Reconstructing paleo-diversity, dynamics and response of eukaryotes to environmental change over the Late-Glacial and Holocene period in lake Lielais Svētiņu using sedaDNA
Date
2021-07-21
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Abstract
Järves 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.
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.
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Keywords
paleoecology, paleolimnology, ice age, Holocene, lacustrine soils, ancient DNA, eukaryotes, biodiversiteet, aquatic ecosystems, Latvia