Fungi and plant co-variation in Arctic Siberia inferred from sedimentary ancient DNA metabarcoding during the last 45.000 years

2021 ◽  
Author(s):  
Barbara von Hippel ◽  
Kathleen R. Stoof-Leichsenring ◽  
Luise Schulte ◽  
Peter Seeber ◽  
Laura S. Epp ◽  
...  
Keyword(s):  
Climate Change ◽  
Ancient Dna ◽  
Mycorrhizal Fungi ◽  
Vegetation Change ◽  
Sediment Cores ◽  
Siberian Larch ◽  
Biotic Interactions ◽  
Arctic Ecosystems ◽  
Arctic Regions ◽  
Arctic Siberia

<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>

scholarly journals Vulnerability of the North Water ecosystem to climate change

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sofia Ribeiro ◽  
Audrey Limoges ◽  
Guillaume Massé ◽  
Kasper L. Johansen ◽  
William Colgan ◽  
...  
Keyword(s):  
Climate Change ◽  
Sea Ice ◽  
Late Holocene ◽  
Sediment Cores ◽  
Arctic Ecosystems ◽  
Little Auk ◽  
The North ◽  
Water Ecosystem ◽  
North Water

AbstractHigh Arctic ecosystems and Indigenous livelihoods are tightly linked and exposed to climate change, yet assessing their sensitivity requires a long-term perspective. Here, we assess the vulnerability of the North Water polynya, a unique seaice ecosystem that sustains the world’s northernmost Inuit communities and several keystone Arctic species. We reconstruct mid-to-late Holocene changes in sea ice, marine primary production, and little auk colony dynamics through multi-proxy analysis of marine and lake sediment cores. Our results suggest a productive ecosystem by 4400–4200 cal yrs b2k coincident with the arrival of the first humans in Greenland. Climate forcing during the late Holocene, leading to periods of polynya instability and marine productivity decline, is strikingly coeval with the human abandonment of Greenland from c. 2200–1200 cal yrs b2k. Our long-term perspective highlights the future decline of the North Water ecosystem, due to climate warming and changing sea-ice conditions, as an important climate change risk.

Climate change and faunal turnover: testing the mechanics of the turnover-pulse hypothesis with South African fossil data

Paleobiology ◽  
10.1666/12043 ◽  
2013 ◽  
Vol 39 (4) ◽  
pp. 609-627 ◽  
Author(s):  
J. Tyler Faith ◽  
Anna K. Behrensmeyer
Keyword(s):  
Climate Change ◽  
Vegetation Change ◽  
Feeding Habits ◽  
Habitat Preferences ◽  
Biotic Interactions ◽  
Cape Floristic Region ◽  
Climate Oscillations ◽  
Faunal Turnover ◽  
Temporal Correlations ◽  
And Migration

The turnover-pulse hypothesis (TPH) makes explicit predictions concerning the potential responses of species to climate change, which is considered to be a major cause of faunal turnover (extinction, speciation, and migration). Previous studies have tested the TPH primarily by examining temporal correlations between turnover pulses and climatic events. It is rarely possible to dissect such correlations and observe turnover as it is occurring or to predict how different lineages will respond to climate change. Thus, whether climate change drives faunal turnover in the manner predicted by the TPH remains unclear. In this study, we test the underlying mechanics of the TPH using well-dated Quaternary ungulate records from southern Africa's Cape Floristic Region (CFR). Changes in sea level, vegetation, and topographic barriers across glacial-interglacial transitions in southern Africa caused shifts in habitat size and configuration, allowing us to generate specific predictions concerning the responses of ungulates characterized by different feeding habits and habitat preferences. Examples from the CFR show how climatically forced vegetation change and allopatry can drive turnover resulting from extinction and migration. Evidence for speciation is lacking, suggesting either that climate change does not cause speciation in these circumstances or that the evolutionary outcome of turnover is contingent on the nature and rate of climate change. Migrations and extinctions are observed in the CFR fossil record over geologically short time intervals, on the order of Milankovitch-scale climate oscillations. We propose that such climate oscillations could drive a steady and moderate level of faunal turnover over 104-year time scales, which would not be resolved in paleontological records spanning 105years and longer. A turnover pulse, which is a marked increase in turnover relative to previous and subsequent time periods, requires additional, temporally constrained climatic forcing or other processes that could accelerate evolutionary change, perhaps mediated through biotic interactions.

