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  • 1
    Publication Date: 2019-04-23
    Description: Benthic foraminifera populate a diverse range of marine habitats. Their ability to use alternative electron acceptors—nitrate (NO3−) or oxygen (O2)—makes them important mediators of benthic nitrogen cycling. Nevertheless, the metabolic scaling of the two alternative respiration pathways and the environmental determinants of foraminiferal denitrification rates are yet unknown. We measured denitrification and O2 respiration rates for 10 benthic foraminifer species sampled in the Peruvian oxygen minimum zone (OMZ). Denitrification and O2 respiration rates significantly scale sublinearly with the cell volume. The scaling is lower for O2 respiration than for denitrification, indicating that NO3− metabolism during denitrification is more efficient than O2 metabolism during aerobic respiration in foraminifera from the Peruvian OMZ. The negative correlation of the O2 respiration rate with the surface/volume ratio is steeper than for the denitrification rate. This is likely explained by the presence of an intracellular NO3− storage in denitrifying foraminifera. Furthermore, we observe an increasing mean cell volume of the Peruvian foraminifera, under higher NO3− availability. This suggests that the cell size of denitrifying foraminifera is not limited by O2 but rather by NO3− availability. Based on our findings, we develop a mathematical formulation of foraminiferal cell volume as a predictor of respiration and denitrification rates, which can further constrain foraminiferal biogeochemical cycling in biogeochemical models. Our findings show that NO3− is the preferred electron acceptor in foraminifera from the OMZ, where the foraminiferal contribution to denitrification is governed by the ratio between NO3− and O2.
    Type: Article , PeerReviewed
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  • 2
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract: Because of a revival in the controversy surrounding ‘aerobic denitrification’, especially in relation to Thiosphaera pantotropha, activity in aerobic batch cultures was evaluated using gas chromatography and mass spectrometry after the addition of 15N-labelled NH4+ and NO2−. Aerobic denitrifying activity in T. pantotropha was present, but only at about 10% of the originally-reported levels. The activity of ‘Pseudomonas denitrificans’ was similar to previously-reported values. Alcaligenes faecalis showed significant aerobic denitrifying activity, producing almost equivalent amounts of N2 and N2O. An unidentified pseudomonad, isolate G4, presumably requires anoxia for enzyme activity as it did not denitrify aerobically, even though it has a constitutive denitrifying pathway.
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  • 3
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: In the Completely Autotrophic Nitrogen removal Over Nitrite (CANON) process, aerobic and anaerobic ammonia oxidizing bacteria cooperate to remove ammonia in one oxygen-limited reactor. Kinetic studies, microsensor analysis, and fluorescence in situ hybridization on CANON biomass showed a partial differentiation of processes and organisms within and among aggregates. Under normal oxygen-limited conditions (∼5 μM O2), aerobic ammonia oxidation (nitrification) was restricted to an outer shell (〈100 μm) while anaerobic ammonia oxidation (anammox) was found in the central anoxic parts. Larger type aggregates (〉500 μm) accounted for 68% of the anammox potential whereas 65% of the nitrification potential was found in the smaller aggregates (〈500 μm). Analysis with ∼5 μM O2 microsensors showed that the thickness of the activity zones varied as a function of bulk O2 and NO−2 concentrations and flow rate.
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  • 4
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Nitrogen is the single most limiting factor for rice production. Detailed knowledge on nitrogen dynamics in rice fields is therefore of major importance for developing sustainable rice production. A combination of state-of-the-art microsensor, stable isotope tracer, and molecular techniques was used to evaluate coupled nitrification–denitrification potentials and community structure of ammonia-oxidizing bacteria in a high yield irrigated rice cropping system in the Philippines, without the use of microcosm incubations. The multiple approaches showed a high degree of concordance among methods and thereby clarified the investigated processes. Numbers and potential activity of ammonia-oxidizing bacteria in the system reflected the availability of substrate in three defined soil factions with a ranking of: surface soil 〉 rhizosphere 〉 bulk soil. No nitrification activity was measured between spit applications of N fertilizer. However, nitrification was induced upon nitrogen amendment in intact soil cores. Despite induction by nitrogen amendment, the loss of nitrogen through coupled nitrification–denitrification was less than 10% of the plant nitrogen uptake. Denaturant gradient gel electrophoresis of amoA fragments revealed no differences in diversity profiles between the soil fractions, and phylogenetic analysis, based on amoA genes retrieved from the rice paddy soil, identified a set of mutually very similar sequences related to Nitrosomonas nitrosa.
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  • 5
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract Microzonation of denitrification in trickling filter biofilms was studied using a combined microsensor for O2 and N2O. Denitrification was measured as a function of concentrations of O2, NO3−, organic matter and NH4+ and was found to occur only in part of the biofilm. At increased concentrations of NO3− the thickness of the denitrifying zone increased and thereby increased the total denitrification whereas addition of dissolved organic matter increased the rates of denitrification within the denitrifying part of the biofilm, expressed per volume biofilm. The presence of NH4+ decreased the rate of NO3− assimilation and thereby increased the availability of NO3− for denitrification. Denitrification was only found at O2 concentrations below approximately 20 μM. The toxic zone normally extended 0.2–0.3 mm below the biofilm surface, but when the biofilm was exposed to light photosynthetically produced O2 pushed the oxic-anoxic interface down to 1.3 mm. Denitrification stopped when O2 was introduced to the denitrifying zone, but even after exposure to O2 for 18 h denitrification began immediately after returning to anoxic conditions. Steady state in denitrification was then reached in only 30 min and the rate found then was identical to the rate before exposure to O2, as well as the rate 15 h after return to anoxia. The immediate onset of denitrification suggest that most of the denitrifiers in the biofilm possessed constitutive enzyme systems for denitrification.
