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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.
Marine sponges are the most ancient metazoans and of large ecological importance as drivers of water and nutrient flows in benthic habitats. Furthermore marine sponges are well known for their association with highly abundant and diverse microbial consortia. Microorganisms inhabit the extracellular matrix of marine sponges where they can make up to 35% of the sponge’s biomass. Many microbial symbionts of marine sponges are highly host specific and cannot, or only in very rare abundances, be found outside of their host environment. Of special interest is the candidate phylum Poribacteria that was first discovered in marine sponges and still remains almost exclusive to their hosts. Phylogenetically Poribacteria were placed into the Planctomycetes, Verrucomicrobia, Chlamydiae superphylum and similarly to many members of this superphylum cell compartmentation has been proposed to occur in members of the Poribacteria. The status as a candidate phylum implies that no member of Poribacteria has been obtained in culture yet. This restricts the investigations of Poribacteria and their interactions with marine sponges to culture independent methods and makes functional characterisation a difficult task.
In this PhD thesis I used the novel method of single-cell genomics to investigate the genomic potential of the candidate phylum Poribacteria. Single-cell genomics enables whole genome sequencing of uncultivated microorganisms by singularising cells from the environment, subsequent cell lysis and multiple displacement amplification of the total genomic DNA. This process yields sufficient amounts of DNA for whole genome sequencing and genome analysis. This technique and its relevance for symbiosis studies are discussed in this PhD thesis.
Through the application of single-cell genomics it was possible to increase the number of single-amplified genomes of the candidate phylum Poribacteria from initially one to a total of six. Analyses of these datasets made it possible to enhance our understanding of the metabolism, taxonomy, and phylum diversity of Poribacteria and thus made these one of the best-characterised sponge symbionts today. The poribacterial genomes represented three phylotypes within the candidate phylum of which one appeared dominant. Phylogenetic and phylogenomic analyses revealed a novel phylogenetic positioning of Poribacteria distinctly outside of the Planctomycete, Verrucomicorbia, Chlamydiae superphylum. The occurrence of cell compartmentation in Poribacteria was also revisited based on the obtained genome sequences and revealed evidence for bacterial microcompartments instead of the previously suggested nucleotide-like structures. An extensive genomic repertoire of glycoside hydrolases, glycotransferases, and other carbohydrate active enzymes was found to be the central shared feature between all poribacterial genomes and showed that Poribacteria are among those marine bacteria with the largest genomic repertoire for carbohydrate degradation. Detailed analysis of the carbohydrate metabolism revealed that Poribacteria have the genomic potential for degradation of a variety of polymers, di- and monosaccharaides that allow these symbionts to feed various nutrient sources accessible through the filter-feeding activities of the sponge host. Furthermore the poribacterial glycobiome appeared to enable degradation of glycosaminoglycan chains, one of the main building blocks of extracellular matrix of marine sponges. Different lifestyles resulting from the poribacterial carbohydrate degradation potential are discussed including the influence of nutrient cycling in sponges, nutrient recycling and scavenging. The findings of this thesis emphasise the long overlooked importance of heterotrophic symbionts such as Poribacteria for the interactions with marine sponges and represent a solid basis for future studies of the influence heterotrophic symbionts have on their sponge hosts.
