Dubilier, Nicole
Lade...
Preferred name
Dubilier, Nicole
Official Name
Dubilier, Nicole
12 Ergebnisse
Einstellungen
Gerade angezeigt 1 - 10 von 12
- Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Molecular characterization of symbiotic associations between chemoautotrophic sulfur-oxidizing microorganisms and nematodes in shallow marine sediments(2006-06-19); ; ; Shallow marine sediments are preferred environments for nematodes harboring endo- or ectosymbiotic microorganisms. In most cases, the symbionts are autotrophic, sulfur-oxidizing bacteria. In the present work molecular biological methods such as comparative 16S rRNA and 18S rRNA sequence analysis, fluorescence in situ hybridization (FISH) and slot blot hybridization with group specific rRNA-targeted oligonucleotide probes were used to investigate and characterize these symbiotic associations and their natural habitat. Thus we investigated the specificity of the symbiotic association between ectosymbiotic bacteria and gut-bearing nematodes of the genus Leptonemella from intertidal sandy sediments near the island of Sylt (Wadden Sea) and we determined the identity and phylogeny of the endosymbionts of mouthless nematode, Astomonema sp. from coral reef sediments in the Bahamas. Also the microbial diversity and community structure of the intertidal Sylt sandy sediments, the preferred habitat of the Leptonemella spp. was determined and characterized over depth (0 to 12 cm) and seasons (March, July, October).Dissertation293 143 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, The Bacterial Ectosymbionts of the Ciliate Kentrophoros(2017-10-24); ; ; Kentrophoros is a single-celled eukaryote that has a symbiosis with sulfur-oxidizing bacteria. This thesis investigates the diversity and functional significance of this symbiosis through molecular ecology and genomics. The bacteria belong to a single lineage in the Gammaproteobacteria that is specifically associated with Kentrophoros. Kentrophoros also constitutes a monophyletic group, despite their morphological diversity, which includes new species discovered during this work. Mitochondrial genes of Kentrophoros show evidence of rapid diversification during their evolutionary history. Genomes of the symbionts encode pathways for sulfur oxidation, but none of the known pathways for autotrophic carbon fixation. Instead they have the genetic potential for uptake and usage of organic carbon substrates, suggesting that this symbiosis is based on chemolithoheterotrophy, instead of chemosynthesis, as previously thought. The ecophysiological consequences of such a metabolism are discussed.Dissertation580 835 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Phylogenetic and functional characterization of symbiotic bacteria in gutless marine worms (Annelida, Oligochaeta)(2005-11-22); ; ; Symbioses between chemoautotrophic bacteria and eukaryotic hosts are widespread in marine environments. In most chemosynthetic endosymbioses, only a single, or at most two bacterial phylotypes co-occur within a host species.In this study the phylogenetic and metabolic diversity of bacterial endosymbionts in gutless marine worms (Annelida, Oligochaeta) from different environments was investigated. Almost all host species harbor a gammaproteobacterial sulfur oxidizer indicating the importance of these Gamma 1 symbionts for the nutrition of the gutless oligochaetes. A second gammaproteobacterial symbiont and deltaproteobacterial symbionts were detected in hosts from coastal silicate sediments, while in hosts from calcareous sands alphaproteobacterial symbionts were identified. Spirochetes were found in hosts from both types of sediments. The phylogenetic diversity of the bacterial symbionts mirrors their different metabolic capabilities. The Deltaproteobacteria have been identified as sulfate reducers and the secondary gammaproteobacterial symbionts are hypothesized to be sulfur oxidizers. Key genes involved in oxidative and reductive sulfur metabolism, CO2 fixation via the Calvin-Benson-Bassham (CBB) cycle, and nitrogen metabolism were successfully detected. Based on phylogenetic analyses it was possible to make potential assignments of genes to a respective symbiont.The use of comparative metagenomics gave first insights into the genome of a gutless oligochaete symbiont. A contiguous sequence of 51 kb from a bacterial artificial chromosome insert contained genes involved in significant metabolic pathways for these symbioses such as sulfur oxidation