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Nucleic acids and proteins in soil:

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Format:	Buch
Sprache:	English
Veröffentlicht:	Berlin [u.a.] Springer 2006
Schriftenreihe:	Soil biology 8
Schlagworte:	Acides nucléiques Protéines Sols - Microbiologie Soil microbiology Enzymaktivität Proteine Bodenmikrobiologie Nucleinsäuren Bodenökologie Aufsatzsammlung
Online-Zugang:	Inhaltsverzeichnis
Beschreibung:	XXIII, 458 S. graph. Darst., Tab.
ISBN:	3540294481 9783540294481

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Datensatz im Suchindex

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adam_text	Contents 1 New Frontiers in Soil Microbiology: How To Link Structure and Function of Microbial Communities? 1 Blaž Stres, James M. liedje 1.1 Introduction: A Framework for the Structure-Function Grand Challenge... 1 1.2 Microbial Community Structure: One-Half of the Structure-Function Paradigm .................... 3 1.3 The Other One-Half: Functional Traits of Microbial Communities ....................... 6 1.4 Newer Approaches for Linking Function with Phylogeny and Structure ........................................... 9 1.5 Future Challenges ........................................................... 12 References ............................................................................. 17 2 Chemical Structure of Organic N and Organic Ρ in Soil 23 Ingrid Kögel-Knabner 2.1 Introduction .................................................................. 23 2.2 Biological Forms of Organic N and Ρ That Enter Soils .......... 24 2.2.1 Proteins and Polypeptides ..................................... 25 2.2.2 Amino Sugar Polymers ......................................... 27 2.2.3 DNA and RNA ..................................................... 28 2.2.4 Minor N-Containing Molecules .............................. 29 2.2.5 Teichoic Acids ...................................................... 29 2.2.6 Inositol Phosphates .............................................. 31 2.2.7 Phospholipids ...................................................... 31 2.3 Techniques To Analyse Soil Organic Nitrogen ..................... 32 2.3.1 Hydrolysis ........................................................... 33 2.3.2 Analytical Pyrolysis and Thermochemolysis ............ 34 2.3.3 Solid-State 15N NMR Spectroscopy .......................... 35 2.3.4 X-ray Absorption Near-Edge Structure Spectroscopy ......................................... 36 2.4 Forms of Organic Nin Soil Organic Matter ......................... 37 χ Contents 2.5 Techniques To Analyse Organic P in Soils ........................... 39 2.5.1 Sequential Extraction and Separation ...................... 40 2.5.2 ^PNMRSpectroscopy .......................................... 40 2.6 Forms of Organic Ρ in Soils .............................................. 42 2.7 Summary ....................................................................... 43 References ............................................................................. 43 3 Nucleic Acid Extraction from Soil 49 Lars R. Bakken, Åsa Frostegård 3.1 Introduction .................................................................. 49 3.2 Lysis and Extraction ........................................................ 51 3.2.1 Cell Rupture Depends on Cell Type and Growth ........ 51 3.2.2 Bead Beating, Efficiency and Bias ........................... 52 3.2.3 Grinding ............................................................. 56 3.2.4 Freeze/Thaw ........................................................ 57 3.2.5 Enzymatic Lysis ................................................... 57 3.2.6 Chemical Agents .................................................. 59 3.2.7 Extraction for Metagenome Libraries ...................... 59 3.3 Purification .................................................................... 60 3.4 RNA Extraction .............................................................. 62 3.5 Cell Extraction ............................................................... 63 3.5.1 Dispersion .......................................................... 64 3.5.2 Separation ........................................................... 65 References ............................................................................. 67 4 Role of Stabilised Enzymes in Microbial Ecology and Enzyme Extraction from Soil with Potential Applications in Soil Proteomics 75 Paolo Nannipieri 4.1 Introduction .................................................................. 75 4.2 Evidence for the Presence of Stabilised Enzymes in Soil ........ 77 4.3 Extraction of Enzymes from Soil ....................................... 79 4.4 The Role of Stabilised Enzymes in Soil Microbial Ecology ..... 82 4.5 Proteomics .................................................................... 