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Thread: Environmental Microbiology of Aquatic and Waste Systems

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    Default Environmental Microbiology of Aquatic and Waste Systems

    Environmental Microbiology of Aquatic and Waste Systems
    by: Nduka Okafor
    year: 2011
    pages: 324
    bookmarked: yes
    paginated: yes
    vector: yes
    cover: yes
    searchable: yes
    doi: 10.1007/978-94-007-1460-1

    This book places the main actors in environmental microbiology, namely the microorganisms, on center stage. Using the modern approach of 16S ribosomal RNA, the book looks at the taxonomy of marine and freshwater bacteria, fungi, protozoa, algae, viruses, and the smaller aquatic animals such as nematodes and rotifers, as well as at the study of unculturable aquatic microorganisms (metagenomics). The peculiarities of water as an environment for microbial growth, and the influence of aquatic microorganisms on global climate and global recycling of nitrogen and sulphur are also examined. The pollution of water is explored in the context of self-purification of natural waters. Modern municipal water purification and disease transmission through water are discussed. Alternative methods for solid waste disposal are related to the economic capability of a society. Viruses are given special attention. By focusing on the basics, this primer will appeal across a wide range of disciplines.

    Common terms and phrases:
    algae anammox Archaea bacteria chlorine cyanobacteria landfill methanogens microorganisms photosynthesis protozoa
    Cover

    Environmental Microbiology of Aquatic and Waste Systems

    ISBN 9789400714595

    Preface

    Contents

    Part I: Introduction

    1: Nature, Properties, and Distribution of Water

    1.1 Physical and Chemical Properties of Water and Their Consequences

    1.1.1 Molecular Structure of Water and Its Strong Surface Tension

    1.1.2 The High Surface Tension of Water and Capillarity in Plants

    1.1.3 The Three Physical States of Water, and the Floatation of Ice

    1.1.4 The Thermal Properties of Water and Their Effect on Climate

    1.1.5 The Change in the Nature of Water at Different Temperatures and Lake Temperatures

    1.1.6 The Low Electrical Conductivity of Pure Water

    1.1.7 The High Chemical Reactiveness of Water

    1.1.8 The pH of Water

    1.1.9 The High Solvent Power of Water

    1.2 Importance and Uses of Water

    1.2.1 Composition of Biological Objects

    1.2.2 Drinking by Man and Animals and Domestic Use

    1.2.3 Irrigation and Aquaculture

    1.2.4 Power Generation

    1.2.5 Transportation

    1.2.6 Recreation

    1.2.7 Human Affairs

    1.3 The Hydrologic Cycle

    1.4 Classification of Waters

    1.4.1 Natural Waters

    1.4.2 Artificial Waters

    1.5 Global Distribution of Water on Earth and Its Study

    References

    2: Peculiarities of Water as an Environmental Habitat for Microorganisms

    2.1 The Peculiar Nature of Water as an Environment for Microbial Habitation

    2.2 Ecological Habitats of Microorganisms in Aquatic Environments

    2.3 Foreign Versus Indigenous Aquatic Bacteria

    2.4 Challenges of Aquatic Life: Factors Affecting the Microbial Population in Natural Waters

    2.5 Methods for the Enumeration of Microorganisms in the Aquatic Environment

    2.5.1 Cultural Methods

    2.5.2 Direct Methods

    2.5.2.1 Light Microscopy

    2.5.2.2 Electron Microscopy

    2.5.2.3 Flow Cytometry

    2.5.3 Determination of Bacterial Mass

    2.5.3.1 Direct Methods

    2.5.3.2 Indirect Methods

    References

    Part II: Biological Aspects of Microorganisms in Aquatic Environments

    3: Aspects of the Molecular Biology of Microorganisms of Relevance to the Aquatic Environment

    3.1 Protein Synthesis

    3.1.1 Transcription

    3.1.2 Translation

    3.2 The Polymerase Chain Reaction

    3.2.1 Some Applications of PCR in Environmental Biotechnology

    3.3 Microarrays

    3.3.1 Applications of Microarray Technology

    3.4 Sequencing of DNA

    3.4.1 Sequencing of Short DNA Fragments

    3.4.2 Sequencing of Genomes or Large DNA Fragments

    3.4.2.1 Use of Bacterial Artificial Chromosomes

    3.4.2.2 Use of the Shotgun Approach

    3.5 The Open Reading Frame and the Identification of Genes

    3.6 Metagenomics

    References

    4: Taxonomy, Physiology, and Ecology of Aquatic Microorganisms

    4.1 Taxonomy of Microorganisms in Aquatic Environments

    4.1.1 Nature of Modern Taxonomy

    4.1.2 Evolution of the Classification of Living Things

    4.1.3 Determining Taxonomic Groups Within Domains

    4.1.3.1 Definition of Species

    4.1.3.2 Nomenclature of Biological Objects

    4.1.3.3 Criteria and Methods for the Identification and Classification of Bacteria and Archae: Morphological, Physiological, Nucleic Acid, and Chemical Properties

