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Aim This study investigates taxonomic and phylogenetic diversity in diatom genera to evaluate assembly rules for eukaryotic microbes across the Siberian tree line. We first analysed how phylogenetic distance relates to taxonomic richness and turnover. Second, we used relatedness indices to evaluate if environmental filtering or competition influences the assemblies in space and through time. Third, we used distance-based ordination to test which environmental variables shape diatom turnover. Location Yakutia and Taymyria, Russia: we sampled 78 surface sediments and a sediment core, extending to 7,000 years before present, to capture the forest-tundra transition in space and time respectively. Taxon Arctic freshwater diatoms. Methods We applied metabarcoding to retrieve diatom diversity from surface and core sedimentary DNA. The taxonomic assignment binned sequence types (lineages) into genera and created taxonomic (abundance of lineages within different genera) and phylogenetic datasets (phylogenetic distances of lineages within different genera). Results Contrary to our expectations, we find a unimodal relationship between phylogenetic distance and richness in diatom genera. We discern a positive relationship between phylogenetic distance and taxonomic turnover in spatially and temporally distributed diatom genera. Furthermore, we reveal positive relatedness indices in diatom genera across the spatial environmental gradient and predominantly in time slices at a single location, with very few exceptions assuming effects of competition. Distance-based ordination of taxonomic and phylogenetic turnover indicates that lake environment variables, like HCO3- and water depth, largely explain diatom turnover. Main conclusion Phylogenetic and abiotic assembly rules are important in understanding the regional assembly of diatom genera across lakes in the Siberian tree line ecotone. Using a space-time approach we are able to exclude the influence of geography and elucidate that lake environmental variables primarily shape the assemblies. We conclude that some diatom genera have greater capabilities to adapt to environmental changes, whereas others will be putatively replaced or lost due to the displacement of the Arctic tundra biome under recent global warming.
Aim This study investigates taxonomic and phylogenetic diversity in diatom genera to evaluate assembly rules for eukaryotic microbes across the Siberian tree line. We first analysed how phylogenetic distance relates to taxonomic richness and turnover. Second, we used relatedness indices to evaluate if environmental filtering or competition influences the assemblies in space and through time. Third, we used distance-based ordination to test which environmental variables shape diatom turnover. Location Yakutia and Taymyria, Russia: we sampled 78 surface sediments and a sediment core, extending to 7,000 years before present, to capture the forest-tundra transition in space and time respectively. Taxon Arctic freshwater diatoms. Methods We applied metabarcoding to retrieve diatom diversity from surface and core sedimentary DNA. The taxonomic assignment binned sequence types (lineages) into genera and created taxonomic (abundance of lineages within different genera) and phylogenetic datasets (phylogenetic distances of lineages within different genera). Results Contrary to our expectations, we find a unimodal relationship between phylogenetic distance and richness in diatom genera. We discern a positive relationship between phylogenetic distance and taxonomic turnover in spatially and temporally distributed diatom genera. Furthermore, we reveal positive relatedness indices in diatom genera across the spatial environmental gradient and predominantly in time slices at a single location, with very few exceptions assuming effects of competition. Distance-based ordination of taxonomic and phylogenetic turnover indicates that lake environment variables, like HCO3- and water depth, largely explain diatom turnover. Main conclusion Phylogenetic and abiotic assembly rules are important in understanding the regional assembly of diatom genera across lakes in the Siberian tree line ecotone. Using a space-time approach we are able to exclude the influence of geography and elucidate that lake environmental variables primarily shape the assemblies. We conclude that some diatom genera have greater capabilities to adapt to environmental changes, whereas others will be putatively replaced or lost due to the displacement of the Arctic tundra biome under recent global warming.
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 co-occurrence of plants and fungi across 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. We obtained 706 unique fungal operational taxonomic units (OTUs) and 243 taxa 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 Tricho-sporiella 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 abun-dance 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 feedbacks between fungus composition and plant diversity changes which will affect forest advance, species diversity, and ecosystem stability in arctic regions.
Organic matter deposited in ancient, ice-rich permafrost sediments is vulnerable to climate change and may contribute to the future release of greenhouse gases; it is thus important to get a better characterization of the plant organic matter within such sediments. From a Late Quaternary permafrost sediment core from the Buor Khaya Peninsula, we analysed plant-derived sedimentary ancient DNA (sedaDNA) to identify the taxonomic composition of plant organic matter, and undertook palynological analysis to assess the environmental conditions during deposition. Using sedaDNA, we identified 154 taxa and from pollen and non-pollen palynomorphs we identified 83 taxa. In the deposits dated between 54 and 51 kyr BP, sedaDNA records a diverse low-centred polygon plant community including recurring aquatic pond vegetation while from the pollen record we infer terrestrial open-land vegetation with relatively dry environmental conditions at a regional scale. A fluctuating dominance of either terrestrial or swamp and aquatic taxa in both proxies allowed the local hydrological development of the polygon to be traced. In deposits dated between 11.4 and 9.7 kyr BP (13.4-11.1 cal kyr BP), sedaDNA shows a taxonomic turnover to moist shrub tundra and a lower taxonomic richness compared to the older samples. Pollen also records a shrub tundra community, mostly seen as changes in relative proportions of the most dominant taxa, while a decrease in taxonomic richness was less pronounced compared to sedaDNA. Our results show the advantages of using sedaDNA in combination with palynological analyses when macrofossils are rarely preserved. The high resolution of the sedaDNA record provides a detailed picture of the taxonomic composition of plant-derived organic matter throughout the core, and palynological analyses prove valuable by allowing for inferences of regional environmental conditions.
