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Microbiology of Atypical Environments

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Contents

Contributors

Cover Picture

Preface

Section 1: Methods for Studying Microorganisms in Space

Chapter 1: Microbiology of the Built Environment in Spacecraft Used for Human Flight

1. Introduction

2. Microbiological Monitoring in Human-Occupied Spacecraft

2.1. Microorganisms in Human-Occupied Spacecraft

3. Ground-Based Tests (Simulating Microgravity in the Laboratory)

4. Microorganisms Associated With Water Recovery

5. Relevance of the Spacecraft Microbiome to Humans during Space Exploration

6. Microbial Influences on Spacecraft Integrity and Function

7. Biofilms and Their Impact on Spaceflight

8. Long-Term Studies

Conclusions

Future Directions

Acknowledgements

References

Chapter 2: The Study of Microbial Survival in Extraterrestrial Environments Using Low Earth Orbit and Ground-Based Experimen

1. Introduction

2. Microbiological Facilities in Space: Past and Present

2.1. The Long Duration Exposure Facility

2.2. EUropean REtrievable Carrier

2.3. BIOPAN

2.4. EXPOSE Facility

2.5. Organism/Organic Exposure to Orbital Stresses Nanosatellite

3. Ground-based Simulation Facilities

3.1. Simulated Mars Conditions

3.2. Simulated Space Conditions

3.3. Simulating Lithopanspermia

3.3.1. Light gas gun

3.3.2. Shock recovery experiments

3.3.3. ESAs STONE experiment

4. Postexposure Analyses

4.1. Microscopic Analysis

4.2. Metabolic Analysis

4.3. Molecular Analyses

5. Life Detection

5.1. Spectroscopic Methods

5.1.1. Infrared spectroscopy

5.1.2. UV-visible spectroscopy

5.1.3. Raman spectrometry

5.2. Gas Chromatography-Mass Spectrometry

Conclusion

References

Further Reading

Chapter 3: Persistence of Fungi in Atypical, Closed Environments: Cultivation to Omics

1. Introduction

2. International Space Station and Other Confined Facilities as Microbial Habitats

2.1. Microbial Sample Collection and Initial Processing

3. Progression From Culture- to Genome-Based Approach in Microbial Characterization of Confined Spaces

3.1. Culture-Based Microbial Analysis

3.2. DNA-Based Microbial Analyses

3.2.1. Pyrosequencing- and Illumina-derived fungal diversity

3.2.2. Metagenomics-derived fungal diversity and functional characterization

Conclusions and Perspectives

Acknowledgements

References

Section 2: Molecular Methods

Chapter 4: Molecular Methods for Studying Microorganisms From Atypical Environments

