BIODIVERSITY AND MOLECULAR SYSTEMATICS OF SUBAERIAL ALGAE FROM AFRICA AND ...

273 Pages·2011·3.7 MB·English

by  John Chambers

BIODIVERSITY AND MOLECULAR SYSTEMATICS OF SUBAERIAL ALGAE FROM
AFRICA AND THE NEOTROPICS

by

HAJ ABDESLAM ALLALI

JUAN LOPEZ-BAUTISTA, COMMITTEE CHAIR

MARTHA POWELL
AMY WARD
JOHN CLARK
CHARLES AMSLER

A DISSERTATION

Submitted in partial fulfillment of the requirements
for the degree of Doctor of Philosophy
in the Department of Biological Sciences
in the Graduate School of
The University of Alabama

TUSCALOOSA, ALABAMA

2011
Copyright Haj Abdeslam Allali 2011
ALL RIGHTS RESERVED
ABSTRACT

Algae are a large and diverse group of photosynthetic organisms that range in size from
microscopic unicellular to multicellular forms. They usually inhabit marine and freshwater
habitats. However, some are terrestrial and are capable of living in soil or above the soil surface
(subaerial). Tropical rainforests, with humid climate and diverse habitats, offer phycologists with
a rich field for biodiversity exploration. In the past, algae in these environments have been the
objective of many studies. However, algae from the African Tropical rainforest have been
greatly overlooked. This investigation is targeting the biodiversity of subaerial algae from an
African tropical rainforest in Gabon (Africa) as well as a Neotropical forest in Panama (Central
America). During this investigation biodiversity studies were based on traditional assessments as
well as state of the art technology such as metagenomic approaches.
In this study, morphology based and molecular phylogenetic protocols have been
integrated to elucidate the biodiversity and systematics of the subaerial green algal order
Trentepohliales from Gabon, Africa. Based on morphological observations 14 species of
Trentepohlia and Printzina (belonging to the order Trentepohliales) were found to occur in
Gabon (six were newly recorded for the continent). Molecular phylogenetics of the
Trentepohliales from Africa suggested that the genera Trentepohlia and Printzina are not
monophyletic lineages. These results also suggested that a taxonomic reassessment of the
Trentepohliales is necessary.
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The African subaerial algal biodiversity was assessed using a novel metagenomic
approach at a broader taxonomic level. Results of this approach suggest that the African
rainforest is home to green algal (Chlorophyta), cyanobacteria, and diatoms (Sramenopiles) taxa.
Finally, Panamanian subaerial diversity was also evaluated using a metagenomic approach with
an ecological application: the biodiversity of the epiphytic flora was compared in four different
tree heights as well as the potential effect of the orientation (East versus West). Results of this
investigation indicate that the distribution of the algal diversity in terms of major groups was
essentially following a similar pattern along the vertical gradient in the forest canopy. In contrast,
the distribution of algal groups and specialized taxa was dissimilar between Western and Eastern
faces of trees.

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LIST OF ABBREVIATIONS AND SYMBOLS

BBM Bold‘s Basal medium (modified with vitamins)
BI Bayesian inference
Bp Base pairs
C Degrees Celsius
DNA Deoxyribonucleic acid
E East
E. coli Escherichia coli
e.g. Exempli gratia (Latin: for example)
et al. Et alia (Latin: and others)
GTR General time reversible
I portion of invariant sites
i.e. Id est (Latin: that is)
km2 Kilometers squared
m Meter
ML Maximum likelihood
MP Maximum parsimony
NSF National Science Foundation (United States of America)
PP Posterior probabilities
PCR Polymerase chain reaction
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rDNA Ribosomal deoxyribonucleic acid
rbcL Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit
RPM Revolutions per minute
RUBISCO Ribulose-1,5-bisphosphate carboxylase oxygenase
SAG Culture collection of algae at the University of Göttingen, Germany
sp. Species
SSU Small subunit
STRI Smithsonian Tropical Research Institute
TBR Tree bisection reconnection
UPA Universal Plastid Amplicon
USA United States of America
UVR Ultraviolet radiation
W West
X-gal 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside
& And
o Degrees
= Equals
Γ Gamma distribution
μL Microliter(s)
‗ Minutes
% Percent
― Seconds

