Bioremediation of PCB-contaminated marine sediments: From identification of indigenous dehalorespirers to enhancement of microbial reductive dechlorination

Marine sediments are the main accumulation reservoir of organic recalcitrant pollutants such as polychlorinated biphenyls (PCBs). In the anoxic conditions typical of these sediments, anaerobic bacteria of the phylum Chloroflexi are able to attack these compounds in a process called microbial reductive dechlorination. Such activity and members of this phylum were detected in PCB-impacted sediments of the Venice Lagoon. The aim of this work was to investigate microbial reductive dechlorination and design bioremediation approaches for marine sediments of the area. Three out of six sediment cultures from different sampling areas exhibited dechlorination activities in the same conditions of the site and two phylotypes (VLD-1 and VLD-2) were detected and correlated to this metabolism. Biostimulation was tested on enriched dechlorinating sediment cultures from the same site using five different electron donors, of which lactate was the best biostimulating agent; complementation of microbial and chemical dechlorination catalyzed by biogenic zerovalent Pd nanoparticles was not effective due to sulfide poisoning of the catalyst. A new biosurfactant-producing strain of Shewanella frigidimarina was concomitantly obtained from hydrocarbon-degrading marine cultures and selected because of the low toxicity of its product. All these findings were then exploited to develop bioremediation lab-scale tests in shaken reactors and static microcosms on real sediments and water of the Venice lagoon, testing i) a bioaugmentation approach, with a selected enriched sediment culture from the same area, ii) a biostimulation approach with lactate as electron donor, iii) a bioavailability enhancement with the supplementation of the newly-discovered biosurfactant, and iv) all possible combinations of the afore-mentioned approaches. The best bioremediation approach resulted to be a combination of bioaugmentation and bioremediation and it could be a starting point to design bioremediation process for actual marine sediments of the Venice Lagoon area.

Microfluidic microbial fuel cell fabrication and rapid screening of electrochemically microbes

The demand for novel renewable energy sources, together with the new findings on bacterial electron transport mechanisms and the progress in microbial fuel cell design, have raised a noticeable interest in microbial power generation. Microbial fuel cell (MFC) is an electrochemical device that converts organic substrates into electricity via catalytic conversion by microorganism. It has represented a continuously growing research field during the past few years. The great advantage of this device is the direct conversion of the substrate into electricity and in the future, MFC may be linked to municipal waste streams or sources of agricultural and animal waste, providing a sustainable system for waste treatment and energy production. However, these novel green technologies have not yet been used for practical applications due to their low power outputs and challenges associated with scale-up, so in-depth studies are highly necessary to significantly improve and optimize the device working conditions. For the time being, the micro-scale MFCs show great potential in the rapid screening of electrochemically active microbes. This thesis presents how it will be possible to optimize the properties and design of the micro-size microbial fuel cell for maximum efficiency by understanding the MFC system. So it will involve designing, building and testing a miniature microbial fuel cell using a new species of microorganisms that promises high efficiency and long lifetime. The new device offer unique advantages of fast start-up, high sensitivity and superior microfluidic control over the measured microenvironment, which makes them good candidates for rapid screening of electrode materials, bacterial strains and growth media. It will be made in the Centre of Hybrid Biodevices (Faculty of Physical Sciences and Engineering, University of Southampton) from polymer materials like PDMS. The eventual aim is to develop a system with the optimum combination of microorganism, ion exchange membrane and growth medium. After fabricating the cell, different bacteria and plankton species will be grown in the device and the microbial fuel cell characterized for open circuit voltage and power. It will also use photo-sensitive organisms and characterize the power produced by the device in response to optical illumination.

