Nannipieri / Smalla Nucleic Acids and Proteins in Soil

1. Auflage 2006
ISBN: 978-3-540-29449-8
Verlag: Springer Berlin Heidelberg
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band 8, 458 Seiten

Reihe: Soil Biology

With millions of different bacterial species living in soil, the microbial community is extremely complex, varying at very small scales. Microbe-driven functions are essential for most processes in soil. Thus, a better understanding of this microbial diversity will be invaluable for the management of the various soil functions. Nucleic Acids and Proteins in Soil combines traditional approaches in soil microbiology and biochemistry with the latest techniques in molecular microbial ecology. Included are methods to analyse the presence and importance of nucleic acids and proteins both inside and outside microbial cells, the horizontal gene transfer which drives bacterial diversity, as well as soil proteomes. Further chapters describe techniques such as PCR, fingerprinting, the challenging use of gene arrays for structural and functional analysis, stable isotope probing to identify in situ metabolic functions, and the use of marker and reporter genes in soil microbial ecology.

Autoren/Hrsg.

Nannipieri, Paolo

Smalla, Kornelia

Inhaltsverzeichnis

1;Preface;6
2;Contents;9
3;Contributors;18
4;New Frontiers in Soil Microbiology: How To Link Structure and Function of Microbial Communities?;23
4.1;1.1 Introduction: A Framework for the Structure–Function Grand Challenge;23
4.2;1.2 Microbial Community Structure: One- Half of the Structure– Function Paradigm;25
4.3;1.3 The Other One-Half: Functional Traits of Microbial Communities;28
4.4;1.4 Newer Approaches for Linking Function with Phylogeny and Structure;31
4.5;1.5 Future Challenges;34
4.6;References;39
5;Chemical Structure of Organic N and Organic P in Soil;45
5.1;2.1 Introduction;45
5.2;2.2 Biological Forms of Organic N and P That Enter Soils;46
5.3;2.3 Techniques To Analyse Soil Organic Nitrogen;54
5.4;2.4 Forms of Organic N in Soil Organic Matter;59
5.5;2.5 Techniques To Analyse Organic P in Soils;61
5.6;2.6 Forms of Organic P in Soils;64
5.7;2.7 Summary;65
5.8;References;65
6;Nucleic Acid Extraction from Soil;71
6.1;3.1 Introduction;71
6.2;3.2 Lysis and Extraction;73
6.3;3.3 Purification;82
6.4;3.4 RNA Extraction;84
6.5;3.5 Cell Extraction;85
6.6;References;89
7;Role of Stabilised Enzymes in Microbial Ecology and Enzyme Extraction from Soil with Potential Applications in Soil Proteomics;96
7.1;4.1 Introduction;96
7.2;4.2 Evidence for the Presence of Stabilised Enzymes in Soil;98
7.3;4.3 Extraction of Enzymes from Soil;100
7.4;4.4 The Role of Stabilised Enzymes in Soil Microbial Ecology;103
7.5;4.5 Proteomics;104
7.6;4.6 Soil Proteomics;106
7.7;4.7 Conclusions;110
7.8;References;111
8;Soil Proteomics: Extraction and Analysis of Proteins from Soils;116
8.1;5.1 Introduction;116
8.2;5.2 Rationale and Context of Soil Proteomics;117
8.3;5.3 Methodology for Soil Proteomics;120
8.4;5.4 Case Studies and Emerging Issues in Soil Proteomics;125
8.5;References;133
9;The Various Sources and the Fate of Nucleic Acids in Soil;137
9.1;6.1 Introduction;137
9.2;6.2 Release of DNA from Organisms;138
9.3;6.3 Presence of DNA in Soil;142
9.4;6.4 Distribution of Extracellular DNA in Soil;144
9.5;6.5 Persistence of DNA in Soil;146
9.6;6.6 The Extracellular Gene Pool Hypothesis;152
9.7;6.7 Conclusions;153
9.8;References;154
10;Stabilization of Extracellular DNA and Proteins by Transient Binding to Various Soil Components;160
10.1;7.1 Introduction;160
10.2;7.2 DNA Interactions with Purified Soil Components;162
10.3;7.3 Protein Interactions with Purified Soil Components;166
10.4;7.4 Interactions of DNA, Combined with Other Cellular Substances, with Pure Soil Components;167
10.5;7.5 DNA Interactions with Natural Soils;169
10.6;7.6 Protein Interactions with Natural Soils;170
10.7;7.7 Concluding Remarks;171
10.8;References;172
11;Assessing Bacterial and Fungal Community Structure in Soil Using Ribosomal RNA and Other Structural Gene Markers;177
11.1;8.1 Introduction;177
11.2;8.2 The General Choices in Molecular Analysis of Soil- Borne Microbial Communities;178
11.3;8.3 General Approaches for Microbial Community Description;185
11.4;8.4 Group-Specific Microbial Community Analyses;190
11.5;8.5 Concluding Remarks;197
11.6;References;198
12;Advances in Microarray-Based Technologies for Soil Microbial Community Analyses;207
12.1;9.1 Introduction;207
12.2;9.2 Types of Environmental Microarrays;208
12.3;9.3 Important Issues in Microarray Analysis;208
