**1. Introduction**

Environmental DNA (eDNA) is defined as genetic material indirectly obtained from a wide variety of environmental samples (e.g., air, water, and soil), rather than directly sampled from macro- and micro-organisms [1]. Since a specific region of DNA sequences accommodates the information about the identification of specific organisms of interest, eDNA collected from an environmental sample encompasses a variety of species information in an ecosystem [2]. The idea of eDNA was initiated from extracting the nucleic acids of microbes directly from environmental samples [1,3–5].

Nowadays, DNA across diverse taxonomic groups has been widely searched in the context of genome projects [6,7]. The rapid advancement of molecular technology, such as amplification using polymerase chain reaction (PCR), facilitates applications of DNA-based approaches that highlight the capacity of analysis to detect a variety of macro- and micro-organisms within the same sample. DNA-based identification has been regarded as efficient alternatives in terms of both time and cost in ecological research [8,9]. This analytical technique can be applied either to a single species/taxon using specific primers or to multiple species/taxa using generic primers in accordance with research objectives. DNA metabarcoding is a rapid method for assessing biodiversity from environmental bulk samples. In particular, rapidly growing next-generation sequencing (NGS) techniques have recently allowed

comprehensive surveys for biological monitoring and assessment [8,10]. To this end, a growing body of literature has put special emphasis on the advantages of metabarcoding, highlighting its usefulness for ecological managemen<sup>t</sup> [2,9,11–15]. Accordingly, a new type of DNA-based identification method has been developed as DNA metabarcoding, and widely introduced with plenty of applicable potentials for biological monitoring and assessment [16–18]. Specifically, eDNA metabarcoding has been newly proposed to assess the status (e.g., healthy, threatened, or degraded) of an ecosystem by detecting single (rare) and/or multiple (abundant) species in terms of biodiversity [12,13,19]. Despite the relatively short history, eDNA metabarcoding is appealing for monitoring and assessment of ecosystems due to its species detectability, cost and effort efficiency, and no environmental disturbance [18].

In coastal marine ecosystems, plankton communities play a pivotal role in food chain flow and biogeochemical cycles [20]. Particularly, zooplankton communities including both mero- and holo-zooplankton exert large influences on fish biomass and fisheries resources especially associated with juvenile growth [21]. Conventional microscopic identification (CMI) methods have mostly been used to estimate the richness and abundance of plankton communities in an aquatic ecosystem [22,23]. CMI might be limited in taxonomic identification, because the resultant data quality depends upon expertise and subjectivity of the scientists, and may cause disturbance to the habitat, and it is difficult to detect rare and endangered species [2,24]. In contrast, an eDNA analysis contains competitive advantages over CMI in detecting rare or invasive species [25]. In addition, given the high cost and large efforts for data collection and analysis in CMI, eDNA metabarcoding sheds light on efficient monitoring and assessment of a target ecosystem [8,18]. Furthermore, the rapid biological responses/changes to ambient physicochemical conditions lead to high demands on a new method that is fast and inexpressive, such as NGS-based metabarcoding [8]. Yet, the applications of eDNA have not been covered as widely as we wished, because of its short history, and to date have focused more on paleoecology and endangered species [13,19].

In the sense that the eDNA metabarcoding is highly appealing for finding cryptic aquatic species in biological monitoring and assessment, our study focuses on testing the potential of eDNA metabarcoding in order to monitor coastal plankton communities and assess biodiversity in comparison to CMI. Hence, the aim of our study is to identify spatial and temporal heterogeneity of plankton community dynamics in Gwangyang Bay of South Korea, characterizing predominant species and ambient water quality conditions. Finally, we discuss the potential values of eDNA metabarcoding as an alternative approach for ecological monitoring and rapid assessment.
