基于环境DNA宏条形码技术研究黄河三角洲典型潮沟系统鱼类多样性及其对水文连通性的响应

doi:10.17520/biods.2023073

生物多样性 ›› 2023, Vol. 31 ›› Issue (7): 23073. DOI: 10.17520/biods.2023073

• 研究报告: 动物多样性 • 上一篇下一篇

基于环境DNA宏条形码技术研究黄河三角洲典型潮沟系统鱼类多样性及其对水文连通性的响应

董志远¹^,², 陈琳琳¹^,², 张乃鹏⁴, 陈莉¹^,³, 孙德斌¹^,², 倪艳梅¹^,³, 李宝泉¹^,²^,^*()

1.中国科学院烟台海岸带研究所海岸带生物学与生物资源保护实验室, 山东烟台 264003
2.中国科学院大学, 北京 100049
3.烟台大学海洋学院, 山东烟台 264003
4.东营市水文中心, 山东东营 257000

收稿日期:2023-03-09 接受日期:2023-04-18 出版日期:2023-07-20 发布日期:2023-04-26
通讯作者: *E-mail: bqli@yic.ac.cn
作者简介:*E-mail: bqli@yic.ac.cn
基金资助:
国家自然科学基金(42176160);国家自然科学基金(42276142);山东省自然科学基金(ZR2021MD084);中国科学院A类战略性先导科技专项(XDA23050202)

Response of fish diversity to hydrological connectivity of typical tidal creek system in the Yellow River Delta based on environmental DNA metabarcoding

Zhiyuan Dong¹^,², Linlin Chen¹^,², Naipeng Zhang⁴, Li Chen¹^,³, Debin Sun¹^,², Yanmei Ni¹^,³, Baoquan Li¹^,²^,^*()

1. Key Laboratory of Coastal Biology and Bioresource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong 264003
2. University of Chinese Academy of Sciences, Beijing 100049
3. School of Ocean, Yantai University, Yantai, Shandong 264003
4. Dongying Municipal Hydrology Center, Dongying, Shandong 257000

Received:2023-03-09 Accepted:2023-04-18 Online:2023-07-20 Published:2023-04-26
Contact: *E-mail: bqli@yic.ac.cn

摘要/Abstract

摘要：

水文连通对于维护滨海湿地生物多样性至关重要, 鱼类多样性作为生物多样性的重要组成部分, 了解其对不同水文连通强度的响应具有重要意义。本研究基于环境DNA宏条形码技术(eDNA metabarcoding)检测黄河三角洲典型潮沟系统鱼类多样性, 分析鱼类物种分布对不同水文连通强度潮沟生境差异的响应特征。利用12S rRNA经典鱼类引物对采集自三级潮沟系统的水样进行高通量测序, 共检测出鱼类55种, 其中本地鱼类27种、非本地鱼类28种, 物种组成以鲈形目为主。各样点序列丰度均较高的鱼类有矛尾刺虾虎鱼(Acanthogobius hasta)、鮻(Planiliza haematocheilus)、长体刺虾虎鱼(Acanthogobius elongatus)等。鱼类多样性在不同水文连通性潮沟间差异明显, 其中, 二级潮沟群落多样性水平、丰富度指数、物种种类及各种鱼类类群中的个体均匀程度等都明显高于其他两级潮沟。RDA分析显示有6种环境因子与鱼类群落结构显著相关(P < 0.05), 分别为: 硅酸盐(SiO₃^2--Si)、硝酸盐(NO₃^--N)、酸碱度(pH值)、盐度(SAL)、铵盐(NH₄⁺-N)、溶解氧(DO)。其中, 优势种矛尾刺虾虎鱼的序列丰度与硅酸盐呈正相关, 鮻的序列丰度与盐度呈负相关。本研究通过与传统采样数据进行比较, 证实了环境DNA宏条形码技术用于监测黄河口典型潮沟水体中鱼类多样性的可行性, 表明潮沟系统水文连通性对鱼类群落结构及多样性均具有明显的影响, 研究结果有助于进一步了解滨海湿地水文连通对生物群落的影响机制。

关键词: 环境DNA宏条形码, 鱼类多样性, 水文连通, 黄河三角洲, 潮沟系统

Abstract

Aims: Hydrological connectivity is essential for maintaining biodiversity in coastal wetlands, and it is important to understand the response of fish diversity, as a major component of biodiversity, to different hydrological connectivity intensities. This study aimed to investigate the response of fish diversity to hydrological connectivity in the typical tidal creek system and verify the applicability of eDNA metabarcoding for monitoring and conserving fish diversity in the Yellow River Delta.

