Transcriptomic response to water accommodated fraction of crude oil exposure in the gill of Japanese flounder, Paralichthys olivaceus

Transcriptome analysis of Sparidentex hasta larvae exposed to water-accommodated fraction of Kuwait crude oil

Anthropogenic activities have been shown to significantly affect marine life. Water pollution and oil spills are particularly deleterious to the fish population, especially during their larval stage. In this study, Sobaity-sea bream Sparidentex hasta (Valenciennes, 1830) larvae were exposed to serial dilutions of water-accommodated fraction of Kuwait crude oil (KCO-WAF) for varying durations (3, 6, 24, 48, 72 or 96 h) in acute exposure regime. Gene expression was assessed using RNA sequencing and validated through RT-qPCR. The RNA sequencing data were aligned to the sequenced genome, and differentially expressed genes were identified in response to treatment with or without KCO-WAF at various exposure times. The highest number of differentially expressed genes was observed at the early time point of 6 h of post-exposure to KCO-WAF. The lowest number of differentially expressed genes were noticed at 96 h of treatment indicating early response of the larvae to KCO-WAF contaminant. The acquired information on the differentially expressed genes was then used for functional and pathway analysis. More than 90% of the differentially expressed genes had a significant BLAST match, with the two most common matching species being Acanthopagrus latus and Sparus aurata. Approximately 65% of the differentially expressed genes had Gene Ontology annotations, whereas > 35% of the genes had KEGG pathway annotations. The differentially expressed genes were found to be enriched for various signaling pathways (e.g., MAPK, cAMP, PI3K-Akt) and nervous system-related pathways (e.g., neurodegeneration, axon guidance, glutamatergic synapse, GABAergic synapse). Early exposure modulated the signaling pathways, while KCO-WAF exposure of larvae for a longer duration affected the neurodegenerative/nervous system-related pathways. RT-qPCR analysis confirmed the differential expression of genes at each time point. These findings provide insights into the underlying molecular mechanisms of the deleterious effects of acute exposure to oil pollution-on marine fish populations, particularly at the early larval stage of Sparidentex hasta.

New insights into the impact of polystyrene micro/nanoplastics on the nutritional quality of marine jacopever (Sebastes schlegelii)

Microplastics (MPs) and nanoplastics (NPs) are ubiquitous in the marine environments due to the wide use and mismanagement of plastics. However, the effect of MPs/NPs on the nutrition quality of economic species is poorly understood, and their underlying mechanisms remained unclear. We therefore investigated the impacts of polystyrene MPs/NPs on the nutrition composition of marine jacopever Sebastes schlegelii from the perspective of assimilation and metabolism. Results showed that NPs reduced more nutrition quality than MPs. Despite no notable impact on intestinal microbiota function, MPs/NPs influenced the assimilation of fish through intestinal damage. Furthermore, NPs induced greater damage to hepatocyte metabolism than MPs, caused by hepatocyte uptake through membrane protein pumps/channels and clathrin/caveolin-mediated endocytosis for NPs, while through phagocytosis/pinocytosis for MPs. NPs triggered more cell apoptosis signals in Ferroptosis and FoxO signaling pathways than MPs, destroying mitochondria structure. Compared with MP treatments, a significant upregulation of genes (PRODH and SLC25A25A) associated with the electron transfer chain of mitochondria was detected in the NP treatments, influencing the tricarboxylic acid cycle and interfering with liver metabolism of proteins, fatty acid, glycerol phospholipids, and carbohydrates. This work provides new insights into the potential impacts of MPs/NPs on the quality and safety of seafood.

Gill and liver transcriptomic responses of Achirus lineatus (Neopterygii: Achiridae) exposed to water-accommodated fraction (WAF) of light crude oil reveal an onset of hypoxia-like condition

Crude oil is one of the most widespread pollutants released into the marine environment, and native species have provided useful information about the effect of crude oil pollution in marine ecosystems. We consider that the lined sole Achirus lineatus can be a useful monitor of the effect of crude oil in the Gulf of Mexico (GoM) because this flounder species has a wide distribution along the GoM, and its response to oil components is relevant. The objective of this study was to compare the transcriptomic changes in liver and gill of adults lined sole fish (Achirus lineatus) exposed to a sublethal acute concentration of water-accommodated fraction (WAF) of light crude oil for 48 h. RNA-Seq was performed to assess the transcriptional changes in both organs. A total of 1073 differentially expressed genes (DEGs) were detected in gills; 662 (61.69%) were upregulated, and 411 (38.30%) were downregulated whereas in liver, 515 DEGs; 306 (59.42%) were upregulated, and 209 (40.58%) were downregulated. Xenobiotic metabolism and redox metabolism, along with DNA repair mechanisms, were activated. The induction of hypoxia-regulated genes and the generalized regulation of multiple signaling pathways support the hypothesis that WAF exposition causes a hypoxia-like condition.

