Dear Ecolog, I have quite a large pitfall collection containing specimens of all sorts--beetles, spiders, grasshoppers, flies. I would like to take a sub-set of this collection and sequence their gut contents to figure out what the major players are eating in different habitats. Family-level determination would be great, genus would be even better--just enough to help me create a more robust food web than the one I'm working with, which largely relies on guesswork and literature that's not relevant to my study area. Microscope analysis is mostly out of the question; a lot of these guys are fluid feeders, and I'm interested in plant DNA as well for the herbivores.
I know that most PCR methods (I'm thinking Zeale et al. 2011, or Garcia-Robledo et al. 2012) can get to genus or better with the Barcode of Life Database. I have been consulting with the core facility at my school, and it sounds like using NGS technology like Illumina and then using multiplexing to get the most for your run is the way to go--get a lot of reads for not a lot of money. My problem is this: what to do about cannibalism? Even a study on fish that directly addresses it (Carreon-Martinez et al. 2011) concedes that DNA contamination from the cannibal itself likely biased results. Dissecting a spider gut and hoping to keep it "clean" takes it to a whole new level. Moreover, I really want to know how much cannibalism is is occurring in this food web--I expect rates of cannibalism are rather high in the Arctic. I know that there are some other methods out there -- monoclonal antibodies and isotope analysis. I worry that isotope analysis won't be specific enough to connect the dots of my food web, and it sounds like the monoclonal antibody studies, when they are interested in cannibalism rates, focus on cannibalism between different life stages of insect. Is there some literature out there that I am missing, or is this maybe a problem without a work-around? Any advice from the listserv would be greatly appreciated. Thanks everyone. Ashley Asmus Ph.D. Student, University of Texas at Arlington
