Microbial Resources

Chapter 1: Planctomycetes—New Models for Microbial Cells and Activities
John Arlington Fuerst

• Abstract
• Introduction
• What are planctomycetes and what properties mark them out as unusual?
• Summary of relevant planctomycete physiology
• Compartmentalization of planctomycete cells
• How might the unusual characteristics of planctomycetes be considered as resources?
• Compartmentalized cells as a potential resource for synthetic biology
• Unusual components of planctomycete cells
• Sulfatases and their uses in stereochemistry/transformations in organic chemistry
• What other properties do planctomycetes harbor relevant to new resources?
• Anammox planctomycetes as a major example of planctomycetes as a microbial resource
• Anammox planctomycetes are resources providing global ecosystem services in the nitrogen cycle
• Conclusions
• Acknowledgments

Chapter 2: A Flavor of Prokaryotic Taxonomy: Systematics Revisited
Paul De Vos Sr.

• Abstract
• Introduction
• The prokaryotic species concept
• Remarks on the generalized use of 16S rRNA sequences
• Chemotaxonomic and phenotypic characterization
• Prokaryote nomenclature
• Identification of prokaryotes
• The gap between prokaryotic diversity and taxonomy of prokaryotes
• A Renaissance in prokaryote taxonomy?
• Hurdles underway
• Toward a new “gold standard”
• WGS is the basic unit for genomic prokaryote taxonomy (GPT)
• Genomic prokaryote taxonomy (GPT)
• Conclusions
• Acknowledgments

Chapter 3: Bioactive Actinomycetes: Reaching Rarity Through Sound Understanding of Selective Culture and Molecular Diversity
Ipek Kurtboke

• Abstract
• Introduction
• Conclusions
• Acknowledgments

Chapter 4: Microbial Resources for Global Sustainability
James Philp and Ronald Atlas

• Abstract
• Introduction
• Replacing fossil fuels with biofuels
• Replacing the oil barrel for chemical production
• Technical barriers to bio-based production
• The convergence with green chemistry
• Gene and genome editing in production strains-the future for bio-based production?
• Shortening the innovation cycle time: the ultimate contribution of synthetic biology?
• Future prospects: overcoming the bottlenecks in bio-based production
• Concluding remarks
• Disclaimer statement

Chapter 5: Modern Natural Products Drug Discovery and Its Relevance to Biodiversity Conservation
William H. Gerwick

• Abstract
• Introduction
• Natural product drug discovery
• Policy regarding bioprospecting
• Biodiversity estimates
• Threats to biodiversity
• Classification of biodiversity resulting from bioprospecting; cyanobacteria as an example
• Biodiversity partnerships, bioprospecting, and conservation efforts
• Future outlooks

Chapter 6: Hydrocarbon-Oxidizing Bacteria and Their Potential in Eco-Biotechnology and Bioremediation
Irina Ivshina

• Abstract
• Introduction
• Bacteriology of hydrocarbon degradation
• Bacterial adaptation to hydrocarbon assimilation
• Environmental biosensors for hydrocarbon pollutants
• Bioremediation of oil-contaminated environments
• Conclusions
• Acknowledgments

Chapter 7: An Overview of the Industrial Aspects of Antibiotic Discovery
Arnold L. Demain and Evan Martens

• Abstract
• Introduction

Chapter 8: Accessing Marine Microbial Diversity for Drug Discovery
William Fenical H. Fenical and Lynette Bueno Perez

• Abstract
• Introduction
• The marine microbial environment
• Sampling marine microenvironments
• Select habitat marine bacteria
• Culturing marine bacteria for drug discovery
• Examples of obligate marine microbial metabolites
• Case studies of marine drug discovery
• Salinosporamide A
• Abyssomicins
• Thiocoralines
• Concluding remarks
• Acknowledgment

Chapter 9: Cryptic Pathways and Implications for Novel Drug Discovery
Kozo Ochi

• Abstract
• Introduction
• Homologous expression of silent genes
• Heterologous expression of silent genes
• Metabolism remodeling and metabolic engineering
• Concluding remarks

Chapter 10: The Nagoya Protocol Applied to Microbial Genetic Resources
Philippe Desmeth

• Abstract
• The convention on biological diversity
• Culture collections: professionals underpinning microbial realm exploitation
• Specificities of microorganisms, ownership of microbiological material
• Continuum in life sciences R&D—extended role of culture collections
• Building a community of connected centers of expertise
• Life sciences practitioners in the arena of political negotiations
• Lack of awareness, ignorance, mistrust, disdain
• The initiatives of the culture collections related to ABS and the Nagoya Protocol
• WDCM, from pioneering to breakthrough, from CCINFO to GCM
• Gaining TRUST, building TRUST

Chapter 11: Fungal Genetic Resources for Biotechnology
Dr. McCluskey

• Abstract
• Introduction
• Conclusions
• Acknowledgment

Chapter 12: Industrial Culture Collections: Gateways from Microbial Diversity to Applications
Olga Genilloud

• Abstract
• Introduction
• Access to microbial diversity: the convention of biological diversity and the nagoya protocol
• Building an industrial culture collection: expanding the diversity of cultured microbial sources
• Strain selection and dereplication tools
• Culture-based approaches and generation of libraries of microbial extracts
• LC-MS profiling and metabolite annotation
• Impact of genomics and genome mining to exploit microbial culture collections
• Applications in biotechnology and role in future NPs discovery

Chapter 13: An Overview of Biological Resource Center-Maintenance of Microbial Resources and Their Management
Ken-ichiro Suzuki

• Abstract
• Introduction
• Acknowledgments

Chapter 14: IP and The Budapest Treaty—Depositing Biological Material for Patent Purposes
Vera Bussas

• Abstract
• Intellectual property rights—why to deposit biological material
• How to deposit biological material—the practical procedure of a patent deposit
• How to request the furnishing of samples of patent organisms
• Complications arising during the deposition procedure
• Notes
• Conclusions
• Acknowledgments

Chapter 15: Biosafety, Transport and Related Legislation Concerning Microbial Resources—An Overview
Vera Bussas, Yogesh Shouche and Avinash Sharma

• Abstract
• Sampling of microorganisms—Convention on Biological Diversity and its Nagoya Protocol
• Isolation of microorganisms—Biosafety Considerations
• Valuable microbial isolates—biosecurity issues
• Shipping of microorganisms—no trivial issue
• Conclusions
• Abbreviations
• Acknowledgments