A potential human footprint on Western Central African rainforests before the Common Era has become the focus of an ongoing controversy. Between 3,000 y ago and 2,000 y ago, regional pollen sequences indicate a replacement of mature rainforests by a forest-savannah mosaic including pioneer trees. Although some studies suggested an anthropogenic influence on this forest fragmentation, current interpretations based on pollen data attribute the "rainforest crisis" to climate change toward a drier, more seasonal climate. A rigorous test of this hypothesis, however, requires climate proxies independent of vegetation changes. Here we resolve this controversy through a continuous 10,500-y record of both vegetation and hydrological changes from Lake Barombi in Southwest Cameroon based on changes in carbon and hydrogen isotope compositions of plant waxes. delta C-13-inferred vegetation changes confirm a prominent and abrupt appearance of C-4 plants in the Lake Barombi catchment, at 2,600 calendar years before AD 1950 (cal y BP), followed by an equally sudden return to rainforest vegetation at 2,020 cal y BP. delta D values from the same plant wax compounds, however, show no simultaneous hydrological change. Based on the combination of these data with a comprehensive regional archaeological database we provide evidence that humans triggered the rainforest fragmentation 2,600 y ago. Our findings suggest that technological developments, including agricultural practices and iron metallurgy, possibly related to the large-scale Bantu expansion, significantly impacted the ecosystems before the Common Era.
Arctic treelines are facing a strong temperature increase as a result of recent global warming, causing possible changes in forest extent, which will alter vegetation-climate feedbacks. However, the mode and strength of the response is rather unclear, as potential changes are happening in areas that are very remote and difficult to access, and empirical data are still largely lacking. Here, we assessed the current population structure and genetic differentiation of Larix Mill. tree stands within the northernmost latitudinal treeline reaching ~ 72° N in the southern lowlands of the Taymyr Peninsula (~ 100° E). We sampled 743 individuals belonging to different height classes (seedlings, saplings, trees) at 11 locations along a gradient from ‘single tree’ tundra over ‘forest line’ to ‘dense forest’ stands and conducted investigations applying eight highly polymorphic nuclear microsatellites. Results suggest a high diversity within sub-populations (HE = 0.826–0.893), coupled, however, with heterozygote deficits in all sub-populations, but pronounced in ‘forest line’ stands. Overall, genetic differentiation of sub-populations is low (FST = 0.005), indicating a region-wide high gene flow, although ‘forest line’ stands harbour few rare and private alleles, likely indicating greater local reproduction. ‘Single tree’ stands, located beyond the northern forest line, are currently not involved in treeline expansion, but show signs of a long-term refuge, namely asexual reproduction and change of growth-form from erect to creeping growth, possibly having persisted for thousands of years. The lack of differentiation between the sub-populations points to a sufficiently high dispersal potential, and thus a rapid northward migration of the Siberian arctic treeline under recent global warming seems potentially unconstrained, but observations show it to be unexpectedly slow.
Changes in species’ distributions are classically projected based on their climate envelopes. For Siberian forests, which have a tremendous significance for vegetation-climate feedbacks, this implies future shifts of each of the forest-forming larch (Larix) species to the north-east. However, in addition to abiotic factors, reliable projections must assess the role of historical biogeography and biotic interactions. Here, we use sedimentary ancient DNA and individual-based modelling to investigate the distribution of larch species and mitochondrial haplotypes through space and time across the treeline ecotone on the southern Taymyr peninsula, which at the same time presents a boundary area of two larch species. We find spatial and temporal patterns, which suggest that forest density is the most influential driver determining the precise distribution of species and mitochondrial haplotypes. This suggests a strong influence of competition on the species’ range shifts. These findings imply possible climate change outcomes that are directly opposed to projections based purely on climate envelopes. Investigations of such fine-scale processes of biodiversity change through time are possible using paleoenvironmental DNA, which is available much more readily than visible fossils and can provide information at a level of resolution that is not reached in classical palaeoecology.
Ecosystem boundaries, such as the Arctic-Boreal treeline, are strongly coupled with climate and were spatially highly dynamic during past glacial-interglacial cycles. Only a few studies cover vegetation changes since the last interglacial, as most of the former landscapes are inundated and difficult to access. Using pollen analysis and sedimentary ancient DNA (sedaDNA) metabarcoding, we reveal vegetation changes on Bol’shoy Lyakhovsky Island since the last interglacial from permafrost sediments. Last interglacial samples depict high levels of floral diversity with the presence of trees (Larix, Picea, Populus) and shrubs (Alnus, Betula, Ribes, Cornus, Saliceae) on the currently treeless island. After the Last Glacial Maximum, Larix re-colonised the island but disappeared along with most shrub taxa. This was probably caused by Holocene sea-level rise, which led to increased oceanic conditions on the island. Additionally, we applied two newly developed larch-specific chloroplast markers to evaluate their potential for tracking past population dynamics from environmental samples. The novel markers were successfully re-sequenced and exhibited two variants of each marker in last interglacial samples. SedaDNA can track vegetation changes as well as genetic changes across geographic space through time and can improve our understanding of past processes that shape modern patterns.