De Novo assembly and characterisation of the greentail prawn (Metapenaeus bennettae) hepatopancreas transcriptome - identification of stress response and detoxification transcripts.

Crude oil is a key contaminant in aquatic environments entering via natural and anthropogenic sources, causing toxicity in marine organisms. Traditionally, biomarkers have been utilised to determine crude oil exposure and effects in aquatic organisms, however advances in genomic technologies has led to increased adoption of transcriptomic approaches for identifying response and detoxification pathways following contaminant exposure. This study presents the first transcriptome for the greentail prawn (Metapenaeus bennettae), a commercially targeted benthic decapod crustacean from eastern and south-eastern Australia. The Trinity generated de novo assembly, after redundancy clustering, resulted in 86,401 contigs, of these 22,252 displayed strong homology to transcripts in the NCBI's non-redundant protein, Swiss-Prot and TrEMBL databases. Furthermore, Gene Ontology was assigned to 15,079 annotated contigs and KEGG Orthology was identified for 1318 annotated contigs. Transcripts encoding common biomarkers utilised to determine crude oil exposure were identified, including those for detoxification phase I and II enzymes; with 40 transcripts encoding for members of the cytochrome P450 gene family and 8 transcripts encoding glutathione S-Transferases (GSTs). Transcripts encoding oxidative stress enzymes including superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) and metallothionein (MT) were identified, as well as stress induced proteins including crustacean hyperglycemic hormone (CHH) and heat shock proteins (Hsps). The annotated transcriptome of the greentail prawn and the identification of detoxification and stress response transcripts, provides a necessary resource for future studies geared toward characterising differential transcriptomic patterns and molecular pathways after exposure to crude oil in this and other crustacean species of environmental and commercial importance.

Monitoring sublethal changes in fish physiology following exposure to a light, unweathered crude oil.

Biomarkers are frequently used to determine the exposure of fish to petroleum hydrocarbons following an oil spill. These biomarkers must be chosen carefully if they are to be used to determine sublethal toxic impacts as well as oil exposure. Many commonly used biomarkers relate to the metabolism of high molecular weight, typically pyrogenic, polycyclic aromatic hydrocarbons (PAHs), which are not abundant in unweathered crude oil. The goal of this study was to compare the efficacy of different biomarkers, including histological examination and transcriptomic profiling, in showing exposure to oil and the potential for sublethal toxic impacts. To achieve these goals, subadults/adults of the spotted dragonet (Repomucenus calcaratus) were exposed to a representative light, unweathered Australian oil for 96 h, so that the physiological changes that occur with exposure could be documented. Fish were then transferred to clean sediment for 90 h to quantify recovery. Biomarker changes, including PAH metabolites, 7-ethoxyresorufin O-deethylase (EROD), and histopathology, are presented in this work. In addition, a de novo transcriptome for the spotted dragonet was assembled, and differential transcript abundance was determined for the gill and liver of petroleum-exposed fish relative to a control. Increased levels of some biliary phenanthrene metabolites were seen throughout the exposure period. EROD levels showed modest, but not significant, increases. Transcriptomic differences were noted in the abundances of transcripts with a role in inflammation, primary metabolism and cardiac function. The patterns of transcript abundance in the gill and the liver changed in a manner that reflected exposure and recovery. The histology showed elevated prevalence of lesions, most notably vacuolization in liver and heart tissue, multi-organ necrosis, and lamellar epithelial lifting and telangiectasia in the gill. These findings suggest that short-term exposures to low molecular weight PAHs could elicit changes in the health of fish that are well predicted by the transcriptome. Furthermore, when light oil is released into the environment, exposure and subsequent risk would be better estimated using phenanthrene metabolite levels rather than EROD. This study also adds to the weight of evidence that exposure to low molecular weight PAHs may cause cardiac problems in fish. Further study is needed to determine the impact of these changes on reproductive capacity, long-term survival, and other population specific parameters.

Transcriptomic, lipid, and histological profiles suggest changes in health in fish from a pesticide hot spot.

Barramundi (Lates calcarifer) were collected at the beginning (1st sampling) and end (2nd sampling) of the wet season from Sandy Creek, an agriculturally impacted catchment in the Mackay Whitsundays region of the Great Barrier Reef catchment area, and from Repulse Creek, located approximately 100 km north in Conway National Park, to assess the impacts of pesticide exposure. Gill and liver histology, lipid class composition in muscle, and the hepatic transcriptome were examined. The first sample of Repulse Creek fish showed little tissue damage and low transcript levels of xenobiotic metabolism enzymes. Sandy Creek fish showed altered transcriptomic patterns, including those that regulate lipid metabolism, xenobiotic metabolism, and immune response; gross histological alterations including lipidosis; and differences in some lipid classes. The second sampling of Repulse Creek fish showed similar alterations in hepatic transcriptome and tissue structure as fish from Sandy Creek. These changes may indicate a decrease in health of pesticide exposed fish.

Hepatic transcriptomic profiles from barramundi, Lates calcarifer, as a means of assessing organism health and identifying stressors in rivers in northern Queensland.

Resource managers need to differentiate between sites with and without contaminants and those where contaminants cause impacts. Potentially, transcriptomes could be used to evaluate sites where contaminant-induced effects may occur, to identify causative stressors of effects and potential adverse outcomes. To test this hypothesis, the hepatic transcriptomes in Barramundi, a perciforme teleost fish, (Lates calcarifer) from two reference sites, two agriculturally impacted sites sampled during the dry season, and an impacted site sampled during the wet season were compared. The hepatic transcriptome was profiled using RNA-Seq. Multivariate analysis showed that transcriptomes were clustered based on site and by inference water quality, but not sampling time. The largest differences in transcriptomic profile were between reference sites and a site sampled during high run-off, showing that impacted sites can be identified via RNA-Seq. Transcripts with altered abundance were linked to xenobiotic metabolism, peroxisome proliferation and stress responses, indicating putative stressors with the potential for adverse outcomes in barramundi.

Global transcriptomic profiling in barramundi (Lates calcarifer) from rivers impacted by differing agricultural land uses.

Most catchments discharging into the Great Barrier Reef lagoon have elevated loads of suspended sediment, nutrients, and pesticides, including photosystem II inhibiting herbicides, associated with upstream agricultural land use. To investigate potential impacts of declining water quality on fish physiology, RNA sequencing (RNASeq) was used to characterize and compare the hepatic transcriptomes of barramundi (Lates calcarifer) captured from 2 of these tropical river catchments in Queensland, Australia. The Daintree and Tully Rivers differ in upstream land uses, as well as sediment, nutrient, and pesticide loads, with the area of agricultural land use and contaminant loads lower in the Daintree. In fish collected from the Tully River, transcripts involved in fatty acid metabolism, amino acid metabolism, and citrate cycling were also more abundant, suggesting elevated circulating cortisol concentrations, whereas transcripts involved in immune responses were less abundant. Fish from the Tully also had an increased abundance of transcripts associated with xenobiotic metabolism. Previous laboratory-based studies observed similar patterns in fish and amphibians exposed to the agricultural herbicide atrazine. If these transcriptomic patterns are manifested at the whole organism level, the differences in water quality between the 2 rivers may alter fish growth and fitness. Environ Toxicol Chem 2017;36:103-112. © 2016 SETAC.