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Excavata: Heterolobosea) Univerzita Karlova v Praze Přírodovědecká fakulta Studijní program: Biologie Studijní obor: Zoologie Bc. Kristýna Uhrová Diverzita nekultivovatelných a obtížně kultivovatelných zástupců čeledi Psalteriomonadidae (Excavata: Heterolobosea) Diversity of noncultivation and difficult cultivation representatives of family Psalteriomonadidae (Excavata: Heterolobosea) Diplomová práce Školitel: doc. RNDr. Ivan Čepička, Ph.D Praha, 2017 Prohlášení: Prohlašuji, že jsem závěrečnou práci zpracovala samostatně a že jsem uvedla všechny použité informační zdroje a literaturu. Tato práce ani její podstatná část nebyla předložena k získání jiného nebo stejného akademického titulu. V Praze, 15. 08. 2017 Podpis 2 Poděkování Na tomto místě bych ráda poděkovala zejména svému školiteli, Ivanu Čepičkovi, za pomoc při sepisování této práce, za odborné rady, poskytnutí materiálu a za trpělivost. Díky Ivane. Dále bych ráda poděkovala Petru Táborskému za cenné rady, Tomáši Pánkovi a velké díky Pavle Hanouskové za pomoc při scanovací elektronové mikroskopii. A v neposlední řadě děkuji svým blízkým za podporu při mém studiu. 3 OBSAH Abstrakt.....................................................................................................................................5 Abstract.....................................................................................................................................6 1. Úvod a cíle..........................................................................................................................7 2. Literální přehled..................................................................................................................8 2.1. Environmentální diverzita protist................................................................................8 2.2. Charakteristika kmene Heterolobosea.........................................................................9 2.3. Charakteristika čeledi Psalteriomonadidae................................................................15 2.4. Taxonomie čeledi Psalteriomonadidae......................................................................19 3. Materiál a metody.............................................................................................................20 3.1. Kultivace izolátů........................................................................................................20 3.1.1. Složení a příprava médií.................................................................................20 3.1.2. Získávání nových izolátů................................................................................21 3.2. Morfologie.................................................................................................................21 3.2.1. Barvení protargolem podle Bodiana, modifikováno podle Nie (1950)..........21 3.2.2. Pozorování pomocí světelného mikroskopu...................................................23 3.2.3. Scanovací elektronová mikroskopie...............................................................23 3.3. Izolace DNA..............................................................................................................23 3.3.1. Amplifikace genu pro SSU rRNA....................................................................24 3.4. Elektroforéza..............................................................................................................25 3.5. Purifikace PCR produktů...........................................................................................25 3.6. Klonování..................................................................................................................25 3.6.1. Příprava ligační směsi.....................................................................................26 3.6.2. Příprava bakteriálních kolonií.........................................................................26 3.7. Sekvenace DNA.........................................................................................................27 3.8. Vyhodnocení sekvencí a fylogenetická analýza........................................................28 4. Výsledky...........................................................................................................................29 4.1. Izoláty........................................................................................................................29 4.2. Fylogenetická analýza...............................................................................................35 4.3. Morfoligie..................................................................................................................40 4.4. Environmentální sekvenování...................................................................................50 