Zooplankton dominate the abundance and biomass of multicellular animals in pelagic marine environments; however, traditional methods to characterize zooplankton communities are invasive and laborious. This study compares zooplankton taxonomic composition revealed through metabarcoding of the cytochrome oxidase I (COI) and 18S rRNA genes to traditional morphological identification by microscopy. Triplicates of three different sample types were collected from three coral reef sites in the Florida Keys National Marine Sanctuary: (1) 1 L surface seawater samples prefiltered through 3 μm filters and subsequently collected on 0.22 μm filters for eDNA (PF-eDNA); (2) 1 L surface seawater samples filtered on 0.22 μm pore-size filters (environmental DNA; eDNA), and (3) zooplankton tissue samples from 64 μm, 200 μm, and 500 μm mesh size net tows. The zooplankton tissue samples were split, with half identified morphologically and tissue DNA (T-DNA) extracted from the other half. The COI and 18S rRNA gene metabarcoding of PF-eDNA, eDNA, and T-DNA samples was performed using Illumina MiSeq. Of the families detected with COI and 18S rRNA gene metabarcoding, 40% and 32%, respectively, were also identified through morphological assessments. Significant differences in taxonomic composition were observed between PF-DNA, eDNA, and T-DNA with both genetic markers. PF-eDNA resulted in detection of fewer taxa than the other two sample types; thus, prefiltering is not recommended. All dominant copepod taxa (> 5% of total abundance) were detected with eDNA, T-DNA, and morphological assessments, demonstrating that eDNA metabarcoding is a promising technique for future biodiversity assessments of pelagic zooplankton in marine systems.

中文翻译：

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通过环境DNA元条形码评估海洋浮游动物群落结构。

浮游动物在中上层海洋环境中主导着多细胞动物的丰度和生物量；然而，表征浮游动物群落的传统方法是侵入性的且费力的。这项研究比较了通过细胞色素氧化酶I（COI）和18S rRNA基因的metabarcode揭示的浮游动物分类学组成与显微镜下的传统形态学鉴定。从佛罗里达礁国家海洋保护区的三个珊瑚礁地点收集了三种不同样品的三份样品：（1）1 L表面海水样品经过3μm过滤器预过滤，然后在0.22μm过滤器上收集eDNA（PF-eDNA）；（2）在0.22μm孔径的过滤器（环境DNA； eDNA）上过滤的1 L地表海水样品，以及（3）网眼尺寸为64μm，200μm和500μm的网状浮游动物浮游动物组织样品。分离浮游动物组织样品，从形态学上鉴定一半，从另一半提取组织DNA（T-DNA）。PF-eDNA，eDNA和T-DNA样品的COI和18S rRNA基因元条形码使用Illumina MiSeq进行。在通过COI和18S rRNA基因元条形码检测到的家族中，还通过形态学评估分别鉴定出40％和32％。两种基因标记的PF-DNA，eDNA和T-DNA在分类学组成上均存在显着差异。PF-eDNA导致比其他两种样品类型检测到更少的分类单元。因此，不建议进行预过滤。通过eDNA，T-DNA和形态学评估检测到所有优势co足类群（> 5％的总丰度），