Toxic effects of fragmented polyethylene terephthalate particles on the marine rotifer Brachionus koreanus: Based on ingestion and egestion assay, in vivo toxicity test, and multi-omics analysis.

Microplastics (MPs) are a major concern in marine ecosystem because MPs are persistent and ubiquitous in oceans and are easily consumed by marine biota. Although many studies have reported the toxicity of MPs to marine biota, the toxicity of environmentally relevant types of MPs is little understood. We investigated the toxic effects of fragmented polyethylene terephthalate (PET) MP, one of the most abundant MPs in the ocean, on the marine rotifer Brachionus koreanus at the individual and molecular level. No significant rotifer mortality was observed after exposure to PET MPs for 24 and 48 h. The ingestion and egestion assays showed that rotifers readily ingested PET MPs in the absence of food but not when food was supplied; thus, there were also no chronic effects of PET MPs. In contrast, intracellular reactive oxygen species levels and glutathione S-transferase activity in rotifers were significantly increased by PET MPs. Transcriptomic and metabolomic analyses revealed that genes and metabolites related to energy metabolism and immune processes were significantly affected by PET MPs in a concentration-dependent manner. Although acute toxicity of PET MPs was not observed, PET MPs are potentially toxic to the antioxidant system, immune system, and energy metabolism in rotifers.

Comparative transcriptome analysis of two Daphnia galeata genotypes displaying contrasting phenotypic variation induced by fish kairomones in the same environment of the Han River, Korea.

BACKGROUND: Phenotypic plasticity is a crucial adaptive mechanism that enables organisms to modify their traits in response to changes in their environment. Predator-induced defenses are an example of phenotypic plasticity observed across a wide range of organisms, from single-celled organisms to vertebrates. In addition to morphology and behavior, these responses also affect life-history traits. The crustacean Daphnia galeata is a suitable model organism for studying predator-induced defenses, as it exhibits life-history traits changes under predation risk. To get a better overview of their phenotypic plasticity under predation stress, we conducted RNA sequencing on the transcriptomes of two Korean Daphnia galeata genotypes, KE1, and KB11, collected in the same environment. RESULTS: When exposed to fish kairomones, the two genotypes exhibited phenotypic variations related to reproduction and growth, with opposite patterns in growth-related phenotypic variation. From both genotypes, a total of 135,611 unigenes were analyzed, of which 194 differentially expressed transcripts (DETs) were shared among the two genotypes under predation stress, which showed consistent, or inconsistent expression patterns in both genotypes. Prominent DETs were related to digestion and reproduction and consistently up-regulated in both genotypes, thus associated with changes in life-history traits. Among the inconsistent DETs, transcripts encode vinculin (VINC) and protein obstructor-E (OBST-E), which are associated with growth; these may explain the differences in life-history traits between the two genotypes. In addition, genotype-specific DETs could explain the variation in growth-related life-history traits between genotypes, and could be associated with the increased body length of genotype KE1. CONCLUSIONS: The current study allows for a better understanding of the adaptation mechanisms related to reproduction and growth of two Korean D. galeata genotypes induced by predation stress. However, further research is necessary to better understand the specific mechanisms by which the uncovered DETs are related with the observed phenotypic variation in each genotype. In the future, we aim to unravel the precise adaptive mechanisms underlying predator-induced responses.

Pathway-dependent toxic interaction between polystyrene microbeads and methylmercury on the brackish water flea Diaphanosoma celebensis: Based on mercury bioaccumulation, cytotoxicity, and transcriptomic analysis.

