Insights into the circulating microbiome of Atlantic and Greenland halibut populations: the role of species-specific and environmental factors

Abstract

Establishing long-term microbiome-based monitoring programs is critical for managing and conserving wild fish populations in response to climate change. In most cases, these studies have been conducted on gut and, to a lesser extent, skin (mucus) microbiomes. Here, we exploited the concept of liquid biopsy to study the circulating bacterial microbiome of two Northern halibut species of economic and ecological importance. Amplification and sequencing of the 16S rRNA gene were achieved using a single drop of blood fixed on FTA cards to identify the core blood microbiome of Atlantic and Greenland halibut populations inhabiting the Gulf of St. Lawrence, Canada. We provide evidence that the circulating microbiome DNA (cmDNA) is driven by genetic and environmental factors. More specifically, we found that the circulating microbiome signatures are species-specific and vary according to sex, size, temperature, condition factor, and geographical localization. Overall, our study provides a novel approach for detecting dysbiosis signatures and the risk of disease in wild fish populations for fisheries management, most notably in the context of climate change.

Figure 1

Map of the sample sites divided into five different areas. The regional temperature is given for each zone (mean ± SE).

Figure 2

Microbiome structure at the phylum level. (A) Mean relative abundance (%) of the four main phyla present in the blood microbiome of Atlantic halibut (H. hippoglossus) and Greenland halibut (R. hippoglossoides). (B) Individual variation in the relative abundance (%) of the main phyla of Atlantic halibut (n = 86) and Greenland halibut (n = 97).

Figure 3

Core blood microbiome analysis. (A) Mean relative abundance (%) of the core genera aggregated (90% prevalence) in the cmDNA of the blood microbiome of the Atlantic halibut (H. hippoglossus) (top) and the Greenland halibut (R. hippoglossoides) (bottom). The mean relative abundance is given in each pie chart, and the number of aggregated ASVs is indicated next to each pie chart. (B) Venn diagram showing common and distinctive genera in the blood microbiome. (C) Heatmaps of the core microbiome. These heatmaps identify the most prevalent bacteria in both halibut species. Atlantic halibut, n = 86, Greenland halibut, n = 97.

Figure 4

Biodiversity analysis. (A) PCoA plot of the β-diversity of the blood microbiome based on weighted UniFrac distances. (B) α-Diversity metrics for the cmDNA of Atlantic halibut (blue) and Greenland halibut (red). ***: p < 0.001. (C and D). Discriminative taxa at the phylum and genus levels in the cmDNA of both halibut populations (p < 0.05). Atlantic halibut, n = 86, Greenland halibut, n = 97.

Figure 5

Maturity analysis. LEfSe analysis of the blood microbiome showing the significantly different taxa in mature (blue) and immature (red) fish in (A) Greenland halibut (Immature, n = 55, mature, n = 42) and (B) Atlantic halibut (Immature, n = 56, mature, n = 25). (C).α-Diversity metrics for immature and mature Greenland halibut. ***: p < 0.001.

Figure 6

Discriminant taxa associated with seawater temperature and size classes. (A) LEfSe analysis of the blood microbiome showing the significantly different taxa in Greenland halibut (A) inhabiting cold (n = 25) and warm (n = 72) seawater and (B) according to their size class (Class 1, n = 36, Class 2, n = 22, Class 3, n = 39).

Figure 7

Spatial analysis. LEfSe analysis of the blood microbiome showing the significantly different taxa in (A) Greenland and (B) Atlantic halibut according to their localization. (C and D). Relative abundance of the discriminative genera in Greenland and Atlantic halibut. (*) p < 0.05; (**) p < 0.01; (***) p < 0.00. Greenland halibut: Estuary–Western Gulf, n = 22, Chaleur Bay, n = 19, Northeast Gulf, n = 22, Laurentian Channel, n = 34. Atlantic halibut: Estuary–Western Gulf, n = 14, Southern Gulf, n = 11, Northeast Gulf, n = 17, Laurentian Channel, n = 44.