@phdthesis{Horn2017,
  author    = {Horn, Hannes},
  title     = {Analysis and interpretation of (meta-)genomic data from host-associated microorganisms},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-152035},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2017},
  abstract  = {Host-microbe interactions are the key to understand why and how microbes inhabit specific environments. With the scientific fields of microbial genomics and metagenomics, evolving on an unprecedented scale, one is able to gain insights in these interactions on a molecular and ecological level. The goal of this PhD thesis was to make (meta-)genomic data accessible, integrate it in a comparative manner and to gain comprehensive taxonomic and functional insights into bacterial strains and communities derived from two different environments: the phyllosphere of Arabidopsis thaliana and the mesohyl interior of marine sponges. This thesis focused first on the de novo assembly of bacterial genomes. A 5-step protocol was developed, each step including a quality control. The examination of different assembly software in a comparative way identified SPAdes as most suitable. The protocol enables the user to chose the best tailored assembly. Contamination issues were solved by an initial filtering of the data and methods normally used for the binning of metagenomic datasets. This step is missed in many published assembly pipelines. The described protocol offers assemblies of high quality ready for downstream analysis. Subsequently, assemblies generated with the developed protocol were annotated and explored in terms of their function. In a first study, the genome of a phyllosphere bacterium, Williamsia sp. ARP1, was analyzed, offering many adaptions to the leaf habitat: it can deal with temperature shifts, react to oxygen species, produces mycosporins as protection against UV-light, and is able to uptake photosynthates. Further, its taxonomic position within the Actinomycetales was infered from 16S rRNA and comparative genomics showing the close relation between the genera Williamsia and Gordonia. In a second study, six sponge-derived actinomycete genomes were investigated for secondary metabolism. By use of state-of-the-art software, these strains exhibited numerous gene clusters, mostly linked to polykethide synthases, non-ribosomal peptide synthesis, terpenes, fatty acids and saccharides. Subsequent predictions on these clusters offered a great variety of possible produced compounds with antibiotic, antifungal or anti-cancer activity. These analysis highlight the potential for the synthesis of natural products and the use of genomic data as screening toolkit. In a last study, three sponge-derived and one seawater metagenomes were functionally compared. Different signatures regarding the microbial composition and GC-distribution were observed between the two environments. With a focus on bacerial defense systems, the data indicates a pronounced repertoire of sponge associated bacteria for bacterial defense systems, in particular, Clustered Regularly Interspaced Short Palindromic Repeats, restriction modification system, DNA phosphorothioation and phage growth limitation. In addition, characterizing genes for secondary metabolite cluster differed between sponge and seawater microbiomes. Moreover, a variety of Type I polyketide synthases were only found within the sponge microbiomes. With that, metagenomics are shown to be a useful tool for the screening of secondary metabolite genes. Furthermore, enriched defense systems are highlighted as feature of sponge-associated microbes and marks them as a selective trait.},
  subject      = {Bakterien},
  language  = {en}
}
@phdthesis{Sickel2016,
  author    = {Sickel, Wiebke},
  title     = {High-throughput biodiversity assessment - Powers and limitations of meta-barcoding},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-144573},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2016},
  abstract  = {Traditional species identification based on morphological characters is laborious and requires expert knowledge. It is further complicated in the case of species assemblages or degraded and processed material. DNA-barcoding, species identification based on genetic data, has become a suitable alternative, yet species assemblages are still difficult to study. In the past decade meta-barcoding has widely been adopted for the study of species communities, due to technological advances in modern sequencing platforms and because manual separation of individual specimen is not required. Here, meta-barcoding is put into context and applied to the study of bee-collected pollen as well as bacterial communities. These studies provide the basis for a critical evaluation of the powers and limitations of meta-barcoding. Advantages identified include species identification without the need for expert knowledge as well as the high throughput of samples and sequences. In microbiology, meta-barcoding can facilitate directed cultivation of taxa of interest identified with meta-barcoding data. Disadvantages include insufficient species resolution due to short read lengths and incomplete reference databases, as well as limitations in abundance estimation of taxa and functional profiling. Despite these, meta-barcoding is a powerful method for the analysis of species communities and holds high potential especially for automated biomonitoring.},
