Dubilier, Nicole
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Item-typ:Veröffentlichung, Metabolic investigation of chemoheterotrophic endosymbionts of gutless oligochaetes(2025-02-25); ; ; The concept of a nested ecosystem and the interchanges among biotic and abiotic factors is one lens through which we can approach the study of the specific associations between organisms that live closely together known as symbioses. The work presented herein builds upon the foundational works on the chemotrophic symbiosis between marine gutless oligochaetes and their various chemoautotrophic and chemoheterotrophic symbionts. To expand on the previously observed taxonomic and metabolic diversity of these symbiotic associations, I focused the work of my dissertation on two of the chemoheterotrophic phyla that occur in various permutations in this symbiosis – Desulfobacterota and Spirochaetota. I provided new insights into the ecology and heterotrophic niche partitioning in these microbiomes, determined metabolic mechanisms that allow for carbon and energy conservation in a symbiotic lifestyle, and optimized a method that leaves room to continue these metabolic explorations in future studies of this and other symbioses.Dissertation35 41 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Phylogeny and diversity of symbionts from whale fall invertebrates(2010-04-08); ; ; Whale falls form oases at the bottom of the ocean that provide an energy source for a diverse and abundant fauna, including a new symbiosis type between Osedax worms and heterotrophic bacteria. Osedax infiltrate whale bones with their root tissues. These roots are filled with bacteria hypothesized to provide their hosts with nutrition by extracting organic compounds from the whale bones. This thesis is made of three thematic parts. The first part is a review on the ecology and evolution of Siboglinidae. The second part focuses on the diversity of the symbionts associated with Osedax mucofloris, where a higher diversity of Oceanospirillales bacteria was identified with eight monophyletic clusters. The symbiont clusters were not uniformly distributed, but one cluster dominated the population and each individual. In addition, when several clusters co-occurred in one individual they were not mixed but spatially separated. Statistical analyses showed that each O. mucofloris individual has a significant effect on symbionts diversity and distribution. Thus, each O. mucofloris individual has its own specific endosymbiont community. Our results suggest a horizontal transmission of the symbionts. Several scenarios explaining the observed symbionts distribution are considered including selection by the host, variability of the available symbionts, and competition between the symbionts. The third part of this thesis focuses on the symbionts of a polycheate worm, a Ctenodrilidae, Raricirrus beryli. Among the epibacteria, bacteria forming a monophyletic cluster with thiotrophic symbionts of bathymodiolin mussels were found. This is the first report of a polychaete host for these bacteria.Dissertation276 287 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Evolution and physiology of the Paracatenula symbiosis(2018-12-10); ; ; This thesis focuses on the symbiosis between the marine flatworm host Paracatenula, which lacks mouth and digestive system, and the alphaproteobacterial symbiont Candidatus Riegeria. Both host and symbiont are unique partners across all known symbioses - no other flatworm besides Paracatenula hosts chemosynthetic symbionts, and Ca. Riegeria is the only known chemosynthetic symbiont within the Alphaproteobacteria. Contained in specialized cells within the trophosome of Paracatenula, the Ca. Riegeria symbionts can comprise up to a half of the total host volume, representing the highest ratio of symbiont-to-host biomass among animal-bacteria symbioses. Ca. Riegeria have been transmitted vertically between host generations for at least 500 million years, leading to the presumption that their genomes contain signatures of reductive genome evolution. Yet only little is known about the genetic repertoire of Ca. Riegeria, their ecophysiology and how reductive genome evolution progressed over their evolutionary history. I have characterized key aspects of the Paracatenula symbiosis emphasizing the physiology of Ca. Riegeria and how it compares to "typical" gammaproteobacterial chemoautotrophs (I). I described the consequences of reductive genome evolution on retained functions and the underlying processes (II). I investigated the role of the symbionts in tissue regeneration as Paracatenula have an enormous regenerative capacity (III). Overall, I demonstrate that Paracatenula and Ca. Riegeria share an intimate biological connection that has been shaped over their long evolutionary history.Dissertation443 205 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Correlative mass spectrometry imaging of animal–microbe symbioses(2020-04-15); ; ; Mass spectrometry imaging provides a new frontier in imaging the spatial distribution of molecular species. However, the chemical images generated with this state-of-the-art