The catabolism and heterotrophic nitrification of the siderophore deferrioxamine B

Summary Three bacteria, two of which were previously noted as active heterotrophic nitrifiers, were examined for their ability to grow and nitrify with the siderophore deferrioxamine B as the carbon source.Pseudomonas aureofaciens displayed limited growth and nitrification while a heterotrophic nitrifyingAlcaligenes sp. was without action concerning its metabolism of deferrioxamine B. The third bacterium, a unique Gram-negative soil isolate, was unable to nitrify deferrioxamine B but grew well when the siderophore was employed as the sole C source. The Gram-negative bacterium removed deferrioxamine B from the medium and left only residual amounts of the compound in solution at the termination of its growth. The organism was without action when the ferrated analogue of deferrioxamine B, ferrioxamine B, sereved as either the C source for growth, for metabolism by resting cells, or as the substrate for cell-free extracts. Deferrioxamine B, by contrast, was rapidly metabolized by resting cells. Cell-free extracts of the bacterium synthesized a monohydroxamate(s) when deferrioxamine B was the substrate. The catabolism of deferrioxamine B, which is synthesized by soil microbes, suggests that soil microflora have the ability to return deferrioxamine B, and perhaps other, siderophores to the C cycle.Abbreviations DFB deferrioxamine B; - FB ferrioxamine B - PhMeSO₂F phenylmethylsulfonyl fluoride     

An iron dioxygenase from Alcaligenes faecalis catalyzing the oxidation of pyruvic oxime to nitrite

Abstract An enzyme which participated in the oxidation of hydroxylamine to nitrite from was partially purified Alcaligenes faecalis , and some of its properties were studied. The enzyme oxidized aerobically pyruvic oxime to nitrite in the presence of hydroxylamine or ascorbate. As molecular oxygen equimolar to nitrite formed was consumed in the enzymatic oxidation of pyruvic oxime to nitrite, the enzyme was thought to be a dioxygenase. It was an iron protein, and a reducing reagent was required to keep the iron in the ferrous state for the action of the enzyme.     

The importance of autotrophic versus heterotrophic oxidation of atmospheric ammonium in forest ecosystems with acid soil

Abstract The role of autotrophic and heterotrophic nitrifying microorganisms in the oxidation of atmospheric ammonium in two acid and one calcareous location of a Dutch woodland area was investigated. In soil slurries nitrate formation was completely inhibited by acetylene, a specific inhibitor of autotrophic ammonium-oxidizing bacteria. A survey of nitrifiers in the forest soils showed that both autotrophic ammonium- and nitrite-oxidizing bacteria were present in high numbers and evidence was obtained that autotrophic bacteria are able to nitrify below pH 4. These results show that autotrophic nitrifying bacteria may account for most of the nitrification in the examined soils. To assess the contribution of heterotrophic nitrifiers, about 200 strains of heterotrophic bacteria and 21 morphologically distinct fungal strains were isolated from the acid soil locations and tested for their ability to nitrify. Only one Penicillium strain produced nitrate in test media, but its nitrate formation when added to acid soils was poor. These findings indicate that in the investigated soil heterotrophs are of minor importance in the oxidation of atmospheric ammonium.     

Geostatistical analysis of soil properties in a secondary tropical dry forest,St. Lucia,West Indies

Spatial variability of soil properties directly influences forest growth. However, spatial variation in soil properties has not been studied within tropical dry forests. As such, it is unclear whether soil properties, like moisture and N availability, display spatial variation at scales similar to that of other ecosystems. To gain insight into this variation, we established a 56 × 56 m sampling grid in tropical dry forest on the Caribbean island of St. Lucia. Samples collected at 4-m intervals were analyzed for forest floor mass, soil texture, pH, organic C, net N mineralization, net nitrification and available P. Geostatistical procedures were used to determine spatial autocorrelation of the aforementioned properties and processes. Semivariogram parameters were used in a block kriging procedure to produce spatial maps of soil properties. At the scale of our study, most soil properties exhibited spatial autocorrelation at distances of 24 m or less. Varying degrees of similarity were found between patterns of forest floor mass, organic C, net N mineralization, net nitrification and available P. No similarity was found between soil texture or pH and other properties. Fine-scale spatial patterns of net N mineralization and net nitrification are likely driven by overstory litter inputs, rather than variation in soil texture and water availability.     

