Published since 1959, Advances in Applied Microbiology continues to be one of the most widely read and authoritative review sources in microbiology.
The series contains comprehensive reviews of the most current research in applied microbiology. Recent areas covered include bacterial diversity in the human gut, protozoan grazing of freshwater biofilms, metals in yeast fermentation processes and the interpretation of host-pathogen dialogue through microarrays.
Eclectic volumes are supplemented by thematic volumes on various topics, including Archaea and sick building syndrome. Impact factor for 2012: 4.974.
Key features:
* Contributions from leading authorities * Informs and updates on all the latest developments in the field
Published since 1959, Advances in Applied Microbiology continues to be one of the most widely read and authoritative review sources in microbiology. The series contains comprehensive reviews of the most current research in applied microbiology. Recent areas covered include bacterial diversity in the human gut, protozoan grazing of freshwater biofilms, metals in yeast fermentation processes and the interpretation of host-pathogen dialogue through microarrays. Eclectic volumes are supplemented by thematic volumes on various topics, including Archaea and sick building syndrome. Impact factor for 2012: 4.974. Contributions from leading authorities Informs and updates on all the latest developments in the field
Front Cover 1
Advances in Applied Microbiology 4
Copyright 5
Contents 6
Contributors 10
Chapter One: Morphogenesis of Streptomyces in Submerged Cultures 12
1. Introduction 13
2. Morphogenesis in Submerged Cultures 15
2.1. Hyphal growth 15
2.2. Submerged sporulation 17
2.3. A special case: Streptomyces L-forms 19
3. Molecular Control of Liquid-Culture Morphogenesis 20
3.1. The tip-organizing center and the cytoskeleton 20
3.2. Extracellular polymers and pellet morphology 23
3.3. Proteins that control liquid-culture morphogenesis 24
3.4. Surface modification of Streptomyces spores 26
4. The SsgA-Like Proteins 27
4.1. SsgA-like proteins and morphotaxonomy of actinomycetes 27
4.2. How does SsgA control hyphal morphogenesis? 29
4.3. SsgA and SsgB control the localization of FtsZ 30
5. Environmental and Reactor Conditions 31
5.1. Culture heterogeneity 31
5.2. Nutrients and morphology 32
5.3. Fragmentation 33
5.4. Relationship between agitation, oxygenation, morphology, and productivity 35
6. Morphology and Antibiotic Production 36
6.1. Impact of morphology on antibiotic production 36
6.2. PCD and antibiotic production 38
7. Outlook: The Correlation Between Morphology and Production 40
Acknowledgments 43
References 43
Chapter Two: Interactions Between Arbuscular Mycorrhizal Fungi and Organic Material Substrates 58
1. Introduction 59
2. AMF Hyphal Foraging Responses 60
3. Early Evidence of AMF Interactions with Organic Matter 66
4. Response by AMF to Organic Materials 68
4.1. Roots and AMF hyphae both experiencing the organic material 70
4.2. AMF hyphae only experiencing the organic material 78
4.3. Influence of organic material amendment on AMF sporulation 81
5. AMF Influence on Organic Material Decomposition 82
6. Interactions with Soil Microorganisms in Organic Substrates 87
7. Interactions with Soil Fauna 91
7.1. Protozoa 93
7.2. Collembola 95
7.3. Earthworms 97
8. Conclusions 98
Acknowledgments 99
References 100
Chapter Three: Transcription Regulation in the Third Domain 112
1. Introduction 113
2. Sugar Utilization 116
2.1. TrmB family 116
2.2. GlpR family 118
3. Sulfur Metabolism 118
4. Electron Carriers 119
5. Methanogenesis 119
5.1. Acetate 120
5.2. Methanol and carbon monoxide 120
5.3. Metal proteins in methanogenesis 121
6. Nitrogen Metabolism 121
7. Amino Acids 122
7.1. Lrp/AsnC family 122
7.2. ACT domain containing 124
8. Cell Structures 125
8.1. Gas vesicles 125
8.2. Flagella 125
9. Heat Shock 126
10. Metals 127
10.1. DtxR family 128
10.2. Fur family 130
10.3. TRASH domain family 131
11. Oxidative Stress Responses 132
12. Viral 133
13. Concluding Remarks 135
References 135
Chapter Four: Bacteria-Phage Interactions in Natural Environments 146
1. Introduction 147
2. Setting the Stage: Bacteria and Phage Distribution in Nature 148
2.1. Bacterial and phage range limits 149
2.2. Phage-mediated selection of bacterial distributions 152
3. Interactions Among Bacteria and Phage 154
3.1. Phage life cycles 154
3.2. Bacterial responses to phage infection 157