  subject      = {Biodiversit{\"a}t},
  language  = {en}
}
@phdthesis{Ankenbrand2018,
  author    = {Ankenbrand, Markus Johannes},
  title     = {Squeezing more information out of biological data - development and application of bioinformatic tools for ecology, evolution and genomics},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-156344},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2018},
  abstract  = {New experimental methods have drastically accelerated the pace and quantity at which biological data is generated. High-throughput DNA sequencing is one of the pivotal new technologies. It offers a number of novel applications in various fields of biology, including ecology, evolution, and genomics. However, together with those opportunities many new challenges arise. Specialized algorithms and software are required to cope with the amount of data, often requiring substantial training in bioinformatic methods. Another way to make those data accessible to non-bioinformaticians is the development of programs with intuitive user interfaces. In my thesis I developed analyses and programs to tackle current problems with high-throughput data in biology. In the field of ecology this covers the establishment of the bioinformatic workflow for pollen DNA meta-barcoding. Furthermore, I developed an application that facilitates the analysis of ecological communities in the context of their traits. Information from multiple public databases have been aggregated and can now be mapped automatically to existing community tables for interactive inspection. In evolution the new data are used to reconstruct phylogenetic trees from multiple genes. I developed the tool bcgTree to automate this process for bacteria. Many plant genomes have been sequenced in current years. Sequencing reads of those projects also contain data from the chloroplasts. The tool chloroExtractor supports the targeted extraction and analysis of the chloroplast genome. To compare the structure of multiple genomes specialized software is required for calculation and visualization of the relationships. I developed AliTV to address this. In contrast to existing programs for this task it allows interactive adjustments of produced graphics. Thus, facilitating the discovery of biologically relevant information. Another application I developed helps to analyze transcriptomes even if no reference genome is present. This is achieved by aggregating the different pieces of information, like functional annotation and expression level, for each transcript in a web platform. Scientists can then search, filter, subset, and visualize the transcriptome. Together the methods and tools expedite insights into biological systems that were not possible before.},
  language  = {en}
}
@phdthesis{VoulgariKokota2020,
  author    = {Voulgari Kokota, Anna},
  title     = {Microbiota interactions and dynamics in megachilid bee nests},
  doi       = {10.25972/OPUS-18249},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-182493},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {Insect microbiota plays an essential role on the hosts' health and fitness, regulating their development, nutrition and immunity. The natural microbiota of bees, in particular, has been given much attention, largely because of the globally reported bee population declines. However, although the worker honey bee has been associated with distinctive and specialized microbiota, the microbiota of solitary bees has not been examined in detail, despite their enormous ecological importance. The main objectives of the present thesis were a) the bacterial community description for various solitary bee species, b) the association of the solitary bee microbiota with ecological factors such as landscape type, c) the relation of the bee foraging preferences with their nest bacterial microbiota, d) the examination of the nest building material contribution to the nest microbiota, e) the isolation of bacterial strains with beneficial or harmful properties for the solitary bee larvae and f) the pathological investigation of bacteria found in deceased solitary bee larvae. The findings of the present study revealed a high bacterial biodiversity in the solitary bee nests. At the same time, the bacterial communities were different for each bee host species. Furthermore, it was shown that the pollen bacterial communities underwent compositional shifts reflecting a reduction in floral bacteria with progressing larval development, while a clear landscape effect was absent. The examination of the nest pollen provisions showed different foraging preferences for each included bee species. Both the pollen composition and the host species