83 4.6 Soil Proteomics .............................................................. 85 4.7 Conclusions ................................................................... 89 References ............................................................................. 90 5 Soil Proteomics: Extraction and Analysis of Proteins from Soils 95 Oladele A. Ogunseitan 5.1 Introduction .................................................................. 95 5.2 Rationale and Context of Soil Proteomics ........................... 96 Contents XI 5.3 Methodology for Soil Proteomics ...................................... 99 5.3.1 Extraction Methods .............................................. 99 5.3.2 Analytical Methods ..............................................101 5.4 Case Studies and Emerging Issues in Soil Proteomics ...........104 5.4.1 Glomalin .............................................................105 5.4.2 Soil Proteins as Metal Biosensors ............................108 5.4.3 Prospects for Proteomic Analysis of Soil Microbial Communities ...............................110 References .............................................................................112 6 The Various Sources and the Fate of Nucleic Acids in Soil 117 Wilfried Wackernagel 6.1 Introduction ..................................................................117 6.2 Release of DNA from Organisms .......................................118 6.2.1 Bacteria ..............................................................118 6.2.2 Plants .................................................................119 6.2.3 Other Organisms ..................................................121 6.3 Presence of DNA in Soil ...................................................122 6.4 Distribution of Extracellular DNA in Soil ...........................124 6.4.1 The Binding of DNA to Soils ..................................124 6.4.2 The Distribution of DNA to Liquid and Solid Soil Phases ............................................125 6.5 Persistence of DNA in Soil ................................................126 6.5.1 Protection of Mineral-Associated DNA against DNases 126 6.5.2 Degradation Kinetics of Introduced DNA in Soil .......128 6.5.3 Methods to Assay the Persistence of Functional DNA in Soils ....................................129 6.5.4 Persistence and Spread of Plant DNA in Agricultural Field Plots ......................................130 6.5.5 Long-Term Field Persistence of Plant DNA in Cellular Material or as Free DNA.........................131 6.6 The Extracellular Gene Pool Hypothesis .............................132 6.7 Conclusions ...................................................................133 References .............................................................................134 7 Stabilization of Extracellular DNA and Proteins by Transient Binding to Various Soil Components 141 Kaare M. Nielsen, Luca Calamai, Giacomo Pietramellara 7.1 Introduction ..................................................................141 7.2 DNA Interactions with Purified Soil Components ................143 7.2.1 DNA Interactions with Sand ..................................143 7.2.2 DNA Interactions with Clay Minerals ......................143 XII Contents 7.2.3 Natural Transformation of Bacteria with DNA Adsorbed or Bound to Clays ....................145 7.2.4 DNA Interactions with Humic Substances ................146 7.2.5 Natural Transformation in the Presence of Humic Substances .............................................146 7.3 Protein Interactions with Purified Soil Components .............147 7.3.1 Protein Interactions with Clay Minerals ...................147 7.3.2 Protein Interactions with Humic Substances ............148 7.4 Interactions of DNA, Combined with Other Cellular Substances, with Pure Soil Components .............................148 7.4.1 DNA-Protein Interactions .....................................149 7.4.2 Adsorption of DNA-Protein Complexes on Different Soil Components ................................149 7.5 DNA Interactions with Natural Soils ..................................150 7.6 Protein Interactions with Natural Soils ...............................151 7.7 Concluding Remarks .......................................................152 References .............................................................................153 8 Assessing Bacterial and Fungal Community Structure in Soil Using Ribosomal RNA and Other Structural Gene Markers 159 George A. Kowalchuk, Barbara Drigo, Etienne Yergeau, Johannes A. van Veen 8.1 Introduction ..................................................................159 8.2 The General Choices in Molecular Analysis of Soil-Borne Microbial Communities ................................160 8.2.1 Community Structure Versus Diversity ...................161 8.2.2 The Benefits and Limitations of PCR-Based Approaches .....................................163 8.2.3 DNA Versus RNA Targets .......................................164 8.2.4 Cloning Inventories Versus Community Profiling Methods .................................................165 8.3 General Approaches for Microbial Community Description .. 