Carbapenem resistance in Acinetobacter baumannii is a growing public health concern and represents a serious problem for treatment of the infection. Several carbapenem-hydrolysing &beta / -lactamases have been identified from A. baumannii so far. In this study carbapenem resistance in A.baumannii strains recovered from intensive care units of Gulhane Military Medical Academy, Turkey, were investigated via multiplex PCR and with parallel phenotypic tests. From June 2006 to January 2010, 138 clinical A. baumannii isolates were collected. Identification and antimicrobial susceptibility tests of the isolates were performed. The MICs of imipenem and meropenem were determined by using E-test method. Carbapenem resistant A. baumannii strains were included for further study. Firstly, the presence of carbapenemases were determined. The presence of Metallo-beta-lactamase (MBL) were also investigated. Detection of the four groups of OXA carbapenemases (OXA- 23, OXA-24, OXA-51 and OXA-58) was carried out using a multiplex PCR assay. Sequence analyses were performed. Non-duplicate, multidrug resistant 61 clinical A. baumannii isolates were found to be resistant to imipenem and meropenem. In the 61 isolates, the MIC50 of imipenem and meropenem were 16 and &gt / 32 / MIC90 were 192 and &gt / 32 respectively. Modified Hodge Tests (MHT) were positive for all 61 A. baumannii strains. None of these isolates showed MBL activity. As determined through multiplex PCR, all of the 61 isolates had blaOXA-51 genes, 50 isolates had blaOXA-23, and 11 isolated had blaOXA-58 genes. Alleles encoding OXA-24-like enzymes were not detected in any isolates. This study indicated that the clinical isolates in our region contained blaOXA-51, blaOXA-23, and blaOXA-58 resistance genes. However, blaOXA-24 gene was either absent or occur in very low frequency.

Olive Mill Wastewater (OMW), by-product of oil industry, is a dark liquid with a characteristic fetid smell, bitter taste and bright appearance / having a high pollution potential, creating serious problems in countries producing olive oil. Azotobacter chroococcum as a Nitrogen-fixing bacteria can bioremediate OMW, by degrading its toxic constituents. With the help of this detoxification process OMW can be used as biofertilizer. In this study, the dynamics of growth and nitrogen fixation at different physiological conditions and nutrient requirements of A. chroococcum in chemically defined N-free medium was determined. These parameters were cultivation conditions such as pH, temperature and aeration and some additives such as inorganic salts, boric acid and nitrogen. Consequently, the maximum cell concentration were obtained when A. chroococcum was grown at neutral pH, 35&amp / #61616 / C, 150 rpm and in medium supplemented with manganese salt at 0.01% concentration. The maximum nitrogen fixation products were attained when A. chroococcum was grown under the same conditions except at pH 8. Further, bioremediation of OMW by A. chroococcum was examined. When A. chroococcum was cultivated in OMW containing basal medium at 10% OMW concentration, a cell density 12 times higher than in the OMW free medium was achieved. Also, it was found to have maximum increase in extracellular protein concentration (112 mg/l) at 10% OMW containing medium and maximum increase in ammonia concentration (9.05 mg/l) at 5% OMW containing medium.

Growth and survival of L. innocua and TAC in artificially inoculated Turkish White Cheese during manufacturing and storage periods, with respect to different level of contamination of L. innocua were investigated. Cheese products were manufactured by the short-set procedure in pilot-plant-sized vats, as in AO&Ccedil / dairy factory. Pasteurized cow&rsquo / s milk was inoculated with L. innocua for obtaining the initial loads of 3.84 and 7.12 log CFU/ml. Bacterial load of inoculated milk, whey, post-ripened curd and post-salted cheese was determined during processing at 20&plusmn / 5&ordm / C. Cheeses were stored in 16% saline solution at 4 &plusmn / 2&ordm / C for up to 45 days. Samples were taken from each treatment and analysed on 5, 10, 15, 20, 30 and 45 days. Total decrease of L. innocua in Turkish White Cheese with each inoculum dose was approximately 2 logs during the storage period. L. innocua values were also compared with TAC values. The results had shown that, if pasteurization is not as sufficient as to kill this bacteria in contaminated raw milk, or if there is post-process contamination, Listeria can survive during the manufacture and storage, although they decrease in number. Storage (ripening) period for consumption of cheeses should be at least 90 and 178 days, in low and high inoculum dose, respectively. Physico-chemical properties of cheese as pH, acidity, salt, fat, moisture contents during storage period were determined. Salt concentration, pH value and storage temperature had a cumulative bactericidal effect on microorganisms. In this respect, effect of implementing HACCP method on reducing the Listerial contamination of Turkish White Cheese was determined for checking the quality problems in a cheese plant and for directing the companies as a guide.