Transformations of ammonia and the environmental impact of nitrifying bacteria

In the sequence of events leading from ammonia to N₂ during the process of biotransformation of inorganic nitrogen compounds, the weakest link, with respect to our knowledge and understanding of the organisms involved, is nitrification. In particular, this is true for the oxidation of ammonia to nitrite. The enzymes have not been thoroughly studied, and the enzymatic mechanisms have not been identified. Almost any biochemical and physiological aspect studied proved to be controversial, and major ecological questions still remain unanswered. Unless the structure and function of the various components of the process are worked out, progress in developing means for controlling nitrification will depend mainly on laborious trial and error and not on knowledgeable manipulation of this group of bacteria.Abbreviations AMO ammonia monooxygenase - HAO hydroxylamine oxidoreductase - MPN most probable number - TCE trichloroethylene     

The variability of nitrifying activity in field soils

The effect of pH on the activity of nitrifying organisms was examined in pasture soils ranging in pH from 4.9 to 7.3, using a short-term nitrification assay (SNA). The optimum pH for nitrifier activity (pH_opt) was generally close to the soil pH, suggesting that the indigenous nitrifier populations adjusted to the prevailing soil pH. A consequence was that the SNA at the soil pH (SNA_pH) bore a near 1:1 relationship with the SNA at the pH_opt (SNA_opt) over a wide range of SNA values. The effect of soil moisture tension on the SNA was less pronounced than that of pH, but an optimum occurred around pF 3.4.     

Interactions among nitrogen-transforming bacteria and nitrogen-fixingPisum sativum L. in laboratory sand columns

Plants of barley (Hordeum vulgare), ryegrass (Lolium perenne), pea (Pisum sativum) or turnip (Brassica campestris rapifera) were grown in pots of unfertilised soil for 10 weeks together with unplanted control pots. A wide range of soil microbiological parameters was measured on bulk soil samples 2, 4, 7 and 10 weeks after seedlings were transplanted. There was no effect of planting or differential effect of plant species upon respiration rate, microbial biomass N, or biomass of microbial predators, but these parameters all varied significantly over time. Respiration, biomass N and nematode biomass all increased, whilst protozoan biomass decreased. Microbial biomass C showed no significant temporal changes or effect of planting. There was evidence for differential plant effects on potential nitrification and denitrification. Nitrification rates were depressed, compared with the fallow, in all treatments except the pea, at some time in the experiment. Conversely denitrification rates were enhanced in all treatments, except the grass, at specific times. Denitrification rates were greater in the pea treatment than the fallow on all occasions. These results demonstrate that plants do not necessarily influence the gross microbiology of the soil, but may affect physiologically distinct sub-components of the microbial biomass.     

Agronomic aspects of wetland rice cultivation and associated methane emissions

Wetland rice cultivation is one of the major sources of atmospheric methane (CH₄). Global rice production may increase by 65% between 1990 and 2025, causing an increase of methane emissions from a 92 Tg CH₄ y^–1 now to 131 Tg in 2025.Methane production depends strongly on the ratio oxidizing: reducing capacity of the soil. It can be influenced by e.g. addition of sulphate, which inhibits methanogenesis. The type and application mode of mineral fertilizers may also affect methane emissions. Addition of organic matter in the form of compost or straw causes an increase of methane emissions, but methane production is lower for materials with a low C/N ratio.High percolation rates in wetland rice soils and occasional drying up of the soil during the cultivation period depresses methane release. Water management practices aimed at reducing emissions are only feasible during specific periods in the rice growing season in flat lowland irrigated areas with high security of water availability and good control of the water supply. Intermittent drying of soils may not be possible on terraced rice lands.Assuming a 10 to 30% reduction in emission rates per unit harvested area, the global emission may amount to 93 Tg CH₄ y^– in 2025. A reduction of global emissions seems very difficult. To develop techniques for reducing CH₄ emissions from wetland rice fields, research is required concerning interactions between soil chemical and physical properties, and soil, water and crop management and methanogenesis. Such techniques should not adversely affect rice yields.     

Heterotrophic cultivation of Paracoccus denitrificans in a horizontal rotating tubular bioreactor

In this work, the heterotrophic cultivation of bacterium Paracoccus denitrificans has been studied in a horizontal rotating tubular bioreactor (HRTB). After development of a microbial biofilm on the inner surface of the HRTB, conditions for one-step removal of acetate and ammonium ion were created. The effect of bioreactor process parameters [medium inflow rate (F) and bioreactor rotation speed (n)] on the bioprocess dynamics in the HRTB was studied. Nitrite and nitrogen oxides (NO and N₂O) were detected as intermediates of ammonium ion degradation. The biofilm thickness and the nitrite concentration were gradually reduced with increase of bioreactor rotation speed when the medium inflow rate was in the range of 0.5–1.5 l h⁻¹. Further increase of inflow rate (2.0–2.5 l h⁻¹) did not have a significant effect on the biofilm thickness and nitrite concentration along the HRTB. Complete acetate consumption was observed when the inflow rate was in the range of 0.5–1.5 l h⁻¹ at all bioreactor rotation speeds. Significant pH gradient (cca 1 pH unit) along the HRTB was only observed at the highest inflow rate (2.5 l h⁻¹). The results have clearly shown that acetate and ammonium ion removal by P. denitificans can be successfully conducted in a HRTB as a one-step process.