identity had a strong effect on the pollen bacteria, indicating that the pollen bacterial communities are the result of a combinatory process. The introduced environmental material also contributed to the nest natural microbiome. However, although the larval microbiota was significantly influenced by the pollen microbiota, it was not much associated with that of the nest material. Two Paenibacillus strains isolated from O. bicornis nests showed strong antifungal activities, while several isolated strains were able to metabolize various oligosaccharides which are common in pollen and nectar. Screening for potential pathogenic bacteria in the nests of O. bicornis unveiled bacterial taxa, which dominated the bacterial community in deceased larvae, while at the same time they were undetectable in the healthy individuals. vi Finally, larvae which were raised in vitro developed distinct bacterial microbiomes according to their diet, while their life span was affected. The present thesis described aspects of the microbiota dynamics in the nests of seven megachilid solitary bee nests, by suggesting which transmission pathways shape the established bacterial communities and how these are altered with larval development. Furthermore, specific bacterial taxa were associated with possible services they might provide to the larvae, while others were related with possible harmful effects. Future studies should integrate microbiota examination of different bee generations and parallel investigation of the microbiota of the nests and their surrounding environment (plant community, soil) to elucidate the bacterial transmission paths which establish the nest microbiota of solitary bees. Functional assays will also allow future studies to characterize specific nest bacteria as beneficial or harmful and describe how they assist the development of healthy bees and the fitness of bee populations.},
  subject      = {Bienen <Familie>},
  language  = {en}
}
@phdthesis{Slaby2017,
  author    = {Slaby, Beate Magdalena},
  title     = {Exploring the microbiome of the Mediterranean sponge \(Aplysina\) \(aerophoba\) by single-cell and metagenomics},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-151869},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2017},
  abstract  = {Sponges (phylum Porifera) are evolutionary ancient, sessile filter-feeders that harbor a largely diverse microbial community within their internal mesohyl matrix. Throughout this thesis project, I aimed at exploring the adaptations of these symbionts to life within their sponge host by sequencing and analyzing the genomes of a variety of bacteria from the microbiome of the Mediterranean sponge Aplysina aerophoba. Employed methods were fluorescence-activated cell sorting with subsequent multiple displacement amplification and single-cell / 'mini-metagenome' sequencing, and metagenomic sequencing followed by differential coverage binning. These two main approaches both aimed at obtaining genome sequences of bacterial symbionts of A. aerophoba, that were then compared to each other and to references from other environments, to gain information on adaptations to the host sponge environment and on possible interactions with the host and within the microbial community. Cyanobacteria are frequent members of the sponge microbial community. My 'mini-metagenome' sequencing project delivered three draft genomes of "Candidatus Synechococcus spongiarum," the cyanobacterial symbiont of A. aerophoba and many more sponges inhabiting the photic zone. The most complete of these genomes was compared to other clades of this symbiont and to closely related free-living cyanobacterial references in a collaborative project published in Burgsdorf I*, Slaby BM* et al. (2015; *shared first authorship). Although the four clades of "Ca. Synechococcus spongiarum" from the four sponge species A. aerophoba, Ircinia variabilis, Theonella swinhoei, and Carteriospongia foliascens were approximately 99\% identical on the level of 16S rRNA gene sequences, they greatly differed on the genomic level. Not only the genome sizes were different from clade to clade, but also the gene content and a number of features including proteins containing the eukaryotic-type domains leucine-rich repeats or tetratricopeptide repeats. On the other hand, the four clades shared a number of features such as ankyrin repeat domain-containing proteins that seemed to be conserved also among other microbial phyla in different sponge hosts and from different geographic locations. A possible novel mechanism for host phagocytosis evasion and phage resistance by means of an altered O antigen of the lipopolysaccharide was identified. To test previous hypotheses on adaptations of sponge-associated bacteria on a broader spectrum of the microbiome of A. aerophoba while also taking a step forward in methodology, I developed a bioinformatic pipeline to combine metagenomic Illumina short-read sequencing data with PacBio long-read data. At the beginning of this project, no pipelines to combine short-read