technique are difficult to analyze and interpret. Especially when investigating the chemical interactions between animals and bacteria the spatial assignment between chemical signatures and individual cells in mixed communities presents a substantial technical challenge. Therefore, I developed correlative mass spectrometry imaging approaches that combine MSI with other visualization strategies such as fluorescence microscopy, to visualize individual bacterial cells and micro computed tomography, to visualize the detailed 3D histology of the host animal. Using the combined visualization techniques, we could reveal new chemical interactions in marine and terrestrial animal-microbe symbioses.Dissertation592 524 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Molecular biology and evolution of the bacterial intranuclear parasite Ca. Endonucleobacter(2020-11-24); ; ; Few bacteria are able to colonize eukaryotic host cells, and even fewer can invade organelles. Among the latter, those which colonize the nucleus (intranuclear bacteria) are a majority. The nucleus is considered as a replication niche that offers bacteria shelter, the opportunity to manipulate nuclear processes and nutrients in form of chromatin. Previous studies have suggested that intranuclear bacteria consume host chromatin, but this would inevitably lead to a collapse of their replication niche. Nuclear colonization has intrinsic risks for bacteria, as eukaryotic cells are able to sense nuclear deformation and respond to it activating apoptosis. Therefore, intranuclear bacteria must count on molecular mechanisms to prevent their host cells to shut down. Although many intranuclear bacteria have been visually characterized, little is known about how they colonize the nucleus, how they thrive within, and which effects they have on their host cells. [...] My findings challenge previous hypotheses about nutritional and survival strategies of intranuclear bacteria, and point out the genomic innovations that might define intranuclear lifestyle in bacteria.Dissertation308 260 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, From genomes to communities - Evolution of symbionts associated with globally distributed marine invertebrates(2021-11-10); ; ; Das Zusammenleben von eukaryotischen Wirten mit vielf ltigen bakteriellen Gemeinschaften ist in der Natur weitverbreitet. Die wahrscheinlich bekanntesten und am besten erforschten Beispiele für solche Lebensgemeinschaften sind die Darmbakterien von Wirbeltieren, und besonders die des Menschen. Die Vielf ltigkeit und Zusammensetzung der menschlichen Darmbakterien werden fortwährend mit der Gesundheit des Wirtes in Zusammenhang gebracht. Dieser Zusammenhang zwischen der menschlichen Darmflora und der Gesundheit des Wirtsorganismus hebt die Wichtigkeit der Erforschung solcher Lebensgemeinschaften hervor. Obwohl immer mehr solcher diverser Lebensgemeinschaften in der Natur gefunden werden und wir verstehen, dass die Assoziation mit Bakterien großen Einfluss auf die Ökologie und Evolution der Wirte hat, verstehen wir verhältnismäßig wenig von den evolutionären Dynamiken, die diesen phylogenetisch diversen Assoziationen zu Grunde liegen. In dieser Doktorarbeit beschäftige ich mich mit der Evolution von Symbionten die mit taxonomisch diversen und weltweit vorkommenden Gruppen mariner, wirbelloser Tiere assoziiert sind. Die hohe taxonomische und biogeographische Diversität dieser Wirte waren Voraussetzung dafür, die Evolution der Symbionten im Kontext von kologischen Effekten und Effekten der Wirtsevolution zu beleuchten.Dissertation315 249 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Investigating the lipid profile of animal-microbe symbioses(2021-07-29); ; ; ; Lipids are important and understudied elements of host-bacteria interactions. Lipids play central roles in defining cellular membranes, they have a structural role but also influence the distribution and activity of transporters, enzymes and receptors. Aside of their functions in the membrane, they have important functions as signaling molecules, energy storages, coenzymes or toxins. In pathogenic interactions, lipids have been shown to participate to every stage of the interaction between the host and the bacteria. A few studies have focused on beneficial symbioses and we only start to discover the importance of lipids in those interactions. Much of the functional importance of the rich chemical diversity of lipids remains unknown. In this study, I aimed to describe the chemical landscape of deep-sea mussels living in close association with chemoautotrophic bacteria (Chapter I) and determine the identity, distribution and potential functions of a metabolite group specific to the association between deep-sea mussels and methane-oxidizing symbionts (Chapter II). This research was expanded to shallow water symbioses formed by gutless annelids and chemoautotrophic bacteria. The study of their sterol pool revealed a new phytosterol synthesis pathway specific to animals (Chapter III).Dissertation247 338 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Geobiological Coupling of Hydrothermal Vent Fluids with Endosymbiotic