Streptococcus uberis is a major causative agent of bovine intramammary infections worldwide. S. uberis infections can persist for several months and resistance to antibiotic therapies has been observed. At present, the failure to bring S. uberis infections under control has been linked to the current lack of information with regards to S. uberis pathogenesis.

Bacteria in most environments exist and grow in association with surfaces, leading to formation of biofilms. In the medical context, biofilms are particularly significant for human health because of their high resistance to antimicrobial and immune system attack. In the health care setting biofilms associated with indwelling devices such as intravenous catheters and endotracheal tubes is a major clinical problem. It has been shown in previous reports that catecholamine stress hormones such as epinephrine, norepinephrine and structurally similar inotrope drugs used to treat heart and kidney problems in seriously-ill patients, are able to promote growth and virulence of certain bacteria. In this thesis, the role of catecholamine inotropes and stress hormones as an environmental factor for the induction of biofilm formation by infectious bacteria relevant to medical devices is considered. In vitro phenotypic characterisation was investigated by mainly using microbiological techniques, microscopy and proteomic analysis. The first section of this thesis shows how clinically attainable levels of catecholamine inotropes stimulated Pseudomonas aeruginosa growth and biofilm formation. The mechanism by which growth stimulation occurs was found to be via delivery of iron from the serum Fe-binding transferrin. P. aeruginosa growth, biofilm formation and motility were all significantly enhanced by catecholamine inotropes (P<0.05). Inotropes may be a risk factor for ventilator associated pneumonia as they stimulated biofilm formation on endotracheal tubing. In the second section which focuses on Escherichia coli and Salmonella Typhimurium, it was found that catecholamine stress hormone effect on growth, motility and biofilm formation was independent of the putative QseC and QseE catecholamine sensing receptors. In the third section, factors related to catecholamines inotropes Staphylococcus epidermidis biofilm stimulation were considered. Collectively, these findings show that levels of catecholamine inotropes found within critically ill patients can promote bacterial biofilm formation, and so contribute to bacterial pathogenesis within the hospital setting.

Most microbial life on earth exists as a collective entities, or 'biofilms'. These biofilms consist of the microbial cells and the extracellular biopolymers (EPS) they exude. The EPS serve many purposes of benefit to the microorganisms, but whereas EPS have received much attention in medical sciences, the science of EPS in soil is relatively undeveloped. Adding EPS to porous media (such as sand or soil) can' improve water-retention which is of great potential benefit to agriculture. ,It is not cost-effective to do this directly however due to the cost of deployment and physical incorporation with soil. Therefore it is more useful to identify managements that increase EPS indirectly using microbes already present in soil. These managements cannot be identified without the use of appropriate and meaningful analytical techniques that characterise the EPS produced by the soil microbial community. ' A range of extraction methods and measurements were compared, with the most representative selected to investigate i) triggers to EPS production ii) interplay between soil-nitrogen and carbon dynamics, and ii) the impact of EPS upon aggregate stability. Ultimately, an extraction method using cation exchange resin was selected. This method appeared to maintain membrane integrity of the majority of cells, thus minimising the likelihood of contaminating the EPS extracts with intracellular material. Using this method, EPS production in soil was shown to be affected by substrate availability, C:N ratio, hydrology, zinc contamination, and the nature of carbon substrates provided:1 Finally, the protein content of EPS was found to be closely related to aggregate stability, which in turn maintains soil functions critical to ecosystem services and agricultural productivity. This thesis represents a step towards understanding soil-native-EPS production: towards applied goals (such as improving soil water retention and understanding the consequences of agricultural managements) and advancing our fundamental knowledge of soil organic matter dynamics

Geothermal environments, in particular their chemistry and microbiology, are of broad scientific interest with respect to the formation of mineral deposits (e.g. Jones et al. 1997) and the ecology of extremophiles, a key component of origin of life studies and astrobiology (e.g. Stetter, 1996). Lipid biomarkers, in comparison to DNA and RNA, are relatively well preserved in geothermal sinters and it is likely that such compounds. once encased in the silica matrix, could persist for extended periods of time (Pancost et al., 2005). Consequently, they can be used to gain insight into microbial diversity and, where preserved in ancient materials, assess past changes in environmental conditions.

Microorganisms are of fundamental importance to global biogeochemical cycling, yet aspects of their ecology are poorly understood. Within the present methods used to study microbial ecology are limitations with regards to sensitivity, applicability and automation. This study aimed to investigate the potential application of novel nucleic acid probes (molecular beacons and locked nucleic acid probes) in microbial ecology.

SUMMARY This study describes some of the processes of macroalgal rafting important for the dispersal of benthic marine invertebrates and structuring intertidal species assemblages in Irish coastal : waters, using a combination of fieldwork and laboratory analyses. A novel method for assessing the density and distribution of seaweed rafts, which takes into consideration sea state was devised as a cost effective approach for surveying drifting algae in coastal and offshore marine environments. During the development of this surver .;, metaodotegy macroalgal rafts. were collected at various locations around the lrish coastlineand species assemblages were characterised. Species richness and abundance relationships were apparentiwhen factoring in.algal carrying capacity, and analysis indicated that rafts are most likely and opportunistic platform for species for survival and potential dispersal, rather than " assemblages where.species-specific responses to raft composition will occur. The abundance of drilling rafts in the offshore environment along with the presence of intertidal invertebrates highlights· the potential importance of such drifting habitats for the survival and movement of intertidal species across large expanses of ocean. The colonisation of Idotea species onto seaweed rafts was investigated to elucidate some of the initial smaller scale processes involved with rafting organisms and to understand some potential: behavioural associations. This was especially important, for species with direct development as they are considered to have low dispersal potential. Results indicate an activ~ colonisation of rafts by Idoteaindividuals from the surrounding water column as supposed to[ust a passive marooning along with algae detaching from the shore. Finally a comparative.analysis of shores that receive high and low levels of drift material from the ocean was undertaken to compare intertidal species assemblages, to expose anr biodiversity signatures of species colonising the shore from 1he arrival of macroalgal rafts. Abundance effects of species were clearly seen in this investigation, with some species displaying significantly higher abundances on high drift shores. These along with species richness effects indicate that.the arrival of rafts to a shore may have some effect .on . intertidal , species assemblages, although exposing any consequences of drift is difficult in such a dynamic and-complex marine environment.

