Applied microbiology

EDITORS PREFACE .................................................................... v IN MEMORY ................................................................................. 1 TABLE OF CONTENTS ............................................................... 3 PART 1 - STARTERS ................................................................. 11 NEW ASPECTS OF FUNGAL STARTER CULTURES FOR FERMENTED FOODS .......................................................................................................................... 13 Abstract ........................................................................................................... 13 1. Introduction ...................................................................................................... 13 Rolf Geisen and Paul Färber .................................................................................... 13 2. Penicillium nalgiovense .................................................................................... 15 2.1. Taxonomic relationships at the molecular level ........................................ 15 2.2. Penicillin production is a common feature of p. nalgiovense .................... 17 2.3. Heterologous Gene Expression in P . nalgiovense .................................... 20 from P . Nalgiovense important for the fermentation process .......................... 21 2.4. Heterologous Gene Expression in P . nalgiovense 2.4. Cloning of genes 3. Penicillium camemberti .................................................................................... 23 4. Penicillium roqueforti ................................................................................. 25 5. Conclusions ...................................................................................................... 27 References ............................................................................................................ 27 STARTERS FOR THE WINE INDUSTRY .............................................................. 31 Aline Lonvaud-Funel ................................................................................................ 31 1. Introduction ...................................................................................................... 31 2. Yeast starters in winemaking ........................................................................... 32 2.1 The objectives of yeast starters .................................................................. 32 Abstract ................................................................................................................ 31 2.2 Properties of yeast used as selective criteria for active dry yeast producers and winemakers ............................................................................................... 34 2.3 Evaluation of the settlement of active dry yeast during alcoholic fermentation : ................................................................................................... 37 3. Malolactic starters in winemaking .................................................................... 38 3.1 Indications for use of malolactic starter and description ............................ 39 3.2 The influence of lactic acid bacteria starters on wine quality and their selection ........................................................................................................... 41 3.3 Efficiency of malolactic starters ................................................................ 42 References ............................................................................................................ 45 4. The future of starters for winemaking .............................................................. 43 5. Conclusion ........................................................................................................ 45 PART 2 - PHYSIOLOGY, BIOSYNTHESIS AND METABOLIC ENGINEERING ........................................................................... 49 METABOLISM AND LYSINE BIOSYNTHESIS CONTROL IN BREVIBACTERIUM FLAVUM: IMPACT OF STRINGENT RESPONSE IN BACTERIAL CELLS .................................................................................................. 51 M. Ruklisha, R. Jonina, L. Paegle and G. Petrovica ...................................................... 51 Abstract ................................................................................................................ 51 2. Materials and Methods ..................................................................................... 52 3. Results and Discussion ..................................................................................... 52 4. Conclusions ...................................................................................................... 56 References ............................................................................................................ 57 ENZYMES BY CELL SURFACE ENGINEERING ................................................ 59 1. Introduction ....................................................................................................... 51 MOLECULAR BREEDING OF ARMING YEASTS WITH HYDROLYTIC Mitsuyoshi Ueda, Toshiyuki Murai, Shouji Takahashi, Motohisa Washida, and Atsuo Tanaka ....................................................................................................................... 59 Abstract ................................................................................................................ 59 1. Introduction ...................................................................................................... 60 2. Principle of Cell Surface Engineering of Yeast ................................................ 63 3. Display of Amylolytic Enzymes on the Yeast Cell Surface ............................. 65 4. Display of Cellulolytic Enzymes on the Yeast Cell Surface ............................ 67 5. Display of Lipase on the Yeast Cell Surface .................................................... 70 6. Cell Surface Engineering as a Novel Field of Biotechnology .......................... 70 References ............................................................................................................ 71 ...................................................................................................................................... 75 Simon Ostergaard, Lisbeth Olsson and Jens Nielsen ................................................ 75 METABOLIC PATHWAY ANALYSIS OF SACCHAROMYCES CEREVISIAE Abstract ................................................................................................................ 75 1. Introduction ...................................................................................................... 75 2. Metabolic pathway analysis .............................................................................. 76 2.1. Metabolic control analysis ........................................................................ 76 2.2. Metabolic flux analysis ............................................................................. 77 3. Steady-state continuous cultivation – an excellent tool for metabolic pathway analysis ................................................................................................................. 79 4. Metabolic pathway analysis applied to Saccharomyces cerevisiae .................. 80 4 4.1. Kinetic studies of the glycolysis ............................................................... 80 Acknowledgements .............................................................................................. 85 4.2. Metabolic pathway analysis of the galactose metabolism ........................ 