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Volume 40 Issue 6
Dec.  2021
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BAI Jie,XING Yingchun,GAO Wanru,et al.Environmental DNA: An emerging tool in studying cave organisms[J].Carsologica Sinica,2021,40(06):1014-1020. doi: 10.11932/karst2020y48
Citation: BAI Jie,XING Yingchun,GAO Wanru,et al.Environmental DNA: An emerging tool in studying cave organisms[J].Carsologica Sinica,2021,40(06):1014-1020. doi: 10.11932/karst2020y48

Environmental DNA: An emerging tool in studying cave organisms

doi: 10.11932/karst2020y48
Funds:

 NSFC-31972868, 31970382

 2019HJ2096001006

 2017B001, 2020A001

  • Received Date: 2020-04-07
  • Publish Date: 2021-12-25
  • China has enormous caves with diverse cave organisms. Many cave creatures have small population size and limited distribution. Therefore, the traditional survey on cave fauna may harm some rare or endangered cave species. Its low efficiency could also restrict the studies of cave biodiversity and conservation. As an emerging survey method, environmental DNA (eDNA) can be used to extract the trace DNA of cave organisms from the environment and to qualitatively or quantitatively investigate the cave biodiversity with the technology such as PCR. After reviewing the principles of eDNA, its advantages and current research status, we put forward a basic process for the application of eDNA in cave biological surveys. We expect that the eDNA can play an important role in future studies of biospeleology in China. To achieve this aim, a thorough database of DNA barcodes and a classic taxonomy for Chinese cave organisms are urgently needed.

     

