Ecological health assessment of waters based on eDNA

  • WANG Hongwei ,
  • LU Canran ,
  • WANG Xi ,
  • ZHUANG Fengyu ,
  • YANG Likun
Expand
  • Institute of Life Science and Green Development, College of Life Sciences, Hebei University, Baoding 071002, China

Received date: 2024-03-21

  Online published: 2025-11-19

Abstract

In recent years, significant strides have been made in strengthening ecological conservation, fostering a synergistic balance between economic development and environmental protection. Notable improvements in water quality metrics have been observed, accompanied by a gradual restoration of aquatic ecosystem health. Conducting ecological health assessments is of paramount importance for accurately tracking the progress of aquatic ecosystem recovery. Rapid and effective biomonitoring of aquatic organisms serves as a prerequisite for understanding restoration trajectories and supporting sustainable management. Environmental DNA(eDNA)technology, which leverages trace nucleic acids in the environment to directly infer species presence and abundance, has emerged as a prominent and innovative approach. This article provides a systematic review of aquatic ecological health assessments utilizing eDNA technology, compares eDNA methods with traditional approaches, and elaborates on both the practical applications and limitations of eDNA techniques. Finally, we discuss future prospects for eDNA technology, aiming to offer insights and references for the advancement of ecological civilization.- DOI:10.3969/j.issn.1000-1565.2025.06.009基于eDNA的水体生态健康评价王宏伟,卢灿然,王玺,庄凤玉,杨丽坤 (河北大学 生命科学学院,生命科学与绿色发展研究院,河北 保定 071002 )摘 要:近年来,随着生态文明建设的加强,经济发展和环境保护双赢, 水质指标得到显著提升,水体健康状况正在逐渐恢复.开展生态健康评价对于更好地把握水生态系统恢复进程尤为重要. 快速、有效的水生生物监测是掌握恢复进程、支撑持续管理的前置条件. 环境DNA(environmental DNA,eDNA)技术借助环境微量核酸直接映射物种存在与丰度,已成为新兴主流手段. 本文系统综述了利用eDNA技术进行的水体生态健康评价,对比了eDNA技术与传统生态评价方法,详细阐述eDNA技术的实际应用及局限性, 并对eDNA技术的未来发展趋势进行展望,希望为生态文明建设提供参考和借鉴.关键词:eDNA;生物多样性;生态健康评价中图分类号:Q89 文献标志码:A 文章编号:1000-1565(2025)06-0637-07Ecological health assessment of waters based on eDNAWANG Hongwei, LU Canran, WANG Xi, ZHUANG Fengyu, YANG Likun(Institute of Life Science and Green Development,College of Life Sciences,Hebei University,Baoding 071002,China)Abstract: In recent years, significant strides have been made in strengthening ecological conservation, fostering a synergistic balance between economic development and environmental protection. Notable improvements in water quality metrics have been observed, accompanied by a gradual restoration of aquatic ecosystem health. Conducting ecological health assessments is of paramount importance for accurately tracking the progress of aquatic ecosystem recovery. Rapid and effective biomonitoring of aquatic organisms serves as a prerequisite for understanding restoration trajectories and supporting sustainable management. Environmental DNA(eDNA)technology, which leverages trace nucleic acids in the environment to directly infer species presence and abundance, has emerged as a prominent and innovative approach. This article provides a systematic review of aquatic ecological health assessments utilizing eDNA technology, compares eDNA methods with traditional approaches, and elaborates on both the practical applications and limitations of eDNA techniques. Finally, we discuss future prospects for eDNA technology, aiming to offer insights and references for the advancement of ecological civilization.- 收稿日期:2024-03-21;修回日期:2024-10-08 基金项目:河北省燕赵黄金台聚才计划骨干人才项目(留学回国平台项目)(C2024026);教育部留学回国基金项目(201808130270);河北省自然科学基金创新研究群体项目(C2022201042);河北省科技特派员项目(2024-2026);河北大学大学生创新创业训练计划项目(2023167;DC2025346);河北省自然科学基金项目(C2025201026) 第一作者:王宏伟(1970—),女,河北大学教授,博士,主要从事水生生物环境监测与保护方向的研究. E-mail:whw66668888@126.com 通信作者:杨丽坤(1982—),女,河北大学实验师,主要从事环境科学方向的研究.E-mail:holly66668888@126.com 第6期王宏伟等:基于eDNA的水体生态健康评价河北大学学报(自然科学版) 第45卷