81 References ............................................................................................................ 85 PART 3 - STATE PARAMETERS AND CULTURE CONDITIONS ................. . ................................................................................... 87 EFFECT OF AERATION IN PROPAGATION ON SURFACE PROPERTIES OF BREWERS’ YEAST .................................................................................................... 89 Andrew Robinson and Susan T. L . Harrison ............................................................. 89 Abstract ................................................................................................................ 89 1. Introduction ...................................................................................................... 89 2. Materials and Methods ..................................................................................... 90 2.1 Propagation conditions .............................................................................. 90 2.2 Hydrophobicity .......................................................................................... 90 2.3 Surface charge ............................................................................................ 91 2.4 Flocculation ............................................................................................... 92 3. Results .............................................................................................................. 92 3.1 Yield coefficients ....................................................................................... 92 3.2 Cell growth rates ........................................................................................ 92 3.3 Hydrophobicity .......................................................................................... 93 3.5 Flocculation ............................................................................................... 95 4. Discussion ......................................................................................................... 96 5. Conclusions ...................................................................................................... 98 Acknowledgements .............................................................................................. 98 References ............................................................................................................ 99 3.4 Zeta potential ............................................................................................. 94 EFFECT OF THE MAIN CULTURE PARAMETERS ON THE GROWTH AND PRODUCTION COUPLING OF LACTIC ACID BACTERIA ............................ 101 A. Amrane and Y. Prigent ....................................................................................... 101 Abstract .............................................................................................................. 101 1. Introduction .................................................................................................... 101 2. Materials and methods .................................................................................... 102 2.1 Microorganism ......................................................................................... 102 2.2 Media ....................................................................................................... 102 2.3 Fermentors and culture conditions ........................................................... 102 2.4 Analytical methods .................................................................................. 103 3. Results and Discussion ................................................................................... 103 3.1. Preculture conditions .............................................................................. 103 3.2. Nutritional limitations ............................................................................. 105 3.3. Initial lactate additions ............................................................................ 106 4. Conclusions .................................................................................................... 107 Acknowledgements ............................................................................................ 107 5 References .......................................................................................................... 107 PSEUDOHYPHAL AND INVASIVE GROWTH IN SACCHAROMYCES CEREVISIAE ............................................................................................................. 109 F.F. Bauer and I.S . Pretorius ................................................................................... 109 Abstract .............................................................................................................. 109 1. Introduction .................................................................................................... 109 2. Signal transduction in Saccharomyces cerevisiae ........................................... 110 3. Molecular nature of signal transduction processes resulting in pseudohyphal differentiation ..................................................................................................... 112 3.1. Signal transduction modules .................................................................. 113 3.1.3. Intermediate signal transduction modules ....................................... 116 3.2. Transcriptional regulators ....................................................................... 122 3.2.1. Ste12p and Tec1 .............................................................................. 123 3.2.2. Msn1p and Mss11p: Central elements in the pseudohyphal growth pathway ..................................................................................................... 123 3.2.3. Sfl1p. Sok2p and Flo8p: Factors depending on the cAMP dependent kinase ........................................................................................................ 124 3.2.4. Other factors .................................................................................... 125 3.3. Effector proteins ..................................................................................... 125 transcriptional regulation .......................................................................... 126 3.3.2. Starch degrading enzymes: a direct metabolic link ......................... 127 4 . Scientific and industrial relevance .................................................................. 127 3.1.1. Nutrient availability is sensed by permeases ................................... 113 3.1.2. Transmission via receptor associated elements ............................... 114 3.3.1. MUC1. a gene encoding a mucin-like protein subjected to complex Acknowledgements ............................................................................................ 129 References ................ ................................................................................... 129 MICROBIAL PRODUCTION OF THE BIODEGRADABLE POLYESTER CHROOCOCCUM 6B: RELATION BETWEEN PHB MOLECULAR WEIGHT. THERMAL STABILITY AND TENSILE STRENGTH ........................................ 135 ......................... 135 Abstract .............................................................................................................. 135 1. Materials and methods .................................................................................... 135 1.1 Microorganism and culture media ........................................................... 135 1.2 Fermentor experiments ............................................................................ 135 1.3 Extraction and purification procedure ...................................................... 