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Martens J, Mueller CW, Joshi P, Rosinger C, Maisch M, Kappler A, Bonkowski M, Schwamborn G, Schirrmeister L, Rethemeyer J. Stabilization of mineral-associated organic carbon in Pleistocene permafrost. Nat Commun 2023; 14:2120. [PMID: 37055417 PMCID: PMC10102184 DOI: 10.1038/s41467-023-37766-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 03/30/2023] [Indexed: 04/15/2023] Open
Abstract
Ice-rich Pleistocene-age permafrost is particularly vulnerable to rapid thaw, which may quickly expose a large pool of sedimentary organic matter (OM) to microbial degradation and lead to emissions of climate-sensitive greenhouse gases. Protective physico-chemical mechanisms may, however, restrict microbial accessibility and reduce OM decomposition; mechanisms that may be influenced by changing environmental conditions during sediment deposition. Here we study different OM fractions in Siberian permafrost deposited during colder and warmer periods of the past 55,000 years. Among known stabilization mechanisms, the occlusion of OM in aggregates is of minor importance, while 33-74% of the organic carbon is associated with small, <6.3 µm mineral particles. Preservation of carbon in mineral-associated OM is enhanced by reactive iron minerals particularly during cold and dry climate, reflected by low microbial CO2 production in incubation experiments. Warmer and wetter conditions reduce OM stabilization, shown by more decomposed mineral-associated OM and up to 30% higher CO2 production. This shows that considering the stability and bioavailability of Pleistocene-age permafrost carbon is important for predicting future climate-carbon feedback.
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Affiliation(s)
- Jannik Martens
- Institute of Geology and Mineralogy, University of Cologne, Cologne, Germany.
- Lamont-Doherty Earth Observatory, Columbia University, New York, NY, USA.
| | - Carsten W Mueller
- Chair for Soil Science, Technical University of Munich, Freising, Germany
- Department of Geosciences and Natural Resource Management, University of Copenhagen, Copenhagen, Denmark
| | - Prachi Joshi
- Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Christoph Rosinger
- Institute of Zoology, University of Cologne, Cologne, Germany
- Institute of Agronomy, University of Natural Resources and Life Sciences, Tulln an der Donau, Austria
- Institute of Soil Research, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Markus Maisch
- Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Andreas Kappler
- Department of Geosciences, University of Tübingen, Tübingen, Germany
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Tübingen, Germany
| | | | - Georg Schwamborn
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Permafrost Research Section, Potsdam, Germany
- Eurasia Institute of Earth Sciences, Istanbul Technical University Maslak, Istanbul, Turkey
| | - Lutz Schirrmeister
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Permafrost Research Section, Potsdam, Germany
| | - Janet Rethemeyer
- Institute of Geology and Mineralogy, University of Cologne, Cologne, Germany.
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2
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Organic matter composition and greenhouse gas production of thawing subsea permafrost in the Laptev Sea. Nat Commun 2022; 13:5057. [PMID: 36030269 PMCID: PMC9420143 DOI: 10.1038/s41467-022-32696-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/10/2022] [Indexed: 11/29/2022] Open
Abstract
Subsea permafrost represents a large carbon pool that might be or become a significant greenhouse gas source. Scarcity of observational data causes large uncertainties. We here use five 21-56 m long subsea permafrost cores from the Laptev Sea to constrain organic carbon (OC) storage and sources, degradation state and potential greenhouse gas production upon thaw. Grain sizes, optically-stimulated luminescence and biomarkers suggest deposition of aeolian silt and fluvial sand over 160 000 years, with dominant fluvial/alluvial deposition of forest- and tundra-derived organic matter. We estimate an annual thaw rate of 1.3 ± 0.6 kg OC m−2 in subsea permafrost in the area, nine-fold exceeding organic carbon thaw rates for terrestrial permafrost. During 20-month incubations, CH4 and CO2 production averaged 1.7 nmol and 2.4 µmol g−1 OC d−1, providing a baseline to assess the contribution of subsea permafrost to the high CH4 fluxes and strong ocean acidification observed in the region. Subsea permafrost underneath the Arctic Ocean is one of the least understood compartments of the global carbon cycle. Here, Wild et al. shed light on its carbon sources, degradation history and potential greenhouse gas release after thaw.
