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In den Weltmeeren findet rund die Hälfte der jährlichen globalen Kohlenstofffixierung statt, davon ein großer Anteil in küstennahen Regionen. Hier kommt es zu wiederkehrenden saisonalen Algenblüten, die durch eine zeitlich begrenzte explosionsartige Vermehrung von Mikroalgen (hauptsächlich Diatomeen und Coccolithophoren) charakterisiert sind. Vor allem Frühjahrsblüten (März-Mai) haben aufgrund ihrer zeitlichen und räumlichen Vorhersagbarkeit einen hohen Stellenwert als Modellsysteme, anhand deren sich der Kohlenstoffkreislauf der Meere untersuchen lässt.
Mikroalgen produzieren eine große Vielfalt an Makromolekülen, die für die mit ihnen vergesellschafteten Bakterien als Nahrungsgrundlage dienen. Besonders im Fokus stehen hier die für den Kohlenstoffkreislauf relevanten Polysaccharide. Im Gegensatz zu anderen natürlichen Makromolekülen wie DNA oder Proteinen können Polysaccharide aus vielen verschiedenen Monomeren mit unterschiedlichsten Bindungen bestehen. Zusätzlich finden sich an diesen Zuckermonomeren viele Modifikationen wie Acetylierungen, Methylierungen oder Sulfatierungen, die die Komplexität weiter erhöhen. Diese Variabilität bedingt eine hohe strukturelle und funktionale Diversität. So können Polysaccharide Speicherstoffe, Zellwandbestandteile oder Teile der extrazellulären Matrix darstellen.
Komplementär hierzu besitzen Polysaccharid-verwertende Bakterien entsprechend komplexe, enzymatische Abbaumechanismen. Besonders hervorzuheben sind hier die Bakterien des Phylums Bacteroidota, die sich in verschiedensten Nischen auf den Abbau von Polysacchariden spezialisiert haben. Sie finden sich in Bodenproben, als Teil der menschlichen Darmflora, oder eben auch als bedeutende Begleiter von Algenblüten.
Bacteroidota (und in marinen Systemen hauptsächlich die zu ihnen gehörenden Flavobakterien) besitzen zum Abbau diverser Polysaccharide sogenannte Polysaccharide utilization loci (PULs), genomische Inseln, die alle notwendigen Proteine zur Aufnahme und Abbau eines bestimmten Polysaccharids codieren. Hierzu gehören hochspezifische Enzyme (Carbohydrate-active enzymes, CAZymes), transkriptionelle Regulatoren sowie Transportersysteme, die initial gespaltene Oligosaccharide über die Membran in das Bakterium transportieren, wo sie von weiteren Enzymen vollständig abgebaut werden. Diese Co-Lokalisation der benötigten Gene und deren gemeinsame Regulation stellt einen enormen Selektionsvorteil der Bacteroidota dar und ist der Grund, warum sie, ähnlich wie Algen, einer jährlich wiederkehrenden Sukzession folgen, die sich gut untersuchen lässt.Die Forschungsartikel, die Teil dieser Doktorarbeit sind, untersuchen das Zusammenspiel von Polysaccharid-produzierenden Algen mit den Bakterien, die sie abbauen, aber auch darauf basierende Beziehungen der Bakterien untereinander. Die erste Publikation beschäftigt sich mit dem weit verbreiteten Speicherpolysaccharid α-Glucan, für das der Großteil der blütenbegleitenden Bakterien einen spezifischen aktiven PUL besitzt. Eine Untersuchung der in der Blüte vorhandenen Algenarten bestätigte, dass die Blüte von β-Glucan-produzierenden Algen dominiert wird. Da Bakterien aber selbst α-Glucane als Speicherpolysaccharide verwenden, konnte gezeigt werden, dass nicht die Algen selbst, sondern die Bakterien Hauptproduzent dieser Polysaccharide während einer Phytoplanktonblüte sind. Bakterielle Proteine, die dem Abbau von Algen-β-Glucan und dem daraus folgenden Aufbau von bakteriellem α-Glucan dienen, waren in Umweltproben und in Laborkulturen unter ähnlichen Bedingungen abundant. Die Untersuchung von extrahiertem bakteriellem Polysaccharid bewies, dass dieses nicht nur α-Glucan enthält, sondern dass dieses Polysaccharid auch in der Lage war, α-Glucan PULs mariner Bakterien zu induzieren. Hier zeigte sich ein innerhalb des marinen Kohlenstoffkreislaufs bisher wenig berücksichtigter Kreislauf, indem Bakterien Polysaccharide anderer Bakterien nutzen, die z.B. durch Viren lysiert wurden.
