Diversité des interactions trophiques à l'interface microorganismes - microcrustacés dans une zone littorale à macrophytes : conséquences sur le transfert des acides gras essentiels

Areas with littoral macrophytes play an important functional role in freshwater systems. In addition to the high productivity recorded in such areas, they also shelter a high diversity of organisms. However, possible links between spatial heterogeneity, biodiversity and energy pathways are still poorly known. As they constitute the major link between microorganisms and species higher in the food web, microcrustaceans play a key role in the transfer of polyunsaturated fatty acids (PUFA) to organisms at higher trophic levels. In this study, we wanted to assess if microcrustaceans diversity encountered in macrophytes littoral zones would lead to a variability of PUFA transfer in the food web. This work combined controlled conditions experiment and studies run in natural environments in order to help the interpretation of results from lipid analysis, isotopic analysis and fatty acid isotope analysis. Our results indicate that there are no differences of PUFA concentrations between cladocerans from a macrophyte littoral zone when they were exposed to the same pool of dietary PUFA. Hence, in heterogeneous feeding habitats such as macrophytes zones where these cladocerans often co-exist, foraging behavior of cladoceran species more than differences of metabolism may be crucial for determining PUFA transfer to upper trophic levels. In addition to seston, our study shows indeed that some cladoceran species are able to forage on the epiphytic and neustonic compartments. Lipid analyses highlight moreover that the diversity of trophic compartments lead to a variability of PUFA inputs to primary consumers. In our study, the epiphytic compartment is indeed significantly more concentrated in PUFA than seston. At the air-water interface, neuston is moreover characterized by important allochthonous organic matter accumulation. During a pollen rain, this organic matter represents an important source of carbon and PUFA for some microcrustacean species. In macrophytes littoral zones, cladocerans complementarity leads to a more complete use of PUFA sources. The association of trophic compartment diversity and microcrustacean diversity probably allows an optimization of PUFA transfer to higher trophic levels.Les zones littorales à macrophytes ont un rôle fonctionnel important dans les hydrosystèmes fluviaux. Outre leur forte productivité, ces milieux se caractérisent également par une forte biodiversité. Cependant, les liens pouvant exister entre hétérogénéité spatiale, biodiversité et flux de matière restent encore peu connus. En milieu aquatique, les microcrustacés représentent un maillon clef entre les microorganismes eucaryotes, qui sont les principaux producteurs d’acide gras polyinsaturés (AGPI), et le compartiment piscicole. Dans ce travail de thèse, nous avons donc cherché à savoir comment la diversité des cladocères rencontrée dans une zone littorale à macrophytes pouvait affecter le transfert des AGPI dans les réseaux trophiques. L’approche vers laquelle s’est orienté ce travail combine à la fois des études menées en milieu contrôlé, permettant des expériences de nutrition, ainsi que des études menées en milieu naturel. Cette double approche permet de faciliter l’interprétation des résultats issus des analyses lipidiques, isotopiques et isotopiques de composés spécifiques. Nos résultats montrent ainsi qu’il n’existe pas de variabilité dans les capacités d’accumulation et de bioconversion des AGPI chez les cladocères coexistant dans une zone littorale à macrophytes. D’après ces résultats, il semble donc que le principal facteur influençant la variabilité des transferts d’AGPI vers le compartiment piscicole soit la stratégie alimentaire et le compartiment trophique exploité par les différentes espèces de microcrustacés. En effet, outre le seston, notre étude montre que certaines espèces de cladocères rencontrées en zone littorale sont capables d’exploiter l’épiphyton et le neuston. Les analyses lipidiques mettent de plus en évidence, que la diversité des compartiments trophiques exploités s’accompagne d’une variabilité d’apports en AGPI. Dans notre étude, l’épiphyton est ainsi significativement plus concentré en AGPI que le seston. A l’interface air-eau, le neuston se caractérise de plus, par une forte accumulation de matière organique d’origine allochtone qui, dans le cas d’une pluie de pollen, représente une source de carbone et d’AGPI non négligeable pour certaines espèces de microcrustacés. Dans les zones littorales à macrophytes, la complémentarité des espèces de cladocères entraine donc une utilisation plus complète des ressources. La diversité des compartiments trophiques, associée à la diversité des microcrustacés, permet donc probablement une optimisation du transfert des AGPI vers les niveaux trophiques supérieurs

Variation in allele frequencies at the bg112 locus reveals unequal inheritance of nuclei in a dikaryotic isolate of the fungus Rhizophagus irregularis.

