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Flow of light energy in benthic photosynthetic microbial mats [Elektronische Ressource] / by Mohammad Ahmad A. al-Najjar

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FlowfightnergynBenthichotosyntheticicrobialats ByMohammadhmad.lajjarAhesisubmittednartialulfilmentofequirementsorheegreefDOCTORFHILOSOPHYNCIENCE“Dr.er.at.“FacultyfBiologyndhemistryUniversityfremenBremenDecember010 The work in this thesis was done during the period from April 2007 to December 2010 in the Max-Planck Institute for Marine Microbiology/Bremen, in the frame of the International Max-Planck Research School for Marine Microbiology (IMPRS MarMic). Supervisors: Dr. Lubos Polerecky, Max-Planck Institute/Bremen Dr. Dirk de Beer, Max-Planck Institute/BremenExamining committee members: First reviewer: Prof. Dr. Bo Barker Jørgensen, MPI /Bremen Second reviewer: Prof. Dr. Ulrich Fischer, Universität Bremen Member: Prof. Dr. Victor Smetacek, AWI/Bremerhaven Member: Dr. Henk Jonkers, Delft University of Technology The Netherlands Thesis contents Microbial mats are extremely interesting ecosystems that have been intensively investigated by researchers from a wide variety of fields. This can be clearly seen from the huge body of literature examined different aspects of microbial mats including structural and functional composition. Microbial mats are highly complex systems with micrometer scale changes in the activity and the structural composition within in the photic zone, primarily, due to the highly heterogeneous light field.

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Published 01 January 2010
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Flowfightnergyn
Benthichotosyntheticicrobialats

By
Mohammadhmad.lajjar
Ahesisubmittednartialulfilment
ofequirementsorheegreef

DOCTORFHILOSOPHYNCIENCE
“Dr.er.at.“
FacultyfBiologyndhemistry
Universityfremen



Bremen
December010



The work in this thesis was done during the period from April 2007 to
December 2010 in the Max-Planck Institute for Marine
Microbiology/Bremen, in the frame of the International Max-Planck
Research School for Marine Microbiology (IMPRS MarMic).










Supervisors:

Dr. Lubos Polerecky, Max-Planck Institute/Bremen
Dr. Dirk de Beer, Max-Planck Institute/Bremen
Examining committee members:
First reviewer: Prof. Dr. Bo Barker Jørgensen, MPI /Bremen

Second reviewer: Prof. Dr. Ulrich Fischer, Universität Bremen
Member: Prof. Dr. Victor Smetacek, AWI/Bremerhaven
Member: Dr. Henk Jonkers, Delft University of Technology
The Netherlands
Thesis contents
Microbial mats are extremely interesting ecosystems that have been intensively investigated
by researchers from a wide variety of fields. This can be clearly seen from the huge body of
literature examined different aspects of microbial mats including structural and functional
composition. Microbial mats are highly complex systems with micrometer scale changes in
the activity and the structural composition within in the photic zone, primarily, due to the
highly heterogeneous light field. The difficulties associated with measuring such small
changes in light field have resulted in dealing with microbial mats as a “black box”.
Therefore, important and fundamental questions such as the fate of light energy and the
energy budget inside the microbial mats, as well as the factors affecting the variations in light
utilizing efficiency between different mat ecosystems have remained unexplored.
The primary aims of this thesis were the ambitious goal of assessing the first energy
budget inside benthic photosynthetic microbial mat ecosystems and the subsequent
understanding of the “black box”. The best way to gain the needed information is by
following the fate of light energy once reaches the surface of a microbial mat. The work in
this thesis used microsensors, pigment analysis using HPLC, a combined imaging approach
(imaging PAM and hyperspectral imaging), molecular and statistical analyses to investigate
the fate of light energy inside microbial mat ecosystems. Gathering glimpses on how light
absorption is affected by mat structure and offer insights into deeper processes in the
microbenthic ecosystem. This was achieved through the three parts of the thesis:
1. Assessing the first energy budget inside a microbial mat ecosystem, demonstrating how
the budget and the spatial distribution of local photosynthetic efficiencies within the euphotic
zone depend on the absorbed irradiance. Furthermore, a model that describes light propagation and conversion in a scattering-absorbing medium was developed. In contrast to
previous attempts, this model requires inputs from the easily measured parameters; the light
attenuation coefficient, the reflectance and the scalar irradiance (Chapter 2).
2. Comparing the efficiency of light energy utilization between the three marine benthic
photosynthetic ecosystems, and showing that maximum photosynthetic efficiency is related
to the accessory pigment/chlorophyll a ratio, depth of the photic zone and light absorption by
non-photosynthetic components relative to absorption by photopigments and the structure of
the upper layer of a given mat. This study provides first insight to how differential
composition and spatial organization of photosynthetic microbial communities affect overall
ecosystem efficiency (Chapter 3).
3. Applying a combined pigment imaging technique (variable chlorophyll fluorescence and
hyperspectral imaging) for a detailed analysis of the spatial heterogeneity in oxygenic
photosynthesis, photopigment composition and light acclimation in cyanobacterial mats.
This, in conjunction with molecular (amplified ribosomal intergenic spacer analysis) and
statistical analyses, were used to assess changes in bacterial community structure as well as
changes in functional and contextual parameters (Chapter 4). Finally, light intensity at which
maximum quantum efficiency, E , and half of quantum efficiency, E , were used instead max 1/2
of the parameter E to evaluate light acclimation state in cyanobacterial mats (Chapter 4). kAcknowledgements

