Identification and characterization of homeobox gene clusters in harpacticoid and calanoid copepods.

In this study, we have identified the entire complement of typical homeobox (Hox) genes (Lab, Pb, Dfd, Scr, Antp, Ubx, Abd-A, and Abd-B) in harpacticoid and calanoid copepods and compared them with the cyclopoid copepod Paracyclopina nana. The harpacticoid copepods Tigriopus japonicus and Tigriopus kingsejongensis have seven Hox genes (Lab, Dfd, Scr, Antp, Ubx, Abd-A, and Abd-B) and the Pb and Ftz genes are also present in the cyclopoid copepod P. nana. In the Hox gene cluster of the calanoid copepod Eurytemora affinis, all the Hox genes were present linearly in the genome but the Antp gene was duplicated. Of the three representative copepods, the P. nana Hox gene cluster was the most compact due to its small genome size. The Hox gene expression profile patterns in the three representative copepods were stage-specific. The Lab, Dfd, Scr, Pb, Ftz, and Hox3 genes showed a high expression in early developmental stages but Antp, Ubx, Abd-A, and Abd-B genes were mostly expressed in later developmental stages, implying that these Hox genes may be closely associated with the development of segment identity during early development.

Effects of low temperature on longevity and lipid metabolism in the marine rotifer Brachionus koreanus.

Low-temperature exposure prolongs lifespans and changes lipid metabolism but the relationship between longevity and lipids is largely unknown. Here, we examine the relationship between longevity and lipid metabolism at low temperatures (20 °C and 15 °C) compared with a 25 °C control. Life parameters, fatty acid composition, and transcriptome changes were analyzed in the monogonont rotifer Brachionus koreanus. In vivo life-parameter data indicate that lifespan and fecundity exhibit opposite correlations at low temperatures. The amount of total fatty acids decreased significantly at low temperatures but areas stained with Nile red increased at 15 °C compared with the control. From RNA-seq-based transcriptional analysis, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway-enrichment analysis were conducted. GO analysis shows that telomeres were positively regulated at low temperatures. KEGG pathway-enrichment results indicate that gene expression involved in lipid metabolism was activated with increased glycerol and/or choline synthesis at low temperatures. We suggest that reduced reproductive rates are associated with a decrease of lecithin, which is involved in the conversion of glycerol to triacylglycerol in response to low temperatures by lowering the temperature of body fluid.

Protective Role of Freshwater and Marine Rotifer Glutathione S-Transferase Sigma and Omega Isoforms Transformed into Heavy Metal-Exposed Escherichia coli.

Glutathione S-transferases (GSTs) play an important role in phase II of detoxification to protect cells in response to oxidative stress generated by exogenous toxicants. Despite their important role in defense, studies on invertebrate GSTs have mainly focused on identification and characterization. Here, we isolated omega and sigma classes of GSTs from the freshwater rotifer Brachionus calyciflorus and the marine rotifer Brachionus koreanus and explored their antioxidant function in response to metal-induced oxidative stress. The recombinant Bc- and Bk-GSTs were successfully transformed and expressed in Escherichia coli. Their antioxidant potential was characterized by measuring kinetic properties and enzymatic activity in response to pH, temperature, and chemical inhibitor. In addition, a disk diffusion assay, reactive oxygen species assay, and morphological analysis revealed that GST transformed into E. coli significantly protected cells from oxidative stress induced by H2O2 and metals (Hg, Cd, Cu, and Zn). Stronger antioxidant activity was exhibited by GST-S compared to GST-O in both rotifers, suggesting that GST-S plays a prominent function as an antioxidant defense mechanism in Brachionus spp. Overall, our study clearly shows the antioxidant role of Bk- and Bc-GSTs in E. coli and provides a greater understanding of GST class-specific and interspecific detoxification in rotifer Brachionus spp.

Interrelationship of salinity shift with oxidative stress and lipid metabolism in the monogonont rotifer Brachionus koreanus.