The genetic state of the arbuscular mycorrhizal fungus species Rhizophagus irregularis differs among isolates, including both homokaryotic and dikaryotic isolates. Via the production of multi-nucleate axexual spores, siblings of dikaryotic isolates may inherit unequal frequencies of nucleotypes. Using bg112, a microsatellite marker, previous studies revealed that lines deriving from single spores of the dikaryotic R. irregularis isolate C3 differed in their proportions of different alleles. A genomic study of single nuclei of R. irregularis, however, suggested that this marker was a multi-copy locus and that therefore it was inappropriate to study the inheritance of nuclei in dikaryotic isolates. In this study, we first analysed whole genome data of several R. irregularis isolates and demonstrated that bg112 is indeed a single copy locus in these genomes. Thus, the bg112 locus is a suitable marker to study the relative frequency of nucleotypes in R. irregularis. Second, by using amplicon sequencing, we confirmed the existence of one allele of bg112 in two homokaryotic isolates (DAOM197198 and C2) and two alleles in the dikaryotic isolate (C3). Finally, we found that the relative proportions of two bg112 alleles differed significantly among dikaryotic single-spore lines derived from isolate C3, indicating that genetically different nucleotypes are inherited unequally in this dikaryotic R. irregularis isolate

Concentration of Airborne Staphylococcus aureus (MRSA and MSSA), Total Bacteria, and Endotoxins in Pig Farms

Pigs are very often colonized by Staphylococcus aureus and transmission of such pig-associated S. aureus to humans can cause serious medical, hygiene, and economic problems. The transmission route of zoonotic pathogens colonizing farm animals to humans is not well established and bioaerosols could play an important role. The aim of this study was to assess the potential occupational risk of working with S. aureus-colonized pigs in Switzerland. We estimated the airborne contamination by S. aureus in 37 pig farms (20 nursery and 17 fattening units; 25 in summer, 12 in winter). Quantification of total airborne bacterial DNA, airborne Staphylococcus sp. DNA, fungi, and airborne endotoxins was also performed. In this experiment, the presence of cultivable airborne methicillin-resistant S. aureus (MRSA) CC398 in a pig farm in Switzerland was reported for the first time. Airborne methicillin-sensitive S. aureus (MSSA) was found in ~30% of farms. The average airborne concentration of DNA copy number of total bacteria and Staphylococcus sp. measured by quantitative polymerase chain reaction was very high, respectively reaching values of 75 (± 28) × 107 and 35 (± 9.8) × 105 copy numbers m-3 in summer and 96 (± 19) × 108 and 40 (± 12) × 106 copy numbers m-3 in winter. Total mean airborne concentrations of endotoxins (1298 units of endotoxin m-3) and fungi (5707 colony-forming units m-3) exceeded the Swiss recommended values and were higher in winter than in summer. In conclusion, Swiss pig farmers will have to tackle a new emerging occupational risk, which could also have a strong impact on public health. The need to inform pig farmers about biological occupational risks is therefore crucia

Etude de la structuration spontanée de films polymères en nano-impression thermique

