Les systèmes de transduction du signal et les transporteurs ABC contribuent de façon conjointe à la réponse adaptative des bactéries aux changements d'environnement. Trois modules, associant un phosphorelais et un transporteur ABC, ont été répertoriés chez B. subtilis et sont impliqués dans la réponse à différents antibiotiques: BceRSAB, PsdRSAB et YxdJKLM. Ils sont caractérisés par une histidine kinase possédant une boucle extracytoplasmique courte et appartenant à la famille des Intramembrane Sensing - Histidine Kinase (IM-HK) et par un transporteur ABC possédant une Membrane Spanning Domain (MSD) à boucle extracytoplasmique exceptionnellement longue. En utilisant une approche phylogénomique, il a été établi que ce type de modules était restreint aux Firmicutes, où ils sont apparus et se sont largement répandus. De plus, cette analyse met en lumière une histoire évolutive très dynamique impliquant de nombreux transferts horizontaux, duplications et pertes de gènes, conduisant à un répertoire de modules Bce-like très varié chez ce phylum. Grâce à une analyse phylogénétique fine, il a été proposé une classification de ces modules en six sous-familles bien définies. Des études fonctionnelles ont été réalisées sur des membres de la sous-famille IV comprenant le module de résistance à la bacitracine BceRSAB de B. subtilis, dont l'expression des gènes codant pour le transporteur requiert, en présence de l'antibiotique, le système de transduction du signal aussi bien que le transporteur lui-même. Les résultats de ces études montrent que d'autres membres de la sous-famille IV, YtsCD de B. licheniformis et BceAB de B. halodurans, sont également impliqués dans la résistance à la bacitracine. Ils suggèrent aussi que dans ces modules le transporteur ABC est le premier senseur de la présence de l'antibiotique et qu'il active le système de transduction une interaction entre une sous unité du transporteur et la kinase du module. De plus, en présence de bacitracine, l'expression des gènes codant pour le transporteur BceAB ainsi que la résistance à cet antibiotique requièrent la présence de la boucle de la MSD BceB ce qui démontre l'importance de cette boucle aussi bien au niveau fonctionnel que structural. Par ailleurs, l'étude que nous avons réalisée suggère que le mécanisme original de régulation des gènes du transporteur BceAB de B. subtilis pourrait être généralisé à tous les modules équivalents présents chez les Firmicutes. Ces modules constitueraient ainsi un mécanisme important de résistance aux antibiotiques peptidiques chez les bactéries de ce phylum qui comprend de nombreux pathogènes.

Over the past century, dust emissions have increased in frequency and intensity due to anthropogenic influences and extended droughts. Dust transports microbes, nutrients, heavy metals and other materials that may then change the biogeochemistry of the receiving environments. The purpose of this study was to find whether unique bacterial communities may provide distinct fingerprints of dust sources in the Western USA. We collaborated with the National Wind Erosion Research Network (NWERN) to identify bacterial core communities (core) of dust from ten NWERN sites, and compared communities to location, soil, and regional characteristics. In order of importance, precipitation levels (F = 43, P = 0.0001, Df = 2, r2 = 0.25), location (F = 16, P = 0.0001, Df = 5, r2 = 0.23), soil texture (F = 14, P = 0.0001, Df = 3, r2 =0.12), seasonality (F = 11, P = 0.0001, Df = 2, r2 = 0.064), and elevation (F = 5.7, P = 0.0002, r2 = 0.033) determined bacterial community composition. Bacterial core communities were defined as taxa present in at least 50% of samples at each site and offered predictable patterns of dust communities in terms of abundant (> 1% relative abundance) and rare (< 1% relative abundance) signatures. We found distinct bacterial core communities that reflected dust source systems, for example, sites contaminated with heavy metals contained Romboutsia, Turicibacter, Clostridium sensu stricto 1, Geodermatophilus, and Microvirga. Sites with association to plants and biocrusts contained Methylobacterium-Methylorubrum, Bradyrhizobium, Paenibacillus thermoaerophilus, Cohnella, and bacterial families Solirubrobacteraceae, Sphingobacteraceae, and Myxococcaceae. The presence of Sphingomonas, Stenotrophomonas, Rhodococcus, and Phenylobacterium were found in hydrocarbon contaminated soils. High stress (UV radiation and desiccation) sites contained Deinococcus, Blastococcus, and Modestobacter. We found that seasonal changes affected microbial community composition in five NWERN sites (CPER, HAFB, Jornada, Red Hills, and Twin Valley) (p < 0.05), while no seasonal effects on bacterial distribution were observed at Moab. Our results identify that the use of core microbiomes may offer a fingerprinting method to identify dust source regions.