Cite this article

WANG Hongwei , LU Canran , WANG Xi , ZHUANG Fengyu , YANG Likun . Ecological health assessment of waters based on eDNA[J]. Journal of Hebei University(Natural Science Edition), 2025 , 45(6) : 637 -643 . DOI: 10.3969/j.issn.1000-1565.2025.06.009

References

[1] 李翠萍,管运涛.环境DNA技术在水生态监测中的应用[J].低碳世界, 2023, 13(5): 10-12. DOI:10.16844/j.cnki.cn10-1007/tk.2023.05.054.
[2] 王宏伟,张伟,杨丽坤,等.中国河流健康评价体系[J]. 河北大学学报(自然科学版), 2011, 31(6): 668-672. DOI:10.3969/j.issn.1000-1565.2011.06.021.
[3] MARTINEZ-HARO M, BEIRAS R, BELLAS J, et al. A review on the ecological quality status assessment in aquatic systems using community based indicators and ecotoxicological tools: What might be the added value of their combination?[J]. Ecol Indic, 2015, 48: 8-16. DOI:10.1016/j.ecolind.2014.07.024.
[4] DÍAZ S, SETTELE J, BRONDÍZIO E S, et al. Pervasive human-driven decline of life on Earth points to the need for transformative change[J]. Science, 2019, 366(6471): eaax3100. DOI:10.1126/science.aax3100.
[5] 易雨君,叶敬旴,丁航,等.水生态评价方法研究进展及展望[J].湖泊科学, 2024, 36(3): 657-669. DOI:10.18307/2024.0300.
[6] VERHEES J J F, VAN DER PUTTEN T A W, VAN HOOF P H, et al. Comparing the effectiveness of short-focal camera trapping, live trapping, and soil eDNA for surveying small mammals: A case study on Eurasian water shrew(Neomys fodiens)[J]. Eur J Wildl Res, 2024, 70(1): 13. DOI:10.1007/s10344-023-01760-5.
[7] WYGAL B T, KRASINSKI K E, METCALFE J Z, et al. Archaeological recovery of late Pleistocene hair and environmental DNA from interior Alaska[J]. Environ Archaeol, 2024, 29(3): 265-280. DOI:10.1080/14614103.2022.2031836.
[8] 吴泳江,蔡明成,孙翰昌,等.环境DNA宏条形码在浮游动植物多样性研究中的应用[J].渔业研究, 2023, 45(4): 399-407. DOI:10.14012/j.cnki.fjsc.2023.04.010.
[9] SAHU A, KUMAR N, PAL SINGH C, et al. Environmental DNA(eDNA): Powerful technique for biodiversity conservation[J]. J Nat Conserv, 2023, 71: 126325. DOI:10.1016/j.jnc.2022.126325.
[10] CIVADE R, DEJEAN T, VALENTINI A, et al. Spatial representativeness of environmental DNA metabarcoding signal for fish biodiversity assessment in a natural freshwater system[J]. PLoS One, 2016, 11(6): e0157366. DOI:10.1371/journal.pone.0157366.
[11] 吕若萱,王秀华,李晨,等.环境DNA方法在水生动物疫病监测方面的应用[J].中国动物检疫, 2023, 40(3): 79-84. DOI:10.3969/j.issn.1005-944X.2023.03.014.
[12] 石大康.底栖动物在评价漓江水质污染中的作用[J].环境科学, 1985, 6(3): 54-58. DOI:10.13227/j.hjkx.1985.03.014.
[13] 廖延科,张萌,冯兵,等.基于P-IBI指数的修河中下游水生态健康评价[J].环境科学与技术, 2024, 47(2): 104-115. DOI:10.19672/j.cnki.1003-6504.2127.23.338.
[14] 王兴顺,张喜.河流健康及其水生生物评价方法研究[J].科技创新与应用, 2024, 14(5): 149-151. DOI:10.19981/j.CN23-1581/G3.2024.05.036.
[15] BREINE J, SIMOENS I, GOETHALS P, et al. A fish-based index of biotic integrity for upstream Brooks in Flanders(Belgium)[J]. Hydrobiologia, 2004, 522(1): 133-148. DOI:10.1023/B: HYDR.0000029991.42922.a4.
[16] 朱迪,陈锋,杨志,等.基于鱼类生物完整性指数的水源地评价[J].水生态学杂志, 2012, 33(2): 1-5. DOI:10.15928/j.1674-3075.2012.02.011.
