A preliminary study into the detection of fish environmental DNA in selected South African estuaries

IF 1.1 4区 环境科学与生态学 Q3 MARINE & FRESHWATER BIOLOGY African Journal of Aquatic Science Pub Date : 2023-10-02 DOI:10.2989/16085914.2023.2288341
Keneilwe Thekiso, Tshoanelo Miya, Dominique A Cowart
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Abstract

Environmental DNA (eDNA) is a powerful technique for the non-invasive and comprehensive monitoring of entire ecosystems. Despite its many advantages, the use of eDNA in South Africa as an assessment tool for fish biodiversity is largely underutilised. This study was performed as an initial screening to assess the efficiency of the eDNA method for characterising fish communities in South African waters using the metabarcoding approach. Water samples were collected from eight estuaries and vacuum filtered using 0.45 μm nylon membrane filters. DNA was extracted from the filters, and sample extracts underwent PCR assaying using MiFish primers for the 12S rRNA gene, prior to being sequenced on the Illumina MiSeq platform. The resulting sequence data produced 1 574 092 raw reads, which resulted in 119 operational taxonomic units (OTUs) after filtering and clustering. Taxonomic assignment of the OTUs produced four different taxonomic groups and one group representing unidentified sequences. The group with the highest number of OTUs (54%) was assigned to fish taxa consisting of 12 families and 22 genera identified across all estuaries, with only 16 taxa identified to species level. As this was a preliminary study, few samples were collected, and therefore several recommendations for a more comprehensive study design are provided. Overall, these results support the hypothesis that the eDNA metabarcoding approach can efficiently detect fish species in South African estuarine environments.
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南非部分河口鱼类环境 DNA 检测初步研究
环境 DNA(eDNA)是一种对整个生态系统进行非侵入性综合监测的强大技术。尽管 eDNA 有很多优点,但在南非,将其作为鱼类生物多样性评估工具的使用率还很低。本研究对 eDNA 方法进行了初步筛选,以评估 eDNA 方法使用代谢编码方法描述南非水域鱼类群落特征的效率。从八个河口采集水样,并使用 0.45 μm 尼龙膜过滤器进行真空过滤。从过滤器中提取 DNA,使用 MiFish 12S rRNA 基因引物对样本提取物进行 PCR 分析,然后在 Illumina MiSeq 平台上进行测序。测序数据产生了 1 574 092 个原始读数,经过过滤和聚类后产生了 119 个可操作的分类单元(OTU)。对 OTUs 进行分类分配后,产生了四个不同的分类组和一个代表未识别序列的组。OTU数量最多的一组(54%)是鱼类分类群,包括在所有河口发现的12个科和22个属,其中只有16个分类群被鉴定为鱼种。由于这是一项初步研究,收集的样本很少,因此提出了一些关于更全面研究设计的建议。总体而言,这些结果支持 eDNA 代谢编码方法可以有效检测南非河口环境中鱼类物种的假设。
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来源期刊
African Journal of Aquatic Science
African Journal of Aquatic Science MARINE & FRESHWATER BIOLOGY-
CiteScore
3.90
自引率
7.10%
发文量
31
审稿时长
>12 weeks
期刊介绍: The African Journal of Aquatic Science is an international journal devoted to the study of the aquatic sciences, covering all African inland and estuarine waters. The Journal publishes peer-reviewed original scientific papers and short articles in all the aquatic science fields including limnology, hydrobiology, ecology, conservation, biomonitoring, management, water quality, ecotoxicology, biological interactions, physical properties and human impacts on African aquatic systems.
期刊最新文献
South African coastal outlets and estuaries: what defines an estuary versus an outlet? Water quality monitoring and measuring physicochemical parameters using wireless sensor networks A bibliometric study on diatom DNA meta-barcording for water quality monitoring: a global perspective Analysis of freshwater diatom deformities in the Karoo, South Africa A preliminary study into the detection of fish environmental DNA in selected South African estuaries
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