In den Firmicutes wird der Induktorausschluss (Katabolitrepression) durch das am Serin46 phosphorylierte HPr (PTS) vermittelt. Der genaue Mechanismus war jedoch unklar. Um diese Frage auf der Grundlage von isolierten Proteinen zu klären, wurde ein zum Escherichia coli Maltose-/Maltodextrin-ABC-Transporter homologes System aus Lactobacillus casei BL23 (MalE1-MalF1G1K12) als Modellsystem genutzt. Im Rahmen der Promotion wurde über isothermale Titrationskalorimetrie und Fluoreszenzspektroskopie gezeigt, dass das Bindeprotein MalE1 lineare und zyklische Maltodextrine, aber keine Maltose bindet. Experimentell ermittelte dreidimensionale Strukturen von MalE1 im Komplex mit diesen Zuckern belegten eine vergleichbar geschlossene Konformation und dienten zusätzlich als Grundlage, um die fehlende Maltosebindung zu erklären. Die Stimulierung der ATPaseaktivität des in Liposomen und Nanodiscs eingebauten Komplexes wurde jedoch hauptsächlich durch eine MalE1-Beladung mit linearen Maltodextrinen bewirkt. Eine bis zu 85 %ige Inhibierung der ATPaseaktivität durch P-Ser46-HPr belegte erstmals in vitro eine Interaktion von mehr als einem phosphorylierten Protein mit dem Transporter. Analog zum EIIAGlc-Inhibitor des homologen Systems aus E. coli wurden über Quervernetzungsexperimente und massenspektrometrische Analysen Interaktionen mit dem MalK1-Dimer als interagierende Komplexeinheit in der Nähe des Walker A-Motivs nachgewiesen. Über Fluoreszenzmessungen in Anwesenheit des ATP-Analogons TNP-ATP wurde eine unbeeinflusste ATP-Bindung und damit eine fehlende Blockade der γ-Phosphatbindestelle des Walker-A Motivs durch die Phosphorylgruppe von P-Ser46-HPr bestimmt. Die folgende Substitution verschiedener positiv geladener MalK1-Reste, die als potenzielle Interaktionsstellen für die Phosphorylgruppe fungieren könnten, identifizierte K63 in der Nähe des Walker A-Motivs als ersten möglichen Partner. Der genaue Mechanismus der Inhibierung bleibt jedoch unklar. / Catabolite repression is a global mechanism which controls the utilization of carbohydrates in bacteria. In Firmicutes HPr, a component of the phosphoenolpyruvate carbohydrate phosphotransferase system, prevents the uptake of less preferred sugars but only when it is phosphorylated at serine46. However the exact mechanism was unclear. To address this question the purified ATP-binding cassette transporter from Lactobacillus casei BL23 (MalE1-MalF1G1K12) was used as a model system, which is homologous to the Escherichia coli maltose/maltodextrin ABC importer. Isothermal titration calorimetry and fluorescence spectroscopy revealed that the binding protein MalE1 binds linear and cyclic maltodextrins but not maltose. Experimentally determined three-dimensional structures from MalE1 in complex with these sugars show a comparably closed conformation and served as a basis to explain the lack of maltose binding. The stimulation of the ATPase activity of the transporter incorporated in liposomes and nanodiscs however, was mainly caused by MalE1 loaded with linear maltodextrins. For the first time an inhibition of ATPase activity by P-Ser46-HPr up to 85 % and an interaction of more than one phosphorylated protein with the transporter was demonstrated. Analogous to the EIIAGlc inhibitor of the homologous system from E. coli, cross-linking experiments and mass spectrometric analyzes revealed interactions with the MalK1 dimer near the Walker A motif. Fluorescence measurements in the presence of the ATP analogue TNP-ATP, however, revealed an unaffected ATP binding and thus a lack of blockade of the γ-phosphate binding site (Walker A motif) by the phosphoryl group from P-Ser46-HPr. The following substitution of several positively charged MalK1 residues that could act as potential sites of interaction for the phosphoryl group, identified K63 near the Walker A motif as the first potential partner. The exact mechanism of inhibition, however, remains unclear.