Salinity is a critical key abiotic factor affecting biological processes such as lipid metabolism, yet the relationship between salinity and lipid metabolism has not been studied in the rotifer. To understand the effects of salinity on the monogonont rotifer B. koreanus, we examined high saline (25 and 35psu) conditions compared to the control (15psu). In vivo life cycle parameters (e.g. cumulative offspring and life span) were observed in response to 25 and 35psu compared to 15psu. In addition, to investigate whether high salinity induces oxidative stress, the level of reactive oxygen species (ROS) and glutathione S-transferase activity (GST) were measured in a salinity- (15, 25, and 35psu; 24h) and time-dependent manner (3, 6, 12, 24h; 35psu). Furthermore composition of fatty acid (FA) and lipid metabolism-related genes (e.g. elongases and desaturases) were examined in response to different salinity conditions. As a result, retardation in cumulative offspring and significant increase in life span were demonstrated in the 35psu treatment group compared to the control (15psu). Furthermore, ROS level and GST activity have both demonstrated a significant increase (P<0.05) in the 35psu treatment. In general, the quantity of FA and mRNA expression of the lipid metabolism-related genes was significantly decreased (P<0.05) in response to high saline condition with exceptions for both GST-S4 and S5 demonstrated a significant increase in their mRNA expression. This study demonstrates that high salinity induces oxidative stress, leading to a negative impact on lipid metabolism in the monogonont rotifer, B. koreanus.

Identification of Hox genes and rearrangements within the single homeobox (Hox) cluster (192.8 kb) of the cyclopoid copepod (Paracyclopina nana).

We report the first identification of the entire complement of the eight typical homeobox (hox) genes (lab, pb, Dfd, scr, antp, ubx, Abd-A, and Abd-B) and the ftz gene in a 192.8 kb region in the cyclopoid copepod Paracyclopina nana. A Hox3 gene ortholog was not present in the P. nana hox gene cluster, while the P. nana Dfd gene was transcribed in the opposite direction to the Daphnia pulex Dfd gene, but in the same direction as the Dfd genes of the fruit fly Drosophila melanogaster and red flour beetle Tribolium castaneum. The location of the lab and pb genes was switched in the P. nana hox cluster, while the order of the remaining hox genes was generally conserved with those of other arthropods. J. Exp. Zool. (Mol. Dev. Evol.) 9999B:XX-XX, 2016. © 2016 Wiley Periodicals, Inc.

Identification of the Full 46 Cytochrome P450 (CYP) Complement and Modulation of CYP Expression in Response to Water-Accommodated Fractions of Crude Oil in the Cyclopoid Copepod Paracyclopina nana.

The 46 cytochrome P450 (CYP) gene superfamily was identified in the marine copepod Paracyclopina nana after searching an RNA-seq database and comparing it with other copepod CYP gene families. To annotate the 46 Pn-CYP genes, a phylogenetic analysis of CYP genes was performed using a Bayesian method. Pn-CYP genes were separated into five different clans: CYP2, CYP3, CYP20, CYP26, and mitochondrial. Among these, the principal Pn-CYP genes involved in detoxification were identified by comparing them with those of the copepod Tigriopus japonicus and were examined with respect to their responses to exposure to a water-accommodated fraction (WAF) of crude oil and to the alkylated forms of two polycyclic aromatic hydrocarbons (PAHs; phenanthrene and fluorene). The expression of two Pn-CYP3027 genes (CYP3027F1 and CYP3027F2) was increased in response to WAF exposure and also was upregulated in response to the two alkylated PAHs. In particular, Pn-CYP3027F2 showed the most notable increase in response to 80% WAF exposure. These two responsive CYP genes (Pn-CYP3027F1 and CYP3027F2) were also phylogenetically clustered into the same clade of the WAF- and alkylated PAH-specific CYP genes of the copepod T. japonicus, suggesting that these CYP genes would be those chiefly involved in detoxification in response to WAF exposure in copepods. In this paper, we provide information on the copepod P. nana CYP gene superfamily and also speculate on its potential role in the detoxification of PAHs in marine copepods. Despite the nonlethality of WAF, Pn-CYP3027F2 was rapidly and significantly upregulated in response to WAF that may serve as a useful biomarker of 40% or higher concentration of WAF exposure. This paper will be helpful to better understand the molecular mechanistic events underlying the metabolism of environmental toxicants in copepods.

