Microbial reclamation of alkaline sodic soils

237 Pages·2016·10.31 MB·English

by  Simon Odell

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Microbial Reclamation of Alkaline Sodic Soils
of
Thesis submitted for the degree
I)octor of PhilosoPhY
at the Universrty of Adelaide bY
Simon Paul Odelt
Deparbnent of Soil and Water
Waite Agricultural Institute
Glen Osmond, South Australia
2000
1l
TABLE OF CONTENTS
Page
x
ABSTRACT
xiv
STATEMENT
xv
ACKNOWLEDGEMENTS
xvi
LIST OF'FIGT]RES
xxi
LIST OF TABLES
xxiv
ABBREVIATIONS
I
CHAPTER 1. Introduction
CHAPTER 2. Literature Review
2.1 Classification and formation of sodic soils 4
2.1.1 Classification of sodic soils 4
2.1.2 Natural formation of sodic soils 5
2.1.3 AnthroPogenic sodic soils 5
2.1.3.I Indiscriminate clearing and over-grazrng of native vegetation 5
2.I.3.2 Inigation of crops with poor quahty water 6
2.2 Chemical reclamation of alkaline sodic soils 6
2.2.1 Sodic soil and gYPs 6
2.2.2 Inigation 8
I
2.2.3
Iron PYrite
2.2.4 10
Water soluble PolYmers
2.2.5 Heating 11
2.3 Biological reclamation of alkaline sodic soils l1
2.3.1 Organic matter and the biological reclamation of sodic soil 1l
t4
2.3.2 Limitations of organic matter treatment
t4
2.3.3 Types of organic matter
t4
2.3.4 Farmyard manure mixtures
l6
2.3.5 Acid cheese whey
t7
2.3.6 Sewage sludge
t9
2.3.7 Straw
2.3.8 Crops and other plants 20
22
2.3.9 Bagasse
2.3.10 Molasses 23
24
2.3.11 Green waste
2.4 Microbiology of sodic soils 24
2.4.1 Effect of alkaline conditions and NaCl on the microflora
of sodic soils 24
2.4.2 Effect of soil moisture content on the microflora of sodic soils 25
2.4.3 Effect of gypsum on the microflora of sodic soils 26
2.4.4 Effect of green manure on the microflora of sodic soils 26
2.4.5 Effect of glucose on the microflora of sodic soils 27
2.5 Methods for studying the microbial populations within soils 27
2.5.t Molecular techniques 28
2.5.2 BIOLOG 29
2.5.3 Immunological methods 29
2.5.4 Fatty Acid Methyl Ester (FAME) analysis 30
2.6 Conclusion 31
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CHApTER 3. Diversity, Alkalitolerance, Halotolerance, and Acid-Producing
Capabilities of Microorganisms Cultured from an Australian Alkaline Sodic Soil
3.1 Introduction 32
3.2 Methods 33
Materials and
3.2.1 ProPerties 35
Soil
solutions
3.2.2 Microbiological culture media and 35
3.2.3 Enumeration of non-filamentous bacteria,
frrngi
filamentous bacteria (actinomycetes) and 35
3.2.4 selection of non-filamentous bacteria to be used in alkali
assays
and NaCl tolerance 37
3.2.5 selection of filamentous bacteria (actinomycetes) to be
assays
used in preliminary alkati and Nacl tolerance 38
characterisation
3.2.6 Selection of fungi for morphological 38
3.2.7 Alkali tolerance of filamentous and non-filamentous
bacteria
Watchem soil 38
3.2.8 NaCl tolerance of of filamentous and non-filamentous
bacteria
Watchem soil 39
3.2.9 combined alkali and Nacl tolerance of filamentous
bacteria
and non-filamentous \ÙVatchem soil 39
3.2.10 Assay for acid production by non-filamentous
isolates 39
bacterial
3.2.11 Fatry Acid Metþl Ester (FAME) identification of
isolates 40
bacterial
3.2.12 Identification of filamentous bacterial isolates 4l
3.2.13 identification 4l
Ftngal
lll
42
3.3 Results
3.3.1 Enumeration of fi lamentous bacteria (actinomycetes),
non-filamentous bacteria, and fungi 42
3.3.2 Alkalitolerance and halotolerance of individual
non-fi lamentous bacteria 43
3.3.2.1 Identifrcation of highly halotolerant non-filamentous
bacteria by FAME analYsis 45
3.3.2.2 Identification of moderately haloalkalitolerant
non-filamentous bacteria by FAME analysis 46
3.3.2.3 Identifi cation of highly haloalkalitolerant non-filamentous
bacteria by FAME analYsis 47
3.3.3 Classification non-filamentous bacteria with a
FAME profile similaritY of <30io 48
3.3.4 Acid production by non-filamentous bacteria:
5l
FAME identified isolates
3.3.5 Acid production by non-filamentous bacteria :
Unidentified isolates 52
3.3.6 Alkali and NaCl tolerance of filamentous Watchem soil
bacteria (actinomycetes): Preliminary studies 54
3.3.7 Identification of filamentous bacteria (actinomycetes) 55
3.3.8 Fungal identification 57
60
3.4 Discussion
3.4.1 Alkalitolerance of the non-filamentous watchem soil bacteria 60
3.4.2 Halotolerance of the non-filamentous Watchem soil bacteria 65
lV
3.4.3 Acid production by the non-filamentous Watchem soil
