河流环境DNA科学图谱及其主题演变
Scientific Mapping and Thematic Evolution of River Environmental DNA
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摘要: 人类活动不断对河流生态系统产生影响，并且施加了巨大的压力。为了制定有效措施缓解河流生态系统的压力，需要获得大量有效的河流水生生物信息。环境DNA （environmental DNA，eDNA）技术作为近期环境科学的研究热点，是监测河流水生生物的有效工具。本文选取了Web of Science数据库（Web of Science Database，WOS）中1990—2020年的2 151篇相关文献进行数据挖掘及其可视化分析。河流eDNA研究的发文量逐年递增，在不同时期该研究领域具有不同的研究热点，研究重心逐渐从水生微生物的研究转向更广泛的生态监测、河流管理等方面。关键词频次分析表明，“biodiversity”“conservation”“metabarcoding”是河流eDNA研究持续的研究热点。学科方向的占比变化表明，河流eDNA在微生物学中的研究占比已经大大降低。在国际合作方面，美国是国际合作文章数量最多的国家，但是瑞士、法国、西班牙与他国合作数量占比却位于前列。eDNA技术在收集河流信息方面简单有效，其应用越来越多地应用于河流入侵物种调查、渔业和河流保护，从而可以为决策者应对环境变化的干预和管理活动提供信息支持。Abstract: Human activities are constantly impacting river ecosystems with tremendous pressure. In order to develop scientific and effective measures to alleviate the pressure on river ecosystems, information on river organisms needs to be obtained. The technology of environmental DNA (eDNA), as one of research hotspots in environmental science, is an effective tool for monitoring river organisms. In this paper, we selected 2 151 relevant papers in Web of Science Database (WOS) from 1990 to 2020 to perform data mining and visualization analysis. The number of research articles on river eDNA has been increasing annually with the constant changing of research hotspots in this field, in which the research focus has shifted gradually from aquatic microorganisms to ecological monitoring and river management. The frequency analysis of keywords showed that "biodiversity", "conservation" and "metabarcoding" continues to be the research hotspot, as they have the highest frequency among keywords. The change in the percentage of subject orientation indicates that the proportion of river eDNA studies in microbiology has been reduced significantly. The United States had the largest number of international cooperation articles. Switzerland, France, and Spain ranked highest in the ratio of collaborative articles with other countries among the total number of articles in their own countries. The eDNA technology, increasingly being utilized in river invasive species surveys, fish farming and river protection, is an effective tool which gathers river information to provide information to support decision makers in their interventions and management activities in response to environmental change.
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Key words:
- river environmental DNA /
- river ecosystem /
- text mining /
- biodiversity /
- invasive species /
- biomonitoring
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唐涛, 蔡庆华, 刘建康. 河流生态系统健康及其评价[J]. 应用生态学报, 2002, 13(9):1191-1194 Tang T, Cai Q H, Liu J K. River ecosystem health and its assessment[J]. Chinese Journal of Applied Ecology, 2002, 13(9):1191-1194(in Chinese)
Dudgeon D, Arthington A H, Gessner M O, et al. Freshwater biodiversity:Importance, threats, status and conservation challenges[J]. Biological Reviews of the Cambridge Philosophical Society, 2006, 81(2):163-182 Freeman M C, Pringle C M, Jackson C R. Hydrologic connectivity and the contribution of stream headwaters to ecological integrity at regional Scales1[J]. Journal of the American Water Resources Association, 2007, 43(1):5-14 Crookes S, Heer T, Castañeda R A, et al. Monitoring the silver carp invasion in Africa:A case study using environmental DNA (eDNA) in dangerous watersheds[J]. NeoBiota, 2020, 56(56):31-47 Barnes M A, Turner C R. The ecology of environmental DNA and implications for conservation genetics[J]. Conservation Genetics, 2016, 17(1):1-17 Ficetola G F, Miaud C, Pompanon F, et al. Species detection using environmental DNA from water samples[J]. Biology Letters, 2008, 4(4):423-425 Ananiadou S, Kell D B, Tsujii J I. Text mining and its potential applications in systems biology[J]. Trends in Biotechnology, 2006, 24(12):571-579 Chen C M. Searching for intellectual turning points:Progressive knowledge domain visualization[J]. Proceedings of the National Academy of Sciences of the United States of America, 2004, 101(Suppl 1):5303-5310 陈俊梅, 张文翔, 刘甜甜, 等. 