Determinants of the bacterial diversity in manipulated and natural soils [Elektronische Ressource] / vorgelegt von Delita Zul

Delita Zul

Sujets

• Biologie

Informations

• Publié par: ludwig-maximilians-universitat_munchen
• Publié le: 01 janvier 2008
• Nombre de lectures: 23
• Langue: English
• Poids de l'ouvrage: 27 Mo

Extrait

Determinants of the Bacterial Diversity
in Manipulated and Natural Soils

Delita Zul

















München 2008





Determinants of the Bacterial Diversity
in Manipulated and Natural Soils










Dissertation
Fakultät für Biologie
Ludwig-Maximilians-Universität München






vorgelegt von

Delita Zul
aus Pariaman, West Sumatera







München, Januar 2008













































ii





































1. Gutacher: Prof. Dr. Jörg Overmann, LMU München
2.: Prof. Dr. Dirk Schüler, LMU München

Tag der Abgabe: 29. Januar 2008
Tag des Promotionskolloquiums: 13. März 2008


iii






















Dedicated to:

my husband (Tony) and my daughter (Uthie)





















iv ACKNOWLEDGEMENTS


First, I would like to thank Prof. Dr. Jörg Overmann for giving me the opportunity to
learn about the amazing bacterial diversity in soil and science, for his supervision of
this work and a financial support through the last months of my thesis. I thank Prof.
Dr. Dirk Schüler for accepting the role as the second referee.
I would like to express my appreciation to all AGO for a good atmosphere in the lab
that has made me feel at home. Many thanks to Dr. Karin Schubert (for her guidance
on spectrophotometer), Evelyn (for her guidance on quantitative PCR and “dirndl”),
Roland (sorry for always stealing your stapler), Jonny (the respiration guy), Isabella,
Martina, and Annemarie (for their emotional support). Special thanks to Kajetan for
always “being available”.
I am grateful to the Technological and Professional Skills Development Sector
Project (TPSDP) for a financial support. My dear colleagues in Department of
Biology, Faculty of Mathematics and Natural Sciences, University of Riau,
Pekanbaru, Indonesia are appreciated for giving me the opportunity to leave my duty
for almost 3.5 years.
Furthermore, I am eternally grateful to my family for giving me the truth and
encouragement. Most of all I gratefully acknowledge my husband, Anthony Hamzah,
for always being there and his endless love (dan untuk semuanya). I do not know
how I could have finished my work without his support and patience. Very special
thanks to my little daughter, Putri Nazeeya Anita (5 yr), for giving me cheerfulness
and support through her question “When will you go home, mom?” (Maafkan mama
Uthie. Mama berjanji tidak akan pernah meninggalkan Uthie lagi. Mama sayang
uthie sebanyak bintang di langit).



München
January 2008

v PUBLICATIONS ORIGINATING FROM THIS THESIS



CHAPTER 2
Zul, D., S. Denzel, A. Kotz, and J. Overmann. 2007. Effects of plant biomass, plant
diversity and water content on the bacterial communities in soil lysimeters:
implications for the determinants of bacterial diversity. Appl. Environ. Microbiol.
73:6916-6929

CHAPTER 3
Zul, D., G. Wanner, and J. Overmann. 2008. Massilia brevitalea sp. nov., a novel
betaproteobacterium isolated from lysimeter soil. Int. J. Syst. Evol. Microbiol. (in
press)

CHAPTER 4
Zul, D., E. Romann, B.U. Fösel, and J. Overmann. 2008. Determinants of the
diversity and activity of a bacterial community in Namibian Savanna Soils.
(manuscript)

















vi CONTRIBUTIONS OF THE AUTHORS


CHAPTER 2
Profiling of the bacterial community compositions were performed by Delita Zul
(Alpha-, Betaproteobacteria, Bacteroidetes, Verrucomicrobia, and Actinobacteria,
species), Sabine Denzel (Acidobacteria and Archaea species), and Andrea Kotz
(Chloroflexi species). Delita Zul (employing the MicroDrop technique) and Sabine
Denzel (employing the dilution technique of soil slurry) performed cultivation of the
soil bacteria. Delita Zul, Andrea Kotz, and one diploma student (Petra Fritsche)
conducted screening of the cultures obtained. Moreover, Delita Zul quantified the
abundance of phylotype beta10 by the real-time PCR. In addition, the diploma
student (Monika Anna Janys) profiled the composition of Firmicutes and
Planctomycetes species.

CHAPTER 3
Massilia brevitalea strain byr 23-80 was isolated, pheno- and genotypically analyzed
by Delita Zul. Prof. Dr. Gerhard Wanner took the electron microscopy pictures and
wrote the corresponding parts of the paper.

CHAPTER 4
Delita Zul carried out the soil respiration measurements, the soil exoenzyme assays,
and cultivation of the soil bacteria. She also did the screening of the cultures obtained
and quantified the abundance of nine major (sub)phyla of Bacteria in soil by use of
the real-time PCR. Moreover, Delita Zul profiled the community composition of
Acidobacteria and Actinobacteria species. Eva Romann counted the total cell
numbers. She also did the clone library construction and analyzed the library data
together with Bärbel U. Fösel.

I hereby confirm the above statements

Delita Zul Prof. Dr. Jörg Overmann
vii TABLE OF CONTENTS

Acknowledgements………………………………………………………………... v
Publications Originating from This Thesis…………………………………........ vi
Contributions of the Authors……………………………………………….......... vii
Table of Contents……………………………… viii
1 Introduction…………………………………………………………………….. 1
1.1 Microbial diversity and its implications……. 1
1.2 Soil as a habitat and ecosystem……………………………………………... 4
1.3 Determinant factors of microbial diversity……………………………......... 6
1.3.1 Plant diversity and water content…………………………………….. 6
1.3.2 Land use and soil properties with special emphasis on Namibia…….. 9
1.4 Cultivation of the non-cultured……………………………………………... 12
1.5 Quantifying microbial diversity and activity………………………….......... 14
1.5.1 Microbial diversity…………………………………………………… 14
1.5.2 Microbial activity…………………………………………………….. 15
1.6 Aims of the present study……………………....... 17
1.7 References………………………………………………………………....... 18
2 Effects of Plant Biomass, Plant Diversity and Water Content on the
Bacterial Communities in Soil Lysimeters: Implications for the
Determinants of Bacterial Diversity…………………………………………... 33
2.1 Abstract…………………………………………………………………....... 33
2.2 Introduction…………………………………………………………………. 34
2.3 Material and methods…………………………. 35
2.3.1 Lysimeter design and sample collection……………………………... 35
2.3.2 Total bacterial cell counts……………………………………………. 37
2.3.3 DNA extraction and purification…………………………………….. 37
2.3.4 PCR amplification, enterobacterial repetitive intergenic consensus
PCR (ERIC-PCR), and denaturing gradient gel electrophoresis
(DGGE) fingerprinting………………………………………………. 38
viii