How do you apply the appropriate ammonia critical level to a vegetation type. For example, for vegetation types such as peatland and woodland would apply the 1ug it would mainly contain lower plants?

This is both a both habitat and site specific consideration.  For bog habitats where lower plants are integral to the habitat function, the lower (1ugm-3) critical level for ammonia is relevant. This more stringent critical level will also be relevant to the woodland if lichen/bryophyte interest is 'an integral part' of the woodland. For protected sites the Site Relevant Critical Loads tool can help as it gives the ammonia critical level for features.

If in doubt, seek site specific advice from the relevant authority (eg conservation agency or site manager).