ENVIRONMENTAL MICROBIOLOGY RESEARCH TRENDS

ENVIRONMENTAL MICROBIOLOGY RESEARCH TRENDS

CONTENTS

PREFACE

Chapter 1 EVALUATION AND VERIFICATION OF SOIL REMEDIATION

ABSTRACT

1. INTRODUCTION

1.1. ENVIRONMENTAL TECHNOLOGY VERIFICATION AND ACCREDITATION

1.2. REMEDIATION TECHNOLOGY VERIFICATION

1.3. CHARACTERISTICS AND MONITORING OF IN SITU SOIL REMEDIATION

1.3.1. Technology Monitoring and the Mass-Balance of Bioremediation

Soil-relevant monitoring-endpoints for bioremediation

Soil microflora- and plant-relevant monitoring-endpoints for bioremediation

Substrate(=contaminant)-relevant monitoring-endpoints for bioremediation

Product-relevant monitoring-endpoints for bioremediation

1.3.2. Environmental Monitoring

In situ and Ex situ

Integrated Monitoring

1.3.3. Post-Remediation Monitoring of Treated Sites

1.4. TWO IN SITU BIOTECHNOLOGIES EVALUATED BY THE MOKKA VERIFICATION SYSTEM

1.4.1. In situ Cyclodextrin Technology (CDT)

1.4.2. Combined in situ Chemical- and Phytostabilisation (CCP)

2. MATERIALS AND METHODS

2.1. CycloDextrin Enhanced Complex Technology (CDT)

2.1.1. Description of the Transformer-Oil Contaminated Site

2.1.2. Laboratory Testing and Microcosm Experiments for the Development of CDT

2.1.3. Field Application of the Complex Cyclodextrin Technology

2.1.4. Integrated Assessment Tool for CDT Monitoring

Chemical Analyses

Soil Toxicity

2.2. Combined Chemical and Phytostabilisation (CCP)

2.2.1. Description of the Toxic-Metal Contaminated Site

2.2.2. Laboratory Testing and Microcosms Experiments

2.2.3. Field Experiments for the Combined Chemical and Phytostabilisation

2.2.4. Integrated Assessment Tools of CCP Monitoring

Chemical Analyses

Environmental Toxicity Testing

2.3. Technology-Verification Tools used for the Evaluation of the Field Demonstrations

2.3.1. Mass-Balance

2.3.2. Risk Assessment

2.3.4. Cost Evaluation

Cost Assessment

Cost-Efficiency Assessment (CEA)

Cost-Benefit Assessment (CBA)

2.3.5. SWOT Analysis

3. RESULTS AND DISCUSSION

3.1. Verification of the CDT Technology

3.1.1. Summary Results of the Microcosm Tests and the In Situ Field Application

3.1.2. Evaluation of the CDT Technology and the Validation of the Verification Tool

Mass Balance of the CDT Technology

Calculation of the substrate’s mass (S)

Calculation of products’ mass (P)

Biodegraded transformer oil calculated on the basis of the CO2 production:

Risks of the Technology

Initial and Final Risk of the Contaminated Soil and Groundwater

Site Specific Environmental Risk of the Application of In Situ CDT

Risk Reduction Alternatives of the CDT Technology

Time Requirement of the Alternatives

Regional and Global Risk Elements in Comparison with the Technology-Alternatives

Cost-efficiency of the CDT

SWOT-analysis of the CDT

3.1.3. Summary of the Technology-Verification Applied for CDT

3.2. Verification of the CCP-technology

3.2.1. Summary Results of the CCP in Lab-Microcosms and Field Experiments

3.2.2. Evaluation of the CPP Technology and Validation of the Verification Tool

Mass Balance of the CCP

Risks Related to the CCP

Initial and Final Risk of the Contaminated Soil

Site Specific Environmental Risk of the Application of CCP

Risk Reduction Alternatives

Time Requirement

Regional and Global Risk Elements in Comparison with the Technology-Alternatives

Costs-Efficiency Assessment

SWOT of the CCP

3.2.3. Summary of the Verification Tool Applied for Combined Chemical and Phytostabilisation

4. CONCLUSION

5. REFERENCES

Chapter 2 DISINFECTION OF EMPTY ANIMAL HOUSES – SCIENTIFIC EVIDENCE FOR APPLIED PROCEDURES

ABSTRACT

INTRODUCTION

PROCEDURES FOR CLEANING AND DISINFECTION OF ANIMAL HOUSES

FACTORS THAT INFLUENCE THE EFFECTIVENESS OF DISINFECTION

General Principles

The Disinfectant

Disinfectant Types and Factors that Influence their Efficacy

Heat

The Micro-Organism

Type of Micro-Organism

General Aspects of Resistance in Micro-Organisms

Membrane-related mechanisms

Biofilm

Enzymatic Breakdown of Disinfectant in Cell

Efflux Pumps

Stress Response Systems in Bacteria and Cross-Resistance

DISINFECTION TESTS

General Principles

Test Principles

Types of Disinfection Tests

APPLIED RESEARCH

Disinfectant Resistance Studies in which Laboratory Conditions were Regulated

Disinfection Resistance Studies Involving Field Strains

Other Laboratory Disinfectant Studies

Field Studies

CONCLUSION

REFERENCES

Chapter 3 NATURAL BACTERIAL BIOFILMS IN THE ENVIRONMENT

ABSTRACT

I. STRUCTURE AND FUNCTIONS OF NATURAL BIOFILMS

I.1. Biofilm Bibliometry

I.2. Biofilm History

I.3. Biofilm Definition

I.4. Biofilm Formation and Structure

I.4.1. Bacterial Adhesion

I.4.2. Biofilm Growth and Matrix Production

I.4.3. Biofilm Maturation

I.5. Biofilm Phenotype?

II. BIOFOULING AND BIOCORROSION

II.1. Biofilm Context and Concept in Biofouling and Biocorrosion

II.2. Biofouling and Biocorrosion Processes

II.2.1. Interface Bacterial Metabolism

II.2.2. Bacteria Respiration and Biocorrosion

II.2.3. Sulfate-Reducing Bacteria (SRB)

II.2.4. Biofilm EPS Presence is also a Promoting Biocorrosion Factor

II.3. Targets and Biofilm Prevention Strategies

II.4. Prospect

II.4.1. Use of Natural Molecules with Antifouling Activity

II.4.2. Development of New Polymers for the Formulation of Paintings

II.4.3. Capping Way

III. PHOTOSYNTHETIC BIOFILMS IN THE ENVIRONMENT

III.1 Similarities and Differences between Phototrophic and Chemotrophic Biofilms

III.2. Structure and Composition of Phosynthetic Biofilms

III.2.1. Adaptations to High Light Intensities

III.2.2. Stratified Sedimentary Biofilms and Microbial Mats

III.3. Wax and Wane of Photosynthetic Biofilms

III.3.1. Photosynthetic Biofilm Development and Succession Phenomena

III.3.2. Role of Predation in Photosynthetic Biofilms

III.4. Photosynthetic Biofilms and the Geological History of Life on Earth

CONCLUSION

ACKNOWLEDGMENTS

REFERENCES

Chapter 4 MICROBIAL AND CHEMICAL ASSAYS TO DETERMINE THE ORIGIN OF FAECAL POLLUTION AND THE PRESENCE OF WATERBORNE PATHOGENS

ABSTRACT

INTRODUCTION

METHODOLOGY FOR THE IDENTIFICATION OF THE ORIGIN OF FAECAL POLLUTION IN WATER SOURCES

Genotyping of F-RNA Phages

Gene Probes used for F-RNA Phage Genotyping

Gene Hybridisation of F-RNA Isolates

Detection of DNA:RNA Hybrids of F-RNA Phages

Faecal Sterols Used as a Tool to Trace the Origins of Faecal Pollution in Water

Cholesterol Used as a Faecal Indicator

Coprostanol Used as a Faecal Indicator

Faecal Sterol Formation and Structure

Extraction of Faecal Sterols from Water

Gas Chromatography-Mass Spectrometry used for the Detection of Faecal Sterols

Sample Collection for F-RNA Genotyping and Chemical Assays (Study 1)

Sample Collection for F-RNA Genotyping During an Intervention Study (Study 2)

RESULTS AND DISCUSSION

Evaluation of DNA:RNA Hybridisation Techniques Using Control Phages

Genotyping of F-RNA Phages from Wastewater and River Samples

Faecal Sterol Assays on Wastewater Samples

Faecal Sterol and F-RNA Phage Genotyping Assays on Environmental Samples

Origin of Male Specific F-RNA Bacteriophage Groups in the Primary Water Sources

Origin of Male Specific F-RNA Bacteriophage Subgroups in the Stored Household Water at the Point-of-Use in the Traditional and CDC Safe Water Storage Containers in Rural Households

Summary of the Use of Male Specific F-RNA Bacteriophages Group Typing to Determine the Faecal Source Origin in Primary Water Sources and Drinking Water Stored in Traditional and CDC Safe Storage Containers in Rural Households

CONCLUSION

ACKNOWLEDGEMENTS

REFERENCES

Chapter 5 THE EFFECTS OF FINE SCALE ENVIRONMENTAL VARIATION ON MICROBIAL COMMUNITY STRUCTURE AND FUNCTION IN AQUATIC ENVIRONMENTS