基于CiteSpace和知网数据库的《湖泊科学》创刊30年(1989-2018年)发表论文的文献计量学分析[J]. 湖泊科学, 2019, 31(4):891-906 Chen J M, Zhang W X, Liu T T, et al. Scientometric analysis of papers published in 1989-2018 of Journal of Lake Sciences based on CiteSpace and CNKI database[J]. Journal of Lake Sciences, 2019, 31(4):891-906(in Chinese)
毛文山, 赵红莉, 蒋云钟, 等. 基于文献计量学的国内水生态环境研究知识图谱构建与应用[J]. 水利学报, 2019, 50(11):1400-1416 Mao W S, Zhao H L, Jiang Y Z, et al. Construction and application of knowledge graph of domestic water eco-environment based on bibliometrics[J]. Journal of Hydraulic Engineering, 2019, 50(11):1400-1416(in Chinese)
Giovannoni S J, Britschgi T B, Moyer C L, et al. Genetic diversity in Sargasso Sea bacterioplankton[J]. Nature, 1990, 345(6270):60-63 van Eck N J, Waltman L. Software survey:VOSviewer, a computer program for bibliometric mapping[J]. Scientometrics, 2010, 84(2):523-538 Handelsman J. Metagenomics:Application of genomics to uncultured microorganisms[J]. Microbiology and Molecular Biology Reviews, 2004, 68(4):669-685 Baker G C, Smith J J, Cowan D A. Review and re-analysis of domain-specific 16S primers[J]. Journal of Microbiological Methods, 2003, 55(3):541-555 Thomsen P F, Kielgast J, Iversen L L, et al. Monitoring endangered freshwater biodiversity using environmental DNA[J]. Molecular Ecology, 2012, 21(11):2565-2573 Butchart S H, Walpole M, Collen B, et al. Global biodiversity:Indicators of recent declines[J]. Science, 2010, 328(5982):1164-1168 Maxam A M, Gilbert W. A new method for sequencing DNA[J]. Proceedings of the National Academy of Sciences of the United States of America, 1977, 74(2):560-564 Hebert P D, Cywinska A, Ball S L, et al. Biological identifications through DNA barcodes[J]. Proceedings Biological Sciences, 2003, 270(1512):313-321 Pompanon F, Coissac É, Taberlet P. Metabarcoding, a new way of analysing biodiversity[J]. Biofutur, 2011, 319(319):30-32 Grad Y H, Lipsitch M, Feldgarden M, et al. Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011[J]. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(8):3065-3070 Goren A, Ozsolak F, Shoresh N, et al. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA[J]. Nature Methods, 2010, 7(1):47-49 Handelsman J, Rondon M R, Brady S F, et al. Molecular biological access to the chemistry of unknown soil microbes:A new frontier for natural products[J]. Chemistry & Biology, 1998, 5(10):R245-R249 Ji Y Q, Ashton L, Pedley S M, et al. Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding[J]. Ecology Letters, 2013, 16(10):1245-1257 Dafforn K, Baird D, Chariton A, et al. Faster, higher and stronger? The pros and cons of molecular faunal data for assessing ecosystem condition[J]. Advances in Ecological Research, 2014, 51:1-40 Guillerault N, Bouletreau S, Iribar A, et al. Application of DNA metabarcoding on faeces to identify European catfish Silurus glanis diet[J]. Journal of Fish Biology, 2017, 90(5):2214-2219 马睿, 陈建徽, 刘建宝, 等. 湖泊沉积物DNA在气候环境变化和生态系统响应研究中的应用[J]. 湖泊科学, 2021, 33(3):653-666 Ma R, Chen J H, Liu J B, et al. Progress in the application of lake sediment DNA in climate and environmental change and ecosystem response[J]. Journal of Lake Sciences, 2021, 33(3):653-666(in Chinese)
