Environmental DNA (eDNA) has emerged as a promising tool for aquatic biodiversity monitoring, yet its collection in lentic ecosystems remains technically constrained by filtration capacity and field logistics. In this study, we applied a novel eDNA concentration system, QuickConcTM, to evaluate freshwater mussel diversity in lakes, and compared its performance with the conventional GF/F filtration method. Water samples were collected from four reservoirs at surface, mid, bottom, and waterside layers, and processed using both filtration techniques. Metabarcoding of mitochondrial 16S rDNA revealed that QuickConcTM captured a higher average number of amplicon sequence variants (ASVs) and exhibited greater species richness and diversity indices (Shannon and Simpson), although the differences were not statistically significant. QuickConcTM samples showed a greater capacity to detect rare taxa and to recover higher ASV richness in certain cases, suggesting its potential to enhance biodiversity resolution. Species composition remained consistent across methods, with Cristaria plicata and Sinanodonta lauta being dominant in both cases. However, slight spatial variations in species assemblages were observed between center and waterside sampling points, highlighting the influence of habitat heterogeneity on eDNA distribution. Overall, our results demonstrate that the QuickConcTM system offers a practical and efficient alternative to traditional filtration methods for eDNA-based freshwater mussel monitoring, particularly in environments with high suspended solids. The findings underline the need for adaptive sampling strategies that consider both methodological and ecological factors when designing eDNA surveys in lentic ecosystems.

Freshwater bivalves contribute to key ecological functions in lake ecosystems, yet their cryptic and benthic lifestyles often hinder detection through conventional surveys. In this study, we applied environmental DNA (eDNA) metabarcoding to assess the diversity and distribution of unionid bivalves in six lakes across Republic of Korea. Water samples were collected from three sampling strategies-Center Surface, Center Mix, and Waterside Surface-and processed using 16S rDNA-targeted primers followed by high-throughput sequencing. A total of four unionid species (Cristaria plicata, Sinanodonta lauta, Unio (Nodularia) douglasiae, and Anodonta woodiana) were detected across 18 sampling points. Notably, eDNA successfully identified unionid presence in all lakes, even where conventional surveys failed to observe individuals. Among the sampling strategies, Center Mix exhibited the highest values for Shannon and Simpson indices as well as ASV richness. Waterside Surface samples generally showed lower diversity and detection frequency. A Venn diagram of ASV occurrences revealed three ASVs shared across all sampling strategies and one unique ASV found only in Center Mix. These results indicate that sampling location significantly affects detection sensitivity and diversity representation in eDNA-based bivalve monitoring. Combined application of Center Mix and Center Surface strategies may enhance both detection efficiency and species diversity coverage in lentic environments.

Environmental DNA (eDNA) analysis has emerged as a powerful tool for biodiversity monitoring due to its efficiency, standardization potential, and cost-effectiveness. We evaluated the applicability of eDNAbased zooplankton monitoring in Korean lakes by comparing three DNA methods-eDNA, iDNA, and eiDNA-with traditional microscopy. Sampling was conducted in six lakes with varying conditions. eDNA was obtained from lake water, iDNA from unpreserved zooplankton incubated in water, and eiDNA from zooplankton incubated in ethanol. DNA metabarcoding detected more taxa than microscopy, but dominant taxa overlapped, mainly Daphnia. While DNA methods showed higher richness, Simpson and Shannon indices were higher in microscopy, reflecting differences in quantification methods. These discrepancies reflect methodological differences in how taxa are quantified and suggest that DNA-based approaches may overrepresent certain groups in richness estimates. In addition, false negatives were observed for several common rotifer species (e.g., Keratella, Polyarthra), likely due to incomplete reference databases and high intraspecific genetic diversity. Conversely, some taxa detected only by DNA-particularly small-bodied or rare crustaceans-may represent false positives relative to microscopy. These findings emphasize the importance of improving reference libraries and interpreting DNA results with caution, while also supporting the utility of DNA-based methods as complementary tools in zooplankton monitoring and national biodiversity assessments.