Atmospheric plasma processes for microbial inactivation: food applications and stress response in Listeria monocytogenes

This PhD thesis is focused on cold atmospheric plasma treatments (GP) for microbial inactivation in food applications. In fact GP represents a promising emerging technology alternative to the traditional methods for the decontamination of foods. The objectives of this work were to evaluate: - the effects of GP treatments on microbial inactivation in model systems and in real foods; - the stress response in L. monocytogenes following exposure to different GP treatments. As far as the first aspect, inactivation curves were obtained for some target pathogens, i.e. Listeria monocytogenes and Escherichia coli, by exposing microbial cells to GP generated with two different DBD equipments and processing conditions (exposure time, material of the electrodes). Concerning food applications, the effects of different GP treatments on the inactivation of natural microflora and Listeria monocytogenes, Salmonella Enteritidis and Escherichia coli on the surface of Fuji apples, soya sprouts and black pepper were evaluated. In particular the efficacy of the exposure to gas plasma was assessed immediately after treatments and during storage. Moreover, also possible changes in quality parameters such as colour, pH, Aw, moisture content, oxidation, polyphenol-oxidase activity, antioxidant activity were investigated. Since the lack of knowledge of cell targets of GP may limit its application, the possible mechanism of action of GP was studied against 2 strains of Listeria monocytogenes by evaluating modifications in the fatty acids of the cytoplasmic membrane (through GC/MS analysis) and metabolites detected by SPME-GC/MS and 1H-NMR analyses. Moreover, changes induced by different treatments on the expression of selected genes related to general stress response, virulence or to the metabolism were detected with Reverse Transcription-qPCR. In collaboration with the Scripps Research Institute (La Jolla, CA, USA) also proteomic profiles following gas plasma exposure were analysed through Multidimensional Protein Identification Technology (MudPIT) to evaluate possible changes in metabolic processes.

Microbial formation of nitrous acid and its exchange processes between soils and atmosphere

Salpetrige Säure (HONO) ist eine wichtige Form von reaktivem Stickstoff, die aufgrund ihrer Photolyse zu Stickstoffmonoxid (NO) und dem Hydroxylradikal (OH), sehr kurzlebig ist. Ein genaues Verständnis der Quellen und Senken von HONO ist eine grundlegende Voraussetzung, um dessen Einfluss auf die Umwelt zu beurteilen. Allerdings wird immer noch nach einer starken HONO-Quelle am Tag gesucht und nächtliche HONO-Deposition auf den Boden wurde bisher stets nur postuliert. Diese Dissertation folgt der Zielsetzung die Prozesse der HONO-Aufnahme und Freisetzung von Böden aufzudecken und die zugrunde liegenden Mechanismen zu verstehen.rnUm die Rolle von HONO-Bodenemissionen zu quantifizieren, wurden 17 Böden in einem dynamischen Kammersystem untersucht. Es konnten HONO-Emissionen derselben Größenordnung wie die bereits gut untersuchten NO-Emissionen festgestellt werden. Unerwarteter Weise wurden die stärksten Emissionen bei Böden mit neutralem pH aus ariden und landwirt¬schaftlichen Gebieten beobachtet. Die Temperaturabhängigkeit der Bodenemissionen