Sharks host bacteria, but what are they?

Methods

Summary

The charter boat we use for sampling purposes is based out of Pompano Dive Center. We take groups of participants out and give them a once in a life-time experience to work closely with sharks, and also to raise conservation awareness at the same time. These trips have been crucial in changing the stigma that surrounds sharks in south Florida, as the participants get to be hands on in setting the lines and pulling them all up (by hand!) to see what they have caught. In addition to the general public, we also bring school field trips of varying ages on board to teach at an earlier age about sharks and the common misconceptions that most people have about them. Sharks are caught and released once samples and measurements are taken. 

The sharks are fished for using a rig that contains a fifty pound weight and a line with a buoy on the top, labelled with “GHRI” (Guy Harvey Research Institute) and the license number that allows us to fish with such gear. Gear is set in groups of 10, with two at each of the following depths: 25ft, 40ft, 60ft, 80ft, and 100ft. Attached to the weight is a 100ft 900lb microfilament line with a circle hook and bait on the end so that the shark can swim and maintain water filtration while we are picking up the gear. When the line is picked up, it is pulled up by hand and the shark is secured with a tail loop and the line from the hook so that measurements and samples can be taken. If at any time the animal is found to be in distress, we release it quickly. The main priority is the well being of the shark at all times. We do not take swabs of Hammerheads, as they stress very easily and can be susceptible to lactic acid buildup that can result in injury or death. 

Samples are collected from as many species as possible in hopes of achieving a wide range of habitats and diets among sharks and will be taken using dual sterile swabs (Henry Schein, Cat. 1228715) which arebe transported in a cooler to the Microbiology and Genetics lab at the Halmos College of Natural Science and Oceanography. For each species that is considered, I intend to sample a minimum of five individuals of each species (with a goal of 10 individuals per species). For each individual, four samples will be taken: mouth, gills, skin, and cloaca. Additionally, swabs of bait, Atlantic Bonito ( Sarda sarda ), will be taken on each trip, and water samples for each individual if possible, which are filtered after each trip, so that any environmental microbes can be characterized and possibly discounted. This would lead to 5 samples per individual and 1 bait sample per trip. I intend to examine at least 3 species with 5 or 6 individuals of each species. This would yield 75-90 samples just from the organisms, with the bait sample total depending on the number of trips to collect the samples needed. 

Microbial community differences will be examined between sampling areas on individuals, as well as compared to other individuals in order to determine species or area specific microbes which could provide insight to be utilized when identifying shark species involved in attacks. Additionally, mouth specific microbes could be identified to determine better treatments for shark bite victims. The composition of each sample can be compared to determine significant differences and similarities between individuals. Spatial examination of the microbial communities of individuals will be accomplished by mapping where each individual was sampled and comparing the community data for individuals in a common area versus different geographical locations. If significant differences are found based on location, it could lead to further study to determine the cause of the spatial microbial differences. If differences in microbial communities are found between species by the data analysis in this study, a protocol could be proposed utilizing the MiSeq technology to further characterize microbial communities, potentially allowing for the accurate identification of the species involved in a shark bite.

Pre Analysis Plan

Hypotheses:

1. Elasmobranch microbiomes contain unique (possibly virulent) microbes when compared to the surrounding environment, which could lead to a high infection rate associated with bites.

2. Individuals have a significant difference in the composition of the microbial community based on the sample area on the organism. Shark mouth sample microbial composition will vary significantly from the skin and gills, as it will reflect the diet of the individual. The cloacal microbial composition should have some similarities to the microbiome of the mouth, but should still have some significant differences.

3. Microbial communities differ based on the species of the shark, and therefore each site should be more similar between individuals of the same species as compared to different species.