Biocrusts and the ecosystem services they provide are becoming more susceptible to fire as exotic annual grass invasions facilitate the spread of desert wildfires. Further, precipitation patterns across the western United States are predicted to change over the next century, and have the potential to dramatically influence fire regimes and the recovery of burned biocrusts. Despite these changes to desert fire and precipitation cycles, our understanding of post-fire biocrust recovery is limited, especially regarding the first two years after fire. To investigate biocrust recovery, we created burn manipulations (i.e., unburned and burned) and tracked crust form and function over two years in one cold and one hot desert ecosystem (UT, USA). We evaluated the entire bacterial community, but focused on Cyanobacteria species that confer soil stability and N fixation capabilities to biocrusts. Specifically, we quantified shifts in biocrust bacterial community composition using target metagenomics of 16S rDNA; monitored biocrust moss and lichen cover; measured N fixation potential; and assessed soil infiltration rates and soil stability. We found little evidence that biocrust form or function recovered from fire within two years. Based on pyrosequencing results, fire altered biocrust community composition in interspace and shrub biocrusts. Cyanobacteria species were almost completely eliminated by fire, constituting 9-21% of unburned plots and less than 0.01% of burned interspace and shrub biocrust communities. Based on cover estimates, no lichen or moss species survived the fire or recovered within two years. N fixation potentials decreased by at least six-fold in burned interspace biocrusts, representing a reduction in soil N inputs into already N-limited desert soils. Soil infiltration rates also drastically declined in burned biocrusts and remained depressed, but only remained depressed for one year. To investigate the interactions between biocrust recovery, fire, and precipitation, we nested precipitation treatments manipulating the amount of monthly rainfall (i.e., ambient, plus 30% and minus 30%) within burn treatments during the second year. Soil NH4+ was the only parameter to be affected by precipitation, and exhibited a positive relationship with precipitation magnitude at the end of one year. Our results demonstrate that fire is a strong destabilizer of the bacterial components of biocrust communities and that the ecosystem services provided by crusts recover at different rates, with N dynamics recovering more slowly than soil ecohydrology.

Soil microbial communities are affected extensively by addition of amendments to their environment. Of particular concern is the addition of poultry litter, which contains a substantial C, energy, and nutrient supply, but also antibiotic resistance genes (ARG), antimicrobials, and a multitude of microbial species. This project seeks to primarily assess if there is a change in bacterial community structure in response to poultry litter amendments to pasture land across geographically independent land across northern Georgia. It may be that changes in the relative abundance of bacterial communities also result in alteration in ARGs, and the community resistance to antibiotics (“resistome”) which in turn increases the potential threat of antibiotic resistance genes. While another part of this study will determine changes in integrons and specific ARGs, this project will focus on changes in bacterial communities and the potential functional changes in the community, which in turn have consequences for ARG levels and its horizontal transfer to various members of the soil community. Addition of waste from livestock is a historical method for increasing nutrients needed in the soil for the cultivation of crops, and in turn causes pronounced shifts in soil microbial communities due to the addition of large amounts of carbon, nutrients, foreign microbes, and other material. This study is unique because it utilizes a novel and relatively large landscape-scale to determine if there are discernable and repeatable patterns of bacterial community structure change in response to amendment regardless of exact soil type or source of chicken litter amendment. In the future, these data can also provide insight into the changes in the relative abundance antibiotic related genes associated with community change. / M.S. / Soil is complicated, both in terms of its physical makeup and the organisms that live inside of it. Predicting changes in soil based on the addition of foreign material such as chemicals or biological waste is not an easy process, and whether or not it is even possible to reliably predict those changes is a matter of some dispute. This study is designed to illustrate that such changes can in fact be reliably and consistently predicted even with regard to the addition of complicated materials to the soil. In this study, specifically, the material in question is chicken litter. A mix of the bedding and waste produced by chickens, litter is commonly handled by composting and is added to soil in farms as a fertilizer rich in organic matter. It is possible to point at specific elements of the soil such as the chemistry and bacteria and see how it is changed with the addition of chicken litter, which allows us to determine the nature and extent of the change that chicken litter has on soil. This study is conducted on a larger scale than similar experiments conducted in the past, making it apparent that these relationships exist on a repeated basis. It is the object of this study to pave the way and make it easier for scientists in the future to determine these relationships in other unique contexts.

