Applied microbiology

This book illustrates the major trends in applied microbiology research with immediate or potential industrial applications. The papers proposed reflect the diversity of the application fields. New microbial developments have been done as well in the food and health sectors than in the environmental technology or in the fine chemical production. All the microbial genera are involved : yeast, fungi and bacteria. The development of biotechnology in parallel with the industrial microbiology has enabled the application of microbial diversity to our socio-economical world. The remarkable properties of microbes, inherent in their genetic and enzymatic material, allow a wide range of applications that can improve our every day life. Recent studies for elucidating the molecular basis of the physiological processes in micro-organisms are essential to improve and to control the metabolic pathways to overproduce metabolites or enzymes of industrial interest. The genetic engineering is of course one of the disciplines offering new horizons for the « fantastic microbial factory » . Studies of the culture parameter incidence on the physiology and the morphology are essential to control the response of the micro-organisms before its successful exploitation at the industrial scale. For this purpose, fundamental viewpoints are necessary. Development of novel approaches to characterise micro-organisms would also facilitate the understanding of the inherent metabolic diversity of the microbial world, in terms of adaptation to a wide range of biotopes and establishment of microbial consortia.

Rolf Geisen and Paul FarberAline Lonvaud-FunelM.Ruklisha and R.Jonina and L.Paegle and G.PetrovicaMitsuyoshi Ueda and Toshiyuki Murai and Shouji Takahashi and Motohisa Washida and Atsuo TanakaSimon Ostergaard and Lisbeth Olsson and Jens NielsenAndrew Robinson and Susan T. L. HarrisonA. Amrane and Y. PrigentF.F. Bauer and I.S. PretoriusQuagliano Javier C. and Miyazaki Silvia SWolf-Rainer Abraham and Christian Hesse and Oliver Pelz and Stefanie Hermann and Michael Tesar and Edward R. B. Moore and Kenneth N. TimmisC. Shiu and Z. Zhang and C.R. ThomasNereida Coello and Luis VidalDong Seog Kim and Jung Ho SuhGy. Barabas and Gy. Vargha and I. Szabo and A. Penyige and J. Szollosi and J. Matko and S. Damjanovich and T. HiranoM. Heyndrickx and N. Rijpens and L. HermanS.M. Cahill and M.E. Upton and A.J. McLoughlin

Editors Preface	p. v
In Memory	p. 1
Table of Contents	p. 3
Part 1 Starters	p. 11
New Aspects of Fungal Starter Cultures for Fermented Foods	p. 13
Abstract	p. 13
1. Introduction	p. 13
2. Penicillium nalgiovense	p. 15
2.1 Taxonomic relationships at the molecular level	p. 15
2.2 Penicillin production is a common feature of p.nalgiovense	p. 17
2.3 Heterologous Gene Expression in P. nalgiovense	p. 20
2.4 Heterologous Gene Expression in P. nalgiovense 2.4 Cloning of genes from P. Nalgiovense important for the fermentation process	p. 21
3. Penicillium camemberti	p. 23
4. Penicillium roqueforti	p. 25
5. Conclusions	p. 27
References	p. 27
Starters for the Wine Industry	p. 31
Abstract	p. 31
1. Introduction	p. 31
2. Yeast starters in winemaking	p. 32
2.1 The objectives of yeast starters	p. 32
2.2 Properties of yeast used as selective criteria for active dry yeast producers and winemakers	p. 34
2.3 Evaluation of the settlement of active dry yeast during alcoholic fermentation	p. 37
3. Malolactic starters in winemaking	p. 38
3.1 Indications for use of malolactic starter and description	p. 39
3.2 The influence of lactic acid bacteria starters on wine quality and their selection	p. 41
3.3 Efficiency of malolactic starters	p. 42
4. The future of starters for winemaking	p. 43
5. Conclusion	p. 45
References	p. 45
Part 2 Physiology, Biosynthesis and Metabolic Engineering	p. 49
Metabolism and Lysine Biosynthesis Control in Brevibacterium Flavum: Impact of Stringent Response in Bacterial Cells	p. 51
Abstract	p. 51
1. Introduction	p. 51
2. Materials and Methods	p. 52
3. Results and Discussion	p. 52
4. Conclusions	p. 56
References	p. 57
Molecular Breeding of Arming Yeasts with Hydrolytic Enzymes by Cell Surface Engineering	p. 59
Abstract	p. 59
1. Introduction	p. 60
2. Principle of Cell Surface Engineering of Yeast	p. 63
3. Display of Amylolytic Enzymes on the Yeast Cell Surface	p. 65
4. Display of Cellulolytic Enzymes on the Yeast Cell Surface	p. 67
5. Display of Lipase on the Yeast Cell Surface	p. 70
6. Cell Surface Engineering as a Novel Field of Biotechnology	p. 70
