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Interactions among free-living prokaryotes and protists in microbial communities
Jirouchová, Kateřina ; Pánek, Tomáš (advisor) ; Fiala, Ivan (referee)
Protists and prokaryotes live in the natural environment in complex microbial communities whose members interact with each other. These communities consist of a few to many species that interact with each other in many ways such as predation/prey, ecto/endosymbiosis, parasitism, modulation of development or behaviour and harmful algicidal/bactericidal interactions, resulting in a complex network of interactions that influence structure of the microbial community as well as metabolism and behaviour of present species. This bachelor thesis is an overview of the interactions between free-living protists and prokaryotes within microbial communities, excluding well-studied interactions such as predation, parasitism, and ecto/endosymbiosis, while focusing on the diversity of lesser- known interactions, highlighting their importance and future research opportunities.
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The diversity of anaerobic ciliates from the subclass Scuticociliatia and their symbionts
Poláková, Kateřina ; Čepička, Ivan (advisor) ; Fiala, Ivan (referee)
Ciliates are the most diversified protists in suboxic and anoxic habitats where they often form symbioses with prokaryotes. Although the diversity of anaerobic ciliates has been overlooked for a long time, anaerobic representatives can be found in most ciliate classes. This study focuses on anaerobic ciliates from the subclass Scuticociliatia, a neglected lineage, which belongs to the species-rich class Oligohymenophorea. One of the main outcomes resulting from this study is the discovery of a novel anaerobic clade of ciliates, from which only one species has been described molecularly to date. We have shown that the clade represents a diversified lineage, likely a new order. Thanks to the sampling of many freshwater and marine anoxic sediments, we have established the largest culture collection of anaerobic scuticociliates in the world. This has enabled us to determine the 18S rRNA gene sequences of 55 cultured anaerobic scuticociliates and to study their morphology both in-vivo and using various silver- impregnation methods. Besides, we applied transmission and scanning electron microscopy techniques to study the ultrastructure of both ciliates and symbionts. To identify the symbionts, we also employed other methods including microbiome sequencing and fluorescence in-situ hybridization. Since all...
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Transmission and detection of the crayfish plague pathogen under experimental conditions
Svoboda, Jiří ; Petrusek, Adam (advisor) ; Fiala, Ivan (referee)
The crayfish plague pathogen, Aphanomyces astaci, is one of the most serious threats to European indigenous crayfish species, e.g., the noble crayfish (Astacus astacus). The only way to protect susceptible crayfish species from the disease is to prevent the dispersion of the pathogen to their populations. One of the most important sources of the crayfish plague pathogen in Central Europe is the spiny-cheek crayfish (Orconectes limosus), a species of North American origin, which can carry the parasite in its cuticle for years. Some literature sources claimed that the pathogen dispersion from the American vectors is restricted to periods of moulting or to the time before and after the crayfish death. However, experimental evidence for such hypotheses was lacking. The main aim of my thesis was to test these predictions, and the alternative scenario that the crayfish plague pathogen can be transmitted from the infected spiny-cheek crayfish also in other periods. For this purpose, experiments were set up to investigate A. astaci transmission from infected spiny-cheek crayfish to non-infected spiny-cheek or noble crayfish. As expected, the pathogen was transmitted to noble crayfish much more easily than to the uninfected American host. Nevertheless, we succeeded in the pathogen transmission also among spiny-cheek...
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Whitehead's philosophy of nature (with special respect to "London period")
Andrle, Michal ; Kratochvíl, Zdeněk (advisor) ; Fiala, Ivan (referee) ; Zuska, Vlastimil (referee)
Autoreferátdisertačrrípráce English version During his long careeťas a thinker and publicist A.N. Whiteheadpassedthrouglrseveral developmentalstages.These rvere invariably marked by a specific intellectualtheme,or ratheran expandinggamutof subjectsthat came into the focus of his analysis.Furthermore, thesephasescan be dated,with a relatively high degreeof accuracy,accordingto the major landmarksin his careersincetheycoincidedalmostpreciselywith his placesof work. Thanks to theselinks' his worksrnaybe dividedinto theťollowingstagesof development: a) workson mathematicsandmathematicallogic ("Cambridgeperiod")(1898- 1910) b) "pan-physical"works, i.e. works on theoreticalphysics,"philosophyof nature" and the"philosophyof naturalsciences"("Londonperiod")(1910- 1924) c) "metaphysical"works("Harvardperiod")(1925- 1938) The individual stagesof his careerdisplay signif,rcantcontinuity (given by the author's personalidiosyncrasies),as well as substantialdiscontinuities(since Whiteheadmodifies termsand themesalongthe way). all of which are essentialto understandingthe development of his work. The major goal of thepresentstudyis to provide a comprehensiveoveryiew of the works on "the philosophyof nature"developedin his "London period".This is accomplishedby meansof a threefoldapproach.The majorityof this studyis...
