Expansion of the HSP70 gene family in Tegillarca granosa and expression profiles in response to zinc toxicity.

Zinc (Zn) is an essential micronutrient in organisms and an abundant element in the Earth's crust. Trace amounts of Zn released from natural sources can enter aquatic ecosystems through weathering and erosion. Zn accumulates in organisms, and when its intracellular concentration exceeds a certain level, it can induce oxidative stress and trigger oxidative stress-mediated heat shock protein (HSP) modulation. HSP70 is the most evolutionarily conserved among the HSP families. Despite extensive research on HSP70 genes in bivalves, the HSP70 gene family of Tegillarca granosa is still poorly characterized. We identified 65 HSP70 genes belonging to 6 families in the T. granosa genome, with 50 HSPa12 and 11 HSPa B2 genes highly expanded. On chromosome 11, 39 HSP70 (60%) genes were identified, and the HSPa12A genes were highly duplicated. A total of 527 and 538 differentially expressed genes were identified in the gills and mantle based on Zn exposure, respectively. The Gene Ontology of cellular anatomical entities was significantly enriched with upregulated differentially expressed genes in the gills and mantle. Eight of the 11 HSPa B2 genes were upregulated in both tissues. Most of the genes identified in both tissues were involved in "protein homeostasis" and "inhibition of apoptosis," which are associated with the HSP70 family's resistance to extrinsic and intrinsic stress. Hence, this study identified that the HSP70 gene family plays a vital role in the adaptation of aquatic organisms to heavy metal (e.g., Zn) stress in contaminated environments by compiling the different physiological responses to preserve homeostasis.

Distribution of nephrons in the head kidney of three species of Sebastes (Teleostei: Scorpaenidae).

Nephrons are generally not distributed in the head kidney of teleost. Nonetheless, in this study, the nephron structure was identified in the head kidney of three species of Sebastes (Sebastes inermis, Sebastes schlegelii and Sebastes thompsoni). The kidney is Y shaped, with the development in the head kidney. The nephron structure was confirmed in the head kidney and body kidney. In addition, the nephron consisted of renal corpuscles and tubules, and the renal corpuscle consisted of the Bowman's capsule and glomerulus. Histologically, previous studies reported that the nephron structure is similar to that of other marine teleost. The renal tubule is a simple columnar epithelial layer with microvilli and cilia on the free surface, which is observed as a brush border. The Rrk (relative area ratio of kidney to body surface) was 5.14%, 7.58% and 5.17% in S. inermis, S. schlegelii and S. thompsoni, respectively. The Gar (glomerular area ratio of the head kidney) was higher in the central area than in the peripheral area, and species, which showed significant difference (P < 0.05), were in the following order: S. thompsoni (1.60%) > S. schlegelii (0.90%) > S. inermis (0.66%).

Chemo-photothermal therapeutic effect of chitosan-gelatin hydrogels containing methotrexate and melanin on a collagen-induced arthritis mouse model.

Heat stimulation can promote osteoblast differentiation and bone formation. Combining photothermal therapy and chemotherapy is an effective strategy for treating rheumatoid arthritis (RA). Herein, we prepared chitosan/gelatin/ß-glycerophosphate-melanin-methotrexate (CMM) hydrogel that could be used to perform simultaneous chemotherapy and photothermal therapy for patients with RA. The CMM solution was successfully converted to a gel state at body temperature. Due to intrinsic photothermal properties of melanin, CMM hydrogel exhibited effective temperature increase both in vitro and in vivo with increasing time of near-infrared (NIR) laser irradiation. After NIR laser irradiation, 50 % of methotrexate was rapidly released from the hydrogel within 3 h. Its release rate showed an instantaneous increase with additional NIR laser irradiation. After CMM hydrogel was injected directly into the paw joint of each collagen-induced arthritis (CIA) mouse followed by irradiation with a NIR laser (808 nm, 0.5 W/cm2, 3 min), swelling and redness at the inflamed area were significantly alleviated at 14 days after treatment. Micro-CT analysis confirmed that treated joints of mice were similar to normal joints. Hence, CMM hydrogel could be used as an attractive RA therapeutic agent for simultaneous chemo-photothermal therapy.

Light and electron microscopy studies of siphon and siphonal sheath formation in the infaunal bivalve Tresus keenae (Bivalvia: Mactridae).