Dejean T, Valentini A, Miquel C, et al. Improved detection of an alien invasive species through environmental DNA barcoding:The example of the American bullfrog Lithobates catesbeianus[J]. Journal of Applied Ecology, 2012, 49(4):953-959 Takahara T, Minamoto T, Doi H. Using environmental DNA to estimate the distribution of an invasive fish species in ponds[J]. PLoS One, 2013, 8(2):e56584 PilliodDavid S, GoldbergCaren S, ArkleRobert S, et al. Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples[J]. Canadian Journal of Fisheries and Aquatic Sciences, 2013, 70(8):1123-1130 Dougherty M M, Larson E R, Renshaw M A, et al. Environmental DNA (eDNA) detects the invasive rusty crayfish Orconectes rusticus at low abundances[J]. The Journal of Applied Ecology, 2016, 53(3):722-732 Vörös J, Márton O, Schmidt B R, et al. Surveying Europe's only cave-dwelling chordate species (Proteus anguinus) using environmental DNA[J]. PLoS One, 2017, 12(1):e0170945 Xu Y Y, Boeing W J. Mapping biofuel field:A bibliometric evaluation of research output[J]. Renewable and Sustainable Energy Reviews, 2013, 28:82-91 Carraro L, Mächler E, Wüthrich R, et al. Environmental DNA allows upscaling spatial patterns of biodiversity in freshwater ecosystems[J]. Nature Communications, 2020, 11(1):3585 Cardinale B J, Duffy J E, Gonzalez A, et al. Biodiversity loss and its impact on humanity[J]. Nature, 2012, 486(7401):59-67 Aylagas E, Borja Á, Muxika I, et al. Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks[J]. Ecological Indicators, 2018, 95:194-202 Ogram A, Sayler G S, Barkay T. The extraction and purification of microbial DNA from sediments[J]. Journal of Microbiological Methods, 1987, 7(2-3):57-66 Sogin M L, Morrison H G, Huber J A, et al. Microbial diversity in the deep sea and the underexplored "rare biosphere"[J]. Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(32):12115-12120 Andersson A F, Lindberg M, Jakobsson H, et al. Comparative analysis of human gut microbiota by barcoded pyrosequencing[J]. PLoS One, 2008, 3(7):e2836 Hajibabaei M, Shokralla S, Zhou X, et al. Environmental barcoding:A next-generation sequencing approach for biomonitoring applications using river benthos[J]. PLoS One, 2011, 6(4):e17497 Deagle B E, Roger K, Jarman S N. Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces[J]. Molecular Ecology, 2009, 18(9):2022-2038 Shu L, Ludwig A, Peng Z G. Standards for methods utilizing environmental DNA for detection of fish species[J]. Genes, 2020, 11(3):296 Tillotson M D, Kelly R P, Duda J J, et al. Concentrations of environmental DNA (eDNA) reflect spawning salmon abundance at fine spatial and temporal scales[J]. Biological Conservation, 2018, 220:1-11 Pan W B, Huang H, Yao P C, et al. Assessment methods of small watershed ecosystem health[J]. Polish Journal of Environmental Studies, 2020, 30(2):1749-1769 Peterson A, Soberón J. Essential biodiversity variables are not global[J]. Biodiversity and Conservation, 2018, 27:1277-1288 王浩. 水生态文明建设的理论基础及若干关键问题[J]. 中国水利, 2016(19):5-7 Wang H. Theoretical basis and key problems of water ecological civilization construction[J]. China Water Resources, 2016 (19):5-7(in Chinese)
Wang P Y, Yan Z G, Yang S W, et al. Environmental DNA:An emerging tool in ecological assessment[J]. Bulletin of Environmental Contamination and Toxicology, 2019, 103(5):651-656 Yang Y Z, Gao Y C, Huang X N, et al. Adaptive shifts of bacterioplankton communities in response to nitrogen enrichment in a highly polluted river[J]. Environmental Pollution, 2019, 245:290-299 Bastos Gomes G, Hutson K S, Domingos J A, et al. Use of environmental DNA (eDNA) and water quality data to predict protozoan parasites outbreaks in fish farms[J]. Aquaculture, 2017, 479:467-473 Peters L, Spatharis S, Dario M A, et al. Environmental DNA:A new low-cost monitoring tool for pathogens in salmonid aquaculture[J]. Frontiers in Microbiology, 2018, 9:3009 刘莹, 韩锰, 王文磊, 等. 高通量技术在微生物培养中的应用进展及分子测序对比分析[J]. 安徽农业科学, 2020, 48(15):16-19 Liu Y, Han M, Wang W L, et al. Application progress of high-throughput technology in microbial culture and comparative analysis of molecular sequencing[J]. Journal of Anhui Agricultural Sciences, 2020, 48(15):16-19(in Chinese)
