Performance assessment and enrichment of anaerobic methane oxidizing microbial communities from marine sediments in bioreactors

271 Pages·2018·9.257 MB·English

by  Gautam, Susma Bhattarai

PERFORMANCE ASSESSMENT
AND ENRICHMENT OF
ANAEROBIC METHANE OXIDISING
MICROBIAL COMMUNITIES
FROM MARINE SEDIMENTS
IN BIOREACTORS
Susma Bhattarai Gautam

Joint PhD degree in Environmental Technology
UNIVERSITE---------------
— PARIS-EST
Docteur de I’Universite Paris-Est
Speciality : Science et Technique de I’Environnement
Dottore di Ricerca in Tecnologie Ambientali
UNESCO-IHE
Institute for Water Education
Degree of Doctor in Environmental Technology
These - Tesi di Dottorato - PhD thesis
Susma Bhattarai Gautam
Performance Assessment and Enrichment of Anaerobic Methane
Oxidizing Microbial Communities from Marine Sediments in Bioreactors
Defended on December 16th, 2016
In front of the PhD committee
Dr. Cartsen Vogt Reviewer
Dr. Artin Hatzikioseyian Reviewer
Prof. dr. ir. Piet. N. L. Lens Promotor
Prof. Michel Madon Co-Promotor
Prof. Giovanni Esposito Co-Promotor
Dr. Eldon R. Rene Co-Promotor
Hab. Dr. Eric van Hullebusch Examiner
3
ETeC oS
Erasmus Joint doctorate programme in Environmental Technology for Contaminated Solids, Soils and
Sediments (ETeCoS3]
Thesis Committee
Thesis Promoter
Prof. dr. ir. Piet N. L. Lens
Professor of Environmental Biotechnology
UNESCO-IHE, Institute for Water Education
Delft, the Netherlands
Thesis Co-Promoters
Prof. Michel Madon
University of Paris-Est, Institut Francilien des Sciences Appliqueees
Champs sur Marne, France
Dr. Giovanni Esposito
Associate Professor of Sanitary and Environmental Engineering
University of Cassino and Southern Lazio, Cassino, Italy
Dr. Eldon R. Rene
UNESCO-IHE, Institute for Water Education
Delft, the Netherlands
Examiner
Hab. Dr. Eric van Hullebusch
Associate Professor of Biogeochemistry
University of Paris-Est, Institut Francilien des Sciences Appliqueees
Champs sur Marne, France
Reviewers
Dr. Cartsen Vogt
Helmholtz Centre for Environmental Research - UFZ
Department of Isotope Biogeochemistry
Leipzig, Germany
Dr. Artin Hatzikioseyian
National Technical University of Athens
Athens, Greece
This research was conducted under the auspices of the Erasmus Mundus Joint
Doctorate Environmental Technologies for Contaminated Solids, Soils, and
Sediments (ETeCoS3) and The Netherlands Research School for the Socio-
Economic and Natural Sciences of the Environment (SENSE).
CRC Press/Balkema is an imprint of the Taylor & Francis Group, an informa business
© 2018, Susma Bhattarai Gautam
All rights reserved. No part of this publication or the information contained herein may
be reproduced, stored in a retrieval system, or transmitted in any form or by any
means, electronic, mechanical, by photocopying, recording or otherwise, without
written prior permission from the publishers.
Although all care is taken to ensure the integrity and quality of this publication and
information herein, no responsibility is assumed by the publishers or the author for
any damage to property or persons as a result of the operation or use of this
publication and or the information contained herein.
Published by: CRC Press/Balkema
PO Box 11320, 2301 EH Leiden, The Netherlands
e-mail: [email protected]
www.crcpress.com - www.taylorandfrancis.com
ISBN: 978-1 -138-33021 -4 (Taylor & Francis Group)

Table of contents
Chapter Title Page no.
Acknowledgements xi
Summary xiii
Samenvatting xv
Somario xvii
Resume xix
CHAPTER 1 General Introduction and Thesis Outline..................................................1
1.1 General introduction and problem statement.....................................................2
1.2 Objectives and scope of the study.....................................................................4
1.3 Outlines of this thesis.........................................................................................5
1.4 References..........................................................................................................6
CHAPTER 2 Physiology and Distribution of Anaerobic Oxidation of Methane by
Archaeal Methanotrophs................................................................................................11
2.1 Introduction........................................................................................................12
2.2 Microbiology of anaerobic methane oxidation.................................................15
2.3 Physiology of AN ME..........................................................................................23
2.4 Drivers for distribution of ANME in natural habitats........................................29
2.5 Ex situ enrichment of ANME.............................................................................40
2.6 Approaches for AOM and ANME studies........................................................49
2.7 Conclusions and outlook..................................................................................57
2.8 References........................................................................................................58
CHAPTER 3 Microbial Sulfate Reducing Activities in Anoxic Sediment from Marine
Lake Grevelingen..........................................................................................................83
Abstract.........................................................................................................................84
3.1 Introduction........................................................................................................84
3.2 Materials and Methods.....................................................................................86
3.3 Results..............................................................................................................90
3.4 Discussion.........................................................................................................97
3.5 Conclusions.....................................................................................................101
3.6 References......................................................................................................101
CHAPTER 4 Anaerobic Methane Oxidizing Microbial Community in a Coastal Marine
Sediment: Anaerobic Methanotrophy Dominated by ANME-3..................................107
4.1 Introduction......................................................................................................108
vii
4.2 Materials and methods....................................................................................111
4.3 Results.............................................................................................................116
4.4 Discussion.......................................................................................................127
4.5 Conclusions.....................................................................................................134
4.6 References......................................................................................................134
CHAPTER 5 Enrichment of Anaerobic Methane Oxidizing ANME-1 from Ginsburg
Mud Volcano (Gulf of Cadiz) Sediment in a Biotrickling Filte.....................................145
5.1 Introduction......................................................................................................146
5.2 Materials and methods....................................................................................148
5.3 Results.............................................................................................................155
5.4 Discussion.......................................................................................................163
5.5 Conclusions.....................................................................................................167
5.6 References.....................................................................................................168
CHAPTER 6 Enrichment of ANME-2 Dominated Anaerobic Oxidation of Methane
Coupled to Sulfate Reduction Consortia from Cold Seep Sediment (Ginsburg Mud
Volcano, Gulf of Cadiz) in a Membrane Bioreactor....................................................177
6.1 Introduction......................................................................................................178
6.2 Materials and Methods....................................................................................181
6.3 Results.............................................................................................................188
6.4 Discussion.......................................................................................................194
6.5 Conclusions.....................................................................................................198
6.6 References......................................................................................................198
CHAPTER 7 Response of Highly Enriched ANME-2a Community to the Different
Pressure and Temperature Conditions......................................................................207
7.1 Introduction......................................................................................................208
7.2 Materials and methods...................................................................................210
7.3 Results............................................................................................................213
7.4 Discussion.......................................................................................................220
7.5 Conclusions.....................................................................................................223
7.6 References......................................................................................................224
CHAPTER 8 General Discussion...............................................................................231
8.1 Introduction......................................................................................................232
8.2 Anaerobic oxidation of methane in coastal sediment.....................................232
8.3 Anaerobic oxidation of methane in bioreactors...............................................236
8.4 Enrichment of ANME in different bioreactor configurations..........................238
8.5 Future perspectives in ANME enrichments...................................................240
8.6 References......................................................................................................241
Biography....................................................................................................................247
Publications.................................................................................................................248
SENSE diploma for specialized PhD trainings..........................................................249
ix