Interactions between lipid metabolism and the microbiome in aquatic organisms: A review.

Marine organisms' lipid metabolism contributes to marine ecosystems by producing a variety of lipid molecules. Historically, research focused on the lipid metabolism of the organisms themselves. Recent microbiome studies, however, have revealed that gut microbial communities influence the amount and type of lipids absorbed by organisms, thereby altering the organism's lipid metabolism. This has highlighted the growing importance of research on gut microbiota. This review highlights mechanisms by which gut microbiota facilitate lipid digestion and diversify the lipid pool in aquatic animals through the accelerated degradation of exogenous lipids and the transformation of lipid molecules. We also assess how environmental factors and pollutants, along with the innovative use of probiotics, interact with the gut microbiome to influence lipid metabolism within the host. We aim to elucidate the complex interactions between lipid metabolism and gut microbiota in aquatic animals by synthesizing current research and identifying knowledge gaps, providing a foundation for future explorations.

Effects of bisphenol A on reproduction, oxidative stress, and lipid regulation in the marine rotifer Brachionus plicatilis.

This study reports the effects of bisphenol A (BPA) on the rotifer Brachionus plicatilis, focusing on growth performance, reproductive output, oxidative stress responses, and lipid metabolism genes. High BPA levels disrupted peak daily offspring production and led to oxidative stress and increased superoxide dismutase and catalase activity. The research identified distinctive monoacylglycerol O-acyltransferase (MGAT) and diacylglycerol O-acyltransferase (DGAT) genes in B. plicatilis, B. rotundiformis, and B. koreanus, enhancing understanding of lipid metabolism in these species. BPA exposure significantly altered MGAT and DGAT expression, and feeding status affected these regulatory patterns. When food was unavailable, BPA reduced DGAT2 and MGAT2a expression. However, under feeding conditions, DGAT2 and MGAT1 levels increased, indicating that nutritional status and BPA exposure interact to affect gene expression.

Multigenerational resilience of the marine rotifer Brachionus plicatilis to high temperature after additive exposure to high salinity and nanoplastics.

To study multigenerational resilience to high temperature (HT) conditions, we exposed Brachionus plicatilis marine rotifers to HT, high salinity (HS), and nanoplastics (NPs), and measured reproductive and life-cycle endpoints. After exposure to HT, rotifer lifespans were reduced, but daily production of offspring increased. However, both combined HT/HS and HT/HS/NP exposure led to additional decreases in longevity and reproductive ability; the antioxidant defense mechanisms of the rotifers were also notably upregulated as measured by reactive oxygen species levels. Fatty-acid profiles were reduced in all conditions. In multigenerational experiments, the negative effects of HT dissipated rapidly; however, the effects of HT/HS and HT/HS/NPs required four generations to disappear completely. The findings indicated that B. plicatilis were able to recover from these environmental stressors. This study demonstrated the resilience of aquatic organisms in response to changing environmental conditions and provides insights into the complex interactions of different abiotic stressors.

Single and combined effects of increased temperature and methylmercury on different stages of the marine rotifer Brachionus plicatilis.

Rapid, anthropogenic activity-induced global warming is a severe problem that not only raises water temperatures but also shifts aquatic environments by increasing the bioavailability of heavy metals (HMs), with potentially complicated effects on aquatic organisms, including small aquatic invertebrates. For this paper, we investigated the combined effects of temperature (23 and 28 °C) and methylmercury (MeHg) by measuring physiological changes, bioaccumulation, oxidative stress, antioxidants, and the mitogen-activated protein kinase signaling pathway in the marine rotifer Brachionus plicatilis. High temperature and MeHg adversely affected the survival rate, lifespan, and population of rotifers, and bioaccumulation, oxidative stress, and biochemical reactions depended on the developmental stage, with neonates showing higher susceptibility than adults. These findings demonstrate that increased temperature enhances potentially toxic effects from MeHg, and susceptibility differs with the developmental stage. This study provides a comprehensive understanding of the combined effects of elevated temperature and MeHg on rotifers. ENVIRONMENTAL IMPLICATION: Methylmercury (MeHg) is a widespread and harmful heavy metal that can induce lethal effects on aquatic organisms in even trace amounts. The toxicity of metals can vary depending on various environmental conditions. In particular, rising temperatures are considered a major factor affecting bioavailability and toxicity by changing the sensitivity of organisms. However, there are few studies on the combinational effects of high temperatures and MeHg on aquatic animals, especially invertebrates. Our research would contribute to understanding the actual responses of aquatic organisms to complex aquatic environments.