In nature, bacteria can exist as a multi species consortium of cells adherent to a surface and able to co-ordinate cellular metabolism via quorum sensing molecules. The effect of biofilm formation can have both positive as well as negative impacts on human society. In order to engineer systems where the positive impacts of biofilms are enhanced and the negative impacts are curbed, a detailed understanding of the environmental signals and molecular mechanisms that trigger the formation and maintenance of biofilms is necessary. As a first step in this direction, the molecular mechanisms underlying the formation of biofilms arc investigated in Bacillus cereus; biofi Im formation in which has positive impacts on society such as. aiding waste water treatment and bioremediation as well as negative impacts such as biofouling of implants and causation of disease. This investigation of cell surface characteristics and production of extracellular polymeric substances via Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, zetapotcntial analysis and various techniques in proteomics suggest that during biofilm formation, the surface chemistry of the cells and the composition of the EPS changes, most likely by glyeosylation of surface and secreted polymers, in order to aid biofilm formation and that biofilms arc predominantly stabilized by electrostatic interactions between the cell surface and EPS polymers. This work also establishes that the presence of other microorganisms in the culture environment, mimicked by the addition of quorum sensing signal, Al-2 affects the surface chemistry, motility, cellular metabolism and EPS production in Bacillus cereus and improves biofilm formation in Bacillus cereus. The use of quorum sensing signals could therefore be a possible mechanism for biofilm control. However, additional investigations into the glycobiome of Bacillus cereus and the regulation of post translation control need to be carried out before quorum sensing signals can be employed to reliably control biofilm formation in Bacillus cereus.

No description available.

This thesis relates to the mathematical modelling of biofilm in two primary areas: biofilm growth, and the effect of microbial immobilisation in biofilm on environmen- tal contaminant transport in the Earth's subsurface. For biofilm growth we construct a model based on polymer solution theory. Parameter estimates motivate a very different model from two published biofilm models also based on polymer solution theory. Analysis of ID solutions provides an expression for growth rate suitable for comparison with experiment. Stability analysis of spatial perturbations to a growing planar front reveals an interfacial instability mechanism similar to that found in a published theoretical study not based on a specific material model. We derive a stability criterion as a critical external nutrient boundary layer thickness, and for the travelling wave solution we identify the finite perturbation wavenumber selected by the instability. For environmental contaminant transport, we identify dissolution of organic phase contaminants and sorption of hydrocarbons onto solid grains as primary lim- itations on bioavailability. We build a pore scale model including both organic phase dissolution and micro- bial uptake and use it to parameterise pore scale Sherwood and Damkohler numbers with respect to pore Peclet number. We illustrate their relation to effective macro- scopic parameters for varying organic phase size relative to pore size. A simple intraparticle diffusion sorption model is extended by considering an external biofilm layer on the particles. A larger scale model considers contaminant transport in a ID flow through a bed of such particles. A physically reasonable pa- rameter regime is suggested, providing analytical solutions for breakthrough curves.

Enterococci are opportunistic pathogens that are frequently a source of nosocomial infections and it is their resistance to antibiotics and their ability to form biofilms that represent important virulence traits. Normally, in healthy individuals it is a harmless commensal that is usually found in the intestine. This thesis firstly studies signal peptidases (SPases), which play an essential role in protein translocation. Interestingly, E. faecium was found to contain three type I SPases. Many proteins that are secreted are virulence factors, and the aim was to delete one or more of the SPases and study the effect of its removal on virulence. Unfortunately no mutants were obtained suggesting that the genes were essential. To establish if the genes were essential an inducible integration vector was constructed, but due to time constraints this could not be tested further. Biofilm formation was studied in both E. faecium and E. faecalis. The presence of the Enterococcal Surface Protein (Esp) in E. faecium was shown to increase hydrophobicity, and therefore also increase biofilm formation. Similarly, E. faecalis isolates that were good biofilm formers were also more hydrophobic in nature. The expression of Esp in E. faecium was studied under different conditions; these studies indicated that the highest level of Esp expression was found in biofilms cells. This growth-dependent manner Esp expression was not observed in E. faecalis BS12297. Surprisingly, Esp in E. faecium was also shown to have a role in ampicillin resistance, which was identified using calorimetry. This method proved to be a sensitive and rapid method to analyse antibiotic resistance. In the gut, bacteria encounter various adverse conditions, such as low pH and the presence of bile salts. Here we investigated the effects of bile salts on biofilm formation in E. faecium and E. faecalis and demonstrated that biofilm formation is induced at physiological concentrations of bile salts. In E. faecium the presence of bile salts caused an increase in initial attachment, microcolony formation and EPS production. Various factors were investigated, including hydrophobicity, cell growth, cell morphology, Esp expression and the production of extracellular polymeric substance (EPS). In E. faecium, only EPS production appeared to play a role, but the stimulation of biofilm formation due to bile salts is still to be fully explained.