136 1.4 Analytical methods .................................................................................. 136 2. Results and discussion .................................................................................... 136 2.1 Effect of MW on PHB thermal stability .................................................... 136 2.2 Effect of aeration rate on PHB MW .......................................................... 137 2.3 PHB tensile strength (σ) at different MW ................................................. 138 2.4 PHB as a matrix for microencapsulation ................................................. 138 POLY-3-HYDROXYBUTYRATE (PHB) FROM AZOTOBACTER Quagliano Javier C. and Miyazaki Silvia S ... 6 3. Conclusions .................................................................................................... 139 References .......................................................................................................... 139 PART 4 - NOVEL APPROACHES TO THE STUDY OF MICROORGANISMS ................................................................ 141 SHARING OF NUTRITIONAL RESOURCES IN BACTERIAL COMMUNITIES DETERMINED BY ISOTOPIC RATIO MASS SPECTROMETRY OF BIOMARKERS .......................................................................................................... 143 Wolf-Rainer Abraham, Christian Hesse, Oliver Pelz, Stefanie Hermann, Michael Tesar, Edward R. B . Moore, and Kenneth N . Timmis ............................................ 143 1. Introduction .................................................................................................... 143 2. Taxon specific biomarkers .............................................................................. 144 2.1. Polar lipids .............................................................................................. 144 2.2. Outer membrane proteins ........................................................................ 145 3. Isotopic fractionation in microorganisms ....................................................... 146 4. Carbon sharing in a pollutant degrading bacterial community ....................... 147 4.1. Origin and characteristics of the microbial consortium .......................... 147 4.2. Incorporation of [U-13C]-metabolites in microbial biomasses ................ 148 4.3. Substrate competition ............................................................................. 149 4.4. Community physiology of the microbial consortium ............................. 150 5. Outlook ........................................................................................................... 152 Acknowledgement .............................................................................................. 152 References .......................................................................................................... 152 A COMPARISON OF THE MECHANICAL PROPERTIES OF DIFFERENT BACTERIAL SPECIES ............................................................................................ 155 C . SHIU, Z . ZHANG AND C.R. THOMAS ........................................................... 155 Abstract .............................................................................................................. 155 1. Introduction .................................................................................................... 155 1.1 Relative resistance of different microorganisms to mechanical disruption ....................................................................................................................... 155 1.2 Cell wall structure .................................................................................... 156 1.3 Bacterial biomechanics ............................................................................ 157 1.4 Micromanipulation ................................................................................... 158 2. Materials and methods .................................................................................... 158 2.1 The micromanipulation system ................................................................ 158 2.2 Culture conditions .................................................................................... 159 3. Results and discussion .................................................................................... 160 4. Conclusions and future developments ............................................................ 161 References .......................................................................................................... 162 7 PART 5 - NOVEL APPLICATIONS .......................................... 163 KOCURIA ROSEA AS A NEW FEATHER DEGRADING BACTERIA ........... 165 Nereida Coello and Luis Vidal ................................................................................ 165 Abstract .............................................................................................................. 165 1. Introduction .................................................................................................... 165 2. Isolation, identification and adaptation of feather-degrading microorganisms 166 2.1. Isolation and degradation of feathers by a microbial isolate ................... 166 2.2. Morphological and ultrastructural characteristics of the feather-degrading isolate ............................................................................................................. 168 3. Microbial growth and feather degradation ...................................................... 168 3.1. Effect of quantity of feathers .................................................................. 168 3.2. Effect of culture temperature on feather degradation and growth of LPB-3 ....................................................................................................................... 171 3.3. Kinetic fermentation ............................................................................... 171 4.1. Fermented feather meal ........................................................................... 171 4.2. Enzymes .................................................................................................. 173 4.3. Pigments ................................................................................................. 173 Acknowledgements ............................................................................................ 174 References .......................................................................................................... 174 4. Industrial applications ..................................................................................... 171 COMPARISON OF Pb2+REMOVAL CHARACTERISTICS BETWEEN BIOMATERIALS AND NON-BIOMATERIALS .................................................. 177 Dong Seog Kim and Jung Ho Suh ........................................................................... 177 Abstract .............................................................................................................. 177 1. Introduction .................................................................................................... 177 2. Materials and methods .................................................................................... 178 2.1. Materials ................................................................................................. 178 2.2. Microorganisms and culture conditions .................................................. 178 2.3. Pb2+ removal experiment ........................................................................ 178 3. Results and discussion .................................................................................... 