Phenotypic and transcriptomic consequences in zebrafish early-life stages following exposure to crude oil and chemical dispersant at sublethal concentrations

To further understand the underlying mechanisms involved in the developmental toxicity of crude oil and chemically dispersed crude oil on fish early-life stages (ELS), zebrafish (Danio rerio) embryos were exposed to GM-2 chemical dispersant (DISP), low-energy water-accommodated fractions (LEWAF), and chemically enhanced WAF (CEWAF) of Merey crude oil at sublethal concentrations for 120 h. We employed the General Morphology Score (GMS) and General Teratogenic Score (GTS) systems in conjunction with high-throughput RNA-Seq analysis to evaluate the phenotypic and transcriptomic responses in zebrafish ELS. Results showed that ΣPAHs concentrations in LEWAF and CEWAF solutions were 507.63 ± 80.95 ng·L^-1 and 4039.51 ± 241.26 ng·L^-1, respectively. The GMS and GTS values indicated that CEWAF exposure caused more severe developmental delay and higher frequencies of teratogenic effects than LEWAF exposure. Moreover, no significant change in heart rate was observed in LEWAF treatment, while CEWAF exposure caused a significant reduction in heart rate. LEWAF and CEWAF exposure exhibited an overt change in eye area, with a reduction of 4.0% and 25.3% (relative to the control), respectively. Additionally, no obvious impact on phenotypic development was observed in zebrafish embryo-larvae following DISP exposure. Significant changes in gene expression were detected in LEWAF and CEWAF treatments, with a total of 957 and 2062 differentially expressed genes (DEGs), respectively, while DISP exposure altered only 91 DEGs. Functional enrichment analysis revealed that LEWAF and CEWAF exposure caused significant perturbations in the pathways associated with phototransduction, retinol metabolism, metabolism of xenobiotics by cytochrome P450, and immune response-related pathways. Our results provide more valid evidence to corroborate the previous suggestion that ocular impairment is an equal or possibly more sensitive biomarker than cardiotoxicity in fish ELS exposed to oil-derived PAHs. All these findings could gain further mechanistic insights into the effects of crude oil and chemical dispersant on fish ELS.

The genome of walking catfish Clarias magur (Hamilton, 1822) unveils the genetic basis that may have facilitated the development of environmental and terrestrial adaptation systems in air-breathing catfishes

The walking catfish Clarias magur (Hamilton, 1822) (magur) is an important catfish species inhabiting the Indian subcontinent. It is considered as a highly nutritious food fish and has the capability to walk to some distance, and survive a considerable period without water. Assembly, scaffolding and several rounds of iterations resulted in 3,484 scaffolds covering ∼94% of estimated genome with 9.88 Mb largest scaffold, and N50 1.31 Mb. The genome possessed 23,748 predicted protein encoding genes with annotation of 19,279 orthologous genes. A total of 166 orthologous groups represented by 222 genes were found to be unique for this species. The Computational Analysis of gene Family Evolution (CAFE) analysis revealed expansion of 207 gene families and 100 gene families have rapidly evolved. Genes specific to important environmental and terrestrial adaptation, viz. urea cycle, vision, locomotion, olfactory and vomeronasal receptors, immune system, anti-microbial properties, mucus, thermoregulation, osmoregulation, air-breathing, detoxification, etc. were identified and critically analysed. The analysis clearly indicated that C. magur genome possessed several unique and duplicate genes similar to that of terrestrial or amphibians’ counterparts in comparison to other teleostean species. The genome information will be useful in conservation genetics, not only for this species but will also be very helpful in such studies in other catfishes.

Variation of Microbial Diversity in Catastrophic Oil Spill Area in Marine Ecosystem and Hydrocarbon Degradation of UCMs (Unresolved Complex Mixtures) by Marine Indigenous Bacteria

The study targeted an assessment of microbial diversity during oil spill in the marine ecosystem (Kaohsiung port, Taiwan) and screened dominant indigenous bacteria for oil degradation, as well as UCM weathering. DO was detected lower and TDS/conductivity was observed higher in oil-spilled area, compared to the control, where a significant correlation (R² = 1; P < 0.0001) was noticed between DO and TDS. The relative abundance (RA) of microbial taxa and diversities (> 90% similarity by NGS) were found higher in the boundary region of spilled-oily-water (site B) compared to the control (site C) and center of the oil spill area (site A) (B_RA/diversity > C_RA/diversity > A_RA/diversity). The isolated indigenous bacteria, such as Staphylococcus saprophyticus (CYCTW1), Staphylococcus saprophyticus (CYCTW2), and Bacillus megaterium (CYCTW3) degraded the C₁₀-C₃₀ including UCM of oil, where Bacillus sp. are exhibited more efficient, which are applicable for environmental cleanup of the oil spill area. Thus, the marine microbial diversity changes due to oil spill and the marine microbial community play an important role to biodegrade the oil, besides restoring the catastrophic disorders through changing their diversity by ecological selection and adaptation process.

