TE buffer contains EDTA, so yes, it can bind to the Mg in your PCR reaction and inhibit the reaction.  Did you add the same volume of extracted DNA to your "poison" reaction as to your sample reaction?  If so, it doesn't sound like there is enough EDTA to inhibit the reaction.

If you still think the TE is a problem, you could try adding extra Mg to the PCR reaction to make up for the Mg binding to the EDTA.  Or, instead of using TE for elution, try using Tris-HCl (5mM, pH 8.5) to avoid the EDTA all together. 

If you are having problems with DNA degradation you might also want to store your samples in the freezer and double check that all your plastics are DNAse free.

Have you tried amplifying the colonies you get on your plates using your fungal primers?  This would help you confirm that the primers are actually able to amplify the fungi present in your sample.  I would also extract using the same technique that you use to extract the DNA from the woodlouse.  Fungal DNA can be very difficult to extract and I find most kits don't do a very good job even on a pure culture, so your woodlouse extraction may simply not contain any fungal DNA.  The technique I usually use to extract fungal DNA is to grind the sample under liquid nitrogen and then use the CTAB extraction.  I've never tried it in a situation like this, but I don't see why it wouldn't work. 

Is there any way you can reduce the amount of woodlouse DNA relative to the fungal DNA in your sample?  If you are interested in fungi in the gut, for instance, maybe you could dissect out the gut and only extract DNA from that, rather than the whole organism.  This would allow you to have a better idea of how much fungal DNA is present in your extract, rather than just looking at the concentration of total DNA.

Good luck!

Thank you for your suggestions

My study eventually is the GI tract of a wood eating catfish, the wood lice is just a practice run to test methodology. We may extract the GI tract at some point if we need to. I haven't amplified the colonies on the plates yet, they have to be replated as single colonies before doing that, so that's in the pipeline.

I've done another DNA extraction using crushed up wood lice rather than using whole ones and bead beating, eluted one tube in TE and one tube in DES water. I have DNA on a low melt gel from the extraction, now I have a gel running after PCR with ITS primers with poison tube in too (easier to just get the poison tubes in there at the same time rather than doing it later!). I don't think it is the TE as the poison work showed there was nothing inhibiting, maybe it was the extraction. We'll see.

I have suggested the CTAB to my supervisor as someone said this too at a conference so I may suggest it again.

Thank you again

I was working with woodlice many years especially with the bacterial community structure of the P. scaber and T. ratzeburgii. Please find in my papers how we did an extraction of DNA from the guts. It is important to define from where you will isolate DNA, what tissue or organ. In woodlouse the gut is cuticle surrounded pipe, which can be quite easily obtained by manipulation with tweezers and eye scissors. 

Regards and good luck.

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I would suggest that since you have been advised to use DES water. Try it. You have seen that due to binding of EDTA in TE buffer to Mg it is inhibiting your reaction.

I have done this, I crushed up 30 wood lice, divided it between 2 tubes, did DNA extraction using kit, eluted one with TE and one with DES water. Ran a low melt gel from the extraction, I have DNA, did PCR using fungal primers, also included a poison tube. I had a band for the poison tube (so no inhibitor), one for the positive control but no band for just wood lice DNA. So there was no problem with the original extraction.

How did you solve your problem? Caroline....