References	p. 71
Metabolic Pathway Analysis of Saccharomyces Cerevisiae	p. 75
Abstract	p. 75
1. Introduction	p. 75
2. Metabolic pathway analysis	p. 76
2.1. Metabolic control analysis	p. 76
2.2. Metabolic flux analysis	p. 77
3. Steady-state continuous cultivation - an excellent tool for metabolic pathway analysis	p. 79
4. Metabolic pathway analysis applied to Saccharomyces cerevisiae	p. 80
4.1. Kinetic studies of the glycolysis	p. 80
4.2. Metabolic pathway analysis of the galactose metabolism	p. 81
Acknowledgements	p. 85
References	p. 85
Part 3 State Parameters and Culture Conditions	p. 87
Effect of Aeration in Propagation on Surface Properties of Brewers' Yeast	p. 89
Abstract	p. 89
1. Introduction	p. 89
2. Materials and Methods	p. 90
2.1 Propagation conditions	p. 90
2.2 Hydrophobicity	p. 90
2.3 Surface charge	p. 91
2.4 Flocculation	p. 92
3. Results	p. 92
3.1 Yield coefficients	p. 92
3.2 Cell growth rates	p. 92
3.3 Hydrophobicity	p. 93
3.4 Zeta potential	p. 94
3.5 Flocculation	p. 95
4. Discussion	p. 96
5. Conclusions	p. 98
Acknowledgements	p. 98
References	p. 99
Effect of the Main Culture Parameters on the Growth and Production Coupling of Lactic Acid Bacteria	p. 101
Abstract	p. 101
1. Introduction	p. 101
2. Materials and methods	p. 102
2.1 Microorganism	p. 102
2.2 Media	p. 102
2.3 Fermentors and culture conditions	p. 102
2.4 Analytical methods	p. 103
3. Results and Discussion	p. 103
3.1. Preculture conditions	p. 103
3.2. Nutritional limitations	p. 105
3.3. Initial lactate additions	p. 106
4. Conclusions	p. 107
Acknowledgements	p. 107
References	p. 107
Pseudohyphal and Invasive Growth in Saccharomyces Cerevisiae	p. 109
Abstract	p. 109
1. Introduction	p. 109
2. Signal transduction in Saccharomyces cerevisiae	p. 110
3. Molecular nature of signal transduction processes resulting in pseudohyphal differentiation	p. 112
3.1. Signal transduction modules	p. 113
3.1.1. Nutrient availability is sensed by permeases	p. 113
3.1.2. Transmission via receptor associated elements	p. 114
3.1.3. Intermediate signal transduction modules	p. 116
3.2. Transcriptional regulators	p. 122
3.2.1. Ste12p and Tec1	p. 123
3.2.2. Msn1p and Mss11p: Central elements in the pseudohyphal growth pathway	p. 123
3.2.3. Sfl1p, Sok2p and Flo8p: Factors depending on the cAMP dependent kinase	p. 124
3.2.4. Other factors	p. 125
3.3. Effector proteins	p. 125
3.3.1. MUC1, a gene encoding a mucin-like protein subjected to complex transcriptional regulation	p. 126
3.3.2. Starch degrading enzymes: a direct metabolic link	p. 127
4. Scientific and industrial relevance	p. 127
Acknowledgements	p. 129
References	p. 129
Microbial Production of the Biodegradable Polyester Poly-3-Hydroxybutyrate (PHB) from Azotobacter Chroococcum 6B: Relation between PHB Molecular Weight, Thermal Stability and Tensile Strength	p. 135
Abstract	p. 135
1. Materials and methods	p. 135
1.1 Microorganism and culture media	p. 135
1.2 Fermentor experiments	p. 135
1.3 Extraction and purification procedure	p. 136
1.4 Analytical methods	p. 136
2. Results and discussion	p. 136
2.1 Effect of M[subscript w] on PHB thermal stability	p. 136
2.2 Effect of aeration rate on PHB M[subscript w]	p. 137
2.3 PHB tensile strength ([sigma]) at different M[subscript w]	p. 138
2.4 PHB as a matrix for microencapsulation	p. 138
3. Conclusions	p. 139
References	p. 139
Part 4 Novel Approaches to the Study of Microorganisms	p. 141
Sharing of Nutritional Resources in Bacterial Communities Determined by Isotopic Ratio Mass Spectrometry of Biomarkers	p. 143
1. Introduction	p. 143
2. Taxon specific biomarkers	p. 144
2.1. Polar lipids	p. 144
2.2. Outer membrane proteins	p. 145
3. Isotopic fractionation in microorganisms	p. 146
4. Carbon sharing in a pollutant degrading bacterial community	p. 147
4.1. Origin and characteristics of the microbial consortium	p. 147
4.2. Incorporation of [U-[superscript 13]C]-metabolites in microbial biomasses	p. 148
4.3. Substrate competition	p. 149
4.4. Community physiology of the microbial consortium	p. 150
5. Outlook	p. 152
Acknowledgement	p. 152
References	p. 152
A Comparison of the Mechanical Properties of Different Bacterial Species	p. 155
Abstract	p. 155
1. Introduction	p. 155
1.1 Relative resistance of different microorganisms to mechanical disruption	p. 155
1.2 Cell wall structure	p. 156
1.3 Bacterial biomechanics	p. 157
1.4 Micromanipulation	p. 158
2. Materials and methods	p. 158
2.1 The micromanipulation system	p. 158
2.2 Culture conditions	p. 159
3. Results and discussion	p. 160
4. Conclusions and future developments	p. 161