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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 endobiotic and free-living trichomonads
Céza, Vít ; Čepička, Ivan (advisor) ; Bardůnek Valigurová, Andrea (referee) ; Fiala, Ivan (referee)
This PhD thesis presents the results of three subprojects focused on the research of so far understudied groups of the phylum Parabasalia. The previous research mostly focused on the parabasalids living in the guts of termites or on demonstrably pathogenic species. Surprisingly, there is only a little information about the impact of an increased contact of non-human primates with humans on the diversity of their intestinal trichomonads. Similarly, free-living trichomonads have been neglected for a long time, although they are likely crucial for understanding the evolution of Parabasalia as a whole. The diversity of the phylum Parabasalia is still poorly understood due to the brief and incomplete descriptions of many species, as well as a lot of missing sequence data. This doctoral project focused on the research of these hitherto understudied research areas. In the first subproject, a complete revision of the genus Hypotrichomonas was carried out, including the descriptions of six new species, some of which were found in previously well studied vertebrate hosts; these species must have been overlooked by the previous authors and the real diversity of intestinal trichomonads is certainly much higher than currently known. Because the most newly described species of Hypotrichomonas are readily...
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The diversity of anaerobic ciliates from the subclass Scuticociliatia and their symbionts
Poláková, Kateřina ; Čepička, Ivan (advisor) ; Fiala, Ivan (referee)
Ciliates are the most diversified protists in suboxic and anoxic habitats where they often form symbioses with prokaryotes. Although the diversity of anaerobic ciliates has been overlooked for a long time, anaerobic representatives can be found in most ciliate classes. This study focuses on anaerobic ciliates from the subclass Scuticociliatia, a neglected lineage, which belongs to the species-rich class Oligohymenophorea. One of the main outcomes resulting from this study is the discovery of a novel anaerobic clade of ciliates, from which only one species has been described molecularly to date. We have shown that the clade represents a diversified lineage, likely a new order. Thanks to the sampling of many freshwater and marine anoxic sediments, we have established the largest culture collection of anaerobic scuticociliates in the world. This has enabled us to determine the 18S rRNA gene sequences of 55 cultured anaerobic scuticociliates and to study their morphology both in-vivo and using various silver- impregnation methods. Besides, we applied transmission and scanning electron microscopy techniques to study the ultrastructure of both ciliates and symbionts. To identify the symbionts, we also employed other methods including microbiome sequencing and fluorescence in-situ hybridization. Since all...
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Whitehead's philosophy of nature (with special respect to "London period")
Andrle, Michal ; Kratochvíl, Zdeněk (advisor) ; Fiala, Ivan (referee) ; Zuska, Vlastimil (referee)
Autoreferátdisertačrrípráce English version During his long careeťas a thinker and publicist A.N. Whiteheadpassedthrouglrseveral developmentalstages.These rvere invariably marked by a specific intellectualtheme,or ratheran expandinggamutof subjectsthat came into the focus of his analysis.Furthermore, thesephasescan be dated,with a relatively high degreeof accuracy,accordingto the major landmarksin his careersincetheycoincidedalmostpreciselywith his placesof work. Thanks to theselinks' his worksrnaybe dividedinto theťollowingstagesof development: a) workson mathematicsandmathematicallogic ("Cambridgeperiod")(1898- 1910) b) "pan-physical"works, i.e. works on theoreticalphysics,"philosophyof nature" and the"philosophyof naturalsciences"("Londonperiod")(1910- 1924) c) "metaphysical"works("Harvardperiod")(1925- 1938) The individual stagesof his careerdisplay signif,rcantcontinuity (given by the author's personalidiosyncrasies),as well as substantialdiscontinuities(since Whiteheadmodifies termsand themesalongthe way). all of which are essentialto understandingthe development of his work. The major goal of thepresentstudyis to provide a comprehensiveoveryiew of the works on "the philosophyof nature"developedin his "London period".This is accomplishedby meansof a threefoldapproach.The majorityof this studyis...
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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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