and CO2 fixation via the CBB cycle indicating that this sequence originated from a thioautotrophic symbiont. This study showed that the symbiotic community in marine gutless oligochaetes with at least three and as many as six different symbiotic phylotypes is much more complex than previously assumed. Despite the high phylogenetic diversity, these associations are clearly specific and stable for most phylotypes within a given host species.Dissertation237 102 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Deep Se(a)quencing : a study of deep sea ectosymbioses using next generation sequencing(2016-06-06); ; ; Deep-sea hydrothermal vent fields and cold seeps are oases for deep-sea life in an otherwise nutrient-poor environment. They release energy-rich inorganic compounds that sustain rich microbial and invertebrate communities on the basis of bacterial chemosynthesis. Many endemic invertebrate species have established symbiotic relationships with chemosynthetic bacteria and thrive in these habitats. Symbioses occur in many forms: in endosymbioses the bacteria are located within a host cell or tissue, whereas in ectosymbioses the bacteria colonize their hosta s body surfaces such as epithelia. Deep-sea research is challenging with isolated and remote study sites requiring extensive logistical operations for sample collection. However, the rise of next-generation sequencing has allowed the gathering of large datasets from small samples and thus allows in-depth exploration of symbiotic systems. This Ph.D. thesis was focused on the investigation of two deep-sea epibiotic systems using next-generation sequencing methods. The first project investigates Epsilonproteobacteria that occur on several deep sea mussels of the subfamily Bathymodiolinae. Previous work with 16S rRNA clone libraries had suggested that the mussels may host epsilonproteobacterial symbionts in addition to the well-known gammaproteobacterial endosymbionts. First I analyzed the localization of the epsilonproteobacterial sequences within the mussela s gill tissue using microscopy and investigated their diversity and phylogeny using 16S rRNA sequencing methods. I was able to show an epibiotic association of the Epsilonproteobacteria and determined that seven out of the twelve mussel species studied were associated with closely-related Epsilonproteobacteria. The phylogenetic reconstruction of the 16S rRNA sequences suggested that the epibionts belong to a new family of Epsilonproteobacteria. In the second part of this project, I aimed to determine the nature of the association and metabolic potential of the epibionts, using metagenome and metatranscriptome analysis of two different bathymodiolin species. Based on genomic data, I was able to reconstruct their inorganic carbon fixation pathway, which was unexpectedly predicted to occur through the Calvin Benson Bassham (CBB) cycle. To date every other chemoautotrophic Epsilonproteobacteria has been described to fix inorganic carbon using the reverse tricarboxylic acid (rTCA) cycle. These epibionts acquired the CBB cycle from two separate horizontal gene transfer (HGT) events and lost the rTCA cycle. The key gene of the CBB, coding for 1,5-ribulose bisphosphate carboxylase, may have been acquired from a relative of the bathymodiolin gammaproteobacterial endosymbionts, whereas all the other CBB genes originate from an unknown Betaproteobacteria. I then discussed the implication of such HGTs and hypothesized that the epibionts are commensal or mutualistic, because most pathogens are not autotrophic. The third part of this project was a comparative analysis of the genomic data of the two epsilonproteobacterial epibionts. My phylogenomic analysis using multigene phylogeny showed that these two epibionts were two different species. I described the genetic potential of these epibionts and presented their reconstructed metabolism. This shows small metabolic differences between both bacterial draft genomes, and an overall array of different metabolic and genetic tools available that gives them a metabolic versatility to adapt to the environment. My second project investigated the ectosymbiotic bacterial populations associated with the deep-sea shrimp Rimicaris hybisae. The R. hybisae shrimp was discovered in 2010 along with two hydrothermal vent fields, Von Damm and Piccard, located on the Mid-Cayman Spreading Center. These two hydrothermal vents had very different environmental conditions and offered a unique setting to study