To understand the habitat ecology of Tresus keenae, an infaunal bivalve, the microanatomical structure of the siphon and the method of siphonal sheath formation were described. The diameter of the incurrent siphon was approximately 1.2 times greater than that of the excurrent siphon. Several irregular tentacles developed inside the distal end of the siphon. The tentacles in the incurrent siphon were approximately twice as long as those in the excurrent siphon. The siphon consisted of six tissue layers, which, from the outside inward, were the siphonal sheath, matrix, outer epithelial layer, connective tissue layer, muscular layer, and inner epithelial layer. The siphonal sheath was composed of an outer cuticle and dense microfilament layer and had vertical ducts. The matrix showed a loose microfilament layer. The outer epithelial layer was simple consisting of ciliated columnar epithelia and secretory cells. There were two types of secretory cells: arenophilic cells and proteinous granular cells. These were all unicellular glands, with cytoplasmic projections developing on the free surface and microstructural features of the cytoplasm showing secretory activity. Histochemical analysis indicated that the secretory granules of the secretory cells, the dense microfilament layer, and the matrix were composed of neutral carboxylated mucopolysaccharides. From these characteristics, it was concluded that the siphonal sheath was formed via the transportation of substances secreted by secretory cells of the outer epithelial layer to the outside through the duct. The hemolymph sinus developed in the connective tissue layer. The muscular layer had alternating longitudinal and circular muscle layers. The inner epithelial layer was simple and consisted of ciliated columnar epithelial cells and secretory cells. Secretory cells are goblet-like cells and contain acidic carboxylated substances. The siphonal sheath was identified starting at approximately 3.5 mm in shell length before the infaunal stage; as it grew, the siphonal sheath thickened, reflecting the infaunal habitat.

Functional analysis of LFRFamide signaling in Pacific abalone, Haliotis discus hannai.

The invertebrate LFRFamide (LFRFa) and short neuropeptide F (sNPF), consisting of 6 to 10 amino acids, are orthologs for bilaterian NPF/Y, which consist of 36 to 40 amino acids. Recently, a molluscan G protein-coupled receptor (GPCR) for NPF was characterized in Pacific abalone (Haliotis discus hannai). To address the functional evolutionary route of the invertebrate LFRFa and NPF signaling system, in this study, we identified cDNAs encoding LFRFa precursors and the sNPF receptor (Hdh-sNPFR) in Pacific abalone. Four LFRFa mature peptides with 6 or 7 amino acids were predicted: GSLFRFa, GGLFRFa, GTLFRFa, and GSTLFRFa. Hdh-sNPFR was identified as a classical rhodopsin-like GPCR and classified into a molluscan sNPFR group. In HEK293 cells, Hdh-sNPFR was mainly localized in the cell membranes and internalized in the cytoplasm following treatment with LFRFa peptides. Reporter assays demonstrated that LFRFa peptides inhibit forskolin-stimulated cAMP accumulation in Hdh-sNPFR-expressing HEK293 cells. LFRFa precursor and Hdh-sNPFR transcripts were more strongly expressed in the cerebral and pleural-pedal ganglia of Pacific abalone than in the peripheral tissues such as the ovary, gills, intestine, and hepatopancreas. The levels of LFRFa transcripts in the ovary, intestine, and hepatopancreas were significantly higher in mature female abalone than in immature females. Injection of LFRFa induced the egg release and spawning behavior of mature abalone, but suppressed food intake. These results suggest that LFRFa peptides are endogenous ligands for Hdh-sNPFR involved in food intake and reproduction through a Gαi-protein dependent signaling pathway.

Gonadal Abnormality and Intersexuality of Oplegnathus fasciatus (Teleostei: Oplegnathidae) Collected from the Southern Coast of Korea: A Case Report.

We report on the gonadal structure abnormality and intersexuality found from a survey regarding the reproductive potential of the rock bream, Oplegnathus fasciatus, along the southern coast of Korea. In total, 448 samples were collected for histological analysis (total length 27.5±6.8 cm; total weight 522.9±385.6 g). The sex ratio (F:M) was 1:0.46 (n=307:141), with 68.5% being females. The frequency of oocyte atresia and ovarian neoplasm in the females was 85.3% and 21.5%, respectively, and the frequency of testicular lobule and cyst deformation and testicular neoplasm in the males was 73.1% and 37.6%, respectively. The scale formation in the ovary and testis was approximately 2.0% for both sexes. The intersexuality was 42.2%, with the intersexuality among females being 49.5%, which was significantly higher than that of males (26.2%). Such findings indicate a negative impact on the reproductive output of the rock bream along the southern coast of Korea; however, a more detailed study is required to ascertain accurate causes.