Methods: Water samples were collected from six sites in a typical tidal creek system in the Yellow River Delta in September 2022. Fish diversity was analyzed by using eDNA metabarcoding, in which, eDNA extracted from the water samples source were amplified by PCR using the 12S rRNA classical fish primers MiFish-E and high-throughput sequencing was performed by Illumina Miseq. The OTU representative sequences were aligned to the NCBI nucleotide sequence database to obtain species taxonomic annotation information. Thirteen environmental physicochemical indicators were measured in the water column. The relationship between fish communities and environmental factors was explored based on redundancy analysis.

Results: A total of 55 fish species were detected, including 27 native and 28 non-native fish species, and Perciformes dominated the fish composition. The fishes with high sequence abundance at each sample site included Acanthogobius hasta, Planiliza haematocheilu, Acanthogobius elongatus, etc. Fish diversity of the tidal creeks with different hydrological connectivity was different. Significantly higher community diversity and richness index, the highest number of species and a more even distribution of the number of individual species were found in the secondary tidal creek than in the other two tidal creeks. SiO₃^2--Si, NO₃^--N, pH, salinity, NH₄⁺-N, and dissolved oxygen were significantly correlated (P < 0.05) with fish community structure shown by RDA analysis. Acanthogobius hasta with higher sequence abundance was positively correlated with silicate, and the sequence abundance of Planiliza haematocheilus was negatively correlated with salinity.

Conclusion: This study confirmed the feasibility of using environmental DNA metabarcoding to monitor fish diversity of typical tidal water bodies in the Yellow River estuary by comparing it with previous traditional sampling data and indicated that hydrological connectivity of tidal creek systems has a significant impact on fish community structure and diversity. The results of this study are helpful to further understand the influence mechanism of coastal wetland hydrological connectivity on biological communities.

Key words: environmental DNA metabarcoding, fish diversity, hydrological connectivity, the Yellow River Delta, tidal creek system

董志远, 陈琳琳, 张乃鹏, 陈莉, 孙德斌, 倪艳梅, 李宝泉 (2023) 基于环境DNA宏条形码技术研究黄河三角洲典型潮沟系统鱼类多样性及其对水文连通性的响应. 生物多样性, 31, 23073. DOI: 10.17520/biods.2023073.

Zhiyuan Dong, Linlin Chen, Naipeng Zhang, Li Chen, Debin Sun, Yanmei Ni, Baoquan Li (2023) Response of fish diversity to hydrological connectivity of typical tidal creek system in the Yellow River Delta based on environmental DNA metabarcoding. Biodiversity Science, 31, 23073. DOI: 10.17520/biods.2023073.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2023073

https://www.biodiversity-science.net/CN/Y2023/V31/I7/23073

图/表 9

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变量 Variable	潮沟级别 Tidal creek level
变量 Variable	一级潮沟 The first-class tidal creek (S1)	二级潮沟 The second-class tidal creek (S2)	三级潮沟 The third-class tidal creek (S3)
总氮 TN (μg/L)	351.893 ± 4.857^b	361.896 ± 11.934^ab	389.191 ± 19.168^a
总磷 TP (μg/L)	15.116 ± 1.175^a	12.586 ± 0.580^b	14.975 ± 0.715^a
磷酸盐 PO₄^3--P (mg/L)	0.033 ± 0.029^a	0.008 ± 0.002^ab	0.004 ± 0.001^b
铵盐 NH₄⁺-N (mg/L)	0.039 ± 0.012^a	0.036 ± 0.004^a	0.170 ± 0.121^b
亚硝酸盐 NO₂^--N (mg/L)	0.019 ± 0.003^b	0.024 ± 0.004^ab	0.027 ± 0.004^a
硅酸盐 SiO₃^2--Si (mg/L)	0.675 ± 0.052^b	0.690 ± 0.107^ab	0.964 ± 0.222^a
硝酸盐 NO₃^--N (mg/L)	0.265 ± 0.041^a	0.238 ± 0.018^a	0.193 ± 0.017^b
温度 T (℃)	21.800 ± 1.595^b	21.450 ± 0.321^b	26.233 ± 2.850^a
溶解氧 DO (mg/L)	7.998 ± 0.804^a	6.692 ± 0.315^b	6.067 ± 1.143^b
电导率 SPC (ms/cm)	26.412 ± 0.245^b	32.538 ± 1.752^ab	36.300 ± 1.715^a
盐度 SAL	16.185 ± 0.170^b	20.362 ± 1.202^ab	22.903 ± 1.121^a
酸碱度 pH	8.408 ± 0.012^a	8.385 ± 0.021^ab	8.248 ± 0.026^b
氧化还原电位 Eh	-71.950 ± 1.104^a	-70.583 ± 1.087^a	-64.033 ± 1.219^b

