Climate change has a major impact on arctic and boreal terrestrial ecosystems as warming leads to northward treeline shifts, inducing consequences for heterotrophic organisms associated with the plant taxa. To unravel ecological dependencies, we address how long-term climatic changes have shaped the palaeo-ecosystems at selected sites in Siberia. We investigated sedimentary ancient DNA from five lakes spanning the last 47,000 years, using the ITS1 marker for fungi and the chloroplast P6 loop marker for vegetation metabarcoding. After bioinformatic processing with the OBItools pipeline, we obtained 706 unique fungal operational taxonomic units (OTUs) and 243 amplicon sequence variants (ASVs) for the plants. We show higher OTU numbers in dry forest tundra as well as boreal forests compared to wet southern tundra. The most abundant fungal taxa in our dataset are Pseudeurotiaceae, Mortierella, Sordariomyceta, Exophiala, Oidiodendron, Protoventuria, Candida vartiovaarae, Pseudeurotium, Gryganskiella fimbricystis, and Trichosporiella cerebriformis. The overall fungal composition is explained by the plant composition as revealed by redundancy analysis. The fungal functional groups show antagonistic relationships in their climate susceptibility. The advance of woody taxa in response to past warming led to an increase in the abundance of mycorrhizae, lichens, and parasites, while yeast and saprotroph distribution declined. We also show co-occurrences between Salicaceae, Larix, and Alnus and their associated pathogens and detect higher mycorrhizal fungus diversity with the presence of Pinaceae. Under future warming, we can expect feedback between fungus compositional and plant diversity changes which will affect forest advance and stability in arctic regions.
SummaryFungi are crucial organisms in most ecosystems as they exert ecological key functions and are closely associated with land plants. Fungal community changes may therefore help reveal biodiversity changes in past ecosystems. Lake sediments contain DNA of organisms in the catchment area, which allows reconstructing past biodiversity by using metabarcoding of ancient sedimentary DNA. We developed a novel PCR primer combination for fungal metabarcoding targeting a short amplicon to account for length bias of amplification due to ancient DNA degradation. In-silico PCRs showed higher diversity using this primer combination than using previously established fungal metabarcoding primers. We analyzed existing data from sediment cores from four artic and one boreal lake in Siberia. These cores had been stored for 2–22 years and examined degradation effects of ancient DNA and storage time-related bias in fungal communities. Amplicon size differed between fungal divisions, however, we observed no significant effect of sample age on amplicon length and GC content, suggesting robust results. We also found no indication of post-coring fungal growth during storage distorting ancient fungal communities. Terrestrial soil fungi, including mycorrhizal fungi and saprotrophs, were predominant in all lakes, which supports the use of lake sedimentary ancient DNA for reconstructing terrestrial communities.
Fungi are crucial organisms in most ecosystems as they exert ecological key functions and are closely associated with land plants. Fungal community changes may, therefore, help reveal biodiversity changes in past ecosystems. Lake sediments contain the DNA of organisms in the catchment area, which allows reconstructing past biodiversity by using metabarcoding of ancient sedimentary DNA. We re-evaluated various commonly used metabarcoding primers, and we developed a novel PCR primer combination for fungal metabarcoding to produce a short amplicon, thus accounting for amplification bias due to the degradation of ancient DNA. In silico PCRs showed higher diversity using this new primer combination, compared with previously established fungal metabarcoding primers. We analyzed data from sediment cores from four artic and one boreal lake in Siberia. These cores had been stored for 2-22 years after coring; we, therefore, examined the degradation effects of ancient DNA and storage time-related bias affecting fungal communities. Amplicon lengths showed considerable variation within and between the major divisions of fungi, for example, amplicons of Basidiomycota were significantly longer than those of Mucoromycota; however, we observed no significant effect of sample age on amplicon length and GC content, suggesting the robustness of our results. We also found no indication of post-coring fungal growth during storage regarding the proportions of common mold taxa, which would otherwise distort conclusions on past fungal communities.Terrestrial soil fungi, including mycorrhizal fungi and saprotrophs, were predominant in all lakes, whereas typical aquatic taxa were only represented to a negligible extent, which supports the use of lake sedimentary ancient DNA for reconstructing terrestrial communities.
Climate change is expected to cause major shifts in boreal forests which are in vast areas of Siberia dominated by two species of the deciduous needle tree larch (Larix). The species differ markedly in their ecosystem functions, thus shifts in their respective ranges are of global relevance. However, drivers of species distribution are not well understood, in part because paleoecological data at species level are lacking. This study tracks Larix species distribution in time and space using target enrichment on sedimentary ancient DNA extracts from eight lakes across Siberia. We discovered that Larix sibirica, presently dominating in western Siberia, likely migrated to its northern distribution area only in the Holocene at around 10,000 years before present (ka BP), and had a much wider eastern distribution around 33 ka BP. Samples dated to the Last Glacial Maximum (around 21 ka BP), consistently show genotypes of L. gmelinii. Our results suggest climate as a strong determinant of species distribution in Larix and provide temporal and spatial data for species projection in a changing climate.
<p>Climate change has a great impact on boreal ecosystems including Siberian larch forests. As a consequence of warming, larch grow is possible in areas where climate used to be too cold, leading to a shift of the tree line into more arctic regions. Most plants co-exist in symbiosis with heterotrophic organisms surrounding their root system. In arctic ecosystems, mycorrhizal fungi are a prerequisite for plant establishment and survival because they support nutrient uptake from nutrient-poor soils and maintain the water supply. Until now, however, knowledge about the co-variation of vegetation and fungi is poor. Certainly, the understanding of dynamic changes in biotic interactions is important to understand adaptation mechanisms of ecosystems to climate change.</p><p>We investigated sedimentary ancient DNA from Lake Levinson Lessing, Taymyr Peninsula (Arctic Siberia, tundra), Lake Lama, Lake Kyutyunda (both northern Siberia, tundra-taiga transition zone) and Lake Bolshoe Toko (southern Siberia, forest area) covering the last about 45.000 years using ITS primers for fungi along with the chloroplast P6 loop marker for vegetation metabarcoding. We found changes in the fungal communities that are in broad agreement with vegetation turnover. To our knowledge, this is the first broad ecological study on lake sediment cores to analyze fungal biodiversity in relation to vegetation change on millennial time scales.</p>
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