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3
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Schulte L, Meucci S, Stoof-Leichsenring KR, Heitkam T, Schmidt N, von Hippel B, Andreev AA, Diekmann B, Biskaborn BK, Wagner B, Melles M, Pestryakova LA, Alsos IG, Clarke C, Krutovsky KV, Herzschuh U. Larix species range dynamics in Siberia since the Last Glacial captured from sedimentary ancient DNA. Commun Biol 2022; 5:570. [PMID: 35681049 PMCID: PMC9184489 DOI: 10.1038/s42003-022-03455-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/06/2022] [Indexed: 11/19/2022] Open
Abstract
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. Using ancient sedimentary DNA from up to 50 kya, dramatic distributional shifts are documented in two dominant boreal larch species, likely guided by environmental changes suggesting climate as a strong determinant of species distribution.
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4
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Courtin J, Andreev AA, Raschke E, Bala S, Biskaborn BK, Liu S, Zimmermann H, Diekmann B, Stoof-Leichsenring KR, Pestryakova LA, Herzschuh U. Vegetation Changes in Southeastern Siberia During the Late Pleistocene and the Holocene. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.625096] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Relationships between climate, species composition, and species richness are of particular importance for understanding how boreal ecosystems will respond to ongoing climate change. This study aims to reconstruct changes in terrestrial vegetation composition and taxa richness during the glacial Late Pleistocene and the interglacial Holocene in the sparsely studied southeastern Yakutia (Siberia) by using pollen and sedimentary ancient DNA (sedaDNA) records. Pollen and sedaDNA metabarcoding data using the trnL g and h markers were obtained from a sediment core from Lake Bolshoe Toko. Both proxies were used to reconstruct the vegetation composition, while metabarcoding data were also used to investigate changes in plant taxa richness. The combination of pollen and sedaDNA approaches allows a robust estimation of regional and local past terrestrial vegetation composition around Bolshoe Toko during the last ∼35,000 years. Both proxies suggest that during the Late Pleistocene, southeastern Siberia was covered by open steppe-tundra dominated by graminoids and forbs with patches of shrubs, confirming that steppe-tundra extended far south in Siberia. Both proxies show disturbance at the transition between the Late Pleistocene and the Holocene suggesting a period with scarce vegetation, changes in the hydrochemical conditions in the lake, and in sedimentation rates. Both proxies document drastic changes in vegetation composition in the early Holocene with an increased number of trees and shrubs and the appearance of new tree taxa in the lake’s vicinity. The sedaDNA method suggests that the Late Pleistocene steppe-tundra vegetation supported a higher number of terrestrial plant taxa than the forested Holocene. This could be explained, for example, by the “keystone herbivore” hypothesis, which suggests that Late Pleistocene megaherbivores were able to maintain a high plant diversity. This is discussed in the light of the data with the broadly accepted species-area hypothesis as steppe-tundra covered such an extensive area during the Late Pleistocene.
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5
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Crump SE, Fréchette B, Power M, Cutler S, de Wet G, Raynolds MK, Raberg JH, Briner JP, Thomas EK, Sepúlveda J, Shapiro B, Bunce M, Miller GH. Ancient plant DNA reveals High Arctic greening during the Last Interglacial. Proc Natl Acad Sci U S A 2021; 118:e2019069118. [PMID: 33723011 PMCID: PMC8020792 DOI: 10.1073/pnas.2019069118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Summer warming is driving a greening trend across the Arctic, with the potential for large-scale amplification of climate change due to vegetation-related feedbacks [Pearson et al., Nat. Clim. Chang. (3), 673-677 (2013)]. Because observational records are sparse and temporally limited, past episodes of Arctic warming can help elucidate the magnitude of vegetation response to temperature change. The Last Interglacial ([LIG], 129,000 to 116,000 y ago) was the most recent episode of Arctic warming on par with predicted 21st century temperature change [Otto-Bliesner et al., Philos. Trans. A Math. Phys. Eng. Sci. (371), 20130097 (2013) and Post et al., SciAdv (5), eaaw9883 (2019)]. However, high-latitude terrestrial records from this period are rare, so LIG vegetation distributions are incompletely known. Pollen-based vegetation reconstructions can be biased by long-distance pollen transport, further obscuring the paleoenvironmental record. Here, we present a LIG vegetation record based on ancient DNA in lake sediment and compare it with fossil pollen. Comprehensive plant community reconstructions through the last and current interglacial (the Holocene) on Baffin Island, Arctic Canada, reveal coherent climate-driven community shifts across both interglacials. Peak LIG warmth featured a ∼400-km northward range shift of dwarf birch, a key woody shrub that is again expanding northward. Greening of the High Arctic-documented here by multiple proxies-likely represented a strong positive feedback on high-latitude LIG warming. Authenticated ancient DNA from this lake sediment also extends the useful preservation window for the technique and highlights the utility of combining traditional and molecular approaches for gleaning paleoenvironmental insights to better anticipate a warmer future.