Projet I : Les endospores représentent un état de dormance des bactéries leur permettant de résister à des conditions extrêmes et de persister pendant des années. La formation d'endospores a façonné l'évolution puisqu’elle se produit exclusivement chez les Firmicutes. Plusieurs études ont rapporté la formation d'endospores chez des espèces en dehors des Firmicutes, en particulier chez deux espèces de Protéobactéries, Rhodobacter johrii et Serratia marscescens, et une espèce d'Actinobacteries, Mycobacterium marinum. Le fait d’identifier les endospores en dehors des Firmicutes pourrait affecter la forme de l'arbre de vie et aiderait dans notre lutte contre les agents pathogènes humains. Par conséquent, nous avons visé d’étudier l'endosporulation chez ces trois espèces en utilisant des approches avancées d'imagerie et d'analyse, y compris la microscopie corrélative alliant la microscopie optique et électronique (CLEM), la tomographie de cryo- électron (cryo-ET) et la lipidomique. Nous avons utilisé la bactérie sporulante bien caractérisée Bacillus subtilis comme contrôle positif de la sporulation. L'examen de R. johrii, S. marcescens et M. marinum en utilisant CLEM et cryo-ET a montré que les objets à phase brillante ne ressemblaient à aucun stade de l'endosporulation. Les cryo-tomogrammes ont montré que les objets à phase brillante chez S. marcescens étaient des débris cellulaires agrégés de cellules mortes, alors qu'ils présentaient des structures granulaires typiques des cellules bactériennes chez les R. johrii et M. marinum. L'analyse lipidomique chez R. johrii a identifié les structures granulaires comme des granules de stockage potentiels enrichis en triacylglycérides (TAG). Nous pensons que les TAG peuvent fournir une source d'énergie pour résister à l'épuisement des nutriments. Des approches biochimiques et bioinformatiques supplémentaires ont soutenu nos conclusions selon lesquelles R. johrii, S. marcescens et M. marinum sont des bactéries non sporulantes. Projet II : Les plasmides jouent un rôle vital dans la propagation des gènes de résistance au sein et entre les espèces bactériennes. Par conséquent, il est essentiel de comprendre les systèmes bactériens impliqués dans le transfert et la maintenance des plasmides pour mieux aider dans notre lutte contre la propagation de la résistance aux antibiotiques. Dans cette thèse de doctorat, nous avons cherché à caractériser l'opéron alp7ARC, en utilisant l'homologue de l'actine bactérienne Alp7A pour séparer le plasmide pLS20 codant pour la résistance à la tétracycline dans B. subtilis. La stabilité du plasmide s'est avérée dépendante de l'opéron alp7ARC, indiquant un rôle essentiel dans la ségrégation plasmidique. Nos résultats préliminaires sur Alp7A ont montré qu'il s'assemble dans une nouvelle nanostructure tubulaire plutôt que des filaments, suggérant un nouveau mécanisme de ségrégation de l'ADN par Alp7A. Nous avons également étudié la structure d'Alp7A in vivo en utilisant une combinaison d'approches, notamment la biologie moléculaire, la Cryo-ET et la fLM. Nous avons également utilisé la CLEM pour localiser Alp7A dans des cellules entières à une résolution macromoléculaire. En outre, nous avons étudié la structure et la fonction d'Alp7A in vitro en transfectant B. subtilis et E. coli avec diverses constructions plasmidiques incorporant des mutations dans le gène d’Alp7A. Nous avons déployé différentes méthodes pour la purification de la protéine Alp7A, y compris la séparation par chromatographie, et le fractionnement au sulfate d'ammonium. J'ai discuté des divers défis que nous avons rencontrés dans ces expériences, tels que la contamination, l'instabilité de la protéine Alp7A et l'épaisseur bactérienne. Enfin, j'ai proposé des approches expérimentales alternatives qui aideraient à étudier le mécanisme de ségrégation des plasmides par Alp7ARC. / Project I: Endospores represent a dormant state of bacteria that allows them to withstand extreme conditions and persist for years. Endospore formation has shaped evolution, whereby it exclusively occurs in Firmicutes. Several studies have reported endospore formation in species outside of Firmicutes, particularly in two species of Proteobacteria, Rhodobacter johrii and Serratia marcescens, and one species of Actinobacteria, Mycobacterium marinum. Identifying endospores outside of Firmicutes would affect the shape of the tree of life and aid in our fight against human pathogens. Therefore, we aimed to investigate endosporulation in these three species using advanced imaging and analytical approaches, including correlative light and electron microscopy (CLEM), cryo-electron tomography (cryo-ET), and lipidomics. We used the