现代分子生物技术在湖泊沉积物古DNA研究中的应用
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摘要
分子生物学技术的发展,为从分子生物学角度探讨湖泊生态系统演化提供了一个新窗口。依据湖泊沉积物中古DNA研究,从古微生物、动植物群落结构组成及数量变化等方面开展研究,可进一步反演湖泊及周边的气候环境变化,探讨生物与气候、人类活动之间的关系。本文首先介绍了湖泊沉积物中古DNA来源、保存特点以及提取方法,其次比较分析了现代分子生物技术在湖泊沉积物古DNA中的应用特点,并阐述了湖泊沉积物古DNA在重建古气候、古生态以及人类活动对古环境影响方面的应用,最后对目前湖泊沉积物古DNA研究方法存在的一些问题进行了总结。
In recent years,the development of new techniques in molecular biology offers a new way for understanding the evolution of lake ecosystem. Ancient DNA could well record the migration and evolution of animals,plants,algae and even microbes,and thus has become an effective tool to reconstruct paleoclimate and paleoenvironment. Studies on the ancient DNA preserved in lake sediments have provided abundant information and high-resolution data that are needed for reconstruction of ancient microbial,plant,or animal community,as well as the ancient environmental conditions. Here,we firstly introduced the preservation characteristics of the ancient DNA and DNA extraction methods from lake sediments,and then reviewed the latest molecular biology techniques for studying ancient DNA preserved in lake sediments. We also discussed the application of ancient DNA in lake sediments including reconstruction of paleoclimate,paleoecology and the impacts of human activities on paleoenvironment. Finally,some problems and possible trends on the research of ancient DNA in lake sediments were summarized.
In recent years,the development of new techniques in molecular biology offers a new way for understanding the evolution of lake ecosystem. Ancient DNA could well record the migration and evolution of animals,plants,algae and even microbes,and thus has become an effective tool to reconstruct paleoclimate and paleoenvironment. Studies on the ancient DNA preserved in lake sediments have provided abundant information and high-resolution data that are needed for reconstruction of ancient microbial,plant,or animal community,as well as the ancient environmental conditions. Here,we firstly introduced the preservation characteristics of the ancient DNA and DNA extraction methods from lake sediments,and then reviewed the latest molecular biology techniques for studying ancient DNA preserved in lake sediments. We also discussed the application of ancient DNA in lake sediments including reconstruction of paleoclimate,paleoecology and the impacts of human activities on paleoenvironment. Finally,some problems and possible trends on the research of ancient DNA in lake sediments were summarized.
引文
单国彬,金文标,林佶侃,等.2006.变性梯度凝胶电泳在环境微生物生态学中的应用.生态学杂志,25(10):1257-1264.
刘学,张志强,郑军卫,等.2014.关于人类世问题研究的讨论.地球科学进展,29(5):640-648.
侯卫国,董海良,蒋宏忱,等.2016.沉积物中古DNA在古生态、古环境和古气候研究中的应用.地学前缘,24(2):286-291.
周晓光,任鲁风,李运涛,等.2010.下一代测序技术:技术回顾与展望.中国科学:生命科学,40(1):23-37.
盛桂莲,赖旭龙,袁俊霞,等.2016.古DNA研究:35年回顾与展望.中国科学:地球科学,46(12):1564-1578.
申慧彦,李世杰.2008.湖泊沉积物中DNA提取与PCR扩增.地球科学进展,23(4):433-438.
魏子艳,金德才,邓晔.2015.环境微生物宏基因组学研究中的生物信息学方法.微生物学通报,42(5):890-901.
王玉倩,薛秀花.2016.实时荧光定量PCR技术研究进展及其应用.生物学通报,51(2):1-6.
冯兆民,舒跃龙.2017.数字PCR技术及其应用进展.病毒学报,33(1):103-107.
杨渐,蒋宏忱,吴耿,等.2016.青海湖1.8万年以来甲藻Dinoflagellate群落变化及其古气候环境的指示意义.盐湖研究,24(2):84-91.
Ahmed E,Han L,Pedersen MW,et al.2016.Ancient DNA in lake sediments:Shotgun metagenomic analyses.Conference:Sci Life Lab mini-symposium:Ancient Environmental DNA.
