SedaDNA abil eukarüootsete organismide mitmekesisuse, dünaamika ja keskkonnamuutuste mõju rekonstrueerimine hilisjääaja ja Holotseeni perioodil Lielais Svētiņu järve näitel

Väitekirja elektrooniline versioon ei sisalda publikatsiooneJärves leiduv ja sinna kandunud bioloogiline materjal mattub seal aja jooksul järve settesse, milles rakuväline DNA võib seonduda savi ja humiinaine osakestega ning seetõttu säilib väga pikka aega. Teadaolevalt vanim järve settest tuvastatud DNA on ligi 270 000 aastat vana. Järve setetes säilinud vana DNA (sedaDNA) võimaldab ajas tagasiulatuvalt rekonstrueerida bioloogilise mitmekesisuse muutusi ning tuvastada, millal ja miks need muutused mitmekesisuses toimusid. Samuti võimaldab sedaDNA uurida keskkonna muutuste mõju kooslustele läbi aja. Koosluste muutuste seoseid keskkonnateguritega on oluline uurida, kuna see aitab seletada ka tänapäevaseid bioloogilise mitmekesisuse muutusi ning koostada prognoose edasise kliimasoojenemise olukorras. SedaDNA on suhteliselt uudne tööriist paleo-ökoloogias, sealjuures on sedaDNA põhised uuringud hüppeliselt kasvanud viimase 5 aasta jooksul tänu DNA sekveneerimis- ja analüüsimeetodite arengule. Käesolevas doktoritöös uuriti, kas Lielais Svētiņu järve settes leiduvat vana DNAd saab kasutada eukarüootide mitmekesisuse rekonstrueerimiseks, keskendudes fototroofide ja seente dünaamikale, ning uuriti tuvastatud koosluste reageerimist muutuvatele keskkonnatingimustele. Lielais Svētiņu järve võib pidada üheks Euroopa kirde regiooni mudeljärveks, sest sinna on kogunenud paks settekiht, piirkonnas on hästi dateeritud hiline inimmõju ning varasematest õietolmu ja mikro-, makrofossiilide uuringutest on kogutud hulgaliselt andmeid. Olemasolev andmestik võimaldab uurida nii looduslikku kui ka inimmõju järve ökosüsteemi kooslustele ja laiemalt piirkonnas toimunud muutusi. Uudse lähenemisena kasutati järves ja selle valgalal toimuvate muutuste hindamiseks indikaatorina seente erinevate ökoloogiliste gruppide esinemist. Esmalt leiti, et sedaDNA võimaldab edukalt tuvastada eukarüootide mitmekesisust ka sügavamatest, s.t vanematest, sette kihtidest. Selgus, et sedaDNA võimaldab rekonstrueerida lisaks järve ökosüsteemile ka järve ümbritsevat maismaa keskkonda. Samuti selgus, et ITS2 markeri abil tuvastatud seente ökoloogilised rollid on kasutatavad potentsiaalsete indikaatoritena peremeesorganismide populatsioonide ja järvesiseste protsesside hindamiseks. Leidsime, et muutused eukarüootide koosluste dünaamikas on põhjustatud nii looduslike kui ka inimtekkeliste tegurite poolt. Fototroofide dünaamikas tuvastati kolm koosluste häiringu perioodi, millest kaks esimest, hilis-jääaja (~12 500-7700) ning Holotseeni temperatuuri maksimumi (~5400-7700) ajajärgu häiringud, olid tõenäoliselt põhjustatud vastavatest järskudest kliimamuutustest või võimalikest jääkatte kestuse ja humifitseerumise protsessidest järves. Kõige selgemini oli eristatav aga liigirikkuse tõus viimase ~2000 aasta jooksul Chlorophyta, planktoni parasiitsete seente ja mükoriissete seente grupis, mis ajaliselt langeb kokku inimmõju järkjärgulise tõusuga selles piirkonnas. Selline koosluste muutus on seletatav suurenenud toitainete liikuvusega järve inimtegevuse tagajärjel. Toitainete hulga tõus aga soosis omakorda fütoplanktoni mitmekesisuse tõusu sel perioodil. Lisaks leidsime tõendeid planktoni parasiitsete seente liigilise mitmekesisuse suurenemise kohta juba alates ~4000 aastast, mis on seotud kliima jahenemise ja tsüanobakterite domineerimise asendumisega eukarüootsete vetikate domineerimisega.Biological material carried into the lake or originating from the lake accumulates over time into lake sediments where the extracellular DNA can bind to clay minerals and humic acids and thus preserve over long periods of time. The oldest known DNA detected from lake sediments dates back to ~270 000 years. Sedimentary ancient DNA (sedaDNA) allows us to reconstruct past biodiversity changes and enables us to identify when and why these changes in diversity appeared. In addition, sedaDNA permits us to study the impact of environmental change on these communities over the long timescale. The studies of relationships between community dynamics and environmental drivers are necessary to understand biodiversity changes and to model possible future scenarios during ongoing climate warming conditions. SedaDNA is a relatively new tool in paleoenvironmental research, where the use of sedaDNA has increased rapidly in the last five years due to the development of DNA sequencing and data analysis methods. This thesis focuses on studying the effectiveness of sedaDNA reconstructing the changes in eukaryotes diversity, focusing on phototroph and fungal dynamics, and exploring the community responses to the environmental changes in the lake Lielais Svētiņu. Lielais Svētiņu can be considered a natural model lake in the North-East Europe region since it has a long sediment record, relatively late human impact in the region and availability of detailed dataset from previous pollen, micro-, and macrofossils studies. This data enables us to study natural and anthropogenic influences on the communities in lake ecosystems and wider changes in the area. As an innovative approach, the fungal ecophysiological groups were tested as new signatures of ecosystem changes in the lake and its surroundings. Firstly, it was found that sedaDNA can be successfully used to assess the biodiversity of eukaryotes also from deeper sediment layers. Also, sedaDNA enables the reconstruction of aquatic ecosystems and terrestrial environments of the lake catchment. In addition, the fungal ecophysiological groups recovered by the ITS2 marker region were found useful as signatures of past host populations and in-lake processes. Also, detected changes in community dynamics of eukaryotes were influenced by natural and anthropogenic factors. Three perturbation periods for phototroph dynamics were detected, of which two – Late-Glacial (~12 500-7700 kyr) and Holocene thermal maximum (~5400-7700 kyr) periods – were likely induced by abrupt climate change or by the effect of ice-cover and humification processes, respectively. The clearest richness change was observed in the last ~2000 kyr when richness rise occurred in Chlorophyta, plankton parasitic fungi and mycorrhizal fungi. These changes were related to the growing anthropogenic impact in the region. Such change in community dynamics can be explained by the higher loading of nutrients in the lake due to human activity. Higher amounts of nutrients, in turn, favored the richness increase in phytoplankton. In addition, the richness rise of plankton parasitic fungi started from ~4000 kyr, which could be explained by climate cooling and cyanobacteria-eukaryotic algae shift.https://www.ester.ee/record=b545275