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Affiliation(s)
- Sarah E Crump
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado, Boulder, CO 80303;
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Bianca Fréchette
- Geotop, Université du Québec à Montréal, Montréal, H2L 2C4, Canada
| | - Matthew Power
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, 6845 Bentley, Australia
| | - Sam Cutler
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
| | - Gregory de Wet
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado, Boulder, CO 80303
- Department of Geosciences, Smith College, Northampton, MA 01063
| | - Martha K Raynolds
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, AK 99775
| | - Jonathan H Raberg
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado, Boulder, CO 80303
| | - Jason P Briner
- Department of Geology, University at Buffalo, Buffalo, NY 14260
| | | | - Julio Sepúlveda
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado, Boulder, CO 80303
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064
- HHMI, University of California, Santa Cruz, CA 95064
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, 6845 Bentley, Australia
- New Zealand Environment Protection Authority, 6011 Wellington, New Zealand
| | - Gifford H Miller
- Institute of Arctic and Alpine Research and Department of Geological Sciences, University of Colorado, Boulder, CO 80303
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6
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Meucci S, Schulte L, Zimmermann HH, Stoof‐Leichsenring KR, Epp L, Bronken Eidesen P, Herzschuh U. Holocene chloroplast genetic variation of shrubs ( Alnus alnobetula, Betula nana, Salix sp.) at the siberian tundra-taiga ecotone inferred from modern chloroplast genome assembly and sedimentary ancient DNA analyses. Ecol Evol 2021; 11:2173-2193. [PMID: 33717447 PMCID: PMC7920767 DOI: 10.1002/ece3.7183] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022] Open
Abstract
Climate warming alters plant composition and population dynamics of arctic ecosystems. In particular, an increase in relative abundance and cover of deciduous shrub species (shrubification) has been recorded. We inferred genetic variation of common shrub species (Alnus alnobetula, Betula nana, Salix sp.) through time. Chloroplast genomes were assembled from modern plants (n = 15) from the Siberian forest-tundra ecotone. Sedimentary ancient DNA (sedaDNA; n = 4) was retrieved from a lake on the southern Taymyr Peninsula and analyzed by metagenomics shotgun sequencing and a hybridization capture approach. For A. alnobetula, analyses of modern DNA showed low intraspecies genetic variability and a clear geographical structure in haplotype distribution. In contrast, B. nana showed high intraspecies genetic diversity and weak geographical structure. Analyses of sedaDNA revealed a decreasing relative abundance of Alnus since 5,400 cal yr BP, whereas Betula and Salix increased. A comparison between genetic variations identified in modern DNA and sedaDNA showed that Alnus variants were maintained over the last 6,700 years in the Taymyr region. In accordance with modern individuals, the variants retrieved from Betula and Salix sedaDNA showed higher genetic diversity. The success of the hybridization capture in retrieving diverged sequences demonstrates the high potential for future studies of plant biodiversity as well as specific genetic variation on ancient DNA from lake sediments. Overall, our results suggest that shrubification has species-specific trajectories. The low genetic diversity in A. alnobetula suggests a local population recruitment and growth response of the already present communities, whereas the higher genetic variability and lack of geographical structure in B. nana may indicate a recruitment from different populations due to more efficient seed dispersal, increasing the genetic connectivity over long distances.