    Morphological and Physiological Methods

    Nucleic Acid Methods

    Chemical Analysis of Microbial Components for Taxonomic Purposes (Chemotaxonomy)

    4.1.4 Bacteria

    4.1.4.1 Taxonomic Groups Among Bacteria

    4.1.4.2 Aspects of the Physiology and Ecology of Microorganisms in the Aquatic Environment

    Photosynthesis

    The Pigments of Photosynthesis

    The Light Reactions

    The Dark or Light-Independent Reactions of Photosynthesis

    Summary: Differences Between Photosynthesis in Plants and in the Bacteria

    Aspects of the Physiology of Photosynthetic Bacteria

    Nitrogen Economy in Aquatic Systems

    Nitrogen Fixation

    Nitrification

    Denitrification

    Anammox

    The Sulfur Cycle in the Aquatic System and Bacteria

    Iron Bacteria

    4.1.5 Archae

    4.1.5.1 General Properties of Archaea

    4.1.5.2 Taxonomic Groups Among Archeae

    Euryarchaeota

    Crenarchaeota

    4.1.6 Microbial Taxonomic Groups Among Eucharia

    4.1.6.1 Protozoa

    4.1.6.2 Fungi

    Taxonomy of Fungi

    4.1.6.3 Algae

    Taxonomy of Algae

    4.1.7 Viruses

    4.1.7.1 Viral Taxonomy and Nomenclature

    4.1.7.2 The Viral Groups

    DNA Viruses (Groups I and II)

    RNA Viruses (Groups III, IV and V)

    Reverse Transcribing Viruses (Groups VI and VII)

    The Structure of the DNA and RNA Viruses

    4.1.7.3 Bacteriophages in the Aquatic Environment

    Life History of Bacteriophages

    Methods for the Study of Bacteriophages

    Isolation and Enumeration of Bacteriophages

    Bacteriophages and Their Bacterial Hosts

    4.1.8 Small Multicellular Macroorganisms in Aquatic Systems

    4.1.8.1 Crustaceans (Including Rotifers)

    4.1.8.2 Nematodes

    References

    Part III: The Ecology of Microorganisms in Natural Waters

    5: Ecology of Microorganisms in Freshwater

    5.1 Microbial Ecology of Atmospheric Waters

    5.2 Microbial Ecology of Surface Waters

    5.2.1 Rivers and Streams

    5.2.2 Lakes and Ponds

    5.2.3 Wetlands

    5.3 Ground Waters

    5.4 Some Microorganisms Usually Encountered in Fresh Water

    5.4.1 Bacteria

    5.4.1.1 New Data Regarding Freshwater Bacteria

    5.4.2 Fungi

    5.4.3 Algae

    5.4.4 Protozoa

    5.5 Succession of Organisms in the Breakdown Materials Added to Aquatic Systems

    5.5.1 The Physiological Basis of Aquatic Microbial Ecology

    5.6 Microbial Loop and the Food Web in a Freshwater System

    References

    6: Ecology of Microorganisms in Saline Waters (Seas and Oceans)

    6.1 The Ocean Environment

    6.2 Some Properties of Sea Water

    6.2.1 Salinity

    6.2.2 Temperature

    6.2.3 Light

    6.2.4 Nutrients

    6.2.5 Oxygen and CO2 in the Marine Environment

    6.2.6 Sea Sediments

    6.3 Microbial Ecology of the Seas and Oceans

    6.3.1 Bacteria

    6.3.2 Archae

    6.3.3 Fungi

    6.3.4 Algae

    6.3.5 Protozoa

    6.3.6 Viruses

    6.3.7 Plankton

    6.4 Unique Aspects of the Existence of Microorganisms in the Marine Environment

    6.4.1 Low Temperature

    6.4.2 High Pressure

    6.4.3 Oxygen

    6.4.4 Food/Nutrients

    6.4.5 Light

    6.4.6 High Temperature

    6.4.7 Size in Marine Microorganisms

    6.5 The Place of Microorganisms in the Food Chains of the Oceans and Seas

    6.6 Marine Microorganisms and Their Influence on Global Climate and Global Nutrient Recycling

    6.6.1 The Influence of Marine Microorganisms on Global Climate and Global Nutrient Recycling

    6.6.1.1 Global Marine Algal Sulfur Recycling, Dimethylsulfoniopropionate, Dimethyl Sulfide and Climate Change

    6.6.1.2 Carbon Recycling by Marine Algae and Reduction of Global Warming

    6.6.1.3 Marine Microorganisms and the Nitrogen Economy of Seas and Oceans

    Nitrogen Fixation in the Ocean

    Anaerobic Oxidations of Ammonium and of Methane

    6.6.1.4 The Global C:N:P Marine Ratio and Its Maintenance Through Microbial Activity: The Redfield Ratio

    References

    Part IV: Pollution and Purification of, and Disease Transmission in, Water

    7: Pollution of Aquatic Systems: Pollution Through Eutrophication, Fecal Materials, and Oil Spills