Die anderen zwei Artikel dieser Arbeit befassen sich mit dem Abbau von Zellwandpolysacchariden durch blütenassoziierte Modellbakterien. In einer der Studien wird detailliert der Abbau eines β-Mannans (ein Polysaccharid das hauptsächlich aus dem Monosaccharid Mannose besteht) durch ein Bakterium des Genus Muricauda beschrieben. Die PUL-Struktur dieses Bakteriums kam in mehreren anderen Phytoplanktonblüten-assoziierten Bakterien vor. Diese Beobachtung wies darauf hin, dass es sich hier um ein Mannan mit zusätzlichen Galactose- und Glucose-Substitutionen handelte. Proteom-Untersuchungen bestätigten, dass das Bakterium derartige Substrate unter Induktion des β-Mannan-PULs nutzen können. β-Mannan konnte durch Antikörpermarkierung in Blütenproben sowie spezifischen Mikroalgenarten (Chaetoceros, Coscinodiscus) nachgewiesen werden. Die in dieser Publikation charakterisieren β-Mannan-PUL-codierten Enzyme waren in der Lage, dieses Signal zu löschen, was bewies, dass Muricauda sp. Mannan-basierte Zellwandpolysaccharide bestimmter Arten von Mikroalgen abbauen kann.
Die dritte Studie geht näher auf den Abbau von Xylanen (bestehend aus Xylose) durch ein blütenassoziiertes Bakterium des Genus Flavimarina ein. In diesem Bakterium wurden anhand der enthaltenen Xylanasen zwei putative Xylan-PULs annotiert. Wachstumsexperimente und Proteom-Untersuchungen zeigten, dass einer dieser PULs hauptsächlich bei Wachstum auf Glucoronoxylan induziert wird, während der andere PUL aufArabinoxylane stärker reagierte. Untersuchung der PUL-CAZymes bestätigte diese Ergebnisse durch Charakterisierung mehrerer Xylanasen sowie Glucoronidasen und Arabinofuranosidasen. Zusätzlich codierten beide PULs für Esterasen, die eine Modifikation der natürlichen Substrate durch Acetylierungen oder Methylierungen nahelegen. Da all diese Merkmale von terrestrischen Xylanen geteilt werden und in Blütenproben aus Küstennahen Regionen Xylane nachgewiesen wurden, ist es möglich, dass Bakterien aus solchen Regionen sowohl Xylane terrestrischen Ursprungs (z.B. durch Flusseinspeisung) sowie marinen Ursprungs abbauen können.
Streptococcus pneumoniae (S. pneumoniae, pneumococci) and Staphylococcus aureus (S. aureus) belong to the Gram-positive, facultative pathogenic bacteria. They are typical commensals of the human upper respiratory tract and most people get colonized at least once during their life. Nevertheless, these potentially pathogenic bacteria are able to spread from the site of colonization to invade into deeper tissues and the blood circulation. Thereby, severe local and invasive infections like bacteremia and life-threatening sepsis can be caused. Once reaching the bloodstream, bacteria get in contact with platelets. Platelets are small, anucleated cells and the second most abundant cell type in the circulation. The role of platelets in hemostasis is well known. Circulating resting platelets sense vessel injury independent of its cause. Platelets bind to injured endothelium and exposed molecules of the underlying extracellular matrix, get activated and release intracellular adhesion proteins and different modulatory molecules. This in turn initiates activation and binding of nearby platelets resulting in closure of vascular injury by formation of small thrombi. Despite being pivotal in maintenance of the endothelial barrier they got increasingly recognized as cells with important immune functions. Platelets excert functions of the immune response by either, i) interacting with immune cells of different pathways of the immune response, ii) releasing immunomodulatory molecules stored in their granules or iii) interacting with invading pathogens via direct or indirect binding.
The basis for this study were results demonstrating direct binding of different S. aureus proteins to platelets resulting in platelet activation. The identified proteins in the mentioned study are the S. aureus proteins Eap, AtlA-1, CHIPS and FlipR. Severe invasive infections with S. pneumoniae are quite often associated with development of thrombocytopenia or disseminated vascular dissemination. This frequent observation hints towards either a direct or indirect interplay of platelets with pneumococci. Hence, this study aims to analyze potential interactions and aims to decipher involved factors on both the platelet- and bacterial site.