scholarly journals Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest

2020 ◽  
Author(s):  
Luise Schulte ◽  
Nadine Bernhardt ◽  
Kathleen Stoof-Leichsenring ◽  
Heike Zimmermann ◽  
Luidmila Pestryakova ◽  
...  
Keyword(s):  
Lake Sediment ◽  
Ancient Dna ◽  
Sediment Cores ◽  
Siberian Larch ◽  
Shotgun Sequencing ◽  
Hybridization Capture ◽  
Chloroplast Genomes ◽  
Long Range Pcr ◽  
Northern Russia ◽  
Genome Scale

<p>Siberian larch (<em>Larix</em> Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the earth. To be able to predict future responses of these forests to a changing climate, it is important to understand also past dynamics of larch populations. One well-preserved archive to study vegetation changes of the past is sedimentary ancient DNA (sedaDNA) extracted from lake sediment cores. We studied a lake sediment core covering 6700 calibrated years BP, from the Taymyr region in northern Siberia. To enrich the sedaDNA for DNA of our focal species <em>Larix</em>, we combine shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete <em>Larix</em> chloroplast genome. In comparison to shotgun sequencing, hybridization capture results in an increase of taxonomically classified reads by several orders of magnitude and the recovery of near-complete chloroplast genomes of <em>Larix</em>. Variation in the chloroplast reads confirm an invasion of <em>Larix gmelinii</em> into the range of <em>Larix sibirica</em> before 6700 years ago. In this time span, both species can be detected at the site, although larch populations have decreased from a forested area to a single-tree tundra at present. This study demonstrates for the first time that hybridization capture applied to ancient DNA from lake sediments can provide genome-scale information and is a viable tool for studying past changes of a specific taxon.</p>

Quantification of past arctic herbivore populations from ancient sedimentary DNA by hybridization capture enrichment, metabarcoding, and droplet digital PCR

2020 ◽  
Author(s):  
Peter Seeber ◽  
Ulrike Herzschuh ◽  
Beth Shapiro ◽  
Hendrik Poinar ◽  
Duane Froese ◽  
...  
Keyword(s):  
Climate Change ◽  
Ancient Dna ◽  
Pcr Amplification ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Arctic Ecosystems ◽  
Coprophilous Fungi ◽  
Hybridization Capture ◽  
Ecosystem Changes ◽  
Read Abundance

<p>The Arctic is currently experiencing dramatic ecosystem changes with immediate effects on biodiversity. Sedimentary ancient DNA is a unique and valuable source of information on ecosystem changes over a long temporal scale. Understanding these past changes may help predict the relative impacts of climate change, herbivory, and anthropogenic effects on present ecosystems. In the BiodivERsA project “Future ArcTic Ecosystems” (FATE), we aim to assess changes in past herbivore abundance over large spatial (circumarctic) and temporal (Last Glacial Maximum until today) scales using three (semi-)quantitative methods on sedimentary ancient DNA of plants, herbivores, and herbivore proxies (i.e. coprophilous fungi and parasites) – metabarcoding, hybridization capture enrichment, and droplet digital PCR (ddPCR).</p><p>Metabarcoding was applied to DNA of plants and also of coprophilous fungi as proxies of herbivore abundance. This approach is an established and important tool for assessing biodiversity from recent environmental DNA; however, quantification of specific taxa may be complicated due to inherent methodological biases (e.g. amplification efficiency due to primer bias), and our current understanding of the factors affecting potential quantification by metabarcoding is still limited. Moreover, ancient DNA is highly fragmented, which may prevent PCR amplification altogether. As an alternative, target enrichment by hybridization capture is a method that does not depend on target PCR amplification and is typically not affected by DNA fragmentation. Furthermore, hybridization capture can be used to target numerous genetic markers of a vast range of highly diverse taxa. We are using hybridization capture to enrich DNA of a range of herbivore species and numerous proxy organisms. Metabarcoding and hybridization capture can be applied to a vast taxonomic range and may be used quantitatively based on relative sequencing read abundance; however, the respective read abundance may be confounded by random and systematic errors and other biases. We are therefore using an additional quantification method – ddPCR – on several selected taxa, which is taxon-specific but facilitates highly accurate quantification of template DNA molecules in a given sample. The combined taxonomic and quantitative results of these three approaches are used to generate highly resolved datasets on past vegetation and herbivores, which allows us to reconstruct past vegetation changes over large spatial (circumarctic) and temporal (Last Glacial Maximum until today) scales.</p><p>Detailed inferences on herbivore abundance and reconstructing past ecological conditions may be important for ecosystem management and conservation in the face of accelerating changes in Arctic ecosystems due to global climate change.</p>