von HONO und NO führten zu der Annahme einer mikrobiellen Freisetzung von HONO, welche durch Reinkulturexperimente mit dem ammoniumoxidierenden Bakterium Nitrosomonas europaea bestätigt werden konnte. Ein konzeptionelles Model für die Freisetzung reaktiver Stickstoffverbindungen aus Böden in Abhängigkeit des Bodenwassergehaltes wurde um HONO-Emissionen erweitert.rnDurch Nachweise mittels Reinkultur- und Inhibitionsexperimenten konnten weitere Untersuchungen der bakteriellen Freisetzung von HONO aus Böden zeigen, dass innerhalb der bakteriellen Nitrifikation nur ammoniumoxidierende Bakterien zur Emission von HONO fähig sind. Durch kontrolliert initiierte Zelllyse konnte gezeigt werden, dass intrazellulär akkumuliertes Hydroxylamin (NH2OH) für die HONO-Freisetzung verantwortlich sind. Zum ersten Mal wurde NH2OH in der Gasphase nachgewiesen und dass dieses über den gesamten Bodenfeuchtebereich von ammoniumoxidierenden Bakterien freigesetzt wird. Es wurde gezeigt, dass die heterogene Reaktion von NH2OH mit Wasserdampf auf einer Glasperlenoberfläche HONO bildet. Diese Reaktion erklärt die beobachtete Freisetzung von HONO bei niedrigen Bodenfeuchten, da nur dann die Oberfläche zur Reaktion zur Verfügung steht und nicht von Wasser bedeckt ist.rnEine 15N Isotopenmarkierungsmethode wurde entwickelt um isotopenmarkiertes gasförmiges HONO zu messen, was die Untersuchung der Bildungsprozesse von HONO und dessen Rolle in biogeochemischen Zyklen ermöglicht. Die Anwendung dieser neuen Methode auf eine Bodenprobe die mit 15N Harnstoff angereichert und in einem dynamischen Kammersystem untersucht wurde, bestätigt die obigen Ergebnisse einer starken mikrobiellen Beteiligung von Bodenbakterien zur HONO Freisetzung.rnBidirektionale Flüsse von HONO wurden für sechs untersuchte Bodenproben gefunden. Die Richtung der Flüsse hängt dabei vom Umgebungsmischungsverhältnis von HONO und dem Bodenwassergehalt ab. Eine wichtige Größe, die die bidirektionalen Flüsse von HONO beschreibt, ist das „Ökosystem spezifische Kompensationsmischungsverhältnis von HONO“, χcomp. Dieser neue Begriff wurde definiert und eingeführt, da die verschiedenen in den Bodenaustausch von HONO involvierten Prozesse nicht mit dem klassischen Kompensationspunktkonzept kompatibel sind. Die Untersuchungen bestätigen neueste Feldbeobachtungen, dass HONO, welches bei hohen Umgebungsmischungsverhältnissen vom Boden adsorbiert wird, bei niedrigen Mischungsverhält-nissen wieder vom Boden desorbiert wird. Folglich wird nächtlich akkumuliertes HONO tagsüber in eine Quelle für HONO umgewandelt. Vier Prozesse - Verteilung von HONO zwischen Gas- und Flüssigphase nach Henrys Gesetz, bakterielle HONO Bildung aus NH2OH, Adsorption und Desorption von HONO - und deren Dominanz in speziellen Bodenfeuchtebereichen wurden identifiziert. Dadurch wurde ein konzeptionelles Model für die Prozesse, die in Aufnahme und Freisetzung von HONO aus Böden involviert sind, als Funktion der Bodenfeuchte entwickelt.rnZusammenfassend hat diese Dissertation die entscheidenden Prozesse im Austausch von HONO zwischen Boden und Atmosphäre aufgeklärt und den der bakteriellen HONO Bildung zugrunde liegenden Mechanismus aufgedeckt. Es konnte gezeigt werden, dass Böden sowohl eine wichtige Quelle als auch eine Senke für HONO sind und sollten folglich in zukünftigen Feldmessungen stärker berücksichtigt werden.rn