Sex of Mussel Mytilus coruscus (Bivalvia: Mytilidae) : Sequential Hermaphroditism.

Samples were collected from the subtidal region of Jumunjin on the eastern coast of Korea in July 2020. A total of 338 mussels of shell height (SH) 20.8-149.8 mm were used for sex ratio analysis. The sex ratio (F:M) in the same population of mussel Mytilus coruscus was approximately 1:0.7. The sex ratio according to the class of SH was different. The sex reversal pattern of M. coruscus appears to go from male → female → male → female, and as such is determined to be sequential hermaphrodites.

Ovarian transcriptome profiles associated with sexual maturation in Pacific abalone (Haliotis discus hannai).

BACKGROUND: There is now abundant information on genes involved in molluscan oogenesis and their associations with ovarian development. However, few studies have investigated the ovarian transcriptome of Pacific abalone (Haliotis discus hannai). OBJECTIVE: The objective of this study was to identify genes related to ovarian development and maturation in Pacific abalone utilizing RNA-sequencing (RNA-seq) and to verify the genes most relevant to different stages of maturation. METHODS: RNA samples from the ovarian tissues of sexually immature and mature abalone were used to construct cDNA libraries, which were paired-end sequenced on an Illumina HiSeq 2500 platform. Reads from individual samples (unigenes) were aligned to reference transcriptome databases for identification of differentially expressed genes (DEGs) between immature and mature ovarian libraries. Reverse transcription-quantitative polymerase chain reaction was used to verify the RNA-seq data. RESULTS: A total of 8779 unigenes were obtained from the ovaries of immature and mature abalone, with a total length of 3323,279 bp and an average length of 379 bp per gene. Gene ontology analysis assigned 5860 unigenes to biological processes, 855 to cellular components, and 1352 to molecular functions. Overall, 470 DEGs were identified, including 213 and 257 genes down-regulated and up-regulated in mature abalone, respectively. Among these, 13 relevant transcripts, including VTG1 and FZD7, were significantly highly expressed in the ovaries of mature abalone (p < 0.05, fold change > 2). CONCLUSION: This H. discus hannai ovary transcriptome provides molecular targets to better understand ovarian development, oogenesis, and sexual maturation, and to enhance Pacific abalone production.

Prolonged exposure to hypoxia inhibits the growth of Pacific abalone by modulating innate immunity and oxidative status.

In aquatic animals, hypoxia is associated with growth retardation, impaired immunity, susceptibility to pathogens, oxidative stress, and mortality. However, the relative long-term effects of hypoxia on bivalves, including abalone, are not well understood. In this study, we examined the effects of exposure to hypoxic (2.5 and 4 mg O2 L-1) and normoxic (8 mg O2 L-1) conditions on the growth, survival, and immune and antioxidant responses of the economically important Pacific abalone Haliotis discus hannai over a 4 month period. We observed that exposure to 2.5 mg O2 L-1 resulted in marked reductions in assessed shell parameters, average meat weight, and survival compared with exposure to 4 and 8 mg O2 L-1. There were also significant reductions in oxygen consumption and ammonia-N excretion in abalone exposed to 2.5 mg O2 L-1. We also detected initial immunosuppression in the 2.5 mg O2 L-1-treated abalone, as evidenced by a significant reduction in total hemocytes and inhibition of antibacterial and lysozyme activities. Furthermore, intracellular malondialdehyde concentrations were significantly elevated at 1 month in the 2.5 mg O2 L-1 treatment group, whereas there were reductions in the levels of glutathione and enzymatic activities of catalase and superoxide dismutase, thereby indicating potential hypoxia-induced oxidative stress and a depression of antioxidant capacity. After 4 months of treatment, severe hypoxia (2.5 mg O2 L-1) had significantly modulated all measured parameters, whereas exposure to 4 and 8 mg O2 L-1 had induced no significant effects. Collectively, our observations indicate that under long-term exposure to hypoxia, Pacific abalone failed to maintain an effective antioxidant defense system and adequate immunity, with the observed biochemical disruptions leading to a reduction in growth and survival.

Gonadal Maturation and Main Spawning Period of Haliotis gigantea (Gastropoda: Haliotidae).

