Snow crab (Chionoecetes opilio) hepatopancreas transcriptome: Identification and testing of candidate molecular biomarkers of seismic survey impact

The eastern slope of the Grand Banks, Newfoundland and Labrador, Canada, represents an area where active seismic exploration overlaps extensively with an important snow crab (Chionoecetes opilio) fishery. Field studies were conducted in 2016 and 2017 to investigate the potential impact of seismic oil and gas surveying exposure on the transcriptome of the snow crab hepatopancreas, which is involved in metabolism and response to environmental stress. In 2016, snow crabs were subjected to 2D seismic noise for 2 h and sampled before (i.e. pre-seismic), and 18 h and 3 weeks after exposure in Carson Canyon (CC). In 2017, the 2D seismic exposure was repeated and samples were collected before and 1 day, 2 days, and 6 weeks after exposure in CC. Additionally, in 2017, snow crabs were subjected to 3D seismic noise for 2 months and sampled during and 6 weeks after exposure at a site north of CC. In both years, snow crabs were also collected from a separate non-seismic exposed site [Lilly Canyon (LC)]. RNA-seq was used to identify candidate seismic-responsive molecular biomarkers in 2016. The quantified transcripts of individuals (i.e. n = 10 from each of the four 2016 groups) were compared using two differential expression analysis methods (DESeq2 and edgeR), identifying a total of 1088 and 389 differentially expressed transcripts, respectively. Real-time quantitative polymerase chain reaction (qPCR) assays were designed and run for 83 of these transcripts to confirm RNA-seq results, identifying 9 transcripts with significantly higher expression after seismic exposure at the CC site, and 14 transcripts with significant differential expression between the CC site and the non-seismic LC site. Functional annotations associated with candidate seismic-responsive genes included oxidoreductase activity, apoptotic process, and inflammatory response. To further investigate the performance and utility of candidate biomarkers identified using the 2016 samples, expression levels of 20 selected transcripts were then examined in 2017 samples using both qPCR and multivariate statistical analyses. Principal component analysis of qPCR data separated exposure groups in 2016 but did not result in clear separation of groups in 2017, although some transcripts showed similar trends in both years. This work has built a strong foundation for future research involving the snow crab hepatopancreas transcriptome and its potential responses to environmental stressors including seismic surveying noise.