167 8.3.1 The rRNA Approach .............................................167 8.3.2 Other General Markers for In Situ Determinations of Microbial Community Structure .........................170 8.4 Group-Specific Microbial Community Analyses ..................172 8.4.1 rRNA Approaches Focused on Specific Phylogenetic Groups .............................173 8.4.2 Specific Approaches Based on Specialised Functional Genes .............................177 8.5 Concluding Remarks .......................................................179 References .............................................................................180 Contents XIII 9 Advances in Microarray-Based Technologies for Soil Microbial Community Analyses 189 Christopher W. Schadt, JizhongZhou 9.1 Introduction ..................................................................189 9.2 Types of Environmental Microarrays .................................190 9.3 Important Issues in Microarray Analysis ............................190 9.3.1 Specificity ...........................................................190 9.3.2 Sensitivity ...........................................................192 9.3.3 Quantitation ........................................................193 9.4 Applications of Different Formats of Microarrays ................194 9.4.1 Phylogenetic Oligonucleotide Arrays (POAs) ......................................................194 9.4.2 Functional Gene Arrays (FGAs) ..............................196 9.4.3 Community Genome Arrays (CG As) .......................197 9.5 Conclusions and Future Perspectives .................................200 References .............................................................................201 10 Stable Isotope Probing: A Critique of Its Role in Linking Phylogeny and Function 205 Mike Manefield, Robert I. Griffiths, Mark J. Bailey, Andrew S. Whiteley 10.1 Introduction ..................................................................205 10.2 Polar Lipid Derived Fatty Acid Based Stable Isotope Probing (PLFA-SIP) ....................................................................207 10.3 DNA- and RNA-Based Stable Isotope Probing (NA-SIP) ........208 10.4 Alternative Stable Isotope Based Approaches ......................211 10.5 Radioactive Isotope Based Approaches ..............................212 10.6 Notes on Isotopie Enrichments .........................................213 10.7 Conclusions ...................................................................213 References .............................................................................214 11 Gene Detection, Expression and Related Enzyme Activity in Soil 217 Martin Krsek, William H. Gaze,N.Z. Morris,Elizabeth M.H. Wellington 11.1 Introduction ..................................................................217 11.2 Molecular Detection of Functional Genes in Soil .................220 11.2.1 Introduction ........................................................220 11.2.2 Antibiotic Biosynthesis Genes ................................222 11.2.3 Detection of Antibiotic and Heavy Metal Resistance Genes ..................................................224 11.2.4 Nutrient Cycle Genes; the Nitrogen Cycle .................227 11.2.5 Biodegradation of Soil Polymers and Cl Compounds 228 11.2.6 Bioremediation Activity ........................................230 XIV Contents 11.2.7 Molecular Detection of Functional Gene Signatures for Detecting Pathogens in Soil ...............................232 11.3 Expression of Functional Genes in Soil ...............................235 11.3.1 Introduction - Methods for the Detection ofmRNAinSoil ...................................................235 11.4 Linking Enzyme Activity to Gene Expression ......................244 11.4.1 Introduction ........................................................244 11.4.2 Decomposer Activity and Bioremediation ................244 11.5 Conclusions ...................................................................246 References .............................................................................246 12 Enzyme Activities in Soil 257 Liliana Gianfreda, Pacifico Ruggiero 12.1 Introduction ..................................................................257 12.2 Type, Distribution, Location and Properties .......................257 12.3 Factors Affecting Soil Enzyme Activities ............................266 12.4 Measurement of Soil Enzyme Activities ..............................267 12.5 Soil Functioning