizal fungi-is there a specific role for protists and ammonia oxidizers?

    Czech Academy of Sciences Publication Activity Database

    Bukovská, Petra; Bonkowski, M.; Konvalinková, Tereza; Beskid, Olena; Hujslová, Martina; Püschel, David; Řezáčová, Veronika; Gutierrez-Nunez, M.S.; Gryndler, Milan; Jansa, Jan

    2018-01-01

    Roč. 28, č. 3 (2018), s. 269-283 ISSN 0940-6360 R&D Projects: GA ČR(CZ) GA18-04892S; GA MŠk(CZ) LK11224 Institutional support: RVO:61388971 Keywords : N-15-labeling * Metatranscriptomics * Organic nitrogen (N) Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 3.047, year: 2016

  8. Year-round metagenomes reveal remarkably stable microbial communities in agricultural soils and novel ammonia oxidizers responding to fertilization

    Science.gov (United States)

    Insight to what underlies the seasonal dynamics of indigenous soil microbial communities in agricultural soils, especially after major activities such as nitrogen fertilization, remain elusive. More detailed understanding of population dynamics will have important implications for modeling efforts a...

  9. Influence of oxygen partial pressure and salinity on the community composition of ammonia-oxidizing bacteria in the Schelde estuary

    NARCIS (Netherlands)

    Bollmann, A.; Laanbroek, H.J.

    2002-01-01

    The influence of environmental factors on the community structure of ammoniaoxidizing bacteria (AOB) was investigated in the Schelde estuary. Simultaneously with the increase of oxygen and salinity, a shift of the dominant AOB was observed. Molecular analysis based on 16S rRNA genes showed that

  10. Molecular Analysis of Ammonia-Oxidizing Bacteria of the ß Subdivision of the Class Proteobacteria in Compost and Composted Materials

    NARCIS (Netherlands)

    Kowalchuk, G.A.; Naoumenko, Z.S.; Derikx, P.J.L.; Felske, A.; Stephen, J.R.; Arkhipchenko, I.A.

    1999-01-01

    Although the practice of composting animal wastes for use as biofertilizers has increased in recent years, little is known about the microorganisms responsible for the nitrogen transformations which occur in compost and during the composting process. Ammonia is the principle available nitrogenous

  11. Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil

    NARCIS (Netherlands)

    Soares, Johnny R.; Cassman, N.; Kielak, A.M.; Pijl, A.S.; do Carmo, J.B.; Lourenço, Késia S.; Laanbroek, H.J.; Cantarella, H.; Kuramae, E.E.

    2016-01-01

    Nitrous oxide (N2O) from nitrogen fertilizers applied to sugarcane has high environmental impact on ethanol production. This study aimed to determine the main microbial processes responsible for the N2O emissions from soil fertilized with different N sources, to identify options to mitigate N2O

  12. Application of a novel functional gene microarray to probe the functional ecology of ammonia oxidation in nitrifying activated sludge.

    Directory of Open Access Journals (Sweden)

    Michael D Short

    Full Text Available We report on the first study trialling a newly-developed, functional gene microarray (FGA for characterising bacterial and archaeal ammonia oxidisers in activated sludge. Mixed liquor (ML and media biofilm samples from a full-scale integrated fixed-film activated sludge (IFAS plant were analysed with the FGA to profile the diversity and relative abundance of ammonia-oxidising archaea and bacteria (AOA and AOB respectively. FGA analyses of AOA and AOB communities revealed ubiquitous distribution of AOA across all samples - an important finding for these newly-discovered and poorly characterised organisms. Results also revealed striking differences in the functional ecology of attached versus suspended communities within the IFAS reactor. Quantitative assessment of AOB and AOA functional gene abundance revealed a dominance of AOB in the ML and approximately equal distribution of AOA and AOB in the media-attached biofilm. Subsequent correlations of functional gene abundance data with key water quality parameters suggested an important functional role for media-attached AOB in particular for IFAS reactor nitrification performance and indicate possible functional redundancy in some IFAS ammonia oxidiser communities. Results from this investigation demonstrate the capacity of the FGA to resolve subtle ecological shifts in key microbial communities in nitrifying activated sludge and indicate its value as a tool for better understanding the linkages between the ecology and performance of these engineered systems.

  13. Archaeal ammonia oxidation in volcanic grassland soils of Iceland. Effects of elevated temperature and N availability on processes and organisms

    NARCIS (Netherlands)

    Daebeler, A.

    2014-01-01

    Thaumarchaea are recognized today as the most abundant and ubiquitously dis­tributed archaeal organisms, especially in the oceans and soil. Their phylogenetic placement as a phylum, the capability of all cultivated Thaumarchaea to oxidize ammonia for energy conservation as well as many further

  14. Underestimation of ammonia-oxidizing bacteria abundance by amplification bias in amoA-targeted qPCR

    DEFF Research Database (Denmark)

    Dechesne, Arnaud; Musovic, Sanin; Palomo, Alejandro

    2016-01-01

    Molecular methods to investigate functional groups in microbial communities rely on the specificity and selectivity of the primer set towards the target. Here, using rapid sand filters for drinking water production as model environment, we investigated the consistency of two commonly used quantit......RNA. In contrast, both approaches performed very similarly at waterworks with high Cluster 7 prevalence. Our results highlight that caution is warranted when comparing AOB abundances obtained using different qPCR primer sets....

  15. Olea europaea Linn (Oleaceae) Fruit Pulp Exhibits ...

    African Journals Online (AJOL)

    of 50 mM Tris-HCl (pH 8.0), 150 mM NaCl, 1 %. Triton X-100, 0.5 % sodium deoxycholate, 0.1 % sodium dodecyl sulfate (SDS), 1 mM EDTA. (Sigma), 1% protease inhibitor cocktail, and 1 % phosphatase inhibitor cocktail (Roche). After centrifugation, the protein concentration of the supernatant was assayed using a Bio-Rad ...

  16. Proteome Regulation during Olea europaea Fruit Development

    DEFF Research Database (Denmark)

    Bianco, Linda; Alagna, Fiammetta; Baldoni, Luciana

    2013-01-01

    occurring during these complex physiological processes. Methodology/Principal Findings: In this work, we started monitoring the proteome variations associated with olive fruit development by using comparative proteomics coupled to mass spectrometry. Proteins extracted from drupes at three different...... if changes observed at the protein level were consistent with changes of mRNAs, proteomic data produced in the present work were compared with transcriptomic data elaborated during previous studies. Conclusions/Significance: This study identifies a number of proteins responsible for quality traits of cv...

  17. Olea europaea Linn (Oleaceae) Fruit Pulp Exhibits ...

    African Journals Online (AJOL)

    as hydroxymethylglutaryl-CoA reductase (HMGR), acyl-CoA:cholesterol acyltransferase (ACAT), cytochrome P450 7A1 (CYP7A1) and peroxisome proliferation-activated receptor alpha (PPAR-á) in rat livers were evaluated using Western blotting. Results: OFP-EA-extract markedly altered the increased plasma TC, TG, LDL ...