Rojahn J, Pearce L, Gleeson D M, et al. The value of quantitative environmental DNA analyses for the management of invasive and endangered native fish[J]. Freshwater Biology, 2021, 66(8):1619-1629 Rees H, Maddison B, Middleditch D J, et al. The detection of aquatic animal species using environmental DNA-A review of eDNA as a survey tool in ecology[J]. Journal of Applied Ecology, 2014, 51:1450-1459 Cantera I, Decotte J B, Dejean T, et al. Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach[J]. Molecular Ecology Resources, 2022, 22(4):1274-1283 Itakura H, Wakiya R, Yamamoto S, et al. Environmental DNA analysis reveals the spatial distribution, abundance, and biomass of Japanese eels at the river-basin scale[J]. Aquatic Conservation Marine and Freshwater Ecosystems, 2019, 29(3):313-361 孙晶莹, 杨江华, 张效伟. 环境DNA(eDNA)宏条形码技术对枝角类浮游动物物种鉴定及其生物量监测研究[J]. 生态毒理学报, 2018, 13(5):76-86 Sun J Y, Yang J H, Zhang X W. Identification and biomass monitoring of zooplankton Cladocera species with eDNA metabarcoding technology[J]. Asian Journal of Ecotoxicology, 2018, 13(5):76-86(in Chinese)
Sepulveda A, Schmidt C, Amberg J, et al. Adding invasive species biosurveillance to the US Geological Survey streamgage network[J]. Ecosphere, 2019, 10(8):e02843 Stewart K A. Understanding the effects of biotic and abiotic factors on sources of aquatic environmental DNA[J]. Biodiversity and Conservation, 2019, 28(5):983-1001 Lacoursière-Roussel A, Rosabal M, Bernatchez L. Estimating fish abundance and biomass from eDNA concentrations:Variability among capture methods and environmental conditions[J]. Molecular Ecology Resources, 2016, 16(6):1401-1414 Francesco F G, Pierre T, Eric C. How to limit false positives in environmental DNA and metabarcoding?[J]. Molecular Ecology Resources, 2016, 16(3):604-607 Doi H, Fukaya K, Oka S I, et al. Evaluation of detection probabilities at the water-filtering and initial PCR steps in environmental DNA metabarcoding using a multispecies site occupancy model[J]. Scientific Reports, 2019, 9(1):3581 Tréguier A, Paillisson J M, Dejean T, et al. Environmental DNA surveillance for invertebrate species:Advantages and technical limitations to detect invasive crayfish "Procambarus clarkii" in freshwater ponds[J]. Journal of Applied Ecology, 2014, 51(4):871-879 Currier C A, Morris T J, Wilson C C, et al. Validation of environmental DNA (EDNA) as a Detection tool for at-risk freshwater pearly mussel species (Bivalvia:Unionidae)[J]. Aquatic Conservation:Marine and Freshwater Ecosystems, 2018, 28(3):545-558 Thomsen P F, Sigsgaard E E. Environmental DNA metabarcoding of wild flowers reveals diverse communities of terrestrial arthropods[J]. Ecology and Evolution, 2019, 9(4):1665-1679 Shogren A J, Tank J L, Andruszkiewicz E, et al. Controls on eDNA movement in streams:Transport, retention, and resuspension[J]. Scientific Reports, 2017, 7(1):5065 Carraro L, Hartikainen H, Jokela J, et al. Estimating species distribution and abundance in river networks using environmental DNA[J]. Proceedings of the National Academy of Sciences of the United States of America, 2018, 115(46):11724-11729 Beng K C, Corlett R T. Applications of environmental DNA (eDNA) in ecology and conservation:Opportunities, challenges and prospects[J]. Biodiversity and Conservation, 2020, 29(7):2089-2121 Rose J P, Wademan C, Weir S, et al. Traditional trapping methods outperform eDNA sampling for introduced semi-aquatic snakes[J]. PLoS One, 2019, 14(7):e0219244 Sales N G, Wangensteen O S, Carvalho D C, et al. Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding[J]. The Science of the Total Environment, 2021, 754:142096 -
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