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Downloaded from https://iwaponline.com/ebooks/book-pdf/521273/wio9781780401775.pdf by IWA Publishing user on 04 February 2019 Identification and quantification of microorganisms in activated sludge and biofilms by FISH and biofilms by sludge in activated Identification and quantification of microorganisms Treatment Wastewater Biological for Handbook FISH 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 FISH Handbook 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 for Biological 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 Wastewater Treatment 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, Identification and quantification of microorganisms and it is important for optimization and troubleshooting of operational problems in present wastewater treatment plants. in activated sludge and biofilms by FISH 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 Editor(s): Per Halkjær Nielsen, Holger Daims and Hilde Lemmer 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. Holger Daims and Hilde Lemmer Editor(s): Per Halkjær Nielsen, Editor(s): Per www.iwapublishing.com ISBN 13: 9781843392316 ISBN: 1843392316 Downloaded from https://iwaponline.com/ebooks/book-pdf/521273/wio9781780401775.pdf by IWA Publishing user on 04 February 2019 FISH Handbook for Biological Wastewater Treatment Downloaded from https://iwaponline.com/ebooks/book-pdf/521273/wio9781780401775.pdf by IWA Publishing user on 04 February 2019 Downloaded from https://iwaponline.com/ebooks/book-pdf/521273/wio9781780401775.pdf by IWA Publishing user on 04 February 2019 FISH Handbook for Biological Wastewater Treatment Identification and quantification of microorganisms in activated sludge and biofilms by FISH Edited by Per Halkjær Nielsen, Holger Daims and Hilde Lemmer Downloaded from https://iwaponline.com/ebooks/book-pdf/521273/wio9781780401775.pdf by IWA Publishing user on 04 February 2019 Published by IWA Publishing Alliance House 12 Caxton Street London SW1H 0QS, UK Telephone: þ44 (0)20 7654 5500 Fax: þ44 (0)20 7654 5555 Email: [email protected] Web: www.iwapublishing.com First published 2009 # 2009 IWA Publishing Cover images provided by Simon Jon Mcllroy, Jeppe Lund Nielsen, and Kilian Stoecker Cover design by www.designforpublishing.co.uk Typeset in India by Alden Prepress Services Private Limited. Index provided by Alden Prepress Services Private Limited. Printed by Page Bros Ltd, Norwich, UK. Apart from any fair dealing for the purposes of research or private study, or criticism or review, as permitted under the UK Copyright, Designs and Patents Act (1998), no part of this publication may be reproduced, stored or transmitted in any form or by any means, without the prior permission in writing of the publisher, or, in the case of photographic reproduction, in accordance with the terms of licences issued by the Copyright Licensing Agency in the UK, or in accordance with the terms of licenses issued by the appropriate reproduction rights organization outside the UK. Enquiries concerning reproduction outside the terms stated here should be sent to IWA Publishing at the address printed above. The publisher makes no representation, express or implied, with regard to the accuracy of the information contained in this book and cannot accept any legal responsibility or liability for errors or omissions that may be made. Disclaimer The information provided and the opinions given in this publication are not necessarily those of IWA and should not be acted upon without independent consideration and professional advice. IWA and the Author will not accept responsibility for any loss or damage suffered by any person acting or refraining from acting upon any material contained in this publication. British Library Cataloguing in Publication Data A CIP catalogue record for this book is available from the British Library Library of Congress Cataloging-in-Publication Data A catalog record for this book is available from the Library of Congress ISBN 10: 1843392316 ISBN 13: 9781843392316 Downloaded from https://iwaponline.com/ebooks/book-pdf/521273/wio9781780401775.pdf by IWA Publishing user on 04 February 2019 Table of contents List of contributors ................................................................................................................... ix Abbreviations ............................................................................................................................... xi 1 INTRODUCTION .................................................................................................................. 1 1.1 Identification of microorganisms in activated sludge and biofilms ................. 1 1.2 The microbiology of biological wastewater treatment ....................................... 2 1.3 Factors of importance for the growth of microorganisms ................................. 4 1.4 The use of this FISH handbook ............................................................................. 6 2 THE NITRIFYING MICROBES: AMMONIA OXIDIZERS, NITRITE OXIDIZERS, AND ANAEROBIC AMMONIUM OXIDIZERS .................................................................... 9 2.1 Introduction ............................................................................................................... 9 2.2 Ammonia oxidizers .................................................................................................. 10 2.2.1 Probes for the detection of AOB ................................................................. 11 2.3 Nitrite oxidizers ........................................................................................................ 13 2.3.1 Probes for the detection of NOB ................................................................. 14 2.4 Anammox bacteria ................................................................................................... 14 2.4.1 Probes for the detection of anammox organisms ....................................... 17 3 IDENTIFICATION OF DENITRIFYING MICROORGANISMS IN ACTIVATED SLUDGE BY FISH .............................................................................................................. 19 3.1 Introduction ............................................................................................................... 19 3.2 Identity of denitrifiers in wastewater treatment systems ................................... 20 3.3 Abundant denitrifiers in full-scale plants ............................................................. 20 3.4 Probes for detection of denitrifiers ....................................................................... 21 4 IDENTIFICATION OF POLYPHOSPHATE-ACCUMULATING AND GLYCOGEN-ACCUMULATING ORGANISMS BY FISH .................................................. 25 4.1 Introduction ............................................................................................................... 25 4.2 Identity of PAOs ....................................................................................................... 26 4.2.1 Probes for detection of PAOs ...................................................................... 28 Downloaded from