3.3. Phage responses to bacterial defenses 158
3.4. Phage host range 158
4. Impact of Phages on Bacterial Populations and Communities 161
4.1. Abundance 161
4.2. Genetic innovation and phage-mediated bacterial gene transfer 166
4.3. Changes in physiology 167
4.4. Virulence 168
5. Bacteria and Phage Dynamics in Nature 169
5.1. Phage-mediated frequency-dependent selection 170
5.2. The Kill the Winner hypothesis 172
5.3. Phage-mediated apparent competition 173
6. Cascading Effects of Bacteria and Phage Interactions 175
6.1. Impact of phages on other nonbacterial species 176
6.2. Role in the ecosystem 177
7. Future Directions 177
7.1. Phage-phage interactions 178
7.2. Potential role for phages in immunology and mediated epidemiology 179
7.3. Impact of phage biocontrol on environmental microbes 180
8. Conclusions 181
Acknowledgments 182
References 182
Chapter Five: The Interactions of Bacteria with Fungi in Soil: Emerging Concepts 196
1. Introduction and the Importance of Microhabitats in the Living Soil 197
2. Bacterial-Fungal Interactions in Soil 199
2.1. Prevalent bacterial communities associated with soil fungi 199
2.2. Interactome of soil fungi and their associated bacteria 201
2.3. Mycorrhization helper bacteria and interactions 202
2.4. Endobacteria and their interactions with mycorrhizal fungi 203
2.5. Sequence of events in bacterial-fungal interactions, taking the B. terrae BS001-Lyophyllum sp. strain Karsten interac ... 204
2.5.1. Cell-to-cell contact-independent interaction 204
2.5.1.1. Secretion 204
2.5.1.2. Capture 204
2.5.1.3. Response 205
2.5.2. Cell-to-cell contact-dependent interaction 205
2.5.2.1. Approximation 206
2.5.2.2. Recognition 206
2.5.2.3. Attachment 206
2.5.2.4. Effector injection 206
2.5.2.5. Extracellular polymeric substance alteration 206
2.5.2.6. Bacterial growth 206
2.5.2.7. Biofilm formation 206
2.5.2.8. Cell wall degradation 207
3. Selected Mechanisms Involved in Bacterial Fitness in Fungal-Affected Microhabitats 207
3.1. Secretion systems 207
3.1.1. Type three secretion system 208
3.1.2. Type four secretion system 209
3.2. Pili and flagella 209
3.3. Chitinase 211
3.4. Biofilm formation genes 212
3.5. Fungal-released compounds in bacterial-fungal interactions 213
4. Genomics of the Interactome of B. terrae BS001 and Lyophyllum sp. Strain Karsten 214
5. Mutational Analysis to Understand Bacterial-Fungal Interactions in Soil 215
6. Horizontal Gene Transfer and Adaptability of Bacteria in the Mycosphere 216
7. Conclusions and Outlook 218
Acknowledgments 219
References 220
Chapter Six: Production of Specialized Metabolites by Streptomyces coelicolor A3(2) 228
1. Introduction 229
2. Morphology and Life Cycle 230
3. Genome Architecture 231
4. Specialized Metabolites of S. coelicolor 232
4.1. Classes of natural products and biosynthetic gene clusters 234
4.1.1. Polyketides and fatty acids 234
4.1.2. Terpenoids 241
4.1.3. Nonribosomal peptides and other peptide-derived compounds 244
4.1.4. Mixed and other natural product class compounds 247
4.2. Mechanisms for transport of specialized metabolites over the cell membrane 251
5. Regulation of Specialized Metabolism 253
5.1. Growth and development 255
5.2. Nutrition 257
5.3. Cross talk 258
5.4. Facilitating export 259
5.5. CPK: Activating a cryptic gene cluster 259
6. Modulation of Antibiotic Titers 260
6.1. Manipulation of RNA polymerase function 261
6.2. Ribosome engineering 262
6.3. Metals 262
6.4. S-Adenosyl methionine 263
6.5. Nucleoid structural changes 263
6.6. Exploiting chemical interactions 264
6.7. Site-specific recombineering for targeted amplification of gene clusters 265
7. Exploiting S. coelicolor as a Generic Host for Antibiotic Production 265
8. Future Perspectives and Concluding Remarks 266
Acknowledgments 267
References 267
Chapter Seven: Synthetic Polyester-Hydrolyzing Enzymes From Thermophilic Actinomycetes 278
1. Introduction 279
2. Identification of Synthetic Polyester Hydrolases From Thermophilic Actinomycetes 280
2.1. Actinomycetes that produce polyester hydrolases 280
2.2. Classification of actinomycete polyester hydrolases 281
3. Preparation of Actinomycete Polyester Hydrolases 283
3.1. Enzymes prepared from actinomycete strains 283
3.2. Recombinant expression of actinomycete polyester hydrolases in heterologous hosts 284
4. Catalytic Properties of Actinomycete Polyester Hydrolases 287
4.1. Hydrolysis of p-nitrophenyl acyl esters 287
4.2. Hydrolysis of organo-soluble esters 290
4.3. Hydrolysis of synthetic polyesters 290
