Front Cover

Advances in Applied Microbiology

Copyright

Contents

Contributors

Chapter One: Morphogenesis of Streptomyces in Submerged Cultures

1. Introduction

2. Morphogenesis in Submerged Cultures

2.1. Hyphal growth

2.2. Submerged sporulation

2.3. A special case: Streptomyces L-forms

3. Molecular Control of Liquid-Culture Morphogenesis

3.1. The tip-organizing center and the cytoskeleton

3.2. Extracellular polymers and pellet morphology

3.3. Proteins that control liquid-culture morphogenesis

3.4. Surface modification of Streptomyces spores

4. The SsgA-Like Proteins

4.1. SsgA-like proteins and morphotaxonomy of actinomycetes

4.2. How does SsgA control hyphal morphogenesis?

4.3. SsgA and SsgB control the localization of FtsZ

5. Environmental and Reactor Conditions

5.1. Culture heterogeneity

5.2. Nutrients and morphology

5.3. Fragmentation

5.4. Relationship between agitation, oxygenation, morphology, and productivity

6. Morphology and Antibiotic Production

6.1. Impact of morphology on antibiotic production

6.2. PCD and antibiotic production

7. Outlook: The Correlation Between Morphology and Production

Acknowledgments

References

Chapter Two: Interactions Between Arbuscular Mycorrhizal Fungi and Organic Material Substrates

1. Introduction

2. AMF Hyphal Foraging Responses

3. Early Evidence of AMF Interactions with Organic Matter

4. Response by AMF to Organic Materials

4.1. Roots and AMF hyphae both experiencing the organic material

4.2. AMF hyphae only experiencing the organic material

4.3. Influence of organic material amendment on AMF sporulation

5. AMF Influence on Organic Material Decomposition

6. Interactions with Soil Microorganisms in Organic Substrates

7. Interactions with Soil Fauna

7.1. Protozoa

7.2. Collembola

7.3. Earthworms

8. Conclusions

Acknowledgments

References

Chapter Three: Transcription Regulation in the Third Domain

1. Introduction

2. Sugar Utilization

2.1. TrmB family

2.2. GlpR family

3. Sulfur Metabolism

4. Electron Carriers

5. Methanogenesis

5.1. Acetate

5.2. Methanol and carbon monoxide

5.3. Metal proteins in methanogenesis

6. Nitrogen Metabolism

7. Amino Acids

7.1. Lrp/AsnC family

7.2. ACT domain containing

8. Cell Structures

8.1. Gas vesicles

8.2. Flagella

9. Heat Shock

10. Metals

10.1. DtxR family

10.2. Fur family

10.3. TRASH domain family

11. Oxidative Stress Responses

12. Viral

13. Concluding Remarks

References

Chapter Four: Bacteria-Phage Interactions in Natural Environments

1. Introduction

2. Setting the Stage: Bacteria and Phage Distribution in Nature

2.1. Bacterial and phage range limits

2.2. Phage-mediated selection of bacterial distributions

3. Interactions Among Bacteria and Phage

3.1. Phage life cycles

3.2. Bacterial responses to phage infection

3.3. Phage responses to bacterial defenses

3.4. Phage host range

4. Impact of Phages on Bacterial Populations and Communities

4.1. Abundance

4.2. Genetic innovation and phage-mediated bacterial gene transfer

4.3. Changes in physiology

4.4. Virulence

5. Bacteria and Phage Dynamics in Nature

5.1. Phage-mediated frequency-dependent selection

5.2. The Kill the Winner hypothesis

5.3. Phage-mediated apparent competition

6. Cascading Effects of Bacteria and Phage Interactions

6.1. Impact of phages on other nonbacterial species

6.2. Role in the ecosystem

7. Future Directions

7.1. Phage-phage interactions

7.2. Potential role for phages in immunology and mediated epidemiology

7.3. Impact of phage biocontrol on environmental microbes

8. Conclusions

Acknowledgments

References

Chapter Five: The Interactions of Bacteria with Fungi in Soil: Emerging Concepts

1. Introduction and the Importance of Microhabitats in the Living Soil

2. Bacterial-Fungal Interactions in Soil

2.1. Prevalent bacterial communities associated with soil fungi

2.2. Interactome of soil fungi and their associated bacteria

2.3. Mycorrhization helper bacteria and interactions

2.4. Endobacteria and their interactions with mycorrhizal fungi

2.5. Sequence of events in bacterial-fungal interactions, taking the B. terrae BS001-Lyophyllum sp. strain Karsten interac ...