    7.1 Nature of Pollution

    7.1.1 The Concept of the Self-purification of Water as Basis for the Understanding of Pollution

    7.1.2 Definition of Pollution

    7.1.3 Kinds of Pollutants

    7.1.4 Pollution by Eutrophication

    7.1.4.1 “Algal Blooms” and Eutrophication

    Factors Encouraging Bloom Formation

    Factors Adversely Affecting Blooms

    7.1.5 Biological Indicators of Pollution by Eutrophication

    7.2 Pollution of Water with Reference to Human Health: Bacterial Indicators of Fecal Pollution

    7.2.1 Microbiological Examination of Water for Fecal Contamination

    7.2.1.1 Principle of Indicator Organisms

    7.2.1.2 Procedure for the Determination of Fecal Contamination

    7.2.1.3 Methods Used in the Enumeration of Indicator Organisms in Water

    7.2.1.4 Standard Water Analysis

    The Presumptive Test

    The Confirmed Test

    The Completed Test

    7.2.1.5 Total Maximum Daily Loads and Microbial Source Tracking in Water Pollution

    Microbial Source Tracking

    Methodologies Employed in MST

    Choice of the MST Method to Use

    7.3 Pollution by Petroleum in Oceans and Seas: Role of Microorganisms in Oil Degradation and Remediation

    7.3.1 Composition of Crude Oil

    7.3.1.1 Categorization of Crude Petroleum

    7.3.2 Oil Spills

    7.3.2.1 Behavior of Oil in an Oil Spill

    7.3.2.2 Remediation of Oil Spills

    References

    8: Disease Transmission in Water

    8.1 Disease Transmission Through Drinking Water

    8.1.1 Communicable Diseases Transmitted Through Drinking Water

    8.1.2 Disease Outbreaks in Drinking Water Due to the Presence of Chemicals, and Biotoxins

    8.1.2.1 Brief Notes on Some Water-Borne Diseases

    Cholera

    Salmonellosis

    Cryptosporidiosis

    Shigellosis

    Tuberculosis

    Atypical Tuberculosis

    Leptospirosis

    Enteropathogenic Escherichia coli

    Aeromonas

    Amoebiasis

    Giardiasis

    Viruses

    Parasitic Worms

    8.2 Disease Transmission in Recreational Waters

    8.2.1 Disease Transmission in Recreational Waters Through Fecal Material

    8.2.1.1 Fecal Bacteria Which Have Caused Disease Outbreaks in Recreational Waters

    8.2.1.2 Fecal Protozoa Which Have Caused Disease Outbreaks in Recreational Waters

    8.2.1.3 Fecal Viruses Which Have Caused Disease Outbreaks in Recreational Waters

    8.2.2 Disease Transmission in Recreational Water Through Non-fecal Material

    8.2.2.1 Disease Transmission by Bacteria in Recreational Water Through Non-fecal Material

    8.2.2.2 Disease Transmission by Viruses in Recreational Water Through Non-fecal Material

    8.2.2.3 Disease Transmission by Protozoa in Recreational Water Through Non-fecal Material

    8.2.2.4 Disease Transmission by Fungi in Recreational Water Through Non-fecal Material: Trichophyton spp. and Epidermophyton floccosum