scholarly journals Ancient plant DNA, macro- and microfossil studies of the lake sediments from the High Arctic lake Tenndammen, Svalbard

2020 ◽  
Author(s):  
Anastasia Poliakova ◽  
Lena M. Håkansson ◽  
Anders Schomacker ◽  
Sandra Garces Pastor ◽  
Inger Greve Alsos
Keyword(s):  
Ancient Dna ◽  
Vegetation History ◽  
Sediment Cores ◽  
Local Environment ◽  
Plant Macrofossils ◽  
High Arctic ◽  
Arctic Ecosystems ◽  
Dna Metabarcoding ◽  
History Of ◽  
Shallow Water Body

<p>Ancient DNA metabarcoding applied together with the investigations of the plant macro-remains, pollen, spores and non-pollen palynomorphs (NPP), open new perspectives and give better taxonomical resolution, allowing to obtain more precise and specific data on the local environment conditions and their changes. So far, only three multiproxy studies that involve both molecular and palaeobotanical/palynological methods are available for the high Arctic archipelago Svalbard. We intend to contribute filling this gap. Therefore, a field trip to Svalbard was undertaken in September, 2019, and three sediment cores were retrieved from the Tenndammen lake (N 78°06.118; E 15°02.024, 7 m asl) which is a small and shallow water body (ca 2.5 m depth). The lake is located in the valley of Colesdalen, a well-known Svalbard’s biodiversity hot spots and a home for about seven to ten thermophilic plant species.</p><p>To investigate the Holocene to modern vegetation history of this place, the 85cm core Te2019 was chosen, it was described for lithology, X-rayed, µXRF-scanned, line-scan photographed with high resolution and sampled for sedaDNA, pollen, spores and NPP studies as well as for studies on plant macrofossils. Ten 14C AMS dates were taken in order to establish an age-depth model. The DNA record contains around 100 taxa, most findings of those are supported by pollen studies (Asteraceae, <em>Betula</em>, Brassicaceae, <em>Salix, Saxifraga, Vaccinium</em>/Ericaceae) and by spores (<em>Equisetum</em> and Bryophyta). In addition, various fungi spores were identified. Investigations of plant macro-remains well support findings of the aquatic (i.e. Warnstorfia fluitans) and terrestrial mosses (e.g. <em>Aulacomnium</em> conf. <em>turgidum, Bryum</em> spp., <em>Distichium capillaceum, Calliergon richardsonii, Scorpidium cossonii, Sphagnum</em> spp., <em>Rhizomnium</em> spp.). Besides, fragments of <em>Salix</em> and <em>Betula</em> leaves and fruit parts, various leaf, stem tissues and flower fragments of <em>Saxifraga</em> species were found within the samples from the same depths with the correspondence to DNA records. Three DNA zones (SvDNA 1 – SvDNA3) and  one subzone within the earliest zone (SvDNA-1a – SvDNA-1b) were established. Relations between DNA, pollen and macrofossil zones were studied. This study is performed within the “Future ArcTic Ecosystems” (FATE) research program: Initiative for investigation on drivers of diversity and future scenarios from ethnoecology, contemporary ecology and ancient DNA.</p>

scholarly journals Hybridization capture of larch (Larix Mill) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forests

