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Morphological and molecular diversity of the free-living representatives of the family Metopidae and the discovery of a new lineage of anaerobic ciliates
Rotterová, Johana ; Čepička, Ivan (advisor) ; Fiala, Ivan (referee)
Anoxic sediments host a wide variety of ciliates. Although it is known that anaerobiosis has independently arisen in several lineages of the main 11 lineages of Ciliophora and anaerobes have been found in at least eight lineages of ciliates, the diversity of anaerobic ciliates of the class Armophorea is severely understudied. Similarly, not much is known about their hydrogenosomes. To deepen our knowledge about the diversity of Armophorea, we have cultivated more than 100 armophorid strains from fresh water, brackish, and marine anoxic sediments worldwide. We determined their SSU rDNA sequences, performed protargol staining techniques, and studied light-microscopic morphology. In addition, we used transmission electron microscopy to assess the ultrastructure of some of the strains. Several novel clades of metopids, the free-living anaerobic ciliates of the class Armophorea, were identified. Importantly, a new deep lineage of marine anaerobic ciliates, muranes, was discovered. According to the SSU rDNA analysis, it is related to SAL group (Spirotrichea, Armophorea, and Litostomatea) with Cariacotrichea, but forms a separate lineage, possibly a novel class. We conclude that anoxic sediments harbour a high diversity of undescribed anaerobic ciliates. Key words: Anaerobiosis, Armophorea, ciliates,...
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The method of DNA barcoding and its use in protists
Rotterová, Johana ; Čepička, Ivan (advisor) ; Fiala, Ivan (referee)
DNA barcoding is a molecular method of species identification based on short regions of DNA sequences. These DNA barcodes should be unique for each species. The sequences within species should be identical or very much alike, while between species they should display a significant amount of differences. The sequences of an undetermined specimen can be compared with sequences vouchered to a particular species in a global DNA barcode database. The database was developed with the aim to simplify traditional taxonomy, eliminate its problems and accelerate its approaches. However, DNA barcoding has its own limitations that may hinder achieving its original goals and a compliance with the concept. The aim of this bachelor thesis consists of explaning the evolution of DNA barcoding through time and assessing the importance of this method at present, particularly in protists. Species identification may be very difficult in many protist groups, which can be explained by several reasons. To appraise this method completely is a hard task, because creation of the database has not yet been finished and official DNA barcodes have not been chosed for many groups. We can only find out in the future, therefore i will only focus on factors that influence the success of DNA barcoding at present.
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Morphological and molecular diversity of the free-living representatives of the family Metopidae and the discovery of a new lineage of anaerobic ciliates
Rotterová, Johana
6 ABSTRACT Anoxic sediments host a wide variety of ciliates. Although it is known that anaerobiosis has independently arisen in several lineages of the main 11 lineages of Ciliophora and anaerobes have been found in at least eight lineages of ciliates, the diversity of anaerobic ciliates of the class Armophorea is severely understudied. Similarly, not much is known about their hydrogenosomes. To deepen our knowledge about the diversity of Armophorea, we have cultivated more than 100 armophorid strains from fresh water, brackish, and marine anoxic sediments worldwide. We determined their SSU rDNA sequences, performed protargol staining techniques, and studied light-microscopic morphology. In addition, we used transmission electron microscopy to assess the ultrastructure of some of the strains. Several novel clades of metopids, the free-living anaerobic ciliates of the class Armophorea, were identified. Importantly, a new deep lineage of marine anaerobic ciliates, muranes, was discovered. According to the SSU rDNA analysis, it is related to SAL group (Spirotrichea, Armophorea, and Litostomatea) with Cariacotrichea, but forms a separate lineage, possibly a novel class. We conclude that anoxic sediments harbour a high diversity of undescribed anaerobic ciliates. Key words: Anaerobiosis, Armophorea, ciliates,...
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Anaerobic ciliates as a model group for studying the biodiversity and symbioses in anoxic environments
Rotterová, Johana ; Čepička, Ivan (advisor) ; Gentekaki, Eleni (referee) ; Silberman, Jeffrey David (referee)
Ciliates are also of the most extensively studied and diverse groups of unicellular eukaryotes, and yet, their anaerobic representatives have been largely neglected; in part due to culturing difficulties. Although all main ciliate lineages contain anaerobes, their diversity and evolution of anaerobiosis are especially poorly understood and just starting to gain attention. In fact, Ciliophora is an excellent model group to study adaptations to life in anoxia, since it, apart from the aerobic majority, includes free-living and endobiotic obligately anaerobic lineages, facultative anaerobes, microaerophiles, and microaerotolerant species. The diversity of Metopida, the free-living order of obligately anaerobic class Armophorea, has been partially revised and significantly broadened during the past years, including numerous redescriptions using modern methods, as well as the description of novel families Tropidoatractidae and Apometopidae, several genera, and multiple species. Oxygen plays a crucial role in ATP production via oxidative phosphorylation that takes place in the mitochondrion in most known eukaryotes. Nevertheless, anaerobic ciliates, among many other eukaryotes that have adapted to low oxygen concentrations or even its absence, have modified their mitochondria and energetic metabolism to...
