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第四本电子书：Nucleic Acids and Proteins in Soil
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Contents 1 New Frontiers in Soil Microbiology: How To Link Structure and Function ofMicrobial Communities? 1 Blaž Stres, James M. Tiedje 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 ofMicrobial 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 P in Soil 23 Ingrid Kögel-Knabner 2.1 Introduction .................................................................. 23 2.2 Biological Forms ofOrganicNand P 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 MinorN-ContainingMolecules .............................. 29 2.2.5 Teichoic Acids...................................................... 29 2.2.6 Inositol Phosphates .............................................. 31 2.2.7 Phospholipids...................................................... 31 2.3 Techniques To Analyse SoilOrganicNitrogen ..................... 32 2.3.1 Hydrolysis........................................................... 33 2.3.2 Analytical Pyrolysis and Thermochemolysis ............ 34 2.3.3 Solid-State 15 NNMR Spectroscopy.......................... 35 2.3.4 X-ray Absorption Near-Edge Structure Spectroscopy ......................................... 36 2.4 Forms ofOrganicNin SoilOrganicMatter ......................... 37 2.5 Techniques To AnalyseOrganic P in Soils ........................... 39 2.5.1 Sequential Extraction and Separation...................... 40 2.5.2 31 PNMR Spectroscopy.......................................... 40 2.6 Forms ofOrganic P in Soils .............................................. 42 2.7 Summary....................................................................... 43 References ............................................................................. 43 3 Nucleic Acid Extraction fromSoil 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 forMetagenome Libraries ...................... 59 3.3 Purification.................................................................... 60 3.4 RNAExtraction.............................................................. 62 3.5 Cell Extraction ............................................................... 63 3.5.1 Dispersion .......................................................... 64 3.5.2 Separation........................................................... 65 References ............................................................................. 67 4 Role of Stabilised Enzymes inMicrobial Ecology and Enzyme Extraction fromSoil 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 fromSoil....................................... 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 5.3 Methodology for Soil Proteomics ...................................... 99 5.3.1 Extraction Methods .............................................. 99 5.3.2 AnalyticalMethods .............................................. 101 5.4 Case Studies and Emerging Issues in Soil Proteomics ........... 104 5.4.1 Glomalin............................................................. 105 5.4.2 Soil Proteins asMetal Biosensors............................ 108 5.4.3 Prospects for Proteomic Analysis of SoilMicrobial 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 OtherOrganisms.................................................. 121 6.3 Presence ofDNA 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 ofDNA in Soil................................................ 126 6.5.1 Protection ofMineral-AssociatedDNAagainstDNases 126 6.5.2 DegradationKinetics of IntroducedDNA in Soil ....... 128 6.5.3 Methods to Assay the Persistence of FunctionalDNA 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 CellularMaterial or as FreeDNA......................... 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 Interactionswith ClayMinerals ...................... 143 7.2.3 Natural Transformation of Bacteria withDNA Adsorbed or Bound to Clays.................... 145 7.2.4 DNA InteractionswithHumic Substances................ 146 7.2.5 Natural Transformation in the Presence ofHumic Substances............................................. 146 7.3 Protein Interactions with Purified Soil Components............. 147 7.3.1 Protein Interactions with ClayMinerals................... 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 onDifferent Soil Components ................................ 149 7.5 DNA Interactions withNatural Soils .................................. 150 7.6 Protein Interactions withNatural Soils............................... 151 7.7 Concluding Remarks....................................................... 152 References ............................................................................. 153 8 Assessing Bacterial and Fungal Community Structure in Soil Using Ribosomal RNA and Other Structural GeneMarkers 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-BorneMicrobial Communities................................ 160 8.2.1 Community StructureVersusDiversity ................... 161 8.2.2 The Benefits and Limitations of PCR-BasedApproaches ..................................... 163 8.2.3 DNA Versus RNA Targets....................................... 164 8.2.4 Cloning Inventories Versus Community ProfilingMethods................................................. 165 8.3 General Approaches for Microbial Community Description .. 167 8.3.1 The rRNAApproach ............................................. 167 8.3.2 Other General Markers for In Situ Determinations ofMicrobial Community Structure ......................... 170 8.4 Group-SpecificMicrobial CommunityAnalyses .................. 172 8.4.1 rRNA Approaches Focused on Specific PhylogeneticGroups............................. 173 8.4.2 Specific Approaches Based on Specialised Functional Genes............................. 177 8.5 Concluding Remarks....................................................... 179 References ............................................................................. 180 。。。。。。。 当您的朋友需要提取此文件时只需: 匿名提取文件连接 http://pickup.mofile.com/2424782350775547 或登录Mofile，使用提取码 2424782350775547 提取文件 [search]Nucleic Acids and Proteins in Soil[/search] http://pickup.mofile.com/2424782350775547 |
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