and long-read data for metagenomics were published, and at time of writing, there are still no projects published with a comparable aim of un-targeted assembly, binning and analysis of a metagenome. I tried a variety of assembly programs and settings on a simulated test dataset reflecting the properties of the real metagenomic data. The developed assembly pipeline improved not only the overall assembly statistics, but also the quality of the binned genomes, which was evaluated by comparison to the originally published genome assemblies. The microbiome of A. aerophoba was studied from various angles in the recent years, but only genomes of the candidate phylum Poribacteria and the cyanobacterial sequences from my above-described project have been published to date. By applying my newly developed assembly pipeline to a metagenomic dataset of A. aerophoba consisting of a PacBio long-read dataset and six Illumina short-read datasets optimized for subsequent differential coverage binning, I aimed at sequencing a larger number and greater diversity of symbionts. The results of this project are currently in review by The ISME Journal. The complementation of Illumina short-read with PacBio long-read sequencing data for binning of this highly complex metagenome greatly improved the overall assembly statistics and improved the quality of the binned genomes. Thirty-seven genomes from 13 bacterial phyla and candidate phyla were binned representing the most prominent members of the microbiome of A. aerophoba. A statistical comparison revealed an enrichment of genes involved in restriction modification and toxin-antitoxin systems in most symbiont genomes over selected reference genomes. Both are defense features against incoming foreign DNA, which may be important for sponge symbionts due to the sponge's filtration and phagocytosis activity that exposes the symbionts to high levels of free DNA. Also host colonization and matrix utilization features were significantly enriched. Due to the diversity of the binned symbiont genomes, a within-symbionts genome comparison was possible, that revealed three guilds of symbionts characterized by i) nutritional specialization on the metabolization of carnitine, ii) specialization on sulfated polysaccharides, and iii) apparent nutritional generalism. Both carnitine and sulfated polysaccharides are abundant in the sponge extracellular matrix and therefore available to the sponge symbionts as substrates. In summary, the genomes of the diverse community of symbionts in A. aerophoba were united in their defense features, but specialized regarding their nutritional preferences.},
  subject      = {Metagenom},
  language  = {en}
}
@phdthesis{Faist2017,
  author    = {Faist, Hanna},
  title     = {Bedeutung und Charakterisierung der bakteriellen Flora in Vitis vinifera mit und ohne Wurzelhalsgallen},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-154359},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2017},
  abstract  = {Am Rebstock werden in der Natur von Agrobacterium vitis, dem Ausl{\"o}ser Wurzelhalsgallenerkrankung, charakteristische Wurzelhalsgallentumore induziert. Virulente Vertreter der Gattung der Agrobacteria schleusen bakterielle DNA in das pflanzliche Genom ein, wodurch die Pflanze Tumore produziert. Die Wurzelhalsgallenerkrankung wird seit einem Jahrhundert als ein Beispiel der Pflanzen-Pathogen-Interaktion untersucht. Die Rolle der bakteriellen Flora im Zusammenhang mit der Wurzelhalsgallenerkrankung beim Rebstock wurde bisher kaum betrachtet. Um dieser Frage nachzugehen, habe ich die endophytische mikrobielle Zusammensetzung von Rebst{\"o}cken mit und ohne Wurzelhalsgalle analysiert. Es werden Proben von drei Zeitpunkten einer Wachstumsperiode (Fr{\"u}hling, Sommer und Herbst) und von den Organen der Rebst{\"o}cke (Wurzeln, Pfropfstelle und einj{\"a}hrige Triebe) sowie dem Boden in einer Weinanlage bei Himmelstadt in Unterfranken genommen. Die Bakterienflora dieser Umweltproben wird mit kultivierungsabh{\"a}ngigen (Isolierung von Bakterien) und kultivierungsunabh{\"a}ngigen (Hochdurchsatzsequenzierungen) Methoden untersucht. Zudem werden i) die Virulenz der verschiedenen Agrobacterium-Isolate in Tumorassays bestimmt, ii) synthetische Bakteriengemeinschaften von in vitro kultivierten Weinpfl{\"a}nzchen mit Wurzelhalsgallen analysiert, iii) die Genome von einem virulenten und einem nicht-virulenten Agrobacteria-Isolat aus der Wurzelhalsgalle verglichen, iv) erste Interaktionsstudien auf festen N{\"a}hrmedien durchgef{\"u}hrt und v) virulente Agrobacteria mittels bildgebender Fluoreszenz-Lebenszeit-Mikroskopie (FLIM) in Wurzelhalsgallen lokalisiert. Die Rebst{\"o}cke dieser Studie haben eine organspezifische Bakterienflora, die innerhalb einer Wachstumsperiode variiert. Nur die Bakterienflora der Pfropfstelle (mit oder ohne Wurzelhalsgalle) aber nicht die des Bodens, der Wurzeln, und der einj{\"a}hrigen Triebe unterscheidet sich strukturell zwischen gesunden und erkrankten Rebst{\"o}cken. Mikroskopisch konnten virulente Agrobacteria punktuell