Alsos IG,Sjogren P,Edwards ME,et al.2015.Sedimentary ancient DNA from Lake Skartjrna,Svalbard:Assessing the resilience of arctic flora to Holocene climate change.Holocene,26:189-192.
An Z,Colman SM,Zhou W,et al.2012.Interplay between the Westerlies and Asian monsoon recorded in Lake Qinghai sediments since 32 ka.Scientific Reports,2:619.
Anderson-Carpenter LL,McLachlan JS,Jackson ST,et al.2011.Ancient DNA from lake sediments:Bridging the gap between paleoecology and genetics.BMC Evolutionary Biology,11:88-95.
Andrew B,John AE,Simon NJ,et al.2005.Isolation,amplification,and identification of ancient copepod DNA from lake sediments.Limnology and Oceanography:Methods,3:533-542.
Belle S,Parent C,Frossard V,et al.2014.Temporal changes in the contribution of methane-oxidizing bacteria to the biomass of chironomid larvae determined using stable carbon isotopes and ancient DNA.Journal of Paleolimnology,52:215-228.
Birks JB,Birks HH.2016.How have studies of ancient DNAfrom sediments contributed to the reconstruction of Quaternary floras?New Phytologist,209:499-506.
Bissett A,Gibson JAE,Jarman SN,et al.2005.Isolation,amplification,and identification of ancient copepod DNAfrom lake sediments.Limnology&Oceanography Methods,3:533-542.
Boessenkool S,Mcglynn G,Epp LS,et al.2014.Use of ancient sedimentary DNA as a novel conservation tool for highaltitude tropical biodiversity.Conservation Biology,28:446-455.
Capo E,Debroas D,Arnaud F,et al.2015.Is planktonic diversity well recorded in sedimentary DNA?Toward the reconstruction of past protistan diversity.Microbial Ecology,70:865-875.
Coolen MJL,Muyzer G,Rijpstra WIC,et al.2004b.Combined DNA and lipid analyses of sediments reveal changes in Holocene haptophyte and diatom populations in an Antarctic lake.Earth and Planetary Science Letters,223:225-239.
Coolen MJL,Muyzer G,Schouten S,et al.2005.Sulfur and methane cycling during the Holocene in Ace Lake Antarctica revealed by lipid and DNA stratigraphy.Nato Science,64:41-65.
Coolen MJL,Overmann J.1998.Analysis of subfossil molecular remains of purple sulfur bacteria in a lake sediment.Applied&Environmental Microbiology,64:4513-4521.
Coolen MJL.2011.7000 years of Emiliania huxleyi viruses in the black sea.Science,333:451-452.
Crutzen PJ,Stoermer EF.2000.The“Anthropocene”.IGBPNews Letter,41:17-18.
D'Andrea WJ,Lage M,Martiny JBH,et al.2015.Alkenone producers inferred fromwell-preserved 18S r DNA in Greenland lake sediments.Journal of Geophysical Research:Biogeosciences,111:397-399.
Domaizon I,Savichtcheva O,Debroas D,et al.2013.DNAfrom lake sediments reveals the long-term dynamics and diversity of Synechococcus assemblages.Biogeosciences,10:3817-3838.
Epp LS,Gussarova G,Boessenkool S,et al.2015.Lake sediment multi-taxon DNA from North Greenland records early post-glacial appearance of vascular plants and accurately tracks environmental changes.Quaternary Science Reviews,117:152-163.
Epp LS,Stoof-Leichsenring KR,Trauth MH,et al.2011.Molecular profiling of diatom assemblages in tropical lake sediments using taxon-specific PCR and Denaturing HighPerformance Liquid Chromatography(PCR-DHPLC).Molecular Ecology Resources,11:842-853.
Fischer SG,Lerman LS.1979.Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis.Cell,16:191-200.
Fu Q,Li H,Moorjani P,et al.2014.Genomesequence of a 45,000-year-old modern humanfrom western Siberia.Nature,514:445-449.
Giguet-Covex C,Pansu J,Arnaud F,et al.2014.Long livestock farming history and human landscape shaping revealed by lake sediment DNA.Nature Communications,23:3211.