A screening of recombinant pneumococcal surface proteins identified proteins belonging to the group of lipoproteins, sortase-anchored proteins and choline-binding proteins to directly activate human platelets. Besides these surface proteins also the intracellular pneumococcal pneumolysin (Ply) induced highly increased values for the platelet activation marker P-selectin. Since Ply is a major virulence factor of
S. pneumoniae the primary focus was set on involvement of this pore forming toxin on platelet activation. Surprisingly, our data revealed Ply induced platelet activation to be a false positive result based on formation of large Ply pores in the platelet membrane. In fact, it was clearly demonstrated that Ply lyses platelets even at low concentrations and thereby rendering them non-functional. Lysis of platelets could be inhibited by the addition of pharmaceutical immunoglobulin preparations as well as antibodies specifically targeting Ply. Inhibition of Ply also resulted in fully rescued platelet function either in washed platelets or in whole blood as shown by thrombus formation. Next to pneumococci also S. aureus expresses pore forming toxins, namely α-hemolysin (Hla) and different pairs of bicomponent pore forming leukocidins. Whereas the different tested leukocidins did not affect platelets, Hla acted in a two-step mechanism on human platelets. The results confirm previous data on Hla induced platelet activation via Hla resulting in e.g., reversible platelet aggregation or surface expression of activation markers. Nevertheless, platelet activation by Hla is followed by dose- and time-dependent lysis of platelets resulting in loss of platelet function and abrogated thrombus formation. Platelet lysis by Hla could neither be rescued with specific monoclonal anti-Hla antibodies nor with pharmaceutical IgG preparations containing anti-Hla IgGs. Taken together, the presented data reveal new pathomechanisms involving disturbance of platelets by bacterial pore forming toxins. Platelet lysis as well as impaired platelet function play an important role in development of severe complications during invasive infections. In life threatening infections caused by S. pneumoniae the usage of antibody formulations containing antibodies targeting Ply might be a promising approach for the prevention or even intervention and improvement of clinical outcome.
In the search for alternative treatment options for infections with multi-resistant germs,
traditionally used medicinal plants are currently being examined more intensively. In this study,
the antimicrobial and anti-biofilm activities of 14 herbal drugs were investigated. Nine of the tested
drugs were traditionally used in Europe for treatment of local infections. For comparison, another
five drugs monographed in the European Pharmacopoeia were used. Additionally, the total tannin
and flavonoid contents of all tested drugs were analyzed. HPLC fingerprints were recorded to ob-
tain further insights into the components of the extracts. The aim of the study was to identify herbal
drugs that might be useable for treatment of infectious diseases, even with multidrug resistant E.
coli, and to correlate the antimicrobial activity with the total content of tannins and flavonoids. The
agar diffusion test and anti-biofilm assay were used to evaluate the antimicrobial potential of dif-
ferent extracts from the plants. Colorimetric methods (from European Pharmacopeia) were used for
determination of total tannins and flavonoids. The direct antimicrobial activity of most of the tested
extracts was low to moderate. The anti-biofilm activity was found to be down to 10 µg mL −1 for
some extracts. Tannin contents between 2.2% and 10.4% of dry weight and total flavonoid contents
between 0.1% and 1.6% were found. Correlation analysis indicates that the antimicrobial and the
anti-biofilm activity is significantly (p < 0.05) dependent on tannin content, but not on flavonoid
content. The data analysis revealed that tannin-rich herbal drugs inhibit pathogens in different
ways. Thus, some of the tested herbal drugs might be useable for local infections with multi-re-
sistant biofilm-forming pathogens. For some of the tested drugs, this is the first report about anti-
biofilm activity, as well as total tannin and flavonoid content.
Primary producers, alongside heterotrophic bacteria and viruses, modulate the essential global carbon cycle. About half of the Earth’s net primary production originates in the marine environment. By effecting these systems and the burial of carbon, bacteria play a significant role in the world’s climate, especially with regard to rising temperatures and increasing anthropogenic carbon dioxide production.
Particles present substrate-rich niches for particle-associated bacteria, but are rare in the marine system. Particle-associated bacteria, comprising of chemotactic motile free-living and particle-attached bacteria, were shown to have higher respiration rates, were larger in cell and genome size and showed a higher hydrolytic activity of extracellular enzymes compared to the free-living fraction.
Understanding the contribution of particle-associated bacteria to the degradation of algal biomass is essential to understand the marine carbon cycle. However, the identification of this group is difficult and required refinement.