in Interzellularen, sklerenchymatischen Geweben und assoziiert mit Leitgef{\"a}ßen nachgewiesen werden. Dadurch ist ausreichend Lebensraum vorhanden, der zus{\"a}tzlich von tumorspezifischen Bakterien besiedelt werden kann. Im Gegensatz zur gesunden Pfropfstelle ist in der Wurzelhalsgalle eine saisonal stabile Kernmikroflora, bestehend aus Vertreter von A. vitis, Pseudomonas, Enterobacteriaceae, Agrobacterium tumefaciens, Gammaproteobacteria und Burkholderiales, vorhanden. Diese Bakterien werden {\"u}berwiegend aus dem Boden rekrutiert und profitieren von der N{\"a}hrstoffsituation in der Wurzelhalsgalle. Wurzelhalsgallen enthalten Opine, die nur von der transformierten Pflanzenzelle produziert werden. Interessanterweise hat in dieser Arbeit ein Agrobacterium-Isolat Gene, die zum Opinkatabolismus beitragen und ein Pseudomonas-Isolat kann Opine als einzige Kohlenstoffquelle nutzen. Trotzdem sind beide Isolate weder virulent noch verdr{\"a}ngen sie die virulenten A. vitis, die ebenso Opine nutzen, aus der Wurzelhalsgalle. In synthetischen Bakteriengemeinschaften an in vitro kultivierten Weinpfl{\"a}nzchen konnte gezeigt werden, dass diese und weitere tumorspezifischen Bakterien, neben A. vitis, nicht essentiell zur Entstehung der Wurzelhalsgalle n{\"o}tig sind aber unterschiedliche Funktionen in der Wurzelhalsgalle {\"u}bernehmen. Ein Serratia-Isolat hemmt das Wachstum von A. vitis auf festen N{\"a}hrmedium, andere f{\"o}rdern oder hemmen das Wachstum der Wurzelhalsgalle. Nach Studien in der Literatur erh{\"o}hen weitere Bakterien die Resistenz des Rebstocks gegen{\"u}ber biotischem und abiotischem Stress. Zusammengefasst identifizierten und isolierte ich in dieser Studie unter 150 unterschiedlichen Bakterien in der Wurzelhalsgalle jene Bakterien, die neben A. vitis von der neuen {\"o}kologischen Nische profitieren und somit wahrscheinlich Opportunisten mit unterschiedlichen Funktionen sind. In Folge von multiplen Interaktionen in der Wurzelhalsgalle entsteht ein {\"o}kologisches Gleichgewicht zwischen den opportunistischen Bakterien, der Wurzelhalsgalle und dem Rebstock, das den Fortbestand des Rebstocks mit Wurzelhalsgalle erm{\"o}glicht.},
  subject      = {Wurzelhalsgalle},
  language  = {de}
}
@phdthesis{Diehl2024,
  author    = {Diehl, Janina Marie Christin},
  title     = {Ecology and evolution of symbiont management in ambrosia beetles},
  doi       = {10.25972/OPUS-32121},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-321213},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2024},
  abstract  = {The relationship between a farmer and their cultivated crops in agriculture is multifaceted, with pathogens affecting both the farmer and crop, and weeds that take advantage of resources provided by farmers. For my doctoral thesis, I aimed to gain a comprehensive understanding of the ecology and symbiosis of fungus farming ambrosia beetles. Through my research, I discovered that the microbial composition of fungus gardens, particularly the mutualists, is significantly influenced by the presence of both adults and larvae. The recognition of both beneficial and harmful symbionts is crucial for the success of ambrosia beetles, who respond differently depending on their life stage and the microbial species they encounter, which can contribute to the division of labour among family groups. The presence of antagonists and pathogens in the fungus garden depends on habitat and substrate quality, and beetle response to their introduction results in behavioural and developmental changes. Individual and social immunity measures, as well as changes in bacterial and fungal communities, were detected as a result of pathogen introduction. Additionally, the ability of ambrosia beetles to establish two nutritional fungal species depends on several factors. These insects must strike a balance between their essential functions and adapt to the constantly changing ecological and social conditions, which demonstrates their adaptive flexibility. However, interpreting data from laboratory studies should be approached with caution, as the natural environment allows for more flexibility and the potential for other beneficial symbionts to become more prominent if required. To aid in my research, I designed primers that use the 'fungal large subunit' (LSU) as genetic marker to identify and differentiate mutualistic and antagonistic fungi in X. saxesenii. The primers were able to distinguish closely related species of the Ophiostomataceae and other fungal symbionts. This allowed me to associate the abundance of key fungal taxa with factors such as the presence of beetles, the nest's age and condition, and the various developmental stages present. My primers are a valuable tool for understanding fungal communities, including their composition and the identification of previously unknown functional symbionts. However, some aspects should be approached with caution due to the exclusion of non-amplified taxa in the relative fungal community compositions.},
  subject      = {{\"O}kologie},
  language  = {en}
}