5. Diskuze.............................................................................................................................51 5.1. Environmentální sekvenování....................................................................................51 5.2. Fylogeneze a morfologie nových druhů....................................................................51 5.3. Diverzita čeledi Psalteriomonadidae..........................................................................55 6. Závěr.................................................................................................................................56 7. Literatura...........................................................................................................................57 4 ABSTRAKT Kmen Heterolobosea je skupinou améboflagelátů, améb a flagelátů patřící do říše Excavata. V současnosti je popsáno asi 150 druhů zástupců kmene Heterolobosea, z nichž je asi 20 druhů obligátně anaerobních. Většina z nich patří do čeledi Psalteriomonadidae. Cílem této práce bylo poznat diverzitu potenciálních obtížně kultivovatelných a nekultivovatelných anaerobních zástupců kmene Heterolobosea. Získali jsme mnoho nových izolátů zejména ze sladkovodních sedimentů. Izolovali jsme DNA z čerstvých kultur a určili jsme sekvence jejich genu pro SSU rRNA za použití primerů specifických pro skupinu Psalteriomonadidae. Získali jsme 123 nových sekvencí, které reprezentují 6 již popsaných druhů, dále bylo objeveno 16 potenciálně nových druhů. Nicméně mnoho nových druhů zaniklo v raných stádiích kultivování. Naše výsledky naznačují, že existuje velká diverzita nekultivovatelných a obtížně kultivovatelných druhů čeledi Psalteriomonadidae. Klíčová slova: diverzita, gen pro SSU rRNA, Heterolobosea, kultivace, Psalteriomonadidae 5 ABSTRACT Heterolobosea is a group of amoeboflagellates, amoebae, and flagellates belonging to the supergroup Excavata. Approximately 150 species of Heterolobosea have been described, from which less than 20 are obligately anaerobic. Most anaerobic species belong to the family Psalteriomonadidae. The aim of this study was to examine the diversity of potentially uncultivable anaerobic heteroloboseids. We obtained multiple new isolates, mainly from freshwater hypoxic sediments, isolated DNA from fresh cultures and determined their SSU rRNA gene sequences using Psalteriomonadidae-specific primers. In total, we have analyzed sequences of 123 new strains, which represented six already described species of Psalteriomonadidae as well as 16 potentially new ones. However, most of the new species died during the early stages of culture. Our results suggest that a great diversity of uncultivable psalteriomonadids exists in the nature. Key words: diversity, SSU rRNA, Heterolobosea, cultivation, Psalteriomonadidae 6 1. ÚVOD A CÍLE PRÁCE Tato práce byla původně zaměřena na environmentální sekvenování vybraných linií anaerobních protist, zejména zástupců čeledi Psalteriomonadidae (Excavata: Heterolobosea: Tetramitia). Tato čeleď byla vybrána, protože byly publikovány PCR primery, které by měly být specifické pro gen pro SSU rRNA jejich zástupců (Pánek et al. 2012, 2014b). Čeleď Psalteriomonadidae patří do kmene Heterolobosea. Kmen Heterolobosea je nepočetnou skupinou, kde bylo posáno přibližně 150 druhů. Avšak je to významný taxon, protože do něho náleží několik významných patogenů člověka. Nicméně náplň diplomové práce se brzy změnila kvůli obtížím při izolování DNA přímo z prostředí a po zjištění, že zmíněné primery nejsou zcela specifické v případě, že ve vzorku výrazně převažuje DNA jiných organismů, a tudíž byly použity i další metody k odhalení diverzity, a to metody mikroskopovací a kultivační. Kvůli již zmíněným problémům při odhalování environmentální diverzity jsme se nakonec zaměřili na charakterizaci kultur, které jsme nasbírali a na kultury z naší sbírky, která byla velmi rozsáhlá. Jednalo se o sladkovodní i mořské izoláty, ze kterých jsme izolovali a následně sekvenovali DNA, která dosud nebyla analyzována. Získali jsme 123 nových sekvencí a objevili jsme 16 potenciálně nových druhů čeledi Psalteriomonadidae. V další fázi této práce jsme se zaměřili na morfologii těchto nově objevených druhů. 7 2. Literální přehled 2.1. Environmentální diverzita protist Protisté jsou skupinou extrémně diverzifikovaných organizmů a jsou dominantní složkou planktonu ve vodním ekosystému (Lie et al. 2014; Massana et al. 2015; Orsi et al. 2011; Šlapeta et al. 2005). Jsou všudypřítomní a početní ve všech typech prostředí. Protista v anoxickém i oxickém prostředí slouží jako hostitelé pro mnoho symbiotických bakterií i archeí (Weber et al. 2014). Protisté hrají důležitou ekologickou roli ve vodních ekosystémech jako primární producenti, konzumenti, predátoři, dekompozitoři a paraziti
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