Sariaslani Advances in Applied Microbiology

1. Auflage 2014
ISBN: 978-0-12-800295-7
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, Band Volume 89, 344 Seiten

Reihe: Advances in Applied Microbiology

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

Autoren/Hrsg.

Sariaslani, Sima

Inhaltsverzeichnis

1;Front Cover;1
2;Advances in Applied Microbiology;4
3;Copyright;5
4;Contents;6
5;Contributors;10
6;Chapter One: Morphogenesis of Streptomyces in Submerged Cultures;12
6.1;1. Introduction;13
6.2;2. Morphogenesis in Submerged Cultures;15
6.2.1;2.1. Hyphal growth;15
6.2.2;2.2. Submerged sporulation;17
6.2.3;2.3. A special case: Streptomyces L-forms;19
6.3;3. Molecular Control of Liquid-Culture Morphogenesis;20
6.3.1;3.1. The tip-organizing center and the cytoskeleton;20
6.3.2;3.2. Extracellular polymers and pellet morphology;23
6.3.3;3.3. Proteins that control liquid-culture morphogenesis;24
6.3.4;3.4. Surface modification of Streptomyces spores;26
6.4;4. The SsgA-Like Proteins;27
6.4.1;4.1. SsgA-like proteins and morphotaxonomy of actinomycetes;27
6.4.2;4.2. How does SsgA control hyphal morphogenesis?;29
6.4.3;4.3. SsgA and SsgB control the localization of FtsZ;30
6.5;5. Environmental and Reactor Conditions;31
6.5.1;5.1. Culture heterogeneity;31
6.5.2;5.2. Nutrients and morphology;32
6.5.3;5.3. Fragmentation;33
6.5.4;5.4. Relationship between agitation, oxygenation, morphology, and productivity;35
6.6;6. Morphology and Antibiotic Production;36
6.6.1;6.1. Impact of morphology on antibiotic production;36
6.6.2;6.2. PCD and antibiotic production;38
6.7;7. Outlook: The Correlation Between Morphology and Production;40
6.8;Acknowledgments;43
6.9;References;43
7;Chapter Two: Interactions Between Arbuscular Mycorrhizal Fungi and Organic Material Substrates;58
7.1;1. Introduction;59
7.2;2. AMF Hyphal Foraging Responses;60
7.3;3. Early Evidence of AMF Interactions with Organic Matter;66
7.4;4. Response by AMF to Organic Materials;68
7.4.1;4.1. Roots and AMF hyphae both experiencing the organic material;70
7.4.2;4.2. AMF hyphae only experiencing the organic material;78
7.4.3;4.3. Influence of organic material amendment on AMF sporulation;81
7.5;5. AMF Influence on Organic Material Decomposition;82
7.6;6. Interactions with Soil Microorganisms in Organic Substrates;87
7.7;7. Interactions with Soil Fauna;91
7.7.1;7.1. Protozoa;93
7.7.2;7.2. Collembola;95
7.7.3;7.3. Earthworms;97
7.8;8. Conclusions;98
7.9;Acknowledgments;99
7.10;References;100
8;Chapter Three: Transcription Regulation in the Third Domain;112
8.1;1. Introduction;113
8.2;2. Sugar Utilization;116
8.2.1;2.1. TrmB family;116
8.2.2;2.2. GlpR family;118
8.3;3. Sulfur Metabolism;118
8.4;4. Electron Carriers;119
8.5;5. Methanogenesis;119
8.5.1;5.1. Acetate;120
8.5.2;5.2. Methanol and carbon monoxide;120
8.5.3;5.3. Metal proteins in methanogenesis;121
8.6;6. Nitrogen Metabolism;121
8.7;7. Amino Acids;122
8.7.1;7.1. Lrp/AsnC family;122
8.7.2;7.2. ACT domain containing;124
8.8;8. Cell Structures;125
8.8.1;8.1. Gas vesicles;125
8.8.2;8.2. Flagella;125
8.9;9. Heat Shock;126
8.10;10. Metals;127
8.10.1;10.1. DtxR family;128
8.10.2;10.2. Fur family;130
8.10.3;10.3. TRASH domain family;131
8.11;11. Oxidative Stress Responses;132
8.12;12. Viral;133
8.13;13. Concluding Remarks;135
