Forced oscillations in a hydrodynamical accretion disk and QPOs

This is the second of a series of papers aimed to look for an explanation on the generation of high frequency quasi-periodic oscillations (QPOs) in accretion disks around neutron star, black hole, and white dwarf binaries. The model is inspired by the general idea of a resonance mechanism in the accretion disk oscillations as was already pointed out by Abramowicz & Klu{\'z}niak (\cite{Abramowicz2001}). In a first paper (P\'etri \cite{Petri2005a}, paper I), we showed that a rotating misaligned magnetic field of a neutron star gives rise to some resonances close to the inner edge of the accretion disk. In this second paper, we suggest that this process does also exist for an asymmetry in the gravitational potential of the compact object. We prove that the same physics applies, at least in the linear stage of the response to the disturbance in the system. This kind of asymmetry is well suited for neutron stars or white dwarfs possessing an inhomogeneous interior allowing for a deviation from a perfectly spherically symmetric gravitational field. We show by a linear analysis that the disk initially in a cylindrically symmetric stationary state is subject to three kinds of resonances: a corotation resonance, a Lindblad resonance due to a driven force and a parametric sonance. The highest kHz QPOs are then interpreted as the orbital frequency of the disk at locations where the response to the resonances are maximal. It is also found that strong gravity is not required to excite the resonances.Comment: Accepte

Evidence for mass accretion driven by spiral shocks onto the white dwarf in SDSS J123813.73–033933.0

We present high-time-resolution photometry and phase-resolved spectroscopy of the short-period (⁠Porb=80.52min⁠) cataclysmic variable SDSS J123813.73–033933.0, observed with the Hubble Space Telescope (HST), the Kepler/K2 mission, and the Very Large Telescope (VLT). We also report observations of the first detected superoutburst. SDSS J1238–0339 shows two types of variability: quasi-regular brightenings recurring every ≃8.5  h during which the system increases in brightness by ≃0.5mag, and a double-hump quasi-sinusoidal modulation at the orbital period. The detailed K2 light curve reveals that the amplitude of the double-humps increases during the brightenings and that their phase undergoes a ≃90° phase shift with respect to the quiescent intervals. The HST  data unambiguously demonstrate that these phenomena both arise from the heating and cooling of two relatively large regions on the white dwarf. We suggest that the double-hump modulation is related to spiral shocks in the accretion disc resulting in an enhanced accretion rate heating two localized regions on the white dwarf, with the structure of the shocks fixed in the binary frame explaining the period of the double humps. The physical origin of the 8.5  h brightenings is less clear. However, the correlation between the observed variations of the amplitude and phase of the double-humps with the occurrence of the brightenings is supportive of an origin in thermal instabilities in the accretion disc

Analyse phylogénétique et comparaison des écosystèmes microbiens de lisier et fumier de porcs et construction d'un système de PCR en temps réel pour détecter une population dominante

Les communautés microbiennes d'un lisier et d'un fumier de porcs ont été caractérisées par clonage, séquençage et analyse phylogénétique des gènes codant pour les ARNr 16S. Les 400 séquences analysées ont révélé une très grande diversité avec respectivement 108 et 153 phylotypes, dont 64% pour le lisier et 91,5% pour le fumier sont phylogénétiquement éloignés d'espèces connues. La communauté microbienne du lisier présente une structure typique des écosystèmes de digestion anaérobie tandis que celle du fumier présente une structure intermédiaire entre anaérobie et aérobie, avec notamment des microorganismes nitrifiants et dénitrifiants. Un système de PCR en temps réel a été développé pour suivre un groupe de séquences proches de la bactérie fécale porcine Streptococcus alactolyticus qui représente 5% et 3% des clones analysés pour le lisier et le fumier. Ce système a été utilisé pour quantifier l'évolution de ce groupe de microorganismes le long d'une filière de traitement du lisier. Il montre que ce groupe évolue peu pendant le stockage anaérobie du lisier

Molecular analysis of the microbial community dynamics in pig slurry during storage and after soil application

The evolution of the microbial community of a pig slurry was followed in a pig farm during 6 months. Sampling was carried out on all the different management steps of effluent: faeces, storage tank, lagoon of storage and soil before and after slurry spreading. Total DNA of these various samples were extracted and analyzed by PCR-SSCP, in particular for the archaea and bacteria domains and for specific bacterial groups. This study shows a relative stability in time of the dominant microbial populations present in the stored pig slurry. However, micro-organisms from the effluent could not be detected any longer in soil after spreading, using the SSCP technique. The dominant archaea of the flora of faeces and pig slurry were identified as hydrogenotrophic archaea methanogens belonging to Methanosphaera, Methanobrevibacter and Methanogenium. No aceticlastic archaea methanogen was found, in spite of the strong acetate content measured in pig slurry. SSCP bacteria profiles obtained, reflect a large bacterial diversity where 9 dominant phylotypes could be characterized. Due to the complexity of the profiles obtained, three dominant bacterial groups were targeted: the Clostridiacea, the Bacillus-Streptococcus-Lactobacillus and the Cytophaga-Flexibacter-Bacteroides. Identification of dominant phylotypes was carried out for these 3 groups. The majority of identified phylotypes are close to uncultivated bacteria. With these results, identification of 5 of the 9 dominant bacterial phylotypes of pig slurry was carried out. The phylotype mostly represented in this ecosystem corresponds to an uncultured bacteria closely related to Clostridium butyricum and four other are close to uncultured Prevotellaceae, Bacteroidaceae and Streptococcaceae