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Affiliation(s)
- Stefano Meucci
- Polar Terrestrial Environmental Systems Research GroupAlfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchPotsdamGermany
- Institute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Luise Schulte
- Polar Terrestrial Environmental Systems Research GroupAlfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchPotsdamGermany
- Institute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
| | - Heike H. Zimmermann
- Polar Terrestrial Environmental Systems Research GroupAlfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchPotsdamGermany
| | - Kathleen R. Stoof‐Leichsenring
- Polar Terrestrial Environmental Systems Research GroupAlfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchPotsdamGermany
| | - Laura Epp
- Department of BiologyUniversity of KonstanzKonstanzGermany
| | | | - Ulrike Herzschuh
- Polar Terrestrial Environmental Systems Research GroupAlfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchPotsdamGermany
- Institute of Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
- Institute of Environmental Sciences and GeographyUniversity of PotsdamPotsdamGermany
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7
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Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. QUATERNARY 2021. [DOI: 10.3390/quat4010006] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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8
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Stoof-Leichsenring KR, Liu S, Jia W, Li K, Pestryakova LA, Mischke S, Cao X, Liu X, Ni J, Neuhaus S, Herzschuh U. Plant diversity in sedimentary DNA obtained from high-latitude (Siberia) and high-elevation lakes (China). Biodivers Data J 2020; 8:e57089. [PMID: 33364896 PMCID: PMC7752886 DOI: 10.3897/bdj.8.e57089] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 09/26/2020] [Indexed: 11/15/2022] Open
Abstract
Background Plant diversity in the Arctic and at high altitudes strongly depends on and rebounds to climatic and environmental variability and is nowadays tremendously impacted by recent climate warming. Therefore, past changes in plant diversity in the high Arctic and high-altitude regions are used to infer climatic and environmental changes through time and allow future predictions. Sedimentary DNA (sedDNA) is an established proxy for the detection of local plant diversity in lake sediments, but still relationships between environmental conditions and preservation of the plant sedDNA proxy are far from being fully understood. Studying modern relationships between environmental conditions and plant sedDNA will improve our understanding under which conditions sedDNA is well-preserved helping to a.) evaluate suitable localities for sedDNA approaches, b.) provide analogues for preservation conditions and c.) conduct reconstruction of plant diversity and climate change. This study investigates modern plant diversity applying a plant-specific metabarcoding approach on sedimentary DNA of surface sediment samples from 262 lake localities covering a large geographical, climatic and ecological gradient. Latitude ranges between 25°N and 73°N and longitude between 81°E and 161°E, including lowland lakes and elevated lakes up to 5168 m a.s.l. Further, our sampling localities cover a climatic gradient ranging in mean annual temperature between -15°C and +18°C and in mean annual precipitation between 36 and 935 mm. The localities in Siberia span over a large vegetational gradient including tundra, open woodland and boreal forest. Lake localities in China include alpine meadow, shrub, forest and steppe and also cultivated areas. The assessment of plant diversity in the underlying dataset was conducted by a specific plant metabarcoding approach. New information We provide a large dataset of genetic plant diversity retrieved from surface sedimentary DNA from lakes in Siberia and China spanning over a large environmental gradient. Our dataset encompasses sedDNA sequence data of 259 surface lake sediments and three soil samples originating from Siberian and Chinese lakes. We used the established chloroplastidal P6 loop trnL marker for plant diversity assessment. The merged, filtered and assigned dataset includes 15,692,944 read counts resulting in 623 unique plant DNA sequence types which have a 100% match to either the EMBL or to the specific Arctic plant reference database. The underlying dataset includes a taxonomic list of identified plants and results from PCR replicates, as well as extraction blanks (BLANKs) and PCR negative controls (NTCs), which were run along with the investigated lake samples. This collection of plant metabarcoding data from modern lake sediments is still ongoing and additional data will be released in the future.