the influence of the environment on ectosymbiotic populations. Von Damm, an ultramafic vent with high concentration of methane and low concentration of hydrogen sulfide, is located at 2500 m depth. Piccard, a basaltic vent field with low concentration of methane but high concentration of hydrogen sulfide, is located at 5000 m depth and is the deepest hydrothermal vent field found so far. I compared the different symbiotic and free-living populations using amplicon libraries of a variable region of the 16S rRNA sequence. I showed that the ectosymbiotic populations associated with R. hybisae are significantly different between the two hydrothermal vent fields and are more similar to their respective free-living bacterial communities. I hypothesize that the R. hybisae shrimp are taking up ectosymbionts from their environment, because they are probably the best-adapted to local environmental conditions.Dissertation306 163 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Diversity, specificity and evolutionary history of marine invertebrate symbioses and functions of the sulfur-oxidizing symbionts(2015-07-09); ; ; Many marine invertebrates have established symbioses with chemosynthetic bacteria that metabolize reduced sulfur compounds and provide nutrition to their host. Two key questions in the field of symbiosis are: (1) How specific and evolutionarily stable are these symbioses? Chapters II, III and IV of this thesis contribute to a more comprehensive understanding of this question by investigating the diversity, specificity and evolutionary history of three sulfur-oxidizing symbioses: deep-sea vestimentiferan tubeworm endosymbioses, shallow water gutless phallodriline oligochaete endo- and stilbonematine nematode ectosymbioses. The studies emphasize the power of molecular analyses to uncover "hidden" symbiont diversity and highlight the remarkably stable and specific stilbonematine ectosymbioses. (2) What are the benefits for the symbiotic partners? Chapter V strengthens the hypothesis of stilbonematine ectosymbionts' nutritional role for their host and the genomic study in Chapter VI discusses potential additional functions of the ectosymbionts for their nematode host.Dissertation277 429 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Characterization of bacterial endo- and ectosymbionts of oligochaete worms from marine sediments: Phylogeny and metabolic potential(2010-06-23); ; ; Two obligate bacterial endosymbioses and a facultative ectosymbiosis of gutless (1, 2) and gut-bearing (3) marine oligochaetes from coastal sediments were characterized. (1, 2) The gutless oligochaetes Olavius algarvensis and O. ilvae live in coastal sediments with very low sulfide concentrations. Similar bacterial consortia were found in both hosts with two sulfide-oxidizing Gammaproteobacteria and two sulfate-reducing Deltaproteobacteria. The presence of sulfate-reducers providing the sulfide-oxidiziers with an internal source of sulfide could explain how the worms could colonize a sulfide-poor environment. (3) Tubificoides benedii lives in Wadden Sea sediments and is adapted to extreme fluctuations of oxygen and sulfide. Its posterior end is facultatively colonized by filamentous bacteria. This community was dominated by two morphologically distinct phylotypes: A thicker Gammaproteobacterium attached to the exterior of the cuticle and a thinner Epsilonproteobacterium penetrated it. Both ectosymbionts belonged to clades that consisted nearly exclusively of bacteria associated with deep-sea hydrothermal vent invertebrates.Dissertation306 179 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Dynamics of Symbiont Abundance in Bathymodiolin Deep-sea Symbioses(2011-10-19); ; ; Deep-sea hydrothermal vents and cold seeps are widespread throughout the world's oceans and represent `oases of life' in a dark and hostile environment. These chemosynthetic habitats are often dominated by mussels of the genus Bathymodiolus. The bivalves harbor bacterial symbionts in their gills that use methane and reduced inorganic compounds such as sulfide and hydrogen as energy sources for chemosynthetic primary production. It is well known that the spatial and temporal gradients of these energy sources can be extremely steep at vents and seeps, and some studies have shown that differences in energy source availability affect symbiont abundance in Bathymodiolus mussels. However, in-depth analyses of physico-chemical gradients and their effect on symbiont abundance