Methods in applied soil microbiology and biochemistry:
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
London [u.a.]
Academic Press
1995
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XIX, 576 S. Ill., graph. Darst. |
| ISBN: | 0125138407 |
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Record in the Search Index
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| adam_text | Contents
Contributors xvii
Chapter 1 Introduction (K Alef, P Nannipieri) 1
Chapter 2 Quality control and quality assurance in applied soil microbiology and
biochemistry 5
Quality - Project Design - Spatial Sampling 5
An introduction (K Totsche) 5
How accurate is the decision, how good is the inference drawn? 5
But what is quality? 6
From sampling to data interpretation (Project design strategies) 7
The zero step: Project design 8
The problem statement - setting up a scientific hypothesis 8
Setting up a statistical hypothesis 9
Prospecting 9
Selection and control of independent variables 9
Selection and control of dependent variables (response) 10
Setting up a statistical model (response function) 10
Setting up and conducting an experiment 10
Data processing and analysis 11
Conclusions and interpretations 11
Experimental designs and sampling strategies - principal activities 12
Randomization 12
Replication 12
Blocking 12
Error control 12
Factorial designs 17
Criteria for selecting an appropriate design 19
The missing value problem 20
Spatial sampling and analysis 20
Rigid sampling plans 21
Proportionate sampling plans 21
Non-proportionate sampling plans 22
Algorithm-orientated sampling plans 23
Mathematical and statistical tools (K Mathes, L Ries) 25
Principles for the selection of a suitable statistical analysis method 25
Analysis of univariate data gained by descriptive field sampling 28
Estimating the unknown population mean 28
Evaluation of spatial data sets 29
What is geostatistics? 29
Contents
Geostatistical analysis and spatial prediction 31
Methodolical comparison of Kriging and inverse distance weighted moving
averages (IDW and IDW + LOGRAN) 33
Time series analysis 38
Establishing differences between field sites in the univariate case 40
Introduction 40
The comparison of two means 41
The comparison of more than two means 42
Quantifying relationships between responses and predictors 42
Regression and correlation analysis in the bivariate case 42
Multiple regression and correlation 43
Structuring of multivariate data sets by descriptive and explanatory analysis 44
Introduction 44
Ordination analysis 44
Cluster analysis 44
References 46
Chapter 3 Soil sampling, handling, storage and analysis 49
Soil sampling (JC Forstet) 49
Representative sampling 49
Sampling device 50
Sample transport 50
Composite samples and subsampling 50
Storage of samples 51
Sterilization of soil and inhibition of microbial activity (K Alef) 52
Sterilization by autoclaving 52
Soil fumigation 52
Irradiation of soils 53
Inhibition of microbial activity by azide, cyanide and toluene 53
Determination of soil pH 55
Measurement of oxygen partial pressures in soil aggregates (J Zauzig) 56
Organic carbon (JC Forster) 59
Total organic carbon 59
Dissolved organic carbon 61
Composition of soil organic matter (/ Kögel-Knabner) 66
Determination of total carbohydrates 66
Characterization of the amount and degree of lignin biodégradation by CuO oxidation 69
Total amino sugars 70
Extractable lipids 72
Hydrolysable proteins 73
Physical fractionation of soil organic matter 74
Soil nitrogen (JC Forster) 79
Determination of total nitrogen 79
Inorganic nitrogen 81
Soil phosphorus (JC Forster) 38
Estimation of total phosphorus 88
Extraction of organic phosphorus 89
Extraction of labile phosphorus 89
Quantification of phosphorus in soil extracts 90
viii
Contents
31P nuclear magnetic resonance spectroscopy of soil extracts 92
Soil sulphur (JC Förster) 94