ABSTRACT

INTRODUCTION

FINE SCALE VARIATION IN MICROBIAL COMMUNITIES IN THE WATER COLUMN OF AQUATIC ENVIRONMENTS

FINE SCALE VARIATION IN BIOFILMS

FINE SCALE VARIATION IN MICROBIAL COMMUNITIES IN SEDIMENTS

THE EFFECTS OF PARTICLE SIZE ON BACTERIAL COMMUNITY STRUCTURE AND ACTIVITY IN WETLAND SEDIMENTS

FINE SCALE SPATIAL VARIATION IN MICROBIAL ACTIVITY ACROSS THE SURFACE OF DECOMPOSING LEAVES

CONCLUSION

REFERENCES

Chapter 6 CHANGES OF MARINE BACTERIAL POPULATIONS IN A SHIP’S BALLAST WATER AND SEDIMENT, AND APPLICATION OF SHOCK PRESSURES TO COMPLETE KILLING OF VIBRIO SP. CELLS ISOLATED FROM BALLAST WATER

1. INTRODUCTION

2. CHANGES OF MARINE BACTERIAL POPULATIONS IN BALLAST WATER AND SEDIMENT OF LNG CARRIER BOUND FROM JAPAN TO QATAR FOR LOADING LNG

2.1. Navigation Route and a Ship Used for Sampling Ballast Water and Sediment

2.2. Changes in the Number of Viable Marine Bacterial Populations in Ballast Water and Sediment

2.3. Vibrio Species Isolated from Ballast Water and Sediment

3. BALLAST WATER MANAGEMENT IN ORDER TO PREVENT DIFFUSION OF NON-NATIVE SPECIES

3. 1. Treatment of Ballast Water by Chemical and Physical Approaches

3.2. Vibrio sp. September 1 and Properties of Shock Pressures

3.3. Inactivation of Vibrio sp. September 1 by Exposure to Shock Pressures

3.4. Additional Effect of Sodium Ascorbate on the Number of Colony-Forming Vibrio sp. September 1 Cells After Exposure to Shock Pressures

3.5. Observation of Morphological Changes of Cells Exposed by Shock Pressures with a Scanning Electron Microscope

CONCLUSION

REFERENCES

Chapter 7 BIODIVERSITY AND ECOLOGY OF EUKARYOTIC ORGANISMS IN EXTREME ACIDIC ENVIRONMENTS, THE RÍO TINTO CASE

ABSTRACT

1. INTRODUCTION

Extreme Environments and Extremophiles

Eukaryotes in Extreme Environments

2. ACIDIC ENVIRONMENTS

3. EUKARYOTIC DIVERSITY AND ECOLOGY IN RIO TINTO

4. EXTREME ACIDIC PHOTOSYNTHETIC BIOFILMS

5. STRUCTURE OF EXTREME ACIDIC PHOTOSYNTHETIC BIOFILMS

6. EXTRACELLULAR MATRIX ASSEMBLY EXTREME ACIDIC EUKARYOTIC BIOFILMS

7. IMPLICATION OF THE EXTRACELLULAR MATRIX IN HEAVY METAL ABSORPTIONS

8. CONCLUSION

ACKNOWLEDGEMENTS

REFERENCES

Chapter 8 ARE RHIZOBIUM AND SOIL ENZYME ACTIVITIES GOOD INDICATORS OF HEAVY METAL SOIL CONTAMINATION?

ABSTRACT

1. INTRODUCTION

2. HEAVY METAL TOLERANCE OF RHIZOBIUM STRAINS ISOLATED FROM BRAÇAL MINE

3. SOIL ENZYME ACTIVITIES

4. CONCLUSION

6. REFERENCES

Chapter 9 VIRUS-BINDING PROTEINS IN WATER ENVIRONMENTS: NATURAL LIGANDS FOR HUMAN VIRUSES

ABSTRACT

INTRODUCTION

OCCURENCE, FUNCTIONS AND PROPERTIES OF VBP

THE ISOLATION OF ADENOVIRUS-BINDING PROTEIN

GENE ACQUISITION OF VIRUS-BINDING PROTEIN

FUTURE APPLICATIONS AND PERSPECTIVES OF VIRUS-BINDING PROTEIN

CONCLUSION

REFERENCES

Chapter 10 ADVANCES IN MARINE BACTERIAL POLLUTION MONITORING

ABSTRACT

INTRODUCTION

Assessment of the Microbiological Quality of Seawater: Importance of Coastal Monitoring

Why the Need for Advanced Technologies and Rapid Methods?

Escherichia coli as the Main Bacterial Indicator of Faecal Pollution

Expertise Developed at the CNR- IAMC- Messina in the Field of Rapid Methods for the Detection of Bacterial Indicators

Aims of the Chapter

MATERIALS AND METHODS

Monitoring Area

FA Method

Combined FA–Viability Staining Protocol

β-glucuronidase Activity Estimates

Real-time PCR

Culture Counts

RESULTS

FA Method

Combined FA–Viability Staining Protocol

β-glucuronidase Activity Estimates

Real-time PCR

CONCLUSION

REFERENCES

INDEX

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