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Application of plant DNA metabarcoding of lake sediments for monitoring vegetation compositions on the Tibetan Plateau

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Science China Earth Sciences 2024年第11期67卷 3594-3609页

作者： Kai WU Kai LI Weihan JIA Kathleen RSTOOF-LEICHSENRING Ulrike HERZSCHUH Jian NI Mengna LIAO Fang TIAN College of Life Sciences Zhejiang Normal UniversityJinhua 321004China polar terrestrial environmental systems research group Alfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchPotsdam 14473Germany Institute of environmental Science and Geography University of PotsdamPotsdam 14476Germany Institute of Biochemistry and Biology University of PotsdamPotsdam 14476Germany College of Resource Environment and Tourism Capital Normal UniversityBeijing 100048China

Benefiting from the rapid development of environmental DNA(eDNA) technologies, sedimentary DNA(sedDNA)emerges as a promising tool for monitoring plant compositions in remote regions. The Tibetan Plateau(TP), renowned for its harsh environment and numerous ponds and lakes, presents a potentially demanding region for the application of sedDNA on vegetation investigations. Here, we used the g and h universal primers for the P6 loop region of the chloroplast trn L(UAA)intron to amplify plant DNA in surface sediments from 59 ponds and small lakes on the southwestern TP. The applicability and limitations of using plant DNA metabarcoding for modern vegetation monitoring and palaeo-vegetation reconstructions have been assessed by comparing sedDNA, pollen, and vegetation survey data. Our results showed that plant DNA metabarcoding recorded 186 terrestrial taxa, of which 30.1% can be identified at the species level. The plant sedDNA approach can effectively disclose the dominant plant taxa(including Asteraceae, Cyperaceae and Poaceae) and significant vegetation assemblages in the vicinity of the investigated sites. The number of taxa and taxonomic resolution of plant sedDNA exceeded that of pollen analysis(75 taxa detected, 5.3% can be identified at species level). Unlike pollen that retains a broad spectrum of regional plant signals(including Pinus and Artemisia), plant sedDNA mirrors very local plants, underscoring its utility in local vegetation monitoring and reconstructions. To conclude, plant DNA metabarcoding of(small) lake sediments warrant increased attention in the future for local vegetation monitoring and reconstructions on the TP.

关键词： Sedimentary DNA(sedDNA) Metabarcoding Pollen Vegetation composition Tibetan Plateau

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Complementarity of lacustrine pollen and sedimentary DNA in representing vegetation on the central-eastern Tibetan Plateau

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Frontiers of Earth Science 2023年第4期17卷 1037-1048页

作者： Fang TIAN Meijiao CHEN Weihan JIA Ulrike HERZSCHUH Xianyong CAO College of Resource Environment and Tourism Capital Normal UniversityBeijing 100048China Alfred Wegener Institute Helmholtz Centre for polar and Marine research Polar Terrestrial Environmental Systems Research GroupPotsdam 14473Germany University of Potsdam Institute of Environmental Science and GeographyPotsdam 14476Germany University of Potsdam Institute of Biochemistry and BiologyPotsdam 14476Germany group of Alpine Paleoecology and Human Adaptation(ALPHA) State Key Laboratory of Tibetan Plateau Earth SystemEnvironment and Resources(TPESER)Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijing 100101China

Plant environmental DNA extracted from lacustrine sediments(sedimentary DNA,sedDNA)has been increasingly used to investigate past vegetation changes and human impacts at a high taxonomic ***,the representation of vegetation communities surrounding the lake is still *** this study,we compared plant sedDNA metabarcoding and pollen assemblages from 27 lake surface-sediment samples collected from alpine meadow on the central-eastern Tibetan Plateau to investigate the representation of sedDNA *** general,the identified components of sedDNA are consistent with the counted pollen taxa and local plant *** to pollen identification,sedDNA data have higher taxonomic resolution,thus providing a potential approach for reconstructing past plant *** sedDNA signal is strongly influenced by local plants while rarely affected by exogenous *** of the overrepresentation of local plants and PCR bias,the abundance of sedDNA sequence types is very variable among sites,and should be treated with caution when investigating past vegetation cover and climate based on sedDNA *** finding suggests that sedDNA analysis can be a complementary approach for investigating the presence/absence of past plants and history of human land-use with higher taxonomic resolution.