Phytoplankton play a vital role as primary producers in freshwater ecosystems, contributing to the nutrient cycle, energy flow, and ecological stability. To accurately assess phytoplankton diversity and community composition, this study compared traditional microscopy and environmental DNA (eDNA) metabarcoding in six small lakes located in the Han, Geum, and Nakdong River basins in Korea. eDNA analysis identified 268 species from 161 genera, approximately 2.4 times higher than microscopy, which detected 113 species from 68 genera. The eDNA data were dominated by picocyanobacteria such as Synechococcus and Cyanobium, while microscopy primarily revealed larger taxa, including Stephanodiscus and Scenedesmus. Nonmetric multidimensional scaling (NMDS) based on Bray-Curtis similarity showed clear separation between the two methods, with average similarity values of 0.0326 (1st survey) and 0.0221 (2nd survey) at the species level. Only 6.8% of the 429 total species were commonly detected by both methods, while overlap at the genus level was 18.8%. Spatial heterogeneity in phytoplankton communities based on eDNA was also evident depending on the sampling location, with the centre of the surface showing the highest species richness and overlap, suggesting its suitability for biodiversity monitoring. These findings demonstrate the high resolution and sensitivity of eDNA metabarcoding in capturing phytoplankton diversity and highlight its complementary role in existing biomonitoring programmes. Further improvements in the quantitative reliability of eDNA-based assessments will require efforts such as copy number normalisation, methodological standardisation, and refinement of reference databases.

This study analyzed and presented zooplankton species occurrence, diversity distribution, and community composition in ninety lakes across South Korea using samples collected through the “Survey of Lake Aquatic Ecosystem Status and Health Assessment.” When comparing our results with the National Species Checklist, we identified factors within each of the three taxa that warrant improvement due to their influence on diversity assessments. To bridge the gap between the ongoing lake ecosystem surveys and the continually updated National Species Checklist-and to enhance the accuracy of diversity evaluations-we conclude that (1) greater taxonomic rigor must be reflected in the national checklist, and (2) the limitations of morphology-based identification (α-taxonomy) must be addressed. Because the National Species Checklist does not distinguish among species, subspecies, and morphospecies, it can give rise to taxonomic oversplitting and taxonomic inflation, leading to ambiguous diversity-index results. Moreover, the low resolution of morphological identification for zooplankton (at the genus, family, or class level) can introduce errors when comparing communities across habitats or detecting non-native introductions. Although alternatives such as environmental DNA and functional diversity exist, they require further refinement before being adopted in policy; therefore, they should be implemented alongside and in comparison with current aquatic ecosystem health assessment methods.

Habenaria radiata, commonly known as the Egret Flower, is a critically endangered terrestrial orchid facing rapid population decline due to overharvesting in Korea. Asymbiotic seed propagation offers a promising conservation method for this rare species. This study investigates the effects of different nutrient media on the germination and plantlet development of immature seeds of H. radiata, with the goal of establishing optimal propagation conditions. Among four media types, with the highest germination rate (75.6%) observed on OBTSG medium, followed by 1/2 MS, OMM, and OSGM. Protocorm development varied across media, with OBTSG and OMM supporting the most robust growth. A two-step culture method involving OBTSG for germination followed by OMM for plantlet development proved most effective, achieving an 84.4% survival rate. These findings highlight the importance of media composition and transitioning for successful propagation. The results provide a practical protocol for in vitro propagation, contributing to both in situ and ex situ conservation efforts aimed at preserving H. radiata and other endangered terrestrial orchids.

Recently, Korean government has incorporated the assessment and restoration of river continuity as a key component of its integrated water management policy. While, methodologies for evaluating discontinuities and degradation, as well as the procedures for assessment and restoration, have been developed and proposed, there is a need for further improvement. Therefore, further research is required to establish a conceptual framework for continuity specific to domestic river ecosystems and to formulate appropriate assessment methods and restoration strategies. In this study we conduct a comparative analysis of the concepts, restoration approaches, and comprehensive evaluation methods for river continuity as proposed by Japan, the United States, and the European Union (EU), all of which have long-standing frameworks for river continuity assessment and restoration projects. Each country demonstrates distinct objectives and guidelines: Japan emphasizes habitat continuity within the context of river and watershed continuity, the United States integrates continuity as a tool for watershed management, and the EU prioritizes biodiversity conservation by advocating for the removal of artificial barriers and promoting the restoration of free-flowing rivers (FFR). By investigating these international examples, this study provides insights that can guide the development of long-term strategies and evaluation criteria for securing aquatic ecosystem continuity in Korea.