7. klassi bioloogiaõpikute analüüs: jõukohasus ja õpilaste motiveerimine

http://tartu.ester.ee/record=b2655082~S6*es

Seenekoosluste tuvastamine jääajajärgsetest järve põhjasetetest 18S rDNA ja ITS2 ala järjestuste põhise meetodiga

Järve põhjasetetest seente mitmekesisuse ja ökoloogilise rolli hindamiseks kasutati ajaloolisele DNAle optimeeritud PCRi koos ITS2 ja 18S rDNA ala praimeritega. Seente mitmekesisuse ja liigrikkuse hindamiseks arvutati Chao1, Shannon-Weaver ja tasakaaluindeksid. Kokku tuvastati 343 seente perekonda, mis kuulusid 8 hõimkonda. Domineerivateks hõimkondadeks olid Basidiomycota ja Ascomycota. Universaalsete 18S rDNA praimerite abil tuvastati lisaks taimi (sh okaspuid), loomi ja protiste. Okaspuude esinemist järve ümbruses toetab Pinus ja Picea taimeperekonna parasiitsete seente tuvastamine settest ITS2 ala abil. Ökoloogiliselt rollilt esines tuvastatud seente seas rohkelt taimeparasiite, taimeseoselisi seeni ja saprotroofe. Esines ka putukate parasiite, koprofiilseid ja seenparasiitseid seeni. Paleoelustiku rekonstrueerimiseks ja organismidevaheliste seoste leidmiseks osutus tulemuslikuks kasutada ITS2 ja 18S rDNA ala koos