1. Introduction

2. Current Status of Microbial Diversity at Atypical Environments

3. Application of Molecular Tools for Studying Atypical Microbial Diversity

3.1. Whole Community Analysis

3.1.1. DNA-DNA hybridization (DDH)

3.1.2. Analysis of G+C content

3.1.3. Complete microbial genome sequencing

3.1.4. Use of metagenomics

3.2. Partial Community Analysis

3.2.1. Clone library method

3.2.2. Genetic fingerprinting techniques

3.2.2.1. DGGE/temperature gradient gel electrophoresis (TGGE)

3.2.2.2. Single-strand conformation polymorphism (SSCP)

3.2.2.3. Rapidly amplified polymorphic DNA (RAPD)

3.2.2.4. ARDRA

3.2.2.5. Terminal restriction fragment length polymorphism (TRFLP)

3.2.2.6. Length heterogeneity PCR (LH-PCR)

3.2.2.7. Ribosomal intergenic spacer analysis (RISA)

3.2.3. DNA microarray

3.2.3.1. 16S rRNA gene microarrays

3.2.3.2. Functional gene arrays (FGA)

3.2.4. qRT-PCR

3.2.5. Fluorescence in situ hybridization (FISH)

3.2.6. Fatty acid methyl ester (FAME) analysis

3.3. Applications of Next-Generation Sequencing (NGS)

3.4. Study of Functional Microbial Diversity

3.4.1. Stable isotope probing (SIP)

3.4.2. Microautoradiography (MAR)

3.4.3. Isotope array

3.5. Applications of Postgenomic Techniques

3.5.1. Metaproteomics

3.5.2. Proteogenomics

3.5.3. Metatranscriptomics

Conclusions and Future Approaches

References

Further Reading

Chapter 5: Measuring Microbial Metabolism in Atypical Environments

1. Defining 'atypical'

1.1. Do Typical Laboratory Explorations Represent the Typical Microbe?

1.1.1. Defining 'atypical' and 'extreme': The habitat and the microbe

1.1.2. Terrestrial microbial persistence

1.1.3. Dormancy, latency, and activity

1.1.4. Experimental time scales: Taking on the challenge

2. Metabolism vs Survival

2.1. Microbial-Societal Interface: The Metabolic Impact of Microbes in Atypical Environments

2.1.1. Microbial dormancy: Academic focus

2.1.2. Microbial metabolism: Societal impact

2.1.3. The relation between metabolic rate and impact

3. Observing Microbial Metabolism: Techniques

3.1. The Historical, the Trendy, and the Novel: Respecting and Harnessing Them

3.1.1. Microscopy: Cell morphology and cell associations under extreme conditions

3.1.2. Energy dynamics: Closed and open energy systems in microbial communities inhabiting extreme environments

3.1.3. Genomics, proteomics, and metabolomics: The building blocks of the cell under extreme conditions

4. Metabolism in Atypical Environments: Gradients, Cycles, and Divergent Timespans

4.1. Environmental Cycles, Gradients, and Interfaces

4.2. The Rate of the Researcher Relative to the Rate of the Subject

References

Further Reading

Chapter 6: Territories of Rock-Inhabiting Fungi: Survival on and Alteration of Solid Air-Exposed Surfaces

1. Rock Surface Biofilms and Rock-Inhabiting Fungi as Their Indicator Organisms

2. Research Development Stages: From Exotic Niches to Realization of the Ubiquitous Presence

2.1. Research in the 1980s: Proof of Existence and Activity

2.2. Research in the 1990s: Black Fungi on White Marble and the First Phylogenetic Analysis

2.3. Research in the 2000s: MCF Are Shown to Be Part of Subaerial Biofilms and Multigene Phylogenetic Methods Are Applied ...

2.4. Research in the 2010s: Advent of Whole-Genome Sequences and Model Organisms

3. Methods to Analyse the Presence and Diversity of RIF

3.1. Microscopy/Visualization of Exact Position on the Substrate

3.2. Diversity Exploration

3.3. Culture Collections=Biodiversity Resource

4. How to Approach ``Life on rocks´´-How Do They Survive?

4.1. Protective Substances of MCF

4.2. Analysing Survival Capabilities and Physiology of MCF

5. How Do MCF Change the Rock Surface?

5.1. Biogenic Influences on Mineral Substrate

5.2. Subtle MCF-Induced Geochemical Changes in the Substrate Can Be Detected by Precise and Sensitive Analytical Methods

5.3. Natural Samples vs Model Laboratory Studies

6. Outlook

References

Chapter 7: Taxonomy of Oral Bacteria

1. Introduction

1.1. The Oral Cavity: Not One, But Many Environments

1.2. The Diversity of the Oral Microbiome

1.3. The Two Major Oral Polymicrobial Diseases and Their Aetiologies

1.3.1. Dental caries

1.3.2. Chronic periodontitis

2. Methods for Characterising Oral Bacteria

2.1. Microscopy

2.2. Bacterial Culture

2.2.1. Characterisation of the oral microbiota with bacterial culture

2.3. Genomic Methods

2.3.1. The 16S rRNA gene

2.3.2. Denaturing gradient gel electrophoresis

2.3.2.1. Characterisation of the oral microbiota with DGGE

2.3.3. 16S rRNA gene sequencing

2.3.3.1. Characterisation of the oral microbiota with 16S rRNA gene sequencing

2.3.4. Metagenomics of the oral microbiome

2.3.4.1. Characterisation of the oral microbiota with metagenomics

2.3.5. Metatranscriptomics of the oral microbiome

2.3.6. The future of characterising the oral microbiome

Conclusions

References

Chapter 8: Aqueous Methods for Extraction/Recovery of Macromolecules From Microorganisms of Atypical Environments: A Focu ...

1. Introduction

2. TPP as an Emerging and Attractive Technique for Macromolecules Recovery

3. Advantages of TPP

4. TPP Process

5. Mechanisms of TPP

6. Factors Affecting TPP Process

6.1. Impact of Ammonium Sulphate

6.2. Impact of t-Butanol (Crude Extract to t-BuOH Ratio)

6.3. Impact of pH

6.4. Impact of Temperature

7. Variants of TPP

7.1. Macroaffinity Ligand-Facilitated TPP (MLF-TPP)

7.2. Enzyme-Assisted TPP (EA-TPP)

7.3. Ultrasound-Assisted TPP (UA-TPP)

7.4. Microwave-Assisted TPP (MA-TPP)

7.5. Metal-Ion Assisted TPP (MIA-TPP)

7.6. Ionic Liquid-Based TPP (IL-TPP)

8. Applications of TPP and Its Potential Uses to Target Macromolecules From Microbial of Atypical Environments

Conclusions

References

Chapter 9: Microbial Community Composition and Predicted Functional Attributes of Antarctic Lithobionts Using Targeted Ne ...