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Morphological and molecular diversity of the free-living representatives of the family Metopidae and the discovery of a new lineage of anaerobic ciliates
Rotterová, Johana
6 ABSTRACT Anoxic sediments host a wide variety of ciliates. Although it is known that anaerobiosis has independently arisen in several lineages of the main 11 lineages of Ciliophora and anaerobes have been found in at least eight lineages of ciliates, the diversity of anaerobic ciliates of the class Armophorea is severely understudied. Similarly, not much is known about their hydrogenosomes. To deepen our knowledge about the diversity of Armophorea, we have cultivated more than 100 armophorid strains from fresh water, brackish, and marine anoxic sediments worldwide. We determined their SSU rDNA sequences, performed protargol staining techniques, and studied light-microscopic morphology. In addition, we used transmission electron microscopy to assess the ultrastructure of some of the strains. Several novel clades of metopids, the free-living anaerobic ciliates of the class Armophorea, were identified. Importantly, a new deep lineage of marine anaerobic ciliates, muranes, was discovered. According to the SSU rDNA analysis, it is related to SAL group (Spirotrichea, Armophorea, and Litostomatea) with Cariacotrichea, but forms a separate lineage, possibly a novel class. We conclude that anoxic sediments harbour a high diversity of undescribed anaerobic ciliates. Key words: Anaerobiosis, Armophorea, ciliates,...
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Prokaryotic symbionts of protists living in the intestine of wood eating cockroaches and termites
Kubánková, Aneta ; Hampl, Vladimír (advisor) ; Rotterová, Johana (referee)
Termites and wood-eating cockroaches are worldwide successful especially because of their ability to digest lignocellulose efficiently. After a long period of coevolution a complex ecosystem of diverse microorganisms was established in their hindgut. A lot of lineages of flagellates live solely within this unique environment and it is impossible to cultivate them in vitro. As termites are unable to survive without their eukaryotic endosymbionts, also protists are strongly linked to prokaryotes colonizing their cytoplasm and cytoplasmic membrane. Numerous phyla of bacteria participate in nitrogen fixation and efficient nitrogen utilization, synthesis of amino acids, cofactors and vitamines. Some of them take part in the degradation of lignocellulose. Representatives of another domain of prokaryotes, Archea, are important in the final stages of lignocellulose fermentation, because they utilize the produced hydrogen gas in a process of methanogenesis. Large part of our knowledge about the composition and function of the termite gut biota was acquired thanks to metagenomic studies.
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Morphological and molecular diversity of the free-living representatives of the family Metopidae and the discovery of a new lineage of anaerobic ciliates
Rotterová, Johana ; Čepička, Ivan (advisor) ; Fiala, Ivan (referee)
Anoxic sediments host a wide variety of ciliates. Although it is known that anaerobiosis has independently arisen in several lineages of the main 11 lineages of Ciliophora and anaerobes have been found in at least eight lineages of ciliates, the diversity of anaerobic ciliates of the class Armophorea is severely understudied. Similarly, not much is known about their hydrogenosomes. To deepen our knowledge about the diversity of Armophorea, we have cultivated more than 100 armophorid strains from fresh water, brackish, and marine anoxic sediments worldwide. We determined their SSU rDNA sequences, performed protargol staining techniques, and studied light-microscopic morphology. In addition, we used transmission electron microscopy to assess the ultrastructure of some of the strains. Several novel clades of metopids, the free-living anaerobic ciliates of the class Armophorea, were identified. Importantly, a new deep lineage of marine anaerobic ciliates, muranes, was discovered. According to the SSU rDNA analysis, it is related to SAL group (Spirotrichea, Armophorea, and Litostomatea) with Cariacotrichea, but forms a separate lineage, possibly a novel class. We conclude that anoxic sediments harbour a high diversity of undescribed anaerobic ciliates. Key words: Anaerobiosis, Armophorea, ciliates,...
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The method of DNA barcoding and its use in protists
Rotterová, Johana ; Čepička, Ivan (advisor) ; Fiala, Ivan (referee)
DNA barcoding is a molecular method of species identification based on short regions of DNA sequences. These DNA barcodes should be unique for each species. The sequences within species should be identical or very much alike, while between species they should display a significant amount of differences. The sequences of an undetermined specimen can be compared with sequences vouchered to a particular species in a global DNA barcode database. The database was developed with the aim to simplify traditional taxonomy, eliminate its problems and accelerate its approaches. However, DNA barcoding has its own limitations that may hinder achieving its original goals and a compliance with the concept. The aim of this bachelor thesis consists of explaning the evolution of DNA barcoding through time and assessing the importance of this method at present, particularly in protists. Species identification may be very difficult in many protist groups, which can be explained by several reasons. To appraise this method completely is a hard task, because creation of the database has not yet been finished and official DNA barcodes have not been chosed for many groups. We can only find out in the future, therefore i will only focus on factors that influence the success of DNA barcoding at present.
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