Total sulphur analysis 94
Sulphur analysis in digests, and salt or aqueous solutions 95
Sulphur analysers for total sulphur determination 96
Soil iron (JC Forstet) 97
Total iron by hydrofluoric acid digestion 97
Amorphous iron by acid ammonium oxalate 98
Iron determination by atomic absorption spectrometry 98
Iron determination by colorimetry 99
Heavy metals (JC Forster) 101
Total heavy metal contents by aqua regia digestion 101
Heavy metal speciation 102
Soil physical analysis (JC Forste/) 105
Determination of the gravimetric water content and soil dry mass 105
Determination of the soil bulk density 105
Determination of the water-holding capacity of soils 106
Determination of the soil water potential 106
Particle size analysis 108
Pretreatments 109
Sieve analysis 111
Pipette analysis 112
Hydrometer methods 112
References 116
Chapter 4 Enrichment, isolation and counting of soil microrganisms 123
Nutrients, sterilization, aerobic and anaerobic culture techniques (KAIef) 124
Nutrients 124
Sterilization of solutions and media 125
Sterilization by moist heat 125
Sterilization by dry heat 125
Sterilization by filtration 125
Sterilization by chemical treatment 126
Sterilization by irradiation 126
Aerobic culture techniques 126
Preparation of agar plates 126
Isolation of pure culture 126
Anaerobic culture technique 127
Removal of oxygen from gases 127
Preparation of anaerobic media 127
Reducing agents and redox indicators 127
Preparation of anaerobic solid media 128
Isolation of pure cultures of anaerobic bacteria 128
Enrichment of aerobic soil bacteria 129
Enrichment of physiological groups (K Alef) 130
Enrichment of cellulose-decomposing aerobic bacteria 130
Enrichment of Pseudomonaceae 130
Enrichment of oligotrophic bacteria 131
Enrichment of nitrifying bacteria 132
ix
Contents
Enrichment of denitrifying bacteria 132
Isolation and identification of aerobic nitrogen-fixing bacteria from soil and plants
(J Döbereiner) 134
Isolation and identification methods 134
Methods for isolation and identification of Azospirillum spp. 137
Isolation and identification of endophytic diazotrophs 139
Enrichment and isolation of obligate anaerobes (K Alef) 142
Enrichment of sulphate reducers 142
Enrichment of carbon dioxide reducers 142
Enrichment of cellulose-decomposing Clostridia 144
Enrichment of fungi 145
Basic methods for counting microorganisms in soil and water (HJ torch,
G Benckieser, JCG OttoW) 146
Cultural methods for enumerating soil and water organisms 147
Most probable number technique 153
Discussion 159
Microscopic methods for counting bacteria and fungi in soil (J Bloem, PR Bolhuis,
MR Veninga, J Wieringa) 162
Preparation of soil suspensions 163
Direct count of bacteria 165
Estimates of activity 170
Measurement of fungi 171
Total hyphal length 171
FDA-active fungal hyphae 172
Isolation and counting of Protozoa (SS Bamforth) 174
Sampling and microscopic examination 174
Species richness 175
Protozoa in general 175
Amoebae 175
Enumeration 176
Total Protozoa 176
Fresh direct counts for ciliates and Testacea 178
Permanent direct counts for Testacea 178
Direct count/culture estimation for ciliates 179
Isolation and counting of Cyanobacteria (S. Oran) 181
Cultivation of Cyanobacteria 181
Selected solid media for laboratory culture 181
Cultivation 182
Counting of Cyanobacteria 183
Most probable number method 183
Direct microscopy 185
References 186
Chapter 5 Estimation of microbial activities 193
Estimation of adenosine triphosphate in soils (KAIef) 194
The trichloracetic acid extraction method (KAIef) 195
The TEA/NRB method (H Van de Werf, G Genouw, W Verstraete) 198
The sulphuric acid-phosphate extraction method (K Alef) 200
The acidic phosphoric acid extraction method (C Ciardi, P Nannipien) 202
_________________________________________________________Contents
Estimation of the adenylate energy charge in soils (PC Brookes) 204
