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Assessing Taxonomic Issues with the Genera Anabaena, Aphanizomenon and Nostoc Using Morphology, 16S Rrna and Efp Genes

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Assessing Taxonomic Issues with the Genera Anabaena, Aphanizomenon and Nostoc Using Morphology, 16S Rrna and Efp Genes Assessing Taxonomic Issues with the Genera Anabaena, Aphanizomenon and Nostoc Using Morphology, 16S rRNA and efp genes by Orietta Beltrami A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Master of Science in Biology Waterloo, Ontario, Canada, 2008 © Orietta Beltrami 2008 I hereby declare that I am the sole author of this thesis. This is a true copy of the thesis, including any required final revisions, as accepted by my examiners. I understand that my thesis may be made electronically available to the general public. ii ABSTRACT Cyanobacteria are an ancient lineage of gram-negative photosynthetic prokaryotes that play an important role in the nitrogen cycle in terrestrial and aquatic systems. Widespread cyanobacterial blooms have prompted numerous studies on the classification of this group, however defining species is problematic due to lack of clarity as to which characters best define the various taxonomic levels. The genera Anabaena, Aphanizomenon and Nostoc form one of the most controversial groups and are typically paraphyletic within phylogenetic trees and share similar morphological characters. This study’s purpose was to determine the taxonomic and phylogenetic relationships among isolates from these three genera using 16S rRNA and bacterial elongation factor P (efp) gene sequences as well as morphological analyses. These data confirmed the non- monophyly of Anabaena and Aphanizomenon and demonstrated that many of the isolates were intermixed among various clades in both gene phylogenies. In addition, the genus Nostoc was clearly not monophyletic and this finding differed from previous studies. The genetic divergence of the genus Nostoc was confirmed based on 16S rRNA gene sequence similarities (≥85.1%), and the isolates of Anabaena were genetically differentiated, contrary to previous studies (16S rRNA gene sequence similarities ≥89.4%). The morphological diversity was larger than the molecular diversity, since the statistical analysis ANOSIM showed that the isolates were morphologically well differentiated; however, the 16S rRNA gene sequence similarities showed some isolates as being related at the species level. Planktonic and benthic strains were not distinguished phylogenetically, although some well-supported clusters were noted. Cellular iii measurements (length and width of vegetative cells, end cells, heterocysts and akinetes) were noted to be the morphological characters that best supported the differentiation among isolates, more than qualitative characterization. Among the metric parameters, the length of akinetes resulted in better differentiation among isolates. The efp gene sequence analyses did not appear to be useful for the taxonomic differentiation at lower taxonomic levels, but gave well-supported clusters for Aphanizomenon that was supported by the morphological analyses. Both gene regions gave similar trees with the exception of the Aphanizomenon isolates which clustered together in phylogenetic trees based on the efp gene. This differed from the 16S rRNA gene in which this genus was paraphyletic with Anabaena species that were similar in morphology to Aphanizomenon. Hence, the application of multiple taxonomic criteria is required for the successful delineation of cyanobacterial species. iv ACKNOWLEDGEMENTS My first acknowledgement is for my supervisor Dr. Kirsten Müller, who gave me the opportunity to work in her lab, provided me with help, advice and constant understanding. I also want to thank Dr. Stephanie Guildford, Dr. Jonathan Witt and Dr. John Semple, for their support. Particularly, thanks to Hedy Kling for her help, support and advice. Special thanks to Amanda Poste and Peter Njuru, who collected the samples for this work and to Dr. Susan Watson, Dr. Friedrich Jütter, Mr. George Izaguirre and Dr. Sarah A. Spaulding who provided me with excellent cyanobacterial cultures and samples. I would also like to thank my labmates: Andrea Gill, Sara Ross, Justin Lorentz, Lynette Lau, Robert Young, Michael Kani and Adam Woodworth for their assistant and their friendly welcoming. Special thanks to Michael Lynch, who provided me with help and advice every time I needed it. Muchísimas gracias para Pablo Conejeros quien me guió y me acompaño durante todo este difícil periodo, y quien en parte me abrió las puertas de Canadá. También gracias por su apoyo y amor incondicionales. Gracias a Iván Salinas, quien me dedico muchísimo tiempo y amistad. A mi papá, mamá y hermanas por su amor y preocupación. Fue una alegría haber conocido a Rita, Leandro, Maricris, Miguel, Andrea, Andres, Alondra, Alejandro, Macarena, Pancho y María José. Muchísimas gracias por su amistad, la que ojala se siga manteniendo en el tiempo. A Laura, Pamela, Chica, Guadalupe, Pilar, Eulogio, Gloria, Paola y todos aquellos que me apoyaron a la distancia. Y especial agradecimiento a mi Flor, que me ha acompañado durante 12 años. v TABLE OF CONTENTS List of Tables ..................................................................................................................... ix List of Illustrations.............................................................................................................. x Chapter 1: General Introduction .................................................................................... 