as Determined by Enzyme Activity ............276 12.5.1 Degradation of Litter and Enzyme Activities in Forest Soil .......................................................276 12.5.2 Effect of pH.........................................................278 12.5.3 Effect of Stresses ..................................................278 12.6 Effects of Land Management Practices on Soil Enzyme Activities .................................................282 12.6.1 Nitrogen Fertilisation ...........................................282 12.6.2 Organic Amendments ...........................................284 12.6.3 Tillage, Cropping and Other Managements ..............286 12.7 Relationship Between Enzyme Activities and Soil Physical Properties and Soil Depth ........................288 12.7.1 Distribution of Enzyme Activities with Soil Particles .................................................288 12.8 Effects of Transgenic Plants and Recombinant Microorganisms on Soil Enzyme Activities. The Potential Role of Rhizosphere Enzyme Activities ...........290 12.9 Relationship Between Enzyme Activities and Their Substrates or Products in Soil .............................292 12.10 Enzymes as Decontaminating Agents .................................293 12.11 Enzyme Activities as Indicators of the Functional Status of the Soil Community .....................................................294 12.12 Future Challenges ...........................................................297 References .............................................................................297 Contents XV 13 How to Assess the Abundance and Diversity of Mobile Genetic Elements (MGE) in Soil Bacterial Communities? 313 Kornelia Smalla, Holger Heuer 13.1 Introduction ..................................................................313 13.2 Cultivation-Dependent Techniques: MGE in Bacterial Isolates from Soil ...................................316 13.2.1 Plasmids Detected in Soil Bacteria by Plasmid Isolation .............................................316 13.2.2 MGE Detected in Soil Bacteria by Probing or PCR .....317 13.2.3 Sequencing of MGE in Bacterial Isolates Allows Insight into MGE-Encoded Traits and Their Evolution ..............................................318 13.3 Genome Sequencing of Soil Bacterial Isolates ......................319 13.4 Cultivation-Independent Methods .....................................320 13.4.1 Microscopic Detection of Phages ............................320 13.4.2 Capturing of MGE by Exogenous Isolation in Biparental and Triparental Matings .....................321 13.4.3 PCR-Based Detection of MGE ................................325 13.5 Conclusions ...................................................................326 References .............................................................................326 14 Bacterial Conjugation in Soil 331 Jan Dirk van Elsas, Sarah Turner, Jack T. Trevors 14.1 Introduction ..................................................................331 14.2 Experimental Approaches to Studying HGT via Conjugation. 336 14.2.1 Conjugation Systems ............................................336 14.2.2 Soil Microcosm Versus Field Studies .......................337 14.2.3 What Did We Learn from Donor-to-Recipient Gene Transfer Studies? ..............338 14.2.4 What Did We Learn from Donor-to-Indigenous-Bacteria Transfer Studies? .......340 14.3 Conjugative Transfer to Total (Potentially Non-culturable) Bacteria .................................342 14.3.1 What Did We Learn from Studies on In Situ Conjugative Gene Transfer? .....................342 14.3.2 What Did We Learn from Sequence Analyses of Soil/Phytosphere Bacteria? .................................343 14.4 Conclusions ...................................................................347 References .............................................................................349 XVI Contents 15 Horizontal Gene Transfer by Natural Transformation in Soil Environment 355 Anne Mercier, Elisabeth Kay, Pascal Simonét 15.1 Introduction ..................................................................355 15.2 Mechanisms of Horizontal Gene Transfer ...........................356 15.3 In Situ Regulation of Natural Transformation in Bacteria ......357 15.4 Natural Transformation: An Unexpected Widespread Gene-Transfer Mechanism in Bacteria? ..............................358 15.5 Bacterial Competence Development in Soil .........................360 15.6 Gene Transfer in the Environment by Alternate Genetic Transformation-Related Mechanisms? ...............................362 15.7 Persistence of Extracellular DNA in Soil .............................362 15.8 Development of Methods To Investigate Gene Transfer .........363 15.9 Gene Transfer by Natural Transformation from Transgenic Plants to Bacteria - A Possible Event? .........365 15.10 Concluding Remarks .......................................................366 References .............................................................................366 16 Reporter Genes in Bacterial Inoculants Can Monitor Life Conditions and Functions in Soil 375 Jan Serensen, Ole Nybroe 16.1 Introduction to Reporter Bacteria .....................................375 16.2 Applications of Reporter Bacteria in Soil ............................379 16.2.1 Non-specific Reporters of Metabolic Activity ............379 16.2.2 Semi-specific Reporters of Stress ............................380 16.2.3 Reporters of Bacterial Growth (Ribosome Synthesis). 