  18. Fate of water borne therapeutic agents and associated effects on nitrifying biofilters in recirculating aquaculture systems

    DEFF Research Database (Denmark)

    Pedersen, Lars-Flemming

    be described as a concentration-dependent exponential decay. HP was found to be enzymatically eliminated by microorganisms, with degradation rates correlated to organic matter content and microbial abundance. Nitrification performance was not affected by HP when applied in dosages less than 30 mg/L, whereas...... prolonged multiple HP dosages at 10 mg/L were found to inhibit nitrite oxidation in systems with low organic loading. PAA decay was found to be concentration-dependent. It had a considerable negative effect on nitrite oxidation over a prolonged period of time when applied at a dosage ≥2 mg/L. PAA and HP...... decay patterns were significantly affected by water quality parameters, i.e. at low organic matter content HP degradation was impeded due to microbial inhibition. FISH analysis on biofilm samples from two different types of RAS showed that Nitrosomonas oligotropha was the dominant ammonia oxidizing...

  19. Cultivation and characteristics of partial nitrification granular sludge in a sequencing batch reactor inoculated with heterotrophic granules.

    Science.gov (United States)

    Wang, Jianfang; Qian, Feiyue; Liu, Xiaopeng; Liu, Wenru; Wang, Shuyong; Shen, Yaoliang

    2016-11-01

    The aim of this study was to develop a simple operation strategy for the cultivation of partial nitrification granules (PNGs) treating an autotrophic medium. For this strategy, aerobic granular sludge adapted to high concentration organics removal was seeded in a sequencing batch reactor (SBR) with a height/diameter ratio of 3.8, and the ratio of organics to the ammonia nitrogen-loading rate (C/N ratio) in the influent was employed as the main control parameter to start up the partial nitrification process. After 86 days of operation, the nitrite accumulation rate reached 1.44 kg/(m 3  day) in the SBR, and the removal efficiency of ammonia nitrogen (NH 4 + -N) was over 95 %. The PNGs showed a dense and compact structure, with an excellent settling ability, a typical extracellular polymeric substance (EPS) composition, and a high ammonia oxidation activity. The high-throughput pyrosequencing results indicated that the microbial community structure in the granules was significantly influenced by the C/N ratio, and ammonia-oxidizing bacteria (AOB), including the r-strategist Nitrosomonas and k-strategist Nitrosospira genre, which accounted for approximately 40 % of the total biomass at the end of operation. The effective suppression of nitrite-oxidizing bacteria (NOB) growth was attributed to oxygen competition on the granular surface among functional bacteria, as well as the high free ammonia or free nitrous acid concentrations during the aeration period.

  20. Unraveling the Long-Term Effects of Cr(VI on the Performance and Microbial Community of Nitrifying Activated Sludge System

    Directory of Open Access Journals (Sweden)

    Xingang Wang

    2017-11-01

    Full Text Available The long-term effects of different influent Cr(VI concentrations (0–0.5 mg L−1 on the nitrification activities and microbial community structures of nitrifying activated sludge system were investigated in this study. Results showed that the performance of ammonia oxidation was significantly inhibited, and the effluent concentration of ammonia nitrogen (NH4+-N increased markedly when the influent Cr(VI loading was equal or greater than 0.2 mg L−1. The specific oxygen utilization rate (SOUR, specific ammonium oxidation rate (SAOR, and specific nitrite oxidation rate (SNOR of the system decreased from 53.24, 6.31, and 7.33 mg N g−1 VSS h−1 to 18.17, 1.68, and 2.88 mg N g−1 VSS h−1, respectively, with an increase of Cr(VI concentration from 0 to 0.5 mg L−1. The protein/polysaccharide (PN/PS ratio increased with the increasing Cr(VI concentration, indicating that excessive PN secreted by microorganisms was conducive to resisting the toxicity of Cr(VI. High-throughput sequencing revealed that the relative abundance of ammonia-oxidizing bacteria (Nitrospira and nitrite-oxidizing bacteria (Nitrosomonas and Nitrosospira all decreased with the increasing Cr(VI concentration, and ammonia-oxidizing bacteria were more sensitive to heavy metal toxicity than nitrite-oxidizing bacteria. The activities of nitrifying activated sludge system could not be completely recovered after a 30-d recovery process.

  1. Characterization of nitrifying granules produced in an aerobic upflow fluidized bed reactor.

    Science.gov (United States)

    Tsuneda, Satoshi; Nagano, Tatsuo; Hoshino, Tatsuhiko; Ejiri, Yoshihiro; Noda, Naohiro; Hirata, Akira

    2003-12-01

    Since nitrification is the rate-determining step in the biological nitrogen removal from wastewater, many research studies have been conducted on the immobilization of nitrifying bacteria. In this research, granulation of nitrifying bacteria in an aerobic upflow fluidized bed (AUFB) reactor in a nitrification process for inorganic wastewater containing 500 g/m(3) of NH(4)(+)-N was investigated. It was observed that spherical, pseudocubic and elliptical granules with a diameter of 346 microm were produced at the bottom of the reactor after 300 days. Denaturing gradient gel electrophoresis analysis revealed that Nitrosomonas-like bacteria were the dominant ammonia-oxidizing species in the granules. Many colonies of Nitrosomonas-like bacteria were found in the outer part of the granules based on the spatial distribution analysis by fluorescence in situ hybridization. By stepwise reduction of the hydraulic retention time, the ammonia removal rate of the AUFB reactor containing these nitrifying granules finally reached 1.5 kg-N/m(3)/day. Results suggested that the use of granules realizes the retention of a large amount of nitrifying bacteria in the reactor, which guarantees a highly efficient nitrification.

  2. Microbial community response reveals underlying mechanism of industrial-scale manganese sand biofilters used for the simultaneous removal of iron, manganese and ammonia from groundwater.

    Science.gov (United States)

    Zhang, Yu; Sun, Rui; Zhou, Aijuan; Zhang, Jiaguang; Luan, Yunbo; Jia, Jianna; Yue, Xiuping; Zhang, Jie

    2018-01-08

    Most studies have employed aeration-biofiltration process for the simultaneous removal of iron, manganese and ammonia in groundwater. However, what's inside the "black box", i.e., the potential contribution of functional microorganisms behavior and interactions have seldom been investigated. Moreover, little attention has been paid to the correlations between environmental variables and functional microorganisms. In this study, the performance of industrial-scale biofilters for the contaminated groundwater treatment was studied. The effluent were all far below the permitted concentration level in the current drinking water standard. Pyrosequencing illustrated that shifts in microbial community structure were observed in the microbial samples from different depths of filter. Microbial networks showed that the microbial community structure in the middle- and deep-layer samples was similar, in which a wide range of manganese-oxidizing bacteria was identified. By contrast, canonical correlation analysis showed that the bacteria capable of ammonia-oxidizing and nitrification was enriched in the upper-layer, i.e., Propionibacterium, Nitrosomonas, Nitrosomonas and Candidatus Nitrotoga. The stable biofilm on the biofilter media, created by certain microorganisms from the groundwater microflora, played a crucial role in the simultaneous removal of the three pollutants.

  3. Process of nitrogen transformation and microbial community structure in the Fe(0)-carbon-based bio-carrier filled in biological aerated filter.