Zooplankton biomass is essential for understanding the quantitative structure of lake food webs and for the functional assessment of biotic interactions. In this study, we aimed to propose a biomass (dry weight) estimation method using the body length of cyclopoid copepods. These copepods play an important role as omnivores in lake zooplankton communities and contribute significantly to biomass. We validated several previously proposed estimation equations against direct measurements and compared the suitability of prosomal length versus total length of copepods to suggest a more appropriate estimation equation. After comparing the regression analysis results of various candidate equations with the actual values measured on a microbalance-using the coefficient of variation, mean absolute error, and coefficient of determination-it was determined that the Total Length-DW exponential regression equation [W=0.7775×e2.0183L; W (μg), L (mm)] could be used to calculate biomass with higher accuracy. However, considering practical issues such as the morphological similarity between species and genera of copepods and the limitations of classifying copepodid stages, we derived a general regression equation for the pooled copepod community rather than a species-specific regression equation.

In ecosystems within limited resources, interspecific competition is inevitable, often leading to the competitive exclusion of inferior species. This study aims to provide foundational information for the conservation and restoration management of Microphysogobio rapidus by evaluating species’ ecological response to biological factors within its habitat. To understand this relationship, we collected food web organisms from site where M. rapidus coexist with Microphysogobio yaluensis, a specie ecologically similar to M. rapidus, and evaluated the trophic levels (TL), isotopic niche space (INS), and the overlap of INS among fishes within the habitat using stable isotope analysis. Our analysis revealed that the M. rapidus exhibited a higher TL than M. yaluensis, with TL of 2.6 and 2.4, respectively. M. yaluensis exhibited a broad INS, significantly influencing the feeding characteristics of most fish. Conversely, M. rapidus showed a narrow INS and asymmetric feeding relationships with other species, in habitats with high competition levels. This feeding characteristics of M. rapidus indicate that the increase in competitors sharing the similar resources lead to a decrease in available resources and, consequently, is expected to result in a decrease in their density.

Small ponds, which exhibit unstable succession pattern of plankton community, are less well studied than large lakes. Recently, the importance of small ponds for local biodiversity conservation has highlighted the necessity of understanding the dynamics of biological community. In the present study, we collected zooplankton from three small reservoirs with monthly basis and analyzed their seasonal dynamics. To understand the complicated zooplankton community dynamics of small reservoirs, we categorized zooplankton species into four groups (LALF Group, Low Abundance Low Frequency; LAHF Group, Low Abundance High Frequency; HALF Group, High Abundance Low Frequency; HAHF Group, High Abundance High Frequency) based on their occurrence pattern (abundance and frequency). We compared the seasonal pattern of each group, and estimated community diversity based on temporal beta diversity contribution of each group. The result revealed that there is a relationship between groups with the same abundance but different occurrence frequencies, and copepod nauplii are common important component for both abundance and frequency. On the other hand, species included with LALF Group throughout the study period are key in terms of monthly succession and diversity. LALF Group includes Anuraeopsis fissa, Hexarthra mira and Lecane luna. However, groups containing species that only occur at certain times of the year and dominate the waterbody, HALF Group, hindered to temporal diversity. The results of this study suggest that the species-specific occurrence pattern is one key trait of species determining its contribution to total annual biodiversity of given community.