Ginolhac A,Vilstrup J,Stenderup J,et al.2012.Improving the performance of true single molecule sequencing for ancient DNA.BMC Genomics,13:177.
Gregory-Eaves S,Pal I,Pick FR.2015.Temporal trends in cyanobacteria revealed through DNA and pigment analyses of temperate lake sediment cores.Journal of Paleolimnology,54:1-15.
Handelsman J,Rondon MR,Brady SF,et al.1998.Molecular biological access to the chemistry of unknown soil microbes:Anew frontier for natural products.Chemistry&Biology,5:245-249.
Heinecke L,Epp LS,MischkeS,et al.2016.Geochemical analyses of macrophytes(Potamogeton sp.)and ancient DNAfrom Lake Karakul,Tajikistan.Geophysical Research Abstracts,18:EGU2016-13233.
Higuchi R,Bowman B,Freiberger M,et al.1984.DNA sequences from the quagga,an extinct member of the horse family.Nature,312:282-284.
Hofreiter M,David S,Hendrik N,et al.2001.Ancient DNA.Nature Reviews Genetics,2:353-362.
Hoss M,Jaruga P,Zastawny TH,et al.1996.DNA damage and DNA sequence retrieval from ancient tissues.Nucleic Acids Research,24:1304-1307.
Hou WG,Dong HL,Li GY,et al.2014.Identification of photosynthetic plankton communities using sedimentary ancient DNA and their response to late-Holocene climate change on the Tibetan Plateau.Scientific Reports,4:6648.
Jiang H,Dong H,Yu B,et al.2007.Microbial response to salinity change in Lake Chaka,a hypersaline lake on Tibetan plateau.Environmental Microbiology,9:2603-2621.
Klouch KZ,Schmidt S,Andrieux-Loyer F,et al.2016.Historical records from dated sediment cores reveal the multidecadal dynamic of the toxic dinoflagellate Alexandrium minutum in the Bay of Brest(France).FEMS Microbiology Ecology,92:101-118.
Knight R,Jansson J,Field D,et al.2012.Unlocking the potential of metagenomics through replicated experimental design.Nature Biotechnology,30:513-520.
Lendvay B,Miklós B,Ilona P,et al.2018.Plant macrofossils from lake sediment as the material to assess ancient genetic diversity:Did deforestation influence Norway spruce(Picea abies)in the South Carpathians.Quaternary International,30:106-116.
Li GY,Dong HL,Hou WG,et al.2016.Temporal succession of ancient phytoplankton community in Qinghai Lake and implication for paleo-environmental Change.Scientific Reports,6:19769.
Limburg PA,Weider LJ.2002.‘Ancient’DNA in the resting egg bank of a microcrustacean can serve as a palaeolimnological database.Proceedings of the Royal Society B:Biological Sciences,269:281-287.
Madeja J.2015.A new tool to trace past human presence from lake sediments:The human-specific molecular marker Bacteroides strain HF 183.Journal of Quaternary Science,30:349-354.
Martínez EG,Antoniades D,Bonilla S,et al.2014.Application of ancient DNA to the reconstruction of past microbial assemblages and for the detection of toxic cyanobacteria in subtropical freshwater ecosystems.Molecular Ecology,23:5791-5802.
Matisoo-Smith E,Roberts K,Welikala N,et al.2008.Recovery of DNA and pollen from New Zealand lake sediments.Quaternary International,184:139-149.
Mitchell D,Willerslev E,Hansen A.2005.Damage and repair of ancient DNA.Mutation Research,571:265-276.
Monchamp ME,Spaak P,Domaizon I,et al.2018.Homogenization of lake cyanobacterial communities over a century of climate change and eutrophication.Nature Ecology Evolution,2:317-322.
Niemeyer B,Epp LS,Stoofleichsenring KR,et al.2017.Acomparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline.Molecular Ecology Resources,17:46-57.
Orlando L,Ginolhac A,Zhang G,et al.2013.Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.Nature,499:74-78.
Paabo S,Poinar H,David S,et al.2004.Genetic analyses from ancient DNA.Annual Reviews of Genetics,38:645-679.
Pal S,Gregory-Eaves I,Pick FR.2015.Temporal trends in cyanobacteria revealed through DNA and pigment analyses of temperate lake sediment cores.Journal of Paleolimnology,54:87-101.