    Science.gov (United States)

    Deng, Shihai; Li, Desheng; Yang, Xue; Zhu, Shanbin; Li, Jinlong

    2016-04-01

    Nitrogen pollutants in low-organic carbon wastewater are difficult to biodegrade. Therefore, the Fe(0)-carbon-based bio-carrier (FCBC) was firstly used as hydrogen producer in a biological-aerated filter (BAF) to make up for the lack of organic carbon in biological nitrogen removal. Physical and chemical properties of FCBC were detected and compared in this study. The nitrogen removal rate for low COD/TN ratio wastewater, nitrogen transformation process, and microbial communities in the FCBC filled in BAF were investigated. Results showed that the nitrogen removal rates was 0.38-0.41 kg N m(-3) day(-1) in the FCBC filled BAF and reached 0.62 kg N m(-3) day(-1) within the filter depth of 60-80 cm, under the conditions of the dissolved oxygen 3.5 ± 0.2 mg L(-1) and the inlet pH 7.2 ± 0.1. Hydrogenophaga (using hydrogen as electron donor), Sphaerotilus (absorbing [Fe(3+)]), Nitrospira (nitrificaion), and Nitrosomonas (ammonia oxidation) were found to be the predominant genera in the reactor. The reaction schemes in the FCBC filled in BAF was calculated: hydrogen and [Fe(3+)] were produced by Fe(0)-C galvanic cells in the FCBC, ammonia was oxidized into nitrate by Nitrosomonas and Nitrospira genera, hydrogen was used as electron donors by Hydrogenophaga genus to reduce nitrate into N2, and [Fe(3+)] was partly absorbed by Sphaerotilus and diverted via sludge discharging.

  4. Nitrate reduction, nitrous oxide formation, and anaerobic ammonia oxidation to nitrite in the gut of soil-feeding termites (Cubitermes and Ophiotermes spp.).

    Science.gov (United States)

    Ngugi, David Kamanda; Brune, Andreas

    2012-04-01

    Soil-feeding termites play important roles in the dynamics of carbon and nitrogen in tropical soils. Through the mineralization of nitrogenous humus components, their intestinal tracts accumulate enormous amounts of ammonia, and nitrate and nitrite concentrations are several orders of magnitude above those in the ingested soil. Here, we studied the metabolism of nitrate in the different gut compartments of two Cubitermes and one Ophiotermes species using (15)N isotope tracer analysis. Living termites emitted N(2) at rates ranging from 3.8 to 6.8 nmol h(-1) (g fresh wt.)(-1). However, in homogenates of individual gut sections, denitrification was restricted to the posterior hindgut, whereas nitrate ammonification occurred in all gut compartments and was the prevailing process in the anterior gut. Potential rates of nitrate ammonification for the entire intestinal tract were tenfold higher than those of denitrification, implying that ammonification is the major sink for ingested nitrate in the intestinal tract of soil-feeding termites. Because nitrate is efficiently reduced already in the anterior gut, reductive processes in the posterior gut compartments must be fuelled by an endogenous source of oxidized nitrogen species. Quite unexpectedly, we observed an anaerobic oxidation of (15)N-labelled ammonia to nitrite, especially in the P4 section, which is presumably driven by ferric iron; nitrification and anammox activities were not detected. Two of the termite species also emitted substantial amounts of N(2) O, ranging from 0.4 to 3.9 nmol h(-1) (g fresh wt.)(-1), providing direct evidence that soil-feeding termites are a hitherto unrecognized source of this greenhouse gas in tropical soils. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

  5. The influence of human exploration on the microbial community structure and ammonia oxidizing potential of the Su Bentu limestone cave in Sardinia, Italy.

    Directory of Open Access Journals (Sweden)

    Stefan Leuko

    Full Text Available The bacterial diversity in the Su Bentu Cave in Sardinia was investigated by means of 16S rRNA gene-based analysis. This 15 km long cave, carved in Jurassic limestone, hosts a variety of calcite speleothems, and a long succession of subterranean lakes with mixed granite and carbonate sands. The lower level is occasionally flooded by a rising groundwater level, but with only scarce input of organic remains (leaves and charcoal fragments. On the quiet cave pools there are visible calcite rafts, whereas walls are locally coated with manganese deposits. In the drier upper levels, where organic input is much more subdued, moonmilk-a hydrated calcium-magnesium carbonate speleothem-can be found. Relative humidity approaches 100% and the measured mean annual cave air temperature is 14.8°C. Samples were obtained in 2014 from calcite rafts, moonmilk, manganese oxide deposits and soil (limestone and granite grains. Microclimatic conditions in the cave near the sampling sites, sample properties, physico-chemical parameters of water, and sediment composition were determined. The microbial community of this system is predominately composed of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Nitrospirae, and Firmicutes. Sampling sites near the entrance of the cave and in close proximity of the underground campsite-located 500 meters deep into the cave-revealed the highest diversity as well as the highest number of human associated microorganisms. Two samples obtained in very close proximity of each other near the campsite, indicate that the human impact is localized and is not distributed freely within the system. Analysis of the abundance of bacterial and archaeal amoA genes revealed a far greater abundance of archaeal amoA genes compared to bacterial representatives. The results of this study highlight that human impact is confined to locations that are utilized as campsites and that exploration leaves little microbial trails. Furthermore, we uncovered a highly specialized microbiome, which is perfectly adapted to survive and thrive in an environment with low nutrient availability.

  6. Effect of Lake Trophic Status and Rooted Macrophytes on Community Composition and Abundance of Ammonia-oxidizing Prokaryotes in Freshwater Sediments

    DEFF Research Database (Denmark)

    Herrmann, Martina; Saunders, Aaron Marc; Schramm, Andreas

    2009-01-01

    /N ratios. AOA communities could be grouped according to lake trophic status and pH; plant species-specific communities were not detected, and no grouping was apparent for AOB communities. Relative abundance, determined by quantitative PCR targeting amoA, was always low for AOB (...) and slightly higher for AOA in unvegetated sediment and AOA in association with M. alterniflorum (0.01 to 2%), while AOA accounted for up to 5% in the rhizospheres of L. uniflora and J. bulbosus. These results indicate that (i) AOA are at least as numerous as AOB in freshwater sediments, (ii) aquatic...

  7. Denaturing Gradient Gel Electrophoretic Analysis of Ammonia-Oxidizing Bacterial Community Structure in the Lower Seine River: Impact of Paris Wastewater Effluents

    NARCIS (Netherlands)

    Cébron, A.; Coci, M.; Garnier, J.; Laanbroek, H.J.

    2004-01-01

    The Seine River is strongly affected by the effluents from the Achères wastewater treatment plant (WWTP) downstream of the city of Paris. We have shown that the effluents introduce large amounts of ammonia and inoculate the receiving medium with nitrifying bacteria. The aim of the present study was

  8. Denaturing gradient gel electrophoretic analysis of ammonia-oxidizing bacterial community structure in the lower Seine River: Impact of Paris wastewater effluents

    NARCIS (Netherlands)

    Cebron, A.; Coci, M.; Garnier, J.; Laanbroek, H.J.

    2004-01-01

    The Seine River is strongly affected by the effluents from the Acheres wastewater treatment plant (WWTP) downstream of the city of Paris. We have shown that the effluents introduce large amounts of ammonia and inoculate the receiving medium with nitrifying bacteria. The aim of the present study was

  9. Denaturing Gradient Gel Electrophoretic Analysis of Ammonia-Oxidizing Bacterial Community Structure in the Lower Seine River: Impact of Paris Wastewater Effluents

    NARCIS (Netherlands)

    Cébron, A.; Coci, M.; Garnier, J.; Laanbroek, H.J.