bacterial isolates 68
3.4.4 Alkalitolerance of filamentous bacteria (actinomycetes)
isolated from the V/atchem soil: Preliminary studies 69
3.4.5 Halotolerance of filamentous bacteria (actinomycetes)
isolated from the Watchem soil: Preliminary studies 70
3.4.6 Fungal identification 7T
3.5 Conclusion 73
CHAPTER 4. volatile Fatty Acid Analysis in Alkaline sodic Soils: Method
Development
4.r Introduction 75
4.2 Method development 76
4.2.1 Instrumentation 76
4.2.2 Determination of chromatography conditions 77
4.2.3 Selection of the MSD analysis mode 78
4.2.4 Selection of ions to monitor 79
4.2.5 Construction of calibration curves 79
4.2.6 Selection of an internal standard 80
4.2.7 Solvent formulation 83
4.2.8 Optimisation of the extraction method 85
4.2.9 Optimum GC-MSD configuration and extraction method 87
v
CHAPTER 5. Microbial Reclamation of an Älkaline Sodic Soil Using the Model
Organic Substrate Glucose
5.1 Introduction 88
5.2 Materials and methods 88
5.2.1 Soil properties 89
5.2.2 Preparation of soil samples 89
5.2.3 Physical and chemical analyses 90
5.2.3.1 Soil pH and EC 90
5.2.3.2 Soluble cation analysis 90
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5.2.3.3 Determination of total carbonate
5.2.3.4 9l
Determination of water soluble carbonate and bicarbonate
5.2.3.5 Measurement of microbial glucose utilisation 9T
s.2.3.6 Volatile fatty acid analysis of soil samples 93
5.2.4 Microbiological analyses 93
5.2.4.1 FAME analysis of soil samples 93
5.2.4.2 Methane analysis of the soil headspace 94
5.2.5 Statistical analyses 94
5.3 Results and Discussion 95
5.3.1 Microbial utilisation of glucose 95
5.3.2 Interpretation of whole soil FAME profiles 96
5.3.3 Volatile fatty acid (VFA) and FAME analysis
of soil samples: W4 treatment 102
5.3.4 Volatile fatty acid (VFA) and FAME analysis
of soil samples: 2W4 treatment 104
vl
5.3.s Volatile fatty acid (VFA) and FAME analysis
of soil samples: 2W2treatment 108
5.3.6 Volatile fatty acid (VFA) and FAME analysis
of soil samples: W2 treatment 110
s.3.7 Volatile fatty acid (VFA) and FAME analysis
t12
of soil samples:Aerobic Control
s.3.8 Volatile fatfy acid (VFA) and FAME analysis
of soil samples:Anaerobic Control 113
5.3.9 Methane analysis of the soil headspace 115
5.3.10 Soil pH 115
5.3.11 Total carbonate/ Soluble Carbonate and Bicarbonate 118
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s.3.12 Soluble Calcium
r23
5.3.13 Soluble Sodium
5.3.14 Soil EC 124
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5.4 Conclusion
CHAPTER 6. Microbial Reclamation of an Alkaline Sodic Soil Using "Complex"
Organic Substrates
6.1 Introduction 127
6.2 Methods 130
Materials and
6.2.1 properties 130
Soil
6.2.2 Ameliorant evaluation experiment 131
6.2.3 Amelioration of the Watchem soil using
ameliorants 132
complex organic
6.2.4 analYsis I32
Total Carbon
v11
6.2.5 Interpretation of whole soil FAME profiles t34
6.3 Results and Discussion 135
6.3.1 Ameliorant evaluation experiment 135
6.3.1.1 Ameliorant evaluation experiment: Control 135
6.3.1.2 Ameliorant evaluation experiment: Wheat straw 135
6.3.1.3 Ameliorant evaluation experiment: Sheep manure r37
6.3.1.4 Ameliorant evaluation experiment: Molasses 138
6.3.1.5 Ameliorant evaluation experiment:
t39
Wheat straw and Sheep manure
6.3.1.6 Ameliorant screening experiment:
t4t
Wheat straw and Molasses
6.3.r.7 Ameliorant screening exPeriment:
Super phosphate, Ammonium nitrate, Molasses
r42
and Wheat straw
6.3.1.8 Ameliorant screening exPeriment:
Selection of ameliorants for further study r43
r45
6.3.2 Small-scale amelioration experiment
t45
6.3.2.1 Total Carbon analysis
6.3.2.2 Volatile Fatty Acid production and
Soil FAME analysis: Control 146
6.3.2.3 Volatile Fatty Acid production and
t47
Soil FAME analysis: Molasses treatment
6.3.2.4
Volatile Fatty Acid production and
Soil FAME analysis: Super treatment 150
v111
6.3.2.5 Soil pIV Total Carbonatel
t54
Soluble Carbonate and Bicarbonate
t56
6.3.2.6 Soluble Calcium
158
6.3.2.7 Soluble Sodium
160
6.3.2.8 Soil EC
6.4 Conclusion 161
CHAPTER 7. General I)iscussion
7.1 Microbial populations within alkaline sodic soils 163
7.2 Microbial reclamation of alkaline sodic soils r66
173
REFERENCES
APPEI\IDIX T. Microbiological growth media and solutions 208
APPEI\DIX 2. FAME protocol for individual bacterial isolates 210
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