Pansu J,Giguet-Covex C,Ficetola GF,et al.2015.Reconstructing long-term human impacts on plant communities:An ecological approach based on lake sediment DNA.Molecular Ecology,24:1485-1498.
Parducci L,Bennett KD,Ficetola GF,et al.2017.Ancient plant DNA in lake sediments.New Phytologist,214:924-942.
Parducci L,Suyama Y.2005.Single-Pollen genotyping of Holocene lake sediments//Isagi Y,Suyama Y,eds.SinglePollen Genotyping.Springer Japan,Ecological Research Monographs 1,DOI:10.1007/978-4-431-53901-8_8.:101-109.
Pedersen MW,Ginolhac A,Orlando L,et al.2013.A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa.Quaternary Science Reviews,75:151-158.
Poulain AJ,Arisbrosou S,Blais JM,et al.2015.Microbial DNA records historical delivery of anthropogenic mercury.ISME Journal,9:2541-2550.
Randlett ME,Coolen MJL,Stockhecke M,et al.2014.Alkenone distribution in Lake Van sediment over the last 270ka:Influence of temperature and haptophyte species composition.Quaternary Science Reviews,104:53-62.
Ravasi DF,Peduzzi S,Guidi V,et al.2012.Development of a real-time PCR method for the detection of fossil 16S r DNAfragments of phototrophic sulfur bacteria in the sediments of Lake Cadagno.Geobiology,10:196-204.
Reid VA,Carvalho GR,George DG,et al.2002.A technique for the molecular genetic analysis of Daphnia,resting eggs from sub-recent lake sediments.Journal of Paleolimnology,27:481-486.
Savichtcheva O,Debroas D,Perga ME,et al.2015.Effects of nutrients and warming on Planktothrix dynamics and diversity:Apalaeolimnological view based on sedimentary DNAand RNA.Freshwater Biology,60:31-49.
Singh G,Sithebe A,Enitan AM,et al.2016.Comparison of droplet digital PCR and quantitative PCR for the detection of Salmonella and its application for river sediments.Journal of Water and Health,15:505-508.
Stoofleichsenring KR,Herzschuh U,Pestryakova LA,et al.2015.Genetic data from algae sedimentary DNA reflect the influence of environment over geography.Scientific Reports,5:12924.
Torit A,Lever MA,Jorgensen BB.2015.Origin,dynamics,and implications of extracellular DNA pools in marine sediments.Marine Genomics,24:185-196.
Willerslev E,Cooper A.2003.Diverse plant and animal genetic records from Holocene and Pleistocene sediments.Science,300:791-795.
Willerslev E,Cooper A.2005.Ancient DNA.Proceedings of the Royal Society B:Biological Sciences,272:3-16.
Xu ZH,Jiang XD,Wang GZ,et al.2011.DNA extraction,amplification and analysis of the 28S rRNA portion in sediment-buried copepod DNA in the Great Wall Bay and Xihu Lake,Antarctica.Journal of Plankton Research,33:917-925.
Yan DN,Xu H,Yang M,et al.2019.Responses of cyanobacteria to climate and human activities at Lake Chenghai over the past 100 years.Ecological Indicators,ECOIND5442.
Yang J,Jiang HC,Dong HL,et al.2015.Sedimentary archaeal amo A gene abundance reflects historic nutrient level and salinity fluctuations in Qinghai Lake,Tibetan Plateau.Scientific Reports,5:18071.
刘学,张志强,郑军卫,等.2014.关于人类世问题研究的讨论.地球科学进展,29(5):640-648.
侯卫国,董海良,蒋宏忱,等.2016.沉积物中古DNA在古生态、古环境和古气候研究中的应用.地学前缘,24(2):286-291.
周晓光,任鲁风,李运涛,等.2010.下一代测序技术:技术回顾与展望.中国科学:生命科学,40(1):23-37.
盛桂莲,赖旭龙,袁俊霞,等.2016.古DNA研究:35年回顾与展望.中国科学:地球科学,46(12):1564-1578.
申慧彦,李世杰.2008.湖泊沉积物中DNA提取与PCR扩增.地球科学进展,23(4):433-438.