1. Introduction

1.1. DNA Sequencing Technology

1.2. Bioinformatics

1.3. Extreme Ecosystems and Lithobiont Microbial Communities

2. Module A: Sample Processing and Data Analysis

2.1. Sample Preparation, DNA Extraction, and NGS

2.1.1. Data output

3. Module B: Bioinformatics Pipeline

3.1. Quality Checking, Trimming, and Merging the Sequence Reads

3.1.1. Data output

3.2. Clustering OTUs and Assigning Representative Sequences

3.2.1. Data output

3.3. Assigning Taxonomy Using Publicly Available Databases

3.3.1. Data output

3.4. Making an OTU Table and Checking Sequence Depth

3.4.1. Data output

4. Module C: Taxonomic Profile, Comparative Analyses, and Functional Profiles

4.1. Taxonomic Profile

4.1.1. Data output

4.2. Comparative Analyses

4.2.1. Data output

4.3. Functional Profile

4.3.1. Data output

4.4. Co-occurrence Analysis

4.4.1. Data output

5. Microbial Community Composition and Predicted Functions of the Rock Samples

5.1. Microbial Community Profile

5.2. Comparative Analyses

5.3. Predicted Functions

5.4. Co-occurrence and Likely Keystone Taxa

6. General Summary

Acknowledgements

References

Further Reading

Section 3: Microscopic Methods

Chapter 10: Methods for Collection and Characterization of Samples From Icy Environments

1. Introduction

1.1. Icy Environments

1.2. Cautionary Note

1.3. Metadata and Sample Labelling

2. Collection Methods

2.1. General

2.2. Bulk Ice

2.3. Permafrost

2.4. Sea Ice Brine

2.5. Cryopeg Brines

3. Imaging

3.1. Light Microscopy

3.1.1. Live-cell observation and enumeration

3.1.1.1. Methods for liquid samples

3.1.1.2. Methods for biofilms

3.1.1.3. Methods for frozen matrices

3.1.2. Staining methods

3.2. Fluorescence Microscopy

3.2.1. Dye considerations

3.2.2. Microscope considerations

3.3. Digital Holographic Microscopy

3.4. Electron Microscopy

3.4.1. Transmission electron microscopy

3.4.2. Scanning electron microscopy

4. Shipping and Preservation

4.1. Freezing

4.2. Keeping Cells Alive

4.3. Considerations for Genomics

References

Chapter 11: Cryo-Electron Microscopy of Extremely Halophilic Microbes

1. Introduction

2. Atypical Environments for Microbes in EM

2.1. Drying

2.2. Substitution of Water

2.3. Vitrification and Cryo-EM

2.4. Environmental EM

3. Atypical Environments for Cryo-EM

3.1. High Temperatures

3.2. Anaerobic Environments

3.3. High Salt Conditions

4. Halophiles and Their Macromolecular Structures in Conventional Electron Microscopy

5. Cryo-EM at Moderate Salt Conditions

6. Cryo-EM at High Salt Conditions

6.1. High Salt Conditions in Cryo-EM of Haloviruses

6.2. High Salt Conditions in Cryo-EM of Halophilic Microbes

6.3. Minimizing the Salt Content of H. salinarum

6.4. Thinning Samples for Cryo-EM Prior to Vitrification

6.5. Cryopreparation of an Extreme Halophile: H. salinarum

6.6. Thinning Samples for Cryo-EM After Vitrification by Focused Ion Beam (FIB) Milling

6.7. A Glimpse on HPF and Cryosectioning

6.8. Cryo-EM of High Salt Specimens

Conclusions

References

Section 4: Organisms

Chapter 12: Methods to Study Magnetotactic Bacteria and Magnetosomes

1. Introduction

2. Method for Studying MTB

2.1. Collection of Samples Containing MTB

2.2. Enrichment and Isolation of MTB

2.3. Mass Culture of MTB

2.4. Morphology and Phylogenetic Diversity of MTB

2.5. Magnetic Properties of MTB

2.5.1. Room-temperature magnetism

2.5.2. Low-temperature magnetism

3. Methods for Studying MS

3.1. Extraction and Purification of MS

3.2. Morphology Characteristics of MS

3.3. Magnetic Properties of MS

3.4. Formation of MS

4. Future Prospects

References

Chapter 13: Molecular Methods to Study Vibrio parahaemolyticus and Vibrio vulnificus From Atypical Environments

1. Introduction

2. V. parahaemolyticus

2.1. V. parahaemolyticus as a Human Pathogen

2.2. Virulence Factors of Human Pathogenic V. parahaemolyticus

2.2.1. TDH

2.2.2. TRH

2.2.3. Type III secretory system

2.2.4. Type VI secretory system

2.3. Methods to Detect V. parahaemolyticus

2.3.1. Conventional culture-based methods to detect V. parahaemolyticus

2.3.1.1. Culture method

2.3.1.2. Enrichment broth

2.3.1.3. Selective agar

2.3.1.4. Traditional methods of enumeration

2.3.2. Molecular-based detection of V. parahaemolyticus

2.3.2.1. Polymerase chain reaction and its variants

2.3.2.2. Loop-mediated isothermal amplification (LAMP)

2.3.2.3. MPN-PCR

2.3.2.4. Colony hybridization

2.3.2.5. Immunological methods

3. V. vulnificus

3.1. V. vulnificus and Its Characteristics

3.2. Conventional Culture-Based Methods

3.2.1. Selective culture media

3.2.1.1. TCBS agar

3.2.1.2. Cellobiose polymyxin colistin (CPC) agar

3.3. Molecular Methods for the Detection of V. vulnificus

3.3.1. DNA hybridization

3.3.2. PCR and its variants

3.3.3. LAMP

Conclusion

Acknowledgements

References

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