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Affiliation(s)
- Kathleen Rosmarie Stoof-Leichsenring
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Potsdam Germany
| | - Sisi Liu
- Institute of Environmental Science and Geography, University of Potsdam, Potsdam, Germany Institute of Environmental Science and Geography, University of Potsdam Potsdam Germany.,Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Potsdam Germany
| | - Weihan Jia
- College of Resource Environment and Tourism, Capital Normal University, Beijing, China College of Resource Environment and Tourism, Capital Normal University Beijing China.,Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Potsdam Germany
| | - Kai Li
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Potsdam Germany.,College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China College of Chemistry and Life Sciences, Zhejiang Normal University Jinhua China
| | - Luidmila A Pestryakova
- Department for Geography and Biology, North-Eastern Federal University of Yakutsk, Yakutsk, Russia Department for Geography and Biology, North-Eastern Federal University of Yakutsk Yakutsk Russia
| | - Steffen Mischke
- Institute of Earth Sciences, University of Iceland, Reykjavík, Iceland Institute of Earth Sciences, University of Iceland Reykjavík Iceland
| | - Xianyong Cao
- Alpine Paleoecology and Human Adaptation Group (ALPHA), Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research, Beijing, China Alpine Paleoecology and Human Adaptation Group (ALPHA), Key Laboratory of Alpine Ecology, Institute of Tibetan Plateau Research Beijing China
| | - Xingqi Liu
- College of Resource Environment and Tourism, Capital Normal University, Beijing, China College of Resource Environment and Tourism, Capital Normal University Beijing China
| | - Jian Ni
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China College of Chemistry and Life Sciences, Zhejiang Normal University Jinhua China
| | - Stefan Neuhaus
- Computing and Data Centre, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany Computing and Data Centre, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
| | - Ulrike Herzschuh
- Institute of Environmental Science and Geography, University of Potsdam, Potsdam, Germany Institute of Environmental Science and Geography, University of Potsdam Potsdam Germany.,Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany Polar Terrestrial Environmental Systems, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Potsdam Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany Institute of Biochemistry and Biology, University of Potsdam Potsdam Germany
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9
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Holm S, Walz J, Horn F, Yang S, Grigoriev MN, Wagner D, Knoblauch C, Liebner S. Methanogenic response to long-term permafrost thaw is determined by paleoenvironment. FEMS Microbiol Ecol 2020; 96:5729939. [PMID: 32031215 PMCID: PMC7046019 DOI: 10.1093/femsec/fiaa021] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 02/06/2020] [Indexed: 01/04/2023] Open
Abstract
Methane production in thawing permafrost can be substantial, yet often evolves after long lag phases or is even lacking. A central question is to which extent the production of methane after permafrost thaw is determined by the initial methanogenic community. We quantified the production of methane relative to carbon dioxide (CO2) and enumerated methanogenic (mcrA) gene copies in long-term (2-7 years) anoxic incubations at 4 °C using interglacial and glacial permafrost samples of Holocene and Pleistocene, including Eemian, origin. Changes in archaeal community composition were determined by sequencing of the archaeal 16S rRNA gene. Long-term thaw stimulated methanogenesis where methanogens initially dominated the archaeal community. Deposits of interstadial and interglacial (Eemian) origin, formed under higher temperatures and precipitation, displayed the greatest response to thaw. At the end of the incubations, a substantial shift in methanogenic community composition and a relative increase in hydrogenotrophic methanogens had occurred except for Eemian deposits in which a high abundance of potential acetoclastic methanogens were present. This study shows that only anaerobic CO2 production but not methane production correlates significantly with carbon and nitrogen content and that the methanogenic response to permafrost thaw is mainly constrained by the paleoenvironmental conditions during soil formation.
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Affiliation(s)
- Stine Holm
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Josefine Walz
- Universität Hamburg, Institute of Soil Science, 20146 Hamburg, Germany.,Universität Hamburg, Center for Earth System Research and Sustainability, 20146 Germany
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Sizhong Yang
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany
| | - Mikhail N Grigoriev
- Russian Academy of Sciences, Siberian Branch, Melnikov Permafrost Institute, 677007 Yakutsk, Russia
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany.,Potsdam University, Institute of Geosciences, 14476 Potsdam, Germany
| | - Christian Knoblauch
- Universität Hamburg, Institute of Soil Science, 20146 Hamburg, Germany.,Universität Hamburg, Center for Earth System Research and Sustainability, 20146 Germany
| | - Susanne Liebner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany.,Potsdam University, Institute of Biochemistry and Biology, 14476 Potsdam, Germany
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10
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Clarke CL, Edwards ME, Gielly L, Ehrich D, Hughes PDM, Morozova LM, Haflidason H, Mangerud J, Svendsen JI, Alsos IG. Persistence of arctic-alpine flora during 24,000 years of environmental change in the Polar Urals. Sci Rep 2019; 9:19613. [PMID: 31873100 PMCID: PMC6927971 DOI: 10.1038/s41598-019-55989-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 12/03/2019] [Indexed: 12/18/2022] Open
Abstract
Plants adapted to extreme conditions can be at high risk from climate change; arctic-alpine plants, in particular, could "run out of space" as they are out-competed by expansion of woody vegetation. Mountain regions could potentially provide safe sites for arctic-alpine plants in a warmer climate, but empirical evidence is fragmentary. Here we present a 24,000-year record of species persistence based on sedimentary ancient DNA (sedaDNA) from Lake Bolshoye Shchuchye (Polar Urals). We provide robust evidence of long-term persistence of arctic-alpine plants through large-magnitude climate changes but document a decline in their diversity during a past expansion of woody vegetation. Nevertheless, most of the plants that were present during the last glacial interval, including all of the arctic-alpines, are still found in the region today. This underlines the conservation significance of mountain landscapes via their provision of a range of habitats that confer resilience to climate change, particularly for arctic-alpine taxa.