魏子艳,金德才,邓晔.2015.环境微生物宏基因组学研究中的生物信息学方法.微生物学通报,42(5):890-901.
王玉倩,薛秀花.2016.实时荧光定量PCR技术研究进展及其应用.生物学通报,51(2):1-6.
冯兆民,舒跃龙.2017.数字PCR技术及其应用进展.病毒学报,33(1):103-107.
杨渐,蒋宏忱,吴耿,等.2016.青海湖1.8万年以来甲藻Dinoflagellate群落变化及其古气候环境的指示意义.盐湖研究,24(2):84-91.
Ahmed E,Han L,Pedersen MW,et al.2016.Ancient DNA in lake sediments:Shotgun metagenomic analyses.Conference:Sci Life Lab mini-symposium:Ancient Environmental DNA.
Alsos IG,Sjogren P,Edwards ME,et al.2015.Sedimentary ancient DNA from Lake Skartjrna,Svalbard:Assessing the resilience of arctic flora to Holocene climate change.Holocene,26:189-192.
An Z,Colman SM,Zhou W,et al.2012.Interplay between the Westerlies and Asian monsoon recorded in Lake Qinghai sediments since 32 ka.Scientific Reports,2:619.
Anderson-Carpenter LL,McLachlan JS,Jackson ST,et al.2011.Ancient DNA from lake sediments:Bridging the gap between paleoecology and genetics.BMC Evolutionary Biology,11:88-95.
Andrew B,John AE,Simon NJ,et al.2005.Isolation,amplification,and identification of ancient copepod DNA from lake sediments.Limnology and Oceanography:Methods,3:533-542.
Belle S,Parent C,Frossard V,et al.2014.Temporal changes in the contribution of methane-oxidizing bacteria to the biomass of chironomid larvae determined using stable carbon isotopes and ancient DNA.Journal of Paleolimnology,52:215-228.
Birks JB,Birks HH.2016.How have studies of ancient DNAfrom sediments contributed to the reconstruction of Quaternary floras?New Phytologist,209:499-506.
Bissett A,Gibson JAE,Jarman SN,et al.2005.Isolation,amplification,and identification of ancient copepod DNAfrom lake sediments.Limnology&Oceanography Methods,3:533-542.
Boessenkool S,Mcglynn G,Epp LS,et al.2014.Use of ancient sedimentary DNA as a novel conservation tool for highaltitude tropical biodiversity.Conservation Biology,28:446-455.
Capo E,Debroas D,Arnaud F,et al.2015.Is planktonic diversity well recorded in sedimentary DNA?Toward the reconstruction of past protistan diversity.Microbial Ecology,70:865-875.
Coolen MJL,Muyzer G,Rijpstra WIC,et al.2004b.Combined DNA and lipid analyses of sediments reveal changes in Holocene haptophyte and diatom populations in an Antarctic lake.Earth and Planetary Science Letters,223:225-239.
Coolen MJL,Muyzer G,Schouten S,et al.2005.Sulfur and methane cycling during the Holocene in Ace Lake Antarctica revealed by lipid and DNA stratigraphy.Nato Science,64:41-65.
Coolen MJL,Overmann J.1998.Analysis of subfossil molecular remains of purple sulfur bacteria in a lake sediment.Applied&Environmental Microbiology,64:4513-4521.
Coolen MJL.2011.7000 years of Emiliania huxleyi viruses in the black sea.Science,333:451-452.
Crutzen PJ,Stoermer EF.2000.The“Anthropocene”.IGBPNews Letter,41:17-18.
D'Andrea WJ,Lage M,Martiny JBH,et al.2015.Alkenone producers inferred fromwell-preserved 18S r DNA in Greenland lake sediments.Journal of Geophysical Research:Biogeosciences,111:397-399.
Domaizon I,Savichtcheva O,Debroas D,et al.2013.DNAfrom lake sediments reveals the long-term dynamics and diversity of Synechococcus assemblages.Biogeosciences,10:3817-3838.
Epp LS,Gussarova G,Boessenkool S,et al.2015.Lake sediment multi-taxon DNA from North Greenland records early post-glacial appearance of vascular plants and accurately tracks environmental changes.Quaternary Science Reviews,117:152-163.
