基于eDNA metabarcoding探究北京市主要河流鱼类分布及影响因素

doi:10.17520/biods.2022240

生物多样性 ›› 2022, Vol. 30 ›› Issue (7): 22240. DOI: 10.17520/biods.2022240

• 研究报告: 动物多样性 • 上一篇下一篇

基于eDNA metabarcoding探究北京市主要河流鱼类分布及影响因素

沈梅¹, 郭宁宁¹, 罗遵兰¹, 郭晓晨², 孙光¹, 肖能文¹^,^*()

1.中国环境科学研究院, 北京 100012
2.山西农业大学林学院, 山西晋中 030801

收稿日期:2022-04-30 接受日期:2022-05-26 出版日期:2022-07-20 发布日期:2022-06-24
通讯作者: 肖能文
作者简介:*E-mail: xiaonw@163.com
基金资助:
巢湖生物资源调查及生态修复示范工程(2021BFFBZ01571-003-04)

Explore the distribution and influencing factors of fish in major rivers in Beijing with eDNA metabarcoding technology

Mei Shen¹, Ningning Guo¹, Zunlan Luo¹, Xiaochen Guo², Guang Sun¹, Nengwen Xiao¹^,^*()

1. State Environmental Protection Key Laboratory of Regional Eco-Process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012
2. College of Forestry, Shanxi Agricultural University, Jinzhong, Shanxi 030801

Received:2022-04-30 Accepted:2022-05-26 Online:2022-07-20 Published:2022-06-24
Contact: Nengwen Xiao

摘要/Abstract

摘要：

使用eDNA宏条形码(eDNA metabarcoding)和地笼法检测了北京市3条水系在夏季和秋季两个季节的鱼类多样性, 旨在研究北京市鱼类群落的空间格局特征, 探索适用于北京鱼类生物多样性监测及保护的新方法。结果表明: 在北京市的34个采样点中, 利用eDNA metabarcoding共检测出鱼类55种, 显著高于传统方法所捕获的鱼类种数(35种), 鱼类组成以鲤形目和鲈形目为主。山区河流清水鱼的多样性要显著高于城区河流, 城区河流(北运河水系)群落结构较为单一, 以鲫(Carassius auratus)、麦穗鱼(Pseudorasbora parva)、泥鳅(Misgurnus anguillicaudatus)等耐污种为优势种; 山区河流(潮白河水系及大清河水系)以宽鳍鱲(Zacco platypus)、拉氏鱥(Rhynchocypris lagowskii)、马口鱼(Opsariichthys uncirostris)等为优势种。不同季节影响清水鱼群落结构的环境因子不同, 夏季主要是总溶解固体和电导率, 秋季主要是海拔和温度。清水鱼丰富度与环境因子及人类活动的相关性表明, 清水鱼的丰富度随着总溶解固体及灯光指数增加而显著降低, 且均与海拔、温度等存在显著相关性。本研究证明了eDNA metabarcoding方法用于监测北京市鱼类多样性及其时空分布的可行性。

关键词: eDNA宏条形码, 鱼类群落, 清水鱼, 生物多样性, 河流

Abstract

Aims: We used eDNA metabarcoding to detect fish diversity in three river systems of Beijing during summer and autumn. The aim of this study is to explore new methods applicable to monitor and protect fish diversity and study the spatio-temporal patterns of fish community in Beijing.
Methods: A total of 34 sites were surveyed simultaneously using the eDNA metabarcoding and ground cage methods. The main processes of the eDNA method are water sample collection and enrichment, DNA extraction with DNeasy Tissue and Blood DNA, PCR amplification with prism of MiFish-U, high-throughput sequencing by Illumina Miseq and bioinformatics analysis. The data of eDNA metabarcoding, environmental factors and human activity were used for statistical analysis between fish communities and influencing factors. The main processes of the ground cage with three replications were placed at each site waiting 24 h to be collected for species identification, and the species with number were recorded for subsequent analysis.
Results: The result showed that 55 fish species were detected by eDNA metabarcoding was higher than that captured by the ground cage (35 species). The fish community composition was dominated by Cypriniformes and Perciformes. The diversity of clearwater fish in mountain rivers is significantly higher than urban rivers. Urban rivers (the Beiyun River System) were dominated by pollution-tolerant species such as Carassius auratus, Pseudorasbora parva and Misgurnus anguillicaudatus, with a relatively homogeneous community structure. Mountain rivers (Chaobai River System and Daqing River System) are dominated by Zacco platypus, Rhynchocypris lagowskii and Opsariichthys uncirostris. The community structure of clearwater fish was affected by electrical conductivity and total dissolved solids in summer but by altitude and temperature in autumn. The correlation between the abundance of clearwater fish with environmental factors and human activities showed that the abundance of clearwater fish decreased significantly with the increase by turbidity of water and human activities, and was significant correlation with altitude and temperature.
Conclusion: The study used eDNA metabarcoding to show the diversity and spatio-temporal patterns of major rivers in Beijing, with a focus on the distribution of clearwater fish. The results demonstrate the feasibility of eDNA metabarcoding for monitoring fish diversity and spatial-temporal distribution in Beijing.

Key words: eDNA metabarcoding, fish community, clearwater fish, biodiversity, river

沈梅, 郭宁宁, 罗遵兰, 郭晓晨, 孙光, 肖能文 (2022) 基于eDNA metabarcoding探究北京市主要河流鱼类分布及影响因素. 生物多样性, 30, 22240. DOI: 10.17520/biods.2022240.