Given their worldwide distribution and toxicity to aquatic organisms, methylmercury (MeHg) and microplastics (MP) are major pollutants in marine ecosystems. Although they commonly co-exist in the ocean, information on their toxicological interactions is limited. Therefore, to understand the toxicological interactions between MeHg and MP (6-µm polystyrene), we investigated the bioaccumulation of MeHg, its cytotoxicity, and transcriptomic modulation in the brackish water flea Diaphanosoma celebensis following single and combined exposure to MeHg and MP. After single exposure to MeHg for 48-h, D. celebensis showed high Hg accumulation (34.83 ± 0.40 µg/g dw biota) and cytotoxicity, which was reduced upon co-exposure to MP. After transcriptomic analysis, 2, 253, and 159 differentially expressed genes were detected in the groups exposed to MP, MeHg, and MeHg+MP, respectively. Genes related to metabolic pathways and the immune system were significantly affected after MeHg exposure, but the effect of MeHg on these pathways was alleviated by MP co-exposure. However, MeHg and MP exhibited synergistic effects on the expression of gene related to DNA replication. These findings suggest that MP can reduce the toxicity of MeHg but that their toxicological interactions differ depending on the molecular pathway.

Analysis of the complete mitogenome of Daphnia galeata from the Han River, South Korea: structure comparison and control region evolution.

Daphnia galeata is an important plankton in aquatic ecosystems. As a widely distributed species, D. galeata has been found throughout the Holarctic region. Understanding the genetic diversity and evolution of D. galeata requires the accumulation of genetic information from different locations. Even though the mitochondrial genome (mitogenome) sequence of D. galeata has already been reported, little is known about the evolution of its mitochondrial control region. In this study, D. galeata samples were collected from the Han River on the Korean Peninsula and its partial nd2 gene was sequenced for haplotype network analysis. This analysis showed that four clades of D. galeata were present in the Holarctic region. Moreover, the D. galeata examined in this study belonged to clade D and was specific to South Korea. The mitogenome of D. galeata from the Han River showed similar gene content and structure compared to sequences reported from Japan. Furthermore, the structure of control region of the Han River was similar to those of Japanese clones and differed substantially from European clone. Finally, a phylogenetic analysis based on the amino acid sequences of 13 protein-coding genes (PCGs) indicated that D. galeata from the Han River formed a cluster with clones collected from Lakes Kasumigaura, Shirakaba, and Kizaki in Japan. The differences in control region structure and stem and loop structure reflect the different evolutionary directions of the mitogenomes from Asian and European clones. These findings improve our understanding of the mitogenome structure and genetic diversity of D. galeata.

Comparative Transcriptome Analysis of Eriocheir sinensis from Wild Habitats in Han River, Korea.

Eriocheir sinensis is an euryhaline crab found from East Asia to Europe and North America. This species can live in freshwater and seawater due to the unique physiological characteristics of their life cycle, which allows them to adapt and inhabit different habitats in a wide range of environments. Despite the wealth of studies focusing on adaptation mechanism of E. sinensis to specific environmental factors, the adaptation mechanisms to wild habitats with coexisting environmental factors are not well understood. In this study, we conducted a transcriptome analysis to investigate gene expression differences related to habitat adaptation of E. sinensis from two wild habitats with different environmental factors in the Han River, Korea. A total of 138,261 unigenes were analyzed, of which 228 were analyzed as differentially expressed genes (DEGs) between the two wild habitats. Among 228 DEGs, 110 DEGs were annotated against databases; most DEGs were involved in energy metabolism, immunity, and osmoregulation. Moreover, DEG enrichment analysis showed that upregulated genes were related to biosynthesis, metabolism, and immunity in an habitat representing relatively high salinity whereas downregulated genes were related to ion transport and hypoxia response in habitats with relatively low salinity and dissolved oxygen. The present findings can serve as foundation for future E. sinensis culture or conservation approaches in natural conditions.

Machine Learning Models for Identification and Prediction of Toxic Organic Compounds Using Daphnia magna Transcriptomic Profiles.