Understanding of stuck fermentations : investigations on the relationship between the microbial diversity and chemical composition of must

Das Ziel dieser Arbeit war es, mehr Informationen über unkonventionelle Gründe für Gärstockungen zu gewinnen und neue Wege zu finden, diese zu überwinden. Mikrobielle Sukzession und die chemische Zusammensetzung bei der Gärung wurden in zwei aufeinander folgenden Jahren in einem Weingut von der oberen Mosel in Deutschland studiert. Es gab keinen Hinweis darauf, dass die isolierten Bakterienspezies oder chemischen Komponenten von Most und Jungwein an schleppenden oder stockenden Gärungen beteiligt waren. Ferner konnte während dieser Arbeit gezeigt werden, dass Saccharomyces bayanus die dominierende Weinhefe in diesem Weingut war statt der klassischen und bekannten Weinhefe Saccharomyces cerevisiae. Während der Gärstockung konnte ein Dreifach-Hybrid Saccharomyces cerevisiae x Saccharomyces kudriavzevii x Saccharomyces bayanus wachsen, Saccharomyces bayanus ersetzen und die Gärung beenden. Beide isolierten Hefestämme Saccharomyces bayanus Stamm HL 77 und der Dreifach-Hybrid Saccharomyces cerevisiae x Saccharomyces kudriavzevii x Saccharomyces bayanus Stamm HL 78 konnten Glucose und Fructose von Anfang an verwerten und konnten bei niedrigen Temperaturen von 15 °C und in der Abwesenheit von Hefe-verwertbarem Stickstoff in Form von Ammonium wachsen, solange Aminosäuren im Medium vorhanden waren, im Gegensatz zu einer kommerziellen Saccharomyces cerevisiae-Starterkultur. Chemische Untersuchungen ergaben, dass Hefe-verwertbarer Stickstoff in dem kooperierenden Weingut mit einem Maximum von 160 mg/l zu Beginn der Gärung vorhanden war und auf 40 mg/L verringert war nach zwei Wochen. Aus diesem Grund sind beide isolierten Hefestämme interessant als Starterkulturen in diesem Weingut und dies kann neben der niedrigen Temperatur im Keller auch ein Grund sein, warum Saccharomyces cerevisiae nicht die dominierende Weinhefe in diesem Fall ist. Der Dreifach-Hybrid Saccharomyces cerevisiae x Saccharomyces kudriavzevii x Saccharomyces bayanus Stamm HL 78 ist in der Lage, Fructose noch effizienter zu nutzen als Saccharomyces bayanus Stamm HL 77 und ist weniger abhängig von der Aminosäurekonzentration. Dieser Stamm wurde bereits erfolgreich bei diesem Projekt eingesetzt, um eine Gärstockung in dem kooperierenden Weingut zu beheben. Es ist bekannt, dass Saccharomyces-Hybride in der Weinherstellung vorkommen aber ihre Rolle bei der Überwindung von Gärstockungen wurde bisher noch nicht beschrieben. Diese Ergebnisse sind nützlich, um Gärstockungen zu vermeiden oder zu überwinden mit der selektiven Verwendung dieser Hefestämme in verschiedenen Stadien der Gärung. Das kooperierende Weingut, welches im oberen Qualitätssegment platziert ist, hatte jedes Jahr Probleme mit Gärstockungen. Daher ist die Anwendung der Dreifach-Hybriden Saccharomyces cerevisiae x Saccharomyces kudriavzevii x Saccharomyces bayanus Stamm HL 78 eine große Chance, Gärstockungen und finanzielle Verluste ohne kommerzielle Starterkulturen oder andere übliche Praktiken, die zu einer Veränderung des Aromaprofils führen können, zu vermeiden. Die beschriebenen Untersuchungen stellen ein Modell dar, um Gärstockungen auch in anderen Weingütern, die Spontangärungen anwenden, zu überwinden.

Implementation of enhanced biological phosphorus removal (ebpr) wastewater treatment processes enriched with different microbial communities

The EBPR (Enhanced Biological Phosphorus Removal) is a type of secondary treatment in WWTPs (WasteWater Treatment Plants), quite largely used in full-scale plants worldwide. The phosphorus occurring in aquatic systems in high amounts can cause eutrophication and consequently the death of fauna and flora. A specific biomass is used in order to remove the phosphorus, the so-called PAOs (Polyphosphate Accumulating Organisms) that accumulate the phosphorus in form of polyphosphate in their cells. Some of these organisms, the so-called DPAO (Denitrifying Polyphosphate Accumulating Organisms) use as electron acceptor the nitrate or nitrite, contributing in this way also to the removal of these compounds from the wastewater, but there could be side reactions leading to the formation of nitrous oxides. The aim of this project was to simulate in laboratory scale a EBPR, acclimatizing and enriching the specialized biomass. Two bioreactors were operated as Sequencing Batch Reactors, one enriched in Accumulibacter, the other in Tetrasphaera (both PAOs): Tetrasphaera microorganisms are able to uptake aminoacids as carbon source, Accumulibacter uptake organic carbon (volatile fatty acids, VFA). In order to measure the removal of COD, phosphorus and nitrogen-derivate compounds, different analysis were performed: spectrophotometric measure of phosphorus, nitrate, nitrite and ammonia concentrations, TOC (Total Organic Carbon, measuring the carbon consumption), VFA via HPLC (High Performance Liquid Chromatography), total and volatile suspended solids following standard methods APHA, qualitative microorganism population via FISH (Fluorescence In Situ Hybridization). Batch test were also performed to monitor the NOx production. Both specialized populations accumulated as a result of SBR operations; however, Accumulibacter were found to uptake phosphates at higher extents. Both populations were able to remove efficiently nitrates and organic compounds occurring in the feeding. The experimental work was carried out at FCT of Universidade Nova de Lisboa (FCT-UNL) from February to July 2014.