Adenylate energy charge as an indicator of microbiological activity in soils
subjected to environmental stress 208
Enzymic procedure TCA-extraction 209
HPLC procedure 212
Soil respiration (K Alef) 214
Estimation of soil respiration in closed jars 215
Estimation of soil respiration with closed bottles 216
Estimation of soil respiration in the sapromat 217
Estimation of soil respiration with the Wösthoff apparatus 218
The infrared gas analysis 218
Aerobic biodégradation of 14C-labelled organic matter in soils (K Alef) 220
Heat output (K Alef) 223
Dimethyl sulphoxide reduction (K Alef) 225
Dehydrogenase activity (K Alef) 228
The TTC method 228
The INT method 230
Estimation of the hydrolysis of fluorescein diacetate (K Alef) 232
Nitrogen mineralization in soils (KAIef) 234
Ammonification 234
Nitrification 234
Estimation of nitrogen mineralization in the laboratory 235
Estimation of the nitrogen mineralization potential of soils by the incubation leaching
method 237
Arginine ammonification 238
Estimation of the nitrification in soil 240
Assay of nitrification (short-term estimations) 241
Estimation of nitrogenase activity of free-living bacteria in soils 243
The use of 15N to study the nitrogen turnover in soils (R Brumme, G Aden) 246
Determination of nitrogen transformation rates in continuous flow systems 246
15N analysis 251
Diffusion method 252
The distillation method 254
[3H] Thymidine incorporation technique to determine soil bacterial growth rate
(H Christensen, S Christensen) 258
References 262
Chapter 6 Anaerobic microbial activities in soil 271
Sampling, transport and storage of anaerobic soils 273
Redox potential measurement (J Zauzig) 27 4
Anaerobic conditions and testing (K Alef) 277
Preparation of oxygen-free gases (K Alef) 277
Preparation of anaerobic solutions 277
Achieving anaerobic conditions and anaerobic testing 278
Assay of the anaerobic ammonification 281
Anaerobic nitrate reduction 282
Assay of dissimilatory nitrate reductase activity 283
Assay of denitrification 285
XI
Contents
Nitrate reduction in sediments and waterlogged soil measured by 15N techniques
(N Risgaard-Petersen, S Rysgaard) 287
Iron (III) reduction test (G Welp, G Brümmei) 296
Bacterial sulphate reduction in soil measured by 35SO42 radiotracer technique
(K Ingversen) 299
Anaerobic heat output (B Alters, A Hartmann, F Beesé) 304
References 307
Chapter 7 Enzyme activities 311
Protease activity (KAIef, P Nannipien) 313
Urease activity (KAIef, P Nannipien) 316
Estimation of urease activity (Tabatabai and Bremner 1972) 317
Estimation of urease activity (Kandeler and Gerber 7988) 318
Amidase activity in soils (WT Frankenberger, Jr, MA Tabatabai) 321
L-Asparaginase activity of soils (WT Frankenberger, Jr, MA Tabatabai) 325
L-Glutaminase activity of soils (WT Frankenberger, Jr, MA Tabatabai) 328
L-Histidine ammonia lyase activity (WT Frankenberger, Jr, MA Tabatabai) 331
Phosphatase activity (K Alef, P Nannipieri, C Trazar-Cepeda) 335
Phosphomonoesterase activity 336
Assay of phosphomonoesterase activity (Hoffmann 1967, modified by Beck 1984a) 336
Phosphomonoesterase activity (Tabatabai and Bremner 1969; Eivazi and
Tabatabai 1977) 338
Phosphodiesterase activity 339
Phosphotriesterase activity 341
Pyrophosphatase activity 342
Cellulase activity (K Alef, P Nannipien) 345
Assay of cellulose activity (Schinner and Von Mersi 1980) 346
Assay of cellulose activity (Hope and Burns 1989) 347
ß-glucosidase activity (K Alef, P Nannipien) 350
Assay of ß-glucosidase activity (Eivazi and Tabatabai 1988; Tabatabai 1982) 350
Assay of ß-glucosidase activity (Hoffman and Dedekan) 351
Saccharase activity (K Alef, P Nannipieri) 353
Assay of saccharase activity (Schinner and Von Mesi 1990) 353
Assay of saccharase activity (Hoffman and Pallant 1965) 354
Xylanase activity (K Alef, P Nannipieri) 356
Lipase activity (K Alef, P Nannipieri) 358