  • BAI Jie,XING Yingchun,GAO Wanru,et al.Environmental DNA: An emerging tool in studying cave organisms[J].Carsologica Sinica,2021,40(06):1014-1020.
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  • 李大通, 罗雁. 中国碳酸盐岩分布面积测量 [J]. 中国岩溶, 1983, 2(2): 147-150.
    王世杰, 张信宝, 白晓永. 中国南方喀斯特地貌分区纲要 [J]. 山地学报, 2015, 33(6):641-648.
    袁道先, 蒋勇军, 沈立成, 等. 现代岩溶学 [M]. 北京: 科学出版社, 2016.
    陈伟海. 洞穴研究进展综述 [J]. 地质论评, 2006, 52(6): 783-792.
    张远海, 朱德浩. 中国大型岩溶洞穴空间分布及演变规律 [J]. 桂林理工大学学报, 2012, 32(1): 20-28.
    LiuW, WynneJ J. Cave millipede diversity with the description of six new species from Guangxi, China [J]. Subterranean Biology, 2019, 30:57-94.
    GolovatchS I. Cave Diplopoda of southern China with reference to millipede diversity in Southeast Asia [J]. Zookeys, 2015, 510(510): 79-94.
    TianM-Y. A new species of the subterranean genus Oodinotrechus Uéno, 1998, from northern Guangxi, China, with additions to the generic diagnosis (coleoptera: carabidae: trechinae) [J]. Journal of Natural History, 2014, 48(33-34): 2097-2104.
    TianM, LuoX. A new species of the highly modified hypogean genus Giraffaphaenops Deuve, 2002 (Coleoptera: Carabidae: Trechinae) [J]. Zootaxa, 2015, 3911(4): 581-588.
    TianM, HuangS, WangX, et al. Contributions to the knowledge of subterranean trechine beetles in southern China’s karsts: five new genera (Insecta, Coleoptera, Carabidae, Trechinae) [J]. Zookeys, 2016, 564:121-156.
    ZhaoY, GozlanR E, ZhangC. Out of sight out of mind: current knowledge of Chinese cave fishes [J]. Journal of Fish Biology, 2011, 79(6): 1545-1562.
    MaL, ZhaoY, YangJ X. Cavefish of China [M]//White W B, Culver D C, Pipan T. Encyclopedia of caves (3rd edition). London: Academic Press, 2019: 237-254.
    NiemillerM L, BichuetteM E, ChakrabartyP, et al. Cavefishes [M]//White W B, Culver D C, Pipan T. Pipan. Encyclopedia of caves (3rd edition). London: Academic Press,2019: 227-236.
    赵亚辉, 张春光. 洞穴鱼类:概念、多样性和研究进展 [J]. 生物多样性, 2006, 14(5): 451-460.
    ParzefallJ. Cave Fishes: The consequences of the Life in Darkness [M]//Sébert P, Onyango D W, Kapoor B G. Fish life in special environments. Enfield: Science Publishers,2008: 53-81.
    MammolaS, CardosoP, CulverD C, et al. Scientists' warning on the conservation of subterranean ecosystems [J]. BioScience, 2019, 69(8): 641-650.
    MammolaS, PianoE, CardosoP, et al. Climate change going deep: The effects of global climatic alterations on cave ecosystems[J].The Anthropocene Review,2019, 6(1-2): 98-116.
    蒋志刚, 江建平, 王跃招, 等. 中国脊椎动物红色名录 [J]. 生物多样性, 2016, 24(5): 500-551.
    GoričkiŠ. Environmental DNA as a conservation tool [M]//White W B, Culver D C, Pipan T. Encyclopedia of Caves (3rd edition). London: Academic Press, 2019: 387-793.
    PedersenM W, OverballeP S, ErminiL, et al. Ancient and modern environmental DNA[J]. Philosophical Transactions of the Royal Society B:Biological Sciences, 2015, 370(1660):20130383.
    OlsenG J. Microbial ecology and evolution: A ribosomal RNA approach [J]. Annual Reviews of Microbiology, 1986, 40:337-365.
    PaceN R, StahlD A, LaneD J, et al. The analysis of natural microbial populations by ribosomal RNA sequences [M]//Marshall K C. Advances in Microbial Ecology. Boston, MA: Springer US, 1986:1-55.
    WillerslevE, HansenA J, BinladenJ, et al. Diverse plant and animal genetic records from Holocene and Pleistocene sediments [J]. Science, 2003, 300(5620): 791-795.
    BhaduryP, AustenM C, BiltonD T, et al. Development and evaluation of a DNA-barcoding approach for the rapid identification of nematodes [J]. Marine Ecology Progress Series, 2006, 320:1-9.
    TaberletP, BoninA, ZingerL, et al. Environmental DNA: for biodiversity research and monitoring [M]. Oxford: Oxford University Press, 2018:9-13.
    WillerslevE, HansenA J, ChristensenB, et al. Diversity of holocene life forms in fossil glacier ice [J]. Proceedings of the National Academy of Sciences, 1999, 96(14): 8017-8021.
    FicetolaG F, MiaudC, PompanonF, et al. Species detection using environmental DNA from water samples [J]. Biology Letters, 2008, 4(4):423-425.
    李萌, 尉婷婷, 史博洋, 等. 环境DNA技术在淡水底栖大型无脊椎动物多样性监测中的应用 [J]. 生物多样性, 2019, 27(5): 480-490.
    ShokrallaS, SpallJ L, GibsonJ F, et al. Next-generation sequencing technologies for environmental DNA research [J]. Molecular Ecology, 2012, 21(8): 1794-1805.
    ThomsenP F, WillerslevE. Environmental DNA-an emerging tool in conservation for monitoring past and present biodiversity [J]. Biological Conservation, 2015, 183:4-18.
    TaberletP, CoissacE, HajibabaeiM, et al. Environmental DNA [J]. Molecular Ecology, 2012, 21(8):1789-1793.
    ValentiniA, TaberletP, MiaudC, et al. Next-Generation monitoring of aquatic biodiversity using environmental DNA metabarcoding [J]. Molecular Ecology,2016,25(4):929-942.
    EvansN T, ShireyP D, WieringaJ G, et al. Comparative cost and effort of fish distribution detection via environmental DNA analysis and electrofishing [J]. Fisheries, 2017, 42(2): 90-99.
    GarganL M, MoratoT, PhamC K, et al. Development of a sensitive detection method to survey pelagic biodiversity using eDNA and quantitative PCR: a case study of devil ray at seamounts [J]. Marine Biology, 2017, 164(5):112-119.
    GoldbergC S, PilliodD S, ArkleR S, et al. Molecular detection of vertebrates in stream water: a demonstration using rocky mountain tailed frogs and idaho giant salamanders [J]. Plos One, 2011, 6(7): e22746.
