I have tried 2 baths of 70% EtOH for 10min followe by 3 rinses with ddH2O and 2 baths of 20% sodium hypochlorite for 10 min each followed by the same rinse. I still am seeing medium to heavy contamination, primarily fungal contamination.
Please try stirring in sodium hypochlorite (5%), for five minutes and then wash the seeds in distilled water for three times
I have attached a paper you may find useful.
I am always very cautious when it comes to disinfecting seed as you can impact germination. Are the seeds affected by the contamination? Sometimes, although the plate may look hideous, the seeds are actually ok. Make sure you have viable seed to begin with, as if you have heavy contamination it can be confusing if your seed goes all mouldy, because you don't know if it is poor seed quality or contamination. What media are you using? I use a 1% agar in sterilized petri dishes and use a para film as an additional seal. Although this may influence your germination (I am not sure what you are testing), I have found GA3 at (0.125mg) incorporated into the agar keeps the plates really clean…but that is a side effect as I use it primariliy to trigger germination (I use it a lot with alpine species).
There is no treatment able to sterilize the surface of seeds without killing (sterilizing) the seeds. The best you can obtain is a reduction of the bacterial load (i.e. a disinfection) by two to four orders of magnitude, which is far from sterilizing the surface.
Sterilisation with hypochlorite only kills the micro-organisms on the outside. This may be enough for your purpose. Seeds can indeed also be sensitive to the oxidative activity of hypochlorite. Moreover, repeated washing may not always remove residual hypochlorite. The latter can be removed by rinsing seeds after two or three washing with water with a mild acid solution (HCl) and subsequently again with water.
An alternative method is vapour sterilisation with chlorine gas. The advantage is that the seeds stay dry. My colleagues perform that routinely with Arabidopsis seeds. See for an example: http://www.plantpath.wisc.edu/fac/afb/vapster.html.
Take care you perform that in a fume hood!
Success
The best way to surface sterilization of seeds Spartina pectinata is mercuric chloride. After it occurs less contamination.
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