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ACKNOWLEDGMENTS

Before all, I would like to thank the many colleagues, family, friends, and faculty who
have helped and supported me throughout my academic career. I am most thankful to the
members of my dissertation committee: Dr. Juan Lopez-Bautista, Dr. Charles Amsler, Dr. John
Clark, Dr. Martha Powell, and Dr. Amelia Ward. I am grateful for their suggestions and
recommendations for this dissertation. I am particularly indebted to Dr. Lopez-Bautista for
awarding me with his trust on this subject when my knowledge about terrestrial algae was very
limited. He made me profit from his invaluable knowledge and valuable expertise. With his
encouragement I could explore this wonderful subject in many parts of the world. I would also
like to extend my sincere thanks to Dr. Fabio Rindi for his greatly appreciated help. His expertise
and tutelage of terrestrial algae made me more knowledgeable about the subject. I would also
like to thank my former fellow Labmate, Dr. Daryl Lam, for his assistance in the lab and his
friendship.
I am also grateful to my dear parents for their moral support all throughout these years of
research. Their prayers and blessings that accompanied me both in the lab and in the fieldwork
helped me to overcome all obstacles. I tell them kindly to find through these lines the expression
of my greatest dedication and love.
I would like to thank the many scientists from around the world that assisted with this research.
Dr. Miguel Leal, Mr. Diosdado Nguema, Mr. Etienne Mounoumoulossi, and Mr. Prince
Bissiemou (Missouri Botanical Garden) for their help with logistics while in Gabon. Without
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them my collections in Gabon would have never been accomplished. I would also like to thank
Dr. Rachel Collin (STRI Bocas del Toro Station) for her support while in Panama. Dr. Collin
provided me with the collection permits and facilitated my collection trips in Panama. Finally, I
extend my thanks to Joe Maher, whose expertise in climbing trees was crucial in gathering
subaerial algal samples while in panama.
This research was sponsored in part by a NSF grant (DEB 0542924) to Dr. Lopez-Bautista.
Research fundings were also provided by The University of Alabama‘s Graduate School, The
UA Graduate Student Association, and the Department of Biological Sciences to Haj A. Allali.
I would also like to extend my thanks to the Phycological Society of America for their funding
through the ―Grants-in-Aid of Research‖ to support field trips and lab work.

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CONTENTS

ABSTRACT .................................................................................................... ii
LIST OF ABBREVIATIONS AND SYMBOLS......................................... iv
ACKNOWLEDGMENTS ............................................................................. vi
LIST OF TABLES .......................................................................................... x
LIST OF FIGURES ....................................................................................... xi
1. INTRODUCTION. ................................................................................. ....1
a. Historical perspective of subaerial algae................................................2
b. Ecology of subaerial algae.....................................................................3
c. Systematics of subaerial algae...............................................................4
d. Problems in systematics of subaerial African algae…………………....6
e. Approach………………………………………………………………10
2. BIODIVERSITY OF TRENTEPOHLIALES IN AN AFRICAN
TROPICAL RAINFOREST…………………………………………….....12

3. MOLECULAR SYSTEMATICS OF THE SUBAERIAL GREEN
ALGAL ORDER TRENTEPOHLIALES FROM WEST
EQUATORIAL AFRICA……………………………………………….....35

4. THE USE OF METAGENOMICS TO INFER ALGAL DIVERSITY
IN A SUBAERIAL COMMUNITY FROM A
TROPICAL RAINFOREST, MONTS DE CRISTAL
NATIONAL PARK, GABON…………………………………………......65

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5. DIVERSITY AND DISTRIBUTION OF EPIPHYTIC
SUBAERIAL ALGAE IN A PANAMANIAN FOREST:
A METAGENOMIC APPROACH……………………………………..148

REFERENCES ............................................................................................ 257
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