Ecological monitoring contributes to the understanding of complex ecosystem functions. The diets of fish reflect the surrounding environment and habitats and may, therefore, act as useful integrating indicators of environmental status. It is, however, often difficult to visually identify items in gut contents to species level due to digestion of soft‐bodied prey beyond visual recognition, but new tools rendering this possible are now becoming available. We used a molecular approach to determine the species identities of consumed diet items of an introduced generalist feeder, brown trout (Salmo trutta), in 10 Tasmanian lakes and compared the results with those obtained from visual quantification of stomach contents. We obtained 44 unique taxa (OTUs) belonging to five phyla, including seven classes, using the barcode of life approach from cytochrome oxidase I (COI). Compared with visual quantification, DNA analysis showed greater accuracy, yielding a 1.4‐fold higher number of OTUs. Rarefaction curve analysis showed saturation of visually inspected taxa, while the curves from the DNA barcode did not saturate. The OTUs with the highest proportions of haplotypes were the families of terrestrial insects Formicidae, Chrysomelidae, and Torbidae and the freshwater Chironomidae. Haplotype occurrence per lake was negatively correlated with lake depth and transparency. Nearly all haplotypes were only found in one fish gut from a single lake. Our results indicate that DNA barcoding of fish diets is a useful and complementary method for discovering hidden biodiversity.

Our study focuses on methodological comparison of plankton community composition in relation to ecological monitoring and assessment with data sampling. Recently, along with the advancement of monitoring techniques, metabarcoding has been widely used in the context of environmental DNA (eDNA). We examine the applicability of eDNA metabarcoding for effective monitoring and assessment of community composition, compared with conventional observation using microscopic identification in a coastal ecosystem, Gwangynag Bay in South Korea. Our analysis is based primarily on two surveys at a total of 15 study sites in early and late summer (June and September) of the year 2018. The results of our study demonstrate the similarity and dissimilarity of biological communities in composition, richness and diversity between eDNA metabarcoding and conventional microscopic identification. It is found that, overall, eDNA metabarcoding appears to provide a wider variety of species composition, while conventional microscopic identification depicts more distinct plankton communities in sites. Finally, we suggest that eDNA metabarcoding is a practically useful method and can be potentially considered as a valuable alternative for biological monitoring and diversity assessments.

The nonlinearity and complexity of coastal ecosystems often cause difficulties when analyzing spatial and temporal patterns of ecological traits. Environmental DNA (eDNA) monitoring has provided an alternative to overcoming the aforementioned issues associated with classical monitoring. We determined aquatic community taxonomic composition using eDNA based on a meta-barcoding approach that characterizes the general ecological features in the Gwangyang Bay coastal ecosystem. We selected the V9 region of the 18S rDNA gene (18S V9), primarily because of its broad range among eukaryotes. Our results produced more detailed spatial patterns in the study area previously categorized (inner bay, main channel of the bay and outer bay) by Kim et al. (2019). Specifically, the outer bay zone was clearly identified by CCA using genus-level identification of aquatic organisms based on meta-barcoding data. We also found significant relationships between environmental factors. Therefore, eDNA monitoring based on meta-barcoding approach holds great potential as a complemental monitoring tool to identify spatial taxonomic distribution patterns in coastal areas.

Anthropogenic connectivity regulation in rivers, such as via weirs and dams, affects the plankton community. We hypothesized that the longitudinal similarity of the zooplankton community in a river could change in a river–reservoir hybrid system (RRHS). The impact of weir construction on zooplankton communities in terms of species diversity, abundance, and community structure was examined biweekly at six sites on the Nakdong River for 14 years (before construction: 2002–2008; after construction: 2012–2018). We checked time-series alignment using a dynamic time-warping method between longitudinal survey sites. After RRHS, the zooplankton community showed an increasing number of species. However, RRHS decreased the longitudinal similarity in terms of number of zooplankton species and population density. Our results demonstrate the negative effect of lateral infrastructures on zooplankton populations due to river fragmentation and habitat alteration.

Vitellogenesis is a pivotal reproductive process of the yolk formation in crustaceans. Vitellogenin (VTG) is the precursor of main yolk proteins and synthesized by endogenous estrogens. The intertidal mud crab (Macrophthalmus japonicus) inhabits sediment and is a good indicator for assessing polluted benthic environments. The purpose of this study was to identify potential responses of M. japonicus VTG under environmental stresses caused by chemical pollutants, such as 1, 10, and 30 µg L⁻¹ concentrations in di(2-ethylhexyl) phthalate (DEHP), bisphenol A (BPA) and irgarol. We characterized the M. japonicus VTG gene and analyzed the transcriptional expression of VTG mRNA in M. japonicus exposed to various chemicals and exposure periods. A phylogenetic analysis revealed that the M. japonicus VTG clustered closely with Eriocheir sinensis (Chinese mitten crab) VTG, in contrast with another clade that included the VTG ortholog of other crabs. The basal level of VTG expression was the highest in the hepatopancreas and ovaries, and tissues. VTG expression significantly increased in the ovaries and hepatopancreas after 24 h exposure to DEHP. Increased responses of VTG transcripts were found in M. japonicus exposed to DEHP and BPA for 96 h; however, VTG expression decreased in both tissues after irgarol exposure. After an exposure of 7 d, VTG expression significantly increased in the ovaries and hepatopancreas for all concentrations of all chemicals. These results suggest that the crustacean embryogenesis and endocrine processes are impaired by the environmental chemical pollutants DEHP, BPA, and irgarol.