变量 Variable	潮沟级别 Tidal creek level
变量 Variable	一级潮沟 The first-class tidal creek (S1)	二级潮沟 The second-class tidal creek (S2)	三级潮沟 The third-class tidal creek (S3)
总氮 TN (μg/L)	351.893 ± 4.857^b	361.896 ± 11.934^ab	389.191 ± 19.168^a
总磷 TP (μg/L)	15.116 ± 1.175^a	12.586 ± 0.580^b	14.975 ± 0.715^a
磷酸盐 PO₄^3--P (mg/L)	0.033 ± 0.029^a	0.008 ± 0.002^ab	0.004 ± 0.001^b
铵盐 NH₄⁺-N (mg/L)	0.039 ± 0.012^a	0.036 ± 0.004^a	0.170 ± 0.121^b
亚硝酸盐 NO₂^--N (mg/L)	0.019 ± 0.003^b	0.024 ± 0.004^ab	0.027 ± 0.004^a
硅酸盐 SiO₃^2--Si (mg/L)	0.675 ± 0.052^b	0.690 ± 0.107^ab	0.964 ± 0.222^a
硝酸盐 NO₃^--N (mg/L)	0.265 ± 0.041^a	0.238 ± 0.018^a	0.193 ± 0.017^b
温度 T (℃)	21.800 ± 1.595^b	21.450 ± 0.321^b	26.233 ± 2.850^a
溶解氧 DO (mg/L)	7.998 ± 0.804^a	6.692 ± 0.315^b	6.067 ± 1.143^b
电导率 SPC (ms/cm)	26.412 ± 0.245^b	32.538 ± 1.752^ab	36.300 ± 1.715^a
盐度 SAL	16.185 ± 0.170^b	20.362 ± 1.202^ab	22.903 ± 1.121^a
酸碱度 pH	8.408 ± 0.012^a	8.385 ± 0.021^ab	8.248 ± 0.026^b
氧化还原电位 Eh	-71.950 ± 1.104^a	-70.583 ± 1.087^a	-64.033 ± 1.219^b

样品名称 Sample name	序列条数 Sequences	碱基数 Bases (bp)	平均读长 Average length (bp)
S1S	500,311	85,254,665	170.40
S1X	500,256	84,418,677	168.75
S2S	471,672	80,731,476	171.16
S2X	479,424	81,634,922	170.28
S3S	556,415	93,868,748	168.70
S3X	614,037	103,314,806	168.26

样品名称 Sample name	序列条数 Sequences	碱基数 Bases (bp)	平均读长 Average length (bp)
S1S	500,311	85,254,665	170.40
S1X	500,256	84,418,677	168.75
S2S	471,672	80,731,476	171.16
S2X	479,424	81,634,922	170.28
S3S	556,415	93,868,748	168.70
S3X	614,037	103,314,806	168.26