[17] 沈强,俞建军,陈晖,等.浮游生物完整性指数在浙江水源地水质评价中的应用[J].水生态学杂志, 2012, 33(2): 26-31. DOI:10.15928/j.1674-3075.2012.02.013.
[18] BAPTISTA D F, BUSS D F, EGLER M, et al. A multimetric index based on benthic macroinvertebrates for evaluation of Atlantic Forest streams at Rio de Janeiro State, Brazil[J]. Hydrobiologia, 2007, 575(1): 83-94. DOI:10.1007/s10750-006-0286-x.
[19] NEFFINGER A J, BREAUX N J, MARGO A D, et al. Developing a bioassessment framework to inform tidal stream management along a hydrologically variable coast[J]. Ecol Indic, 2024, 160: 111804. DOI:10.1016/j.ecolind.2024.111804.
[20] 曹家乐,张亚辉,张瑾,等.国内外水生态健康评价研究进展[J].环境工程技术学报, 2022, 12(5): 1402-1410. DOI:10.12153/j.issn.1674-991X.20210425.
[21] 彭斌,顾森,赵晓晨,等.广西河流水生态安全评价指标体系探究[J].中国水利, 2016(3): 46-49. DOI:10.3969/j.issn.1000-1123.2016.03.018.
[22] 孙徐阳,李卫明,粟一帆,等.香溪河流域水生态系统健康评价[J].环境科学研究, 2021, 34(3): 599-606. DOI:10.13198/j.issn.1001-6929.2020.06.27.
[23] 李晓玲,刘洋,王丛丛,等.基于环境DNA技术的夏季东海鱼类物种多样性研究[J].海洋学报, 2022, 44(4): 74-84.
[24] ZHANG C X, LIU H J, WANG S P, et al. An advanced early warning technology for coral bleaching crisis based on the electrochemical biosensing of coral-symbiotic zooxanthellae eDNA[J]. Microchem J, 2024, 207: 111775. DOI:10.1016/j.microc.2024.111775.
[25] 蒋佩文,李敏,张帅,等.基于环境DNA宏条码和底拖网的珠江河口鱼类多样性[J].水生生物学报, 2022, 46(11): 1701-1711. DOI:10.7541/2022.2021.0265.
[26] 吕嘉诚,林渊源,李爱军,等.基于环境DNA宏条形码的柴河浮游藻类研究[J].环境科学导刊, 2022, 41(6): 1-7. DOI:10.13623/j.cnki.hkdk.2022.06.003.
[27] PRIETO A E, HARDION L, DEBORTOLI N, et al. A comparative analysis of eDNA metabarcoding and field surveys: Exploring freshwater plant communities in rivers[J]. Sci Total Environ, 2024, 954: 176200. DOI:10.1016/j.scitotenv.2024.176200.
[28] 卢依雯,张璐,李海玲,等.环境DNA技术在环境监测与动物生产管理中的应用进展[J].环境监测管理与技术, 2023, 35(3): 11-16. DOI:10.19501/j.cnki.1006-2009.2023.03.013.
[29] MATHON L, BALETAUD F, LEBOURGES-DHAUSSY A, et al. Three-dimensional conservation planning of fish biodiversity metrics to achieve the deep-sea 30 × 30 conservation target[J]. Conserv Biol, 2025, 39(2): e14368. DOI:10.1111/cobi.14368.
[30] SATO Y, TSURUI-SATO K, UCHIMA Y, et al. A systematic survey of environmental DNA in Palau’s lakes and waterfalls reveals an increase in Leptospira levels after flooding[J]. One Health, 2024, 19: 100898. DOI:10.1016/j.onehlt.2024.100898.
[31] TIMANA-MENDOZA C, REYES-CALDERON A, VENAIL P, et al. Assessing fish diversity in abandoned mining ponds in Madre de Dios, Peru, using environmental DNA[J]. Environ DNA, 2024, 6(1): e520. DOI:10.1002/edn3.520.
[32] MVULA A, SAWADA H, YAMANAKA H, et al. Identifying migration hotspots of the potamodromous fish Opsariichthys uncirostris in Lake Biwa tributaries using environmental DNA and visual counts during its reproductive season[J]. Ecol Res, 2024, 39(2): 228-241. DOI:10.1111/1440-1703.12433.
[33] 李冰,冯秀,朱仁,等.雅鲁藏布江中游拉萨裸裂尻鱼环境DNA检测及生物量评估[J].水生态学杂志, 2024, 45(2): 84-91. DOI:10.15928/j.1674-3075.202201120016.
