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Molecular methodologies were used to characterize fungal communities associated with lichen-dominated biological soil crusts (BSCs) at two sites on the Colorado Plateau (USA) in order to investigate their diversity and abundance, in relation to that of bacteria, as well as how these parameters corresponded to overall soil crust cover and the presence of anthropogenic disturbance. Fungal community diversity and composition were assessed with denaturing gradient gel electrophoresis (DGGE) fingerprinting of PCR amplified ribosomal genes and by sequencing. Quantitative PCR, specific for fungi as well as bacteria, was used to evaluate relative microbial densities. Two sites with similar soil characteristics, both of which contained well developed BSCs dominated by lichens, were studied. Results indicated that while a considerable diversity of fungi is present within these BSCs, much higher than what has previously been determined for cyanobacteria-dominated crusts, fungi contribute less biomass and are less diverse than their bacterial counterparts. Fungal diversity in lichen-dominated BSCs was negatively correlated with disturbance and positively correlated with crust cover. (C) 2010 Elsevier Ltd. All rights reserved.