Die oberirdischen Oberflächen von Pflanzen sind von komplexen mikrobiellen Konsortien besiedelt deren Zusammensetzung von verschiedenen Faktoren abhängig ist. In der vorliegenden Promotionsarbeit wurden zwei Eigenschaften pflanzlicher Oberflächen auf mögliche Auswirkungen auf ihre bakterielle Besiedelung hin untersucht. Dazu wurden Wildtyplinien und Mutanten von Arabidopsis thaliana eingesetzt. Zunächst wurde die bakterielle Besiedelung von A. thaliana Wildtyplinien in kultivierungsbasierten Experimenten untersucht. Es wurde hierbei ein Überblick über die kultivierbare Diversität auf Pflanzen, die unter kontrollierten Bedingungen im Klimaschrank gewachsen waren und Pflanzen, die einen Freilandaufenthalt durchlaufen hatten, gewonnen. Der Einfluss von nicht-drüsigen Trichomen von A. thaliana auf die Quantität und Diversität der bakteriellen Besiedelung wurde am A. thaliana Col-0-Wildtyp mit normaler Behaarung und der trichomlosen gl1-Mutante untersucht. Mithilfe von DAPI-Färbungen und nachfolgender Zellzählung wurden die bakteriellen Gemeinschaften der beiden Pflanzenlinien quantifiziert. Dabei zeigten sich keine pflanzenlinienspezifischen Unterschiede. Durch die Amplifizierung der bakteriellen 16S rRNA-Gene der Gemeinschaft und den nachfolgenden Einsatz der Denaturierenden Gradientengelelektrophorese (DGGE) wurde ein Überblick über die Diversität der vorherrschenden Bakteriengruppen gewonnen. Obwohl Trichome als bevorzugte Siedlungsplätze von Bakterien gelten, wurden hier auch hinsichtlich der Diversität der bakteriellen Gemeinschaften keine Unterschiede zwischen den untersuchten Pflanzenlinien gefunden. Als weiteres artspezifisches Merkmal von Pflanzenoberflächen wurde die Zusammensetzung der kutikulären Wachse als Einflussfaktor untersucht. Dafür wurden vier eceriferum-Mutanten (cer) von A. thaliana in Landsberg erecta (Ler) Wildtyp-Hintergrund eingesetzt, die sich hinsichtlich der kutikulären Wachszusammensetzung ihrer Blätter unterschieden. Zur Untersuchung der Diversität der bakteriellen Besiedelung wurde zunächst ein DGGE-Screening durchgeführt. Hier zeigten sich deutliche pflanzenlinienspezifische Unterschiede, die vor allem die Gemeinschaften der cer9- und der cer16-Mutante betrafen. Zur genaueren Charakterisierung der bakteriellen Gemeinschaften der fünf Pflanzenlinien wurde die Amplicon-Pyrosequenzierung eingesetzt. Hierbei stellte sich die bakterielle Diversität auf allen Pflanzenlinien entsprechend des Phyllosphärenhabitats moderat divers und ungleich verteilt dar. Die Identifizierung der sequenzierten Phylotypen ließ eine bakterielle Kerngemeinschaft erkennen. Weiterhin wurden 35 Phylotypen identifiziert, die differenziell auf einzelnen Pflanzenlinien auftraten. Hier handelte es sich um den pflanzenlinienspezifischen Teil der bakteriellen Gemeinschaften. Die statistische Analyse zeigte deutlich divergente Muster für die analysierten Bakteriengemeinschaften der fünf Pflanzenlinien. Vor allem die Gemeinschaften der cer6-, cer9- und cer16-Linie konnten in einer UniFrac-basierten Clusteranalyse von den anderen Pflanzenlinien abgegrenzt werden. Diese Ergebnisse zeigen klar, dass die Mutationen in der Wachsbiosynthese zu divergenten bakteriellen Gemeinschaften führten.
Untersuchungen zur Diversität, Abundanz und vertikalen Weitergabe von Bakterien in marinen Schwämmen
(2013)
Marine Schwämme (Phylum Porifera) gehören mit ihrem ersten Auftreten im Präkambrium vor ungefähr 580 Millionen Jahren zu den ältesten Vertretern der Metazoen weltweit. Ähnlich lange leben sie wahrscheinlich schon in Symbiose mit Mikroorganismen. In der vorliegenden Doktorarbeit soll der karibische Schwamm Ectyoplasia ferox als Modellsystem zur Erforschung der Schwamm-assoziierten mikrobiellen Konsortien, deren Weitergabe und Interaktionen mit dem Schwamm, vorgestellt werden. Mit Hilfe von 16S rRNA-Genbanken sowie der denaturierenden Gradienten-Gelelektrophorese (DGGE) konnte gezeigt werden, dass Symbionten aus sechs der in E. ferox gefundenen acht Phyla sowie der „sponge-associated unclassified lineage” SAUL vertikal an die nächste Schwammgeneration weitergegeben werden. Mittels phylogenetischer Analysen wurden insgesamt 21 „vertical transmission“ (VT) Cluster identifiziert, von denen 19 in „sponge specific“ Cluster (SSC) bzw. „sponge coral“ Clustern (SCC) lagen. Daraus kann man schließen, dass ein Großteil des mikrobiellen Konsortiums von E. ferox über die reproduktiven Stadien weitergegeben wird. Auch konnten zwei Cyanobakterien identifiziert werden, die nicht in den reproduktiven Stadien vorhanden waren und höchstwahrscheinlich horizontal aus dem umgebenden Meerwasser aufgenommen wurden. Eine Reduzierung von 50% der Symbionten im Mesohyl nach dem „spawning“ zeigte erstmalig experimentell auf, dass Schwammsymbionten aus dem Schwamm in das umgebende Meerwasser gelangen können. In dieser Arbeit wurde zum ersten Mal der „presence vs. activity“-Vergleich zur Feststellung der metabolischen Aktivität von Bakterien auf die DGGE-Methode übertragen. Es konnte gezeigt werden, dass die meisten mikrobiellen Symbionten im Adult-Schwamm, Embryo- sowie Larvalstadium metabolisch aktiv waren. Erste Versuche die Anzahl von Symbionten in den Larven von E. ferox mittels Antibiotika zu reduzieren, verliefen positiv. So wiesen die mit Antibiotika behandelten Larven in der DGGE eine deutliche Reduzierung der Bandenintensität auf. Die Verfügbarkeit aller reproduktiver Stadien von E. ferox sowie die Möglichkeit die Larven im Labor experimentell zu manipulieren, machen E. ferox zu einem geeigneten Modellschwamm für zukünftige Studien bezüglich der vertikalen Weitergabe von Symbionten.