8.14;References;135
9;Chapter Four: Bacteria-Phage Interactions in Natural Environments;146
9.1;1. Introduction;147
9.2;2. Setting the Stage: Bacteria and Phage Distribution in Nature;148
9.2.1;2.1. Bacterial and phage range limits;149
9.2.2;2.2. Phage-mediated selection of bacterial distributions;152
9.3;3. Interactions Among Bacteria and Phage;154
9.3.1;3.1. Phage life cycles;154
9.3.2;3.2. Bacterial responses to phage infection;157
9.3.3;3.3. Phage responses to bacterial defenses;158
9.3.4;3.4. Phage host range;158
9.4;4. Impact of Phages on Bacterial Populations and Communities;161
9.4.1;4.1. Abundance;161
9.4.2;4.2. Genetic innovation and phage-mediated bacterial gene transfer;166
9.4.3;4.3. Changes in physiology;167
9.4.4;4.4. Virulence;168
9.5;5. Bacteria and Phage Dynamics in Nature;169
9.5.1;5.1. Phage-mediated frequency-dependent selection;170
9.5.2;5.2. The Kill the Winner hypothesis;172
9.5.3;5.3. Phage-mediated apparent competition;173
9.6;6. Cascading Effects of Bacteria and Phage Interactions;175
9.6.1;6.1. Impact of phages on other nonbacterial species;176
9.6.2;6.2. Role in the ecosystem;177
9.7;7. Future Directions;177
9.7.1;7.1. Phage-phage interactions;178
9.7.2;7.2. Potential role for phages in immunology and mediated epidemiology;179
9.7.3;7.3. Impact of phage biocontrol on environmental microbes;180
9.8;8. Conclusions;181
9.9;Acknowledgments;182
9.10;References;182
10;Chapter Five: The Interactions of Bacteria with Fungi in Soil: Emerging Concepts;196
10.1;1. Introduction and the Importance of Microhabitats in the Living Soil;197
10.2;2. Bacterial-Fungal Interactions in Soil;199
10.2.1;2.1. Prevalent bacterial communities associated with soil fungi;199
10.2.2;2.2. Interactome of soil fungi and their associated bacteria;201
10.2.3;2.3. Mycorrhization helper bacteria and interactions;202
10.2.4;2.4. Endobacteria and their interactions with mycorrhizal fungi;203
10.2.5;2.5. Sequence of events in bacterial-fungal interactions, taking the B. terrae BS001-Lyophyllum sp. strain Karsten interac ...;204
10.2.5.1;2.5.1. Cell-to-cell contact-independent interaction;204
10.2.5.1.1;2.5.1.1. Secretion;204
10.2.5.1.2;2.5.1.2. Capture;204
10.2.5.1.3;2.5.1.3. Response;205
10.2.5.2;2.5.2. Cell-to-cell contact-dependent interaction;205
10.2.5.2.1;2.5.2.1. Approximation;206
10.2.5.2.2;2.5.2.2. Recognition;206
10.2.5.2.3;2.5.2.3. Attachment;206
10.2.5.2.4;2.5.2.4. Effector injection;206
10.2.5.2.5;2.5.2.5. Extracellular polymeric substance alteration;206
10.2.5.2.6;2.5.2.6. Bacterial growth;206
10.2.5.2.7;2.5.2.7. Biofilm formation;206
10.2.5.2.8;2.5.2.8. Cell wall degradation;207
10.3;3. Selected Mechanisms Involved in Bacterial Fitness in Fungal-Affected Microhabitats;207
10.3.1;3.1. Secretion systems;207
10.3.1.1;3.1.1. Type three secretion system;208
10.3.1.2;3.1.2. Type four secretion system;209
10.3.2;3.2. Pili and flagella;209
10.3.3;3.3. Chitinase;211
10.3.4;3.4. Biofilm formation genes;212
10.3.5;3.5. Fungal-released compounds in bacterial-fungal interactions;213
10.4;4. Genomics of the Interactome of B. terrae BS001 and Lyophyllum sp. Strain Karsten;214
10.5;5. Mutational Analysis to Understand Bacterial-Fungal Interactions in Soil;215
10.6;6. Horizontal Gene Transfer and Adaptability of Bacteria in the Mycosphere;216
