Impact of soil pedogenesis on the diversity and composition of fungal communities across the California soil chronosequence of Mendocino.

Understanding how soil pedogenesis affects microbial communities and their in situ activities according to ecosystem functioning is a central issue in soil microbial ecology, as soils represent essential nutrient reservoirs and habitats for the biosphere. To address this question, soil chronosequences developed from a single, shared mineralogical parent material and having the same climate conditions are particularly useful, as they isolate the factor of time from other factors controlling the character of soils. In our study, we considered a natural succession of uplifted marine terraces in Mendocino, CA, ranging from highly fertile in the younger terrace (about 100,000 years old) to infertile in the older terraces (about 300,000 years old). Using ITS amplicon pyrosequencing, we analysed and compared the diversity and composition of the soil fungal communities across the first terraces (T1 to T3), with a specific focus in the forested terraces (T2 and T3) on soil samples collected below trees of the same species (Pinus muricata) and of the same age. While diversity and richness indices were highest in the grassland (youngest) terrace (T1), they were higher in the older forested terrace (T3) compared to the younger forested terrace (T2). Interestingly, the most abundant ectomycorrhizal (ECM) taxa that we found within these fungal communities showed high homology with ITS Sanger sequences obtained previously directly from ECM root tips from trees in the same study site, revealing a relative conservation of ECM diversity over time. Altogether, our results provide new information about the diversity and composition of the fungal communities as well as on the dominant ECM species in the soil chronosequence of Mendocino in relation to soil age and ecosystem development.

Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities.

The impacts of plant species on the microbial communities and physico-chemical characteristics of soil are well documented for many herbs, grasses and legumes but much less so for tree species. Here, we investigate by rRNA and ITS amplicon sequencing the diversity of microorganisms from the three domains of life (Archaea, Bacteria and Eukaryota:Fungi) in soil samples taken from the forest experimental site of Breuil-Chenue (France). We discovered significant differences in the abundance, composition and structure of the microbial communities associated with two phylogenetically distant tree species of the same age, deciduous European beech (Fagus sylvatica) and coniferous Norway spruce (Picea abies Karst), planted in the same soil. Our results suggest a significant effect of tree species on soil microbiota though in different ways for each of the three microbial groups. Fungal and archaeal community structures and compositions are mainly determined according to tree species, whereas bacterial communities differ to a great degree between rhizosphere and bulk soils, regardless of the tree species. These results were confirmed by quantitative PCR, which revealed significant enrichment of specific bacterial genera, such as Burkholderia and Collimonas, known for their ability to weather minerals within the tree root vicinity.

Improved gfp and inaZ broad-host-range promoter-probe vectors.

A new set of broad-host-range promoter-probe vectors has been constructed. One subset contains the pVS1 and p15a replicons and confers resistance to either gentamicin or kanamycin. The other set contains the broad-host-range replicon from pBBR1 and confers resistance to kanamycin, tetracycline, ampicillin, or spectinomycin/streptomycin. Both plasmid sets are highly stable and are maintained without selection for more than 30 generations in several bacterial taxa. Each plasmid contains a promoter-probe cassette that consists of a multicloning site, containing several unique restriction sites, and gfp or inaZ as a reporter gene. The cassette is bound by transcriptional terminators to permit the insertion of strong promoters and to insulate the cassette from external transcription enabling the detection of weak or moderate promoters. The vector suite was augmented with derivatives of the kanamycin-resistant gfp promoter-probe plasmids that encode Gfp variants with different half-life times.

Genetic characterization of insertion sequence ISJP4 on plasmid pJP4 from Ralstonia eutropha JMP134.