well-characterized sporulating bacterium Bacillus subtilis as a positive control of sporulation. Examination of R. johrii, S. marcescens, and M. marinum using CLEM and cryo-ET showed that phase-bright objects did not resemble any stages of endosporulation. Cryo-tomograms revealed that the phase-bright objects in S. marcescens were aggregated cellular debris of dead cells, whereas they displayed granular structures typical of bacterial cells in R. johrii and M. marinum. Lipidomic analysis in R. johrii identified the granular structures as potential storage granules enriched with triacyl-glycerides (TAGs). We speculate that TAGs may provide an energy source to withstand the nutrient depletion. Additional biochemical and bioinformatics approaches supported our conclusions that R. johrii, S. marcescens, and M. marinum are non-sporulating bacteria. Project II: Plasmids play a vital role in the spread of resistance genes within and across bacterial species. Therefore, it is essential to understand the bacterial systems involved in the transfer and maintenance of plasmids to better aid in our fight against the spread of antibiotic resistance. In this doctorate, we aimed to characterize the alp7ARC operon, employing the bacterial actin homolog Alp7A to segregate the tetracycline resistance-encoding plasmid pLS20 in B. subtilis. The stability of the plasmid was shown to be dependent on the alp7ARC operon, indicating an essential role in plasmid segregation. Preliminary results on Alp7A showed that it assembles into a novel tubular nanostructure rather than filaments, suggesting a novel mechanism for DNA segregation by Alp7A. We further studied the structure of Alp7A in vivo using combination of approaches, including molecular biology, cryo-ET, and fLM. We also used CLEM to localize Alp7A in whole cells to a macromolecular resolution. Besides, we investigated the structure and function of Alp7A in vitro by transfecting E. coli with various plasmid constructs and purification by several methods, including affinity chromatography and ammonium sulfate precipitation. I discussed the diverse challenges we encountered in these experiments, such as bacterial thickness, contamination, and Alp7A protein instability. Finally, I proposed alternative experimental approaches for investigating the mechanism of plasmid segregation by Alp7ARC.

The work was comprehensively focused on the development of adhesive forms of probiotics in the form of a biofilm on combined carriers with a prebiotic component. The second part dealed with the influence of food on the multiplication and survival of selected types of probiotic bacteria. Subsequently, the effect of individualized probiotic supplements on changes in the human intestinal microbiome was monitored. Suitable adherent probiotic strains for biofilm formation were selected and tested. Methods have been introduced and different variants of carriers for culturing and binding bacteria have been tested. In vitro experiments verified the stability of biofilm stucture and its resistance to low pH, bile and antibiotics in comparison with the planktonic cell form. The antimicrobial effect of probiotic strains in the form of a biofilm was studied. The cultivation of the multispecies biofilm on the combined carrier was optimized and the stability of the biofilm and the final viability of probiotic bacteria were confirmed. Furthermore, the influence of various foods and beverages on the viability of probiotic bacteria was evaluated with emphasis on the simulation of passage through the gastrointestinal tract. Both models, solutions with standardised concentrations of alcohol, sugar, salts, proteins or different pH and different types of real foods and beverages were tested. The effect of food and beverages was tested on monocultures of Lactobacillus acidophilus, Bifidobacterium breve and on probiotic capsules containing a mixed culture of probiotic microorganisms. The survival of probiotics in various food matrices in the simulated gastrointestinal tract was quantitatively different. We managed to define foods suitable for supporting the multiplication of probiotic bacteria. A separate part of the work was focused on the targeted modulation of the intestinal microbiome by individualized probiotics that were prepared on the basis of molecular biological analyzes of the intestinal microbiome aimed at detecting the percentage of lactobacilli, bifidobacteria and phylum Firmicutes and Bacteroidetes. Personalized probiotic supplementation confirmed the positive effect of this approach on microbiome changes, especially on the increase of the content of lactobacilli, bifidobacteria and the overall diversity of the microbiome.