The role of the interplay between polymer architecture and bacterial surface properties on the microbial adhesion to polyoxazoline-based ultrathin films

Surface platforms were engineered from poly(L-lysine)-graft-poly(2-methyl-2-oxazoline) (PLL-g-PMOXA) copolymers to study the mechanisms involved in the non-specific adhesion of Escherichia coli (E. coli) bacteria. Copolymers with three different grafting densities (PMOXA chains/Lysine residue of 0.09, 0.33 and 0.56) were synthesized and assembled on niobia (Nb O ) surfaces. PLL-modified and bare niobia surfaces served as controls. To evaluate the impact of fimbriae expression on the bacterial adhesion, the surfaces were exposed to genetically engineered E. coli strains either lacking, or constitutively expressing type 1 fimbriae. The bacterial adhesion was strongly influenced by the presence of bacterial fimbriae. Non-fimbriated bacteria behaved like hard, charged particles whose adhesion was dependent on surface charge and ionic strength of the media. In contrast, bacteria expressing type 1 fimbriae adhered to the substrates independent of surface charge and ionic strength, and adhesion was mediated by non-specific van der Waals and hydrophobic interactions of the proteins at the fimbrial tip. Adsorbed polymer mass, average surface density of the PMOXA chains, and thickness of the copolymer films were quantified by optical waveguide lightmode spectroscopy (OWLS) and variable-angle spectroscopic ellipsometry (VASE), whereas the lateral homogeneity was probed by time-of-flight secondary ion mass spectrometry (ToF-SIMS). Streaming current measurements provided information on the charge formation of the polymer-coated and the bare niobia surfaces. The adhesion of both bacterial strains could be efficiently inhibited by the copolymer film only with a grafting density of 0.33 characterized by the highest PMOXA chain surface density and a surface potential close to zero.

Reversible microbial colonization of germ-free mice reveals the dynamics of IgA immune responses

The lower intestine of adult mammals is densely colonized with nonpathogenic (commensal) microbes. Gut bacteria induce protective immune responses, which ensure host-microbial mutualism. The continuous presence of commensal intestinal bacteria has made it difficult to study mucosal immune dynamics. Here, we report a reversible germ-free colonization system in mice that is independent of diet or antibiotic manipulation. A slow (more than 14 days) onset of a long-lived (half-life over 16 weeks), highly specific anticommensal immunoglobulin A (IgA) response in germ-free mice was observed. Ongoing commensal exposure in colonized mice rapidly abrogated this response. Sequential doses lacked a classical prime-boost effect seen in systemic vaccination, but specific IgA induction occurred as a stepwise response to current bacterial exposure, such that the antibody repertoire matched the existing commensal content.

Adherence to the medical regime in patients with heart failure

To assess adherence to medical treatment in patients with heart failure (HF) using a specific questionnaire and measurement of the serum concentration of digoxin.

Effects of adherence to guidelines for the control of major cardiovascular risk factors on outcomes in the REduction of Atherothrombosis for Continued Health (REACH) Registry Europe

To examine the impact of cardiovascular risk factor control on 3-year cardiovascular event rates in patients with stable symptomatic atherothrombotic disease in Europe.

Longitudinal analysis of patterns and predictors of changes in self-reported adherence to antiretroviral therapy: Swiss HIV Cohort Study

Adherence to combination antiretroviral therapy (cART) is a dynamic process, however, changes in adherence behavior over time are insufficiently understood.