Toxicity evaluation and microbiota response of the lined sole Achirus lineatus (Chordata: Achiridae) exposed to the light petroleum water-accommodated fraction (WAF)

Exposure to contaminants might directly affect organisms and alter their associated microbiota. The objective of the present study was to determine the impact of the petroleum-water-accommodated fraction (WAF) from a light crude oil (API gravity 35) on a benthic fish species native from the Gulf of Mexico (GoM). Ten adults of Achirus lineatus (Linnaeus, 1758) were exposed to a sublethal WAF/water solution of 50% v/v for 48 hr. Multiple endpoints were measured including tissue damage, presence of polycyclic aromatic hydrocarbons (PAHs) metabolites in bile and gut microbiota analyses. Atrophy and fatty degeneration were observed in livers. Nodules and inflammation were detected in spleen, and structural disintegration and atrophy in the kidney. In gills hyperplasia, aneurysm, and gills lamellar fusion were observed. PAHs metabolites concentrations in bile were significantly higher in exposed organisms. Gut microbiome taxonomic analysis showed significant shifts in bacterial structure and composition following WAF exposure. Data indicate that exposure to WAF produced toxic effects in adults of A. lineatus, as evidenced by histological alterations and dysbiosis, which might represent an impairment to long-term subsistence of exposed aquatic organisms.

Genome sequence of walking catfish (Clarias batrachus) provides insights into terrestrial adaptation

Background

Walking catfish (Clarias batrachus) is a freshwater fish capable of air-breathing and locomotion on land. It usually inhabits various low-oxygen habitats, burrows inside the mudflat, and sometimes “walks” to search for suitable environments during summer. It has evolved accessory air-breathing organs for respiring air and corresponding mechanisms to survive in such challenging environments. Thereby, it serves as a great model for understanding adaptations to terrestrial life.

Results

Comparative genomics with channel catfish (Ictalurus punctatus) revealed specific adaptations of C. batrachus in DNA repair, enzyme activator activity, and small GTPase regulator activity. Comparative analysis with 11 non-air-breathing fish species suggested adaptive evolution in gene expression and nitrogenous waste metabolic processes. Further, myoglobin, olfactory receptor related to class A G protein-coupled receptor 1, and sulfotransferase 6b1 genes were found to be expanded in the air-breathing walking catfish genome, with 15, 15, and 12 copies, respectively, compared to non-air-breathing fishes that possess only 1–2 copies of these genes. Additionally, we sequenced and compared the transcriptomes of the gill and the air-breathing organ to characterize the mechanism of aerial respiration involved in elastic fiber formation, oxygen binding and transport, angiogenesis, ion homeostasis and acid-base balance. The hemoglobin genes were expressed dramatically higher in the air-breathing organ than in the gill of walking catfish.

Conclusions

This study provides an important genomic resource for understanding the adaptive mechanisms of walking catfish to terrestrial environments. It is possible that the coupling of enhanced abilities for oxygen storage and oxygen transport through genomic expansion of myoglobin genes and transcriptomic up-regulation of hemoglobin and angiogenesis-related genes are important components of the molecular basis for adaptation of this aquatic species to terrestrial life.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5355-9) contains supplementary material, which is available to authorized users.

Ultraviolet radiation significantly enhances the molecular response to dispersant and sweet crude oil exposure in Nematostella vectensis

Estuarine organisms are subjected to combinations of anthropogenic and natural stressors, which together can reduce an organisms' ability to respond to either stress or can potentiate or synergize the cellular impacts for individual stressors. Nematostella vectensis (starlet sea anemone) is a useful model for investigating novel and evolutionarily conserved cellular and molecular responses to environmental stress. Using RNA-seq, we assessed global changes in gene expression in Nematostella in response to dispersant and/or sweet crude oil exposure alone or combined with ultraviolet radiation (UV). A total of 110 transcripts were differentially expressed by dispersant and/or crude oil exposure, primarily dominated by the down-regulation of 74 unique transcripts in the dispersant treatment. In contrast, UV exposure alone or combined with dispersant and/or oil resulted in the differential expression of 1133 transcripts, of which 436 were shared between all four treatment combinations. Most significant was the differential expression of 531 transcripts unique to one or more of the combined UV/chemical exposures. Main categories of genes affected by one or more of the treatments included enzymes involved in xenobiotic metabolism and transport, DNA repair enzymes, and general stress response genes conserved among vertebrates and invertebrates. However, the most interesting observation was the induction of several transcripts indicating de novo synthesis of mycosporine-like amino acids and other novel cellular antioxidants. Together, our data suggest that the toxicity of oil and/or dispersant and the complexity of the molecular response are significantly enhanced by UV exposure, which may co-occur for shallow water species like Nematostella.