are lacking. One of the basic requirements for these analyses is a reliable quantification method for the symbionts. The goal of my thesis was therefore to develop an accurate and efficient protocol for determining symbiont abundance in bathymodiolin mussels.Dissertation310 170 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Acquisition and activity of bacterial symbionts in marine invertebrates(2012-10-26); ; ; Chemosynthetic symbioses evolved multiple times in a wide diversity of host species and from many different bacterial lineages. The symbionts provide nutrition to the hosts by fixing CO2 into biomass using reduced inorganic compounds as energy sources. This gives the hosts a physiological advantage to colonize and thrive in nutrient poor habitats. Two key questions that have emerged in symbiosis research are 1) how do the hosts acquire their symbionts and 2) what reduced compounds can be used by the symbionts as energy source to fix CO2 into biomass. This PhD thesis consists of two parts that will each deal with one of these two fundamental questions. In the first part of this thesis, two manuscripts describe the symbiont colonization of host tissues in the deep-sea mussel Bathymodiolus from hydrothermal vents. Bathymodiolus harbors its chemosynthetic symbionts intracellularly in gill tissues and, as in all bivalves, the gills grow throughout the mussel's life. This raises the question how the newly developed gill tissues are colonized by symbionts. Symbiont colonization of newly formed gill tissues was investigated using fluorescence in situ hybridization with symbiont-specific probes on semi-thin sections of whole juveniles. In addition, posterior ends of adult gills were also analyzed, as new gill filament formation occurs here. In the smallest juveniles, symbionts had colonized a wide range of epithelial tissues, revealing a widespread distribution of symbionts in many different juvenile organs. In contrast, juveniles larger than 9 mm had symbionts only in their gills. These observations indicate an ontogenetic shift in symbiont colonization from an indiscriminate infection of almost all epithelia in early life stages to spatially restricted colonization of gills in later developmental stages of Bathymodiolus. Analyses of the posterior end of both juvenile and adult gill tissues further showed that all gill filaments except the first most recently formed 7 to 9 filaments harbored symbionts. Newly formed gill tissues of Bathymodiolus are thus initially symbiont free and only later become infected with symbionts as they extend and differentiate, suggesting a life long de novo colonization by the endosymbionts of aposymbiotic host cells. In the second part of this thesis I investigated the physiological capabilities of the symbionts of Olavius algarvensis. This marine worm lacks both a digestive and excretory system. Instead it relies on a symbiotic community of two gammaproteobacterial sulfur oxidizers, two deltaproteobacterial sulfate reducers, and a spirochete for nutrition and waste recycling. External energy sources for the symbiotic association have remained enigmatic because of extremely low concentrations of reduced sulfur compounds and organic substrates in the worms habitat. Using a metaproteomic approach and incubation experiments I showed that hydrogen (H2) and carbon monoxide (CO) are additional energy sources for the symbiosis of O. algarvensis. The finding of elevated CO and H2 concentrations in the worm s habitat further confirmed the ecological importance of both substrates for the worm symbiosis. One of the sulfur-oxidizing symbionts incorporated high amounts of CO2 into its biomass in the presence of CO, which was determined using 13C-labeled bicarbonate in the incubation medium and subsequent nanoSIMS analyses. The metaproteomic study further revealed a high expression of proteins involved in highly efficient pathways and high-affinity uptake transporters for the recycling and conservation of energy, nitrogen, and carbon sources. This indicates that the nutrient-poor nature of the worm s habitat exerted a strong selective pressure in shaping this association.Dissertation216 149 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Transmission of bacterial symbionts in the gutless oligochaete Olavius algarvensis(2016-01-27); ; ; The essential role that symbioses between bacteria and animals play for life on earth has been a major topic of scientific research for the past fifty years. We now understand