University of Groningen
The ecology and evolution of bacteriophages of mycosphere-inhabiting Paraburkholderia spp.
Pratama, Akbar Adjie
IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below.
Document Version
Publisher's PDF, also known as Version of record
Publication date: 2018
Link to publication in University of Groningen/UMCG research database
Citation for published version (APA):
Pratama, A. A. (2018). The ecology and evolution of bacteriophages of mycosphere-inhabiting Paraburkholderia spp. Rijksuniversiteit Groningen.
Copyright
Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).
Take-down policy
If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.
Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons the number of authors shown on this cover page is limited to 10 maximum.
The ecology and evolution of
bacteriophages of mycosphere-inhabiting
Paraburkholderia spp.
The research reported in this thesis was carried out at the Microbial Ecology cluster, which is part of the Genomics Research in Ecology and Evolution in Nature (GREEN) research group, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, The Netherlnads, according to the requirement of the Graduate School of Science (Faculty of Science and Engineering, University of Groningen).
Akbar Adjie Pratama receive a PhD grant from Lembaga Pengelola Dana Pendidikan, Kementrian Keuangan, Republik Indonesia (Indonesian Endowment Fund for Education).
Layout: Nikki Vermeulen | Ridderprint BV Printing: Ridderprint BV | www.ridderprint.nl Cover: Akbar Adjie Pratama
ISBN: 978-94-034-1044-9 (printed version) ISBN: 978-94-034-1043-2 (electronic version)
The ecology and evolution of
bacteriophages of mycosphere-inhabiting
Paraburkholderia spp.
PhD thesis
to obtain the degree of PhD at the University of Groningen
on the authority of the Rector Magnificus Prof. E. Sterken
and in accordance with the decision by the College of Deans. This thesis will be defended in public on Monday 5 November 2018 at 14.30 hours
by
Akbar Adjie Pratama
born on 30 July 1987 in Jakarta, Indonesia
Supervisor
Prof. dr. ir. J.D. (Jan Dirk) van Elsas
Assessment committee
Prof. dr. K. Smalla Prof. dr. J. Kok Prof. dr. R. Lavigne
Content
Chapter 1
General introduction 9
SECTION I: Genomics-based dissection of mycosphere-inhabiting Paraburkholderia strains, yielding a basis for bioinformatics-assisted searches for prophages
Chapter 2
Draft genome sequences of three fungal-interactive Paraburkholderia terrae strains BS007, BS110 and BS437 35 Chapter 3
Species boundaries and ecological features among P. terrae DSM 17804T,
P. hospita DSM 17164T and P. caribensis DSM 13236T 57
SECTION II: Conceptualisation and theoretical perspective on (soil) viruses Chapter 4
The “neglected” soil virome – potential role and impact 87 Chapter 5
The significance of mutualistic phages for bacterial ecology and evolution 109 SECTION III: Paraburkholderia viruses and their evolutionary trajectory
Chapter 6
A novel inducible prophage from the mycosphere inhabitant P. terrae BS437 127 Chapter 7
Evolutionary history of bacteriophages in the Genus Paraburkholderia 167 Chapter 8
The dynamics and diversity of the mycosphere viromes 211 Chapter 9 Synthesis 233 References 252 Summary/Samenvatting 276 Acknowledgements 281 Author affiliations 284