Oxidative stress-mediated deleterious effects of hypoxia in the brackish water flea Diaphanosoma celebensis.

In this study, we investigated the acute toxicity, in vivo effects, oxidative stress, and gene expression changes caused by hypoxia on the brackish water flea Diaphanosoma celebensis. The no-observed-effect concentration (NOEC) of 48 h of hypoxia exposure was found to be 2 mg/L O2. Chronic exposure to NOEC caused a significant decline in lifespan but had no effect on total fecundity. The induction of reactive oxygen species increased in a time-dependent manner over 48 h, whereas the content of antioxidant enzymes (superoxide dismutase and catalase) decreased. The transcription and translation levels were modulated by hypoxia exposure. In particular, a significant increase in hemoglobin level was followed by up-regulation of hypoxia-inducible factor 1α gene expression and activation of the mitogen-activated protein kinase pathway. In conclusion, our findings provide a better understanding of the molecular mechanism of the adverse effects of hypoxia in brackish water zooplankton.

Effect of culture density and antioxidants on naupliar production and gene expression of the cyclopoid copepod, Paracyclopina nana.

Although attempts have been made to use mass cultures of marine copepods as live foods in marine aquaculture, some limitations such as low density culture still exist. The brackish water cyclopoid copepod, Paracyclopina nana has the potential for mass culturing as live food. In this study, we not only investigated the effect of culture density on the naupliar production and specific gene expressions of P. nana, but also the effect of several antioxidants under the conditions of a high density culture. The naupliar production of the copepod decreased with increasing culture density. The expression of glutathione reductase (GR), selenium-dependent glutathione peroxidase (SeGPx), glutathione S-transferase kappa (GST kappa), heat shock protein 40 (Hsp40), and Hsp70 genes of P. nana increased in the high density treatment but vitellogenin genes (Vg1 and Vg2) showed downregulation. In the condition with 20 inds./mL, vitamin C had a significant decrease but sodium selenite induced the naupliar production of P. nana greatly. The expressions of GR, SeGPx, Hsp70, and Vg genes increased with the vitamin C treatment. Sodium selenite caused a decrease of SeGPx and Hsp40 but GST kappa increased in the treatment with 20 inds./mL. These results suggest that sodium selenite is a positive antioxidant which can increase the culture efficiency of the copepod.

Effects of temperature and combinational exposures on lipid metabolism in aquatic invertebrates.

Studies of changes in fatty acids in response to environmental temperature changes have been conducted in many species, particularly mammals. However, few studies have considered aquatic invertebrates, even though they are particularly vulnerable to changes in environmental temperature. In this review, we summarize the process by which animals synthesize common fatty acids and point out differences between the fatty acid profiles of vertebrates and those of aquatic invertebrates. Unlike vertebrates, some aquatic invertebrates can directly synthesize polyunsaturated fatty acids (PUFAs), which can be used to respond to temperature changes. Various studies have shown that aquatic invertebrates increase the degree of saturation in their fatty acids through an increase in saturated fatty acid production or a decrease in PUFAs as the temperature increases. In addition, we summarize recent studies that have examined the complex effects of temperature and combinational stressors to determine whether the degree of saturation in aquatic invertebrates is influenced by other factors. The combined effects of carbon dioxide partial pressure, food quality, starvation, salinity, and chemical exposures have been confirmed, and fatty acid profile changes in response to high temperature were greater than those from combinational stressors.

Genome-wide identification of fatty acid synthesis genes, fatty acid profiles, and life parameters in two freshwater water flea Daphnia magna strains.