1 1.1 Cyanobacteria ..................................................................................................... 1 1.2 Toxicology of Cyanobacteria.............................................................................. 2 1.3 Ecogeographical Distribution of Cyanobacteria................................................. 5 1.3.1 Ecogeographical Distribution of Anabaena................................................ 5 1.3.2 Ecogeographical Distribution of Aphanizomenon ...................................... 6 1.3.3 Ecogeographical Distribution of Nostoc..................................................... 7 1.4 Problems in taxonomy and phylogeny of Cyanobacteria ................................... 9 1.4.1 Taxonomic and Phylogenetic Problems among Genera Anabaena, Aphanizomenon and Nostoc...................................................................................... 12 1.4.1.1 The Anabaena-Aphanizomenon Complex ................................................ 12 1.4.1.2 The Nostoc-Anabaena Complex............................................................... 16 1.4.2 Taxonomic and Phylogenetic Problems within Genera Anabaena, Aphanizomenon and Nostoc...................................................................................... 17 1.4.2.1 Anabaena-strain Gaps............................................................................... 17 1.4.2.2 Aphanizomenon-strain Gaps ..................................................................... 19 1.4.2.3 Nostoc-strain Gaps.................................................................................... 19 1.5 Morphological Identification for Taxonomic and Phylogenetic Analysis on Anabaena, Aphanizomenon and Nostoc species ........................................................... 20 1.5.1 Anabaena and Aphanizomenon Morphological Differentiation ............... 22 vi 1.5.2 Anabaena and Nostoc Morphological Differentiation.............................. 22 1.5.3 Anabaena Species Morphological Identification...................................... 24 1.5.4 Aphanizomenon Species Morphological Identification ............................ 24 1.5.5 Nostoc Species Morphological Identification........................................... 25 1.6 Induction of Heterocysts and Akinetes Differentiation .................................... 26 1.7 Molecular Identification for Taxonomic and Phylogenetic Analysis on Anabaena, Aphanizomenon and Nostoc species ........................................................... 27 1.7.1 Sequence Analysis of 16S rRNA Gene .................................................... 27 1.7.2 Sequence Analysis of efp Gene of Protein Elongation Factor P (EF-P)... 28 1.8 Thesis Objectives.............................................................................................. 29 Chapter 2: Methods ........................................................................................................ 32 2.1 Cyanobacterial Isolates ..................................................................................... 32 2.2 Isolation and Culture Conditions ...................................................................... 32 2.3 Morphological Analysis.................................................................................... 36 2.4 Induction of Akinetes and Heterocysts Differentiation .................................... 36 2.5 DNA Extraction ................................................................................................ 39 2.6 PCR Amplification of the 16S rRNA Gene...................................................... 39 2.7 Sequencing of the 16S rRNA Gene ................................................................... 40 2.8 PCR Amplification of the efp Gene.................................................................. 41 2.9 Sequencing of the efp Gene .............................................................................. 43 2.10 Phylogenetic Analyses...................................................................................... 43 2.11 Statistical Analyses of Morphological Data ..................................................... 44 vii Chapter 3: Results..........................................................................................................
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