179 3.1. Pb2+ removal characteristics .................................................................... 179 3.2. Initial Pb2+ removal rate .......................................................................... 182 4. Conclusions .................................................................................................... 183 References .......................................................................................................... 183 HYDROCARBON UTILISATION BY STREPTOMYCES SOIL BACTERIA . 185 Gy. Barabás, Gy. Vargha, I. Szabó, A. Penyige, J. Szöllõsi, J. Matkó, S. Damjanovich and T . Hirano .................................................................................... 185 Abstract .............................................................................................................. 185 1. Materials and methods .................................................................................... 185 1.1 Test organisms . oligocarbophylic streptomyces ...................................... 185 1.2 Biomass preparation ................................................................................ 186 8 1.3 Incorporation of radioactivity from labelled n-Hexadecane into mycelia . ....................................................................................................................... 186 1.4 Fluorescence measurements ..................................................................... 186 1.5 Analysis of fatty acids .............................................................................. 187 1.6 Investigations with GTP analogues .......................................................... 187 3. Conclusion ...................................................................................................... 190 References .......................................................................................................... 190 PART 6 - FOOD SECURITY AND FOOD PRESERVATION ... 191 2. Results and discussion .................................................................................... 187 MOLECULAR DETECTION AND TYPING OF FOODBORNE BACTERIAL PATHOGENS: A REVIEW ...................................................................................... 193 M . Heyndrickx, N . Rijpens and L . Herman ............................................................. 193 Abstract .............................................................................................................. 193 1. Introduction .................................................................................................... 194 2. Characteristics of the foodborne bacterial pathogens ..................................... 194 3. Molecular detection and identification of foodborne bacterial pathogens ...... 198 3.1 Nucleic acid based identification methods ............................................... 198 3.2 The use of virulence genes as target for molecular identification ............ 198 3.3 The use of RRNA genes as target for molecular identification ............... 199 for molecular identification ........................................................................... 200 3.5 The available molecular identification systems ....................................... 201 3.6 PCR detection of bacterial pathogens in food products ........................... 203 3.6.1 Influence of food components on PCR performance ....................... 203 3.6.2 Sensitivity and contamination of PCR ............................................. 203 3.6.3 The detection of the viability of cells by DNA based technology .... 204 3.7 Evaluation and validation of DNA based methods .................................. 205 4. Molecular typing of foodborne bacterial pathogens ....................................... 208 4.1 Terminology and general information ..................................................... 208 4.1.1 Necessity of bacterial typing of foodborne pathogens ..................... 208 4.1.2 Species-subspecies-variety-clone-strain-isolate ............................... 209 4 .. 2 Prospects in molecular typing ................................................................. 220 5. Molecular typing of some specific bacterial foodborne pathogens ............... 221 5.1 Salmonella ............................................................................................... 221 5.3 Listeria monocytogenes .......................................................................... 227 5.5 Some other foodborne bacterial pathogens .............................................. 229 References .......................................................................................................... 229 3.4 The use of specific sequences with a known or unknown function as target 3.8 DNA amplification methods for quantification of foodborne pathogens . 207 4.1.3 Molecular typing techniques used for bacterial pathogens .............. 210 4.1.4 Analysis of DNA fingerprints .......................................................... 219 5.2 Campylobacter jejuni ............................................................................... 226 5.4 Escherichia coli 0157 .............................................................................. 228 9 BIOENCAPSULATION TECHNOLOGY IN MEAT PRESERVATION ........... 239 Cahill, S.M., Upton, M.E., and McLoughlin. A.J. .................................................. 239 Abstract .............................................................................................................. 239 1. Introduction .................................................................................................... 240 2. Meat preservation ........................................................................................... 241 2.1 Biological fermentation ........................................................................... 241 2.2 Chemical acidification ............................................................................. 243 3. The application of encapsulation technology to meat preservation ................ 243 3.1. The application of encapsulation technology to a microbial fermentation ....................................................................................................................... 243 3.1.3. Commercial applications ................................................................. 247 3.2.1. Encapsulation matrices and the encapsulation process ................... 248 3.2.2. The benefits of acidulant encapsulation .......................................... 249 3.2.3 Commercial availability ................................................................... 249 4. Control of emerging pathogens ...................................................................... 250 5. The application of encapsulation technology to bacteriocin delivery ............. 251 5.1 Bacteriocins ............................................................................................. 251 5.2.1 Encapsulation of nisin ...................................................................... 252 6. Conclusions and future work .......................................................................... 261 References .......................................................................................................... 261 INDEX ....................................................................................... 267 3.1.1. Encapsulation matrices and the encapsulation process ................... 244 3.1.2. The benefits of meat starter culture encapsulation .......................... 246 3.2. The application of encapsulation technology to chemical acidification . 248 5.2 Nisin ......................................................................................................... 251 10