This study was carried out to obtain information on the developmental biology and the management of biological resources of the abalone Haliotis gigantea in Korea. The sex ratio (female:male) in the present study was 1:1.7 and the proportion of females was 36.6% (n=106/290). Their gonadal structures displayed definitive seasonal changes which were similar in pattern to the changes in the gonad index (GI). The GI showed a pattern of definitive seasonal changes in both males and females it was high in the fall and low in the spring. The reproductive cycle could be categorized into the following six stages: inactive, early active, late active, ripe, spent, and degenerative stage. Based on the monthly changes in GI and stages of gonadal development, October to November was determined to be the main spawning period for H. gigantea on Jeju Island, Korea.

Neural Ganglia Transcriptome and Peptidome Associated with Sexual Maturation in Female Pacific Abalone (Haliotis discus hannai).

Genetic information of reproduction and growth is essential for sustainable molluscan fisheries and aquaculture management. However, there is limited knowledge regarding the reproductive activity of the commercially important Pacific abalone Haliotisdiscushannai. We performed de novo transcriptome sequencing of the ganglia in sexually immature and mature female Pacific abalone to better understand the sexual maturation process and the underlying molecular mechanisms. Of the ~305 million high-quality clean reads, 76,684 transcripts were de novo-assembled with an average length of 741 bp, 28.54% of which were annotated and classified according to Gene Ontology terms. There were 256 differentially expressed genes between the immature and mature abalone. Tandem mass spectrometry analysis, as compared to the predicted-peptide database of abalone ganglia transcriptome unigenes, identified 42 neuropeptide precursors, including 29 validated by peptidomic analyses. Label-free quantification revealed differential occurrences of 18 neuropeptide families between immature and mature abalone, including achatin, FMRFamide, crustacean cardioactive peptide, and pedal peptide A and B that were significantly more frequent at the mature stage. These results represent the first significant contribution to both maturation-related transcriptomic and peptidomic resources of the Pacific abalone ganglia and provide insight into the roles of various neuropeptides in reproductive regulation in marine gastropods.

Changes in Hematological Parameters and Heat Shock Proteins in Juvenile Sablefish Depending on Water Temperature Stress.

Juvenile Sablefish Anoplopoma fimbria were used to assess the effects of water temperature (8, 10, 12, 14, 16, 18, and 20°C) on hematological parameters and heat shock proteins 70 and 90 for 4 months. Hematological parameters, including red blood cell count, hematocrit, and hemoglobin, were significantly decreased at 18°C. The inorganic plasma components calcium and magnesium were not altered by water temperature. The organic plasma components glucose and cholesterol were notably elevated at 18°C, whereas total protein was reduced. The enzymatic components, including aspartate aminotransferase, alanine aminotransaminase, and alkaline phosphatase, were notably elevated at 16°C or 18°C. The results of this study indicate that a temperature higher than the proper temperature affects the hematological parameters and heat shock proteins of juvenile Sablefish.

Transcriptome profiling suggests roles of innate immunity and digestion metabolism in purplish Washington clam.

The purplish Washington clam (Saxidomus purpuratus) in the family Veneridae is distributed widely along the intertidal zones of northeast Asia and is increasingly being utilized as a commercially important food resource. Bivalves maintain homeostasis by regulating their food intake and digestion, innate immunity, and biotransformation in a mollusk-specific organ, the digestive gland. To understand digestive gland-specific pathways, we generated a high-quality de novo assembly of the digestive gland transcriptome of this clam using the Illumina Miseq platform. A total of 9.9 million raw reads were obtained and assembled using the Oases assembly platform, resulting in 27,358 contigs with an N50 of 433 bp. Functional gene annotations were performed using Gene Ontology, Eukaryotic Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes pathway analyses. In the transcriptome, many crucial genes involved in innate immunity and digestion metabolism were detected. A number of enzymes associated with drug metabolism were annotated, as much as that identified from the whole transcriptome of the Pacific oyster Crassostrea gigas. We provide valuable sequence information of S. purpuratus to predict functional understandings of the bivalve-specific digestive gland. This resource will be valuable for researchers comparing gene compositions and their expression levels in the digestive glands of bivalves.

Expression profile and reproductive regulation of APGWamide in Pacific abalone (Haliotis discus hannai).