4.3.1. Methods for the detection of enzymatic polyester hydrolysis activity 292
4.3.2. Kinetic analysis of the enzymatic hydrolysis of polyesters 295
4.3.3. Mechanism of the enzymatic hydrolysis of synthetic polyesters 297
5. Structural Properties of Actinomycete Polyester Hydrolases 297
5.1. Comparison of the protein crystal structures of Est119, LC-cutinase, and TfCut2 297
5.2. Relationship between the surface properties of actinomycete polyester hydrolases and their hydrolytic activity 304
5.3. Structural features of polyester hydrolases that affect their thermal stability 305
6. Genetic Engineering of Actinomycete Polyester Hydrolases 306
7. Conclusions 308
Acknowledgments 309
References 309
Index 318
Contents of Previous Volumes 326
Interactions Between Arbuscular Mycorrhizal Fungi and Organic Material Substrates
Angela Hodge1 Department of Biology, University of York, York, United Kingdom
1 Corresponding author: email address: angela.hodge@york.ac.uk
Abstract
Arbuscular mycorrhizal (AM) associations are widespread and form between ca. two-thirds of all land plants and fungi in the phylum Glomeromycota. The association is a mutualistic symbiosis with the fungi enhancing nutrient capture for the plant while obtaining carbon in return. Although arbuscular mycorrhizal fungi (AMF) lack any substantial saprophytic capability they do preferentially associate with various organic substrates and respond by hyphal proliferation, indicating the fungus derives a benefit from the organic substrate. AMF may also enhance decomposition of the organic material. The benefit to the host plant of this hyphal proliferation is not always apparent, particularly regarding nitrogen (N) transfer, and there may be circumstances under which both symbionts compete for the N released given both have a large demand for N. The results of various studies examining AMF responses to organic substrates and the interactions with other members of the soil community will be discussed.
Keywords
Arbuscular mycorrhizal fungi
Organic materials
Hyphal proliferation
Saprophytic capability
Decomposition
1 Introduction
The arbuscular mycorrhizal (AM) association is a classic mutualism in which both partners benefit. The fungi involved are in the phylum Glomeromycota, an ancient group of fungi as shown by fossil evidence from the Ordovician period as spores (Redecker, Kodner, & Graham, 2000) and from the Devonian as a symbiosis, which shows remarkable similarity to the present day symbiosis structure (Remy, Taylor, Haas, & Kerp, 1994), namely the arbuscule.
Upon perception of plant root exudates, chiefly strigolactone compounds (Akiyama, Matsuzaki, & Hayashi, 2005; Besserer et al., 2006), AM fungal (AMF) spore germination is stimulated and hyphal growth and extensive branching occurs in addition to alterations in fungal physiological activity. The AMF, in turn, signals to the plant via the collectively termed mycorrhizal factors (Myc factors) (Chabaud, Venard, Defaux-Petras, Becard, & Barker, 2002; Kosuta et al., 2003). Their detection by the plant results in calcium oscillations in the root epidermal cells (Kosuta et al., 2008) and an activation of plant symbiosis related genes (Kosuta et al., 2003). The AMF then forms an infection peg called a hyphopodium (a type of appressorium), while the plant cells produce a prepenetration apparatus that allows hyphal growth into the epidermal cells and colonization of the root cortex. Following root colonization, the fungus extends its hyphae into the soil extending the zone of influence of the root into the “mycorrhizosphere” and allowing a larger volume of soil to be foraged for nutrients. Traditionally, the main benefit of being AM is viewed as enhanced acquisition of poorly mobile phosphate ions (Karasawa, Hodge, & Fitter, 2012; Smith & Smith, 2011), although a range of other benefits has been identified such as increased nitrogen (N) capture, including from organic matter zones or “patches” (Hodge, Campbell, & Fitter, 2001; Leigh, Hodge, & Fitter, 2009), and improved pathogen resistance (Newsham, Fitter, & Watkinson, 1995). In return, the fungal symbiont receives carbohydrates from its host (Bryla & Eissenstat, 2005), leading to estimates of the AM symbiosis representing a flow of carbon equivalent to ca. 5 billion tons of carbon (C) per year and significantly contributing to the global carbon cycle (Bago, Pfeffer, & Shachar-Hill, 2000; Hughes, Hodge, Fitter, & Atkin, 2008).
