环境DNA(eDNA)技术作为新兴生物多样性监测方法,具有非侵入性、高效性及灵敏性的特点.为探究基于宏基因组测序的eDNA技术对喀斯特湖泊硅藻监测的适用性,以贵州草海为例,采集草海湖滨带的水样及表层沉积物样品,运用宏基因组学与eDNA相结...环境DNA(eDNA)技术作为新兴生物多样性监测方法,具有非侵入性、高效性及灵敏性的特点.为探究基于宏基因组测序的eDNA技术对喀斯特湖泊硅藻监测的适用性,以贵州草海为例,采集草海湖滨带的水样及表层沉积物样品,运用宏基因组学与eDNA相结合的方法,分析浮游及沉积硅藻的群落组成、生物多样性及KEGG代谢功能.结果表明:①草海硅藻群落共注释到4纲23目36科54属78种,在科分类阶元上以舟形藻科和海链藻科为优势类群.硅藻群落的Chao1指数平均值为42.88±15.35,Shannon-Wiener指数平均值为2.09±0.29.②硅藻群落KEGG通路功能最具代表性的是全局和概述图谱(global and overview maps),其次是能量代谢、翻译;优势KO基因主要为atpF基因、secA基因、rplT基因、rpoA基因、argH基因.③主坐标分析(PCoA)和相似性分析(ANOSIM)表明硅藻群落存在显著的环境介质差异;LEfSe分析揭示浮游硅藻群落的差异标志物主要为海链藻属(Thalassiosira)、小环藻属(Cyclotella),沉积硅藻主要是管状藻属(Fistulifera)、褐指藻属(Phaeodactylum)、微壳藻属(Nanofrustulum)等;Wilcoxon秩和检验表明,浮游硅藻的差异基因集中在叶酸生物合成通路、嘧啶代谢,沉积硅藻的差异基因集中在光合作用、氧化磷酸化等代谢功能.研究显示,高灵敏性的eDNA宏基因组技术能有效描述草海湖泊硅藻群落及多样性,在喀斯特湖泊生物多样性监测及水生态环境健康评估具有广阔的应用前景.展开更多
Environmental DNA(eDNA)has been used as an important tool for fish diversity analysis,which can greatly solve the problems in traditional survey methodology.However,little work has been done on the actual monitoring a...Environmental DNA(eDNA)has been used as an important tool for fish diversity analysis,which can greatly solve the problems in traditional survey methodology.However,little work has been done on the actual monitoring accuracy of eDNA.In this study,we analyzed the current status of fish resources in Erhai Lake in Yunnan,SW China,by dividing the lake into three sectors according to habitat differences,and compared the results of eDNA and traditional capture methods to investigate the shortcomings of the current analysis of eDNA results.A total of 27 fish species were detected by eDNA and traditional capture methods,including 20 and 19 fish species,respectively,and additional differences in fish composition between the two methods.The alpha diversity showed higher fish abundance and lower fish diversity by eDNA method compared to the traditional capture method,demonstrating that eDNA was not superior for use in fish diversity analysis.Fish community similarity analysis showed that community differences were generally significant for eDNA(P<0.05).RDA analysis indicated that environmental factors did not significantly affect fish communities monitored by the eDNA method.However,water temperature,aquatic plants,and water depth had