    PedersenM W, GinolhacA, OrlandoL, et al. A comparative study of ancient environmental DNA to pollen and macrofossils from lake sediments reveals taxonomic overlap and additional plant taxa [J].Quaternary Science Reviews,2013,75:161-168.
    BoussarieG, BakkerJ, WangensteenO S, et al. Environmental DNA illuminates the dark diversity of sharks [J]. Science Advances, 2018, 4(5): eaap9661.
    FranklinT W, MckelveyK S, GoldingJ D, et al. Using environmental DNA methods to improve winter surveys for rare carnivores: DNA from snow and improved noninvasive techniques [J]. Biological Conservation, 2019, 229:50-58.
    DejeanT, ValentiniA, DuparcA, et al. Persistence of environmental DNA in freshwater ecosystems [J]. Plos One, 2011, 6(8): e23398.
    PedersenM W, RuterA, SchwegerC, et al. Postglacial viability and colonization in north America's ice-free corridor [J]. Nature, 2016, 537(7618): 45-49.
    TringeS G, RubinE M. Metagenomics: DNA sequencing of environmental samples [J]. Nature Reviews Genetics, 2005, 6(11): 805-814.
    IUCN. The IUCN red list of threatened species. Version 2020-1[J]. IUCN Red List of Threatened Species (2020), 2020.
    GoričkiŠ, StankovićD, SnojA, et al. Environmental DNA in subterranean biology: range extension and taxonomic implications for Proteus [J]. Scientific Reports, 2017, 7(1): 1-11.
    AljančičG, GoričkiŠ, NăpăruşM, et al. Endangered Proteus: combining DNA and GIS analyses for its conservation [J]. Dinaric Karst Poljes-Floods for Life, 2014, 70: 5.
    VörösJ, MártonO, SchmidtB R, et al. Surveying Europe’s only cave-dwelling chordate species (Proteus Anguinus) using environmental DNA [J]. Plos One, 2017, 12(1): e0170945.
    NiemillerM L, PorterM L, KeanyJ, et al. Evaluation of eDNA for groundwater invertebrate detection and monitoring: a case study with endangered Stygobromus (Amphipoda: Crangonyctidae) [J]. Conservation Genetics Resources, 2018, 10(2): 247-257.
    FraserC I, ConnellL, LeeC K, et al. Evidence of plant and animal communities at exposed and subglacial (cave) geothermal sites in Antarctica [J]. Polar Biology, 2018, 41(3): 417-421.
    MacaladyJ L, DattaguptaS, SchaperdothI, et al. Niche differentiation among sulfur-oxidizing bacterial populations in cave waters [J]. The Isme Journal, 2008, 2(6): 590-601.
    CheepthamN. Advances and Challenges in Studying Cave Microbial Diversity [M]. Cave Microbiomes: A Novel Resource for Drug Discovery. Springer. 2013: 1-34.
    TsujiS, TakaharaT, DoiH, et al. The detection of aquatic macroorganisms using environmental DNA analysis-a review of methods for collection, extraction, and detection [J]. Environmental DNA, 2019, 1(2): 99-108.
    BohmannK, EvansA, GilbertM T P, et al. Environmental DNA for wildlife biology and biodiversity monitoring [J]. Trends in Ecology & Evolution, 2014, 29(6): 358-367.
    ElenaV, JonasB, SimonJ G, et al. Novel universal primers for metabarcoding environmental DNA surveys of marine mammals and other marine vertebrates [J]. Environmental DNA, 2020, 2(4):460-467.
    HebertP D, CywinskaA, BallS L, et al. Biological identifications through DNA barcodes [J]. Proceedings of the Royal Society of London Series B: Biological Sciences, 2003, 270(1512): 313-321.
    HollingsworthM L, AndraC A, ForrestL L, et al. Selecting barcoding loci for plants: evaluation of seven candidate loci with species‐level sampling in three divergent groups of land plants[J].Molecular Ecology Resources,2009,9(2):439-457.
    BellemainE, CarlsenT, BrochmannC, et al. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases [J]. BMC Microbiology, 2010, 10(1): 189.
    SchochC L, SeifertK A, HuhndorfS, et al. Nuclear ribosomal internal transcribed spacer (its) region as a universal DNA barcode marker for fungi [J]. Proceedings of the National Academy of Sciences, 2012, 109(16): 6241-6246.
    RiazT, ShehzadW, ViariA, et al. Ecoprimers: inference of new DNA barcode markers from whole genome sequence analysis [J]. Nucleic Acids Research, 2011, 39(21): 145.
    BrownW M, WilsonG A C. Rapid evolution of animal mitochondrial DNA [J]. Proceedings of the National Academy of Sciences of the United States of America, 1979, 76(4):1967-1971.
    LatellaL. Chapter 16-Biodiversity: China [M]//White W B, Culver D C, Pipan T. Encyclopedia of caves (3rd edition). London: Academic Press, 2019: 127-135.
    赵亚辉, 张春光. 中国特有金线鲃属鱼类:物种多样性、洞穴适应、系统演化和动物地理 [M]. 北京: 科学出版社, 2009.
    TianM, HuangS, WangX, et al. Contributions to the knowledge of subterranean trechine beetles in southern China's karsts: five new genera (Insecta, Coleoptera, Carabidae, Trechinae) [J]. Zookeys, 2016, 564(3):121-156.
    陈善元, 张仁东, 李维贤, 等. 六种鱼巴亚科鱼类线粒体细胞色素b基因序列分析 [J]. 云南大学学报(自然科学版), 2003, 25(5): 453-457.
    XiaoC, LiM, LiW, et al. Mitochondrial DNA variation in two subspecies of Sinocyclocheilus as revealed by DNA sequences [J]. Journal of Yunnan University (Natural Sciences), 1998, 20(3): 218-220.
    XiaoH, ChenS Y, LiuZ M, et al. Molecular phylogeny of Sinocyclocheilus (Cypriniformes: Cyprinidae) inferred from mitochondrial DNA sequences [J]. Molecular Phylogenetics and Evolution, 2005, 36(1): 67-77.
    李雪健. 中国条鳅科洞穴鱼类的经典分类、适应演化和动物地理 [D]. 上海:上海海洋大学, 2018.
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