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Inferring Past Environmental Changes in High Arctic Lake Ecosystems Using Ancient DNA

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Inferring Past Environmental Changes in High Arctic Lake Ecosystems Using Ancient DNA Biology Department Research Group Protistology and Aquatic Ecology _____________________________________________________________________________________ Inferring past environmental changes in High Arctic lake ecosystems using ancient DNA Laura Decorte Studentnumber: 01402099 Supervisors: Prof. Dr. Elie Verleyen, Prof. Dr. Wim Vyverman, Dr. Bjorn Tytgat Scientific tutor: Lotte De Maeyer Master’s dissertation submitted to obtain the degree of Master of Science in Biology Academic year: 2019 - 2020 © Faculty of Sciences – research group Protistology and Aquatic Ecology All rights reserved. This thesis contains confidential information and confidential research results that are property to the UGent. The contents of this master thesis may under no circumstances be made public, nor complete or partial, without the explicit and preceding permission of the UGent representative, i.e. the supervisor. The thesis may under no circumstances be copied or duplicated in any form, unless permission granted in written form. Any violation of the confidential nature of this thesis may impose irreparable damage to the UGent. In case of a dispute that may arise within the context of this declaration, the Judicial Court of Gent only is competent to be notified. Content 1 Introduction ..................................................................................................................................... 2 2 Objectives ........................................................................................................................................ 4 3 Material and methods ..................................................................................................................... 5 3.1 Description of study site .......................................................................................................... 5 3.2 Sample collection .................................................................................................................... 7 3.2.1 Samples of present-day community ................................................................................ 7 3.2.2 Lake sediment cores ........................................................................................................ 7 3.3 Analysis of present-day lake and surface sediment DNA samples .......................................... 7 3.3.1 Bioinformatic analyses, taxonomical assignment and downstream analysis ................. 7 3.4 Core analysis ............................................................................................................................ 8 3.4.1 Radiocarbon dating ......................................................................................................... 8 3.4.2 Fossil pigment analysis .................................................................................................... 8 3.4.3 Ancient DNA analysis ....................................................................................................... 8 4 Results ........................................................................................................................................... 12 4.1 Present-day lake and surface sediment samples .................................................................. 12 4.1.1 Alpha diversity ............................................................................................................... 12 4.1.2 Taxonomic composition of the samples ........................................................................ 12 4.2 Lake sediment core ............................................................................................................... 14 4.2.1 Chronology .................................................................................................................... 14 4.2.2 Core description ............................................................................................................ 15 4.2.3 Fossil pigments .............................................................................................................. 15 4.2.4 Ancient DNA .................................................................................................................. 17 5 Discussion ...................................................................................................................................... 22 5.1 Representation of aquatic and catchment community in surface lake sediments ............... 22 5.2 Protocol for aDNA processing ............................................................................................... 23 5.3 Lake evolution and environmental reconstruction ............................................................... 23 5.3.1 Deglaciation and colonization after the Last Glacial Maximum .................................... 23 5.3.2 Late Glacial and early-mid Holocene ............................................................................. 24 5.4 Perspectives ........................................................................................................................... 25 6 Conclusion ..................................................................................................................................... 26 7 Summary........................................................................................................................................ 27 7.1 English summary ................................................................................................................... 27 7.2 Nederlandse samenvatting ................................................................................................... 29 8 Acknowledgments ......................................................................................................................... 32 9 Reference list ................................................................................................................................. 33 10 Appendix .................................................................................................................................... 41 1 1 Introduction The Arctic is the most sensitive region in terms of climate change, with warming being two to three times higher than the global annual average (IPCC 2018). Since the end of the Little Ice Age (LIA) in the late nineteenth century, most Arctic glaciers have been retreating (Dowdeswell et al. 1997). Glacier retreat exposes new terrestrial habitats that can be colonized (Pessi et al. 2019), which promotes the greening of the Arctic. This happens in a few successional steps where cryptogamic covers (plants that reproduce by spores) play an important role (Screen & Simmonds 2010, Kern et al. 2019). The first colonizers of deglaciated, exposed soils generally are biological soil crusts (BSCs), consisting of algae, cyanobacteria, fungi, lichens and mosses (Yoshitake et al. 2018). They act as ecosystem engineers as they contribute to soil stabilisation, water content of the soil and nutrient cycling (Pointing & Belnap 2012). This way, BSCs are very important for further colonization by higher plants. They have a direct positive influence on vegetation density, species richness and cover and as such contribute to the greening of the Arctic (Breen & Lévesque 2006). The dominant primary producers in High Arctic tundra biomes are dwarf shrubs, forbs, graminoids and cryptogamic covers (Kern et al. 2019). The tundra biome is impacted by climate warming in such a way that it is showing an increased shrub dominance (Myers-Smith et al. 2015). Pearson et al. (2013) also predict a widespread redistribution of Arctic vegetation. They claim that in general, low-lying vegetation with sparse plant cover will decrease, while larger shrubs and trees will increase their range. Climate warming also induces changes in Arctic freshwater ecosystems through lengthening of the summer growing season. More in particular, increased spring and autumn temperatures are resulting in a decrease in the duration of lake ice cover. Moreover in deep lakes, warming temperatures and less ice cover may induce longer periods of thermal stratification. These changes in ice phenology (timing of ice break-up and freeze-up) and stratification lead to shifts in the life strategy of diatoms, generally marked by increasing abundances of small-celled cyclotelloid taxa and decreasing abundances of heavier diatoms like Aulacoseira taxa (Rühland et al. 2015). Furthermore, the decreased duration of lake ice cover may lead to increased development of mosses in the littoral zone, which in turn favours epiphytic diatom taxa associated with mossy substrates (Rühland et al. 2015). Interestingly, lake sediments, that accumulate over time, contain plenty of information about the response of the biological communities in the lake and their surrounding catchment to environmental changes (Smol & Douglas 2007). As sediments accumulate continuously, often anoxic conditions are created, which offers excellent preservation conditions (Parducci et al. 2017). An Arctic wide evaluation of diatoms in lake sediments has revealed significant and widespread changes in diatom community structure and ecological reorganisations in many High Arctic lakes within the last ~150 years (Smol et al. 2005). In addition to diatoms, many studies on sediment cores in the Arctic up to now were focussed on pollen and macrofossils to assess the effect of climate changes on the vegetation in their catchments (e.g. Peros & Gajewski 2009, Zhang et al. 2018). Pollen data, however, give a relatively low taxonomic resolution
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