significant(P<0.05)effects on fish communities in the traditional capture method,suggesting that eDNA results are insensitive to the effects of environmental factors.Our results illustrate the effectiveness of eDNA in fish identification and the issues in quantification compared to traditional capture methods.Therefore,combining eDNA with traditional methods is a more effective method for analyzing eDNA metabarcoding,following which the protocols of both quantitative methods can be designed to explore the regularity of eDNA quantification.展开更多
利用环境DNA宏条形码(environmental DNA metabarcoding;eDNA metabarcoding)检测长江上游珍稀特有鱼类国家级自然保护区重庆段鱼类多样性,探索适用于长江鱼类多样性监测和保护的新方法,为后期长江“十年禁渔”效果评估提供一定的基础...利用环境DNA宏条形码(environmental DNA metabarcoding;eDNA metabarcoding)检测长江上游珍稀特有鱼类国家级自然保护区重庆段鱼类多样性,探索适用于长江鱼类多样性监测和保护的新方法,为后期长江“十年禁渔”效果评估提供一定的基础资料。研究于2021年3月在保护区重庆段共设置6个采样点,通过水样采集、eDNA捕获及提取、PCR扩增及测序和数据库对比分析等环境DNA宏条形码标准化分析流程来检测鱼类的多样性组成。结果表明保护区重庆段6个采样点中共检测出74种鱼类(不包括未鉴定到种水平的3属),隶属于6目16科52属,其中国家级保护鱼类2种,长江上游特有鱼类10种,重庆市重点保护鱼类1种,外来物种8种。鲤属(Cyprinus)、鲫属(Carassius)、草鱼属(Ctenopharyngodon)和黄颡鱼属(Tachysurus)在各采样点均被检测到且为优势种。各样点鱼类组成的Alpha和Beta多样性的各项指数差异不大,表明保护区鱼类的生态结构较为均衡和稳定。总体上,在现阶段的长江流域鱼类资源监测中,可根据监测任务的需要,将环境DNA技术与传统的监测方法结合使用,用于快速调查长江流域鱼类的多样性组成及分布等。展开更多
[目的]建立高效实用的水样环境DNA提取方案。[方法]采用滤膜法和沉淀法对2个不同大小的水域进行eDNA提取并对所获得的eDNA进行PCR扩增。其中,滤膜法设置50、100、200 mL 3个水样体积试验组,每组3个平行;沉淀法设置10、20、40 mL 3个水...[目的]建立高效实用的水样环境DNA提取方案。[方法]采用滤膜法和沉淀法对2个不同大小的水域进行eDNA提取并对所获得的eDNA进行PCR扩增。其中,滤膜法设置50、100、200 mL 3个水样体积试验组,每组3个平行;沉淀法设置10、20、40 mL 3个水样体积试验组,每组3个平行。[结果]大型水塘水样经滤膜法处理后获得的eDNA浓度更高;小型水池采用滤膜法和大型水塘采用沉淀法处理水样后经PCR检测可获得更明显的扩增结果。[结论]该研究建立的滤膜法和沉淀法可用于不同水环境eDNA的提取。展开更多
文摘环境DNA(eDNA)技术作为新兴生物多样性监测方法,具有非侵入性、高效性及灵敏性的特点.为探究基于宏基因组测序的eDNA技术对喀斯特湖泊硅藻监测的适用性,以贵州草海为例,采集草海湖滨带的水样及表层沉积物样品,运用宏基因组学与eDNA相结合的方法,分析浮游及沉积硅藻的群落组成、生物多样性及KEGG代谢功能.结果表明:①草海硅藻群落共注释到4纲23目36科54属78种,在科分类阶元上以舟形藻科和海链藻科为优势类群.硅藻群落的Chao1指数平均值为42.88±15.35,Shannon-Wiener指数平均值为2.09±0.29.②硅藻群落KEGG通路功能最具代表性的是全局和概述图谱(global and overview maps),其次是能量代谢、翻译;优势KO基因主要为atpF基因、secA基因、rplT基因、rpoA基因、argH基因.③主坐标分析(PCoA)和相似性分析(ANOSIM)表明硅藻群落存在显著的环境介质差异;LEfSe分析揭示浮游硅藻群落的差异标志物主要为海链藻属(Thalassiosira)、小环藻属(Cyclotella),沉积硅藻主要是管状藻属(Fistulifera)、褐指藻属(Phaeodactylum)、微壳藻属(Nanofrustulum)等;Wilcoxon秩和检验表明,浮游硅藻的差异基因集中在叶酸生物合成通路、嘧啶代谢,沉积硅藻的差异基因集中在光合作用、氧化磷酸化等代谢功能.研究显示,高灵敏性的eDNA宏基因组技术能有效描述草海湖泊硅藻群落及多样性,在喀斯特湖泊生物多样性监测及水生态环境健康评估具有广阔的应用前景.
