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[资源] 第四本电子书：Nucleic Acids and Proteins in Soil

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
。。。。。。。

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