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The Southeast Rügen Biosphere Reserve boasts a diversity of plant communities. The Granitz is the largest contiguous forest in the reserve. Up to the early Middle Ages, the Granitz was a mixed deciduous forest composed mainly of alder (Alnus spp.), lime tree (Tillia spp.) and oak (Quercus spp.). In the following centuries, the common beech (Fagus sylvatica) became the dominant tree. None-the-less, the coastal slope beech forest is one of the most species rich forest communities in northern Germany. In the humid gorges leading to the sea, we find sycamore maple (Acer pseudoplatanus) and wood fescue (Festuca altissima). Where the cliffs are inactive, Ribes alpinum, honeysuckle (Lonicera spp.), common dogwood (Cornus sanguinea), and goat willow (Salix caprea) grow in the understory. Liverwort (Hepatica nobilis), wood anemone (Anemone nemorosa), primrose (Primula sp.), lily of the valley (Convallaria majalis), spring vetch (Lathyrus vernus) and woodruff (Galium odoratum) are found in the herb layer.

Outside of the forests, the landscape is dominated by pastures. In particular, the dry grasslands of the Zicker Hills represent a remarkable and long coexistence between humans and nature. In this xeric and nutrient-poor habitat, a centuries-old tradition of extensive grazing has resulted in a unique vegetation and high species richness. Thermophilic plant species such as oregano (Origanum vulgare), swallow-wort (Vincetoxicum hirundinaria) and large veronica (Veronica teucrium) can be found here. Salt marches on the bodden side of Rügen are flooded only four or five times per year during particularly strong storms. These pastures are optimal habitats for salt tolerant species such as sea pink (Armeria arenaria), sea aster (Aster tripolium), sea arrowgrass (Triglochin maritimum) and glasswort (Salicornia sp.). Sea-milkwort (Glaux maritima), maritime plantain (Plantago maritima) and sea rocket (Cakile maritima) also thrive here. Unfortunately, local flood control measures impinge on the natural flooding cycle and threaten the salt marsh character of this habitat. A limited degree of grazing by cattle has been permitted in the reserve in order to counter expansion of common reed in the salt marsh.

In contrast to the degraded habitats elsewhere, beach and dune communities within the biosphere reserve still harbour the full complement of plant species. There are only a small number of bogs in Southeast Rügen. “Big Meadow” is located among the forested hills of the Granitz. This somewhat misleadingly named clearing is a kettle bog with a 9m thick peat layer and intact bog vegetation with peat mosses and common cottongrass (Eriophorum angustifolium). Sundew (Drosera spp.), Vaccinium spp., tussock cottongrass (Eriophorum vaginatum) and marsh Labrador tea (Rhododendron tomentosum) grow here.

The aggressive agricultural policies of the East German government resulted in the irreversible destruction of natural habitats on a large scale. Land amelioration and over-fertilization converted many wetlands into intensively used pastures and hayfields, whereas land consolidation resulted in the removal of many hedgerows and ponds. None-the-less, a number of species that are endangered elsewhere in Germany are still found in Southeast Rügen, for example Melampyrum nemorosum, Hypochaeris maculata, marsh cinquefoil (Potentilla palustris), common cowslip (Primula veris) and meadow saxifrage (Saxifraga granulata).

Large Veronica