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FISH Handbook for Biological Wastewater Treatment

FISH Handbook for Biological Wastewater Treatment

Per Halkjaer Nielsen | Holger Daims | Hilde Lemmer | Idil Arslan-Alaton | Tugba Olmez-Hanci

(2009)

Additional Information

Book Details

Abstract

The FISH Handbook for Biological Wastewater Treatment provides all the required information for the user to be able to identify and quantify important microorganisms in activated sludge and biofilms by using fluorescence in situ hybridization (FISH) and epifluorescence microscopy. It has for some years been clear that most microorganisms in biological wastewater systems cannot be reliably identified and quantified by conventional microscopy or by traditional culture-dependent methods such as plate counts. Therefore, molecular biological methods are vital and must be introduced instead of, or in addition to, conventional methods. At present, FISH is the most widely used and best tested of these methods. 
This handbook presents all relevant information from the literature and, based on the extensive experience of the authors, advice and recommendations are given for reliable FISH identification and quantification. The overall purpose of the book is to help scientists, consultants, students, and plant operators to get an overview of important microorganisms in biological wastewater treatment and to explain how FISH can be used for detecting and quantifying these microbes. A proper and reliable identification of dominant microorganisms is of great importance for research and new developments in the wastewater treatment industry, and it is important for optimization and troubleshooting of operational problems in present wastewater treatment plants.   
The book encompasses an overview of dominant microorganisms present in the wastewater treatment systems, which oligonucleotide probes (gene probes) to select for detection of these microbes by FISH, how to perform FISH (detailed protocols), how to quantify the microbes, and how to solve common problems of FISH. The book addresses several functional groups: nitrifiers, denitrifiers, polyphosphate-accumulating organisms, glycogen-accumulating organisms, bacteria involved in hydrolysis and fermentation, filamentous bacteria from bulking sludge, and scum-forming bacteria. A comprehensive collection of FISH-images showing dominant representatives of these groups helps readers to use FISH in the context of wastewater treatment.

Table of Contents

Section Title Page Action Price
Half title 1
Title 3
Copyright 4
Table of contents 5
List of contributors 9
Abbreviations 11
Chapter 1: Introduction 12
1.1 IDENTIFICATION OF MICROORGANISMS IN ACTIVATED SLUDGE AND BIOFILMS 12
1.2 THE MICROBIOLOGY OF BIOLOGICAL WASTEWATER TREATMENT 13
1.3 FACTORS OF IMPORTANCE FOR THE GROWTH OF MICROORGANISMS 15
1.4 THE USE OF THIS FISH HANDBOOK 17
Chapter 2: The nitrifying microbes: Ammonia oxidizers, nitrite oxidizers, and anaerobic ammonium oxidizers 20
2.1 INTRODUCTION 20
2.2 AMMONIA OXIDIZERS 21
2.2.1 Probes for the detection of AOB 22
2.3 NITRITE OXIDIZERS 24
2.3.1 Probes for the detection of NOB 25
2.4 ANAMMOX BACTERIA 25
2.4.1 Probes for the detection of anammox organisms 28
Chapter 3: Identification of denitrifying microorganisms in activated sludge by FISH 30
3.1 INTRODUCTION 30
3.2 IDENTITY OF DENITRIFIERS IN WASTEWATER TREATMENT SYSTEMS 31
3.3 ABUNDANT DENITRIFIERS IN FULL-SCALE PLANTS 31
3.4 PROBES FOR DETECTION OF DENITRIFIERS 32
Chapter 4: Identification of polyphosphate-accumulating and glycogen-accumulating organisms by FISH 36
4.1 INTRODUCTION 36
4.2 IDENTITY OF PAOs 37
4.2.1 Probes for detection of PAOs 39
4.3 IDENTITY OF GAOs 39
4.3.1 Probes for detection of GAOs 40
Chapter 5: Identification of filamentous bacteria by FISH 44
5.1 INTRODUCTION 44
5.2 FISH DETECTION OF FILAMENTOUS BACTERIA 47
5.3 FILAMENTOUS BACTERIA DETECTION AND IDENTIFICATION 49
5.3.1 Beggiatoa morphotype 52
5.3.2 Haliscomenobacter hydrossis morphotype 52
5.3.3 Leucothrix mucor morphotype 56
5.3.4 Microthrix parvicella morphotype 56
5.3.5 Nostocoida limicola morphotypes 59
5.3.6 Nocardioform actinomycetes/Mycolata morphotype 63
5.3.7 Sphaerotilus natans and Leptothrix discophora morphotype 67
5.3.8 Streptococcus morphotype 67
5.3.9 Thiothrix and Type 021N morphotypes 68
5.3.10 0041/0675 morphotype 70
5.3.11 0092 morphotype 72
5.3.12 1701 morphotype 74
5.3.13 1851 morphotype 76
5.3.14 1863 morphotype 76
5.3.15 0803, 0914 morphotypes and other still unidentified filamentous species 78
Chapter 6: Identification of other microorganisms in activated sludge and biofilms by FISH 80
6.1 INTRODUCTION 80
6.2 EPIPHYTIC BACTERIA INVOLVED IN PROTEIN HYDROLYSIS 80
6.3 SULFATE-REDUCING BACTERIA 81
6.4 FERMENTING BACTERIA 81
6.5 ESCHERICHIA COLI AS INDICATOR ORGANISM FOR ENTERO-PATHOGENS 81
Chapter 7: Protocol for Fluorescence in situ Hybridization (FISH) with rRNA-targeted oligonucleotides 84
7.1 INTRODUCTION 84
7.2 FISH PROTOCOL 86
7.2.1 Materials and solutions 86
7.2.2 Equipment and supplies needed for FISH 87
7.3 PROTOCOL 87
7.3.1 Sample collection and fixation 87
7.3.2 Sample preparation 88
7.3.3 Immobilization of the samples on glass slides 88
7.3.4 Dehydration 89
7.3.5 Permeabilization by enzymatic or chemical treatment 89
7.3.6 Preparation and quality check of probes 90
7.3.7 Hybridization 90
7.3.8 Counterstaining with DAPI 92
7.4 MICROSCOPY 92
7.5 RECOMMENDATIONS AND TROUBLESHOOTING 92
Chapter 8: Quantitative FISH for the cultivation-independent quantification of microbes in wastewater treatment plants 96
8.1 INTRODUCTION 96
8.2 QUANTITATIVE FISH: A BRIEF OVERVIEW 97
8.3 A PROTOCOL FOR QUANTITATIVE FISH AND IMAGE ANALYSIS TO MEASURE BIOVOLUME FRACTIONS 99
8.4 CONCLUDING REMARKS 102
Chapter 9: Color image section 104
Nitrifiers 104
Denitrifiers 105
PAOs/GAOs 107
Filamentous bacteria 109
Chapter 10: Reference list 120
Index 132