Biological hydrogen production is a renewable, carbon-neutral and clean route for hydrogen production. Purple non-sulfur (PNS) bacteria have the ability to produce biohydrogen via photofermentation process. The type of the bacterial strain used in photofermentation is known to have an important effect on hydrogen yield. In this study, the effect of different co-cultures of PNS bacteria on photofermentation process was investigated in search of improving the hydrogen yield. For this purpose, growth, hydrogen production and substrate utilization of single and co-cultures of different PNS bacteria (R. capsulatus (DSM 1710), R. capsulatus hup- v (YO3), R. palustris (DSM 127) and R. sphaeroides O.U.001 (DSM 5864)) were compared on artificial H2 production medium in 150 mL photobioreactors under continuous illumination and anaerobic conditions. In general, higher hydrogen yields were obtained via co-cultivation of two different PNS bacteria when compared with single cultures. Further increase in hydrogen yield was observed with co-cultivation of three different PNS bacteria. Co-cultures of two different PNS bacteria have resulted in up to 1.4 and 2.1 fold increase in hydrogen yield and hydrogen productivity. Whereas co-cultures of three different PNS bacteria have resulted in up to 1.6 and 2.0 fold increase in hydrogen yield and hydrogen productivity compared to single cultures. These results indicate that, defined co-cultures of PNS bacteria produce hydrogen at a higher yield and productivity, due most probably to some synergistic relationship. Further studies regarding the physiological and molecular changes need to be carried out for deeper understanding of the mechanism of hydrogen production in co-cultures.

One of the most important parameters affecting hydrogen production in photofermentation process is the type of carbon and nitrogen sources. For this reason in this research, the effect of different nitrogen sources (5mM ammonium chloride and 2mM glutamate) and acetate concentrations (40

The members of the genus Bacillus produce a wide variety of secondary metabolites with antimetabolic and pharmacological activities. These metabolites are mostly small peptides and have unusual components and chemical bonds. These metabolites are synthesized nonribosomally by multifunctional enzyme complexes called peptide synthetases. One of those small peptides, bacilysin, is a dipeptide antibiotic composed of L-alanine and L-anticapsin which is produced and excreted by certain strains of Bacillus subtilis. Proteins that are responsible to synthesize bacilysin are encoded by bac operon. It has been shown that the biosynthesis of bacilysin is under the control of quorum sensing global regulatory pathway through the action of ComQ/ComX, PhrC (CSF), ComP/ComA in a Spo0K (Opp)-dependent manner. The objective of the study is to identify the functional roles of bacilysin biosynthesis in the regulatory cascade and idiophase cell physiology operating in B. subtilis by using gel-based and gel-free proteomics techniques. For this, we employed comparative proteome-wide analysis of the bacilysin producer B. subtilis PY79 and its bacilysin nonproducer derivative bacA::lacz::erm OGU1 strain which was recently constructed by our group. Identification via GeLC analysis of 76 differentially expressed proteins from total soluble proteome of wild-type PY79 and bacilysin minus OGU1 strain indicated the direct or indirect multiple effects of bacilysin on metabolic pathways, global regulatory systems and sporulation.

In this study, a new bacteriocin isolated from a Leuconostoc mesenteroides subsp. cremoris strain was purified to homogeneity by pH mediated cell adsorption-desorption, solid phase extraction with Amberlite XAD-16, cation-exchange chromatography and hydrophobic interaction chromatography. The purification resulted in an electrophoretically pure protein that was smaller than 6 kDa as judged by SDS-PAGE. The bacteriocin was found to be very hydrophobic and cationic and could be adsorbed by synthetic calcium silicate due to its cationic and especially hydrophobic nature. It was observed that this bacteriocin was sensitive to &amp / #945 / -amylase in addition to proteinase K, trypsine, pepsine and chymotrypsine and had a bactericidal mode of action with a concomitant cell lysis. The results indicated that bacteriocin produced by Leuconostoc mesenteroides subsp. cremoris was more stable to combined effect of pH and heat than nisin, lacticin 481, lacticin 3147 and lactococcin G and was bactericidal between pH 2.0-12. It was found that the bacteriocin produced by Leuconostoc mesenteroides subsp. cremoris was stable to organic solvents and could be extracted with chloroform containing solvents efficiently for purification. The bacteriocin produced by Leuconostoc mesenteroides subsp. cremoris was found to have a strong inhibitory activity against Listeria innoqua, Listeria monocytogenes, Bacillus cereus, Enterococcus faecalis, Lactobacillus delbrueckii, Lactobacillus cremoris, other Leuconostoc meenteroides strains and gram-negative bacterium Pseudomonas fluorescens. Some of the insensitive bacteria were observed to be sensitive when high concentration of the bacteriocin was used.

