Aerobic and anaerobic growth of rifampin-resistant denitrifying bacteria in soil

Effects of drought and N-fertilization on N cycling in two grassland soils

Changes in frequency and intensity of drought events are anticipated in many areas of the world. In pasture, drought effects on soil nitrogen (N) cycling are spatially and temporally heterogeneous due to N redistribution by grazers. We studied soil N cycling responses to simulated summer drought and N deposition by grazers in a 3-year field experiment replicated in two grasslands differing in climate and management. Cattle urine and NH4NO3 application increased soil NH4(+) and NO3(-) concentrations, and more so under drought due to reduced plant uptake and reduced nitrification and denitrification. Drought effects were, however, reflected to a minor extent only in potential nitrification, denitrifying enzyme activity (DEA), and the abundance of functional genes characteristic of nitrifying (bacterial and archaeal amoA) and denitrifying (narG, nirS, nirK, nosZ) micro-organisms. N2O emissions, however, were much reduced under drought, suggesting that this effect was driven by environmental limitations rather than by changes in the activity potential or the size of the respective microbial communities. Cattle urine stimulated nitrification and, to a lesser extent, also DEA, but more so in the absence of drought. In contrast, NH4NO3 reduced the activity of nitrifiers and denitrifiers due to top-soil acidification. In summary, our data demonstrate that complex interactions between drought, mineral N availability, soil acidification, and plant nutrient uptake control soil N cycling and associated N2O emissions. These interactive effects differed between processes of the soil N cycle, suggesting that the spatial heterogeneity in pastures needs to be taken into account when predicting changes in N cycling and associated N2O emissions in a changing climate.

A steady-state biofilm model for simultaneous reduction of nitrate and perchlorate, part 1: model development and numerical solution

A multispecies biofilm model is developed for simultaneous reduction of nitrate and perchlorate in the H(2)-based membrane biofilm reactor. The one-dimension model includes dual-substrate Monod kinetics for a steady-state biofilm with five solid and five dissolved components. The solid components are autotrophic denitrifying bacteria, autotrophic perchlorate-reducing bacteria, heterotrophic bacteria, inert biomass, and extracellular polymeric substances (EPS). The dissolved components are nitrate, perchlorate, hydrogen (H(2)), substrate-utilization-associated products, and biomass-associated products (BAP). The model explicitly considers four mechanisms involved in how three important operating conditions (H(2) pressure, nitrate loading, and perchlorate loading) affect nitrate and perchlorate removals: (1) competition for H(2), (2) promotion of PRB growth due to having two electron acceptors (nitrate and perchlorate), (3) competition between nitrate and perchlorate reduction for the same resources in the PRB: electrons and possibly reductase enzymes, and (4) competition for space in the biofilm. Two other special features are having H(2) delivered from the membrane substratum and solving directly for steady state using a novel three-step approach: finite-difference for approximating partial differential and/or integral equations, Newton-Raphson for solving nonlinear equations, and an iterative scheme to obtain the steady-state biofilm thickness. An example result illustrates the model's features.

Competition between Two Isolates of Denitrifying Bacteria Added to Soil

We examined the competitive relationship between two isolates of denitrifying bacteria, both of which grow well under aerobic conditions but differ in their ability to grow under denitrifying conditions. The growth and persistence of the two isolates, added to sterile soil or added to soil previously colonized by the other isolate, were monitored under aerobic and denitrifying (anaerobic) conditions. When isolates were added together to sterile soil, the isolate added at the higher density reduced the growth of the isolate added at the lower density. The magnitude of the growth reduction varied depending on the competitive abilities of the individual isolates and the aeration state of the soil. Prior colonization of soil with one of the isolates conferred a competitive advantage on the colonized isolate but did not lead to the disappearance of the challenging isolate. Fluctuations in aeration state caused large changes in the population density of one isolate and altered the competitive relationship between the two isolates. The competitive effectiveness of each isolate varied with cell density, the degree of prior colonization of the soil by the other isolate, and the aeration state of the soil.

Co-existence of anammox and denitrification for simultaneous nitrogen and carbon removal--Strategies and issues

The discovery of anaerobic ammonium oxidation (anammox) has greatly improved the understanding of the nitrogen cycle. Anammox provides great promise for the removal of nitrogen from wastewater, containing high concentration of ammonium. However, the presence of organic carbon is considered as unfavorable to this autotrophic process, i.e. anammox. Most of the real wastewaters contain both organic carbon and nitrogen. Under this circumstance, several processes have been established primarily for the complete removal of organic carbon. Subsequently, the wastewater containing no or low organic carbon and nitrogen is treated via a variety of nitrogen removal processes. The co-existence of anammox and denitrification could be useful for the simultaneous removal of nitrogen and organic carbon in a single system rather than a sequential chain of treatment. This review addresses the microbiology, strategies, consequences and the future research challenges in the co-existence of anammox and denitrification.