La lithographie de nano-impression par déstabilisation spontanée de polymère est unevariante de la technique de nano-impression thermique, et permet de limiter le contact directentre moule et polymère. Le but de cette thèse est d étudier cette déstabilisation spontanée etde déterminer si elle peut conduire à la formation de nanostructures en dupliquant de façonpositive un moule nano-structuré. Ce procédé est influencé, en particulier, par la température,le champ électrique externe ou interne au niveau des interfaces moule air polymère, ainsique par la distance d séparant les structures du moule et la surface du polymère.Les études réalisées au cours de cette thèse se sont concentrées sur l influence de cesdifférents paramètres. Nous avons montré que la formation de motifs dépend plus de l effetde charges que de la température, dans la mesure où le polymère peut néanmoins fluer. Nousavons surtout mis en évidence le scénario de structuration suivant : une duplication positiveapparaît dans un premier temps, et est suivie, dans certains cas, d un remplissage des cavitésdu moule conduisant à une duplication négative. Un modèle théorique a été utilisé pourcalculer la longueur d onde de déstabilisation la plus favorable, et une comparaison avec nosrésultats expérimentaux a permis d expliquer pourquoi et dans quels cas la structurationfinale est positive ou négative. Une investigation a été accomplie sur la déstabilisationspontanée de substrats souples, mais la grande épaisseur des films conduit à unedéstabilisation de grande longueur d onde, et donc à un remplissage complet du moule.NanoImprint lithography by spontaneous polymer destabilization is an alternative toThermal NanoImprint, which limits physical contact between polymer and mold surfaces.The purpose of this thesis is to investigate this spontaneous destabilization and to work out ifit can lead to the formation of nanostructures by duplicating positively a structured mold.This process is in particular affected by temperature or electric field present at mold - air -polymer interfaces and by the distance d between the structures of the mold and the polymersurface.The studies of this thesis were focused on the influence of these process parameters. Itwas shown that the structuration depends more of charges effect than temperature, since thepolymer can creep. We highlighted the following scenario of structuration: a positiveduplication appears first and is followed, in some cases, by the filling of the mold cavitiesleading to a negative duplication. A theoretical model was used to calculate the mostfavorable destabilization wavelength, and a comparison with experimental results helped toexplain why and under which circumstances the final structuration is positive or negative. Aninvestigation was performed on the spontaneous destabilization of flexible substrate but thebigger thickness of flexible films led to a destabilisation with a wide wavelength and so tothe filling of molds cavities.SAVOIE-SCD - Bib.électronique (730659901) / SudocGRENOBLE1/INP-Bib.électronique (384210012) / SudocGRENOBLE2/3-Bib.électronique (384219901) / SudocSudocFranceF

Assessment of airborne virus contamination in wastewater treatment plants.

Occupational exposure to bioaerosols in wastewater treatment plants (WWTP) and its consequence on workers' health are well documented. Most studies were devoted to enumerating and identifying cultivable bacteria and fungi, as well as measuring concentrations of airborne endotoxins, as these are the main health-related factors found in WWTP. Surprisingly, very few studies have investigated the presence and concentrations of airborne virus in WWTP. However, many enteric viruses are present in wastewater and, due to their small size, they should become aerosolized. Two in particular, the norovirus and the adenovirus, are extremely widespread and are the major causes of infectious gastrointestinal diseases reported around the world. The third one, hepatitis E virus, has an emerging status. This study׳s objectives were to detect and quantify the presence and concentrations of 3 different viruses (adenovirus, norovirus and the hepatitis E virus) in air samples from 31 WWTPs by using quantitative polymerase chain reaction (qPCR) during two different seasons and two consecutive years. Adenovirus was present in 100% of summer WWTP samples and 97% of winter samples. The highest airborne concentration measured was 2.27 × 10(6) genome equivalent/m(3) and, on average, these were higher in summer than in winter. Norovirus was detected in only 3 of the 123 air samples, and the hepatitis E virus was not detected. Concentrations of potentially pathogenic viral particles in WWTP air are non-negligible and could partly explain the work-related gastrointestinal symptoms often reported in employees in this sector

Genetic variation and evolutionary history of a mycorrhizal fungus regulate the currency of exchange in symbiosis with the food security crop cassava.