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Affiliation(s)
- C L Clarke
- School of Geography and Environmental Science, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.
| | - M E Edwards
- School of Geography and Environmental Science, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - L Gielly
- Laboratoire d'Ecologie Alpine (LECA), Université Grenoble Alpes, C2 40700 38058, Grenoble, Cedex 9, France
| | - D Ehrich
- Department of Arctic and Marine Biology, UiT- The Arctic University of Norway, Tromsø, NO-9037, Norway
| | - P D M Hughes
- School of Geography and Environmental Science, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - L M Morozova
- Institute of Plant and Animal Ecology, Ural Branch of Russian Academy of Sciences, Ekaterinburg, Russia
| | - H Haflidason
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, Bergen, 5007, Norway
| | - J Mangerud
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, Bergen, 5007, Norway
| | - J I Svendsen
- Department of Earth Science and Bjerknes Centre for Climate Research, University of Bergen, Allégaten 41, Bergen, 5007, Norway
| | - I G Alsos
- Tromsø University Museum, UiT - The Arctic University of Norway, NO-9037, Tromsø, Norway
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11
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Zimmermann HH, Harms L, Epp LS, Mewes N, Bernhardt N, Kruse S, Stoof-Leichsenring KR, Pestryakova LA, Wieczorek M, Trense D, Herzschuh U. Chloroplast and mitochondrial genetic variation of larches at the Siberian tundra-taiga ecotone revealed by de novo assembly. PLoS One 2019; 14:e0216966. [PMID: 31291259 PMCID: PMC6619608 DOI: 10.1371/journal.pone.0216966] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/30/2019] [Indexed: 01/10/2023] Open
Abstract
Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix.
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MESH Headings
- Chromosome Mapping
- DNA, Ancient
- DNA, Chloroplast/genetics
- DNA, Mitochondrial/genetics
- DNA, Plant/genetics
- Genetic Variation
- Genetics, Population
- Genome, Chloroplast
- Genome, Mitochondrial
- Genome, Plant
- Haplotypes
- History, Ancient
- Larix/classification
- Larix/genetics
- Polymorphism, Single Nucleotide
- Siberia
- Taiga
- Tundra
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Affiliation(s)
- Heike H. Zimmermann
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- * E-mail: (HHZ); (UH)
| | - Lars Harms
- Scientific Computing, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Laura S. Epp
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Nick Mewes
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Nadine Bernhardt
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Stefan Kruse
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Kathleen R. Stoof-Leichsenring
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | | | - Mareike Wieczorek
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
| | - Daronja Trense
- Institute for Integrated Natural Sciences, Biology, Koblenz-Landau University, Koblenz, Germany
| | - Ulrike Herzschuh
- Polar Terrestrial Environmental Systems Research Group, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Institute of Environmental Sciences and Geography, University of Potsdam, Potsdam, Germany
- * E-mail: (HHZ); (UH)
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12
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Parducci L, Alsos IG, Unneberg P, Pedersen MW, Han L, Lammers Y, Salonen JS, Väliranta MM, Slotte T, Wohlfarth B. Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00189] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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13
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Carcaillet C, Blarquez O. Glacial refugia in the south-western Alps? THE NEW PHYTOLOGIST 2019; 222:663-667. [PMID: 30734310 DOI: 10.1111/nph.15673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/31/2018] [Indexed: 06/09/2023]
Affiliation(s)
- Christopher Carcaillet
- Laboratory for Ecology of Natural and Anthropised Hydrosystems (UMR 5023 CNRS ENTPE), Université Claude Bernard-Lyon, Villeurbanne, F-69622, France
- Paris Sciences & Lettres University (PSL), École Pratique des Hautes Études (EPHE), 4-14 rue Ferrus, F-75014, Paris, France
| | - Olivier Blarquez
- Département de Géographie, Université de Montréal, C.P. 6128 Succ. Centre Ville, Montréal, QC, H3C 3J7, Canada
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14
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Epp LS, Kruse S, Kath NJ, Stoof-Leichsenring KR, Tiedemann R, Pestryakova LA, Herzschuh U. Temporal and spatial patterns of mitochondrial haplotype and species distributions in Siberian larches inferred from ancient environmental DNA and modeling. Sci Rep 2018; 8:17436. [PMID: 30498238 PMCID: PMC6265258 DOI: 10.1038/s41598-018-35550-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 11/01/2018] [Indexed: 12/01/2022] Open
Abstract
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.
