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

doi:10.17520/biods.2023073

Abstract

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

Zhiyuan Dong, Linlin Chen, Naipeng Zhang, Li Chen, Debin Sun, Yanmei Ni, Baoquan Li. Response of fish diversity to hydrological connectivity of typical tidal creek system in the Yellow River Delta based on environmental DNA metabarcoding[J]. Biodiv Sci, 2023, 31(7): 23073.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2023073

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

Figures/Tables 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