Chitinase activity (KAIef, P Nannipieri) 360
Catalase activity (K Alef, P Nannipieri) 362
Arylsulphatase activity (KAIef, P Nannipieri) 364
References 366
Chapter 8 Microbial biomass 375
The fumigation incubation method (RG Jörgensen) 376
The fumigation extraction method (RG Jörgensen) 382
Fumigation and extraction 382
Fumigation and extraction after pre-extraction 384
Microbial biomass carbon by dichromate oxidation 385
Biomass carbon by ultraviolet persulphate oxidation 386
XII
Contents
The fumigation extraction method for determining microbial biomass nitrogen
(RG Jörgensen) 388
Fumigation and extraction 388
Determination of total nitrogen extracted by potassium sulphate 388
Determination of inorganic and organic nitrogen 389
The use of the ninhydrin nitrogen reaction for determining microbial biomass nitrogen
(RG Jörgensen) 391
Fumigation and extraction 391
Determination of ninhydrin-reactive nitrogen 391
Fumigation extraction method for biomass phosphorus (RG Jörgensen) 394
The substrate-induced respiration method (GP Sparling) 397
The determination of active microbial biomass by the respiration stimulation method
(H Van de Werf, G Genouw, W Verstraete) 405
Microscopic methods (K Alef) 409
ATP content as a parameter to estimate microbial biomass (KAIef) 410
References 411
Chapter 9 Community structure 419
Differentation by selective inhibition techniques (K Alef, GP Sparling) 420
Biomarkers (L Zelles, K Alef) 422
Ergosterol 422
Estimation of ergosterol (Zelles 1987) 422
Estimation of ergosterol (Grant and West 1986) (KAIef) 424
Muramic acid (L Zelles) 424
Estimation of teichoic acid components 426
Lipopolysaccharide (lipid A) fatty acids 429
Phospholipid fatty acids 431
Diaminopimelic acid 436
Glucosamine 437
Estimation of glucosamine (Zelles 1988) 437
Estimation of glucosamine (Grant and West 1986) 438
Isolation and identification of DNA from soil (A Saano, K Lindström) 440
Isolation of DNA from soil 440
The method of Selenska and Klingmüller (1991) 440
The method of Tsau and Olson (1991) 442
The method of Picard et al (1992) 443
Methods for the characterizaton of DNA from soil 444
DNA-DNA hybridization 444
Restriction fragment length polymorphism 449
Polymerase chain reaction 450
The use of antibody techniques in soil (JWL van Vuurde, JK Van der Wolf) 452
References 458
Chapter 10 Field methods 463
Estimation of soil respiration (K Alef) 464
Measurement of CO2 evolution rates (long-term assay) 464
Measurement of CO2 evolution rates (short-term assay) 465
Measurement of CO2 and O2 concentrations at various soil depths 466
XIII
Contents
Automated monitoring of biological trace gas production and consumption (R. Brumme,
F Beese) 468
Quantification of total denitrification losses from undisturbed field soils by the acetylene
inhibition technique (G Benckieser, HJ Lorch, JCG Ottov/j 473
Lysimeter (P Burauel, W Steffen F Führ) 479
Extraction of soil solution with porous suction cups (H Deschauer) 482
Litter bag method (HA Verhoef) 485
References 488
Chapter 11 Bioremediation of Soil 491
Technical safety and guidelines (H Burmeier) 492
The problem 492
Statutory basis 492
Accidents 492
Determination of danger 493
Planning and preparing for work 493
Site equipment 494
Protective measures 497
Reclamation and regeneration measures 497
Technical protective measures 497
Protective equipment for construction machines, appliances and tools 498
Technical ventilation 498
Enclosing 498
Securing areas near the surface of contaminated sites 499
Organizational protective measures 499
Personal safety equipment 500
Personal protection 500
Respiratory protection 501
Discussion 502
Microbiological characterization of contaminated soils (K Alef) 503
Sampling, transport and storage of soil 503
Estimation of microbial activity 503
Estimation of soil respiration in the presence of substrate 503