Within the content of this thesis, it was aimed to understand the changes in the biomass and abundance of heterotrophic bacteria and marine cyanobacteria Synechococcus in time with respect to multitude of ambient physical, chemical and biological factors. For this, monthly samples from discrete depths in the offshore (0-20-40-60-80-100-125-150-175-200 m) and in the near shore (surface and 10 m) stations over a period of one year in the Cilician Basin (eastern Mediterranean) were collected via rosette sampler. Epifluorescent microscope and the image analysis system were used to estimate abundance and biomass of both groups. Coastal station was more abundant and had much higher bacterial (heterotrophic bacteria) and cyanobacterial (Synechococcus) biomass than the offshore station as it receives substantial amount of freshwater from the nearby Lamas River throughout the year. The surface annual averages for bacterial and cyanobacterial abundance and biomass were 9600000 cells/ml - 56.5 microgram C/l and 400000 cells/ml - 24.1 microgram C/l, respectively, at the coastal station. The surface annual averages for bacterial and cyanobacterial abundance and biomass were 8100000 cells/ml &ndash / 49.1 microgram C/l and 210000 cells/ml &ndash / 10.6 microgram C/l, respectively, at the offshore station. Bacterial population always found to exceed Synechococcus abundance within the water column. In general, bacterial and cyanobacterial abundance and biomass tend to decrease with depth. On a seasonal basis, bacterial population was found excessively dominant at the surface or near-surface waters during the second half of the year. Synechococcus were also found more abundant during late summer and autumn. Temperature and nitrate concentration seemed to affect efficiently the abundance of both populations in the area. Based on Spearman Rank Correlation analysis, highly significant correlations between bacterial abundance as well as biomass and ambient temperature were observed at both stations. However, a significant correlation was found between Synechococcus and temperature only at the offshore station. Significant negative correlations are found between nitrate and bacterial abundance and biomass at both stations and between Synechococcus abundance and biomass only at the offshore station. At the offshore station, salinity was also found to be positively correlated with the bacterial and cyanobacterial abundance and biomass.

The insect pathogen Bacillus thuringiensis (Bt) holds great promise as an effective and friendly way for management of the pests with safety for nontarget animals and humans. However, high capital investment due to high production and formulation cost of commercial Bt preparations has caused prohibitive effect on companies. The present study mainly aimed at developing a low cost medium that supports the growth of different Bt strains and their specific bioinsecticidal &amp / #948 / -endotoxins (crystal proteins). A comparison was made between the representative members of three different subspecies of Bt to observe toxin yields in response to certain nutritional conditions. Three different Bt subspecies were Bt kurstaki (strain 81), Bt israelensis (strain HD500) and Bt tenebrionis (strain 3203), producing lepidoptera- and diptera-specific Cry1 and Cry2, diptera-specific Cry4Ba and Cry11Aa and coleoptera-specific Cry3Aa toxins, respectively. Studies were conducted to optimize glucose and inorganic phosphate concentrations in standard DSM medium for the production of these Bt-based biopesticides. General suppression of toxin yields in high glucose medium (10 g/L) thought the generality of carbon catabolite regulation for biosynthesis of different types of toxins. Inorganic phosphate (Pi) level was important for Cry4Ba, Cry11Aa and Cry3Aa biosynthesis while Cry1 and Cry2 production was not responsive to high Pi. Wastewater sludge, fruit residues and broiler litter were next tested as cheap raw materials for Bt-based biopesticide production in batch cultures. Broiler litter seemed to be a much better substrate among all since some degree of production of each toxin was observed at almost every stage of fermentation. The processing of broiler litter was found to significantly improve toxin yields. The medium prepared from processed broiler litter was successfully used to cultivate all Bt stains and obtain bioinsecticidal proteins in high yields which were comparable or higher than those that can be obtained on standard semi-synthetic media.

Lactic acid bacteria are associated with preservation of foods, including milk, meat and vegetables. Yoghurt is produced by the cooperative action of two starter bacteria / S. thermophilus and L. delbrueckii subsp. bulgaricus. In this study, identification and typing of yoghurt starter bacteria were aimed. Traditional home made yoghurts were collected from different areas of Turkey, identification of those isolates at species and subspecies level and typing at strain level were achieved using PCR based methods. In our study, identification of yogurt starter bacteria was studied using species specific primers and ARDRA. These methods were inefficient in identification of yoghurt starter bacteria, at species and subspecies level. Consequently, a reliable and quick method for accurate identification of yoghurt starter bacteria was developed. The new method focuses on amplification of methionine biosynthesis genes, for selective identification of yoghurt starter bacteria together with some cheese starters. Further discrimination by ARDRA enabled differentiation of yoghurt starter bacteria from cheese starters. Confirmation of the proposed method has been accomplished by partial sequencing of the 16S rRNA gene. After correct identification of starter bacteria had been achieved, the strains were typed at strain level using RAPD-PCR and MLST. RAPD-PCR with primer 1254 resulted better fingerprints, compared to primer M13 at strain level. Comparisons of the two typing methods showed that RAPD-PCR revealed strain diversity better than MLST, however MLST was a more robust and reliable method and resulted in clustering of the strains depending on the isolation source.