Quantification of a novel group of nitrate-reducing bacteria in the environment by real-time PCR

Nitrate reduction is performed by phylogenetically diverse bacteria. Analysis of narG (alpha subunit of the membrane bound nitrate reductase) trees constructed using environmental sequences revealed a new cluster that is not related to narG gene from known nitrate-reducing bacteria. In this study, primers targeting this as yet uncultivated nitrate-reducing group were designed and used to develop a real-time SYBR(R) Green PCR assay. The assay was tested with clones from distinct nitrate-reducing groups and applied to various environmental samples. narG copy number was high ranging between 5.08x10(8) and 1.12x10(11) copies per gram of dry weight of environmental sample. Environmental real-time PCR products were cloned and sequenced. Data was used to generate a phylogenetic tree showing that all environmental products belonged to the target group. Moreover, 16S rDNA copy number was quantified in the different environments by real-time PCR using universal primers for Eubacteria. 16S rDNA copy number was similar or slightly higher than that of narG, between 7.12x10(9) and 1.14x10(11) copies per gram of dry weight of environmental sample. Therefore, the yet uncultivated nitrate-reducing group targeted in this study seems to be numerically important in the environment, as revealed by narG high absolute and relative densities across various environments. Further analysis of the density of the nitrate-reducing community as a whole by real-time PCR may provide insights into the correlation between microbial density, diversity and activity.     

Denitrifying bacteria in bulk and maize-rhizospheric soil: diversity and N2O-reducing abilities

The aim of this study was to determine the effect of the rhizosphere of maize on the diversity of denitrifying bacteria. Community structure comparison was performed by constructing a collection of isolates recovered from bulk and maize planted soil. A total of 3240 nitrate-reducing isolates were obtained and 188 of these isolates were identified as denitrifiers based on their ability to reduce nitrate to N2O or N2. 16S rDNA fragments amplified from the denitrifying isolates were analysed by restriction fragment length polymorphism. Isolates were grouped according to their restriction patterns, and 16S rDNA of representatives from each group were sequenced. A plant dependent enrichment of Agrobacterium-related denitrifiers has been observed resulting in a modification of the structure of the denitrifying community between planted and bulk soil. In addition, the predominant isolates in the rhizosphere soil were not able to reduce N2O while dominant isolates in the bulk soil evolve N2 as a denitrification product.     

Influence of maize mucilage on the diversity and activity of the denitrifying community

In order to understand the effect of the maize rhizosphere on denitrification, the diversity and the activity of the denitrifying community were studied in soil amended with maize mucilage. Diversity of the denitrifying community was investigated by polymerase chain reaction (PCR) amplification of total community DNA extracted from soils using gene fragments, encoding the nitrate reductase (narG) and the nitrous oxide reductase (nosZ), as molecular markers. To assess the underlying diversity, PCR products were cloned and 10 gene libraries were obtained for each targeted gene. Libraries containing 738 and 713 narG and nosZ clones, respectively, were screened by restriction fragment analysis, and grouped based on their RFLP (restriction fragment length polymorphism) patterns. In all, 117 and 171 different clone families have been identified for narG and nosZ and representatives of RFLP families containing at least two clones were sequenced. Rarefaction curves of both genes did not reach a clear saturation, indicating that analysis of an increasing number of clones would have revealed further diversity. Recovered NarG sequences were related to NarG from Actinomycetales and from Proteobacteria but most of them are not related to NarG from known bacteria. In contrast, most of the NosZ sequences were related to NosZ from alpha, beta, and gammaProteobacteria. Denitrifying activity was monitored by incubating the control and amended soils anaerobically in presence of acetylene. The N2O production rates revealed denitrifying activity to be greater in amended soil than in control soil. Altogether, our results revealed that mucilage addition to the soil results in a strong impact on the activity of the denitrifying community and minor changes on its diversity.     

LDL-mediated targeting of liposomes to leukemic lymphocytes in vitro.

We describe a method for the covalent coupling of low-density lipoproteins (LDL) to the surface of small unilamellar vesicles, and the delivery of the liposome content to leukemic L2C lymphocytes in vitro. We demonstrate the stability of the linkage between LDL and liposomes, the preservation of vesicle integrity and the affinity of the LDL for their specific receptors after the coupling reaction. Hygromycin B, an impermeant inhibitor of protein synthesis, was encapsulated in the targeted liposomes, and delivered into the cytoplasm of leukemic L2C lymphocytes by the LDL pathway, as demonstrated by the lethal effect on cells measured by 51chromium-release assay.     

