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Molecular Microbial Eukaryote Diversity in Five Rift Valley Lakes and Description of Three Ciliates Species from Lake Bogoria, Kenya

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Molecular Microbial Eukaryote Diversity in Five Rift Valley Lakes and Description of Three Ciliates Species from Lake Bogoria, Kenya MOLECULAR MICROBIAL EUKARYOTE DIVERSITY IN FIVE RIFT VALLEY LAKES AND DESCRIPTION OF THREE CILIATES SPECIES FROM LAKE BOGORIA, KENYA Inaugural-Dissertation zur Erlangung des Doktorgrades Dr. rer. nat. der Fakultät für Biologie an der Universität Duisburg-Essen vorgelegt von Ong’ondo Geoffrey Odhiambo aus Kisumu, Kenia Juni, 2014 1. Gutachter: Prof. Dr. Jens Boenigk 2. Gutachter: Prof. Dr. Michael Schagerl Tag der mündlichen Prüfung: 19. 09. 2014 DEDICATIONS In loving memory of my late father, Henry Martin Ong’ondo (1944 – 1983) ii TABLE OF CONTENTS TABLE OF CONTENTS .......................................................................................................... iii LIST OF ABBREVIATIONS AND ACRONYMS ...................................................................vii LIST OF FIGURES ................................................................................................................ viii LIST OF TABLES ...................................................................................................................... x CHAPTER 1 ............................................................................................................................... 1 1.0 GENERAL INTRODUCTION .............................................................................................. 1 1.1 Background ................................................................................................................... 1 1.2 Ecology of the rift valley lakes ...................................................................................... 2 1.3 Thesis outline ................................................................................................................ 4 CHAPTER 2 ............................................................................................................................... 5 2.0 MATERIALS AND METHODS ........................................................................................... 5 2.1 Study sites ..................................................................................................................... 5 2.1.1 Lake Baringo ......................................................................................................... 5 2.1.2 Lake Turkana ......................................................................................................... 5 2.1.3 Lake Oloidien ........................................................................................................ 6 2.1.4 Lake Elmenteita ..................................................................................................... 7 2.1.5 Lake Bogoria ......................................................................................................... 7 2.2 Sample collection .......................................................................................................... 7 2.3 Microscopy ................................................................................................................. 10 2.3.1 Live observations ................................................................................................. 10 2.3.2 Fixation and staining ............................................................................................ 10 2.3.3 Counts and measurements .................................................................................... 10 2.4 DNA extraction, amplification and sequencing............................................................ 10 2.5 High-throughput data processing and analyses ............................................................ 11 2.6 Phylogenetic placement of the 454 reads ..................................................................... 11 iii 2.7 Stastical analysis ......................................................................................................... 12 CHAPTER 3 ............................................................................................................................. 13 3.0 MOLECULAR DIVERSITY OF EUKARYOTIC PROTISTS ............................................ 13 3.1 Introduction ................................................................................................................ 13 3.2 Results ........................................................................................................................ 14 3.2.1 Environmental parameters .................................................................................... 14 3.2.1 Overall protist diversity........................................................................................ 14 3.2.3 Protist diversity in the lakes ................................................................................. 14 3.2.4 Taxonomic richness ............................................................................................. 16 3.2.4 Spatial distribution ............................................................................................... 17 3.2.5 Phylogenetic affiliation of the ciliates .................................................................. 18 3.3 Discussion................................................................................................................... 21 3.3.1 Molecular protist diversity and taxonomic richness .............................................. 21 3.3.2 Spatial distribution of the protist community ........................................................ 22 3.3.3 Phylogenic affiliation of the ciliates ..................................................................... 23 CHAPTER 4 ............................................................................................................................. 25 4.0 MOLECULAR MICROBIAL DIVERSITY AND CILIATE MORPHOSPECIES IN LAKE BOGORIA ................................................................................................................................ 25 4.1 Introduction ................................................................................................................ 25 4.2 Results ........................................................................................................................ 26 4.2.1 Protist taxonomic richness and abundance ............................................................ 26 4.2.2 Protistan and fungal phylogenetic affiliations ....................................................... 26 4.2.3 Ciliate molecular abundance, morphospecies and taxonomic composition ............ 27 4.3 Discussion................................................................................................................... 28 4.3.1 Protist and fungal taxonomic richness and sequence abundance ............................ 28 4.3.2 Protist and fungal taxon phylogenetic affiliations ................................................. 29 iv 4.3.3 Ciliate molecular abundance, morphospecies and taxonomic composition ............ 30 CHAPTER 5 ............................................................................................................................. 32 5.0 DIVERSITY AND COMPOSITION OF CHLOROPHYTES ............................................. 32 5.1 Introduction ....................................................................................................... …….32 5.2 Results ........................................................................................................................ 33 5.2.1 Chlorophyta distribution ............................................................................................ 33 5.2.2 Diversity and phylogenetic affiliation................................................................... 33 5.2.2.1 Chlorophyceae .................................................................................................... 34 5.2.2.2 Trebouxiophyceae .............................................................................................. 34 5.2.2.3 Prasinophyceae .................................................................................................... 34 5.3 Discussion................................................................................................................... 39 5.2.1 Chlorophyta distribution ............................................................................................ 39 5.2.2 Diversity and phylogenetic affiliation................................................................... 39 5.2.2.1 Chlorophyceae ..................................................................................................... 39 5.2.2.2 Trebouxiophyceae ................................................................................................ 41 5.2.2.3 Prasinophyceae .................................................................................................... 42 CHAPTER 6 ............................................................................................................................. 43 6.0 DESCRIPTION OF THREE NEW CILIATE SPECIES .................................................... 43 6.1 Introduction ................................................................................................................ 43 6.2 Results ........................................................................................................................ 45 6.2.1 Frontonia alkalina sp. candidatus. ....................................................................... 45 6.2.2 Euplotes endoroisi sp. candidatus. ........................................................................ 53 6.2.3 Condylostoma bogoriense sp. candidatus ............................................................
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