A differential concentration-dependent effect of IVIg on neutrophil functions: relevance for anti-microbial and anti-inflammatory mechanisms

Background Polymorphonuclear neutrophils (PMN) play a key role in host defences against invading microorganisms but can also potentiate detrimental inflammatory reactions in case of excessive or misdirected responses. Intravenous immunoglobulins (IVIg) are used to treat patients with immune deficiencies and, at higher doses, in autoimmune, allergic and systemic inflammatory disorders. Methodology/Principal Findings We used flow cytometry to examine the effects of IVIg on PMN functions and survival, using whole-blood conditions in order to avoid artifacts due to isolation procedures. IVIg at low concentrations induced PMN activation, as reflected by decreased L-selectin and increased CD11b expression at the PMN surface, oxidative burst enhancement, and prolonged cell survival. In contrast, IVIg at higher concentrations inhibited LPS-induced CD11b degranulation and oxidative burst priming, and counteracted LPS-induced PMN lifespan prolongation. Conclusions/Significance IVIg appears to have differential, concentration-dependent effects on PMN, possibly supporting the use of IVIg as either an anti-microbial or an anti-inflammatory agent.

Adherence to ESMO clinial recommendations for prophylaxis of chemotherapy-induced nausea and vomiting

We assessed adherence to the European Society of Medical Oncology (ESMO)/Multinational Association of Supportive Care in Cancer recommendations for prophylaxis of chemotherapy-induced nausea and vomiting (CINV) at our institution.

Microbial community analysis of Lake Chillisquaque, a small water system in Central Pennsylvania

Cyanobacteria are photosynthetic organisms that require the absorption of light for the completion of photosynthesis. Cyanobacteria can use a variety of wavelengths of light within thevisible light spectrum in order to harvest energy for this process. Many species of cyanobacteria have light-harvesting proteins that specialize in the absorption of a small range of wavelengths oflight along the visual light spectrum; others can undergo complementary chromatic adaptation and alter these light-harvesting proteins in order to absorb the wavelengths of light that are mostavailable in a given environment. This variation in light-harvesting phenotype across cyanobacteria leads to the utilization of environmental niches based on light wavelength availability. Furthermore, light attenuation along the water column in an aquatic system also leads to the formation of environmental niches throughout the vertical water column. In order to better understand these niches based on light wavelength availability, we studied the compositionof cyanobacterial genera at the surface and depth of Lake Chillisquaque at three time points throughout the year: September 2009, May 2010, and July 2010. We found that cyanobacterialgenera composition changes throughout the year as well as with physical location in the water column. Additionally, given the light attenuation noted throughout the Lake Chillisquaque, we are able to conclude that light is a major selective factor in the community composition of Lake Chillisquaque.

Determinants of sustained viral suppression in HIV-infected patients with self-reported poor adherence to antiretroviral therapy

Background Good adherence to antiretroviral therapy (ART) is critical for successful HIV treatment. However, some patients remain virologically suppressed despite suboptimal adherence. We hypothesized that this could result from host genetic factors influencing drug levels. Methods Eligible individuals were Caucasians treated with efavirenz (EFV) and/or boosted lopinavir (LPV/r) with self-reported poor adherence, defined as missing doses of ART at least weekly for more than 6 months. Participants were genotyped for single nucleotide polymorphisms (SNPs) in candidate genes previously reported to decrease EFV (rs3745274, rs35303484, rs35979566 in CYP2B6) and LPV/r clearance (rs4149056 in SLCO1B1, rs6945984 in CYP3A, rs717620 in ABCC2). Viral suppression was defined as having HIV-1 RNA <400 copies/ml throughout the study period. Results From January 2003 until May 2009, 37 individuals on EFV (28 suppressed and 9 not suppressed) and 69 on LPV/r (38 suppressed and 31 not suppressed) were eligible. The poor adherence period was a median of 32 weeks with 18.9% of EFV and 20.3% of LPV/r patients reporting missed doses on a daily basis. The tested SNPs were not determinant for viral suppression. Reporting missing >1 dose/week was associated with a lower probability of viral suppression compared to missing 1 dose/week (EFV: odds ratio (OR) 0.11, 95% confidence interval (CI): 0.01–0.99; LPV/r: OR 0.29, 95% CI: 0.09–0.94). In both groups, the probability of remaining suppressed increased with the duration of continuous suppression prior to the poor adherence period (EFV: OR 3.40, 95% CI: 0.62–18.75; LPV/r: OR 5.65, 95% CI: 1.82–17.56). Conclusions The investigated genetic variants did not play a significant role in the sustained viral suppression of individuals with suboptimal adherence. Risk of failure decreased with longer duration of viral suppression in this population.