Modifications of LDL-receptor-mediated endocytosis rates in CEM lymphoblastic cells grown in lipoprotein-depleted fetal calf serum

The efficiency of supplying cholesterol by the LDL endocytic pathway of lymphoblastic T CEM cells was compared when incubated in the presence of either fetal calf serum (FCS) or lipoprotein-depleted fetal calf serum (LDFCS). In the presence of FCS, there were 8600 +/- 2000 LDL receptors/cell with a Kd of (2.2 +/- 0.8).10(-8) M and a receptor cycling time of about 7 min; about 90% of the internalized LDL was degraded. LDL degradation produced 98% of total cellular cholesterol and only 2% came from endogenous synthesis. The absence of LDL in the culture medium of lymphoblastic CEM cells deeply modified certain metabolic and structural characteristics of the cells. Their cholesterol content decreased; the total number of LDL receptors increased 6-fold, whereas their affinity for the ligand decreased by the same factor (Kd = (1.2 +/- 0.2).10(-7) M); the receptor cycling time increased 3-fold. Finally, LDL degraded by cholesterol-depleted CEM cells amounted to about 40% of that degraded by untreated CEM cells.     

Cholinephosphotransferase and ethanolaminephosphotransferase activities in Plasmodium knowlesi-infected erythrocytes. Their use as parasite-specific markers

CDPcholine: 1,2-diacylglycerol cholinephosphotransferase (EC 2.7.8.2) and CDPethanolamine: 1,2-diacylglycerol ethanolaminephosphotransferase (EC 2.7.8.1) activities were investigated in Plasmodium knowlesi-infected erythrocytes obtained from Macaca fascicularis monkeys. Disrupted infected erythrocytes possess a cholinephosphotransferase activity (1.3 +/- 0.2 nmol phosphatidylcholine/10(7) infected cells per h) 1.5-times higher than the ethanolaminephosphotransferase activity. Optimal activities of both enzymes were observed in the presence of 12 mM MnCl2, which was about 3-times as effective as 40 mM MgCl2 as a cofactor. The two activities had similar dependences on pH and thermal inactivation. Their Arrhenius plots show an identical break at 17 degrees C and the corresponding activation energies below and above the critical temperature were similar for the two activities. Sodium deoxycholate, sodium dodecyl sulfate, Triton X-100, beta-D-octylglucoside and lysophosphatidylcholine strongly inhibited the two activities above their critical micellar concentration, but the first three detergents stimulated the activities at lower concentrations. Saponin (0.004-0.5%) either did not affect the two activities or else increased them. Cholinephosphotransferase and ethanolaminephosphotransferase activities had apparent Km values for the CDP ester of 23.4 and 18.6 microM, respectively. CDPcholine and CDPethanolamine competitively inhibited the ethanolaminephosphotransferase and cholinephosphotransferase activities, respectively. The high selectivity of these activities for individual molecular species of diradylglycerol suggests that substrate specificity is responsible for the various molecular species of Plasmodium-infected erythrocyte phospholipids. However, cholinephosphotransferase and ethanolaminephosphotransferase had different dependences on 1,2-dilauroylglycerol and 1-oleylglycerol, which were substrates for cholinephosphotransferase but not for ethanolaminephosphotransferase under our conditions. These data provide the first characterization of an enzyme involved in the intense lipid metabolism in Plasmodium-infected erythrocytes, and the presence of cholinephosphotransferase demonstrates a biosynthesis of phosphatidylcholine by the Kennedy pathway after infection. Our data suggest that cholinephosphotransferase and ethanolaminephosphotransferase activities could be catalyzed by the same enzyme. Furthermore, since host erythrocytes are devoid of these enzymatic activities, cholinephosphotransferase is a parasite-specific membrane-associated enzyme which can be used as a probe or marker.     

The influence of the internal content of negatively charged liposomes on their interaction with high-density lipoprotein

The release of the internal content of negatively charged phosphatidylcholine/phosphatidylserine vesicles under the influence of high density lipoprotein was studied. Under standard conditions (the same composition outside and inside the compartment) the leakage of negative liposomes increased significantly. However, a high internal concentration of calcein provoked a sealing effect, exhibited both in sucrose and in calcein release. This sealing effect is not related to the size of vesicles, the fluidity of the membrane, the distribution of phosphatidylserine molecules, or the membrane potential. Our data indicate that surface potential influences this effect, probably in addition to a lateral pressure effect such as with cholesterol. The surface potential, as measured by the water-lipid partition coefficient of fatty acids, is strongly affected by internal ionic strength when liposomes contain calcein as well as other polyanions (6-carboxyfluorescein, sodium citrate).     

