Nucleic acids and proteins in soil:
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| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Berlin [u.a.]
Springer
2006
|
| Series: | Soil biology
8 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XXIII, 458 S. graph. Darst., Tab. |
| ISBN: | 3540294481 9783540294481 |
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| 300 | |a XXIII, 458 S. |b graph. Darst., Tab. | ||
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| 490 | 1 | |a Soil biology |v 8 | |
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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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| building | Verbundindex |
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| discipline_str_mv | Biologie Agrarwissenschaft Agrar-/Forst-/Ernährungs-/Haushaltswissenschaft / Gartenbau Pflanzenbau Geographie |
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| indexdate | 2024-07-09T20:33:53Z |
| institution | BVB |
| isbn | 3540294481 9783540294481 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-014573599 |
| oclc_num | 65427444 |
| open_access_boolean | |
| owner | DE-M49 DE-BY-TUM DE-703 DE-634 DE-11 |
| owner_facet | DE-M49 DE-BY-TUM DE-703 DE-634 DE-11 |
| physical | XXIII, 458 S. graph. Darst., Tab. |
| publishDate | 2006 |
| publishDateSearch | 2006 |
| publishDateSort | 2006 |
| publisher | Springer |
| record_format | marc |
| series | Soil biology |
| series2 | Soil biology |
| 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 |