    2004-01-01

    The Seine River is strongly affected by the effluents from the Achères wastewater treatment plant (WWTP) downstream of the city of Paris. We have shown that the effluents introduce large amounts of ammonia and inoculate the receiving medium with nitrifying bacteria. The aim of the present study

  10. Greater Fusarium wilt suppression after complex than after simple organic amendments as affected by soil pH, total carbon and ammonia-oxidizing bacteria

    NARCIS (Netherlands)

    Senechkin, I.V.; Overbeek, van L.S.; Bruggen, van A.H.C.

    2014-01-01

    A field experiment was conducted to compare effects of four types of organic amendments on soil chemical, microbiological and disease suppression characteristics in an organic farm. The amendments were plant-derived fresh compost (C), steer-derived slurry (S), slurry plus dung (SD) and slurry,

  11. Impact of Support and Potassium-Poisoning on the V2O5-WO3/ZrO2 Catalyst Performance in Ammonia Oxidation

    DEFF Research Database (Denmark)

    Due-Hansen, Johannes; Kustov, Arkadii; Christensen, Claus H.

    2009-01-01

    A series of WO3-promoted zirconia supports were synthesized and calcined between 400 and 800C. Subsequently vanadium oxide was introduced to obtain 3.5 wt% V2O5. The influence of the calcination temperature and potassium-poisoning (K/V = 0.2, molar ratio) on the catalytic activity in the selective...... catalytic reduction (SCR) of NO with NH3 was previously studied. Here, we focus on the influence of these parameters on the catalytic activity for the undesirable oxidation of ammonia, which decrease the N2 selectivity of the SCR process. It is found that potassium doping of the catalysts results...

  12. Genome Sequences of Two Freshwater Betaproteobacterial Isolates, Limnohabitans Species Strains Rim28 and Rim47, Indicate Their Capabilities as Both Photoautotrophs and Ammonia Oxidizers

    Czech Academy of Sciences Publication Activity Database

    Zeng, Yonghui; Kasalický, Vojtěch; Šimek, Karel; Koblížek, Michal

    2012-01-01

    Roč. 194, č. 22 (2012), s. 6302-6303 ISSN 0021-9193 R&D Projects: GA MŠk(CZ) ED2.1.00/03.0110; GA MŠk(CZ) EE2.3.30.0032; GA ČR GA206/08/0015 Institutional research plan: CEZ:AV0Z50200510 Institutional support: RVO:60077344 Keywords : NICHE SEPARATION * BACTERIA Subject RIV: EE - Microbiology, Virology Impact factor: 3.194, year: 2012

  13. Effect of freshwater mussels on the vertical distribution of anaerobic ammonia oxidizers and other nitrogen-transforming microorganisms in upper Mississippi river sediment

    Directory of Open Access Journals (Sweden)

    Ellen M. Black

    2017-07-01

    Full Text Available Targeted qPCR and non-targeted amplicon sequencing of 16S rRNA genes within sediment layers identified the anaerobic ammonium oxidation (anammox niche and characterized microbial community changes attributable to freshwater mussels. Anammox bacteria were normally distributed (Shapiro-Wilk normality test, W-statistic =0.954, p = 0.773 between 1 and 15 cm depth and were increased by a factor of 2.2 (p < 0.001 at 3 cm below the water-sediment interface when mussels were present. Amplicon sequencing of sediment at depths relevant to mussel burrowing (3 and 5 cm showed that mussel presence reduced observed species richness (p = 0.005, Chao1 diversity (p = 0.005, and Shannon diversity (p < 0.001, with more pronounced decreases at 5 cm depth. A non-metric, multidimensional scaling model showed that intersample microbial species diversity varied as a function of mussel presence, indicating that sediment below mussels harbored distinct microbial communities. Mussel presence corresponded with a 4-fold decrease in a majority of operational taxonomic units (OTUs classified in the phyla Gemmatimonadetes, Actinobacteria, Acidobacteria, Plantomycetes, Chloroflexi, Firmicutes, Crenarcheota, and Verrucomicrobia. 38 OTUs in the phylum Nitrospirae were differentially abundant (p < 0.001 with mussels, resulting in an overall increase from 25% to 35%. Nitrogen (N-cycle OTUs significantly impacted by mussels belonged to anammmox genus Candidatus Brocadia, ammonium oxidizing bacteria family Nitrosomonadaceae, ammonium oxidizing archaea genus Candidatus Nitrososphaera, nitrite oxidizing bacteria in genus Nitrospira, and nitrate- and nitrite-dependent anaerobic methane oxidizing organisms in the archaeal family “ANME-2d” and bacterial phylum “NC10”, respectively. Nitrosomonadaceae (0.9-fold (p < 0.001 increased with mussels, while NC10 (2.1-fold (p < 0.001, ANME-2d (1.8-fold (p < 0.001, and Candidatus Nitrososphaera (1.5-fold (p < 0.001 decreased with mussels. Co-occurrence of 2-fold increases in Candidatus Brocadia and Nitrospira in shallow sediments suggests that mussels may enhance microbial niches at the interface of oxic–anoxic conditions, presumably through biodeposition and burrowing. Furthermore, it is likely that the niches of Candidatus Nitrososphaera and nitrite- and nitrate-dependent anaerobic methane oxidizers were suppressed by mussel biodeposition and sediment aeration, as these phylotypes require low ammonium concentrations and anoxic conditions, respectively. As far as we know, this is the first study to characterize freshwater mussel impacts on microbial diversity and the vertical distribution of N-cycle microorganisms in upper Mississippi river sediment. These findings advance our understanding of ecosystem services provided by mussels and their impact on aquatic biogeochemical N-cycling.

  14. Nitrate reduction, nitrous oxide formation, and anaerobic ammonia oxidation to nitrite in the gut of soil-feeding termites (Cubitermes and Ophiotermes spp.)

    KAUST Repository

    Ngugi, David

    2011-11-28

    Soil-feeding termites play important roles in the dynamics of carbon and nitrogen in tropical soils. Through the mineralization of nitrogenous humus components, their intestinal tracts accumulate enormous amounts of ammonia, and nitrate and nitrite concentrations are several orders of magnitude above those in the ingested soil. Here, we studied the metabolism of nitrate in the different gut compartments of two Cubitermes and one Ophiotermes species using 15N isotope tracer analysis. Living termites emitted N 2 at rates ranging from 3.8 to 6.8nmolh -1 (g fresh wt.) -1. However, in homogenates of individual gut sections, denitrification was restricted to the posterior hindgut, whereas nitrate ammonification occurred in all gut compartments and was the prevailing process in the anterior gut. Potential rates of nitrate ammonification for the entire intestinal tract were tenfold higher than those of denitrification, implying that ammonification is the major sink for ingested nitrate in the intestinal tract of soil-feeding termites. Because nitrate is efficiently reduced already in the anterior gut, reductive processes in the posterior gut compartments must be fuelled by an endogenous source of oxidized nitrogen species. Quite unexpectedly, we observed an anaerobic oxidation of 15N-labelled ammonia to nitrite, especially in the P4 section, which is presumably driven by ferric iron; nitrification and anammox activities were not detected. Two of the termite species also emitted substantial amounts of N 2O, ranging from 0.4 to 3.9nmolh -1 (g fresh wt.) -1, providing direct evidence that soil-feeding termites are a hitherto unrecognized source of this greenhouse gas in tropical soils. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

  15. The relative abundance of predicted genes associated with ammonia-oxidation, nitrate reduction, and biomass decomposition in mineral soil are altered by intensive timber harvest.

