Explaining food web dynamics, stability, and functioning depend substantially on understanding of feeding relations within a community. Bulk stable isotope ratios (SIRs) in natural abundance are well‐established tools to express direct and indirect feeding relations as continuous variables across time and space. Along with bulk SIRs, the SIRs of individual amino acids (AAs) are now emerging as a promising and complementary method to characterize the flow and transformation of resources across a diversity of organisms, from microbial domains to macroscopic consumers. This significant AA‐SIR capacity is based on empirical evidence that a consumer's SIR, specific to an individual AA, reflects its diet SIR coupled with a certain degree of isotopic differences between the consumer and its diet. However, many empirical ecologists are still unfamiliar with the scope of applicability and the interpretative power of AA‐SIR. To fill these knowledge gaps, we here describe a comprehensive approach to both carbon and nitrogen AA‐SIR assessment focusing on two key topics: pattern in AA‐isotope composition across spatial and temporal scales, and a certain variability of AA‐specific isotope differences between the diet and the consumer. On this basis we review the versatile applicability of AA‐SIR to improve our understanding of physiological processes as well as food web functioning, allowing us to reconstruct dominant basal dietary sources and trace their trophic transfers at the specimen and community levels. Given the insightful and opportunities of AA‐SIR, we suggest future applications for the dual use of carbon and nitrogen AA‐SIR to study more realistic food web structures and robust consumer niches, which are often very difficult to explain in nature.

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.

To identify key factors that control primary production (P.P.) and trigger cyanobacterial harmful algal blooms (cHABs), we investigated spatio-temporal variations in P.P. in a continuous weir system in the Nakdong River once or twice a month from April to October 2018. P.P. was measured through an in-situ incubation experiment using a ¹³C tracer. Relative proportion of pigment-based phytoplankton composition was calculated by the CHEMTAX program based on pigment analysis using a high-performance liquid chromatography (HPLC). P.P. was higher in spring (1130 ± 1140 mg C m⁻² d⁻¹) and summer (1060 ± 814 mg C m⁻² d⁻¹) than autumn (180 ± 220 mg C m⁻² d⁻¹), and tended to increase downstream. P.P. was negatively related to PO₄³⁻ (r = −0.41, p < 0.01) due to utilization by phytoplankton during the spring and summer when it was high. The relative proportion of pigment-based cyanobacteria (mainly Microcystis sp.) was positively correlated with water temperature (r = 0.79, p < 0.01) and hydraulic retention time (HRT, r = 0.67, p < 0.01), suggesting that these two factors should affect cHABs in summer. Therefore, to control HRT could be one of the solutions for reducing cHABs in a continuous weir system.

We integrated stomach content analysis (SCA) and stable isotope analysis (SIA) to understand ontogenetic niche shifts in the invasive freshwater fish, bluegill, Lepomis macrochirus, inhabiting the Yedang Reservoir in Korea. Based on the total length (TL), we classified L. macrochirus as small (23–57 mm), medium (61–99 mm), or large (100–163 mm). Across all study sites, the index of relative importance (IRI) of zooplankton was high for small individuals, whereas those of benthic macroinvertebrates were high for the medium and large groups. Isotopic niche width estimates based on carbon and nitrogen isotope ratios (δ space) also increased with growth, indicating an ontogenetic niche shift in L. macrochirus. In particular, the δ space and diet plasticity of large fish was higher in the littoral population, implying L. macrochirus are generalist feeders as adults. Individuals classified as small showed confined and constant δ space, regardless of habitat condition. Thus, together with the results on the significantly high IRI of zooplankton, these individuals seem to have strong specialistic feeding ecology. Our study demonstrates the applicability strength of combining SCA and SIA for ecological niche research by providing clear evidence of an ontogenetic niche shift in L. macrochirus and elucidates their feeding ecology.

Leiocassis longirostris, a large benthic catfish, has been classified as Regionally Extinct (RE) in South Korea since the 1970s. Assessing the success of ongoing restocking efforts in the Geum River is challenging due to limitations in traditional capture-based monitoring methods. We developed a highly sensitive, species-specific quantitative real-time PCR (qPCR) assay targeting the mitochondrial cytochrome b gene (mt-cyb) for this restocked fish. Assay validation confirmed high specificity against a panel of 25 co-occurring fish species, including 8 related siluriforms, and an excellent limit of detection of 10 copies per reaction. We applied this assay to environmental DNA (eDNA) extracted from paired water and sediment samples collected from 13 stations across the Geum River Basin. eDNA was detected at three water and five sediment stations. Notably, detection rates and average concentrations were consistently higher in a sediment sample (peaking at 1609.93 copies L⁻¹), an observation consistent with the species’ benthic ecology. These findings provide the first molecular evidence that restocked L. longirostris may disperse and persist in the mid to lower reaches of the Geum River. This validated eDNA qPCR tool is essential for guiding the integrated monitoring and adaptive management strategies required to support the long-term recovery of this ecologically important species. This study is the first species-specific qPCR of the bagrid catfish in South Korea.