The medium-large cladoceran species Simocephalus spp. predominantly occur in habitats with developed aquatic vegetation. Accordingly, due to Simocephalus’ high contribution to zooplankton community biomass in the lake’s littoral zone and wetland habitats, estimating their biomass is important to understand the matter cycling based on biological interactions within the aquatic food web. In this study, we reviewed the length-weight regression equations used previously to estimate Simocephalus biomass, directly measured S. serrulatus’ body specification (length, width and area) and their biomass (dry weight) using instruments such as a microscopic digital camera and a microscale, and performed regression analysis between each other. When S. serrulatus biomass was estimated using the equation (Kawabata and Urabe, 1998) presented in 『Biomonitoring Survey and Assessment Manual』, Korea, errors between estimates and measures were relatively large compared to the S. serrulatus species-specific biomass estimate equation developed by Lemke and Benke (2003). In addition, both equations showed not only increasing trends in error (estimate-measure) with increasing S. serrulatus’ body length, but also in error variance among similar-sized individuals. The results of regression analysis with dry weight by body specifications indicated that the most appropriate equation for estimating the biomass of S. serrulatus was derived from the width-dry weight exponential regression equation (R2=0.9555). The review and development study of such species-specific biomass estimation equations for zooplankton can be used as a tool to understand their role and function in aquatic ecosystem food webs.

Recently, Korean government has introduced Multi Metric Indices (MMI) using various biocommunity information for aquatic ecosystem monitoring and ecosystem health assessment at the national level. MMI is a key tool in national ecosystem health assessment programs. The MMI consists of indices that respond to different target environmental factors, including environmental disturbance (e.g. nutrients, hydrological and hydraulic situation of site etc.). We used zooplankton community information collected from Korean lakes to estimate the availability of candidate zooplankton MMI indices that can be used to assess lake ecosystem health. First, we modified the candidate indices proposed by the U.S. EPA to suit Korean conditions. The modified indices were subjected to individual index suitability analysis, correlation analysis with environmental variables, and redundancy analysis among indices, and 19 indices were finally selected. Taxonomic diversity was suggested to be an important indicator for all three taxonomic groups (cladoceran, copepod, rotifer), on the other hand, the indices using biomass for large cladocerans and copepods, while the indices using abundance were suggested for small cladocerans and rotifers.

Through sample-size-based rarefaction analyses, we tried to suggest the appropriate degree of sample concentration and sub-sample extraction, as a way to estimate more accurate zooplankton species diversity when assessing biodiversity. When we collected zooplankton from three reservoirs with different environmental characteristics, the estimated species richness (S) and Shannon’s Hʹ values showed different changing patterns according to the amount of sub-sample extracted from the whole sample by reservoir. However, consequently, their zooplankton diversity indices were estimated the highest values when analyzed by extracting the largest amount of sub-sample. As a result of rarefaction analysis about sample coverage, in the case of deep eutrophic reservoir (Juam) with high zooplankton species and individual numbers, it was analyzed that 99.8% of the whole samples were represented by only 1 mL of sub-sample based on 100 mL of concentrated samples. On the other hand, in Soyang reservoir, which showed very small species and individual numbers, a relatively low representation at 97% when 10 mL of sub-sample was extracted from the same amount of concentrated sample. As such, the representation of sub-sample for the whole zooplankton sample varies depending on the individual density in the sample collected from the field. If the degree of concentration of samples and the amount of subsample extraction are adjusted according to the collected individual density, it is believed that errors that occur when comparing the number of species and diversity indices among different water bodies can be minimized.

동물플랑크톤 군집 연구에 DNA 바코딩과 같은 DNA 분 석 기법의 적용은 분류형태학을 기반으로 하는 전통적인 종 동정 시 발생할 수 있는 문제 (e.g. 개체의 표현형 가소성에 의한 오동정, 유사종 및 자매종, 유생 시기의 종 동정의 어려움)를 보완할 수 있다. 최근 DNA 시퀀싱 기술의 발전으로 다양한 수생태계의 동물플랑크톤 군집은 물론, 육안 및 현미경을 통해 구분하는 데 한계가 있는 동물플랑크톤의 위 내용물에 대한 DNA 기반 군집 분석 또한 가능하게 되었으며, 이는 동물플랑크톤의 섭식 먹이원 분석을 통한 생물학적 상호 작용을 이해를 돕는다. 본 논문은 동물플랑크톤 연구에 DNA 분석 기법이 활용된 사례 (e.g. DNA 바코딩을 이용한 계통분 류학적 연구, 메타바코딩을 이용한 군집 분석, 위 내용물 분석)를 소개하고 분석 방법을 요약하여, 최종적으로 향후 이를 활용하고자 하는 연구자들에게 연구 접근성을 높일 수 있도록 방법론적인 기초 지식을 제공하고자 하였다.