The impact of agricultural management on soil aggregation and carbon storage is regulated by climatic thresholds across a 3000 km European gradient

Organic carbon and aggregate stability are key features of soil quality and are important to consider when evaluating the potential of agricultural soils as carbon sinks. However, we lack a comprehensive understanding of how soil organic carbon (SOC) and aggregate stability respond to agricultural management across wide environmental gradients. Here, we assessed the impact of climatic factors, soil properties and agricultural management (including land use, crop cover, crop diversity, organic fertilization, and management intensity) on SOC and the mean weight diameter of soil aggregates, commonly used as an indicator for soil aggregate stability, across a 3000 km European gradient. Soil aggregate stability (−56%) and SOC stocks (−35%) in the topsoil (20 cm) were lower in croplands compared with neighboring grassland sites (uncropped sites with perennial vegetation and little or no external inputs). Land use and aridity were strong drivers of soil aggregation explaining 33% and 20% of the variation, respectively. SOC stocks were best explained by calcium content (20% of explained variation) followed by aridity (15%) and mean annual temperature (10%). We also found a threshold-like pattern for SOC stocks and aggregate stability in response to aridity, with lower values at sites with higher aridity. The impact of crop management on aggregate stability and SOC stocks appeared to be regulated by these thresholds, with more pronounced positive effects of crop diversity and more severe negative effects of crop management intensity in nondryland compared with dryland regions. We link the higher sensitivity of SOC stocks and aggregate stability in nondryland regions to a higher climatic potential for aggregate-mediated SOC stabilization. The presented findings are relevant for improving predictions of management effects on soil structure and C storage and highlight the need for site-specific agri-environmental policies to improve soil quality and C sequestration.     

Dissimilatory nitrite-reductase provides a competitive advantage to Pseudomonas sp. RTC01 to colonise the centre of soil aggregates

Abstract: The effect of soil aggregation on denitrification has been studied in different ways: artificial or natural aggregates individually analysed or comparison of denitrifying activity of different size classes of aggregates. However, until now, no work has been conducted to evaluate the role of denitrification in the microbial colonisation of soil aggregates. Over a one-month period, we examined on remoulded nonsterile soil aggregates the survival of inoculated wild-type Pseudomonas strain and of its corresponding isogenic Tn5 mutant (Nir⁻) lacking the ability to synthesize the dissimilative nitrite-reductase. Simultaneously, the evolution of the O₂ repartition inside the soil aggregates was assessed by the use of microelectrodes. The inner and outer portions were roughly anoxic and oxic, respectively, during the entire experiment while the intermediate portion showed fluctuating aeration conditions. The values of the Nir⁻ to wild-type + Nir⁻ ratio were found in the following order: inner < intermediate < outer portion, demonstrating that the nitrite-reductase may provide a competitive advantage to the Pseudomonas strain to colonise the centre of soil aggregates. However, a clear differentiation between inner and outer aggregates portions was not observed with the indigenous microflora (denitrifiers-to-total heterotrophs, biomass or physiological abilities).     

Peaks of in situ N2O emissions are influenced by N2O‐producing and reducing microbial communities across arable soils

Agriculture is the main source of terrestrial N₂O emissions, a potent greenhouse gas and the main cause of ozone depletion. The reduction of N₂O into N₂ by microorganisms carrying the nitrous oxide reductase gene (nosZ) is the only known biological process eliminating this greenhouse gas. Recent studies showed that a previously unknown clade of N₂O‐reducers (nosZII) was related to the potential capacity of the soil to act as a N₂O sink. However, little is known about how this group responds to different agricultural practices. Here, we investigated how N₂O‐producers and N₂O‐reducers were affected by agricultural practices across a range of cropping systems in order to evaluate the consequences for N₂O emissions. The abundance of both ammonia‐oxidizers and denitrifiers was quantified by real‐time qPCR, and the diversity of nosZ clades was determined by 454 pyrosequencing. Denitrification and nitrification potential activities as well as in situ N₂O emissions were also assessed. Overall, greatest differences in microbial activity, diversity, and abundance were observed between sites rather than between agricultural practices at each site. To better understand the contribution of abiotic and biotic factors to the in situ N₂O emissions, we subdivided more than 59,000 field measurements into fractions from low to high rates. We found that the low N₂O emission rates were mainly explained by variation in soil properties (up to 59%), while the high rates were explained by variation in abundance and diversity of microbial communities (up to 68%). Notably, the diversity of the nosZII clade but not of the nosZI clade was important to explain the variation of in situ N₂O emissions. Altogether, these results lay the foundation for a better understanding of the response of N₂O‐reducing bacteria to agricultural practices and how it may ultimately affect N₂O emissions.