Primary Producers of Bathymodiolus Mussels from Hydrothermal Vents on the Mid-Atlantic Ridge(2008-09-11); ; ; This thesis was accomplished within the Priority Program SPP 1144 "From Mantle to Ocean" which investigates the energy-, material-, and life cycles at hydrothermal vents on the slow-spreading Mid-Atlantic Ridge. Two hydrothermal settings which differ prominently in their fluid composition are examined within the SPP: the ultramafic-hosted Logatchev vent field (14 45'N) and a cluster of basalt-hosted vent fields at 4 48'S. In contribution to the SPP the research group "Hydrothermal Symbioses" investigates the conversion of geochemical energy into biomass, particularly of hydrothermal vent mussels belonging to the genus Bathymodiolus through their chemoautotrophic and methanotrophic endosymbionts. To address this energy transfer the symbiosis research project focuses on the diversity, abundance, distribution, biomass, and activity of these endosymbiotic bacteria in regard to differing physico-chemical conditions. This PhD project aimed to (i) describe the physico-chemical conditions in Logatchev mussel habitats by means of in situ measurements, (ii) investigate the endosymbiotic diversity of B. puteoserpentis (Logatchev) using the 16S rRNA gene as a phylogenetic marker, and (iii) evaluate the activity of endosymbiotic bacteria as judged from H2 and H2S consumption and CO2 assimilation in response to the two differing hydrothermal settings. (I) In situ measurements using microsensors revealed abundant H2S and O2 in diffuse fluids emanating from the mussel beds. Thus, Logatchev mussel habitats, previously suggested to be deficient in free sulfide, comply with the requirements of aerobic sulfur-oxidation. (II) Cloning and sequencing of the 16S rRNA gene revealed three phylotypes in B. puteoserpentis. Two were related to sulfur- and methane-oxidizing symbionts. The third phylotype was identified as an intranuclear bacterial parasite which was subsequently found to be widespread in hydrothermal vent and cold seep mussels of the genus Bathymodiolus and termed "Candidatus Endonucleobacter bathymodioli". FISH and deconvolution microscopy revealed an unusual cell cycle, the first to be reported from an intranuclear parasite of metazoans. (III) Consumption of H2 and H2S along with CO2 assimilation, indicative of energy conservation and thus actively metabolizing endosymbionts, implied that endosymbiotic chemoautotrophy may be sulfur-based at basalt-hosted vent settings but hydrogen-based at ultramafic-hosted vents. Indeed, the mussel population inhabiting the ultramafic-hosted Logatchev vent field may oxidize 270-670 liters of hydrogen per hour. Endosymbionts of B. puteoserpentis may therefore play an appreciable role as H2-oxidizing primary producers and thus in converting H2-derived geochemical energy into biomass. In fact, H2 has not been shown previously to be utilized by symbionts of invertebrates from reducing environments.Dissertation506 172 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Bacterial-invertebrate symbioses: from an asphalt cold seep to shallow water(2010-10-18); ; ; Symbiotic associations are complex partnerships that can lead to new metabolic capabilities and the establishment of novel organisms. The diversity of these associations is very broad and there are still many mysteries about the origin and the exact relationship between the organisms that are involved in a symbiosis (host and symbiont). Some of these associations are essential to the hosts, such as the chemosynthetic symbioses occurring in invertebrates of the deep-sea. In others the host probably would rather not be the host, as in the case of parasitic microbes. My PhD research focuses on symbiotic and parasitic associations in chemosynthetic and non-chemosynthetic invertebrates. This thesis describes and discusses three different aspects of associations between bacteria and marine invertebrates. The first aspect focuses on chemosynthetic associations from a unique asphalt seep called Chapopote in the Gulf of Mexico (GoM). Phylogenetic analyses of host genes (cytochrome-c-oxidase subunit I) and bacterial genes (16S rRNA) in two Bathymodiolus mussel species and an Escarpia tubeworm showed that both the hosts and their chemosynthetic symbionts are very similar to their congeners from the northern GoM. Unexpectedly, a novel symbiont most closely related to hydrocarbon degrading bacteria of the genus Cycloclasticus was discovered in B. heckerae. Stable carbon isotope values in B. heckerae tissues of lipids typical for Cycloclasticus spp. were consistently heavier by 2.5permil than other lipids indicating that the novel symbiont might use isotopically heavy hydrocarbons from the asphalt seep as an energy and carbon source. The discovery of a novel symbiont that may be able to metabolize hydrocarbons is particularly intriguing because until now only methane and reduced sulfur compounds have been identified as energy sources in chemosynthetic symbioses. The large amounts of hydrocarbons available at Chapopote would provide these mussel symbioses with a rich source of nutrition. The second aspect