Estimation of soil respiration in the absence of substrate 504
Quantification of microbial populations in contaminated soil 504
Basic chemical analysis in contaminated soils 506
The determination of hydrocarbon content by intrared spectroscopy (H Platen) 506
The gravimetric determination of non-volatile lipophilic substances (H Platen) 510
The gas Chromatographie analysis of BTX (benzene, toluene and xylenes) and other
aromatic and aliphatic volatile hydrocarbons (H Platen) 512
Analysis of volatile halogenated hydrocarbons in soil (/ Laurent) 517
Analysis of polycyclic aromatic hydrocarbons in soil (S Schieffet) 522
Determination of the extractable halogenated hydrocarbons in soil samples
(H-M Berstermann) 526
Degradation parameters (W. Müller-Markgraf) 529
The objective of optimization studies 529
Respirometry 530
Inhibition test 533
Closed-loop soil-slurry reactor 535
xiv
Contents
Technical aspects 535
Nutrient salt demand 538
Aeration, oxygen demand and alternative electron acceptors 539
Adsorption, desorption and bioavailability 539
Temperature and pH 541
Co-substrates 541
Special organisms (bioaugmentation) 542
Soil columns and lysimeters 542
Conclusions 546
Microbiological decontamination of soils 547
On-site and off-site techniques (R Eisermann) 547
Decontamination in bioreactors (U Gaugtitz) 552
In-situ bioremediation of the saturated soil (Th Held, G. Rippen) 557
Reuse of decontaminated soils 565
References 566
Index 569
XV
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| id | DE-604.BV010338977 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T17:50:47Z |
| institution | BVB |
| isbn | 0125138407 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-006881533 |
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| physical | XIX, 576 S. Ill., graph. Darst. |
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| publisher | Academic Press |
| record_format | marc |
| spelling | Methods in applied soil microbiology and biochemistry ed. by Kassem Alef ... London [u.a.] Academic Press 1995 XIX, 576 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Bodenchemie (DE-588)4146134-4 gnd rswk-swf Boden (DE-588)4007348-8 gnd rswk-swf Biochemie (DE-588)4006777-4 gnd rswk-swf Mikrobiologie (DE-588)4316357-9 gnd rswk-swf Boden (DE-588)4007348-8 s Mikrobiologie (DE-588)4316357-9 s DE-604 Biochemie (DE-588)4006777-4 s Bodenchemie (DE-588)4146134-4 s Alef, Kassem 1948- Sonstige (DE-588)140624635 oth HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=006881533&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Methods in applied soil microbiology and biochemistry Bodenchemie (DE-588)4146134-4 gnd Boden (DE-588)4007348-8 gnd Biochemie (DE-588)4006777-4 gnd Mikrobiologie (DE-588)4316357-9 gnd |
| subject_GND | (DE-588)4146134-4 (DE-588)4007348-8 (DE-588)4006777-4 (DE-588)4316357-9 |
| title | Methods in applied soil microbiology and biochemistry |
| title_auth | Methods in applied soil microbiology and biochemistry |
| title_exact_search | Methods in applied soil microbiology and biochemistry |
| title_full | Methods in applied soil microbiology and biochemistry ed. by Kassem Alef ... |
| title_fullStr | Methods in applied soil microbiology and biochemistry ed. by Kassem Alef ... |
| title_full_unstemmed | Methods in applied soil microbiology and biochemistry ed. by Kassem Alef ... |
| title_short | Methods in applied soil microbiology and biochemistry |
| title_sort | methods in applied soil microbiology and biochemistry |
| topic | Bodenchemie (DE-588)4146134-4 gnd Boden (DE-588)4007348-8 gnd Biochemie (DE-588)4006777-4 gnd Mikrobiologie (DE-588)4316357-9 gnd |
| topic_facet | Bodenchemie Boden Biochemie Mikrobiologie |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=006881533&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT alefkassem methodsinappliedsoilmicrobiologyandbiochemistry |