Mei Shen, Ningning Guo, Zunlan Luo, Xiaochen Guo, Guang Sun, Nengwen Xiao (2022) Explore the distribution and influencing factors of fish in major rivers in Beijing with eDNA metabarcoding technology. Biodiversity Science, 30, 22240. DOI: 10.17520/biods.2022240.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2022240

https://www.biodiversity-science.net/CN/Y2022/V30/I7/22240

图/表 9

图1 北京市主要河流采样点分布图

Fig. 1 Distribution map of sampling sites of major rivers in Beijing

图2 eDNA metabarcoding识别鱼类物种在目和科分类学水平上的数量及所占比例

Fig. 2 Number and proportion of fish species identified by eDNA metabarcoding at the taxonomic level of order and family

图3 3条水系在秋、夏季节鱼类群落组成分布。红色圆点表示北运河水系; 绿色圆点表示潮白河水系; 蓝色圆点表示大清河水系。

Fig. 3 Distribution of fish communities in the three river systems during the autumn and summer. Red dots represent Beiyun River System; Green dots represent Chaobai River System; Blue dots represent Daqing River System.

表1 3条水系鱼类群落优势种的优势度指数

Table 1 Dominance index of dominant species in three river systems

北运河水系 Beiyun River System		潮白河水系 Chaobai River System		大清河水系 Daqing River System
物种 Species	优势度指数 Dominance index (Y)	物种 Species	优势度指数 Dominance index (Y)	物种 Species	优势度指数 Dominance index (Y)
鲫 Carassius auratus	0.5175	鲫 Carassius auratus	0.2556	宽鳍鱲 Zacco platypus	0.1517
麦穗鱼 Pseudorasbora parva	0.0888	拉氏鱥 Rhynchocypris lagowskii	0.1031	鲫 Carassius auratus	0.1475
小黄黝鱼 Micropercops swinhonis	0.0453	宽鳍鱲 Zacco platypus	0.0807	拉氏鱥 Rhynchocypris lagowskii	0.0968
泥鳅 Misgurnus anguillicaudatus	0.0448	鲇 Silurus asotus	0.0474	小黄黝鱼 Micropercops swinhonis	0.0540
高体鳑鲏 Rhodeus ocellatus	0.0345	子陵吻鰕虎鱼 Rhinogobius giurinus	0.0350	马口鱼 Opsariichthys uncirostris	0.0408
? Hemiculter leucisculus	0.0205	麦穗鱼 Pseudorasbora parva	0.0242	华鳈 Sarcocheilichthys sinensis	0.0406
-	-	-	-	褐吻鰕虎鱼 Rhinogobius brunneus	0.0400
-	-	-	-	子陵吻鰕虎鱼 Rhinogobius giurinus	0.0376
-	-	-	-	鲇 Silurus asotus	0.0340
-	-	-	-	北鳅 Lefua costata	0.0241
-	-	-	-	鲤 Cyprinus carpio	0.0233

表2 清水鱼在3条水系的检测的样点数情况

Table 2 Number of detected site of clearwater fish in each river system

物种 Species	样点数 Number of detected site
物种 Species	北运河水系 Beiyun River System	潮白河水系 Chaobai River System	大清河水系 Daqing River System	总计 Total
北方须鳅 Barbatula nuda	1	1	0	2
华鰁 Sarcocheilichthys sinensis	4	5	4	13
黄尾鲴 Xenocypris davidi	6	11	4	21
宽鳍鱲 Zacco platypus	7	9	6	22
拉氏鱥 Rhynchocypris lagowskii	9	9	6	24
马口鱼 Opsariichthys uncirostris	10	9	5	24
北鳅 Lefua costata	0	0	2	2
达里湖高原鳅 Triplophysa dalaica	0	3	2	5
鳜 Siniperca chuatsi	6	5	4	15
细鳞鲑 Brachymystax lenok	1	3	0	4

图4 34个点位清水鱼的序列丰度

Fig. 4 Sequence abundance of clearwater fish across 34 sampling sites

图5 北京市3条水系清水鱼α多样性检验

Fig. 5 α diversity of clearwater fish in three river systems of Beijing. * indicates P < 0.05, ns indicates P > 0.05。

图6 冗余分析(RDA)探究清水鱼群落结构与测量环境变量之间的关系。DO: 溶解氧; TDS: 总溶解固体; T: 温度; H: 海拔; EC: 电导率。黄色圆点表示北运河水系; 绿色圆点表示潮白河水系; 蓝色圆点表示大清河水系。

Fig. 6 RDA exploring the relationship between community structure and measured environmental variables. DO, Dissolved oxygen; TDS, Total dissolved solids; T, Temperature; H, Height; EC, Electrical conductivity。Yellow dots represent Beiyun River System; Green dots represent Chaobai River System; Blue dots represent Daqing River System.

图7 清水鱼丰富度与环境因子及灯光指数的相关性。H: 海拔; pH: 酸碱度; T: 温度;DO: 溶解氧; TDS: 总溶解固体; EC: 电导率; NL: 夜间灯光; a: 秋季; b: 夏季。

Fig. 7 Correlation of clearwater fish abundance with environmental factors and lighting indices. H, Height; pH, Potential of hydrogen; T, Temperature; DO, Dissolved oxygen; TDS, Total dissolved solids; EC, Electrical conductivity; NL, Night light; a, Autumn; b, Summer.

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基于eDNA metabarcoding探究北京市主要河流鱼类分布及影响因素

Explore the distribution and influencing factors of fish in major rivers in Beijing with eDNA metabarcoding technology

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