Environmental DNA metabarcoding for fish diversity assessment in a macrotidal estuary: A comparison with established fish survey methods
Environmental DNA metabarcoding for fish diversity assessment in a macrotidal estuary: A comparison with established fish survey methods
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DOI：
10.1016/j.ecss.2023.108522
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发表时间：
2023-10
期刊：
影响因子：
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通讯作者：
Thomas I. Gibson;Gary Carvalho;Amy Ellison;Enrica Gargiulo;Tristan Hatton-Ellis;Lori Lawson-Handley-
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文献类型：
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作者：
Thomas I. Gibson;Gary Carvalho;Amy Ellison;Enrica Gargiulo;Tristan Hatton-Ellis;Lori Lawson-Handley-
鱼类是河口大型动物的主要组成部分，对于评估这些受到威胁的生态系统的健康状况很重要。一些研究已经应用环境DNA(EDNA)元生物编码来评估河口鱼类的生物多样性。然而，没有一个将物理化学变量的测量与跨整个盐度梯度的空间广泛的抽样设计结合在一起。这项研究的目的是比较在大潮河口(英国北威尔士迪河)通过EDNA Metabarcode地表水样本的EDNA MetabarCoding检测到的鱼的空间组合组成与传统渔具调查的结果。此外，还研究了不同季节的埃德纳组合组成。2018年秋季，在13个测站进行了空间系统设计，采集了三份埃德纳样本，同时还采集了围网、远洋渔船和横梁拖网样本。2019年夏季，13个原始站中的8个站在上下游河口再次采集了埃德娜样本。从样本中提取DNA，并使用建立的针对硬骨鱼的检测方法进行代谢编码分析。关键的发现是，在秋季，Edna检测到了26种渔具捕获的物种中的17种(71%)，其中包括最丰富的物种。总体而言，Edna在每30个样本中检测到的物种丰富度高于围网或飞网(但不包括光束拖网)。此外，盐度与组合组成之间存在明显的相关性，这种相关性在不同季节是一致的。总体而言，该研究表明，EDNA元编码可通过生成更全面的河口鱼类生物多样性图景并为生态推断和管理行动提供更多信息，从而改进现有的鱼类抽样方法。
Fishes are a dominant component of the macrofauna in estuaries and are important for assessing the health of these threatened ecosystems. Several studies have applied environmental DNA (eDNA) metabarcoding to assess the biodiversity of fishes in estuaries. However, none have combined measurement of physicochemical variables with a spatially extensive sampling design across the full salinity gradient. This study aimed to compare spatial fish assemblage composition detected via eDNA metabarcoding of surface water samples with conventional fishing gear surveys in a macrotidal estuary (river Dee, North Wales, UK). In addition, eDNA assemblage composition across seasons was investigated. In autumn 2018, triplicate eDNA samples were taken at 13 stations in a spatially systematic design alongside with seine, fyke and beam trawl sampling. In summer 2019, eDNA samples from eight of the 13 original stations were collected again in the upper and lower estuary. DNA was extracted from samples and subjected to metabarcoding analysis using an established assay targeting teleost fishes. The key findings were that in autumn, eDNA detected 17 of the 26 (71%) species caught by fishing gears, which included the most abundant species. Overall, eDNA detected a greater species richness, per 30 samples, than seine or fyke nets (but not beam trawling). Additionally, there was a clear correlation between salinity and assemblage composition, which was consistent across seasons. Overall, the study indicates that eDNA metabarcoding could enhance existing fish sampling methods, by generating a more comprehensive picture of estuarine fish biodiversity and providing additional information for ecological inference and management actions.