A wide range of environmental factors heavily impact aquatic ecosystems, in turn, affecting human health. Toxic organic compounds resulting from anthropogenic activity are a source of pollution in aquatic ecosystems. To evaluate these contaminants, current approaches mainly rely on acute and chronic toxicity tests, but cannot provide explicit insights into the causes of toxicity. As an alternative, genome-wide gene expression systems allow the identification of contaminants causing toxicity by monitoring the organisms' response to toxic substances. In this study, we selected 22 toxic organic compounds, classified as pesticides, herbicides, or industrial chemicals, that induce environmental problems in aquatic ecosystems and affect human-health. To identify toxic organic compounds using gene expression data from Daphnia magna, we evaluated the performance of three machine learning based feature-ranking algorithms (Learning Vector Quantization, Random Forest, and Support Vector Machines with a Linear kernel), and nine classifiers (Linear Discriminant Analysis, Classification And Regression Trees, K-nearest neighbors, Support Vector Machines with a Linear kernel, Random Forest, Boosted C5.0, Gradient Boosting Machine, eXtreme Gradient Boosting with tree, and eXtreme Gradient Boosting with DART booster). Our analysis revealed that a combination of feature selection based on feature-ranking and a random forest classification algorithm had the best model performance, with an accuracy of 95.7%. This is a preliminary study to establish a model for the monitoring of aquatic toxic substances by machine learning. This model could be an effective tool to manage contaminants and toxic organic compounds in aquatic systems.

Seasonal Diversity of Microeukaryotes in the Han River, Korea Through 18S rRNA Gene Metabarcoding.

Freshwater ecosystems contain a large diversity of microeukaryotes that play important roles in maintaining their structure. Microeukaryote communities vary in composition and abundance on the basis of temporal and environmental variables and may serve as useful bioindicators of environmental changes. In the present study, 18S rRNA metabarcoding was employed to investigate the seasonal diversity of microeukaryote communities during four seasons in the Han River, Korea. In total, 882 unique operational taxonomic units (OTUs) were detected, including various diatoms, metazoans (e.g., arthropods and rotifers), chlorophytes, and fungi. Although alpha diversity revealed insignificant differences based on seasons, beta diversity exhibited a prominent variation in the community composition as per seasons. The analysis revealed that the diversity of microeukaryotes was primarily driven by seasonal changes in the prevailing conditions of environmental water temperature and dissolved oxygen. Moreover, potential indicator OTUs belonging to diatoms and chlorophytes were associated with seasonal and environmental factors. This analysis was a preliminary study that established a continuous monitoring system using metabarcoding. This approach could be an effective tool to manage the Han River along with other freshwater ecosystems in Korea.

Development of polymorphic microsatellite markers for the Trichoglossus haematodus and cross-species amplification in Trichoglossus moluccanus.

BACKGROUD: Trichoglossus haematodus is the most popular parrots globally and one of the most bred species in Korea's zoos. However, despite its popularity, there are limited studies on the population genetics of this species. METHODS AND RESULTS: In this study, 10 polymorphic microsatellite markers were developed for T. haematodus. The number of alleles ranged from 6 to 9 (mean 7.9). Null alleles were present in two loci (TH-07 and TH-08). The observed heterozygosity ranged from 0.4444 to 1.0000 (mean 0.7000). One locus (TH-08) indicated a significant deviation from the Hardy-Weinberg equilibrium after Bonferroni correction (p < 0.005). The mean inbreeding coefficient (FIS) of the 10 loci was positive, suggesting that there is inbreeding in the population. Since the polymorphism information content (PIC) values were more than 0.7 in all loci, all markers developed in this study were classified as informative. The parentage exclusion probabilities considering all loci were higher than 0.99 in all three cases (P1, P2, and P3). The cross-species amplification of the 10 markers was tested in T. moluccanus, a close relative species of T. haematodus. These markers were also informative for T. moluccanus with PIC values higher than 0.7 in all loci. Additionally, the parentage exclusion probabilities (P1, P2 and P3) for T. moluccanus were above 0.99. However, due to the small number of T. haematodus and T. moluccanus investigated in this study, the 10 microsatellite markers should be analyzed with more individuals of these two species in future studies. CONCLUSIONS: The markers developed in this study might be helpful for investigations of genetic diversity and parentage analysis of T. haematodus and T. moluccanus.

