R. Lensi

Link between spatial structure of microbial communities and degradation of a complex mixture of volatile organic compounds in peat biofilters

Aims:  To investigate the relationships between the operation of the volatile organic compound (VOC) removal biofilter and the structure of microbial communities, and to study the impact on degradation activities and the structuring of microbial communities of biofilter malfunctions related to the qualitative composition of the polluted air.

Denitrifiers and denitrifying activity in size fractions of a mollisol under permanent pasture and continuous cultivation

Abstract The variability of the denitrification process in soils was investigated through the distribution of denitrifiers and potential denitrifying activity in the various microenvironments of a mollisol sampled under permanent pasture (PP) and under continuous cultivation (CC). Five size-separates ( 250 μm fraction to the total potential denitrification was negligible due to the very small number of denitrifying organisms associated with this fraction. Moreover, a high DSA was found only in the POM of the soil under permanent pasture and not in the soil under continuous cultivation.

Dynamics of residual enzyme activities, denitrification potential, and physico-chemical properties in a γ-sterilized soil

Abstract The use or sterilized reinoculated soils appears to be valuable in the study of relationships between numbers and activity of microorganisms, especially in the case of denitrifiers. In this context, residual enzymatic activities and physico-chemical changes after γ-irradiation have been studied. The dynamics of disappearance of the residual activities of denitrifying enzymes, CO; release and β-glucosiduse activity were followed for 8 weeks. Evolution of some physico-chemical properties after γ-irradiation were also tested: pH, N and C status, concentrations of exchangeable cations, soil porosity. The soil treatments were wet or dry γ-sterilized and wet or dry stored after irradiation. Complete sterilization was achieved by a 25 kGy dose in all treatments. No important changes were noticed concerning the pore volume distribution. Very small variations in pH and exchangeable cation concentrations were considered negligible. On the contrary, an increase in soluble organic C. especially in the wet treatment, was attributed both to the lysis of killed cells and to the release of organic acids. particularly through the action of peroxides in wet conditions. The measurement of the enzymatic activities showed the resistance of enzymes to irradiation, leading for example to CO2 production, to lysis of β-glucosidic bonds or to variations in the N status through deamination of nitrogenous organic compounds or progressive protcolysis of microbial cells. Nevertheless, the location of enzymes was considered as a factor controlling resistance to γ-rays and to its subsequent activity. We suggested that denitrifying enzymes were remaining active in non-proliferating cells and that the loss of potential denitrifying activity, observed for the 8 weeks period, resulted from cell lysis. It was concluded that γ-irradiation of dry soil is less damaging than that of wet soil. Nevertheless, the soil must stabilize before use and a control (uninoculated irradiated soil) must be compared in order not to attribute residual activities of the irradiated soil to the introduced microbial populations.

Role of Respiratory Nitrate Reductase in Ability of Pseudomonas fluorescens YT101 To Colonize the Rhizosphere of Maize

ABSTRACT 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 denitrifyingPseudomonas 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.

Relationships between root density of the African grass Hyparrhenia diplandra and nitrification at the decimetric scale: an inhibition–stimulation balance hypothesis

Previous studies have shown that Lamto savannah exhibits two different types of nitrogen cycle with high and low nitrification sites and suggested that the perennial grass Hyparrhenia diplandra is responsible for this duality at a subpopulation level, with one ecotype being thought to be able to inhibit nitrification. The present work aimed to investigate the relationships between nitrification and the roots of H. diplandra at two scales. (i) Site–scale experiments gave new insight into the hypothesized control of nitrification by H. diplandra tussocks: the two ecotypes exhibited opposite influences, inhibition in a low nitrification site (A) and stimulation in a high nitrification site (B). (ii) Decimetric–scale experiments demonstrated close negative or positive relationships (in sites A or B, respectively) between the roots and nitrification (in the 0–10 cm soil layer), showing an unexpectedly high sensitivity of the nitrification process to root density. In both soils, the correlation between the roots and nitrification decreased with depth and practically disappeared in the 20–30 cm soil layer (where the nitrification potential was found to be very low). Therefore, the impact of H. diplandra on nitrification may be viewed as an inhibition–stimulation balance.