2.5.1. Cell-to-cell contact-independent interaction

2.5.1.1. Secretion

2.5.1.2. Capture

2.5.1.3. Response

2.5.2. Cell-to-cell contact-dependent interaction

2.5.2.1. Approximation

2.5.2.2. Recognition

2.5.2.3. Attachment

2.5.2.4. Effector injection

2.5.2.5. Extracellular polymeric substance alteration

2.5.2.6. Bacterial growth

2.5.2.7. Biofilm formation

2.5.2.8. Cell wall degradation

3. Selected Mechanisms Involved in Bacterial Fitness in Fungal-Affected Microhabitats

3.1. Secretion systems

3.1.1. Type three secretion system

3.1.2. Type four secretion system

3.2. Pili and flagella

3.3. Chitinase

3.4. Biofilm formation genes

3.5. Fungal-released compounds in bacterial-fungal interactions

4. Genomics of the Interactome of B. terrae BS001 and Lyophyllum sp. Strain Karsten

5. Mutational Analysis to Understand Bacterial-Fungal Interactions in Soil

6. Horizontal Gene Transfer and Adaptability of Bacteria in the Mycosphere

7. Conclusions and Outlook

Acknowledgments

References

Chapter Six: Production of Specialized Metabolites by Streptomyces coelicolor A3(2)

1. Introduction

2. Morphology and Life Cycle

3. Genome Architecture

4. Specialized Metabolites of S. coelicolor

4.1. Classes of natural products and biosynthetic gene clusters

4.1.1. Polyketides and fatty acids

4.1.2. Terpenoids

4.1.3. Nonribosomal peptides and other peptide-derived compounds

4.1.4. Mixed and other natural product class compounds

4.2. Mechanisms for transport of specialized metabolites over the cell membrane

5. Regulation of Specialized Metabolism

5.1. Growth and development

5.2. Nutrition

5.3. Cross talk

5.4. Facilitating export

5.5. CPK: Activating a cryptic gene cluster

6. Modulation of Antibiotic Titers

6.1. Manipulation of RNA polymerase function

6.2. Ribosome engineering

6.3. Metals

6.4. S-Adenosyl methionine

6.5. Nucleoid structural changes

6.6. Exploiting chemical interactions

6.7. Site-specific recombineering for targeted amplification of gene clusters

7. Exploiting S. coelicolor as a Generic Host for Antibiotic Production

8. Future Perspectives and Concluding Remarks

Acknowledgments

References

Chapter Seven: Synthetic Polyester-Hydrolyzing Enzymes From Thermophilic Actinomycetes

1. Introduction

2. Identification of Synthetic Polyester Hydrolases From Thermophilic Actinomycetes

2.1. Actinomycetes that produce polyester hydrolases

2.2. Classification of actinomycete polyester hydrolases

3. Preparation of Actinomycete Polyester Hydrolases

3.1. Enzymes prepared from actinomycete strains

3.2. Recombinant expression of actinomycete polyester hydrolases in heterologous hosts

4. Catalytic Properties of Actinomycete Polyester Hydrolases

4.1. Hydrolysis of p-nitrophenyl acyl esters

4.2. Hydrolysis of organo-soluble esters

4.3. Hydrolysis of synthetic polyesters

4.3.1. Methods for the detection of enzymatic polyester hydrolysis activity

4.3.2. Kinetic analysis of the enzymatic hydrolysis of polyesters

4.3.3. Mechanism of the enzymatic hydrolysis of synthetic polyesters

5. Structural Properties of Actinomycete Polyester Hydrolases

5.1. Comparison of the protein crystal structures of Est119, LC-cutinase, and TfCut2

5.2. Relationship between the surface properties of actinomycete polyester hydrolases and their hydrolytic activity

5.3. Structural features of polyester hydrolases that affect their thermal stability

6. Genetic Engineering of Actinomycete Polyester Hydrolases

7. Conclusions

Acknowledgments

References

Index

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