2020 ◽  
Author(s):  
Luise Schulte ◽  
Nadine Bernhardt ◽  
Kathleen R. Stoof-Leichsenring ◽  
Heike H. Zimmermann ◽  
Luidmila A. Pestryakova ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Sediment Cores ◽  
Siberian Larch ◽  
Shotgun Sequencing ◽  
Hybridization Capture ◽  
Chloroplast Genomes ◽  
Dna Metabarcoding ◽  
Long Range Pcr ◽  
Northern Russia ◽  
Genome Scale

AbstractSiberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches, in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA – metabarcoding – focuses on small fragments which cannot resolve Larix to species level nor allow the detailed study of population dynamics. Here we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back up to 6700 years in age from the Taymyr region in northern Siberia. In comparison to shotgun sequencing, hybridization capture results in an increase of taxonomically classified reads by several orders of magnitude and the recovery of near-complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborate an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied to ancient DNA from lake sediments can provide genome-scale information and is a viable tool for studying past changes of a specific taxon.

scholarly journals Fungal biodiversity in Arctic paleoecosystems assessed by metabarcoding of lake sedimentary ancient DNA

2021 ◽  
Author(s):  
Peter A. Seeber ◽  
Barbara von Hippel ◽  
Havard Kauserud ◽  
Ulrike Loeber ◽  
Kathleen Stoof-Leichsenring ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Mycorrhizal Fungi ◽  
Sediment Cores ◽  
Gc Content ◽  
Fungal Growth ◽  
Fungal Communities ◽  
Amplicon Length ◽  
Amplicon Size ◽  
Biodiversity Changes ◽  
Sample Age

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 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.

Twelfth Century AD

2017 ◽  
Author(s):  
Lonnie G. Thompson ◽  
Alan L. Kolata
Keyword(s):  
Climate Change ◽  
Southern Oscillation ◽  
Sediment Cores ◽  
Critical Role ◽  
Lake Titicaca ◽  
Independent Evidence ◽  
Tropical Regions ◽  
Ice Cap ◽  
Paleoclimate Records ◽  
Past Climate Change

Climate is a fundamental and independent variable of human existence. Given that 50 percent of the Earth’s surface and much of its population exist between 30oN and 30oS, paleoenvironmental research in the Earth’s tropical regions is vital to our understanding of the world’s current and past climate change. Most of the solar energy that drives the climate system is absorbed in these regions. Paleoclimate records reveal that tropical processes, such as variations in the El Niño-Southern Oscillation (ENSO), have affected the climate over much of the planet. Climatic variations, particularly in precipitation and temperature, play a critical role in the adaptations of agrarian cultures located in zones of environmental sensitivity, such as those of the coastal deserts, highlands, and altiplano of the Andean region. Paleoclimate records from the Quelccaya ice cap (5670 masl) in highland Peru that extend back ~1800 years show good correlation between precipitation and the rise and fall of pre-Hispanic civilizations in western Peru and Bolivia. Sediment cores extracted from Lake Titicaca provide independent evidence of this correspondence with particular reference to the history of the pre-Hispanic Tiwanaku state centered in the Andean altiplano. Here we explore, in particular, the impacts of climate change on the development and ultimate dissolution of this altiplano state.

scholarly journals Edible mycorrhizal fungi of the world: What is their role in forest sustainability, food security, biocultural conservation and climate change?

2021 ◽  
Author(s):  
Jesús Pérez‐Moreno ◽  
Alexis Guerin‐Laguette ◽  
Andrea C. Rinaldi ◽  
Fuqiang Yu ◽  
Annemieke Verbeken ◽  
...  
Keyword(s):  
Climate Change ◽  
Food Security ◽  
Mycorrhizal Fungi ◽  
Forest Sustainability ◽  
The World ◽  
Biocultural Conservation
Sign in / Sign up

Export Citation Format

Share Document