Effect of soil type and plant species on the fluorescent pseudomonads nitrate dissimilating community

The distribution of nitrogen dissimilative abilities among 618 isolates of fluorescent pseudomonads was studied. These strains were isolated from two uncultivated soils (C and D; collected at Châteaurenard and Dijon, France, respectively) and from rhizosphere, rhizoplane and root tissue of two plant species (flax and tomato) cultivated on these two soils. According to their ability to dissimilate nitrogen, the isolates have been distributed into three metabolic types: non-dissimilators, NO2- accumulators and denitrifiers. While the three metabolic types were recovered in all the compartments of soil D experiments, only two (non-dissimilators and denitrifiers) were recovered in all the compartments of soil C experiments. Even under the contrasting conditions of the two soil types, both plants were able to select the nitrate dissimilating community among the total community of fluorescent Pseudomonas, but the mode of this selection seems to be dependent on both plant and soil type. The soil type appears to be unable to significantly modulate the strong selective effect of tomato. Indeed, similar dissimilator to non-dissimilator ratios were found in the root tissue of this plant species cultivated in both soils. In contrast, the different dissimilator to non-dissimilator ratios observed in flax roots between soils C and D suggest that the selective effect of flax was modulated by the soil type. Taxonomic identifications showed that the 618 isolates were distributed among three species (P. chlororaphis, P. fluorescens, P. putida) plus an intermediate type between P. fluorescens and P. putida. However, no clear relationship between the distribution of the metabolic types (functional diversity) and the distribution of bacterial species has been found.

Denitrification in waterlogged soils: In situ temperature-dependent variations

Abstract A method to measure nitrous oxide (N2O) produced by denitrification in the field is described. The system shows a relationship between N2O emission and the daily temperature variations of the surface soil. We compare the results with those obtained by complementary use of acetylene. A conversion factor between emitted N2O (without C2H2) and reduced NO−3 is discussed.

PURIFICATION OF THE DISSIMILATIVE NITRATE REDUCTASE OF PSEUDOMONAS FLUORESCENS AND THE CLONING AND SEQUENCING OF ITS CORRESPONDING GENES

The dissimilative membrane-bound nitrate reductase from Pseudomonas fluorescens strain AK15 was purified and the alpha subunit of the enzyme partially sequenced. On the basis of this partial amino acid sequence and of conserved stretches of amino acids between Escherichia coli and Bacillus subtilis, degenerate primers were design to amplify the narG gene and part of the narH gene in a PCR approach. The deduced amino acid sequence of narG shows 72% and 52% and narH 78% and 62% identity to the homologous subunit of E. coli and B. subtilis, respectively.

Spatial distribution of nitrification and denitrification in an acid forest soil

Abstract The spatial distribution of nitrification and denitrification has been studied in a forest located in central France. The potential for nitrification in the A1 soil horizon showed a high variability at a 1 m scale and was even absent at locations where a thick upper litter was present these locations, the highest nitrification ability was found in the first 2 cm of the litter, demonstrating that recent stages may be colonized by nitrifiers. These findings suggested that the process may be governed by O2 diffusion. In the litter, the potential for nitrification was found to be equally distributed between the Abies alba needles and the aggregates of organic matter particles mainly resulting from faunal activity. At the same scale the denitrification process was never absent and showed lttle variability. Consequently, the distribution of this process has been studied at the scale of 0.2 mm x 0.5 mm aggregates. All the aggregates appeared to be fully colonized by soil bacteria. However, some aggregates did not exhibit any denitrifying ability when they were individually incubated in rich or minimal medium. This suggests that a limit of the spatial distribution of denitrifying organisms was reached at a 0.5 mm scale, which is the size of currently encountered aggregates in this forest soil.

Evaluation of dispersion methods for enumeration of microorganisms from peat and activated carbon biofilters treating volatile organic compounds

To enumerate microorganisms having colonized biofilters treating volatile organic compounds, it is necessary firstly to evaluate dispersion methods. Crushing, shaking and sonication were then tested for the removal of microflora from biofilters packing materials (peat and activated carbon). Continuous or discontinuous procedures, and addition of glass beads had no effect on the number of microorganisms removed from peat particles. The duration of treatment also had no effect for shaking and crushing, but the number of microorganisms after 60 min of treatment with ultrasound was significantly higher than that obtained after 0.5 min. The comparison between these methods showed that crushing was the most efficient for the removal of microorganisms from both peat and activated carbon. The comparison between three chemical dispersion agents showed that 1% Na-pyrophosphate was less efficient, compared with 200 mM phosphate buffer or 1% Na-hexametaphosphate. To optimize the cultivation of microorganisms, three different agar media were compared. Tryptic soy agar tenfold diluted (TSA 1/10) was the most suitable medium for the culture of microflora from a peat biofilter. For the activated carbon biofilter, there was no significant difference between Luria Bertoni, TSA 1/10, and plate count agar. The optimized extraction and enumeration protocols were used to perform a quantitative characterization of microbial populations in an operating laboratory activated carbon biofilter and in two parallel peat biofilters.