The role of gut microbial community and metabolomic shifts in adaptive resistance of Atlantic killifish (Fundulus heteroclitus) to polycyclic aromatic hydrocarbons

Abstract

Altered gut microbiomes may play a role in rapid evolution to anthropogenic change but remain poorly understood. Atlantic killifish (Fundulus heteroclitus) in the Elizabeth River, VA have evolved resistance to polycyclic aromatic hydrocarbons (PAHs) and provide a unique opportunity to examine the links between shifts in the commensal microbiome and organismal physiology associated with evolved resistance. Here, 16S rRNA sequence libraries derived from fish guts and sediments sampled from a highly PAH contaminated site revealed significant differences collected at similar samples from an uncontaminated site. Phylogenetic groups enriched in the libraries derived from PAH-resistant fish were dissimilar to their associated sediment libraries, suggesting the specific environment within the PAH-resistant fish intestine influence the gut microbiome composition. Gut metabolite analysis revealed shifts between PAH-resistant and non-resistant subpopulations. Notably, PAH-resistant fish exhibited reduced levels of tryptophan and increased levels of sphingolipids. Exposure to PAHs appears to impact several bacterial in the gut microbiome, particularly sphingolipid containing bacteria. Bacterial phylotypes known to include species containing sphingolipids were generally lower in the intestines of fish subpopulations exposed to high concentrations of PAHs, inferring a complex host-microbiome relationship. Overall, killifish microbial community shifts appear to be related to a suppression of overall metabolite level, indicating a potential role of the gut in organismal response to anthropogenic environmental change. These results on microbial and metabolomics shifts are potentially linked to altered bioenergetic phenotype observed in the same PAH-resistant killifish populations in other studies.

Keywords: Adaptive resistance; Atlantic killifish; Gut metabolome; Gut microbes; Polycyclic aromatic hydrocarbons.

Figure 1.

Concentrations of amino acids from fish guts of King’s Creek (KC; grey bars) and Republic Creosote, Inc. (RCI; black bars) samples. Triplicate measurements from each of three samples were averaged and the bars and error bars represent means and standard deviation of those samples (n=3). Single and double asterisks (*) indicate significant difference at p<0.05 and p<0.01, respectively. Abbreviations follow standard 3-letter nomenclature for amino acids.

Figure 2.

Sphingolipids and relative abundance of some bacterial groups associated with sphingolipids. (Top) Bar graph showing levels of quantified sphingolipids in fish guts from KC (grey) and RCI (black) samples. Values shown are averages of triplicate samples with error bars representing standard deviations. Asterisks (*) above bars represent samples with significantly greater values (p < 0.05). (Bottom) Stacked bar graph showing average relative abundance of taxa potentially containing sphingolipid-producing bacteria. KC, sediment sample does not include the outlier library. Error bars account for propagation of error of either range (KC, sed.) or standard deviation (all other samples) for all four taxa.

Figure 3.

Principal coordinate analysis (PCoA) of libraries constructed from King’s Creek (K) and Republic Creosoting, Inc. (R) associated sediments (S) and fish guts (G). Triplicates of each library are shown (numbered 1-4), with some symbols partially obscuring others representing libraries in the same treatment.