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Affiliation(s)
- Laura S Epp
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany.
| | - Stefan Kruse
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany
| | - Nadja J Kath
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, 14476, Potsdam, Germany
| | - Kathleen R Stoof-Leichsenring
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany
| | - Ralph Tiedemann
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, 14476, Potsdam, Germany
| | - Luidmila A Pestryakova
- Department for Geography and Biology, North-Eastern Federal University of Yakutsk, Belinskogo 58, 67700, Yakutsk, Russia
| | - Ulrike Herzschuh
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Periglacial Research Section, Telegrafenberg A43, 14473, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, 14476, Potsdam, Germany
- Institute of Earth and Environmental Science, University of Potsdam, Karl-Liebknecht-Str 24-25, 14476, Potsdam, Germany
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15
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Alsos IG, Lammers Y, Yoccoz NG, Jørgensen T, Sjögren P, Gielly L, Edwards ME. Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation. PLoS One 2018; 13:e0195403. [PMID: 29664954 PMCID: PMC5903670 DOI: 10.1371/journal.pone.0195403] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 03/21/2018] [Indexed: 11/18/2022] Open
Abstract
Metabarcoding of lake sediments have been shown to reveal current and past biodiversity, but little is known about the degree to which taxa growing in the vegetation are represented in environmental DNA (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA at 11 lakes in northern Norway. Out of 489 records of taxa growing within 2 m from the lake shore, 17–49% (mean 31%) of the identifiable taxa recorded were detected with eDNA. Of the 217 eDNA records of 47 plant taxa in the 11 lakes, 73% and 12% matched taxa recorded in vegetation surveys within 2 m and up to about 50 m away from the lakeshore, respectively, whereas 16% were not recorded in the vegetation surveys of the same lake. The latter include taxa likely overlooked in the vegetation surveys or growing outside the survey area. The percentages detected were 61, 47, 25, and 15 for dominant, common, scattered, and rare taxa, respectively. Similar numbers for aquatic plants were 88, 88, 33 and 62%, respectively. Detection rate and taxonomic resolution varied among plant families and functional groups with good detection of e.g. Ericaceae, Roseaceae, deciduous trees, ferns, club mosses and aquatics. The representation of terrestrial taxa in eDNA depends on both their distance from the sampling site and their abundance and is sufficient for recording vegetation types. For aquatic vegetation, eDNA may be comparable with, or even superior to, in-lake vegetation surveys and may therefore be used as an tool for biomonitoring. For reconstruction of terrestrial vegetation, technical improvements and more intensive sampling is needed to detect a higher proportion of rare taxa although DNA of some taxa may never reach the lake sediments due to taphonomical constrains. Nevertheless, eDNA performs similar to conventional methods of pollen and macrofossil analyses and may therefore be an important tool for reconstruction of past vegetation.
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Affiliation(s)
- Inger Greve Alsos
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
- * E-mail:
| | - Youri Lammers
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Nigel Giles Yoccoz
- Department of Arctic and Marine Biology, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Tina Jørgensen
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Per Sjögren
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
| | - Ludovic Gielly
- University Grenoble Alpes, LECA, Grenoble, France
- CNRS, LECA, Grenoble, France
| | - Mary E. Edwards
- Tromsø Museum, University of Tromsø –The Arctic University of Norway, Tromsø, Norway
- Geography and Environment, University of Southampton, Highfield, Southampton, United Kingdom
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