My highest appreciation goes to my direct supervisor Dr. Lubos Polerecky, for the
time and the information that he kindly provided during my PhD. I do highly thank
Dr. Dirk de Beer for offering me this chance to do this work in the microsensor
group, in addition to his active participation in the PhD committee meetings,
discussions and improving the manuscript for the published paper. I deeply
appreciate the continuous support and encouragements that I received from Prof. Dr.
Bo Barker Jørgensen and for his constant interest in my work. I appreciate him
because he accepted being my ‘Doktorvater’. Prof. Dr. Ulrich Fischer is also thanked
for being the second reviewer of my thesis. I further thank, Prof. Dr. Michael Kühl
for his continuous interest in my work, his comments and suggestions are particularly
appreciated. The fruitful discussions with Prof. Dr. Friedrich Widdel, Dr. Henk
Jonkers, and Dr. Alban Ramette are highly acknowledged. I do thank Prof. Dr.
Waleed Hamza from UAE University, as well as, Dr. Alistair Grinham for the fruitful
collaborations and supplying the samples. I also thank technicians of the microsensor
group at MPI for being always helpful, building the microsensors and their smile
faces always. Many thanks to my colleagues in “microsens” for the friendly work
atmosphere. I also thank Abdul monem Al-Raei for his support and for being always
there, ready to provide help. I thank the MarMic graduate school, especially Dr.
Christiane Glöckner, for the supportive and pleasant atmosphere. The continuous
support and prayers from my parents in Jordan is one of the important energy sources
that powered my motivation during my PhD. The last but not the least, I can’t find
enough words suitable to acknowledge the support, encouragements, spiritual
motivation and patience I gained, without conditions, from my greatest family; my
(w/l)ife Siham and the greatest kids (Malek, Moath and Bushra). The financial
support from Yosuf Jameel scholarship and the MPI-Bremen is highly appreciated.

Bremen, December 2010




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Contents
Chapter 1 Introduction
1

Energy sources 2
Biofuel production form photosynthetic
3
organisms as promising option
Cyanobacteria and evolution of photosynthesis 4
Conversion of solar energy into chemical
7
energy in photosynthesis
Importance of measuring rates of photosynthesis
8
accurately
Quantum efficiency of photosynthetic 10
Photosynthetic microbial mats 18
Aims of the thesis
26

Chapter 2 Conversion and conservation of light energy in
a photosynthetic microbial mat ecosystem 38

Chapter 3 Comparison of light utilization efficiency in
photosynthetic microbial mats 81

Chapter 4 Spatial Distribution of Photosynthetic Efficiency
107
and Light Acclimation in Microbial Mat Ecosystems
Chapter 5
Abstracts of Contributed Work: 133
5.2 Modular spectral imaging system for
discrimination of pigments in cells and
134
microbial communities

5.1 Hyper-spectral imaging of biofilm
136
growth dynamics
Chapter 6
Concluding Discussion and Summary 137
6.1 Discussion 138
6.2 Summary
151
6.3 Zusammenfassung
152