Directly adjacent to the (tfdT-) tfdCDEF gene cluster for chlorocatechol breakdown on plasmid pJP4 of Ralstonia eutropha (formerly Alcaligenes eutrophus) JMP134, we identified a 0.9-kb DNA element, designated ISJP4, with the typical features of a bacterial insertion sequence. ISJP4 occurs as a single complete copy on plasmid pJP4. About 9 kb away from this copy, in the tfdA-tfdS intergenic region, we found a 71-bp duplication of the ISJP4 right-hand extremity. In addition, we discovered a complete copy of ISJP4 on the chromosome of the R. eutropha JMP134 strain that we use routinely in our laboratory. We suppose that this copy resulted from a recent transposition of the plasmid-borne ISJP4, since it was shown to be lacking from the chromosomes of R. eutropha JMP222 and JMP289, two previously pJP4-cured derivatives of JMP134. By comparing both complete copies and their flanking regions, we could establish that element ISJP4 has a size of 915 bp and is bordered by 18-bp inverted repeats with one mismatch. Based on sequence similarity of its coding regions, ISJP4 could be classified into the IS5 group of the IS4 family of bacterial insertion sequences, where it is mostly related to IS402 of Burkholderia cepacia. A TAA direct repeat, presumably resulting from a duplication of the target site, flanked the chromosomal copy of ISJP4. We could demonstrate that a piece of DNA that is flanked by two complete copies of ISJP4 can be transposed. Even more so, one complete ISJP4 plus its tfdA-tfdS intergenic remnant were sufficient to mediate transposition of intervening DNA. A possible role of ISJP4 in the formation of the tfd pathway genes will be discussed.

Exercise increases the lung clearance of inhaled technetium-99m DTPA.

The regional lung clearance of a deposited aerosol of [99mTc] diethylenetriaminepentaacetic acid was successively computed at rest and at exercise in seven nonsmoking volunteers in upright posture. The subjects were seated on a bicycle with their backs against a gamma camera. At rest there was a gradient of clearance from the apex to the base of the lung, the apical clearance being significantly higher. At exercise this regional gradient was enhanced by a large and significant increase of the apical clearances (3.40 +/- 0.63% min-1 s.d. compared with 1.82 +/- 0.75% min-1 s.d. at rest, n = 7, p less than 0.01). By contrast the changes of the basal clearances were slight and unsignificant (1.46 +/- 0.71% min-1 s.d. compared with 1.40 +/- 0.82% min-1 s.d.). This increase of the apical lung clearance could be attributed primarily to the increase of apical blood flow induced by exercise and to the subsequent increase of the permeability surface area product.

Quaternary ammonium compound stresses induce specific variations in fatty acid composition of Pseudomonas aeruginosa.

The involvement of cell membrane fatty acids in resistance of Pseudomonas aeruginosa to Quaternary Ammonium Compounds (QACs) stresses was investigated. The strain was grown in a medium with increasing concentrations of different biocides: two QACs, and two non-QACs. In the presence of two QACs only, the strain was able to grow with increasing concentrations. During cellular adaptation to QACs, the resistance to the same biocide increased. A principal component analysis was performed with whole of fatty acid compositions which highlighted a specific variation for the cultures in presence of QACs. These modifications gave evidence of the outer membrane involvement in cellular response to the presence of QACs.

Effect of temperature and physiological state on the fatty acid composition of Pseudomonas aeruginosa.

The influence of temperature and physiological state on fatty acid profiles of cell membranes of a gram-negative bacteria was studied in this work. It has been shown that fatty acid composition is largely modified by these two parameters. Lipids play an important role in the composition and the function of cell membranes. These modifications of membrane structures are very important to understand because of their consequences on cell viability.

[Ergotism of therapeutic origin. A report of 4 new cases (author's transl)]. / Ergotisme d'origine thérapeutique. Quatre nouvelles observations.

The observations concern ischemic accidents with various localizations (lower limbs, tongue, uterus, intestine, heart, liver) corresponding to 4 observations for which ergot derivatives (ergotamine tartrate) can be responsible. The most typical accidents are localized at the level of limbs and especially of lower limbs. In the greatest part of observations, a specific terrain (puerperium, vasomotor disorders, suspicion of temporal arteritis) can be considered and favouring factors (infection, and especially associated medicinal treatments with triacetyloleandomycin [2 observations] and Doxycyclin [1 observation]). The posologies of ergot alcaloïds were either superior to the limit prescription or normal. The duration of prescription was variable, but generally short. The arteriography confirms a vascular spasm. In an observation with very severe evolution, various ischemic localizations inducing amputation, two intestinal resections and an hemodialysis for lactic acidosis were noted. These ischemic accidents have to be noticed as early as possible in order to start a treatment; the best one seems to be the association of sodium nitroprussiate in intravenous perfusion with peri-dural anesthesia in an antalgic aim.

