qPCR , eDNA and standard curve - (Mar/07/2016 )

I wish to use qPCR to detect a specific species of fish from eDNA in the water of aquaria tanks. Since eDNA is fragmented and therefore of differing sizes I would think it not suitable for use as a standard curve. Could i use PCR product instead?

You should clone your PCR product into a plasmid and transform a bacteria to get more plasmid, that can be isolated in high concentrations, measured and diluted with similar diluent as your real sample is (in human gDNA, plasmids are linearized and mixed with rRNA to simulate complexity of genomic DNA, you may not need that with your eDNA). This is how standards are commonly prepared.

PCR product can be used, when made fresh, if you need it just few times, but it's not that easy to quantify precisely and in time the ends will start to degrade (plasmid  is more stable) and also, you can't very well simulate the real template.

I have since seen a recent paper use/order synthetic oligonucleotides (100 bases) then serial diluted for use as qPCR standard. This would be simpler since mine is a "one off". Are there obvious issues with this idea?

You have a PCR product smaller than 100 bp? The oligos, unless modified will have the same degradation problems as normal DNA, only benefit from PCR product is purity (and maybe longer overhangs, but I can't magine that on 100 bp oligo).

Putting PCR product into ready to use TA vector is very simple and if you have lab with wide scale of methods in use, you are likely to have all needed, from bacteria/vectors, incubators and kits for isolation. Of course if you have no microbiology stuff, then it is difficult.

Depends if it's for a single-time experiment or you want to do it in long term. In the first case I would go with PCR product, as I did in past, otherwise I would take the efford or pay someone to make a proper standard, stable and in large quantities.