of this thesis deals with bacteria that infect the nuclei of marine invertebrates and were recently found to be widespread in deep-sea Bathymodiolus mussels. Because of their potentially lethal effect on bivalve populations, I looked for the presence of intranuclear bacteria in economically important and commercially available bivalve species, i.e. oysters (Crassostrea gigas), razor clams (Siliqua patula and Ensis directus), blue mussels (Mytilus edulis), Manila clams (Venerupis philippinarum), and common cockles (Cerastoderma edule). Fluorescence in situ hybridization (FISH) revealed the presence of intranuclear bacteria in all investigated bivalves except oysters and blue mussels. Preliminary tests with real-time PCR showed massive amounts of intranuclear bacteria in some of the bivalve species, raising the question if these might affect not only the health of the bivalves but possibly also of the humans that eat them. In the third and final aspect of my thesis, I examined the general diversity of bacteria in the gill tissues of deep-sea and shallow-water mussels and clams. Comparative 16S rRNA sequence analysis and cultivation experiments revealed a much higher diversity than previously recognized. This thesis shows that bivalves are ideal models for studying the microbiota of marine invertebrates because of the high diversity of both highly specific and more generalized symbiotic and parasitic bacteria in their gill tissues.Dissertation324 237 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Bioplastic-eating animals: Polyhydroxyalkanoate degrading enzymes in a chemosymbiotic worm(2023-12-11); ; ; ; Bacteria and halophilic archaea synthesize the bioplastic polyhydroxyalkanoate (PHA). PHA represents an important carbon and energy storage compound build up under nutrient limitation. PHA can make up to 90% of the microorganism’s dry weight. When growth conditions are lifted, the microorganisms degrade PHA into their monomers, dimers or a mix of oligomers. Microorganism will metabolize the resulting degradation products to yield CO2, CH4, H2O and energy. To degrade PHA, microorganisms, including bacteria, archaea, fungi and a few protist species, use a PHA depolymerase enzyme (PHAD). Until now, it was largely thought that animals were unable to produce the PHAD enzyme to breakdown PHA. In Chapter I of my dissertation, I identified the first animal PHAD in the gutless worm Olavius algarvensis. I characterized the enzyme structure, function and expression pattern. The host PHAD degrades extracellular PHA and expresses all genes needed to generate energy from PHA degradation, which likely indicates that the worm benefits from the PHA degradation. Surprisingly, I discovered that additional 67 metazoan species from nine distinct animal phyla encode for at least one PHAD. All of the animal species that encode for a PHAD access PHA through their diet. My in-depth analysis of the earthworm PHAD in Chapter III contradicted my hypothesis that animals encode for a PHAD to meet their nutritional requirements. Using immunohistochemistry assays, I found that the Lumbricus rubellus PHAD was localized in the epidermis. One possible explanation for my findings is that the PHAD degrades PHA of invading bacteria. Alternatively, earthworms might excrete their PHADs to their habitat to target extracellular PHA in the soil. Therefore, I predict that animal PHADs might have multiple benefits for metazoans. PHADs degrade PHA either intracellularly or extracellularly. Intracellular PHADs function on native PHA inside the cell. In contrast, extracellular PHADs function on denatured PHA that occurs outside the cell. The affinity of the PHAD for either intracellular or extracellular PHA is reflected in the enzymes structure. PHADs are typically classified based on sequence homology of the predicted protein. In Chapter II of my dissertation, I showed that the classification of PHADs from the gammaproteobacterial group Chromatiales is often misleading. One challenge is that there is less known about the protein structure of intracellular PHADs, which makes predicting the type of PHAD by sequence homology alone uncertain. Using AlphaFold2 to generate and compare PHAD models from multiple Chromatiales PHAD enzymes, I showed that true intracellular PHADs lack a signal peptide and have an altered substrate binding site. Enzyme assays on selected Chromatiales species, including Thiocapsa rosea, confirmed the initial hypothesis. Experimental evidence is thus crucial to reveal the true functions of PHADs. It is important to correctly classify the type of PHAD because it alters our interpretation of PHA degradation in natural ecosystems and consequently our understanding of carbon cycling. In conclusion, my dissertation adds new data to the field of PHA degradation. I revealed that experimental evidence is needed to classify PHADs. Additionally, I identified a novel group of PHADs that likely function after lysis of microbial species. Significantly, I showed that PHA degradation is not limited to bacteria, fungi, archaea, protists but that the ability to degrade PHA is widespread in animals.Dissertation253 163