Homogeneity and Synchronous Dynamics of Microbial Communities in Particulate Biofilms: from Major Populations to Minor Groups

International audienceNatural or engineered microbial populations often show variations over time. These variations may be due to environmental fluctuations or intrinsic factors. Thus, studying the dynamics of microbial diversity for different communities living in a spatially homogeneous landscape is of interest. As a model ecosystem, nitrifying biofilm communities were grown in a two litre inverse turbulent bed reactor (ITBR) containing an estimated 200 million small particles (about 150 μm in diameter). Each particulate biofilm is considered as a distinct community growing in the neighborhood of other similar particles, in a homogeneous and well-controlled environmental context. A molecular approach was adopted to test how microbial community structures might evolve: either in synchrony, converging or diverging. The shape of biofilm was observed by microscopy for each particle. The biomass content was evaluated by quantitative PCR and showed similar values for each particle. The microbial community structure was evaluated by Capillary Electrophoresis-Single Strand Conformation Polymorphism (CE-SSCP) fingerprinting and showed extraordinary homogeneity between particles, even though transitory community structures were observed when reactor operating conditions were modified. This homogeneity was observed for the Bacteria primer set but, more interestingly, was also observed when minor non-nitrifying bacteria making up the biofilm, representing about 5% and 10% of total cells, were targeted

Impact de la gestion et du stockage du lisier de porcs sur la dynamique de la flore microbienne du lisier par des approches culturales et moléculaires

Intensive pig production in developed countries generates a large amount of pig slurry. This biological effluent contains about 1010 microorganisms per ml (Rivière et al., 1974). Its microbial transformation over the farm management generates air pollution by emission of a great number of gas compounds (ammonia, green house gas, odours) (Zhu et al., 2000). Moreover, it may contain pathogenic microorganisms and present a potential risk to the recipient ecosystem and finally to human populations. The objective of the present work was to monitor the evolution of a pig slurry microbial community throughout its management process. Dominant microbial populations were followed with a molecular typing technique using small-subunit ribosomal DNA analysis: PCR-SSCP (Polymerase Chain Reaction and Single Strand Conformation Polymorphism electrophoresis) (Delbès et al., 2000) while faecal indicators were numerated with culturable techniques. Materials and methods Sampling was carried out on a commercial pig farm, holding 220 sows plus finishers, that produces about 4500 m3 of pig slurry per year. 54 samples were collected from December 2002 to June 2003: faeces, slurries and soils. Analysis of the slurry microbial community was performed by PCR amplification of the microbial 16S rDNA V3 region using either general bacterial primers or specific primers targeting the Clostridiacea, the Bacillus-Lactobacillus-Streptococcus (BSL), and the Cytophaga-Flexibacter-Bacteroides (CFB) groups according to Dabert et al. (2004). PCR products were separated and visualised by SSCP capillary electrophoresis on an ABI 310 genetic analyser. The microbial community appears as a profile of peaks that corresponds to dominant microbial populations of the ecosystem. Peaks migrating at the same position are assumed to correspond to the same species. Faecal indicator were monitored using plating on selective media or MPN (Most Probable Number) technique using normalised culturable media. Number of microorganisms was expressed as a function of the samples dry matter content determined by drying at 105°C. Results and discussion Dynamics of the pig slurry microbial community was followed by aligning the SSCP electrophoregrams obtained from all slurry samples. The bacterial SSCP profiles appeared very complex with a high number of peaks reflecting the pig slurry microbial diversity (black arrows, fig. 1a). The comparison of the SSCP profiles revealed an unexpected stability of the pig manure slurry microbial community during time within the storage pit. From December 2002 to March 2003, the profiles remained about the same with no major apparent changes in peak number and composition. As expected, no change in SSCP profiles was observed when manure went through the auger press. On the opposite, SSCP profiles observed from lagoon samples showed a slow evolution of the community through time (data not shown). Finally, none of the peaks present in the profile from the lagoon liquid used for spreading were found in soil profiles after spreading. This could be explained by the high dilution rate of manure microorganisms within soil at the time of spreading, and shows that we reached the detection limits of the PCR-SSCP approach. Globally, the same results were obtained with the analysis of the specific microbial groups Clostridiacea, BSL, and CFB The dynamics of the faecal indicator microorganisms observed using the cultural approach revealed also a relative stability of the numeration over time for the different sampling locations (data not shown). However, in the same way as before, numeration changed from one step of slurry management to another (figure 1b). Slight variations took place when the faeces were mixed with urine to form slurry, but important numeration decay happened principally between the slurry from the storage tank and the separated liquid and solid phases from the lagoon and compost respectively. Pig slurry spreading did not seem to change significantly soil numeration of the studied groups. Conclusion The microbial community of pig slurry was studied from faeces to soil spreading with two complementary approaches. The molecular approach allows the detection of uncultured dominant microorganisms, originating from the pork faecal flora, which persist through the different manure management steps. The cultural approach allows to monitor faecal indicators. Both approach conducted to the same conclusions: the manure slurry microbial community does not evolve rapidly during passive anaerobic storage. Significant changes occurs primarily when manure move from one step of the management process to another

