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As the name indicates, marsh gentian favors wet soils. It is one of the few plants that grows in wet heathlands. It tolerates strong acidic conditions and heavy metals. Among heather, marsh gentian prefers the least nutrient-poor soil, which often means edges of paths where light or treading stimulates the breakdown of humus. It is a rare, protected plant, found almost exclusively in nature areas. Besides bog regions, it can be found in the dunes on Texel, Ameland and Terschelling. It is threatened by drainage, fertilizers and pesticides.

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