Epp LS,Stoof-Leichsenring KR,Trauth MH,et al.2011.Molecular profiling of diatom assemblages in tropical lake sediments using taxon-specific PCR and Denaturing HighPerformance Liquid Chromatography(PCR-DHPLC).Molecular Ecology Resources,11:842-853.
Fischer SG,Lerman LS.1979.Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis.Cell,16:191-200.
Fu Q,Li H,Moorjani P,et al.2014.Genomesequence of a 45,000-year-old modern humanfrom western Siberia.Nature,514:445-449.
Giguet-Covex C,Pansu J,Arnaud F,et al.2014.Long livestock farming history and human landscape shaping revealed by lake sediment DNA.Nature Communications,23:3211.
Ginolhac A,Vilstrup J,Stenderup J,et al.2012.Improving the performance of true single molecule sequencing for ancient DNA.BMC Genomics,13:177.
Gregory-Eaves S,Pal I,Pick FR.2015.Temporal trends in cyanobacteria revealed through DNA and pigment analyses of temperate lake sediment cores.Journal of Paleolimnology,54:1-15.
Handelsman J,Rondon MR,Brady SF,et al.1998.Molecular biological access to the chemistry of unknown soil microbes:Anew frontier for natural products.Chemistry&Biology,5:245-249.
Heinecke L,Epp LS,MischkeS,et al.2016.Geochemical analyses of macrophytes(Potamogeton sp.)and ancient DNAfrom Lake Karakul,Tajikistan.Geophysical Research Abstracts,18:EGU2016-13233.
Higuchi R,Bowman B,Freiberger M,et al.1984.DNA sequences from the quagga,an extinct member of the horse family.Nature,312:282-284.
Hofreiter M,David S,Hendrik N,et al.2001.Ancient DNA.Nature Reviews Genetics,2:353-362.
Hoss M,Jaruga P,Zastawny TH,et al.1996.DNA damage and DNA sequence retrieval from ancient tissues.Nucleic Acids Research,24:1304-1307.
Hou WG,Dong HL,Li GY,et al.2014.Identification of photosynthetic plankton communities using sedimentary ancient DNA and their response to late-Holocene climate change on the Tibetan Plateau.Scientific Reports,4:6648.
Jiang H,Dong H,Yu B,et al.2007.Microbial response to salinity change in Lake Chaka,a hypersaline lake on Tibetan plateau.Environmental Microbiology,9:2603-2621.
Klouch KZ,Schmidt S,Andrieux-Loyer F,et al.2016.Historical records from dated sediment cores reveal the multidecadal dynamic of the toxic dinoflagellate Alexandrium minutum in the Bay of Brest(France).FEMS Microbiology Ecology,92:101-118.
Knight R,Jansson J,Field D,et al.2012.Unlocking the potential of metagenomics through replicated experimental design.Nature Biotechnology,30:513-520.
Lendvay B,Miklós B,Ilona P,et al.2018.Plant macrofossils from lake sediment as the material to assess ancient genetic diversity:Did deforestation influence Norway spruce(Picea abies)in the South Carpathians.Quaternary International,30:106-116.
Li GY,Dong HL,Hou WG,et al.2016.Temporal succession of ancient phytoplankton community in Qinghai Lake and implication for paleo-environmental Change.Scientific Reports,6:19769.
Limburg PA,Weider LJ.2002.‘Ancient’DNA in the resting egg bank of a microcrustacean can serve as a palaeolimnological database.Proceedings of the Royal Society B:Biological Sciences,269:281-287.
Madeja J.2015.A new tool to trace past human presence from lake sediments:The human-specific molecular marker Bacteroides strain HF 183.Journal of Quaternary Science,30:349-354.
Martínez EG,Antoniades D,Bonilla S,et al.2014.Application of ancient DNA to the reconstruction of past microbial assemblages and for the detection of toxic cyanobacteria in subtropical freshwater ecosystems.Molecular Ecology,23:5791-5802.
Matisoo-Smith E,Roberts K,Welikala N,et al.2008.Recovery of DNA and pollen from New Zealand lake sediments.Quaternary International,184:139-149.
Mitchell D,Willerslev E,Hansen A.2005.Damage and repair of ancient DNA.Mutation Research,571:265-276.