Most land plants form symbioses with arbuscular mycorrhizal fungi (AMF). Diversity of AMF increases plant community productivity and plant diversity. For decades, it was known that plants trade carbohydrates for phosphate with their fungal symbionts. However, recent studies show that plant-derived lipids probably represent the most essential currency of exchange. Understanding the regulation of plant genes involved in the currency of exchange is crucial to understanding stability of this mutualism. Plants encounter many different AMF genotypes that vary greatly in the benefit they confer to plants. Yet the role that fungal genetic variation plays in the regulation of this currency has not received much attention. We used a high-resolution phylogeny of one AMF species (Rhizophagus irregularis) to show that fungal genetic variation drives the regulation of the plant fatty acid pathway in cassava (Manihot esculenta); a pathway regulating one of the essential currencies of trade in the symbiosis. The regulation of this pathway was explained by clearly defined patterns of fungal genome-wide variation representing the precise fungal evolutionary history. This represents the first demonstrated link between the genetics of AMF and reprogramming of an essential plant pathway regulating the currency of exchange in the symbiosis. The transcription factor RAM1 was also revealed as the dominant gene in the fatty acid plant gene co-expression network. Our study highlights the crucial role of variation in fungal genomes in the trade of resources in this important symbiosis and also opens the door to discovering characteristics of AMF genomes responsible for interactions between AMF and cassava that will lead to optimal cassava growth

Amino acid pattern and glutamate metabolism during dehydration stress in the 'resurrection' plant Sporobolus stapfianus: a comparison between desiccation-sensitive and desiccation-tolerant leaves

The present study analyses changes in nitrogen compounds, amino acid composition, and glutamate metabolism in the resurrection plant Sporobolus stapfianus during dehydration stress. Results showed that older leaves (OL) were desiccation-sensitive whereas younger leaves (YL) were desiccation-tolerant. OL lost their soluble protein more rapidly, and to a larger extent than YL. Enzymes of primary nitrogen assimilation were affected by desiccation and the decrease in the glutamine synthetase (GS, EC 6.3.1.2) and ferredoxin-dependent GOGAT (Fd-GOGAT, EC 1.4.7.1) activities was higher in OL than in YL, thus suggesting higher sensibility to dehydration. Moreover, YL showed higher total GS enzyme activity at the end of the dehydration stress and was shown to maintain high chloroplastic GS protein content during the entire stress period. Free amino acid content increased in both YL and OL between 88% and 6% relative water content. Interestingly, OL and YL did not accumulate the same amino acids. OL accumulated large amounts of proline and gamma-aminobutyrate whereas YL preferentially accumulated asparagine and arginine. It is concluded (i) that modifications in the nitrogen and amino acid metabolism during dehydration stress were different depending on leaf development and (ii) that proline and gamma-aminobutyrate accumulation in S. stapfianus leaves were not essential for the acquisition of desiccation tolerance. On the contrary, the accumulation of large amounts of asparagine and arginine in the YL during dehydration could be important and serve as essential nitrogen and carbon reservoirs useful during rehydration. In this context, the role of GS for asparagine accumulation in YL is discussed

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Coexistence of genetically different Rhizophagus irregularis isolates induces genes involved in a putative fungal mating response.

Arbuscular mycorrhizal fungi (AMF) are of great ecological importance because of their effects on plant growth. Closely related genotypes of the same AMF species coexist in plant roots. However, almost nothing is known about the molecular interactions occurring during such coexistence. We compared in planta AMF gene transcription in single and coinoculation treatments with two genetically different isolates of Rhizophagus irregularis in symbiosis independently on three genetically different cassava genotypes. Remarkably few genes were specifically upregulated when the two fungi coexisted. Strikingly, almost all of the genes with an identifiable putative function were known to be involved in mating in other fungal species. Several genes were consistent across host plant genotypes but more upregulated genes involved in putative mating were observed in host genotype (COL2215) compared with the two other host genotypes. The AMF genes that we observed to be specifically upregulated during coexistence were either involved in the mating pheromone response, in meiosis, sexual sporulation or were homologs of MAT-locus genes known in other fungal species. We did not observe the upregulation of the expected homeodomain genes contained in a putative AMF MAT-locus, but observed upregulation of HMG-box genes similar to those known to be involved in mating in Mucoromycotina species. Finally, we demonstrated that coexistence between the two fungal genotypes in the coinoculation treatments explained the number of putative mating response genes activated in the different plant host genotypes. This study demonstrates experimentally the activation of genes involved in a putative mating response and represents an important step towards the understanding of coexistence and sexual reproduction in these important plant symbionts