    Science.gov (United States)

    Mushinski, R. M.; Zhou, Y.; Gentry, T. J.; Boutton, T. W.

    2017-12-01

    Forest ecosystems in the southern United States are substantially altered by anthropogenic disturbances such as timber harvest and land conversion, with effects being observed in carbon and nutrient pools as well as biogeochemical processes. Furthermore, the desire to develop renewable energy sources in the form of biomass extraction from logging residues may result in alterations in soil community structure and function. While the impact of forest management on soil physicochemical properties of the region has been studied, its' long-term effect on soil bacterial community composition and metagenomic potential is relatively unknown, especially at deeper soil depths. This study investigates how intensive organic matter removal intensities associated with timber harvest influence decadal-scale alterations in bacterial community structure and functional potential in the upper 1-m of the soil profile, 18 years post-harvest in a Pinus taeda L. forest of eastern Texas. Amplicon sequencing of the 16S rRNA gene was used in conjunction with soil chemical analyses to evaluate treatment-induced differences in community composition and potential environmental drivers of associated change. Furthermore, functional potential was assessed by using amplicon data to make metagenomic predictions. Results indicate that increasing organic matter removal intensity leads to altered community composition and the relative abundance of dominant OTUs annotated to Burkholderia and Aciditerrimonas. The relative abundance of predicted genes associated with dissimilatory nitrate reduction and denitrification were highest in the most intensively harvested treatment while genes involved in nitrification were significantly lower in the most intensively harvested treatment. Furthermore, genes associated with glycosyltransferases were significantly reduced with increasing harvest intensity while polysaccharide lyases increased. These results imply that intensive organic matter removal may create long-term alterations in bacterial community structure with concurrent alterations to mineral soil carbon and nutrient cycling which may have future consequences on forest regeneration and subsequent stand productivity.

  16. Effects of Simulated Rare Earth Recycling Wastewaters on Biological Nitrification.

    Science.gov (United States)

    Fujita, Yoshiko; Barnes, Joni; Eslamimanesh, Ali; Lencka, Malgorzata M; Anderko, Andrzej; Riman, Richard E; Navrotsky, Alexandra

    2015-08-18

    Increasing rare earth element (REE) supplies by recycling and expanded ore processing will result in generation of new wastewaters. In some cases, disposal to a sewage treatment plant may be favored, but plant performance must be maintained. To assess the potential effects of such wastewaters on biological treatment, model nitrifying organisms Nitrosomonas europaea and Nitrobacter winogradskyi were exposed to simulated wastewaters containing varying levels of yttrium or europium (10, 50, and 100 ppm), and the extractant tributyl phosphate (TBP, at 0.1 g/L). Y and Eu additions at 50 and 100 ppm inhibited N. europaea, even when virtually all of the REE was insoluble. Provision of TBP with Eu increased N. europaea inhibition, although TBP alone did not substantially alter activity. For N. winogradskyi cultures, Eu or Y additions at all tested levels induced significant inhibition, and nitrification shut down completely with TBP addition. REE solubility was calculated using the previously developed MSE (Mixed-Solvent Electrolyte) thermodynamic model. The model calculations reveal a strong pH dependence of solubility, typically controlled by the precipitation of REE hydroxides but also likely affected by the formation of unknown phosphate phases, which determined aqueous concentrations experienced by the microorganisms.

  17. Genetic variation within the olive ( Olea europaea L. ) cultivar Oblica ...

    African Journals Online (AJOL)

    Oblica is the predominant olive cultivar in Croatia, spread widely in all the olive growing regions. Morphological variability within the cultivar is well documented but often it has been attributed to environmental factors rather than to genetic ones. In order to investigate intracultivar variability on the molecular level, olive ...

  18. Heavy metal accumulation in under crown Olea europaea L forest ...

    African Journals Online (AJOL)

    Heavy metal concentration in plants increased in site irrigation with wastewater. Zn, Pb and Ni exceeded their permitted limits in soils and Pb, Cr and Ni exceeded their permitted limits in roots of plants irrigated with wastewater. It was concluded that the use of wastewater in urban forest enriched the soils with heavy metals ...

  19. Genetic variation within the olive (Olea europaea L.) cultivar Oblica ...

    African Journals Online (AJOL)

    USER

    2010-05-17

    May 17, 2010 ... 1Institute for Adriatic Crops and Karst Reclamation Split, Put Duilova 11, 21000 Split, Croatia. 2Science and Research Centre of Koper, University of Primorska, Garibaldijeva 18, 6000 Koper, Slovenia. 3University of Zagreb, Faculty of Agriculture, Svetosimunska 25, 10000 Zagreb, Croatia. 4University of ...

  20. Flowering in the wild olive ( Olea europaea L.) tree (oleaster ...

    African Journals Online (AJOL)

    flowers with absence or reduced stamens and flowers with absence of pistil) are frequently observed and may reduce fruit set. This study investigates the phenology evolution and the male and female abortion of the oleaster tree (or the wild olive ...

  1. Mycorrhizal status of Olea europaea spp. oleaster in Morocco

    African Journals Online (AJOL)

    SARAH

    2013-01-31

    Jan 31, 2013 ... Physico-chemical analyzes of soil: The main physicochemical soils characteristics (pH, electrical conductivity, organic matter, carbon, nitrate, Nitrogen, ammoniacal nitrogen, mineral nitrogen, phosphore and potassium) were determined by conventional analyzes performed by the soil analysis laboratory of ' ...

  2. Comparative molecular analysis of old olive ( Olea europaea L ...

    African Journals Online (AJOL)

    We compared the genetic profiles of six old olive cultivars from an Eastern Mediterranean Region of Turkey to 15 modern Turkish olive cultivars from different geographical origins. The RAPD profiles successfully clarified the molecular relationships among the genotypes tested. Seventeen RAPD primers generated 153 ...

  3. Factors influencing phenolic compounds in table olives (Olea europaea).

    Science.gov (United States)

    Charoenprasert, Suthawan; Mitchell, Alyson

    2012-07-25

    The Mediterranean diet appears to be associated with a reduced risk of several chronic diseases including cancer and cardiovascular and Alzheimer's diseases. Olive products (mainly olive oil and table olives) are important components of the Mediterranean diet. Olives contain a range of phenolic compounds; these natural antioxidants may contribute to the prevention of these chronic conditions. Consequently, the consumption of table olives and olive oil continues to increase worldwide by health-conscious consumers. There are numerous factors that can affect the phenolics in table olives including the cultivar, degree of ripening, and, importantly, the methods used for curing and processing table olives. The predominant phenolic compound found in fresh olive is the bitter secoiridoid oleuropein. Table olive processing decreases levels of oleuropein with concomitant increases in the hydrolysis products hydroxytyrosol and tyrosol. Many of the health benefits reported for olives are thought to be associated with the levels of hydroxytyrosol. Herein the pre- and post-harvest factors influencing the phenolics in olives, debittering methods, and health benefits of phenolics in table olives are reviewed.

  4. Olea europaea Linn (Oleaceae) Fruit Pulp Extract Suppresses Sterol ...

    African Journals Online (AJOL)

    regarded as an energy sensor in most tissues. AMPK regulates cellular lipid metabolism by increasing ... cells relative to that of control vehicle-treated cells. Nile red stain test. Human HepG2 hepatocytes .... assay and expressed as percentage of the vehicle controls. Data expressed are means ± SD of three independent ...