Monchamp ME,Spaak P,Domaizon I,et al.2018.Homogenization of lake cyanobacterial communities over a century of climate change and eutrophication.Nature Ecology Evolution,2:317-322.
Niemeyer B,Epp LS,Stoofleichsenring KR,et al.2017.Acomparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline.Molecular Ecology Resources,17:46-57.
Orlando L,Ginolhac A,Zhang G,et al.2013.Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.Nature,499:74-78.
Paabo S,Poinar H,David S,et al.2004.Genetic analyses from ancient DNA.Annual Reviews of Genetics,38:645-679.
Pal S,Gregory-Eaves I,Pick FR.2015.Temporal trends in cyanobacteria revealed through DNA and pigment analyses of temperate lake sediment cores.Journal of Paleolimnology,54:87-101.
Pansu J,Giguet-Covex C,Ficetola GF,et al.2015.Reconstructing long-term human impacts on plant communities:An ecological approach based on lake sediment DNA.Molecular Ecology,24:1485-1498.
Parducci L,Bennett KD,Ficetola GF,et al.2017.Ancient plant DNA in lake sediments.New Phytologist,214:924-942.
Parducci L,Suyama Y.2005.Single-Pollen genotyping of Holocene lake sediments//Isagi Y,Suyama Y,eds.SinglePollen Genotyping.Springer Japan,Ecological Research Monographs 1,DOI:10.1007/978-4-431-53901-8_8.:101-109.
Pedersen MW,Ginolhac A,Orlando L,et al.2013.A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa.Quaternary Science Reviews,75:151-158.
Poulain AJ,Arisbrosou S,Blais JM,et al.2015.Microbial DNA records historical delivery of anthropogenic mercury.ISME Journal,9:2541-2550.
Randlett ME,Coolen MJL,Stockhecke M,et al.2014.Alkenone distribution in Lake Van sediment over the last 270ka:Influence of temperature and haptophyte species composition.Quaternary Science Reviews,104:53-62.
Ravasi DF,Peduzzi S,Guidi V,et al.2012.Development of a real-time PCR method for the detection of fossil 16S r DNAfragments of phototrophic sulfur bacteria in the sediments of Lake Cadagno.Geobiology,10:196-204.
Reid VA,Carvalho GR,George DG,et al.2002.A technique for the molecular genetic analysis of Daphnia,resting eggs from sub-recent lake sediments.Journal of Paleolimnology,27:481-486.
Savichtcheva O,Debroas D,Perga ME,et al.2015.Effects of nutrients and warming on Planktothrix dynamics and diversity:Apalaeolimnological view based on sedimentary DNAand RNA.Freshwater Biology,60:31-49.
Singh G,Sithebe A,Enitan AM,et al.2016.Comparison of droplet digital PCR and quantitative PCR for the detection of Salmonella and its application for river sediments.Journal of Water and Health,15:505-508.
Stoofleichsenring KR,Herzschuh U,Pestryakova LA,et al.2015.Genetic data from algae sedimentary DNA reflect the influence of environment over geography.Scientific Reports,5:12924.
Torit A,Lever MA,Jorgensen BB.2015.Origin,dynamics,and implications of extracellular DNA pools in marine sediments.Marine Genomics,24:185-196.
Willerslev E,Cooper A.2003.Diverse plant and animal genetic records from Holocene and Pleistocene sediments.Science,300:791-795.
Willerslev E,Cooper A.2005.Ancient DNA.Proceedings of the Royal Society B:Biological Sciences,272:3-16.
Xu ZH,Jiang XD,Wang GZ,et al.2011.DNA extraction,amplification and analysis of the 28S rRNA portion in sediment-buried copepod DNA in the Great Wall Bay and Xihu Lake,Antarctica.Journal of Plankton Research,33:917-925.
Yan DN,Xu H,Yang M,et al.2019.Responses of cyanobacteria to climate and human activities at Lake Chenghai over the past 100 years.Ecological Indicators,ECOIND5442.
Yang J,Jiang HC,Dong HL,et al.2015.Sedimentary archaeal amo A gene abundance reflects historic nutrient level and salinity fluctuations in Qinghai Lake,Tibetan Plateau.Scientific Reports,5:18071.