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Community Structure of Skin Microbiome of Gulf Killifish, Fundulus grandis, Is Driven by Seasonality and Not Exposure to Oiled Sediments in a Louisiana Salt Marsh

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Abstract

Mucus of fish skin harbors complex bacterial communities that likely contribute to fish homeostasis. When the equilibrium between the host and its external bacterial symbionts is disrupted, bacterial diversity decreases while opportunistic pathogen prevalence increases, making the onset of pathogenic bacterial infection more likely. Because of that relationship, documenting temporal and spatial microbial community changes may be predictive of fish health status. The 2010 Deepwater Horizon oil spill was a potential stressor to the Gulf of Mexico’s coastal ecosystem. Ribosomal intergenic spacer analysis (RISA) and pyrosequencing were used to analyze the bacterial communities (microbiome) associated with the skin and mucus of Gulf killifish (Fundulus grandis) that were collected from oiled and non-oiled salt marsh sites in Barataria Bay, LA. Water samples and fin clips were collected to examine microbiome structure. The microbiome of Gulf killifish was significantly different from that of the surrounding water, mainly attributable to shifts in abundances of Cyanobacteria and Proteobacteria. The Gulf killifish’s microbiome was dominated by Gammaproteobacteria, specifically members of Pseudomonas. No significant difference was found between microbiomes of fish collected from oiled and non-oiled sites suggesting little impact of oil contamination on fish bacterial assemblages. Conversely, seasonality significantly influenced microbiome structure. Overall, the high similarity observed between the microbiomes of individual fish observed during this study posits that skin and mucus of Gulf killifish have a resilient core microbiome.

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Acknowledgments

We thank the Louisiana Department of Wildlife and Fisheries for facilitating access to collection sites; Carlos Ruiz (SFAAS), George Benz, and Eric Salmon (both from Middle Tennessee State University) for the help in collecting fish; and the Gulf of Mexico Research Initiative (SAB), National Science Foundation (SAB), and National Oceanic and Atmospheric Administration (PI, Arias) for the funding.

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  1. Andrea M. Larsen

    Present address: Mote Marine Laboratory, 1600 Ken Thompson Parkway, Sarasota, FL, 34236, USA

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  1. School of Fisheries, Aquaculture, and Aquatic Sciences, Auburn University, 203 Swingle Hall, Auburn, AL, 36849, USA

    Andrea M. Larsen, Stephen A. Bullard, Matthew Womble & Covadonga R. Arias

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Larsen, A.M., Bullard, S.A., Womble, M. et al. Community Structure of Skin Microbiome of Gulf Killifish, Fundulus grandis, Is Driven by Seasonality and Not Exposure to Oiled Sediments in a Louisiana Salt Marsh. Microb Ecol 70, 534–544 (2015). https://doi.org/10.1007/s00248-015-0578-7

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