381 16.2.4 Reporters of Nutrient Limitation ............................382 16.2.5 Reporters for Specific Carbon and Nitrogen Sources.. 383 16.2.6 Reporters for Oxygen Limitation (Anaerobiosis) .......384 16.2.7 Reporters of Aromatics and Their Degradation .........384 16.3 Current and Future Trends ...............................................388 References .............................................................................391 17 Reporter Gene Technology in Soil Ecology; Detection of Bioavailability and Microbial Interactions 397 Mette Burmelle, Lars Hestbjerg Hansen, Soren J. S0rensen 17.1 Introduction ..................................................................397 17.2 Reporter Genes ...............................................................398 17.2.1 Reporter Genes Encoding Luciferases ......................398 17.2.2 Reporter Genes Based on Chromogenic Detection .... 400 17.2.3 Reporter Genes Encoding Fluorescence ...................401 17.2.4 Reporter Genes Encoding Ice-Nudeation Activity .....404 Contents XVII 17.3 Whole-Cell Biosensors .....................................................404 17.4 Bioavailability ................................................................409 17.4.1 Use of Biosensors To Measure Bioavailability of Metals in Soil ...................................................410 17.4.2 In Situ Versus Extract Measurements of Bioavailability ..................................................411 17.5 Detection of Microbial Interactions ...................................412 17.5.1 Production of Oxytetracycline ................................412 17.5.2 Production of Communication Signals ....................413 17.6 Concluding Remarks .......................................................414 References .............................................................................415 18 Marker Genes As Tools To Study Deliberately Released Soil Bacteria 421 Christoph С. Tebbe, Rona Miethling-Graff 18.1 Introduction: The Importance of Tagging Microbial Inoculants for Environmental Applications ..........421 18.2 Genetic Tools for Tagging Inoculants .................................422 18.3 Selective Markers ............................................................425 18.4 Luminescence and Fluorescence Markers ...........................426 18.5 Objectives for Field Releases of Genetically Engineered Bacteria ....................................429 18.6 Field Release of Sinorhizobium meliloti L33 and LI - A Case Study ..................................................................431 18.7 Evaluation of Strategies To Eliminate S. meliloti from Soil .....437 18.8 Conclusions: Biosafety and Usefulness of Small-Scale Field Release Studies with Marker Gene-Tagged Bacteria ......438 References .............................................................................439 Subject Index 449
adam_txt	Contents 1 New Frontiers in Soil Microbiology: How To Link Structure and Function of Microbial Communities? 1 Blaž Stres, James M. liedje 1.1 Introduction: A Framework for the Structure-Function Grand Challenge. 1 1.2 Microbial Community Structure: One-Half of the Structure-Function Paradigm . 3 1.3 The Other One-Half: Functional Traits of Microbial Communities . 6 1.4 Newer Approaches for Linking Function with Phylogeny and Structure . 9 1.5 Future Challenges . 12 References . 17 2 Chemical Structure of Organic N and Organic Ρ in Soil 23 Ingrid Kögel-Knabner 2.1 Introduction . 23 2.2 Biological Forms of Organic N and Ρ That Enter Soils . 24 2.2.1 Proteins and Polypeptides . 25 2.2.2 Amino Sugar Polymers . 27 2.2.3 DNA and RNA . 28 2.2.4 Minor N-Containing Molecules . 29 2.2.5 Teichoic Acids . 29 2.2.6 Inositol Phosphates . 31 2.2.7 Phospholipids . 31 2.3 Techniques To Analyse Soil Organic Nitrogen . 32 2.3.1 Hydrolysis . 33 2.3.2 Analytical Pyrolysis and Thermochemolysis . 34 2.3.3 Solid-State 15N NMR Spectroscopy . 35 2.3.4 X-ray Absorption Near-Edge Structure Spectroscopy . 36 2.4 Forms of Organic Nin Soil Organic Matter . 37 χ Contents 2.5 Techniques To Analyse Organic P in Soils . 39 2.5.1 Sequential Extraction and Separation . 40 2.5.2 ^PNMRSpectroscopy . 