Localization of bacteria in lichens from Alpine soil crusts by fluorescence in situ hybridization

•Localization of bacteria in lichen–soil interface was analyzed by FISH and CLSM.•Six species of Alpine soil crust lichens were selected.•An improved FISH protocol is presented for soil crust material.•Specific FISH probes were applied to detect the major bacterial groups.•The proposed protocol enables to study other ecologically important soil crust habitats.