Application of environmental DNA in monitorining surface sediment and its relationship to environment variables
WEI Nan1,2,, WANG Xiahui1,,, ZHANG Chunpeng3 1.Chinese Academy of Environmental Planning, Ministry of Ecology and Environment, Beijing 100012, China 2.Department of Urban Engineering, The University of Tokyo, Tokyo 113-8656, Japan 3.Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, China
Abstract:Environmental DNA (eDNA) is an emerging tool for environmental and ecological monitoring in recent years. To clarify the effects of environment variables on the variation of eDNA in surface sediment, through the lab-scale experiments which could simulate marine environment and choose benthic organism Grandidierella japonica as target species with 4 groups of different bioabundance, the relationship between the variation of eDNA in surface sediment and ambient environment variables was investigated by using environmental DNA technology. After Grandidierella japonica were cultured for 4 days, and they were taken out from the experimental devices, then the following experiments start-up. The surface sediment samples and water samples were collected at 0, 6, 12, 18, 24, 72, 144, 264, 384 h from the start-up of the eperiments, the eDNA was extracted from these surface sediment samples and target eDNA copy numbers were determined by quantitative PCR with species-specific primers. The results showed that after removal of Grandidierella japonica, environmental DNA in surface sediment decreased to low level within 72 hours, which was similar to the decreasing characteristics of environmental DNA in water. The general linear modelling regression showed that the eDNA decay rate was significantly and negatively (P=0.000 5) related to the water salinity and significantly and positively (P=0.04) related to the pH value, indicating that environment DNA in surface sediment could reflect the changes of surrounding environment at a certain degree. This study provide a reference for promoting the application of eDNA and profoundly studying its effects on environment variables. Key words:environmental biomonitoring/ environmental DNA/ surface sediment/ environment variables/ benthic organism.
图1实验期间各实验组表层沉积物中环境DNA片段浓度的变化 Figure1.Variation of eDNA content in surface sediment during experimental period
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1.Chinese Academy of Environmental Planning, Ministry of Ecology and Environment, Beijing 100012, China 2.Department of Urban Engineering, The University of Tokyo, Tokyo 113-8656, Japan 3.Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun 130021, China Received Date: 2019-10-09 Accepted Date: 2020-03-01 Available Online: 2020-08-18 Keywords:environmental biomonitoring/ environmental DNA/ surface sediment/ environment variables/ benthic organism Abstract:Environmental DNA (eDNA) is an emerging tool for environmental and ecological monitoring in recent years. To clarify the effects of environment variables on the variation of eDNA in surface sediment, through the lab-scale experiments which could simulate marine environment and choose benthic organism Grandidierella japonica as target species with 4 groups of different bioabundance, the relationship between the variation of eDNA in surface sediment and ambient environment variables was investigated by using environmental DNA technology. After Grandidierella japonica were cultured for 4 days, and they were taken out from the experimental devices, then the following experiments start-up. The surface sediment samples and water samples were collected at 0, 6, 12, 18, 24, 72, 144, 264, 384 h from the start-up of the eperiments, the eDNA was extracted from these surface sediment samples and target eDNA copy numbers were determined by quantitative PCR with species-specific primers. The results showed that after removal of Grandidierella japonica, environmental DNA in surface sediment decreased to low level within 72 hours, which was similar to the decreasing characteristics of environmental DNA in water. The general linear modelling regression showed that the eDNA decay rate was significantly and negatively (P=0.000 5) related to the water salinity and significantly and positively (P=0.04) related to the pH value, indicating that environment DNA in surface sediment could reflect the changes of surrounding environment at a certain degree. This study provide a reference for promoting the application of eDNA and profoundly studying its effects on environment variables.
为探究环境变量对环境DNA含量变化的影响，本研究采用广义线性模型(general linear model，GLM)进行回归分析。假设环境DNA降解规律服从指数降解模型，以qPCR检测出的表层沉积物环境DNA片段含量在t时刻的降解速率(由指数降解模型求得[9])作为因变量，以环境变量中的生物丰度、总活菌量、pH、盐度、溶解氧作为自变量，缺失数据由前后2个时间点均值代替。由于水质电导率与盐度为相关非独立关系变量，因此，回归分析中未将电导率纳入自变量中。本研究所涉及的数据分析均在R语言(版本3.6.0)[16]及其集成开发环境R Studio[17]上进行。
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