  5. Hydrophilic C terminus of Salicornia europaea vacuolar Na/H ...

    Indian Academy of Sciences (India)

    Plant vacuolar Na+/H+ antiporters play important roles in cellular ion homeostasis,vacuolar pH regulation and sequestration of Na+ ions into the vacuole. Previous research showed that hydrophilic C-terminal region of Arabidopsis AtNHX1 negatively regulates the Na+/H+ transporting activity. In this study, we truncated the ...

  6. Olea europaea Linn (Oleaceae) Fruit Pulp Extract Exhibits Potent ...

    African Journals Online (AJOL)

    HP

    expression and tumor necrosis factor-alpha (TNF-α) production were measured using enzyme-linked immunosorbent assay (ELISA) and Western blot analysis. Results: OFP-EA extract significantly (p<0.001 at 20-200 µg/ml, respectively) scavenged the free radicals in a dose-dependent fashion. The increased levels of No ...

  7. Experimental measurement of the biomass of Olea europaea L ...

    African Journals Online (AJOL)

    The C stock evaluation methodology made in this research and the calculation of biomass expansion factor can be considered as the first scientific contribution in estimating productivity, CO2 sequestration, carbon stocks and yield of olive groves. Key words: Biomass, biomass expansion factor, Intergovernmental Panel on ...

  8. Bioassays for the determination of nitrification inhibition

    Energy Technology Data Exchange (ETDEWEB)

    Grunditz, Camilla

    1999-07-01

    Requirements for nitrogen reduction in wastewater treatment plants were introduced in Sweden in the early 1990's. This was a governmental move to reduce the nitrogen discharges to the Baltic and Kattegat in order to prevent eutrophication. The nitrification process in wastewater treatment plants is performed by nitrifying bacteria. These are susceptible to inhibition and it is of great importance that the influent water does not contain toxic compounds. Therefore, there is a need for assays for the determination of nitrification inhibition. This thesis describes the development and applications of such bioassays. Pure cultures of Nitrosomonas sp. and Nitrobacter sp. were isolated from activated sludge of a wastewater treatment plant. These cultures were used as test organisms in the development of bioassays for nitrification inhibition measurements. The assays are based on two different principles; cell suspensions of the bacteria, performed in test tubes, and mediated amperometric biosensors with the bacteria immobilised. Ammonia oxidation and nitrite oxidation are studied separately without interference from other organisms, which makes it easier to interpret the results. The cell suspension assays were applied to samples of industrial and municipal wastewater. The Nitrosomonas and Nitrobacter assays showed to have different inhibition patterns. A large percentage of the Swedish municipal wastewater treatment plants were found to receive inhibitory influent water, but the inhibition level was generally low. Compared to an assay based on activated sludge, the screening method, the pure culture assays found more samples of influent water strongly inhibitory or stimulating. The highest correlation was found between the screening method and the Nitrosomonas assay. The Nitrobacter assay was found to be the most sensitive method. Assessment of toxicity of a number of chemical substances was studied using the biosensors, together with the cell suspension assays

  9. Multiplicação in vitro de oliveira (Olea europaea L. Olive (Olea europaea L. in vitro multiplication

    Directory of Open Access Journals (Sweden)

    Leonardo Ferreira Dutra

    2004-02-01

    Full Text Available Com o objetivo de induzir a multiplicação em explantes de oliveira, segmentos nodais oriundos de plântulas mantidas in vitro foram excisados e inoculados em tubos de ensaio contendo meio de cultura MS suplementado com 2 g L-1 de carvão ativado, BAP (0, 1, 2 e 4 mg L-1 e ANA (0; 0,01; 0,1 e 1 mg L-1, solidificado com 6 g L-1 de ágar e pH ajustado para 5,8. Durante 100 dias, os explantes foram mantidos em sala de crescimento a 25±1ºC, intensidade luminosa de 32 µmoles.m-2.s-1 e fotoperíodo de 16 horas. Não houve indução de brotações nos segmentos nodais. O maior comprimento da parte aérea foi obtido com 0,1 mg L-1 de ANA na ausência de BAP. O meio de cultura sem BAP proporcionou maior peso de matéria fresca da parte aérea.This work had the objective to induce olive multiplication. Nodal segments from in vitro plantlets were excised and inoculated in test tubes containing MS culture medium supplemented with activated charcoal (2 g L-1, BAP (0, 1, 2 and 4 mg L-1, NAA (0; 0.01; 0.1 and 1 mg L-1, agar (6 g L-1 and pH adjusted to 5.8. The explant were maintained in growth room to 25±1°C, 32 µmoles.m-2.s-1 light intensity and 16 hours photoperiod for 100 days. There was not shoots induction in the nodal segments. Larger length of aerial part were obtained with ANA 0.1 mg L-1 in the BAP absence. Culture medium without BAP provides larger weight of fresh matter of the aerial part.

  10. Application of hierarchical oligonucleotide primer extension (HOPE) to assess relative abundances of ammonia- and nitrite-oxidizing bacteria

    KAUST Repository

    Scarascia, Giantommaso

    2017-04-04

    Background: Establishing an optimal proportion of nitrifying microbial populations, including ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), complete nitrite oxidizers (comammox) and ammonia-oxidizing archaea (AOA), is important for ensuring the efficiency of nitrification in water treatment systems. Hierarchical oligonucleotide primer extension (HOPE), previously developed to rapidly quantify relative abundances of specific microbial groups of interest, was applied in this study to track the abundances of the important nitrifying bacterial populations. Results: The method was tested against biomass obtained from a laboratory-scale biofilm-based trickling reactor, and the findings were validated against those obtained by 16S rRNA gene-based amplicon sequencing. Our findings indicated a good correlation between the relative abundance of nitrifying bacterial populations obtained using both HOPE and amplicon sequencing. HOPE showed a significant increase in the relative abundance of AOB, specifically Nitrosomonas, with increasing ammonium content and shock loading (p < 0.001). In contrast, Nitrosospira remained stable in its relative abundance against the total community throughout the operational phases. There was a corresponding significant decrease in the relative abundance of NOB, specifically Nitrospira and those affiliated to comammox, during the shock loading. Based on the relative abundance of AOB and NOB (including commamox) obtained from HOPE, it was determined that the optimal ratio of AOB against NOB ranged from 0.2 to 2.5 during stable reactor performance. Conclusions: Overall, the HOPE method was developed and validated against 16S rRNA gene-based amplicon sequencing for the purpose of performing simultaneous monitoring of relative abundance of nitrifying populations. Quantitative measurements of these nitrifying populations obtained via HOPE would be indicative of reactor performance and nitrification functionality.

