American lobster postlarvae alter gene regulation in response to ocean warming and acidification

Abstract

Anthropogenic carbon emissions released into the atmosphere is driving rapid, concurrent increases in temperature and acidity across the world's oceans. Disentangling the interactive effects of warming and acidification on vulnerable life stages is important to our understanding of responses of marine species to climate change. This study evaluates the interactive effects of these stressors on the acute response of gene expression of postlarval American lobster (Homarus americanus), a species whose geographic range is warming and acidifying faster than most of the world's oceans. In the context of our experiment, we found two especially noteworthy results: First, although physiological end points have consistently been shown to be more responsive to warming in similar experimental designs, our study found gene regulation to be considerably more responsive to elevated pCO₂. Furthermore, the combined effect of both stressors on gene regulation was significantly greater than either stressor alone. Using a full factorial experimental design, lobsters were raised in control and elevated pCO₂ concentrations (400 ppm and 1,200 ppm) and temperatures (16°C and 19°C). A transcriptome was assembled from an identified 414,517 unique transcripts. Overall, 1,108 transcripts were differentially expressed across treatments, several of which were related to stress response and shell formation. When temperature alone was elevated (19°C), larvae downregulated genes related to cuticle development; when pCO₂ alone was elevated (1,200 ppm), larvae upregulated chitinase as well as genes related to stress response and immune function. The joint effects of end-century stressors (19°C, 1,200 ppm) resulted in the upregulation of those same genes, as well as cellulase, the downregulation of calcified cuticle proteins, and a greater upregulation of genes related to immune response and function. These results indicate that changes in gene expression in larval lobster provide a mechanism to respond to stressors resulting from a rapidly changing environment.

Keywords: Homarus americanus; RNA‐seq; crustaceans; gene expression; joint stressors; larvae; ocean acidification; ocean warming.

FIGURE 1

Heat map depicting expression of the 1,108 differentially expressed genes subject to single and joint stressor treatments, relative to control treatment of 400 ppm, 16°C. This represents only 0.27% of all transcripts identified. Colors represent absolute value of log2 fold change. Red represents a downregulation relative to the control, whereas green represents upregulation. More than half of these genes (55%) were functionally annotated and subject to further analysis (Figures 2, 3, 4, 5, 6)

FIGURE 2

Percent of total (a) and annotated (b) differentially expressed transcripts as quantified by DESeq2 analysis within elevated temperature treatment (400 ppm 19°C), elevated pCO₂ treatment (1,200 ppm 16°C), and joint temperature and pCO₂ treatment (1,200 ppm 19°C). All differential expression is relative to control treatment (400 ppm 16°C)

FIGURE 3

Volcano plots from DESeq2 analysis depicting the statistical significance (−Log10(p‐values)) of transcripts against the Log2 transformed magnitude of change of each transcript across samples of treatments of elevated temperature (a), elevated pCO₂ (b), and elevated temperature and pCO₂ (c), relative to the control condition. Values in green represent statistically significant upregulated and red represent downregulated genes in treatment samples relative to control treatment

FIGURE 4

Comparison of number of annotated, statistically significant (p < .05), differentially expressed transcripts identified by DESeq2 and edgeR analysis within elevated temperature (a), elevated pCO₂ (b), and joint elevated temperature and pCO₂ treatments (c)

FIGURE 5

Response of lobster postlarval exoskeleton formation transcripts to elevated temperature and pCO₂ by DESeq2 (orange) and edgeR (green) analyses. Depicted are Log2 fold change of 28 genes of interest at elevated temperature (a), elevated pCO₂ (b), joint elevated temperature & pCO₂ and (c) relative to gene expression under control conditions. Darkened colors indicate statistically significant outcomes (p < .05)

FIGURE 6

Response of lobster postlarval immune function transcripts to elevated temperature and pCO₂ by DESeq2 (orange) and edgeR (green) analyses. Depicted are Log2 fold change of 42 transcripts of interest at elevated temperature (a), elevated pCO₂ (b), joint elevated temperature and pCO₂ treatment and (c) relative to gene expression under control conditions. Darkened colors indicate statistically significant outcomes (p < .05)