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.

The commercial feed additive, native rumen microbes (RC), derived from a diverse microbial community isolated from the rumen of Hanwoo steers is being explored to enhance rumen fermentation and improve ruminant feed utilization. This study evaluated the impact of native rumen microbes supplementation on methane emissions, microbial diversity, and fermentation efficiency on in vitro assessment. Treatments were as follows: CON (basal diet, without RC); T1 (basal diet + 0.1% RC); T2 (basal diet + 0.2% RC). Rumen fermentation parameters, total gas, and methane production were assessed at 12, 24, and 48 h of incubations. The in vitro gas production was carried out using the Ankom RF Gas Production System. Supplementation of RC significantly reduced the total gas production at 12, 24, and 48 hours of incubation (p < 0.05). Volatile fatty acid concentrations were increased, while acetate and propionate were decreased (p < 0.05) at 48 h by the supplementation of RC. Notably, the 0.1% inclusion level of RC significantly reduced methane production by 28.30% and 21.21% at 12 and 24 hours. Furthermore, microbial diversity analysis revealed significant shifts (p < 0.05) in bacterial composition between the control and treatment groups, while supplementation also promoted the growth of bacterial populations, such as Succiniclasticum. These findings suggest that native rumen microbes supplementation, particularly at 0.1% inclusion level, can enhance rumen microbial composition while significantly reducing methane production in vitro.

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.

Lakes and reservoirs represent key freshwater ecosystems that host diverse aquatic organisms and perform essential functions such as water cycling, nutrient retention, and ecosystem service provision. Due to their semi-closed hydrological structure and limited inflow-outflow dynamics, lakes exhibit complex biological communities shaped by regional climate, topography, and land use. However, these ecosystems are increasingly exposed to multifactorial stressors-including climate change, urbanization, nutrient enrichment, and invasive species-that are causing significant structural and functional shifts in aquatic biodiversity. This review provides an integrative overview of (1) the structural and ecological characteristics of lake ecosystems and the primary drivers of biodiversity alteration, (2) the ecological functions and bioindicator potential of key organism groups including phytoplankton, zooplankton, aquatic macrophytes, benthic macroinvertebrates, and fish, and (3) the emerging role of environmental DNA (eDNA) metabarcoding in lake biodiversity monitoring. We highlight both the technical principles and challenges of eDNA analysis and discuss its potential to complement traditional survey methods for the development of integrated ecosystem health assessments. Positioned at the forefront of the 2025 special issue of Ecology and Environment, this article establishes a conceptual and methodological foundation for a national-scale freshwater biodiversity monitoring framework in Korean lakes.

The long-tailed goral (Naemorhedus caudatus) is classified as an endangered species in South Korea due to population declines driven by human development and habitat fragmentation. This study aimed to investigate genetic characteristics and microsatellite genotypes in long-tailed goral populations using fecal samples collected from Uljin and Samcheok regions, which are geographically important habitats for the distribution and dispersal of this species in South Korea. The mean expected heterozygosity (HE) and observed heterozygosity (HO) across 10 microsatellite loci were 0.600 and 0.461 for the Uljin population and 0.644 and 0.571 for the Samcheok population, respectively. These values indicate a moderate level of genetic diversity compared to other closely related species. Genetic differentiation between the two populations had a low level, while a moderate gene flow was observed. The genetic evidence obtained in this study suggests that these two populations share a similar genetic pool, resulting in a low level of genetic differentiation between them. Therefore, they should be considered as one continuous population. Results of this study provide fundamental data and valuable genetic insights for long-term management of the long-tailed goral population in Uljin and Samcheok regions.