While beneficial sponge-microbe associations have received much attention in recent years, less effort has been undertaken to investigate the interactions of sponges with potentially pathogenic microorganisms. Thus, the aim of this study was to examine two selected Caribbean disease conditions, termed “Sponge Orange Band” and “Sponge White Patch”, via ecological and molecular methods. Sponge Orange Band (SOB) disease affects the prominent Caribbean barrel sponge Xestospongia muta that is counted among the high-microbial-abundance (HMA) sponges, whereas Sponge White Patch (SWP) disease affects the abundant rope sponge Amphimedon compressa that belongs to the low-microbial-abundance (LMA) sponges. I have documented for both Caribbean sponge diseases a disease progression going along with massive tissue destruction as well as loss of the characteristic microbial signatures. Even though new bacteria were shown to colonize the bleached areas, the infection trials revealed in both cases no indication for the involvement of a microbial pathogen as an etiologic agent of disease leaving us still in the dark about the cause of Sponge Orange Band as well as Sponge White Patch disease.
Marine sponges and their associated bacteria have been proven to be a rich source of novel secondary metabolites with therapeutic usefulness in infection and autoimmunity. This Ph.D. project aimed to isolate bioactive secondary metabolites from the marine sponges Amphimedon compressa, Aiolochroia crassa and Theonella swinhoei as well as from bacteria associated with different Caribbean sponges, specifically actinomycetes and sphingomonads. In this study, amphitoxin was isolated from the crude methanol extract of the sponge A. compressa and it was found to have antibacterial and anti-parasitic activities. Amphitoxin showed protease inhibitory activity when tested against the mammalian protease cathepsin B and the parasitic proteases rhodesain and falcipain-2. Furthermore, miraziridine A was identified in the dichloromethane extract of the sponge T. swinhoei collected offshore Israel in the Red Sea. Miraziridine A, a natural peptide isolated previously from the marine sponge Theonella aff. mirabilis, is a potent cathepsin B inhibitor with an IC50 value of 1.4 g/mL (2.1 M). Secondary metabolites from sponge-derived bacteria were also isolated and identified. A total of 79 strains belonging to 20 genera of the order Actinomycetales and seven strains belonging to two genera of the order Sphingomonadales were cultivated from 18 different Caribbean sponges and identified by 16S rRNA gene sequencing. Seven of these strains are likely to represent novel species. Crude extracts from selected strains were found to exhibit protease inhibition against cathepsins B and L, rhodesain, and falcipain-2 as well as immunomodulatory activities such as induction of cytokine release by human peripheral blood mononuclear cells. The isolates Sphingobium sp. CO105 and Lapillicoccus sp. BA53 were selected for cultivation, extraction and purification of bioactive metabolites based on initial bioactive screening results. The isoalloxazine isolumichrome was isolated from the strain Sphingobium sp. CO105 which inhibited the protease rhodesain with an IC50 of 0.2 M. The strain Lapillicoccus sp. BA53 was found to produce p-aminosalicylic acid methyl ester, which showed activity against the proteases cathepsins B and L, falcipain-2 and rhodesain. These results highlight the significance of marine sponge-associated bacteria to produce bioactive secondary metabolites with therapeutic potential in the treatment of infectious diseases and disorders of the immune system.