关键词： Tibetan Plateau plant DNA metabarcoding pollen lake sediment plant diversity vegetation history

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Reefs in the Early Paleozoic Taebaek group,Korea:A Review

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Acta Geologica Sinica(English Edition) 2016年第1期90卷 352-367页

作者： LEE Jeong-Hyun HONG Jongsun WOO Jusun OH Jae-Ryong LEE Dong-Jin CHOH Suk-Joo Department of Earth and environmental Sciences Korea University Department of Earth and Planetary Sciences University of Tennessee Division of polar Earth-System Sciences Korea Polar Research Institute Department of Earth and environmental Sciences Andong National University

Various early Paleozoic （Cambrian Series 3-Middle Ordovician） reefs are found in the Taebaek group, eastern Korea, located in the eastern margin of the Sino-Korean Block. They occur in every carbonate-dominant lithostratigraphic unit of the group, but their morphology and composition differ markedly. The Daegi Formation （middle Cambrian： Cambrian Series 3） contains siliceous sponge-Epiphyton reefs formed in a shallow subtidal environment, which is one of the earliest metazoan-bearing microbial reefs after the archaeocyath extinction. The Hwajeol Formation （upper Cambrian： Furongian） encloses sporadic dendrolites consisting of Angulocellularia, which developed in a relatively deep subtidal environment, representing a rare deeper water example. The onset of the Ordovician radiation resulted in the formation of microbialite-Archaeoscyphia-calathiid patch reefs in shallow subtidal deposits of the Lower Ordovician Dumugol Formation. Subsequent late Early Ordovician relative sea-level fall established extensive peritidal environments, forming microbial mats and stromatolites of the Lower-Middle Ordovician Makgol Formation. Ensuing Ordovician radiation resulted in one of the earliest metazoan skeletal reefs of the Middle Ordovician Duwibong Formation, constructed by stromatoporoid Cystostroma and bryozoan Nicholsonella, and developed around shallow shoals. These reefs reflect ongoing evolution and sea-level change during the early Paleozoic, and exemplify a rare glimpse of peri-Gondwanan records of reef evolution, which warrant detailed investigations and comparison with their counterparts in other regions.

关键词： carbonate sedimentology metazoans stromatolites Porifera Cambrian-Ordovician Taebaeksan Basin Korea

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湖泊沉积植物古DNA的现代过程

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植物生态学报 2022年第7期46卷 735-752页

作者：吴铠李凯贾伟瀚廖梦娜倪健浙江师范大学化学与生命科学学院浙江金华321004 polar terrestrial environmental systems research group Alfred Wegener Institute Helmholtz Centre for Polar and Marine ResearchPotsdam 14473Germany Institute of environmental Science and Geography University of PotsdamPotsdam 14476Germany

对植被历史变化过程的研究是理解现代植被组成、分布及其对全球变化响应的基础。近年来,随着分子古生态学的发展,分析沉积介质中的陆生植物古DNA信号,以研究植被及植物多样性演变的历史过程正在成为研究热点,湖泊沉积植物古DNA已成为古... 详细信息

对植被历史变化过程的研究是理解现代植被组成、分布及其对全球变化响应的基础。近年来,随着分子古生态学的发展,分析沉积介质中的陆生植物古DNA信号,以研究植被及植物多样性演变的历史过程正在成为研究热点,湖泊沉积植物古DNA已成为古植被和古生态学研究的成熟代用指标。然而与第四纪孢粉分析相比较,湖泊沉积植物古DNA的现代过程依然不明确,成为其进一步发展和应用的限制因素。基于此,该文综述了湖泊沉积植物古DNA技术研究进展,尝试阐明湖泊沉积植物古DNA的现代过程,包括植物DNA的来源、沉积和保存过程及其影响因素,以及植物DNA与现代植被的关系等。已有研究表明,湖泊沉积植物古DNA主要来自湖泊周边或流域范围,其丰度和组成除受到源植物生物量的影响外,同样受到沉积物的搬运和沉积过程中DNA降解作用、土壤以及沉积物中颗粒的吸附过程和稀释作用等因素的影响。湖泊沉积物中植物DNA的保存则主要受到微生物活动、湖水的化学性质(电导率和pH值)、湖泊深度、沉积物组成等一系列生物与非生物因素的共同影响。湖泊沉积植物古DNA可以揭示其沉积时代的植物群落类型以及气候环境信息,但目前并不能够用来定量重建古植被变化过程。鉴于湖泊沉积植物古DNA现代过程的复杂性,对研究结果的解释要格外小心。与孢粉分析相比,湖泊沉积植物古DNA研究仍处于起步阶段,但随着分子生物技术的进步、实验设计的优化、物种条形码的扩充及参考数据库的完善等,以DNA宏条形码和宏基因组学为主要技术手段的植物古DNA技术,必将推动我国植物古生态研究的进一步发展。