Relative involvement of nitrate and nitrite reduction in the competitiveness of Pseudomonas fluorescens in the rhizosphere of maize under non-limiting nitrate conditions

Competition between different isogenic mutants of Pseudomonas fluorescens unable to carry out the first steps of the denitrification pathway was compared in soil micro-columns non-planted or planted with maize. A new isogenic mutant of P. fluorescens YT101 affected in both nitrate and nitrite respirations was constructed and used as a model of non-denitrifying strain (FM69MS strain). The outcome of the selection exerted by the plant after co-inoculation of FM69MS at the same ratio either with an isogenic denitrifier unable to reduce nitrate (Nar(-) mutant) or with an isogenic NO2 (-) accumulator (Nir(-) mutant) was investigated in non-limiting NO3 (-) conditions. Regardless of the inoculated mixture, both strains were able to grow in both rhizosphere and non-planted soil. The proportion of Nar(-) or Nir(-) strain in the Nar(-)+FM69MS or Nir(-)+FM69MS total introduced population remained stable in non-planted soil. In the rhizosphere, we observed a higher competitiveness of the Nir(-) mutant compared with FM69MS, whereas the latter showed the same competitiveness as the Nar(-) mutant. These results provide the first demonstration that NO3 (-) reduction is the main nitrogen-dissimilating step controlling the competitiveness of P. fluorescens in the rhizosphere.

Role of respiratory nitrate reductase in ability of Pseudomonas fluorescens YT101 to colonize the rhizosphere of maize

Selection of the denitrifying community by plant roots (i.e., increase in the denitrifier/total heterotroph ratio in the rhizosphere) has been reported by several authors. However, very few studies to evaluate the role of the denitrifying function itself in the selection of microorganisms in the rhizosphere have been performed. In the present study, we compared the rhizosphere survival of the denitrifying Pseudomonas fluorescens YT101 strain with that of its isogenic mutant deficient in the ability to synthesize the respiratory nitrate reductase, coinoculated in nonplanted or planted soil. We demonstrated that under nonlimiting nitrate conditions, the denitrifying wild-type strain had an advantage in the ability to colonize the rhizosphere of maize. Investigations of the effect of the inoculum characteristics (density of the total inoculum and relative proportions of mutant and wild-type strains) on the outcome of the selection demonstrated that the selective effect of the plant was expressed only during the phase of bacterial multiplication and that the intensity of selection was dependent on the magnitude of this phase. Moreover, application of the de Wit replacement series technique to our results suggests that the advantage of the wild-type strain was maximal when the ratio between the two strains in the inoculum was close to 1:1. This work constitutes the first direct demonstration that the presence of a functional structural gene encoding the respiratory nitrate reductase confers higher rhizosphere competence to a microorganism.

Use of tn5 mutants to assess the role of the dissimilatory nitrite reductase in the competitive abilities of two pseudomonas strains in soil

We examined the influence of soil aeration state and plant root presence on the comparative survival of wild-type bacteria and isogenic Tn5 (Nir(sup-)) mutants lacking the ability to synthesize nitrite reductase. Two denitrifying Pseudomonas strains with different nitrite reductase types were used. Enumeration of bacteria in sterile and nonsterile soils was based on differential antibiotic resistance. The validity of the bacterial models studied (i.e., equal growth of wild-type and mutant bacteria under aerobic conditions and significantly better growth of wild-type bacteria under denitrifying conditions) was verified in pure-culture studies. In sterile soil, both strains survived better under aerobic than under anaerobic conditions. The lower efficiency of denitrification than O(inf2) respiration in supporting bacterial growth explained this result, and the physical heterogeneity of soil did not strongly modify the results obtained in pure-culture studies. In nonsterile soil, one of the Pseudomonas strains survived better under anaerobic conditions while the other competed equally with the indigenous soil microflora under aerobic and anaerobic conditions. However, when the Nir(sup-)-to-total inoculant ratios (wild type plus Nir(sup-) mutant) were analyzed, it appeared that the presence of nitrite reductase conferred on both Pseudomonas strains a competitive advantage for anaerobic environment or rhizosphere colonization. This is the first attempt to demonstrate with isogenic nondenitrifying mutants that denitrification can contribute to the persistence and distribution of bacteria in fluctuating soil environments.