Sequential filtration, the most commonly used technique for the separation of bacterial fractions, provides only access to a part of the particle-associated microbiome, and includes with large and clustered bacteria undesired false-positives. To overcome these limitations, separation by gravity in Imhoff sedimentation cones was explored in this thesis to access, identify and define particle-associated microbiomes, in comparison and conjunction with the established separation techniques like sequential filtration and centrifugation.
The cultivability on agar plates was assessed, aiming at the question which portion of the colony-forming bacteria belong to free-living non-motile or motile bacteria or to particle-attached bacteria. As continuous cultivation on plates often involves loss of cultures, colonies of the original plate were used to obtain partial 16S rRNA sequences of individual colonies and of plate microbiomes.
For future studies on particle-associated bacteria, a representative strain collection was established from particle-attached bacteria retained on 3 μm filters and from particle-associated bacteria collected together with settled algae in sedimentation cones.
To understand the contribution of top-down selection to a yearly recurring bacterioplankton bloom at our sampling site Helgoland, particle-associated strains were included in isolation experiments for flavophages, since Flavobacteriia are among the most important responder to the yearly observed blooms.
Overall, this thesis provides new insights into the isolation and cultivation of particle-associated bacteria – an important, but currently not fully understood fraction of organisms within the marine system.
Bacteria are an integral part of modern biotechnology. They are used to make a variety of products, such as foods, drugs, as well as a multitude of chemicals. In order to increase their production rates molecular biotechnology offers many tuning points, starting from the selection of an applicable host, over its geno- and phenotypical characterization, followed by genetic manipulations for an optimized metabolism and stabilisation of production processes. This work comprises the optimization of Bacillus subtilis as an expression system. It describes the steps taken for selection and genomic characterization of the B. subtilis wild type strain ATCC 6051, the subsequent optimizations of the strain in respect to growth and productivity, as well as the characterization of its behaviour in a variety of cultivation conditions. The B. subtilis strain most commonly found in laboratories around the world is the first sequenced Gram-positive organism B. subtilis 168. Zeigler et al. showed that strain 168 is not a real wild type. Instead it was created through random mutagenesis with X-rays and selected for transformability. This strain has been used as the basis for popular B. subtilis strains in heterologous gene expression such as the extracellular protease deficient WB strains. Growth experiments showed the real wild type strain ATCC 6051 to be superior to its mutated ancestor 168, making it a solid basis for the construction of an optimized B. subtilis expression system. In order to gain a full understanding of the genomic and corresponding physiological differences between the two systems, B. subtilis ATCC 6051 was sequenced and compared to the genome of B. Subtilis 168. Several variations on geno- and phenotypic level could be revealed, that resulted in particular from genes involved in natural competency, the metabolism of amino acids and chemotaxis. This genomically well characterized B. subtilis ATCC 6051 was improved in respect to its application as an expression host. Improvements were achieved through the inactivation of both sporulation and reduction of autolysis, leading to a more robust behaviour during the overproduction and secretion of a reporter enzyme. A positive effect on the activity of an acetoin induced promoter by the addition of second copies for its transcription factors SigmaL and AcoR could be observed. Anaerobic zones and areas with excess glucose caused by insufficient mixing are common conditions in large scale bioprocesses and lead to oscillating conditions for the cells. In turn, this oscillation provokes an excretion of so called overflow metabolites, which can negatively affect the bacterial productivity. Detailed scientific characterizations of industrial scale processes under such oscillating conditions are scarce due to the high costs and logistics involved. A B. Subtilis sporulation mutant was thus examined in respect to its extra- and intracellular metabolites in a scale-down, two-compartment reactor giving hints about conditions the host is exposed to and how it reacts. To improve tolerance thresholds and utilization capacity for such metabolites in B. subtilis, the glyoxylate cycle was transferred from its close relative Bacillus licheniformis into the genome of B. subtilis. This feature enabled our B. subtilis ACE mutant to grow on acetate. The improved strain showed higher tolerance towards excess glucose in a fed-batch as well as higher productivity during the expression of a reporter enzyme in comparison to the wild type. The ACE strain and B. licheniformis showed an increased formation of glycolate during growth with the glyoxylate cycle. This with regard to bacteria undescribed metabolite seems to play a role as a by-product of the glyoxylate cycle. Summarizing, this thesis deals with the characterization and optimization of B. subtilis for growth on overflow metabolites, enhancements of the acoA-expression system and the influence of sporulation and lysis mutants on its activity. Complementary, the host was begun to be characterized in respect to its behaviour in industrial scale processes.
