BOOK
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 |