10.7;7. Conclusions and Outlook;218
10.8;Acknowledgments;219
10.9;References;220
11;Chapter Six: Production of Specialized Metabolites by Streptomyces coelicolor A3(2);228
11.1;1. Introduction;229
11.2;2. Morphology and Life Cycle;230
11.3;3. Genome Architecture;231
11.4;4. Specialized Metabolites of S. coelicolor;232
11.4.1;4.1. Classes of natural products and biosynthetic gene clusters;234
11.4.1.1;4.1.1. Polyketides and fatty acids;234
11.4.1.2;4.1.2. Terpenoids;241
11.4.1.3;4.1.3. Nonribosomal peptides and other peptide-derived compounds;244
11.4.1.4;4.1.4. Mixed and other natural product class compounds;247
11.4.2;4.2. Mechanisms for transport of specialized metabolites over the cell membrane;251
11.5;5. Regulation of Specialized Metabolism;253
11.5.1;5.1. Growth and development;255
11.5.2;5.2. Nutrition;257
11.5.3;5.3. Cross talk;258
11.5.4;5.4. Facilitating export;259
11.5.5;5.5. CPK: Activating a cryptic gene cluster;259
11.6;6. Modulation of Antibiotic Titers;260
11.6.1;6.1. Manipulation of RNA polymerase function;261
11.6.2;6.2. Ribosome engineering;262
11.6.3;6.3. Metals;262
11.6.4;6.4. S-Adenosyl methionine;263
11.6.5;6.5. Nucleoid structural changes;263
11.6.6;6.6. Exploiting chemical interactions;264
11.6.7;6.7. Site-specific recombineering for targeted amplification of gene clusters;265
11.7;7. Exploiting S. coelicolor as a Generic Host for Antibiotic Production;265
11.8;8. Future Perspectives and Concluding Remarks;266
11.9;Acknowledgments;267
11.10;References;267
12;Chapter Seven: Synthetic Polyester-Hydrolyzing Enzymes From Thermophilic Actinomycetes;278
12.1;1. Introduction;279
12.2;2. Identification of Synthetic Polyester Hydrolases From Thermophilic Actinomycetes;280
12.2.1;2.1. Actinomycetes that produce polyester hydrolases;280
12.2.2;2.2. Classification of actinomycete polyester hydrolases;281
12.3;3. Preparation of Actinomycete Polyester Hydrolases;283
12.3.1;3.1. Enzymes prepared from actinomycete strains;283
12.3.2;3.2. Recombinant expression of actinomycete polyester hydrolases in heterologous hosts;284
12.4;4. Catalytic Properties of Actinomycete Polyester Hydrolases;287
12.4.1;4.1. Hydrolysis of p-nitrophenyl acyl esters;287
12.4.2;4.2. Hydrolysis of organo-soluble esters;290
12.4.3;4.3. Hydrolysis of synthetic polyesters;290
12.4.3.1;4.3.1. Methods for the detection of enzymatic polyester hydrolysis activity;292
12.4.3.2;4.3.2. Kinetic analysis of the enzymatic hydrolysis of polyesters;295
12.4.3.3;4.3.3. Mechanism of the enzymatic hydrolysis of synthetic polyesters;297
12.5;5. Structural Properties of Actinomycete Polyester Hydrolases;297
12.5.1;5.1. Comparison of the protein crystal structures of Est119, LC-cutinase, and TfCut2;297
12.5.2;5.2. Relationship between the surface properties of actinomycete polyester hydrolases and their hydrolytic activity;304
12.5.3;5.3. Structural features of polyester hydrolases that affect their thermal stability;305
12.6;6. Genetic Engineering of Actinomycete Polyester Hydrolases;306
12.7;7. Conclusions;308
12.8;Acknowledgments;309
12.9;References;309
13;Index;318
14;Contents of Previous Volumes;326

Leseproben

Chapter Two 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: [e-mail] 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...