Molecular Diet Analysis of Asian Clams for Supplementary Biodiversity Monitoring: A Case Study of Nakdong River Estuary.

Environmental DNA (eDNA) extracted from the gut contents of filter feeders can be used to identify biodiversity in aquatic ecosystems. In this study, we used eDNA from the gut contents of the Asian clam Corbicula fluminea to examine biodiversity within estuarine ecosystem. Field sampling was conducted at three points in the Nakdong River Estuary, which is characterised by closed estuarine features resulting from the presence of an estuarine barrage. The collected C. fluminea samples were dissected to separate the gut contents, and the extracted eDNA was amplified using 18S V9 primer targeting all eukaryote-derived DNA. The amplified DNA was sequenced using a next-generation sequencing (NGS) technique, and a BLASTn search was performed based on the National Centre for Biotechnology Information (NCBI) database for taxa identification. We obtained 23 unique operational taxonomic units (OTUs), including fish (approximately 8.70%), copepods (approximately 17.39%), and green algae (approximately 21.74%), representing a wide range of habitats. Furthermore, 8 out of the 20 families were identified through comparisons with reference data from conventional field surveys, and the OTUs of elusive migratory fish were detected. The results support the application of C. fluminea as an eDNA sampler for supplementary biodiversity monitoring.

Complete mitochondrial genome of Ischnura asiatica (Brauer, 1865) assembled from next-generation sequencing data.

Ischnura asiatica (Brauer, 1865) is a freshwater damselfly belonging to the family Coenagrionidae that is distributed across most of Korea, primarily in areas with low water flow, such as ponds and wetlands. The complete mitochondrial genome of I. asiatica was sequenced by next-generation sequencing. The circular mitochondrial genome was found to be 15,769 bp long, with of 13 protein-coding, two ribosomal RNA, and 22 transfer RNA genes (GenBank accession no. OM310774). Maximum likelihood, phylogenetic analysis showed that this species clustered with other species belonging to the family Coenagrionidae. This study contributes to the phylogeny of damselflies and other members of the family Coenagrionidae.

Effects of algal food quality on sexual reproduction of Daphnia magna.

The objective of our study was to investigate sexual reproduction of Daphnia magna associated with mating behaviors and hatching rates, according to different algal food sources. Since a diatom is known to contain more abundant long-chain poly unsaturated fatty acids (PUFAs), we hypothesized that the diatom-consuming D. magna would exhibit more successful reproduction rates. Upon the hypothesis, we designed three experiments using two algal species, a green alga (Chlorella vulgaris) and a diatom (Stephanodiscus hantzschii). From the results, we found that the mating frequency and copulation duration increased in the treatment with S. hantzschii, resulting in a significant increase of hatching rates of resting eggs. In the other two repetitive mating strategies (e.g., one female vs. multiple males, and one male vs. multiple females), we found that the hatching rates of resting eggs were greater in the S. hantzschii treatment. In addition to the mating strategy, male body size significantly increased in the diatom treatment, hence average diameter of penis was also statistically different among the treatments (greater diameter in the S. hantzschii treatment). To examine the effect of algal food quality, we estimated quantity of fatty acids in the two algal species. Our result showed that S. hantzschii had a higher proportion of long-chain PUFAs than C. vulgaris. Furthermore, a stable isotope analysis revealed that carbon and nitrogen originated from S. hantzschii were more assimilated to D. magna. In summary, our study manifested that diatom consumption of D. magna leads to more successful sexual reproduction. We then discussed how the diatom consumption of zooplankton influences food web dynamics in a freshwater ecosystem.

HEpD: a database describing epigenetic differences between Thoroughbred and Jeju horses.

With the advent of next-generation sequencing technology, genome-wide maps of DNA methylation are now available. The Thoroughbred horse is bred for racing, while the Jeju horse is a traditional Korean horse bred for racing or food. The methylation profiles of equine organs may provide genomic clues underlying their athletic traits. We have developed a database to elucidate genome-wide DNA methylation patterns of the cerebrum, lung, heart, and skeletal muscle from Thoroughbred and Jeju horses. Using MeDIP-Seq, our database provides information regarding significantly enriched methylated regions beyond a threshold, methylation density of a specific region, and differentially methylated regions (DMRs) for tissues from two equine breeds. It provided methylation patterns at 784 gene regions in the equine genome. This database can potentially help researchers identify DMRs in the tissues of these horse species and investigate the differences between the Thoroughbred and Jeju horse breeds.