The freshwater water flea Daphnia magna is a planktonic animal belonging to the Cladocera. To evaluate differences between two D. magna strains (KIT and NIES) in terms of life parameters and fatty acid profiles, we examined several endpoints. In the D. magna KIT strain, the numbers of total and cumulative offspring were lower at 23 °C and higher at 14 °C than in the D. magna NIES strain. However, at 14 °C, the D. magna KIT strain showed an increased lifespan. Although the n-3/n-6 polyunsaturated fatty acids (PUFA) ratio was always decreased at a low temperature, the PUFA ratio in the KIT strain had a higher value on day 3 than the NIES strain, which gave it higher adaptability to low temperature. In addition, we identified the elongation of very long chain fatty acids (elovl) and fatty acid desaturase (fad) genes, which are involved in fatty acid biosynthesis pathways, in the genomes of both D. magna KIT and NIES. The Elovl and Fad genes in both D. magna strains were highly conserved, including tandem duplicated Elovl 1/7 genes. This study provides new information about the molecular basis for the difference in temperature sensitivity between two strains of D. magna.

Comparative genome analysis of the monogonont marine rotifer Brachionus manjavacas Australian strain: Potential application for ecotoxicology and environmental genomics.

This is the first study to analyze the whole-genome sequence of B. manjavacas Australian (Aus.) strain through combination of Oxford Nanopore long-read seq, resulting in a total length of 108.1 Mb and 75 contigs. Genome-wide detoxification related gene families in B. manjavacas Aus. strain were comparatively analyzed with those previously identified in other Brachionus spp., including B. manjavacas German (Ger.) strain. Most of the subfamilies in detoxification related families (CYPs, GSTs, and ABCs) were highly conserved and confirmed orthologous relationship with Brachionus spp., and with accumulation of genome data, clear differences between genomic repertoires were demonstrated the marine and the freshwater species. Furthermore, strain-specific genetic variations were present between the Aus. and Ger. strains of B. manjavacas. This whole-genome analysis provides in-depth review on the genomic structural differences for detoxification-related gene families and further provides useful information for comparative ecotoxicological studies and evolution of detoxification mechanisms in Brachionus spp.

The genome of the freshwater monogonont rotifer Brachionus rubens: Identification of phase I, II, and III detoxification genes.

Monogonont rotifers are common species in aquatic environments and make model species for ecotoxicology studies. Whole genomes of several species of the genus Brachionus have been assembled, but no information on the freshwater rotifer Brachionus rubens has been reported. In this study, the whole-genome sequence of B. rubens was successfully assembled using NextDenovo. The total length of the genome was 132.7 Mb (N50 = 2.51 Mb), including 122 contigs. The GC contents accounted for 29.96% of the genome. Aquatic organisms are always exposed to various external stresses, and a comprehensive genomic analysis is needed to better understand the adverse effects on organisms. This paper focuses on the ecotoxicological aspect and conducted genome analysis of representative gene families involved in detoxification mechanisms against environmental stressors. Specifically, we identified cytochrome P450 genes (CYPs) of phase I, glutathione S-transferase genes (GSTs) of phase II, and ATP-binding cassette transporter genes (ABCs) of phase III in the genome of B. rubens. Gene duplications were found in CYP, GST, and ABC genes, as is the case for other Brachionus rotifers. Our results suggest that these detoxification-related gene families have evolved in a species-specific and/or lineage-specific manner. This paper improves our understanding of how the freshwater Brachionus rotifers respond to environmental stressors in a molecular ecotoxicology context.

Trophic Enrichment Factors of Carbon and Nitrogen Isotopic Ratios (Δ13C and Δ15N) in Four Marine Ciliates.

Understanding the magnitude and causes of isotopic fractionation between organisms and their dietary resources is crucial for gaining knowledge on stable isotope ecology. However, little is known regarding the diet-tissue fractionation values of marine ciliates, which play a critical role in the reconstruction of microbial food webs. In the present study, we conducted experiments on two benthic (Pseudokeronopsis pararubra and Protocruzia labiata) and two pelagic (Strombidium sulcatum and Uronemella filificum) marine ciliates, where they were fed with isotopically constant foods (Chaetoceros calcitrans and Isochrysis galbana) under laboratory culture conditions to determine their carbon and nitrogen isotopic fractionation values (Δ13C and Δ15N). The stable isotope values (δ13C and δ15N) of ciliates for all experiments rapidly increased after the initial feeding, with half-lives ranging from 6.1 to 23.0h for δ13C and from 3.1 to 24.9h for δ15N. The Δ13C and Δ15N for all ciliates represented significantly positive enrichments, with overall mean fractionations of 0.6±0.2 and 1.2±0.4, respectively. Irrespective of the dietary type, both Δ13C and Δ15N were very similar for the same ciliate species. These results suggest that Δ13C and Δ15N for marine ciliates are similar to those found in common marine organisms with very little food-dependent variation. Overall, quantifying the specific isotopic fractionation of marine ciliates is expected to provide fundamental information on the trophic transfer of carbon, nitrogen, and energy flow through the microbial pathway in marine ecosystems.