Neuropeptides in the central nervous system regulate reproductive activities in vertebrates. Ala-Pro-Gly-Trp-NH2 (APGWamide), a neuromediator expressed in the neural ganglia of mollusks, controls sexual maturation and reproduction. To clarify the role of APGWamide in sexual behavior regulation and gamete cell maturation in mollusks, we cloned the cDNA of APGWamide precursor (Hdh-APGWamide) and examined the spatiotemporal expression of the transcript in the Pacific abalone Haliotis discus hannai. The 222-amino acid sequence of the precursor deduced from the cDNA sequence showed typical features of gastropod APGWamide precursors. Phylogenetic analysis revealed that Hdh-APGWamide is classified with other gastropod APGWamide precursors, which form a separate branch from those of the bivalves. Hdh-APGWamide mRNA was highly expressed in the neural ganglia in both sexes. In females, the three ganglia (pleuro-pedal ganglion, PPG; branchial ganglion, and cerebral ganglion) showed similar expression in immature and mature animals, whereas in males, the level in the PPG only was higher at maturity (P < 0.05). In vivo injection of APGWamide or 5-hydroxytryptamine (10-3 M) increased the frequency of spawning and the number of released sperm cells by mature males (P < 0.05), while concentrations above 10-7 M enhanced germinal vesicle breakdown in fully developed cultured oocytes (P < 0.05). Thus, the phylogenetic branch of the APGWamide precursor gene in Haliotidae was separate from the other branches under the phylum Mollusca, and this gene exhibited ganglion-specific expression, indicating that it may induce final maturation and spawning in both sexes of Haliotis spp.

Toxic effects of juvenile sablefish, Anoplopoma fimbria by ammonia exposure at different water temperature.

Juvenile sablefish, Anoplopoma fimbria (mean length 17.1±2.4cm, and mean weight 75.6±5.7g) were used to evaluate toxic effects on antioxidant systems, immune responses, and stress indicators by ammonia exposure (0, 0.25, 0.75, and 1.25mg/L) at different water temperature (12 and 17°C) in 1 and 2 months. In antioxidant responses, superoxide dismutase (SOD) and catalase (CAT) were significantly increased by ammonia exposure, whereas glutathione (GSH) was decreased. In immune responses, lysozyme and phagocytosis activity were significantly increased by ammonia exposure. In stress indicators, plasma glucose, heat shock protein 70 (HSP 70), and cortisol were significantly increased. At high water temperature (17°C), alterations by ammonia exposure were more distinctly. The results of this study indicated that ammonia exposure can induce toxic effects in the sablefish, and high water temperature can affect the ammonia exposure toxicity.

Growth performance, oxidative stress, and non-specific immune responses in juvenile sablefish, Anoplopoma fimbria, by changes of water temperature and salinity.

Juvenile sablefish, Anoplopoma fimbria (mean length 15.5 ± 1.9 cm, mean weight 68.5 ± 4.8 g), were used to evaluate the effects on growth, oxidative stress, and non-specific immune responses by changes of water temperature (8, 10, 12, 14, 16, 18, and 20 °C) and salinity (100 (35.0), 90 (31.5), 80 (28.0), 70 (24.5), 60 (21.0), 50 (17.5), and 40% (14.0) (‰)) for 4 months. The growth performance was significantly increased at the temperature of 12 and 14 °C, and the feed efficiency was notably decreased at the temperature of 18 °C. The growth performance and feed efficiency were also significantly decreased at low salinity. The antioxidant responses such as superoxide dismutase and catalase were significantly increased by the high temperature and decreased by the low salinity. The immune responses such as lysozyme and phagocytosis were elevated by the temperature of 18 °C and decreased by the salinity of 50%. The results of this study indicate that the growth performance of juvenile sablefish, A. fimbria, is influenced by the temperature and salinity, and the excessive temperature and salinity levels can affect the antioxidant and immune responses.

Characterization and spatiotemporal expression of gonadotropin-releasing hormone in the Pacific abalone, Haliotis discus hannai.