    8.3 Disease Transmission Through Shellfish Growing in Fecally Contaminated Water

    8.3.1 Description of Shellfish

    8.3.2 Monitoring the Aquatic Environment of Shellfish Growth

    8.3.2.1 Procedure for Monitoring Shellfish Growing Areas in the US

    Classification of Shellfish Growing Areas

    8.4 Recent Developments Regarding Knowledge of Pathogens in Drinking Water

    References

    9: Municipal Purification of Water

    9.1 The Need for Water Purification

    9.2 The Quality of the Raw Water to Be Purified

    9.3 Processes for the Municipal Purification of Water

    9.3.1 Pretreatments

    9.3.2 Storage and Sedimentation Without Coagulation

    9.3.3 Aeration

    9.3.4 Coagulation and Flocculation

    9.3.5 Sedimentation

    9.3.6 Filtration

    9.3.7 Chlorination (and Other Methods of) Disinfection

    9.3.7.1 Reactions of Chlorine with Chemicals Found in Water

    9.3.7.2 The Present Practice of Water Chlorination

    9.3.7.3 Mode of Action of Chlorine Disinfection

    9.3.7.4 Factors Affecting the Efficacy of Disinfection in Water by Chlorine (and the other Halogens)

    9.3.7.5 Tests for Chlorine in Water

    9.3.7.6 Alternative Methods of Disinfection Besides Chlorine and Other Halogens

    9.3.7.7 Ozone

    Factors affecting the Efficacy of Ozonation in Water

    Mode of Action of Ozone

    9.3.8 Ultraviolet Light

    9.3.8.1 Mode of Action and Use of UV

    9.3.9 Iron and Manganese Control

    9.3.10 Softening of Water

    9.3.11 Fluoridation

    9.3.12 Algae Control (and Control of Taste and Odors)

    9.3.12.1 Methods for the Control of Algae and Taste and Odor

    9.3.13 Color and Turbidity Removal

    9.3.14 Miscellaneous Treatments Water Purification

    9.3.14.1 Plumbosolvency Removal

    9.3.14.2 Radium (Radioactivity) Removal

    9.3.14.3 Reverse Osmosis

    9.3.14.4 Ion Exchange

    9.3.14.5 Electrodeionization

    9.4 Purification of Bottled Water

    9.5 Standards Required of Water

    9.5.1 Standards Required for Drinking Water

    9.5.1.1 The Microbiological Standards

    9.5.1.2 Turbidity

    9.5.1.3 Chemical Standards

    9.5.2 Standards Required for Recreational Waters

    9.5.3 Standards Required for Shellfish Harvesting Waters

    References

    Part V: Waste Disposal in Aquatic and Solid Media

    10: Waste Disposal in the Aqueous Medium: Sewage Disposal

    10.1 Nature of Wastes

    10.2 Methods for the Determination of Organic Matter Content in Sewage and Wastewaters

    10.2.1 Determination of Dissolved Oxygen

    10.2.1.1 The Biological or Biochemical Oxygen Demand Test

    10.2.1.2 Permanganate Value Test

    10.2.1.3 Chemical Oxygen Demand

    10.2.1.4 Total Organic Carbon

    10.2.1.5 Total Suspended Solids

    10.2.1.6 Volatile Suspended Solids

    10.3 Systems for the Treatment of Sewage

    10.3.1 Aerobic Breakdown of Raw Waste Waters

    10.3.1.1 The Activated Sludge System

    Microbiology of the Activated Sludge Process

    Bulking in Activated Sludge Systems

    Nutrition of Organisms in the Activated Sludge Process

    Modifications of the Activated Sludge System

    Efficiency of Activated Sludge Treatments

    10.3.1.2 The Trickling Filter

    Microbiology of the Trickling Filter

    10.3.1.3 Rotating Discs

    10.3.1.4 Oxidation Ponds

    The Microbiology of the Oxidation Pond

    10.3.2 Anaerobic Sewage Systems

    10.3.2.1 Treatment of the Sludge from Aerobic Sewage Treatment Systems: Anaerobic Breakdown of Sludge

    10.3.2.2 The Septic Tank

    10.3.2.3 The Imhoff Tank

    10.3.2.4 Cesspools

    10.4 Advanced Wastewater Treatment

    10.4.1 Methods Used in Advanced Wastewater Treatment

    References*

    11: The Disposal of Municipal Solid Wastes

    11.1 The Nature of Wastes in General

    11.2 The World-Wide Development of Interest in the Environment

    11.2.1 The Stockholm Conference, 1972: Beginning of World-Wide Interest in the Protection of the Environment

    11.2.2 Environmental Regulation in the European Union

    11.2.3 Environmental Regulations in Japan

    11.2.4 Governmental Regulation of the Environment in Ghana

    11.2.5 Egypt’s Environmental Affairs Agency

    11.3 Nature of Municipal Solid Wastes

    11.3.1 Integrated Solid Waste Management

    11.3.1.1 Source Reduction

    11.3.1.2 Recycling

    11.3.1.3 Incineration with Energy Recovery

    Modern and Emerging (and Safer?) Methods of the Thermal Treating of MSW

    11.3.1.4 Composting

    Preprocessing

    Compost Processing Conditions

    Compost Post Processing or the Curing Stage

    Microbiology of Composting

    11.3.1.5 Landfills Used in the Disposal of MSW

    Factors to be Considered in Planning an MSW Landfill

    Parts of a Landfill

    Operation of a Landfill

    Problems of Landfills

    11.4 Anaerobic Breakdown of Organic Matter in Landfills (and Aquatic Sediments)

    11.4.1 Some Properties of Methanogens

    11.4.2 Landfill Gas

    11.4.2.1 Landfill Methane Capture Technology

    11.5 Options for Municipal Solid Wastes Management

    References

    Index
    Last edited by rocky; 22nd May 2012 at 09:00 PM.
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