40 2.6 Forms of Organic Ρ in Soils . 42 2.7 Summary . 43 References . 43 3 Nucleic Acid Extraction from Soil 49 Lars R. Bakken, Åsa Frostegård 3.1 Introduction . 49 3.2 Lysis and Extraction . 51 3.2.1 Cell Rupture Depends on Cell Type and Growth . 51 3.2.2 Bead Beating, Efficiency and Bias . 52 3.2.3 Grinding . 56 3.2.4 Freeze/Thaw . 57 3.2.5 Enzymatic Lysis . 57 3.2.6 Chemical Agents . 59 3.2.7 Extraction for Metagenome Libraries . 59 3.3 Purification . 60 3.4 RNA Extraction . 62 3.5 Cell Extraction . 63 3.5.1 Dispersion . 64 3.5.2 Separation . 65 References . 67 4 Role of Stabilised Enzymes in Microbial Ecology and Enzyme Extraction from Soil with Potential Applications in Soil Proteomics 75 Paolo Nannipieri 4.1 Introduction . 75 4.2 Evidence for the Presence of Stabilised Enzymes in Soil . 77 4.3 Extraction of Enzymes from Soil . 79 4.4 The Role of Stabilised Enzymes in Soil Microbial Ecology . 82 4.5 Proteomics . 83 4.6 Soil Proteomics . 85 4.7 Conclusions . 89 References . 90 5 Soil Proteomics: Extraction and Analysis of Proteins from Soils 95 Oladele A. Ogunseitan 5.1 Introduction . 95 5.2 Rationale and Context of Soil Proteomics . 96 Contents XI 5.3 Methodology for Soil Proteomics . 99 5.3.1 Extraction Methods . 99 5.3.2 Analytical Methods .101 5.4 Case Studies and Emerging Issues in Soil Proteomics .104 5.4.1 Glomalin .105 5.4.2 Soil Proteins as Metal Biosensors .108 5.4.3 Prospects for Proteomic Analysis of Soil Microbial Communities .110 References .112 6 The Various Sources and the Fate of Nucleic Acids in Soil 117 Wilfried Wackernagel 6.1 Introduction .117 6.2 Release of DNA from Organisms .118 6.2.1 Bacteria .118 6.2.2 Plants .119 6.2.3 Other Organisms .121 6.3 Presence of DNA in Soil .122 6.4 Distribution of Extracellular DNA in Soil .124 6.4.1 The Binding of DNA to Soils .124 6.4.2 The Distribution of DNA to Liquid and Solid Soil Phases .125 6.5 Persistence of DNA in Soil .126 6.5.1 Protection of Mineral-Associated DNA against DNases 126 6.5.2 Degradation Kinetics of Introduced DNA in Soil .128 6.5.3 Methods to Assay the Persistence of Functional DNA in Soils .129 6.5.4 Persistence and Spread of Plant DNA in Agricultural Field Plots .130 6.5.5 Long-Term Field Persistence of Plant DNA in Cellular Material or as Free DNA.131 6.6 The Extracellular Gene Pool Hypothesis .132 6.7 Conclusions .133 References .134 7 Stabilization of Extracellular DNA and Proteins by Transient Binding to Various Soil Components 141 Kaare M. Nielsen, Luca Calamai, Giacomo Pietramellara 7.1 Introduction .141 7.2 DNA Interactions with Purified Soil Components .143 7.2.1 DNA Interactions with Sand .143 7.2.2 DNA Interactions with Clay Minerals .143 XII Contents 7.2.3 Natural Transformation of Bacteria with DNA Adsorbed or Bound to Clays .145 7.2.4 DNA Interactions with Humic Substances .146 7.2.5 Natural Transformation in the Presence of Humic Substances .146 7.3 Protein Interactions with Purified Soil Components .147 7.3.1 Protein Interactions with Clay Minerals .147 7.3.2 Protein Interactions with Humic Substances .148 7.4 Interactions of DNA, Combined with Other Cellular Substances, with Pure Soil Components .148 7.4.1 DNA-Protein Interactions .149 7.4.2 Adsorption of DNA-Protein Complexes on Different Soil Components .149 7.5 DNA Interactions with Natural Soils .150 7.6 Protein Interactions with Natural Soils .151 7.7 Concluding Remarks .152 References .153 8 Assessing Bacterial and Fungal Community Structure in Soil Using Ribosomal RNA and Other Structural Gene Markers 159 George A. Kowalchuk, Barbara Drigo, Etienne Yergeau, Johannes A. van Veen 8.1 Introduction .159 8.2 The General Choices in Molecular Analysis of Soil-Borne Microbial Communities .160 8.2.1 Community Structure Versus Diversity .161 8.2.2 The Benefits and Limitations of PCR-Based Approaches .163 8.2.3 DNA Versus RNA Targets .164 8.2.4 Cloning Inventories Versus Community Profiling Methods .165 8.3 General Approaches for Microbial Community Description . 167 8.3.1 The rRNA Approach .167 8.3.2 Other General Markers for In Situ Determinations of Microbial Community Structure .170 8.4 Group-Specific Microbial Community Analyses .172 8.4.1 rRNA Approaches Focused on Specific Phylogenetic Groups .173 8.4.2 Specific Approaches Based on Specialised Functional Genes .177 8.5 Concluding Remarks .179 References .180 Contents XIII 9 Advances in Microarray-Based Technologies for Soil Microbial Community Analyses 189 Christopher W. Schadt, JizhongZhou 9.1 Introduction .189 9.2 Types of Environmental Microarrays .190 9.3 Important Issues in Microarray Analysis .190 9.3.1 Specificity .190 9.3.2 Sensitivity .192 9.3.3 Quantitation .193 9.4 Applications of Different Formats of Microarrays .194 9.4.1 Phylogenetic Oligonucleotide Arrays (POAs) .194 9.4.2 Functional Gene Arrays (FGAs) .196 9.4.3 Community Genome Arrays (CG As) .197 9.5 Conclusions and Future