  11. Fluctuation of microbial activities after influent load variations in a full-scale SBR. Recovery of the biomass after starvation

    Energy Technology Data Exchange (ETDEWEB)

    Cabezas, Angela; Draper, Patricia; Etchebehere, Claudia [Universidad de la Republica, Montevideo (Uruguay). Catedra de Microbiologia, Facultad de Quimica y Facultad de Ciencias

    2009-10-15

    Due to variations in the production levels, a full-scale sequencing batch reactor (SBR) for post-treatment of tannery wastewater was exposed to low and high ammonia load periods. In order to study how these changes affected the N-removal capacity, the microbiology of the reactor was studied by a diverse set of techniques including molecular tools, activity tests, and microbial counts in samples taken along 3 years. The recover capacity of the biomass was also studied in a lab-scale reactor operated with intermittent aeration without feeding for 36 days. The results showed that changes in the feeding negatively affected the nitrifying community, but the nitrogen removal efficiencies could be restored after the concentration stress. Species substitution was observed within the nitrifying bacteria, Nitrosomonas europaea and Nitrobacter predominated initially, and after an ammonia overload period, Nitrosomonas nitrosa and Nitrospira became dominant. Some denitrifiers, with nirS related to Alicycliphilus, Azospirillum, and Marinobacter nirS, persisted during long-term reactor operation, but the community fluctuated both in composition and in abundance. This fluctuating community may better resist the continuous changes in the feeding regime. Our results showed that a nitrifying-denitrifying SBR could be operated with low loads or even without feeding during production shut down periods. (orig.)

  12. Thermophilic biological nitrogen removal in industrial wastewater treatment.

    Science.gov (United States)

    Lopez-Vazquez, C M; Kubare, M; Saroj, D P; Chikamba, C; Schwarz, J; Daims, H; Brdjanovic, D

    2014-01-01

    Nitrification is an integral part of biological nitrogen removal processes and usually the limiting step in wastewater treatment systems. Since nitrification is often considered not feasible at temperatures higher than 40 °C, warm industrial effluents (with operating temperatures higher than 40 °C) need to be cooled down prior to biological treatment, which increases the energy and operating costs of the plants for cooling purposes. This study describes the occurrence of thermophilic biological nitrogen removal activity (nitritation, nitratation, and denitrification) at a temperature as high as 50 °C in an activated sludge wastewater treatment plant treating wastewater from an oil refinery. Using a modified two-step nitrification-two-step denitrification mathematical model extended with the incorporation of double Arrhenius equations, the nitrification (nitrititation and nitratation) and denitrification activities were described including the cease in biomass activity at 55 °C. Fluorescence in situ hybridization (FISH) analyses revealed that Nitrosomonas halotolerant and obligatehalophilic and Nitrosomonas oligotropha (known ammonia-oxidizing organisms) and Nitrospira sublineage II (nitrite-oxidizing organism (NOB)) were observed using the FISH probes applied in this study. In particular, this is the first time that Nitrospira sublineage II, a moderatedly thermophilic NOB, is observed in an engineered full-scale (industrial) wastewater treatment system at temperatures as high as 50 °C. These observations suggest that thermophilic biological nitrogen removal can be attained in wastewater treatment systems, which may further contribute to the optimization of the biological nitrogen removal processes in wastewater treatment systems that treat warm wastewater streams.

  13. Differential responses of nitrifying archaea and bacteria to methylene blue toxicity.

    Science.gov (United States)

    Sipos, A J; Urakawa, H

    2016-02-01

    Methylene blue, a heterocyclic aromatic chemical compound used to treat fish diseases in the ornamental fish aquaculture industry, is believed to impair nitrification as a side effect. However, very little is known about the toxicity of methylene blue to nitrifying micro-organisms. Here, we report the susceptibility of six bacterial and one archaeal ammonia-oxidizing micro-organisms to methylene blue within the range of 10 ppb to 10 ppm. Remarkably high susceptibility was observed in the archaeal species Nitrosopumilus maritimus compared to the bacterial species. Ammonia oxidation by Nitrosopumilus maritimus was inhibited 65% by 10 ppb of methylene blue. Of the bacterial species examined, Nitrosococcus oceani was the most resistant to methylene blue toxicity. For similar inhibition of Nitrosococcus oceani (75% inhibition), one thousand times more methylene blue (10 ppm) was needed. The examination of single cell viability on Nitrosomonas marina demonstrated that methylene blue is lethal to the cells rather than reducing their single cell ammonia oxidation activity. The level of susceptibility to methylene blue was related to the cell volume, intracytoplasmic membrane arrangement and the evolutionary lineage of nitrifying micro-organisms. Our findings are relevant for effectively using methylene blue in various aquaculture settings by helping minimize its impact on nitrifiers during the treatment of fish diseases. In the future, resistant nitrifiers such as Nitrosococcus oceani may be purposely added to aquaculture systems to maintain nitrification activity during treatments with methylene blue. The susceptibility of six bacterial and one archaeal nitrifying micro-organisms to methylene blue was tested. Remarkably high susceptibility was observed in the archaeal species compared to the bacterial species. The level of resistance to methylene blue was related to the cell volume, cytomembrane system and the taxonomic position of the nitrifying micro

  14. Density and distribution of nitrifying guilds in rapid sand filters for drinking water production: Dominance of Nitrospira spp.

    Science.gov (United States)

    Tatari, Karolina; Musovic, Sanin; Gülay, Arda; Dechesne, Arnaud; Albrechtsen, Hans-Jørgen; Smets, Barth F

    2017-12-15

    We investigated the density and distribution of total bacteria, canonical Ammonia Oxidizing Bacteria (AOB) (Nitrosomonas plus Nitrosospira), Ammonia Oxidizing Archaea (AOA), as well as Nitrobacter and Nitrospira in rapid sand filters used for groundwater treatment. To investigate the spatial distribution of these guilds, filter material was sampled at four drinking water treatment plants (DWTPs) in parallel filters of the pre- and after-filtration stages at different locations and depths. The target guilds were quantified by qPCR targeting 16S rRNA and amoA genes. Total bacterial densities (ignoring 16S rRNA gene copy number variation) were high and ranged from 10 9 to 10 10 per gram (10 15 to 10 16 per m 3 ) of filter material. All examined guilds, except AOA, were stratified at only one of the four DWTPs. Densities varied spatially within filter (intra-filter variation) at two of the DWTPs and in parallel filters (inter-filter variation) at one of the DWTPs. Variation analysis revealed random sampling as the most efficient strategy to yield accurate mean density estimates, with collection of at least 7 samples suggested to obtain an acceptable (below half order of magnitude) density precision. Nitrospira was consistently the most dominant guild (5-10% of total community), and was generally up to 4 orders of magnitude more abundant than Nitrobacter and up to 2 orders of magnitude more abundant than canonical AOBs. These results, supplemented with further analysis of the previously reported diversity of Nitrospira in the studied DWTPs based on 16S rRNA and nxrB gene phylogeny (Gülay et al., 2016; Palomo et al., 2016), indicate that the high Nitrospira abundance is due to their comammox (complete ammonia oxidation) physiology. AOA densities were lower than AOB densities, except in the highly stratified filters, where they were of similar abundance. In conclusion, rapid sand filters are microbially dense, with varying degrees of spatial heterogeneity, which

  15. Kinetics of NH3-oxidation, NO-turnover, N2O-production and electron flow during oxygen depletion in model bacterial and archaeal ammonia oxidisers.