关键词：湖泊沉积植物古DNA 埋藏学植被代表性古植被古生态学

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Cambrian Stem-group Cnidarians with a New Species from the Cambrian Series 3 of the Taebaeksan Basin, Korea

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Acta Geologica Sinica(English Edition) 2016年第3期90卷 827-837页

作者： Tae-Yoon S.PARK Ji-Hoon KIHM Jusun WOO Yong-Yi ZHEN Michael ENGELBRETSEN Jongsun HONG Suk-Joo CHOH Dong-Jin LEE Division of polar-Earth System Sciences Korea Polar Research Institute Geological Survey of New South Wales W.B.Clarke Geoscience Centre research Affiliate Biological Sciences Macquarie University Department of Earth and environmental Sciences Korea University Department of Earth and environmental Sciences Andong National University

Five species, Lipopora lissa Jell and Jell, 1976, Lipopora daseia Jell and Jell, 1976, Tretocylichne perplexa Engeibretsen, 1993 from Australia, Cambroctoconus orientalis Park, Woo, Lee, Lee, Lee, Han and Chough, 2011 from China, and Cambroctoconus kyrgyzstanicus Peel, 2014 from Kyrgyzstan, belonging to the Cambrian stem-group cnidarians have been documented in the fossil record. Cambroctoconus coreaensis sp. nov., interpreted here as a stem-group cnidarian, from the Seokgaejae section in the Daegi Formation, Taebaek group （Cambrian Series 3）, Taebaeksan Basin, central-eastern Korean Peninsula, has a slender cup-shaped skeleton. A cladistic analysis produced 21 most parsimonious trees, which invariably placed the six stem-group cnidarians below the crown-group, but their relationships within the stem-group are unresolved. Nine out of the 21 trees suggest a monophyletic relationship for the Cambrian stem-group cnidarians, whereas in six other trees a monophyly of Cambroctoconus and Tretocylichne appeared as the sister-group to the crown-group cnidarians with Lipopora at the most basal branch. This result may reflect the fact that crown-group cnidarians evolved in the Precambrian, and suggests that the diversity of stem-group cnidarians was a result of an independent radiation in the Cambrian.

关键词： Phylogeny Cnidaria Cambrian Drumian Taebaeksan Basin Korea

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Modelling impacts of acid deposition and groundwater level on habitat quality and plant species diversity

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Ecological Processes 2016年第1期5卷 273-291页

作者： J.Kros J.P.Mol-Dijkstra G.W.W.Wamelink G.J.Reinds Avan Hinsberg W.de Vries Wageningen environmental research Wageningen University and ResearchP.O.Box 476700 AA WageningenThe Netherlands Netherlands environmental Assessment Agency PO Box 3033720 BABilthovenWageningenThe Netherlands environmental systems Analysis group Wageningen University and ResearchP.O.Box 476700 AA WageningenThe Netherlands

Introduction:We quantified the effects of the site factors pH and nitrate(NO_(3))concentration in soil solution and groundwater level on the vegetation of terrestrial ecosystems for the Netherlands in response to changes in atmospheric nitrogen(N)and sulphur(S)deposition and groundwater level over the period *** assessment was made with the SMART2 model,a simple one-layer model including geochemical buffer processes,element cycling by litterfall,mineralisation and uptake,nitrogen transformation processes and element input through deposition,weathering and upward ***:To assess the effects of changes in abiotic site factors on the vegetation,we developed a simple plant diversity indicator for grassland,heathland and forest,based on the occurrence of target plant species and competing *** occurrence was calculated from the preferred ranges of each species for the NO_(3) concentration and pH in soil solution and mean spring groundwater *** in the plant diversity indicator were assessed from effects of changes in the occurrence of target and competing plant species in response to changes in mean spring groundwater level and in pH and NO_(3) concentration,as calculated with *** were made for combinations of five vegetation structure types(three forest types,semi-natural grassland and heathland)and seven soil types(three sandy soils,two clay soils,peat and loess soils)using a 250×250 m *** used data for atmospheric deposition and groundwater level in the past to assess trends between 1990 and 2010 and evaluated two future scenarios for the period 2010-2030:a Business as Usual and an Improved Environment ***:Comparison of model predictions on pH and NO_(3) with measured soil solution concentrations for forest showed a reasonable to good agreement for pH but rather poor for NO_(3).The largest impacts were found for the combination of the two Improved Environment ***:Reductions in N