With current requirements to move toward more sustainable agricultural systems and so reduce the amount of fertilizer inputs together with their associated high energy costs and environmental problems (particularly in the case of N-based fertilizers) and use of nonrenewable resources (e.g., rock phosphate) there has been renewed interest in exploiting this ancient symbiosis. However, most of the modern farming practices (high nutrient input, pesticide treatments, ploughing, etc.,) are detrimental to AM establishment, while crop breeders have largely ignored AM symbiosis as a “useful” trait focusing, instead, on varieties that respond well to high nutrient inputs. Despite this, there has been considerable research on the ability of AMF to acquire nutrients from organic materials, albeit mainly conducted under rather artificial conditions, which show AMF respond to organic matter. This response, however, can vary with the type of amendment added and the experimental conditions used as discussed below. Although changes to the nomenclature of many AMF species have recently been proposed (e.g., Krüger, Krüger, Walker, Stockinger, & Schußler, 2012; Redecker et al., 2013), in this review the names reported are as they appear in the original studies, with the new name given in Table 2.1. This approach has been taken for the following reasons: firstly, some AMF names have changed several times as new approaches have become available to resolve phylogenetic classification (e.g., see Stockinger et al., 2009), but, unfortunately, the exact origin of the AMF isolate used is not always obvious from the information given in the original paper. Secondly, as with any new system, it takes time for the new names to be established, and there is still some debate over the classification of several AMF species with further corrections recently made (see Redecker et al., 2013).
Table 2.1
The previous name (as used in this review) and, where appropriate, the new name of the various AMF species cited in this review
| Archaeospora trappi | Unchanged |
| Gigaspora decipiens | Unchanged |
| Gigaspora gigantea | Unchanged |
| Gigaspora margarita | Unchanged |
| Glomus claroideum | Claroideoglomus claroideum |
| Glomus clarum | Rhizophagus clarus |
| Glomus geosporum | Funneliformis geosporum |
| Glomus hoi | Currently unchanged but pending clarification | Some uncertainty as to exact positioning of this species. Moreover, current evidence suggests “G. hoi” referred to in this review (which in all cases is isolate “UY110”), is unlikely to be “G. hoi” but further clarification is required (see Redecker et al., 2013). |
| Glomus intraradices | Rhizophagus intraradices | Several isolates previously identified as R. intraradices (Basionym G. intraradices) were subsequently identified as R. irregularis (Basionym G. irregulare) including the isolate most commonly used in root organ culture studies (see Stockinger, Walker, & Schußler, 2009). |
| Glomus irregulare | Rhizophagus irregularis |
| Glomus mosseae | Funneliformis mosseae |
| Glomus monosporum | Unchanged | Original culture lost before DNA sequencing could be conducted to confirm identity. |
| Glomus versiforme | Diversispora epigaea |
| Scutellospora calospora | Unchanged |
| Scutellospora dipurpurescens | Unchanged |
Note, in some cases there is some uncertainty as to the exact positioning or even the identity of the AMF species used (see “Comments” column), therefore further changes are likely (see Redecker et al., 2013).
2 AMF Hyphal Foraging Responses
AMF have two phases: one inside the root (internal phase), the other outside the root (external phase) and it is the latter that explores the soil environment for nutrients. Studies using inorganic nutrient addition to compartments that only AMF hyphae had access to, suggest AMF can effectively forage their environment for resources and may show some similarities to how roots respond to heterogeneously supplied nutrients. AMF were equally effective at acquiring inorganic P for their associated host plant regardless if the P was distributed in a uniform or patchy manner (Cui & Caldwell, 1996), which suggests AMF are effective at foraging the soil environment for resources irrespective of their distribution. However, differences among AMF species in their strategies for space colonization, both inside the root and in the external substrate, have also been reported...
| Erscheint lt. Verlag | 21.8.2014 |
|---|---|
| Mitarbeit |
Herausgeber (Serie): Geoffrey M. Gadd, Sima Sariaslani |
| Sprache | englisch |
| Themenwelt | Medizin / Pharmazie ► Allgemeines / Lexika |
| Naturwissenschaften ► Biologie ► Mikrobiologie / Immunologie | |
| Technik ► Umwelttechnik / Biotechnologie | |
| ISBN-10 | 0-12-800295-6 / 0128002956 |
| ISBN-13 | 978-0-12-800295-7 / 9780128002957 |
| Haben Sie eine Frage zum Produkt? |
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