Sedimentary Ancient DNA (sedaDNA) Reveals Fungal Diversity and Environmental Drivers of Community Changes throughout the Holocene in the Present Boreal Lake Lielais Svētiņu (Eastern Latvia)

Fungi are ecologically important in several ecosystem processes, yet their community composition, ecophysiological roles, and responses to changing environmental factors in historical sediments are rarely studied. Here we explored ancient fungal DNA from lake Lielais Svētiņu sediment throughout the Holocene (10.5 kyr) using the ITS metabarcoding approach. Our data revealed diverse fungal taxa and smooth community changes during most of the Holocene with rapid changes occurring in the last few millennia. More precisely, plankton parasitic fungi became more diverse from the Late Holocene (2–4 kyr) which could be related to a shift towards a cooler climate. The Latest Holocene (~2 kyr) showed a distinct increase in the richness of plankton parasites, mycorrhizal, and plant pathogenic fungi which can be associated with an increased transfer rate of plant material into the lake and blooms of planktonic organisms influenced by increased, yet moderate, human impact. Thus, major community shifts in plankton parasites and mycorrhizal fungi could be utilized as potential paleo-variables that accompany host-substrate dynamics. Our work demonstrates that fungal aDNA with predicted ecophysiology and host specificity can be employed to reconstruct both aquatic and surrounding terrestrial ecosystems and to estimate the influence of environmental change

Environmental drivers and abrupt changes of phytoplankton community in temperate lake Lielais Svetinu, Eastern Latvia, over the last Post-Glacial period from 14.5 kyr

Understanding the long-term dynamics of ecological communities on the centuries-to-millennia scale is important for explaining the emergence of present-day biodiversity patterns and for predicting possible future scenarios. Fossil pigments and ancient DNA present in various sedimentary deposits can be analysed to study long-term changes in ecological communities. We analysed recent compilations of data, including fossil pigments, microfossils, and molecular inventories from the sedimentary archives, to understand the impact of gradual versus abrupt climate changes on the ecosystem status of a regional model lake over the last similar to 14.5 kyr. Such long and complete paleo-archives are scarce in North-Eastern Europe. The study site lies in a sensitive area, both climatically and in respect to vegetation. Namely the maritime-continentality line runs west to east in the central Baltic area to NE Europe and its south-north transect lies within the gradual decay of the nemoral forest into a boreal environment. Therefore, the selected location is an ideal sampling point to decipher long term environmental changes in the temperate climate zone. The main objective of the present study was to find out external factors influencing phototroph dynamics at temperate Lake Lielais Svetinu over the post-glacial period (similar to 14.5 kyr). We were able to model climate change together with vegetation change and the appearance of anthropogenic forcing, either as a gradual change or as abrupt events that influenced the phototrophs, which are keystone groups within the lacustrine ecosystem. Most interestingly, the gradual increase of species richness of phototrophs was linked to similar increase in fungal parasites of the same group - phototrophs. Abrupt climate change in the Late Glacial period caused abrupt events in the ecosystem but equally abrupt events were caused by gradual changes during the stable period of the Holocene Thermal Maximum (HTM). In addition, we highlight the increased frequency and degree of perturbation in pristine lakes due to low impact human activity over a larger region. Both observations demonstrate an impaired relationship between gradual external drivers and ecosystem response and apply to future scenarios of climate warming and increased human impact in north-eastern Europe. (C) 2021 The Authors. Published by Elsevier Ltd