关键词： Nutrient cycling Soil modelling Biodiversity Acidification Scenario analysis

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Holocene temperature variation recorded by branched glycerol dialkyl glycerol tetraethers in a loess-paleosol sequence from the north-eastern Tibetan Plateau

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Frontiers of Earth Science 2023年第4期17卷 1012-1025页

作者： Tianxiao WANG Duo WU Tao WANG Lin CHEN Shilong GUO Youmo LI Chenbin ZHANG Key Laboratory of Western China’s environmental systems(Ministry of Education) College of Earth and Environmental SciencesLanzhou UniversityLanzhou 730000China Alpine Paleoecology and Human Adaptation group(ALPHA) Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijing 100101China

Reconstructing Holocene temperature evolution is important for understanding present temperature variations and for predicting future climate change,in the context of global *** evolution of Holocene global temperature remains disputed,due to differences between proxy reconstructions and model simulations,a discrepancy known as the῾Holocene temperature conundrum᾽.More reliable and quantitative terrestrial temperature records are needed to resolve the spatial heterogeneity of existing *** this study,based on the analysis of branched glycerol dialkyl glycerol tetraethers(brGDGTs)from a loess-paleosol sequence from the Ganjia Basin in the north-eastern Tibetan Plateau(NETP),we quantitatively reconstructed the mean annual air temperature(MAAT)over the past 12 *** MAAT reconstruction shows that the temperature remained low during the early Holocene(12−8 ka),followed by a rapid warming at around 8 *** 8 to 4 ka,the MAAT record reached its highest level,followed by a cooling trend from the late Holocene(4−0 ka).The variability of the reconstructed MAAT is consistent with trends of annual temperature records from the Tibetan Plateau(TP)during the *** attribute the relatively low temperatures during the early Holocene to the existence of ice sheets at high-latitude regions in the Northern Hemisphere and the weaker annual mean insolation at 35°*** the mid to late Holocene,the long-term cooling trend in the annual temperature record was primarily driven by declining summer *** study provides key geological evidence for clarifying Holocene temperature change in the TP.

关键词： sHolocene Ganjia Basin loess temperature variation BrGDGTs

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Dust storms in northern China and their significance for the concept of the Anthropocene

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Science China Earth Sciences 2022年第5期65卷 921-933页

作者： Jianbao LIU Jie CHEN Shengqian CHEN Xinwei YAN Haoran DONG Fahu CHEN Key Laboratory of Western China’s environmental systems(Ministry of Education) College of Earth and Environmental ScienceLanzhou UniversityLanzhou 730000China group of Alpine Paleoecology and Human Adaptation(ALPHA) State Key Laboratory of Tibetan Plateau Earth SystemResources and Environment(TPESRE)Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijing 100101China

A key scientific issue in the study of the Anthropocene is the determination of the corresponding stratigraphic marker in geological *** arid and semi-arid regions of Asia are the second largest dust source on Earth,and their release,transport and deposition of dust affect global climate change,as well as marine and terrestrial biogeochemical *** the past~2000 years,human activity has outpaced natural climatic variability as the dominant control of dust storms in northern ***,exploring the potential of anthropogenic Asian dust as a marker of the Anthropocene and its impacts on lake ecosystems may contribute to an improved definition of the characteristics and timing of the *** this context,we measured spectrally-inferred chlorophyll a from the sediments of an undisturbed alpine lake in northern China,and compared the results with dust storm data from the same cores and with regional climatic *** dust is a widely distributed,globally significant signal of human activity,and it is also well preserved in various geological archives;hence,we propose anthropogenic dust can be considered as a potential marker of the *** dust signals in stratigraphic records during the past~2000 years differ substantially from those during the early and middle Holocene,which demonstrates that,at least since~2000 years ago,human activity has exceeded the natural forcing of dust transport in northern *** therefore propose that there are spatial and temporal differences in the onset of the Anthropocene,as defined by anthropogenic dust deposition,which is therefore *** spectrally-inferred chlorophyll a record is consistent with dust storm activity over the past~2000 years(except since the 1950s),suggesting that anthropogenic dust storms were the dominant control on lake primary *** to the 1950s the interactions of the East Asian summer monsoon(EASM),human activity,dust storms and lake ecos