Evaluation de la survie de la flore fécale porcine au travers des filière de gestion des lisiers

National audienceThe impact of pig manure treatment was studied on bacterial populations of 17 piggeries using cultural methods and 16S rRNA targeted PCR Single-Strand-Conformation-Polymorphism analysis (SSCP). While both methods are conceptually and technically very different and even if they did not target the same microbial populations, the data obtained followed the same trends. Simple anaerobic storage did not promote a strong microbial community shift or reduction of faecal indicator numeration. Aerobic treatment followed by anaerobic storage induced strong microbial community shifts and resulted in a reduction of between one to two logarithmic units of the numbers of E coli and enterococci. This was not sufficient to totally eliminate Salmonella and Listeria monocytogenes. The dominant microbial community of the raw manures appeared very stable with the strong dominance of a few species whereas SSCP profiles of treated manures showed a greater diversity of bacterial population. The possible utilisation of molecular typing methods like SSCP is discussed as a tool to monitor microbial communities' diversity and stability, as well as a tool to identify and track specific manure indicators

Suivi de la communauté microbienne d'un lisier de porc le long d'une filière d'élevage, approches moléculaire et culturale

The microbial community evolution of a swine manure was monitored within a piggery equipped with a flushing system for a period of 6 months. Samples were withdrawn over all the manure management process : breeding house pits, homogenised storage pit, inlet and outlet of the compressor screw, storage lagoon, and finally soil before and after spreading of the manure from the lagoon. The microbial community was characterised and monitored using two different methodologies. The first one used techniques from molecular microbiology which allow the dominant microorganisms from manure to be identified and monitored without a need for culture (total bacteria, Archaea, Clostridiacea, Bacteroides Prevotella, and Lactobacillus-Streptococcus). The second, based on cultural techniques, was used to enumerate indicative bacteria, usually subdominant, as enterobacteria, enterococcus, coliforms, Escherichia coli, and potentially pathogenic bacteria as Salmonella, Listeria monocytogenes, and Staphylococcus aureus. Both approaches revealed a stability of the microbial populations during time within each step of the manure management process separately. However, qualitative and quantitative microbial population changes were observed when manure was shifting from one step of the process to another one (ex. going from the storage pit to the lagoon). Finally, microorganisms present within the effluent before spreading in the fields were not detectable anymore within soil after the spreading, whatever the technique used (molecular or cultural).L'évolution de la communauté microbienne d'un lisier a été suivie dans un élevage de porcs équipé d'un système de flushage pendant une période de 6 mois. Des prélèvements ont été réalisés sur toute la filière de gestion des déjections : préfosses des bâtiments, fosse de stockage homogénéisée, entrée et sorties de vis compacteuse, lagune de stockage, et enfin sol avant et après épandage du lisier issu du lagunage. La communauté microbienne a été caractérisée et suivie par deux méthodologies différentes. La première utilisant les techniques de microbiologie moléculaire permet d'identifier et de suivre les micro-organismes dominants du lisier sans avoir à les cultiver (bactéries totales, Clostridium - Eubacterium, Bacteroides - Prevotella, et Lactobacillus-Streptococcus). La seconde, utilisant les techniques culturales, a été utilisée pour suivre les bactéries indicatrices, généralement sous-dominantes telles que les entérobactéries, entérocoques, coliformes, Escherichia coli, et des bactéries potentiellement pathogènes telles que les Salmonelles, Listeria monocytogenes, et Staphylococcus aureus. Les deux approches montrent une stabilité dans le temps des populations microbiennes rencontrées sur chaque étape de la filière prise séparément. En revanche, des changements de populations microbiennes et de numération sont observés lorsque le lisier passe d'une étape de la filière à une autre (ex. passage fosse lagune). Enfin, les micro-organismes présents dans les effluents avant épandage ne sont plus détectables dans le sol après épandage, quelle que soit l'approche utilisée (moléculaire ou culturale)