[Acute basal ganglia necrosis with favorable course during Mycoplasma encepahlitis]. / Nécrose aiguë des noyaux gris d'évolution favorable lors d'une encéphalite à mycoplasme.

BACKGROUND: Acute bilateral striatal necrosis complicating the course of a post-infectious encephalitis is rare. CASE REPORT: A previously healthy 5-year-old boy presented with an atypical pneumonia; he rapidly developed, encephalitis revealed by a generalized status epilepticus. After transient improvement, he became confused and mutic, with dystonic postures of his limbs. Painful stimulation resulted in prolonged facial grimacing and doleful cry. CT scan and MRI showed abnormal signals in the whole basal ganglia, typical of bilateral striatal necrosis. Serologic tests for Mycoplasma pneumoniae were positive. The child recovered almost completely. CONCLUSION: A parainfectious process is probably responsible for the transient bilateral striatal necrosis seen in this patient who had Mycoplasma pneumoniae infection several days before the onset of neurologic symptoms. MRI seemed more reliable than CT-scan for the diagnosis of this condition.

[Anesthesia protocol in the swine. Effects of bleeding on circulation and acid-base equilibrium]. / Protocole d'anesthésie du porc. Effets de la saignée sur la circulation et l'équilibre acido-basique.

Haemodynamic parameters and their variations after the loss of 250 and 500 ml of blood under anaesthesia were studied in nine, 11 to 12 week-old, domestic swine weighing 37.4 +/- 2.6 kg. Premedication consisted of 2 ml azaperone i.m. Anaesthesia was induced with thiopentone, followed by suxamethonium to allow the easy placement of a cuffed endotracheal tube. Anaesthesia was maintained with phenoperidine and pancuronium. The animals were mechanically ventilated with a 50/50 nitrous oxide-oxygen mixture. A catheter was inserted in each of the femoral artery, upper hepatic vein, vena cava and portal vein. Right atrial, pulmonary and wedge pressures were measured; stroke volume, systemic and pulmonary resistances were calculated (fC 90 c X min-1, Pa 82 mmHg, Pra 4.7 mmHg, Ppa 24 mmHg, Ppw 11.6 mmHg, Q 4.45 l X min-1 and Rsa 1460 dyn X s X cm-5). The swine were then bled. After a bleed of 250 ml (t1), the haemodynamic parameters were significantly modified. After another bleed of 250 ml (t2), the heart rate only was significantly higher than at t1; but the blood transfusing could not re-establish a normal haemodynamic state. Blood samples were obtained to measure pH and total CO2 in a systemic artery, and the upper hepatic veins, vena cava and portal vein: the results suggested that the liver took part in the removal of acid metabolites.

["Monosonic" one canal digital implant]. / L'implant cochléaire monocanal numérique "Monosonic".

In order to decrease the gap between the single and multichannel cochlear implant efficacy we tried to improve the speech coding strategy of the Monomac, the constant current single channel system which we designed in 1987. Owing to a research computerized system, different strategies have been successively studied in the laboratory on 12 new implanted patients during the first weeks of the post-operative period to avoid habituation differences. Results led us to design a miniaturized digital emitter, the Monosonic. This emitter allows the speech therapist to program the frequency band wideness (80-1000 Hz) of the transmitted information, and the threshold level and dynamic range of the stimulating square wave as a function of its frequency. Other strategies are discussed, which have not been yet studied, but may be also programmed.

[Presentation of the prototype of a fully implanted cochlear prosthesis]. / Présentation du prototype d'une prothèse cochléaire entièrement implantée.