Population growth of the Cladoceran, Daphnia magna: a quantitative analysis of the effects of different algal food.

In this study, we examined the effects of two phytoplankton species, Chlorella vulgaris and Stephanodiscus hantzschii, on growth of the zooplankton Daphnia magna. Our experimental approach utilized stable isotopes to determine the contribution of food algae to offspring characteristics and to the size of adult D. magna individuals. When equal amounts of food algae were provided (in terms of carbon content), the size of individuals, adult zooplankton, and their offspring increased significantly following the provision of S. hantzschii, but not after the provision of C. vulgaris or of a combination of the two species. Offspring size was unaffected when C. vulgaris or a mixture of the two algal species was delivered, whereas providing only S. hantzschii increased the production of larger-sized offspring. Stable isotope analysis revealed significant assimilation of diatom-derived materials that was important for the growth of D. magna populations. Our results confirm the applicability of stable isotope approaches for clarifying the contribution of different food algae and elucidate the importance of food quality for growth of D. magna individuals and populations. Furthermore, we expect that stable isotope analysis will help to further precisely examine the contribution of prey to predators or grazers in controlled experiments.

Application of DNA barcoding for identification of freshwater carnivorous fish diets: Is number of prey items dependent on size class for Micropterus salmoides?

Understanding predator-prey interactions is a major challenge in ecological studies. In particular, the accurate identification of prey is a fundamental requirement in elucidating food-web structure. This study took a molecular approach in determining the species identity of consumed prey items of a freshwater carnivorous fish (largemouth bass, Micropterus salmoides), according to their size class. Thirty randomly selected gut samples were categorized into three size classes, based on the total length of the bass. Using the universal primer for the mtDNA cytochrome oxidase I (COI) region, polymerase chain reaction (PCR) amplification was performed on unidentified gut contents and then sequenced after cloning. Two gut samples were completely empty, and DNA materials from 27 of 28 gut samples were successfully amplified by PCR (success rate: 96.4%). Sequence database navigation yielded a total of 308 clones, containing DNA from 26 prey items. They comprised four phyla, including seven classes, 12 orders, and 12 families based on BLAST and BOLD database searches. The results indicate that largemouth bass show selective preferences in prey item consumption as they mature. These results corroborate a hypothesis, presence of ontogenetic diet shift, derived through other methodological approaches. Despite the practical limitations inherent in DNA barcoding analysis, high-resolution (i.e., species level) identification was possible, and the predation patterns of predators of different sizes were identifiable. The utilization of this method is strongly recommended for determining specific predator-prey relationships in complex freshwater ecosystems.

Delayed influence of dam storage and discharge on the determination of seasonal proliferations of Microcystis aeruginosa and Stephanodiscus hantzschii in a regulated river system of the lower Nakdong River (South Korea).

This study presents the relationship between the dam hydrology and phytoplankton proliferations in a regulated river system in East Asia. A long-term ecological study reveals that multi-purpose dam regulation on river flow in the Nakdong River (South Korea) affects proliferating patterns of phytoplankton, especially during summer (June-August) and winter (December-next February) as Microcystis aeruginosa and Stephanodiscus hantzschii, respectively, dominate each season by over 80%. Eutrophication was observed in the lower Nakdong River (South Korea) (mean+/-standard deviation: nitrate-N, 2.8+/-0.9 mg L(-1); phosphate-P, 40.3+/-31.3 microg L(-1); chlorophyll a, 45.2+/-84.9 microg L(-1); n=449), and the limnological characteristics responded to climatic variations such as monsoon and summer typhoons. The river basin experiences concentrated rainfall during the rainy season (June-September, over ca. 60% of total annual rainfall). Correlation and cross-correlation for time-delayed relationship revealed the hydrological environments (i.e., quantity of dam storage and discharge) had significantly negative relationship with the population dynamics of the two bloom-forming species for up to the next 2 years. S. hantzschii had clearer relationship with dam storage and discharge, which might be due to the seasonality exhibited by the species. The results support the necessity of "smart flow control" which may enable destruction of bloom formation by the two species with an adequate pulse of discharge generated by upstream dams in the far-east Asian river systems. This would increase the efficiency of water resource management system.