Clara L. Mackenzie’s research while affiliated with Fisheries and Oceans Canada and other places

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Publications (1)

Continuous sea surface temperature (SST) and dissolved oxygen (DO) conditions (logged at 15 min intervals) between June 1 and September 15, 2022 at the subtidal site at the Deep Bay Marine Field Station farm during the common garden experiment. SST and DO values represent means of logger data (n = 2). The horizontal red and blue lines indicate 20 °C (onset of thermal stress) and 2 mg/L oxygen (hypoxia), respectively. The black dashed boxes indicate marine heatwave events. The yellow squares indicate gene expression sampling timepoints with pre-heatwave, heatwave, and post-heatwave samples taken May 31, July 26, and September 15, respectively. Microbiome sampling timepoints occurred on April 12 (pre-transfer, not shown) and in parallel with gene expression sampling on May 31 (pre-heatwave) and September 15 (post-heatwave). Note that SST and DO data visualized in this plot were previously presented in Fig. 3b of Mackenzie et al. (2024), as part of a parallel study
Principal components analysis of gene expression in Pacific oysters from Intertidal → Subtidal (I → S) and Subtidal (S) treatments across all timepoints (pre-heatwave (Pre-HW), heatwave (HW), and post-heatwave (Post-HW)) in the common garden experiment. Refer to Table 1 for full gene names
Heatmap and hierarchical cluster analyses of gene expression in Pacific oysters from Intertidal → Subtidal (I → S) and Subtidal (S) culture treatments across all timepoints (pre-heatwave (Pre-HW), heatwave (HW), and post-heatwave (Post-HW)) in the common garden experiment. Cluster analyses suggested four sub-groups (SG1 – SG4), indicated by the light grey boxes. SG1 largely comprised pre-HW samples, SG2 mostly HW samples, and SG3 predominantly post-HW samples, while SG4 included a mix of samples across treatment groups and timepoints. Refer to Table 1 for full gene names
Principal components analysis of gene expression in Pacific oysters from Intertidal → Subtidal (I → S) and Subtidal (S) treatments at the post-heatwave timepoint in the common garden experiment. Refer to Table 1 for full gene names
Microbiome characteristics of Pacific oysters from Intertidal → Subtidal (I → S) and Subtidal (S) culture treatments across all timepoints (pre-transfer (Pre-T), pre-heatwave (Pre-HW), and post-heatwave (Post-HW)) in the common garden experiment: (a) Violin plots of observed amplicon sequence variant (ASV) richness (after removing rare and singleton ASVs), with letters indicating the results of a Tukey’s HSD post-hoc test. Groups with the same letter(s) are not significantly different and sample groups that are significantly different have different letters; (b) Principal coordinates analysis highlighting variability in oyster microbiome bacterial genera across culture treatments and timepoints; (c) Boxplots of the 25 most abundant bacteria, agglomerated at the genus level, in the oyster microbiomes, grouped by timepoint (across culture treatment) and displayed in descending order of average relative abundance across the dataset. Note that where genus-level ASV groups could not be confidently annotated to genus, groups were labeled with the next most confident annotation (order, class, or family level). The median is indicated by the horizontal lines in the boxplot, the lower and upper hinges correspond to the first and third quartiles, the whiskers extend from the upper or lower hinge to the largest or smallest value no further than 1.5 × the interquartile range (IQR) from the hinge. Outliers, exceeding 1.5 × IQR are shown as black circles. Taxonomic groups are bolded if at least one significant difference was observed between timepoints. The between timepoint comparisons and their significance level are shown above the boxplots. * indicates a Holm-adjusted p-value of ≤ 0.05, ** indicates p-adjusted ≤ 0.01, *** indicates p-adjusted ≤ 0.001, and **** indicates p-adjusted ≤ 0.0001 of a Wilcoxon Rank Sums Test

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A common garden comparison of the microbiome and gene expression of intertidally- and subtidally-cultured Pacific oysters (Crassostrea gigas) in relation to extreme warming events
  • Article
  • Full-text available

May 2025

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23 Reads

Clara L. Mackenzie

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Monique R. Raap

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Christopher M. Pearce

In order to investigate how shellfish culture in the intertidal zone may serve as a means of conferring resilience prior to subtidal deployment for commercial grow-out, a common garden experiment was carried out with juvenile Pacific oysters. Individuals were cultured under intertidal or subtidal conditions for one year, following which intertidal animals were transplanted to the subtidal site and both treatment groups were cultured together under subtidal conditions for a period of five months. During that time, microbiome and gene expression were tracked in relation to a marine heatwave event. Multivariate analyses of samples indicated a significant effect of time on gene expression, but no significant effect of culture treatment prior to and during the heatwave. Significant differences in the expression of oxidative stress and immune response genes in post-heatwave samples in comparison to pre-heatwave and heatwave samples, and between culture treatment groups post-heatwave, were detected. Results also indicated significant differences in microbiome according to culture treatment and timepoint, with increased richness observed in intertidally-cultured oysters and over time. Similarly, while the overall composition of the oyster microbiome did not vary between culture treatments, changes were observed over time. At the end of the field trial, a laboratory-based temperature and Vibrio challenge experiment was conducted to compare genomic responses of both culture treatment groups following 24-h exposure to coinciding acute warming and pathogen stressor conditions. A significant interactive effect of temperature and culture treatment on gene expression was observed, further suggesting that stress response may be influenced by prior culture treatment.

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