Fish gut microbiome changes as biological responses after an oil exposure

Giovanna Monticelli1, Isha Sehgal1, Andrea Bagi2 and Daniela Maria Pampanin1,2, (1)University of Stavanger, Department of Chemistry, Bioscience and Environmental Engineering, Stavanger, Norway, (2)NORCE, Norwegian Research Centre, Stavanger, Norway
The fish gut microbial community is involved in different functions, e.g. digestion processes and immune system responses, and can be influenced by various factors, including the exposure to contaminants.

Studies have shown the importance of the understanding of gut microbiome changes in humans and other mammals; however a limited knowledge is available in fish species. In this study, Atlantic cod (Gadus morhua) has been used a sentinel organism to evaluate microbial community changes after exposure to dispersed crude oil as a proxy of oil contamination in the ocean.

Juveniles were exposed to 0.05 ppm dispersed crude oil for 28 days. Samples were collected after 1,3,7 and 28 days. The Qiagen Fast DNA Stool Mini Kit was used for the DNA extraction and the Illumina MiSeq platform was used for sequencing the 16s rRNA V4-V5 region. Sequencing results were processed using QIIME2 and various R packages. An average of 359,912 quality filtered reads was generated and 3438 amplicon sequence variants (ASVs) were identified after data processing of the 32 samples (16 exposed and 16 control fish guts).

The most abundant orders were Vibrionales, Mycoplasmatales, Actinobacteridae, Alteromonadales, Rhodobacterales, and Pseudomonadales, while Photobacterium, Aliivibrio and Mycoplasma were the most abundant genera. Photobacterium presence was significantly lower in gut samples of exposed fish, after 1, 3 and 28 days. The sequencing depth of 99181 reads/sample was enough for sequence diversity coverage. The DESeq2 function in R was used to find out ASVs that were either enriched or depleted in exposed samples compared to controls. The analysis depicted the upregulation of 9 and downregulation of 65 ASVs.

In general, values for diversity metrics indicated that the microbial diversity was reduced in gut samples of fish exposed to dispersed crude oil. The results will be followed up in terms of microbial community function evaluation on gene expression analysis.