The complete mitochondrial genome of Scyra compressipes Stimpson, 1857 (Decapoda: Epialtidae).

The family Epialtidae is the most diversified family within superfamily Majoidea but there is no report for complete mitogenome of any species in this family. This study was performed to sequence a complete mitogenome of Scyra compressipes Stimpson, 1857, as the first mitochondrial genome report from the Epialtidae. The complete mitogenome sequence of S. compressipes was 16,415 bp and it consisted of 36 genes, including 13 protein-coding genes (PCGs), two rRNA genes, and 21 tRNA genes excluding tRNA-Leu (UAG). tRNA genes ranged from 63 bp to 72 bp in length. The base composition of a complete mitogenome of S. compressipes is 34.7% A, 15.3% C, 10.2% G, and 39.8% T. The phylogenetic position of S. compressipes in the superfamily Majoidea was examined based on 13 PCGs. The phylogenetic analysis showed that S. compressipes was most closely related to Maguimithrax spinosissimus, a representative of the family Mithracidae.

Characterization of the complete mitochondrial genome of Okenia hiroi (Baba, 1938) (Nudibranchia, Goniodorididae).

Okenia is a speciose genus of the family Goniodorididae with more than 50 valid species. The phylogenetic relationships within the genus are little known. The mitogenome is a good marker to understand the phylogenetic relationships of relative species. This study was performed to sequence the mitogenome of O. hiroi. The mitogenome of O. hiroi was 14,583 bp in size and was composed of 37 genes, including 13 protein-coding genes, two ribosomal RNA genes, and 22 tRNA genes. The nucleotide composition was 30.5% A, 13.6% C, 16.5% G, and 39.4% T. The phylogenetic analysis showed that O. hiroi is sister to Notodoris gardineri (Aegiridae). This study recorded the first mitochondrial genome sequence of the family Goniodorididae.

An Investigation of the Variations in Complete Mitochondrial Genomes of Lingula anatina in the Western Pacific Region.

Lingula anatina is a brachiopod widely distributed in the western Pacific region. Even though L. anatina has been targeted for a number of biological studies, there is still limited information on intraspecific genetic variations of L. anatina. In this study, L. anatina specimens were collected from Korea and Vietnam, and complete mitochondrial genome (mitogenome) sequences were analyzed and compared with previous records. The total mitogenomes of L. anatina were 24,875 bp and 25,305 bp in size for Korean and Vietnamese specimens, respectively. Those mitogenomes are extraordinarily longer than the typical mitogenome size for an animal but shorter than the previous record from Yanagawa (Japan) for this species. The gene orders and the sizes of the protein-coding genes are also different from those for the Japanese specimen. Furthermore, the nonsynonymous (Ka) and synonymous (Ks) substitution rates in protein-coding genes (PCGs) were calculated to test the idea of evolutionary rate differences in mitochondrial genomes. The analyses showed relatively low Ka and Ks for the complete mitogenomes from Buan (Korea), Doson (Vietnam) and Yanagawa (Japan). The Ka/Ks ratio was less than 1 in comparisons of three localities, indicating the existence of purifying selection in this species. The phylogenetic analyses showed that L. anatina diverged among localities in the western Pacific region.

The complete mitochondrial genome of Hemigrapsus penicillatus (De Haan, 1835) (Decapoda, Varunidae).

Hemigrapsus penicillatus is a small grapsoid crab which is found in Japan, Taiwan, Korea, and China coasts. In this study a complete mitogenome of Korean H. penicillatus was analyzed and phylogenetic relationships in the family Varunidae were investigated. The mitogenome size is 16,486 bp with 34.1% A, 18.1% C, 11.4% G, and 36.4% T nucleotide distributions. Genome structure and gene orientations are identical with previous records from the family and mitochondrial protein-coding gene based phylogenetic tree suggested that the closest species to H. penicillatus is H. sanguineus. This is the second complete mitogenome record from the genus Hemigrapsus and the first record for the species.