Perspectives .200 References .201 10 Stable Isotope Probing: A Critique of Its Role in Linking Phylogeny and Function 205 Mike Manefield, Robert I. Griffiths, Mark J. Bailey, Andrew S. Whiteley 10.1 Introduction .205 10.2 Polar Lipid Derived Fatty Acid Based Stable Isotope Probing (PLFA-SIP) .207 10.3 DNA- and RNA-Based Stable Isotope Probing (NA-SIP) .208 10.4 Alternative Stable Isotope Based Approaches .211 10.5 Radioactive Isotope Based Approaches .212 10.6 Notes on Isotopie Enrichments .213 10.7 Conclusions .213 References .214 11 Gene Detection, Expression and Related Enzyme Activity in Soil 217 Martin Krsek, William H. Gaze,N.Z. Morris,Elizabeth M.H. Wellington 11.1 Introduction .217 11.2 Molecular Detection of Functional Genes in Soil .220 11.2.1 Introduction .220 11.2.2 Antibiotic Biosynthesis Genes .222 11.2.3 Detection of Antibiotic and Heavy Metal Resistance Genes .224 11.2.4 Nutrient Cycle Genes; the Nitrogen Cycle .227 11.2.5 Biodegradation of Soil Polymers and Cl Compounds 228 11.2.6 Bioremediation Activity .230 XIV Contents 11.2.7 Molecular Detection of Functional Gene Signatures for Detecting Pathogens in Soil .232 11.3 Expression of Functional Genes in Soil .235 11.3.1 Introduction - Methods for the Detection ofmRNAinSoil .235 11.4 Linking Enzyme Activity to Gene Expression .244 11.4.1 Introduction .244 11.4.2 Decomposer Activity and Bioremediation .244 11.5 Conclusions .246 References .246 12 Enzyme Activities in Soil 257 Liliana Gianfreda, Pacifico Ruggiero 12.1 Introduction .257 12.2 Type, Distribution, Location and Properties .257 12.3 Factors Affecting Soil Enzyme Activities .266 12.4 Measurement of Soil Enzyme Activities .267 12.5 Soil Functioning as Determined by Enzyme Activity .276 12.5.1 Degradation of Litter and Enzyme Activities in Forest Soil .276 12.5.2 Effect of pH.278 12.5.3 Effect of Stresses .278 12.6 Effects of Land Management Practices on Soil Enzyme Activities .282 12.6.1 Nitrogen Fertilisation .282 12.6.2 Organic Amendments .284 12.6.3 Tillage, Cropping and Other Managements .286 12.7 Relationship Between Enzyme Activities and Soil Physical Properties and Soil Depth .288 12.7.1 Distribution of Enzyme Activities with Soil Particles .288 12.8 Effects of Transgenic Plants and Recombinant Microorganisms on Soil Enzyme Activities. The Potential Role of Rhizosphere Enzyme Activities .290 12.9 Relationship Between Enzyme Activities and Their Substrates or Products in Soil .292 12.10 Enzymes as Decontaminating Agents .293 12.11 Enzyme Activities as Indicators of the Functional Status of the Soil Community .294 12.12 Future Challenges .297 References .297 Contents XV 13 How to Assess the Abundance and Diversity of Mobile Genetic Elements (MGE) in Soil Bacterial Communities? 313 Kornelia Smalla, Holger Heuer 13.1 Introduction .313 13.2 Cultivation-Dependent Techniques: MGE in Bacterial Isolates from Soil .316 13.2.1 Plasmids Detected in Soil Bacteria by Plasmid Isolation .316 13.2.2 MGE Detected in Soil Bacteria by Probing or PCR .317 13.2.3 Sequencing of MGE in Bacterial Isolates Allows Insight into MGE-Encoded Traits and Their Evolution .318 13.3 Genome Sequencing of Soil Bacterial Isolates .319 13.4 Cultivation-Independent Methods .320 13.4.1 Microscopic Detection of Phages .320 13.4.2 Capturing of MGE by Exogenous Isolation in Biparental and Triparental Matings .321 13.4.3 PCR-Based Detection of MGE .325 13.5 Conclusions .326 References .326 14 Bacterial Conjugation in Soil 331 Jan Dirk van Elsas, Sarah Turner, Jack T. Trevors 14.1 Introduction .331 14.2 Experimental Approaches to Studying HGT via Conjugation. 336 14.2.1 Conjugation Systems .336 14.2.2 Soil Microcosm Versus Field Studies .337 14.2.3 What Did We Learn from Donor-to-Recipient Gene Transfer Studies? .338 14.2.4 What Did We Learn from Donor-to-Indigenous-Bacteria Transfer Studies? .340 14.3 Conjugative Transfer to Total (Potentially Non-culturable) Bacteria .342 14.3.1 What Did We Learn from Studies on In Situ Conjugative Gene Transfer? .342 14.3.2 What Did We Learn from Sequence Analyses of Soil/Phytosphere Bacteria? .343 14.4 Conclusions .347 References .349 XVI Contents 15 Horizontal Gene Transfer by Natural Transformation in Soil Environment 355 Anne Mercier, Elisabeth Kay, Pascal Simonét 15.1 Introduction .355 15.2 Mechanisms of Horizontal Gene Transfer .356 15.3 In Situ Regulation of Natural Transformation in Bacteria .357 15.4 Natural Transformation: An Unexpected Widespread Gene-Transfer Mechanism in Bacteria? .358 15.5 Bacterial Competence Development in Soil .360 15.6 Gene Transfer in the Environment by Alternate Genetic Transformation-Related Mechanisms? .362 15.7 Persistence of Extracellular DNA in Soil .362 15.8 Development of Methods To Investigate Gene Transfer .363 15.9 Gene Transfer by Natural Transformation from Transgenic Plants to Bacteria - A Possible Event? .365 15.10 Concluding Remarks .366 References .366 16 Reporter Genes in Bacterial Inoculants Can Monitor Life Conditions and Functions in Soil 375 Jan Serensen, Ole Nybroe 16.1 Introduction to Reporter Bacteria .375 16.2 Applications of Reporter Bacteria in Soil .379 16.2.1 Non-specific Reporters of Metabolic Activity .379 16.2.2 Semi-specific Reporters of Stress .380 16.2.3 Reporters of Bacterial Growth (Ribosome Synthesis). 