Green technological approach to synthesis hydrophobic stable crystalline calcite particles with one-pot synthesis for oil-water separation during oil spill cleanup

The process of separating oil and water from oil/water mixtures is an attractive strategy to answer the menace caused by industrial oil spills and oily wastewater. In addition, water coproduced during hydrocarbon exploitation, which can be an economic burden and risk for freshwater resources, can become an important freshwater source after suitable water-oil separation. For oil-water separation purposes, considerable attention has been paid to the preparation of hydrophobic-oleophilic materials with modified surface roughness. However, due to issues of thermodynamic instability, costly and complex methods as well as lack of ecofriendly compounds, most of hydrophobic surface modified particles are of limited practical application. The study presents a facile procedure, to synthesize crystalline particles of calcite, which is the most stable polymorph of CaCO₃ from industrial CaCO₃ using oleic acid as an additive in a one-pot synthesis method. The XRD results show that the synthesized particles were a well-crystallized form of calcite. The FTIR results reflect the appearance of the alkyl groups from the oleic acid in synthesized particles which promotes the production of calcite with 'rice shape' (1.64 μm) (aggregated by spherical nanoparticle of 19.56 nm) morphology with concomitant changes in its surface wettability from hydrophilic to hydrophobic. The synthesized particles exhibited near to super hydrophobicity with ∼99% active ratio and a contact angle of 143.8°. The synthesized hydrophobic calcite particles had an oleophilic nature where waste diesel oil adsorption capacity of synthesized calcium carbonate (HCF) showed a very high (>99%) and fast (7 s) oil removal from oil-water mixture. The functional group of long alkyl chain including of CO bounds may play critical roles for adsorption of diesel oils. Moreover, the thermodynamically stable crystalline polymorph calcite (compared to vaterite) exhibited excellent recyclability. The isothermal study reflects the comparatively high value of correlation coefficient (R² = 0.94) for the Langmuir isotherm compared to those of the Freundlich isotherm (R² = 0.82) showed that the adsorption of diesel oil onto the hydrophobic CaCO₃ adsorbent was much better described by the Langmuir isotherm. The kinetics study of second-order rate expression (R² = 0.99) more fitted with the experimental data compare to first-order model (R² = 0.92). The synthesized calcite exhibited a significant dual oleophilic and hydrophobic nature that can be applicable for oil adsorption/or removal purpose in oil contaminated areas in environment and/or industrial oily wastewater for green, simple, and inexpensive environmental cleanup.

Crude oil impairs immune function and increases susceptibility to pathogenic bacteria in southern flounder

Exposure to crude oil or its individual constituents can have detrimental impacts on fish species, including impairment of the immune response. Increased observations of skin lesions in northern Gulf of Mexico fish during the 2010 Deepwater Horizon oil spill indicated the possibility of oil-induced immunocompromisation resulting in bacterial or viral infection. This study used a full factorial design of oil exposure and bacterial challenge to examine how oil exposure impairs southern flounder (Paralichthys lethostigma) immune function and increases susceptibility to the bacteria Vibrio anguillarum, a causative agent of vibriosis. Fish exposed to oil prior to bacterial challenge exhibited 94.4% mortality within 48 hours of bacterial exposure. Flounder challenged with V. anguillarum without prior oil exposure had <10% mortality. Exposure resulted in taxonomically distinct gill and intestine bacterial communities. Mortality strongly correlated with V. anguillarum levels, where it comprised a significantly higher percentage of the microbiome in Oil/Pathogen challenged fish and was nearly non-existent in the No Oil/Pathogen challenged fish bacterial community. Elevated V. anguillarum levels were a direct result of oil exposure-induced immunosuppression. Oil-exposure reduced expression of immunoglobulin M, the major systemic fish antibody, and resulted in an overall downregulation in transcriptome response, particularly in genes related to immune function, response to stimulus and hemostasis. Ultimately, sediment-borne oil exposure impairs immune function, leading to increased incidences of bacterial infections. This type of sediment-borne exposure may result in long-term marine ecosystem effects, as oil-bound sediment in the northern Gulf of Mexico will likely remain a contamination source for years to come.