基金Supported by the Project of Basic Investigation on Ecological Environment Quality of Erhai Lake(No.TPDL-2021-C 265)the Ecological Effects,Population Regulation and Management Strategies of Invasion of Japanese Smelt(Hypomesus nipponensis)in Erhai Lake funded by the government of Dali City,Yunnan Province,China(No.[2018]447)。
文摘Environmental DNA(eDNA)has been used as an important tool for fish diversity analysis,which can greatly solve the problems in traditional survey methodology.However,little work has been done on the actual monitoring accuracy of eDNA.In this study,we analyzed the current status of fish resources in Erhai Lake in Yunnan,SW China,by dividing the lake into three sectors according to habitat differences,and compared the results of eDNA and traditional capture methods to investigate the shortcomings of the current analysis of eDNA results.A total of 27 fish species were detected by eDNA and traditional capture methods,including 20 and 19 fish species,respectively,and additional differences in fish composition between the two methods.The alpha diversity showed higher fish abundance and lower fish diversity by eDNA method compared to the traditional capture method,demonstrating that eDNA was not superior for use in fish diversity analysis.Fish community similarity analysis showed that community differences were generally significant for eDNA(P<0.05).RDA analysis indicated that environmental factors did not significantly affect fish communities monitored by the eDNA method.However,water temperature,aquatic plants,and water depth had significant(P<0.05)effects on fish communities in the traditional capture method,suggesting that eDNA results are insensitive to the effects of environmental factors.Our results illustrate the effectiveness of eDNA in fish identification and the issues in quantification compared to traditional capture methods.Therefore,combining eDNA with traditional methods is a more effective method for analyzing eDNA metabarcoding,following which the protocols of both quantitative methods can be designed to explore the regularity of eDNA quantification.
文摘利用环境DNA宏条形码(environmental DNA metabarcoding;eDNA metabarcoding)检测长江上游珍稀特有鱼类国家级自然保护区重庆段鱼类多样性,探索适用于长江鱼类多样性监测和保护的新方法,为后期长江“十年禁渔”效果评估提供一定的基础资料。研究于2021年3月在保护区重庆段共设置6个采样点,通过水样采集、eDNA捕获及提取、PCR扩增及测序和数据库对比分析等环境DNA宏条形码标准化分析流程来检测鱼类的多样性组成。结果表明保护区重庆段6个采样点中共检测出74种鱼类(不包括未鉴定到种水平的3属),隶属于6目16科52属,其中国家级保护鱼类2种,长江上游特有鱼类10种,重庆市重点保护鱼类1种,外来物种8种。鲤属(Cyprinus)、鲫属(Carassius)、草鱼属(Ctenopharyngodon)和黄颡鱼属(Tachysurus)在各采样点均被检测到且为优势种。各样点鱼类组成的Alpha和Beta多样性的各项指数差异不大,表明保护区鱼类的生态结构较为均衡和稳定。总体上,在现阶段的长江流域鱼类资源监测中,可根据监测任务的需要,将环境DNA技术与传统的监测方法结合使用,用于快速调查长江流域鱼类的多样性组成及分布等。
文摘[目的]建立高效实用的水样环境DNA提取方案。[方法]采用滤膜法和沉淀法对2个不同大小的水域进行eDNA提取并对所获得的eDNA进行PCR扩增。其中,滤膜法设置50、100、200 mL 3个水样体积试验组,每组3个平行;沉淀法设置10、20、40 mL 3个水样体积试验组,每组3个平行。[结果]大型水塘水样经滤膜法处理后获得的eDNA浓度更高;小型水池采用滤膜法和大型水塘采用沉淀法处理水样后经PCR检测可获得更明显的扩增结果。[结论]该研究建立的滤膜法和沉淀法可用于不同水环境eDNA的提取。