Description of the prototype of a fully implanted cochlear implant demonstrating the feasibility of a prosthesis with no external component within the next few years. The battery is reloaded by means of electromagnetic induction, and the sound message is received by a subcutaneous microphone, which already has a satisfactory bandwitch and signal-to-noise ratio. This system can be generally applied to most types of permanent intracorporeal stimulation.

Comparative genomics of bacteria from the genus Collimonas: linking (dis)similarities in gene content to phenotypic variation and conservation.

Collimonas is a genus of soil bacteria comprising three recognized species: C. fungivorans, C. pratensis and C. arenae. Collimonads share the ability to degrade chitin (chitinolysis), feed on living fungal hyphae (mycophagy), and dissolve minerals (weathering), but vary in their inhibition of fungi (fungistasis). To better understand this phenotypic variability, we analysed the genomic content of four strains representing three Collimonas species (Ter14, Ter6, Ter91 and Ter10) by hybridization to a microarray based on reference strain C. fungivorans Ter331. The analysis revealed genes unique to strain Ter331 (e.g. those on the extrachromosomal element pTer331) and genes present in some but not all of the tested strains. Among the latter were several candidates that may contribute to fungistasis, including genes for the production and secretion of antifungals. We hypothesize that differential possession of these genes underlies the specialization of Collimonas strains towards different fungal hosts. We identified a set of 136 genes that were common in all tested Collimonas strains, but absent from the genomes of three other members of the family Oxalobacteraceae. Predicted products of these 'Collimonas core' genes include lytic, secreted enzymes such as chitinases, peptidases, nucleases and phosphatases with a putative role in mycophagy and weathering.

Collimonas arenae sp. nov. and Collimonas pratensis sp. nov., isolated from (semi-)natural grassland soils.

A polyphasic taxonomic study was performed to compare 26 novel bacterial isolates obtained from (semi-)natural grassland soils and a heathland soil in the Netherlands with 16 strains that had previously been assigned to the genus Collimonas. Genomic fingerprinting (BOX-PCR), whole-cell protein electrophoresis, matrix-assisted laser desorption ionization time-of-flight mass spectrometry of intact cells and physiological characterization (Biolog) of the isolates confirmed the existence of different strain clusters (A-D) within the genus Collimonas. Until now, only cluster C strains have been formally classified, as Collimonas fungivorans. In this study, DNA-DNA hybridizations were performed with a selection of strains representing the four clusters. The results showed that cluster B strains also belong to C. fungivorans and that strains of clusters A and D represent two novel species within the genus Collimonas. The latter novel species could be differentiated by means of phenotypic and genotypic characteristics and are classified as Collimonas arenae sp. nov. (cluster A; type strain Ter10(T) =LMG 23964(T) =CCUG 54727(T)) and Collimonas pratensis sp. nov. (cluster D; type strain Ter91(T) =LMG 23965(T) =CCUG 54728(T)).

An instrumented station for the survey of ozone and climate change in the southern tropics.

The assessment of changes induced by human activities on Earth atmospheric composition and thus on global climate requires a long-term and regular survey of the stratospheric and tropospheric atmospheric layers. The objective of this paper is to describe the atmospheric observations performed continuously at Reunion Island (55.5 degrees east, 20.8 degrees south) for 15 years. The various instruments contributing to the systematic observations are described as well as the measured parameters, the accuracy and the database. The LiDAR systems give profiles of temperature, aerosols and ozone in the troposphere and stratosphere, probes give profiles of temperature, ozone and relative humidity, radiometers and spectrometers give stratospheric and tropospheric integrated columns of a variety of atmospheric trace gases. Data are included in international networks, and used for satellite validation. Moreover, some scientific activities for which this station offers exceptional opportunities are highlighted, especially air mass exchanges nearby dynamical barriers: (1) On the vertical scale through the tropical tropopause layer (stratosphere-troposphere exchange). (2) On the quasi-horizontal scale across the southern subtropical barrier separating the tropical stratospheric reservoir from mid- and high latitudes.

