We compared two sampling methods, eDNA metabarcoding and microscope identification (MSI), for the analysis of zooplankton diversity in reservoirs with its inflow and outflow streams. The dynamic patterns of Cladocera and Rotifera at different time points were similar between the two sampling methods, but there was a slight difference in the Copepoda. Specifically, the members of the Copepoda subclass could not be easily classified using the MSI method, whereas eDNA metabarcoding could detect minor taxa of Cladocera and Rotifera. Upon comparing the list of zooplankton communities in Korea with the gene database of NCBI, only ~56% of the zooplankton genera reported in Korea could be detected based on the 18S rRNA gene. However, eDNA metabarcoding detected a more diverse range of zooplankton despite the lack of genetic information. As water temperature increased after May, the zooplankton diversity decreased according to the MSI method but increased according to the eDNA metabarcoding method. Although eDNA metabarcoding has some limitations, it was able to detect a wider diversity of zooplankton compared to the MSI. eDNA metabarcoding provides a more reliable means to identify zooplankton.

For the sustainable use of lake ecosystem services—water resources, aquatic habitats for biodiversity conservation, and aesthetic values as waterfront space—ecosystem health assessments using biota are implemented as important national environmental monitoring projects. Zooplankton play a key role as an important linkage in the material circulation as secondary producers in lake ecosystems. At the same time, they influence the composition and biomass of other communities through biological interactions. In this review, we summarize useful zooplankton indices for ecosystem health assessment and suggest considerations for their use. Suggestions are provided for the practical application of indirectly measured zooplankton biomass, as well as the potential and limitations of eDNA application, which has recently been actively utilized in biological monitoring.

Assessing the biomass of zooplankton compensates for the difference between number of individuals and the accumulated body weight of the community, which helps assess aquatic ecosystem food web functions. Daphnia are crustaceans that play an intermediate role in biological interactions within food webs. The morphology and body specification of Daphnia differ during growth; hence, it is essential to apply species-specific equations to estimate biomass. We evaluated the length–weight regression equations used previously to estimate Daphnia magna biomass and conducted regression analyses using various body specifications and biomass measurements taken directly using devices such as a microbalance and microscopic camera. Biomass estimated using an equation from the Environmental Protection Agency was significantly different from the direct measurement: average biomass was lower, indicating that the equation possibly underestimated actual biomass. The biomass of D. magna had a higher multiple R² value when length was compared with width and area, and a linear regression equation was the most suitable equation for biomass estimation. Because body specifications and biomass are affected by various environmental factors, the development of accurate species-specific biomass estimation equations will contribute to obtaining fundamental data with which the biological responses of zooplankton to aquatic ecosystem changes can be assessed.

To adapt to ecological and environmental conditions, species can change their ecological niche (e.g., interactions among species) and function (e.g., prey‐predation, diet competition, and habitat segregation) at the species and guild levels. Stable isotope analysis of bulk carbon and nitrogen of organisms has conventionally been used to evaluate such adaptabilities in the scenopoetic and bionomic views as the isotopic niche width. Compound‐specific stable isotope analysis (CSIA) of nitrogen within amino acids provides trophic information without any disruption of scenopoetic views in the isotope ratios, unlike conventional bulk isotope analysis provides both information and therefore frequently hinders its usefulness for trophic information. We performed CSIA of amino acids to understand the trophic variability of the pike gudgeon Pseudogobio esocinus and largemouth bass Micropterus salmoides as representative specialist and generalist fish species, respectively, from 16 ecologically variable habitats in the four major rivers of Korea. There was little variation (1σ) in the trophic position (TP) among habitats for P. esocinus (± 0.2); however, there was considerably large variation for M. salmoides (± 0.6). The TP of M. salmoides was negatively correlated with the benthic invertebrate indices of the habitats, whereas the TP of P. esocinus showed no significant correlation with any indices. Thus, these two representative fish species have different trophic responses to ecological conditions, which is related to known differences in the trophic niche between specialists (i.e., small niche width) and generalists (i.e., large niche width). Over the past four decades, the conventional bulk isotope analysis has not been capable of deconvoluting “scenopoetic” and “bionomic” information. However, in the present study, we demonstrated that the CSIA of amino acids could isolate trophic niches from the traditional ecological niche composed of trophic and habitat information and evaluated how biological and ecological indices influence the trophic response of specialists and generalists.

We designed an experiment to analyze the gut content of Rotifera based on DNA barcoding and tested it on Asplanchna sp. in order to ensure that the DNA extracted from the rotifer species is from the food sources within the gut. We selected ethanol fixation (60%) to minimize the inflow effects of treated chemicals, and commercial bleach (the final concentration of 2.5%, for 210 s) to eliminate the extracellular DNA without damage to the lorica. Rotifers have different lorica structures and thicknesses. Therefore, we chose a pretreatment method based on Asplanchna sp., which is known to have weak durability. When we used the determined method on a reservoir water sample, we confirmed that the DNA fragments of Chlorophyceae, Diatomea, Cyanobacteria, and Ciliophora were removed. Given this result, Diatomea and cyanobacteria, detected from Asplanchna, can be considered as gut contents. However, bacteria were not removed by bleach, thus there was still insufficient information. Since the results of applying commercial bleach to rotifer species confirmed that pretreatment worked effectively for some species of rotifers food sources, in further studies, it is believed to be applicable to the gut contents analysis of more diverse rotifers species and better DNA analysis techniques by supplementing more rigorous limitations.

Three-dimensional excitation emission matrix (EEM) fluorescence spectroscopy was used to investigate the characteristics of dissolved organic matter (DOM) in five typical eutrophic agricultural reservoirs. Based on catchment ecosystem, the five reservoirs were divided into three pollution sources of livestock, living, and farmland sources. The quantities and qualities of DOM in the reservoirs were analyzed. Our results showed that DOM characteristics were different in eutrophic reservoirs based on source. More protein-like components were observed in the reservoirs with the living sources, while more humic-like components were seen in the reservoir with farmland sources. Additionally, correlation analysis showed different sources for protein-like and humic-like components. Protein-like components originated mainly from phytoplankton (endogenous sources), and humic-like components were from terrestrial sources. Furthermore, the high values of specific fluorescence parameters were consistent with a dominant role of endogenous DOM in eutrophic water bodies, with FI values (fluorescence index) of approximately 1.9, and β:α values (freshness index) greater than 0.7. This result indicated that mixed features dominated endogenous sources in the reservoirs, regardless of terrestrial pollution sources. By comparing our fluorescence characteristics and historical references, we confirmed that catchment ecosystems related to human activities are important factors in determination of the characteristics of DOM in aquatic environments. However, complex and extensive eutrophication requires endogenous control of water bodies, which will play a central role in improving water environments and sustainable use of reservoirs. Therefore, this study provides an effective basis for water quality assessment of eutrophic agricultural reservoirs.