12.4;9.4 Applications of Different Formats of Microarrays;212
12.5;9.5 Conclusions and Future Perspectives;218
12.6;References;219
13;Stable Isotope Probing: A Critique of Its Role in Linking Phylogeny and Function;222
13.1;10.1 Introduction;222
13.2;10.2 Polar Lipid Derived Fatty Acid Based Stable Isotope Probing ( PLFA- SIP);224
13.3;10.3 DNA- and RNA-Based Stable Isotope Probing (NA-SIP);225
13.4;10.4 Alternative Stable Isotope Based Approaches;228
13.5;10.5 Radioactive Isotope Based Approaches;229
13.6;10.6 Notes on Isotopic Enrichments;230
13.7;10.7 Conclusions;230
13.8;References;231
14;Gene Detection, Expression and Related Enzyme Activity in Soil;234
14.1;11.1 Introduction;234
14.2;11.2 Molecular Detection of Functional Genes in Soil;237
14.3;11.3 Expression of Functional Genes in Soil;252
14.4;11.4 Linking Enzyme Activity to Gene Expression;261
14.5;11.5 Conclusions;263
14.6;References;263
15;Enzyme Activities in Soil;273
15.1;12.1 Introduction;273
15.2;12.2 Type, Distribution, Location and Properties;273
15.3;12.3 Factors Affecting Soil Enzyme Activities;282
15.4;12.4 Measurement of Soil Enzyme Activities;283
15.5;12.5 Soil Functioning as Determined by Enzyme Activity;292
15.6;12.6 Effects of Land Management Practices on Soil Enzyme Activities;298
15.7;12.7 Relationship Between Enzyme Activities and Soil Physical Properties and Soil Depth;304
15.8;12.8 Effects of Transgenic Plants and Recombinant Microorganisms on Soil Enzyme Activities. The Potential Role of Rhizosphere Enzyme Activities;306
15.9;12.9 Relationship Between Enzyme Activities and Their Substrates or Products in Soil;308
15.10;12.10 Enzymes as Decontaminating Agents;309
15.11;12.11 Enzyme Activities as Indicators of the Functional Status of the Soil Community;310
15.12;12.12 Future Challenges;313
15.13;References;313
16;How to Assess the Abundance and Diversity of Mobile Genetic Elements in Soil Bacterial Communities?;328
16.1;13.1 Introduction;328
16.2;13.2 Cultivation-Dependent Techniques: MGE in Bacterial Isolates from Soil;331
16.3;13.3 Genome Sequencing of Soil Bacterial Isolates;334
16.4;13.4 Cultivation-Independent Methods;335
16.5;13.5 Conclusions;341
16.6;References;341
17;Bacterial Conjugation in Soil;346
17.1;14.1 Introduction;346
17.2;14.2 Experimental Approaches to Studying HGT via Conjugation;351
17.3;14.3 Conjugative Transfer to Total ( Potentially Non- culturable) Bacteria;357
17.4;14.4 Conclusions;362
17.5;References;364
18;Horizontal Gene Transfer by Natural Transformation in Soil Environment;369
18.1;15.1 Introduction;369
18.2;15.2 Mechanisms of Horizontal Gene Transfer;370
18.3;15.3 In Situ Regulation of Natural Transformation in Bacteria;371
18.4;15.4 Natural Transformation: An UnexpectedWidespread Gene- Transfer Mechanism in Bacteria?;372
18.5;15.5 Bacterial Competence Development in Soil;374
18.6;15.6 Gene Transfer in the Environment by Alternate Genetic Transformation- Related Mechanisms?;376
18.7;15.7 Persistence of Extracellular DNA in Soil;376
18.8;15.8 Development of Methods To Investigate Gene Transfer;377
18.9;15.9 Gene Transfer by Natural Transformation from Transgenic Plants to Bacteria – A Possible Event?;379
18.10;15.10 Concluding Remarks;380
18.11;References;380
19;Reporter Genes in Bacterial Inoculants Can Monitor Life Conditions and Functions in Soil;388
19.1;16.1 Introduction to Reporter Bacteria;388
19.2;16.2 Applications of Reporter Bacteria in Soil;392
19.3;16.3 Current and Future Trends;401
19.4;References;404
20;Reporter Gene Technology in Soil Ecology; Detection of Bioavailability and Microbial Interactions;409
20.1;17.1 Introduction;409
20.2;17.2 Reporter Genes;410
20.3;17.3 Whole-Cell Biosensors;416
20.4;17.4 Bioavailability;421
20.5;17.5 Detection of Microbial Interactions;424
20.6;17.6 Concluding Remarks;426
20.7;References;427
21;Marker Genes As Tools To Study Deliberately Released Soil Bacteria;432
21.1;18.1 Introduction: The Importance of Tagging Microbial Inoculants for Environmental Applications;432
21.2;18.2 Genetic Tools for Tagging Inoculants;433
21.3;18.3 Selective Markers;436
21.4;18.4 Luminescence and Fluorescence Markers;437
21.5;18.5 Objectives for Field Releases of Genetically Engineered Bacteria;440
21.6;18.6 Field Release of Sinorhizobium meliloti L33 and L1 – A Case Study;442
21.7;18.7 Evaluation of Strategies To Eliminate S. meliloti from Soil;448
21.8;18.8 Conclusions: Biosafety and Usefulness of Small-Scale Field Release Studies with Marker Gene- Tagged Bacteria;449
21.9;References;450
22;Subject Index;459