    Science.gov (United States)

    Hink, Linda; Lycus, Pawel; Gubry-Rangin, Cécile; Frostegård, Åsa; Nicol, Graeme W; Prosser, James I; Bakken, Lars R

    2017-12-01

    Ammonia oxidising bacteria (AOB) are thought to emit more nitrous oxide (N 2 O) than ammonia oxidising archaea (AOA), due to their higher N 2 O yield under oxic conditions and denitrification in response to oxygen (O 2 ) limitation. We determined the kinetics of growth and turnover of nitric oxide (NO) and N 2 O at low cell densities of Nitrosomonas europaea (AOB) and Nitrosopumilus maritimus (AOA) during gradual depletion of TAN (NH 3  + NH4+) and O 2 . Half-saturation constants for O 2 and TAN were similar to those determined by others, except for the half-saturation constant for ammonium in N. maritimus (0.2 mM), which is orders of magnitudes higher than previously reported. For both strains, cell-specific rates of NO turnover and N 2 O production reached maxima near O 2 half-saturation constant concentration (2-10 μM O 2 ) and decreased to zero in response to complete O 2 -depletion. Modelling of the electron flow in N. europaea demonstrated low electron flow to denitrification (≤1.2% of the total electron flow), even at sub-micromolar O 2 concentrations. The results corroborate current understanding of the role of NO in the metabolism of AOA and suggest that denitrification is inconsequential for the energy metabolism of AOB, but possibly important as a route for dissipation of electrons at high ammonium concentration. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  16. Optimizing source-separated feces degradation and fertility using nitrifying microorganisms.

    Science.gov (United States)

    Hashemi, Shervin; Han, Mooyoung

    2018-01-15

    Resource-oriented sanitation (ROS) systems play an important role in handling source-separated human sanitary wastes intended to be used for other purposes. Usually, the purpose of employing such systems is to render the source-separated human feces suitable as fertilizer or soil conditioner. However, the high volume, low degradation rate, and lack of fertility management pose challenges to such enterprises. Accordingly, treatment by applying controlled amounts of nitrifying microorganisms could be useful. The effect of adding different amounts of Nitrosomonas Europaea bio-seed, along with a certain amount of Nitrobacter Winogradskyi bio-seed, to source-separated human feces was investigated. The results show that adding 7000-8000 or more N. Europaea cells, along with 10,000 N. Winogradskyi cells, to 1 g feces, resulted in up to 90% degradation of the organic matter by enhancing the growth of heterotrophic microorganisms. Moreover, the nitrogen composition and pH of the degraded feces were optimized to meet the criteria for standard fertilizer. The results can be useful for managing source-separated feces in ROS systems in accordance with the specific aims of such systems, i.e., reducing feces volume by bio-degradation and increasing the fertility to meet the standard criteria for fertilizer. Copyright © 2017 Elsevier Ltd. All rights reserved.

  17. Analysis of microbial community and nitrogen transition with enriched nitrifying soil microbes for organic hydroponics.

    Science.gov (United States)

    Saijai, Sakuntala; Ando, Akinori; Inukai, Ryuya; Shinohara, Makoto; Ogawa, Jun

    2016-06-27

    Nitrifying microbial consortia were enriched from bark compost in a water system by regulating the amounts of organic nitrogen compounds and by controlling the aeration conditions with addition of CaCO 3 for maintaining suitable pH. Repeated enrichment showed reproducible mineralization of organic nitrogen via the conversion of ammonium ions ([Formula: see text]) and nitrite ions ([Formula: see text]) into nitrate ions ([Formula: see text]). The change in microbial composition during the enrichment was investigated by PCR-DGGE analysis with a focus on prokaryote, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and eukaryote cell types. The microbial transition had a simple profile and showed clear relation to nitrogen ions transition. Nitrosomonas and Nitrobacter were mainly detected during [Formula: see text] and [Formula: see text] oxidation, respectively. These results revealing representative microorganisms acting in each ammonification and nitrification stages will be valuable for the development of artificial simple microbial consortia for organic hydroponics that consisted of identified heterotrophs and autotrophic nitrifying bacteria.

  18. Performance of a sequencing-batch membrane bioreactor (SMBR) with an automatic control strategy treating high-strength swine wastewater.

    Science.gov (United States)

    Sui, Qianwen; Jiang, Chao; Yu, Dawei; Chen, Meixue; Zhang, Junya; Wang, Yawei; Wei, Yuansong

    2018-01-15

    Due to high-strength of organic matters, nutrients and pathogen, swine wastewater is a major source of pollution to rural environment and surface water. A sequencing-batch membrane bioreactor (SMBR) system with an automatic control strategy was developed for high-strength swine wastewater treatment. Short-cut nitrification and denitrification (SND) was achieved at nitrite accumulation rate of 83.6%, with removal rates of COD, NH 4 + -N and TN at 95%, 99% and 93%, respectively, at reduced HRT of 6.0 d and TN loading rate of 0.02kgN/(kgVSS d). With effective membrane separation, the reduction of total bacteria (TB) and putative pathogen were 2.77 logs and 1%, respectively. The shift of microbial community was well responded to controlling parameters. During the SND process, ammonia oxidizing bacteria (AOB) (Nitrosomonas, Nitrosospira) and nitrite oxidizing bacteria (NOB) (Nitrospira) were enriched by 52 times and reduced by 2 times, respectively. The denitrifiers (Thauera) were well enriched and the diversity was enhanced. Copyright © 2017. Published by Elsevier B.V.

  19. Microbial community structure and biodiversity of size-fractionated granules in a partial nitritation-anammox process.

    Science.gov (United States)

    Luo, Jinghuan; Chen, Hui; Han, Xiaoyu; Sun, Yanfang; Yuan, Zhiguo; Guo, Jianhua

    2017-06-01

    The performance of a granule-based partial nitritation-anammox process is expected to be affected by the granule size distribution, but little is known about the impact of granule size on microbial community structure and diversity. To reveal how the microbial composition and diversity vary with granule size, granules from a partial nitritation-anammox reactor were size-fractionated into five classes (1.0 mm). Microbial communities and diversity in these size-fractionated granules were investigated using 16S rRNA gene high-throughput sequencing. It was found that larger granules harbor more diverse microbial communities than small granules. Both quantitative PCR and 16S rRNA gene sequencing indicated that the abundance of anammox bacteria (dominated by Candidatus Brocadia) exhibited an increasing trend with granule size. In contrast, the abundance of ammonia-oxidizing bacteria (Nitrosomonas) decreased with increasing granule size. Moreover, larger granules harbored more diverse anammox bacteria, with four genera found in the largest granules while only two with limited abundance were detected in the smallest granules. The findings highlight an important role for granule size in shaping community structure and biodiversity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  20. Nitrifying granules cultivation in a sequencing batch reactor at a low organics-to-total nitrogen ratio in wastewater.

    Science.gov (United States)

    Cydzik-Kwiatkowska, A; Wojnowska-Baryła, I

    2011-05-01

    It is possible to cultivate aerobic granular sludge at a low organic loading rate and organics-to-total nitrogen (COD/N) ratio in wastewater in the reactor with typical geometry (height/diameter = 2.1, superficial air velocity = 6 mm/s). The noted nitrification efficiency was very high (99%). At the highest applied ammonia load (0.3 ± 0.002 mg NH (4) (+) -N g total suspended solids (TSS)(-1) day(-1), COD/N = 1), the dominating oxidized form of nitrogen was nitrite. Despite a constant aeration in the reactor, denitrification occurred in the structure of granules. Applied molecular techniques allowed the changes in the ammonia-oxidizing bacteria (AOB) community in granular sludge to be tracked. The major factor influencing AOB number and species composition was ammonia load. At the ammonia load of 0.3 ± 0.002 mg NH (4) (+) -N g TSS(-1) day(-1), a highly diverse AOB community covering bacteria belonging to both the Nitrosospira and Nitrosomonas genera accounted for ca. 40% of the total bacteria in the biomass.