Gonadotropin-releasing hormone (GnRH) is a key neuropeptide regulating reproduction in humans and other vertebrates. Recently, GnRH-like cDNAs and peptides were reported in marine mollusks, implying that GnRH-mediated reproduction is an ancient neuroendocrine system that arose prior to the divergence of protostomes and deuterostomes. Here, we evaluated the reproductive control system mediated by GnRH in the Pacific abalone Haliotis discus hannai. We cloned a prepro-GnRH cDNA (Hdh-GnRH) from the pleural-pedal ganglion (PPG) in H. discus hannai, and analyzed its spatiotemporal gene expression pattern. The open reading frame of Hdh-GnRH encodes a protein of 101 amino acids, consisting of a signal peptide, a GnRH dodecapeptide, a cleavage site, and a GnRH-associated peptide. This structure and sequence are highly similar to GnRH-like peptides reported for mollusks and other invertebrates. Quantitative polymerase chain reaction demonstrated that Hdh-GnRH mRNA was more strongly expressed in the ganglions (PPG and cerebral ganglion [CG]) than in other tissues (gonads, gills, intestine, hemocytes, muscle, and mantle) in both sexes. In females, the expression levels of Hdh-GnRH mRNA in the PPG and branchial ganglion (BG) were significantly higher at the ripe and partial spent stages than at the early and late active stages. In males, Hdh-GnRH mRNA levels in the BG showed a significant increase in the partial spent stage. Unexpectedly, Hdh-GnRH levels in the CG were not significantly different among the examined stages in both sexes. These results suggest that Hdh-GnRH mRNA expression profiles in the BG and possibly the PPG are tightly correlated with abalone reproductive activities.

Alternative Splicing Profile and Sex-Preferential Gene Expression in the Female and Male Pacific Abalone Haliotis discus hannai.

In order to characterize the female or male transcriptome of the Pacific abalone and further increase genomic resources, we sequenced the mRNA of full-length complementary DNA (cDNA) libraries derived from pooled tissues of female and male Haliotis discus hannai by employing the Iso-Seq protocol of the PacBio RSII platform. We successfully assembled whole full-length cDNA sequences and constructed a transcriptome database that included isoform information. After clustering, a total of 15,110 and 12,145 genes that coded for proteins were identified in female and male abalones, respectively. A total of 13,057 putative orthologs were retained from each transcriptome in abalones. Overall Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyzed in each database showed a similar composition between sexes. In addition, a total of 519 and 391 isoforms were genome-widely identified with at least two isoforms from female and male transcriptome databases. We found that the number of isoforms and their alternatively spliced patterns are variable and sex-dependent. This information represents the first significant contribution to sex-preferential genomic resources of the Pacific abalone. The availability of whole female and male transcriptome database and their isoform information will be useful to improve our understanding of molecular responses and also for the analysis of population dynamics in the Pacific abalone.

Effects of hypoxia caused by mussel farming on benthic foraminifera in semi-closed Gamak Bay, South Korea.

Seawater monitoring and geochemical and benthic foraminiferal analysis of sediments were conducted to identify the effects of hypoxia created by a mussel farm on benthic foraminifera in a semi-closed bay. Extremely polluted reductive conditions with a high content of organic matter (OM) at >12.0% and oxygen minimum zones (OMZs) with dissolved oxygen (DO) <0.4mg∙L(-1) were formed below the mussel farm in the northwest area of Gamak Bay, and gradually diffused toward the south. Highly similar patterns of variation were observed in species diversity, abundance frequency, and benthic foraminiferal assemblage distributed from Elphidium subarcticum-Ammonia beccarii in the northwest area through E. subarcticum-A. beccarii-Trochammina hadai, E. subarcticum-A. beccarii-Elphidiumclavatum, and E. clavatum-Ammonia ketienziensis in the southern area. These phenomena were caused by hydrodynamics in the current water mass. It was thought that E. subarcticum is a bioindicator of organic pollution caused by the mussel farm.

Effect of abalone farming on seawater movement and benthic foraminiferal assemblage of Zostera marina in the inner bay of Wando, South Korea.

Tidal current survey as well as geochemical and benthic foraminiferal analyses of sediment cores were conducted in an abalone farm and a Zostera bed to understand the degree to which the abalone farm facilities installed along a channel in a shallow sea affect the benthic environment and ecology. In the abalone farm, Ammonia beccarii-Pseudoparrella naraensis-Elphidium somaense-Rosalina globularis-Trochammina hadai and P. naraensis-E. somaense-A. beccarii-T. hadai assemblages appeared owing to an increase in the total nitrogen content from the biodeposits. The Zostera bed consisted of A. beccarii-P. naraensis-Buccella frigida-T. hadai assemblage owing to the gradual expansion of a brackish shallow-water environment by the rapidly decreasing current speed, and it may have flourished. Moreover, the total sulfur, Zn, Cr, and Cu contents in the sediments decreased remarkably more than those of the pre-abalone farming did, caused by the vigorous activity of Zostera marina physiology.