References	p. 162
Part 5 Novel Applications	p. 163
Kocuria Rosea as a New Feather Degrading Bacteria	p. 165
Abstract	p. 165
1. Introduction	p. 165
2. Isolation, identification and adaptation of feather-degrading microorganisms	p. 166
2.1. Isolation and degradation of feathers by a microbial isolate	p. 166
2.2. Morphological and ultrastructural characteristics of the feather-degrading isolate	p. 168
3. Microbial growth and feather degradation	p. 168
3.1. Effect of quantity of feathers	p. 168
3.2. Effect of culture temperature on feather degradation and growth of LPB-3	p. 171
3.3. Kinetic fermentation	p. 171
4. Industrial applications	p. 171
4.1. Fermented feather meal	p. 171
4.2. Enzymes	p. 173
4.3. Pigments	p. 173
Acknowledgements	p. 174
References	p. 174
Comparison of Pb[superscript 2+] Removal Characteristics Between Biomaterials and Non-Biomaterials	p. 177
Abstract	p. 177
1. Introduction	p. 177
2. Materials and methods	p. 178
2.1. Materials	p. 178
2.2. Microorganisms and culture conditions	p. 178
2.3. Pb[superscript 2+] removal experiment	p. 178
3. Results and discussion	p. 179
3.1. Pb[superscript 2+] removal characteristics	p. 179
3.2. Initial Pb[superscript 2+] removal rate	p. 182
4. Conclusions	p. 183
References	p. 183
Hydrocarbon Utilisation by Streptomyces Soil Bacteria	p. 185
Abstract	p. 185
1. Materials and methods	p. 185
1.1 Test organisms. oligocarbophylic streptomyces	p. 185
1.2 Biomass preparation	p. 186
1.3 Incorporation of radioactivity from labelled n-Hexadecane into mycelia	p. 186
1.4 Fluorescence measurements	p. 186
1.5 Analysis of fatty acids	p. 187
1.6 Investigations with GTP analogues	p. 187
2. Results and discussion	p. 187
3. Conclusion	p. 190
References	p. 190
Part 6 Food Security and Food Preservation	p. 191
Molecular Detection and Typing of Foodborne Bacterial Pathogens: a Review	p. 193
Abstract	p. 193
1. Introduction	p. 194
2. Characteristics of the foodborne bacterial pathogens	p. 194
3. Molecular detection and identification of foodborne bacterial pathogens	p. 198
3.1 Nucleic acid based identification methods	p. 198
3.2 The use of virulence genes as target for molecular identification	p. 198
3.3 The use of RRNA genes as target for molecular identification	p. 199
3.4 The use of specific sequences with a known or unknown function as target for molecular identification	p. 200
3.5 The available molecular identification systems	p. 201
3.6 PCR detection of bacterial pathogens in food products	p. 203
3.6.1 Influence of food components on PCR performance	p. 203
3.6.2 Sensitivity and contamination of PCR	p. 203
3.6.3 The detection of the viability of cells by DNA based technology	p. 204
3.7 Evaluation and validation of DNA based methods	p. 205
3.8 DNA amplification methods for quantification of foodborne pathogens	p. 207
4. Molecular typing of foodborne bacterial pathogens	p. 208
4.1 Terminology and general information	p. 208
4.1.1 Necessity of bacterial typing of foodborne pathogens	p. 208
4.1.2 Species-subspecies-variety-clone-strain-isolate	p. 209
4.1.3 Molecular typing techniques used for bacterial pathogens	p. 210
4.1.4 Analysis of DNA fingerprints	p. 219
4.2 Prospects in molecular typing	p. 220
5. Molecular typing of some specific bacterial foodborne pathogens	p. 221
5.1 Salmonella	p. 221
5.2 Campylobacter jejuni	p. 226
5.3 Listeria monocytogenes	p. 227
5.4 Escherichia coli 0157	p. 228
5.5 Some other foodborne bacterial pathogens	p. 229
References	p. 229
Bioencapsulation Technology in Meat Preservation	p. 239
Abstract	p. 239
1. Introduction	p. 240
2. Meat preservation	p. 241
2.1 Biological fermentation	p. 241
2.2 Chemical acidification	p. 243
3. The application of encapsulation technology to meat preservation	p. 243
3.1 The application of encapsulation technology to a microbial fermentation	p. 243
3.1.1. Encapsulation matrices and the encapsulation process	p. 244
3.1.2. The benefits of meat starter culture encapsulation	p. 246
3.1.3. Commercial applications	p. 247
3.2 The application of encapsulation technology to chemical acidification	p. 248
3.2.1. Encapsulation matrices and the encapsulation process	p. 248
3.2.2. The benefits of acidulant encapsulation	p. 249
3.2.3 Commercial availability	p. 249
4. Control of emerging pathogens	p. 250
5. The application of encapsulation technology to bacteriocin delivery	p. 251
5.1 Bacteriocins	p. 251
5.2 Nisin	p. 251
5.2.1 Encapsulation of nisin	p. 252
6. Conclusions and future work	p. 261
References	p. 261
Index	p. 267

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