Reactive oxygen species (ROS) can damage all cellular macromolecules and also produce secondary reactive intermediates, like reactive electrophilic species (RES) that include quinones or aldehydes. Low molecular weight (LMW) thiols are small thiol-containing compounds that play essential roles in the defense against ROS and RES in all organisms. The best studied LMW thiol is the tripeptide glutathione (GSH). Firmicutes bacteria including Bacillus und Staphylococcus species have been recently discovered to utilize the redox buffer bacillithiol (BSH). LMW thiols function as redox buffers to maintain the reduced state of the cytoplasm. Under conditions of oxidative stress, LMW thiols also react with protein thiols to form mixed LMW thiol – protein disulfides, termed S-thiolations, as major protection mechanism. Investigating the role of BSH in oxidative stress response and ROS-induced S-thiolations in Firmicutes bacteria was one subject of this PhD thesis. Specifically, the regulatory mechanisms and post-translational thiol-modifications in response to NaOCl stress were studied in the model bacterium for low-GC Gram-positive bacteria Bacillus subtilis. The transcriptome profile after NaOCl stress was indicative of disulfide stress and overlapped strongly with the response to diamide. NaOCl stress caused induction of the thiol- and oxidative stress-specific Spx, CtsR, PerR and OhrR regulons. Thiol redox proteomics identified only few NaOCl-sensitive proteins with reversible thiol-oxidations. Using mass spectrometry, eleven proteins were identified that were oxidized to mixed BSH protein disulfides (S-bacillithiolated) in B. subtilis cells after NaOCl-exposure. Methionine synthase MetE is the most abundant S-bacillithiolated protein in B. subtilis and other Bacillus species after NaOCl exposure. S-bacillithiolation of OhrR repressor leads to upregulation of the OhrA peroxiredoxin that confers together with BSH specific protection against NaOCl. S-bacillithiolation of MetE, YxjG, PpaC, and SerA causes hypochlorite-induced methionine starvation as supported by the induction of the S-box regulon. To further assess the conservation of targets for S-bacillithiolations in other Firmicutes bacteria, we studied the S-bacillithiolomes of Bacillus megaterium, Bacillus pumilus, Bacillus amyloliquefaciens, and Staphylococcus carnosus under NaOCl stress conditions. In total, 54 S-bacillithiolated proteins were identified, including 29 unique proteins and 8 conserved proteins involved in amino acid and cofactor biosynthesis, nucleotide metabolism, translation, protein quality control, redox and antioxidant functions. Together our data support a major role of BSH redox buffer in redox control and thiol protection of conserved and essential proteins against irreversible oxidation by S-bacillithiolations in Firmicutes bacteria. In response to ROS and RES, bacteria also activate the expression of antioxidant and detoxification enzymes, such as catalases, peroxidases, thiol-dependent peroxiredoxins and other specific oxidoreductases to detoxify ROS and RES. These defense mechanisms are often controlled by redox-sensitive transcription factors. B. subtilis encodes redox-sensing MarR-type regulators belonging to the OhrR and DUF24-families that are conserved among bacteria. Hence, we were further interested in this PhD thesis to study at the molecular and structural level the redox-sensing mechanisms of novel redox-sensing MarR/DUF24-type regulators in B. subtilis. We have characterized the regulatory mechanisms of HypR, YodB and CatR that sense and respond to hypochlorite, diamide and quinones stress. HypR is the first DUF24-family regulator whose crystal structure was resolved. HypR senses specifically disulfide stress and controls positively expression of the flavin oxidoreductase HypO after NaOCl and diamide stress. HypR resembles a 2-Cys-type regulator with a reactive nucleophilic N-terminal Cys14 and a second C-terminal Cys49. Besides HypR, B. subtilis encodes further MarR/DUF24-family members including the paralogous YodB and CatR repressors that sense quinones and diamide. YodB controls the azoreductase AzoR1, the nitroreductase YodC, and the Spx regulator. YodB resembles a 2-Cys-type MarR/DUF24-family regulator with three Cys residues (Cys6, Cys101, and Cys108) that form intermolecular disulfides in vivo under oxidative stress. YodB and its paralog CatR were further identified as repressors of the catDE operon encoding a catechol-2,3-dioxygenase that also contributes to quinone resistance. Although CatR is a 1-Cys-type regulator, our data showed that CatR also forms intermolecular disulfide in response to diamide and quinones in vitro. Thus, HypR, YodB and CatR are controlled by 2-Cys-type thiol-disulfide redox switches to sense disulfide and RES stress conditions, and to control specific RES detoxification enzymes.