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Increased deposition of atmospheric N largely from intensive agriculture is affecting biodiversity and the composition of natural and semi-natural vegetation in Europe. The value of species based bioindicators such as the Ellenberg N index and measurements of total tissue N and free amino acids in key plant species, is described with reference to a mixed woodland downwind of a livestock farm in the Scottish Borders, operated for over 20 years with a measured spatial gradient of ammonia concentration (29–1.5 μg m
−3). All the indicators examined showed a relationship with N deposition and provided some indication of vegetation change. Total tissue N and arginine concentrations were most closely linked with ammonia concentrations and N deposition, with
r
2 values of >0.97 and >0.78 respectively.
Tissue N and amino acid concentrations in mosses are good indicators of enhanced N deposition.