	目 Order	科 Family	种 Species
本地鱼类物种	鲽形目 Pleuronectiformes	舌鳎科 Cynoglossidae	短吻红舌鳎 Cynoglossus joyneri
Native fish species	鲱形目 Clupeiformes	鲱科 Dorosomatidae	青鳞小沙丁鱼 Sardinella zunasi
			斑鰶 Konosirus punctatus
		鳀科 Engraulidae	赤鼻棱鳀 Thryssa kammalensis
			鳀 Engraulis japonicus
			凤鲚 Coilia mystus
	颌针鱼目 Beloniforme	鱵科 Hemiramphidae	间下鱵 Hyporhamphus intermedius
	胡瓜鱼目 Osmeriformes	胡瓜鱼科 Osmeridae	西太公鱼 Hypomesus nipponensis
	鲈形目 Perciformes	花鲈科 Lateolabracidae	花鲈 Lateolabrax japonicus
		蓝子鱼科 Siganidae	褐蓝子鱼 Siganus fuscescens
		鲹科 Carangidae	吉打副叶鲹 Alepes djedaba
		石首鱼科 Sciaenidae	小黄鱼 Larimichthys polyactis
		鱚科 Sillaginidae	少鳞鱚 Sillago japonica
		虾虎鱼科 Gobiidae	矛尾刺虾虎鱼 Acanthogobius hasta
			长体刺虾虎鱼 Acanthogobius elongatus
			矛尾虾虎鱼 Chaeturichthys stigmatias
			七棘裸身虾虎鱼 Gymnogobius heptacanthus
			普氏细棘虾虎鱼 Acentrogobius pflaumii
			六丝钝尾虾虎鱼 Amblychaeturichthys hexanema
			棕刺虾虎鱼 Acanthogobius luridus
			拉氏狼牙虾虎鱼 Odontamblyopus lacepedii
	鳗鲡目 Anguilliformes	康吉鳗科 Congridae	星康吉鳗 Conger myriaster
	鳐形目 Rajiformes	鳐科 Rajidae	斑鳐 Okamejei kenojei
	鲉形目 Scorpaeniformes	六线鱼科 Hexagrammidae	大泷六线鱼 Hexagrammos otakii
		鲬科 Platycephalidae	鲬 Platycephalus indicus
	鲻形目 Mugiliformes	鲻科 Mugilidae	鮻 Planiliza haematocheilus
			鲻 Mugil cephalus
非本地鱼类物种	鲱形目 Clupeiformes	鲱科 Clupeidae	隆背小沙丁鱼 Sardinella gibbosa
Non-native fish species			花点鲥 Hilsa kelee
	鳉形目 Cyprinodontiformes	青鳉科 Oryziatidae	青鳉 Oryzias latipes
	鲤形目 Cypriniformes	鲤科 Cyprinidae	鲫 Carassius auratus
			似鳊 Pseudobrama simoni
			尖棘鱲 Zacco acutipinnis
			鲤 Cyprinus carpio
			温州光唇鱼 Acrossocheilus wenchowensis
			三角鲂 Megalobrama terminalis
			长鳍马口鱼 Opsariichthys evolans
			刺鲃 Spinibarbus caldwelli
			贝氏? Hemiculter bleekeri
		爬鳅科 Balitoridae	梅花山拟腹吸鳅 Pseudogastromyzon meihuashanensis
			原缨口鳅 Vanmanenia stenosoma
	鲈形目 Perciformes	金线鱼科 Nemipteridae	日本金线鱼 Nemipterus thosaporni
		丽鱼科 Cichlidae	齐氏非鲫 Coptodon zillii
			非鲫 Oreochromis mossambicus
			加利略帚齿非鲫 Sarotherodon galilaeus
			尼罗非鲫 Oreochromis niloticus
		雀鲷科 Pomacentridae	白带金翅雀鲷 Chrysiptera brownriggii
		塘鳢科 Eleotridae	刺盖塘鳢 Eleotris acanthopomus
		虾虎鱼科 Gobiidae	波氏吻虾虎鱼 Rhinogobius cliffordpopei
			雀斑吻虾虎鱼 Rhinogobius lentiginis
			名古屋吻虾虎鱼 Rhinogobius nagoyae
			武义吻虾虎鱼 Rhinogobius wuyiensis
	鲇形目 Siluriformes	鲿科 Bagridae	黄颡鱼 Tachysurus fulvidraco
		鲇科 Siluridae	怀头鲇 Silurus soldatovi
		甲鲇科 Loricariidae	豹纹脂身鲇 Pterygoplichthys pardalis

基于环境DNA宏条形码技术研究黄河三角洲典型潮沟系统鱼类多样性及其对水文连通性的响应

Response of fish diversity to hydrological connectivity of typical tidal creek system in the Yellow River Delta based on environmental DNA metabarcoding

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采样站点 Sampling station	观察物种数 Observed species	ACE指数 ACE index	Chao 1指数 Chao 1 index	Shannon指数 Shannon index	Simpson指数 Simpson index	测序深度指数 Good's coverage
S1S	325	328.28	328.11	3.95	0.84	0.999977
S1X	327	329.57	328.62	3.14	0.62	0.999980
S2S	324	335.00	350.25	4.44	0.87	0.999958
S2X	316	325.00	323.50	3.25	0.73	0.999958
S3S	325	337.51	335.69	3.60	0.78	0.999946
S3X	288	302.85	302.88	3.64	0.81	0.999935

	排序轴 Axes
	1	2	3	4
特征值 Eigenvalues	0.62	0.251	0.046	0.028
相关系数 Species-environment correlations	0.969	0.992	0.986	0.947
物种数据累积百分比方差 Cumulative percentage variance of species data (%)	62	87.2	91.8	94.7
物种-环境关系累积百分比方差 Cumulative percentage variance of species-environment relation (%)	65.3	91.7	96.6	99.6
总特征值 Sum of all eigenvalues	1
总特征值 Sum of all eigenvalues	1	总典范特征值 Sum of all canonical eigenvalues	0.951

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