Trial pre-registration service that accepts non-clinical trials, or specifically ecology?
Did you try OSF.io?

They offer a free service where you can preregister trials and give them a timestamp with a DOI number etc.

I do not know if this is exactly what you are looking for, but it's the easiest solution for preregistering and I am quite sure that it would be enough to get the "preregistration" badge when you are finally ready to publish. 

Here is more info on how to do it and what is essential for preregistration.