关键词： Anthropocene Stratigraphic marker Dust storms Lake primary production Time-transgressive Great Acceleration

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Spatial and temporal variability of marine-origin matter along a transect from Zhongshan Station to Dome A,Eastern Antarctica

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Journal of environmental Sciences 2016年第8期28卷 190-202页

作者： Chuanjin Li Cunde Xiao Guitao Shi Minghu Ding Dahe Qin Jiawen Ren The State Key Laboratory of the Cryospheric Sciences The Cold and Arid Regions Environmental and Engineering Research InstituteChinese Academy of Sciences Lanzhou 730000 China Climate System Institute Chinese Academy of Meteorological Sciences Beijing 100081 China polar research Institute of China Shanghai 200136 China

The spatiotemporal distribution pattern of marine-origin matter on the Antarctica ice sheet was used to study variations in the source regions, transport mechanisms and postdepositional influences. We present data on sea salt ions, sulfur components and stable isotopes from surface and snow pit samples collected along the transect route from Zhongshan Station to Dome A during the austral summer in 2012–2013. A general decreasing trend in the accumulation, sea salt ions and sulfur components occurred with increasing distance from the coast and increasing elevation. However, different sources of the marine components, transport pathways and post-depositional influences were responsible for their different spatial distribution patterns. The marine ions in the coastal snow pit varied seasonally, with higher sea salt ion concentrations in the winter and lower concentrations in the summer; the opposite pattern was found for the sulfur compounds. The sea ice area surrounding Antarctica was the main source region for the deposited sea salt and the open sea water for the sulfur compounds. No significant trends in the marine-origin components were detected during the past 3 decades. Several periods of elevated deposition of sea salt ions were associated with lower temperatures（based on δD and δ18O） or intensified wind fields. In comparison to the sea salt ions, the sulfur concentrations exhibited the opposite distribution patterns and were associated with changes in the surrounding sea ice extent.

关键词： Marine-origin matter Transect Dome A Eastern Antarctica

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Distribution of isotopes and chemicals in precipitation in Shule River Basin,northwestern China:an implication for water cycle and groundwater recharge

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Journal of Arid Land 2016年第6期8卷 973-985页

作者： ZHAO Wei MA Jinzhu GU Chunjie QI Shi ZHU Gaofeng HE Jiahua Key Laboratory of Western China’s environmental systems (Ministry of Education) College of Earth Environmental SciencesLanzhou University

The distribution of stable isotopes and ions in precipitation in the Shule River Basin, northwestern China, were investigated to understand the regional water cycle and precipitation input to groundwater recharge. The study found that the mean annual concentrations of Ca2＋, Na＋, SO42-, CI-, Mg2＋, NO3-, and K＋ in the basin were lower than those in other arid areas of northwestern China. The average concentrations of ions in the lower reaches of the Shule River were higher than those in the upper reaches. The results showed that the main ionic concentrations decreased with the increase of precipitation amount, indicating that heavy precipitation cannot only wash crustal aerosols out of the atmosphere, but also create a dilution effect. CI- and Na＋ in precipitation had a strong and positive correlation, suggesting a common origin for the two ions. However, the excess of Na＋, combined with non-marine SO42- and NO3-, indicated that some ions were contributed by terrestrial origins. In the extremely arid regions of northwestern China, the evaporation process obviously changes the original relationship between δ2H and δ18O in precipitation, and leads to dexcess values 〈8‰. δ18O and temperature were significantly correlated, suggested that temperature strongly affected the characteristics of isotopes in the study area. The δ18O value indicates a dominant effect of westerly air masses and southwest monsoon in warm months, and the integrated influence of westerly and Siberian-Mongolian polar air masses in cold months. The d-excess values were generally lower in warm months than those in cold months, indicating that post-condensation processes played a significant role in the water cycle. The results provide reliable precipitation input information that can be used in future groundwater recharge calculations in the study area.

关键词： precipitation stable isotopes ions westerly air masses Shule River Basin

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