[34] WANG S P, YAN Z G, HÄNFLING B, et al. Methodology of fish eDNA and its applications in ecology and environment[J]. Sci Total Environ, 2021, 755: 142622. DOI:10.1016/j.scitotenv.2020.142622.
[35] THOMSEN P F, KIELGAST J, IVERSEN L L, et al. Detection of a diverse marine fish fauna using environmental DNA from seawater samples[J]. PLoS One, 2012, 7(8): e41732. DOI:10.1371/journal.pone.0041732.
[36] MIYA M, SATO Y, FUKUNAGA T, et al. MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: Detection of more than 230 subtropical marine species[J]. R Soc Open Sci, 2015, 2(7): 150088. DOI:10.1098/rsos.150088.
[37] 徐念,常剑波.长江中下游干流环境DNA样本鱼类物种检测的初步研究[J].水生态学杂志, 2016, 37(5): 49-55. DOI:10.15928/j.1674-3075.2016.05.007.
[38] 梁绪虹,王丛丛,刘洋,等.基于环境DNA技术的黑潮-亲潮交汇区夏季鱼类物种多样性分析[J].上海海洋大学学报, 2024, 33(4): 911-926. DOI:10.12024/jsou.20230904320.
[39] LI W H, SONG T J, HOU X L, et al. Application of eDNA metabarcoding for detecting anura on a tropical island[J]. Diversity, 2021, 13(9): 440. DOI:10.3390/d13090440.
[40] 杨海乐,杜浩,祁洪芳,等.青藏高原沙柳河流域自然径流驱动的流域生物信息流量化特征:以环境微生物为指标[J].生态学报, 2021, 41(9): 3475-3487.
[41] 王萌,金小伟,林晓龙,等.基于环境DNA-宏条形码技术的底栖动物监测及水质评价研究进展[J].生态学报, 2021, 41(18): 7440-7453. DOI:10.5846/stxb202009162411.
[42] 张迪涛,张鹏,王司阳,等.基于微生物完整性指数的水生态系统健康评价:以武汉市东西湖区湖泊群为例[J].中国环境科学, 2023, 43(6): 3055-3067. DOI:10.19674/j.cnki.issn1000-6923.20230104.008.
[43] ZHANG M L, ZOU Y T, XIAO S, et al. Environmental DNA metabarcoding serves as a promising method for aquatic species monitoring and management: A review focused on its workflow, applications, challenges and prospects[J]. Mar Pollut Bull, 2023, 194: 115430. DOI:10.1016/j.marpolbul.2023.115430.
[44] LEESE F, BOUCHEZ A, ABARENKOV K, et al. Why we need sustainable networks bridging countries, disciplines, cultures and generations for aquatic biomonitoring 2.0: A perspective derived from the DNAqua-Net COST action[M] //Advances in ecological research,Academic Press, 2018,58: 63-99. DOI:10.1016/bs.aecr.2018.01.001.
[45] 王玉蓉,文茄汀,张建民.eDNA技术及其在河流生态系统的研究进展[J].水力发电学报, 2020, 39(5): 90-98. DOI:10.11660/slfdxb.20200509.
[46] EICHMILLER J J, BAJER P G, SORENSEN P W. The relationship between the distribution of common carp and their environmental DNA in a small lake[J]. PLoS One, 2014, 9(11): e112611. DOI:10.1371/journal.pone.0112611.
[47] SHOGREN A J, TANK J L, ANDRUSZKIEWICZ E, et al. Controls on eDNA movement in streams: Transport, retention, and resuspension[J]. Sci Rep, 2017, 7(1): 5065. DOI:10.1038/s41598-017-05223-1.
[48] 李苗,陈小勇.环境DNA技术在鱼类生态学中的应用研究进展[J].生态学报, 2023, 43(17): 6951-6967. DOI:10.20103/j.stxb.202208172362.
[49] JO T S, SASAKI Y. Evaluating the quantitative performance of environmental DNA metabarcoding for freshwater zooplankton community: A case study in Lake Biwa, Japan[J]. Environ Sci Pollut Res, 2024, 31(47): 58069-58082. DOI:10.1007/s11356-024-35025-8. (
Outlines

/

〈 〉