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  • 6
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology reviews 24 (2000), S. 0 
    ISSN: 1574-6976
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Flooded rice paddies are one of the major biogenic sources of atmospheric methane. Apart from this contribution to the ‘greenhouse’ effect, rice paddy soil represents a suitable model system to study fundamental aspects of microbial ecology, such as diversity, structure, and dynamics of microbial communities as well as structure–function relationships between microbial groups. Flooded rice paddy soil can be considered as a system with three compartments (oxic surface soil, anoxic bulk soil, and rhizosphere) characterized by different physio-chemical conditions. After flooding, oxygen is rapidly depleted in the bulk soil. Anaerobic microorganisms, such as fermentative bacteria and methanogenic archaea, predominate within the microbial community, and thus methane is the final product of anaerobic degradation of organic matter. In the surface soil and the rhizosphere well-defined microscale chemical gradients can be measured. The oxygen profile seems to govern gradients of other electron acceptors (e.g., nitrate, iron(III), and sulfate) and reduced compounds (e.g., ammonium, iron(II), and sulfide). These gradients provide information about the activity and spatial distribution of functional groups of microorganisms. This review presents the current knowledge about the highly complex microbiology of flooded rice paddies. In Section 2 we describe the predominant microbial groups and their function with particular regard to bacterial populations utilizing polysaccharides and simple sugars, and to the methanogenic archaea. Section 3 describes the spatial and temporal development of microscale chemical gradients measured in experimentally defined model systems, including gradients of oxygen and dissolved and solid-phase iron(III) and iron(II). In Section 4, the results of measurements of microscale gradients of oxygen, pH, nitrate–nitrite, and methane in natural rice fields and natural rice soil cores taken to the laboratory will be presented. Finally, perspectives of future research are discussed (Section 5).
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  • 7
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract: Cells of the aerobic denitrifier and heterotrophic nitrifier Thiosphaera pantotropha and of the traditional denitrifier Paracoccus denitrificans were immobilized in a 1.5 mm thick agar layer (biofilm) and submersed in liquid medium. A combined microsensor for O2 and N2O was used to record microprofiles of these two species in biofilms where the reduction of N2O was inhibited by acetylene. Nitrification in T. pantotropha was not affected by the addition of acetylene and by using a diffusion-reaction model to simulate the N2O profiles it was possible to calculate depth profiles of both nitrification and denitrification. The validity of the calculations when both nitrification and denitrification were operating in concert was confirmed by performing identical calculations on data obtained for a P. denitrificans biofilm. At high NO3− concentrations, part of the NO3− reduced by T. pantotropha biofilms was reduced only to NO2− and N2O production thus did not reflect total NO3− reduction. When NO2− and no NO3− was present in the water above the biofilm N2O production was recorded in the anoxic zone directly below the oxic zone. Nitrous oxide production was never detected in the oxic zone of the biofilms, although aerobic denitrification was described for the original isolate of this bacterium. The growth rate of T. pantotropha in the oxic region of the biofilms was estimated to be 0.42 h−1 which is slightly higher than rates previously obtained in liquid culture. In the T. pantotropha biofilms nitrification was calculated to account for more than 50% of the O2 consumption whereas this process only consumed about 10% of the O2 in liquid culture.
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  • 8
    ISSN: 1574-6941
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
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  • 9
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract A diatom biofilm was grown in a chamber developed for culture of biofilms in chemical gradients. The diatoms grew on a polycarbonate membrane filter which separated a sterile reservoir, with added phosphate, from a reservoir without phosphate. Within 3 weeks of inoculation, a thick biofilm developed on the surface of the filter. The biofilms were homogeneous and therefore suitable for calculations of O2 diffusion fluxes from concentration profiles of O2. Profiles of O2, pH, and gross photosynthesis at different light intensities and liquid medium concentrations of dissolved inorganic carbon and O2 were measured with microelectrodes. Respiratory activity in a layer of the biofilm was determined as the difference between gross photosynthesis and outflux of O2 from that layer. The photosynthetic activity in a well-developed biofilm grown at 360 μEinst m−2 s−1 and 2.4 mM HCO3− was limited by the supply of inorganic carbon. Exposure to light above 360 μEinst m−2 s−1 stimulated gross photosynthesis as well as respiratory processes without affecting net outflux of O2. Higher concentrations of inorganic carbon, on the other hand, enhanced gross photosynthesis without concurrent increase in respiratory rate, resulting in an increased outflux of O2. High concentrations of O2 in the liquid medium decreased the net outflux of O2 with little effect on the gross photosynthesis. The effects of inorganic carbon and O2 on the metabolic activities of the biofilm were consistent with the presence of photorespiratory activity.
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  • 10
    Publication Date: 2014-08-11
    Description: Despite its huge ecological importance, microbial oxygen respiration in pelagic waters is little studied, primarily due to methodological difficulties. Respiration measurements are challenging because of the required high resolution of oxygen concentration measurements. Recent improvements in oxygen sensing techniques bear great potential to overcome these limitations. Here we compare 3 different methods to measure oxygen consumption rates at low oxygen concentrations, utilizing amperometric Clark type sensors (STOX), optical sensors (optodes), and mass spectrometry in combination with 18-18O2 labeling. Oxygen concentrations and consumption rates agreed well between the different methods when applied in the same experimental setting. Oxygen consumption rates between 30 and 400 nmol L−1 h−1 were measured with high precision and relative standard errors of less than 3%. Rate detection limits in the range of 1 nmol L−1 h−1 were suitable for rate determinations in open ocean water and were lowest at the lowest applied O2 concentration.
    Type: Article , PeerReviewed
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