Appetite of an epiphyte: quantitative monitoring of bacterial sugar consumption in the phyllosphere.

We report here the construction, characterization, and application of a bacterial bioreporter for fructose and sucrose that was designed to monitor the availability of these sugars to microbial colonizers of the phyllosphere. Plasmid pP(fruB)-gfp[AAV] carries the Escherichia coli fruB promoter upstream from the gfp[AAV] allele that codes for an unstable variant of green fluorescent protein (GFP). In Erwinia herbicola, this plasmid brings about the accumulation of GFP fluorescence in response to both fructose and sucrose. Cells of E. herbicola (pP(fruB)-gfp[AAV]) were sprayed onto bean plants, recovered from leaves at various time intervals after inoculation, and analyzed individually for GFP content by quantitative analysis of digital microscope images. We observed a positive correlation between single-cell GFP accumulation and ribosomal content as determined by fluorescence in situ hybridization, indicating that foliar growth of E. herbicola occurred at the expense of fructose and/or sucrose. One hour after inoculation, nearly all bioreporter cells appeared to be actively engaged in fructose consumption. This fraction dropped to approximately 11% after 7 h and to approximately 1% a day after inoculation. This pattern suggests a highly heterogeneous availability of fructose to individual E. herbicola cells as they colonize the phyllosphere. We estimated that individual cells were exposed to local initial fructose abundances ranging from less than 0.15 pg fructose to more than 4.6 pg.

Predictive and interpretive simulation of green fluorescent protein expression in reporter bacteria.

We have formulated a numerical model that simulates the accumulation of green fluorescent protein (GFP) in bacterial cells from a generic promoter-gfp fusion. The model takes into account the activity of the promoter, the time it takes GFP to mature into its fluorescent form, the susceptibility of GFP to proteolytic degradation, and the growth rate of the bacteria. From the model, we derived a simple formula with which promoter activity can be inferred easily and quantitatively from actual measurements of GFP fluorescence in growing bacterial cultures. To test the usefulness of the formula, we determined the activity of the LacI-repressible promoter P(A1/O4/O3) in response to increasing concentrations of the inducer IPTG (isopropyl-beta-D-thiogalactopyranoside) and were able to predict cooperativity between the LacI repressors on each of the two operator sites within P(A1/O4/O3). Aided by the model, we also quantified the proteolytic degradation of GFP[AAV], GFP[ASV], and GFP[LVA], which are popular variants of GFP with reduced stability in bacteria. Best described by Michaelis-Menten kinetics, the rate at which these variants were degraded was a function of the activity of the promoter that drives their synthesis: a weak promoter yielded proportionally less GFP fluorescence than a strong one. The degree of disproportionality is species dependent: the effect was more pronounced in Erwinia herbicola than in Escherichia coli. This phenomenon has important implications for the interpretation of fluorescence from bacterial reporters based on these GFP variants. The model furthermore predicted a significant effect of growth rate on the GFP content of individual bacteria, which if not accounted for might lead to misinterpretation of GFP data. In practice, our model will be helpful for prior testing of different combinations of promoter-gfp fusions that best fit the application of a particular bacterial reporter strain, and also for the interpretation of actual GFP fluorescence data that are obtained with that reporter.

Electrophoretic study of the macromolecular compounds excreted by yeasts: application to differentiation between strains of the same species.

The macromolecular compounds excreted during growth by yeasts as exocellular fractions were studied and found to contain a high proportion of carbohydrates. On the basis of the specificity of these fractions, an attempt was made to distinguish between nine strains of a single species of yeast-Saccharomyces cerevisiae. Each strain came from a different source. The electrophoretic patterns of the exocellular fractions tested made it possible to distinguish between the nine strains, on the basis of Lodder's criteria for the morphological and physiological identification of yeasts. We considered that strains giving exocellular fractions distinguishable by electrophoresis belonged to distinct clones. Consequently, this technique enables us to go further than diagnosis of the species.