that eukaryotic life could not have evolved without the intricate influence of bacteria, which impact physiological, metabolic, nutritional, developmental and evolutionary processes in many eukaryotic phlya. One model system for such associations is the well-studied symbiosis between the gutless oligochaete Olavius algarvensis, from the island of Elba, Italy, and its obligate consortium of chemoautotrophic sulphide-oxidizing gamma-proteobacteria and sulphate reducing delta-proteobacteria. The complete nutritional dependency of the host to its symbionts has led to the reduction of the digestive tract and the excretory system. The aim of this thesis is to investigate how this symbiosis is maintained over consecutive generations. In particular I examine whether symbionts are transmitted into the next host generation vertically by smearing from the parent worm during oviposition, horizontally by uptake from the environment, or by both these modes. To answer this question further investigation into worm ecology, development and molecular methodological advancement had to be made.Dissertation464 249 - Some of the metrics are blocked by yourconsent settings
Item-typ:Veröffentlichung, Phylogenetic diversity and metabolic versatility of the bacterial endosymbionts in marine gutless oligochaete worms(2009-12-14); ; ; Marin gutless oligochaete worms (Annelida, Phallodrilinae) live in an obligate association with bacterial endosymbionts. Each host, belonging to one of the two genera Olavius or Inanidrilus, harbours a specific, but morphologically, phylogenetically and metabolically diverse symbiont community. The primary symbionts of gutless oligochaetes, called Gamma 1, are large chemoautotrophic sulfur-storing bacteria that form a monophyletic clade within the Gammaproteobacteria and had been found in all host species studied so far. Secondary symbionts of gutless oligochaetes belong to the Alpha-, Gamma- and Deltaproteobacteria and to the Spirochaetes. In this PhD thesis the diversity and function of gutless oligochaete symbiont communities was investigated.In a first part, the phylogenetic and metabolic diversity of I. exumae was studied. The symbiont community of this host differed markedly from that of other gutless oligochaetes. Sulfate-reducing deltaproteobacterial symbionts co-occurred with alpha-proteobacterial symbionts in this host, showing that these do not mutually exclude each other as previously assumed. Furthermore, a large novel gammaproteobacterial symbiont only distantly related to the Gamma 1 symbionts, but morphologically similar, dominated the symbiont community, while no indication was found for a Gamma 1 symbiont. The presence of sulfur and genes diagnostic for autotrophy and sulfur oxidation indicate that this new symbiont is a sulfur-storing chemoautotroph. Thus, the novel symbiont seems to share its morphology and its function with the Gamma 1 symbionts and may have replaced the Gamma 1 symbiont in I. exumae.To learn more about the ecophysiology of gutless oligochaete symbioses, the autotrophic activity was investigated in a second project with tracer incubation experiments. Analyses of radiolabelled inorganic carbon uptake and sulfur content of individual Olavius algarvensis worms showed that in the presence of oxygen, internally stored sulfur was used as an energy source for the incorporation of inorganic carbon into biomass. In the absence of oxygen, inorganic carbon was taken up at lower rates. The electron donors and electron acceptors used under anoxic conditions could not be unambiguously identified. However, increased carbon fixation occurred in the presence of nitrate, sulfide and thiosulfate in a few worms.Identification of the autotrophic symbionts in the O. algarvensis symbiont community was achieved in a third project by applying in situ hybridization combined with microautoradiography (MARFISH) or high resolution mass spectrometry (nanoSIMS-HISH). The Gamma 1 symbionts immediately incorporated inorganic carbon into biomass under oxic conditions in the absence of external energy sources suggesting the usage of internally stored sulfur as electron donor. Uptake rates of individual cells varied, but were on average in the range of those found for free-living sulfur bacteria and chemoautotrophic symbionts. For the first time, the autotrophic symbiont could be directly identified and the inorganic carbon uptake analyzed for individual symbionts within the gutless oligochaete symbiosis.Dissertation258 335