The glutathione S-transferase genes in marine rotifers and copepods: Identification of GSTs and applications for ecotoxicological studies.

Various xenobiotics are constantly being released and accumulated into the aquatic environments and consequently, the aquatic organisms are continuously being exposed to exogenous stressors. Among various xenobiotic detoxifying enzymes, Glutathione S-transferase (GST) is one of the major xenobiotic detoxifying enzyme which is widely distributed among living organisms and thus, understanding of the nature of GSTs is crucial. Previous studies have shown GST activity in response to various xenobiotics yet, full identification of GSTs in marine invertebrates is still limited. This review covers information on the importance of GSTs as a biomarker for emerging chemicals and their response to wide ranges of environmental pollutants as well as in-depth phylogenetic analysis of marine invertebrates, including recently identified GSTs belonging to rotifers (Brachionus spp.) and copepods (Tigriopus japonicus and Paracyclopina nana), with unique class-specific features of GSTs, as well as a new suggestion of GST evolutionary pathway.

The genome of the marine rotifer Brachionus koreanus sheds light on the antioxidative defense system in response to 2-ethyl-phenanthrene and piperonyl butoxide.

BRACHIONUS: spp. (Rotifera: Monogononta) have been introduced as ecotoxicological model-organisms that are widely distributed in aquatic environments. Among the Brachionus spp., the monogonont rotifer Brachionus koreanus has been widely used for ecology, ecotoxicology, and evolution, thus, providing the whole genome data of B. koreanus is important for further understandings of in-depth molecular mechanisms. In this study, the completed assembly and characterization of the B. koreanus genome resulted in a total length of 85.7 Mb with 14,975 annotated genes. The final number of scaffolds was 567 with an N50 value and a GC content of 1.86 Mb and 24.35 %, respectively. Based on the fully constructed genome database, a total of 24 CYPs, 23 GSTs, two SODs, and a single CAT genes were identified and analyzed antioxidant activities (CAT, SOD, and GST), and transcriptional regulation of the entire CYPs, GSTs, SODs, and CAT in response to 2-ethyl-phenanthrene (2-ethyl-PHE) and piperonyl butoxide (PBO), to demonstrate the usefulness of the whole genome library of B. koreanus in response xenobiotic-induced oxidative stress. The assembled B. koreanus genome will provide a better understanding on the molecular ecotoxicology in the view of molecular mechanisms underlying toxicological responses, particularly on xenobiotic detoxification processes in the rotifer B. koreanus.

The genome of the harpacticoid copepod Tigriopus japonicus: Potential for its use in marine molecular ecotoxicology.

The copepod Tigriopus japonicus has been widely used as an experimental species in the field of ecotoxicology. We have sequenced and assembled the whole genome of T. japonicus with comparative analysis of gene families that represent detoxification phases in two additional public genomes of Tigriopus spp., namely, T. californicus and T. kingsejongensis. The total length of the T. japonicus assembled genome was 196.6 Mb with an N50 value of 10.65 Mb and consisted of 339 scaffolds and 25,143 annotated genes. The detoxification gene families encoding cytochrome P450s (CYP450s), glutathione S-transferases (GSTs), and ATP-binding cassette (ABC) proteins in Tigriopus spp. have shown species-dependent diversity in several gene sets, suggesting that these genes have undergone a species-specific expansion to increase their fitness to different marine habitats and environmental pressures. Our study will provide a better understanding of the detoxification system in Tigriopus spp. and will contribute to various areas of research, including ecotoxicology.