381 16.2.4 Reporters of Nutrient Limitation .382 16.2.5 Reporters for Specific Carbon and Nitrogen Sources. 383 16.2.6 Reporters for Oxygen Limitation (Anaerobiosis) .384 16.2.7 Reporters of Aromatics and Their Degradation .384 16.3 Current and Future Trends .388 References .391 17 Reporter Gene Technology in Soil Ecology; Detection of Bioavailability and Microbial Interactions 397 Mette Burmelle, Lars Hestbjerg Hansen, Soren J. S0rensen 17.1 Introduction .397 17.2 Reporter Genes .398 17.2.1 Reporter Genes Encoding Luciferases .398 17.2.2 Reporter Genes Based on Chromogenic Detection . 400 17.2.3 Reporter Genes Encoding Fluorescence .401 17.2.4 Reporter Genes Encoding Ice-Nudeation Activity .404 Contents XVII 17.3 Whole-Cell Biosensors .404 17.4 Bioavailability .409 17.4.1 Use of Biosensors To Measure Bioavailability of Metals in Soil .410 17.4.2 In Situ Versus Extract Measurements of Bioavailability .411 17.5 Detection of Microbial Interactions .412 17.5.1 Production of Oxytetracycline .412 17.5.2 Production of Communication Signals .413 17.6 Concluding Remarks .414 References .415 18 Marker Genes As Tools To Study Deliberately Released Soil Bacteria 421 Christoph С. Tebbe, Rona Miethling-Graff 18.1 Introduction: The Importance of Tagging Microbial Inoculants for Environmental Applications .421 18.2 Genetic Tools for Tagging Inoculants .422 18.3 Selective Markers .425 18.4 Luminescence and Fluorescence Markers .426 18.5 Objectives for Field Releases of Genetically Engineered Bacteria .429 18.6 Field Release of Sinorhizobium meliloti L33 and LI - A Case Study .431 18.7 Evaluation of Strategies To Eliminate S. meliloti from Soil .437 18.8 Conclusions: Biosafety and Usefulness of Small-Scale Field Release Studies with Marker Gene-Tagged Bacteria .438 References .439 Subject Index 449
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spelling	Nucleic acids and proteins in soil P. Nannipieri ... (eds.) Berlin [u.a.] Springer 2006 XXIII, 458 S. graph. Darst., Tab. txt rdacontent n rdamedia nc rdacarrier Soil biology 8 Acides nucléiques Protéines Sols - Microbiologie Soil microbiology Enzymaktivität (DE-588)4152470-6 gnd rswk-swf Proteine (DE-588)4076388-2 gnd rswk-swf Bodenmikrobiologie (DE-588)4659394-9 gnd rswk-swf Nucleinsäuren (DE-588)4172117-2 gnd rswk-swf Bodenökologie (DE-588)4332816-7 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Bodenökologie (DE-588)4332816-7 s Nucleinsäuren (DE-588)4172117-2 s Proteine (DE-588)4076388-2 s DE-604 Bodenmikrobiologie (DE-588)4659394-9 s Enzymaktivität (DE-588)4152470-6 s b DE-604 Nannipieri, Paolo Sonstige oth Soil biology 8 (DE-604)BV019353150 8 Digitalisierung UB Bayreuth application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014573599&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis
spellingShingle	Nucleic acids and proteins in soil Soil biology Acides nucléiques Protéines Sols - Microbiologie Soil microbiology Enzymaktivität (DE-588)4152470-6 gnd Proteine (DE-588)4076388-2 gnd Bodenmikrobiologie (DE-588)4659394-9 gnd Nucleinsäuren (DE-588)4172117-2 gnd Bodenökologie (DE-588)4332816-7 gnd
subject_GND	(DE-588)4152470-6 (DE-588)4076388-2 (DE-588)4659394-9 (DE-588)4172117-2 (DE-588)4332816-7 (DE-588)4143413-4
title	Nucleic acids and proteins in soil
title_auth	Nucleic acids and proteins in soil
title_exact_search	Nucleic acids and proteins in soil
title_exact_search_txtP	Nucleic acids and proteins in soil
title_full	Nucleic acids and proteins in soil P. Nannipieri ... (eds.)
title_fullStr	Nucleic acids and proteins in soil P. Nannipieri ... (eds.)
title_full_unstemmed	Nucleic acids and proteins in soil P. Nannipieri ... (eds.)
title_short	Nucleic acids and proteins in soil
title_sort	nucleic acids and proteins in soil
topic	Acides nucléiques Protéines Sols - Microbiologie Soil microbiology Enzymaktivität (DE-588)4152470-6 gnd Proteine (DE-588)4076388-2 gnd Bodenmikrobiologie (DE-588)4659394-9 gnd Nucleinsäuren (DE-588)4172117-2 gnd Bodenökologie (DE-588)4332816-7 gnd
topic_facet	Acides nucléiques Protéines Sols - Microbiologie Soil microbiology Enzymaktivität Proteine Bodenmikrobiologie Nucleinsäuren Bodenökologie Aufsatzsammlung
url	http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014573599&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
volume_link	(DE-604)BV019353150
work_keys_str_mv	AT nannipieripaolo nucleicacidsandproteinsinsoil

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