The broad distribution and high colonization rates of plant roots by a variety of endophytic fungi suggest that these symbionts have an important role in the function of ecosystems. Semiarid and arid lands cover more than one-third of the terrestrial ecosystems on Earth. However, a limited number of studies have been conducted to characterize root-associated fungal communities in semiarid grasslands. We conducted a study of the fungal community associated with the roots of a dominant grass, Bouteloua gracilis, at the Sevilleta National Wildlife Refuge in New Mexico. Internal transcribed spacer ribosomal DNA sequences from roots collected in May 2005, October 2005, and January 2006 were amplified using fungal-specific primers, and a total of 630 sequences were obtained, 69% of which were novel (less than 97% similarity with respect to sequences in the NCBI database). B. gracilis roots were colonized by at least 10 different orders, including endophytic, coprophilous, mycorrhizal, saprophytic, and plant pathogenic fungi. A total of 51 operational taxonomic units (OTUs) were found, and diversity estimators did not show saturation. Despite the high diversity found within B. gracilis roots, the root-associated fungal community is dominated by a novel group of dark septate fungi (DSF) within the order Pleosporales. Microscopic analysis confirmed that B. gracilis roots are highly colonized by DSF. Other common orders colonizing the roots included Sordariales, Xylariales, and Agaricales. By contributing to drought tolerance and nutrient acquisition, DSF may be integral to the function of arid ecosystems.Symbiotic associations of fungi and plants are ancient and phylogenetically diverse (4,9,11,42,43,60,64,69). Some of these fungi, notably mycorrhizal fungi, have received extensive study, but accumulating evidence indicates that many of the fungi associated with plant roots are dark septate fungi (DSF). These fungi are usually described as endophytes, whose functions have only recently been studied (43,44,76). DSF comprise a taxonomically diverse group (34, 37) characterized by melanized septate hyphae. Endophytes with hyaline hyphae are also common (e.g., see references 48, 53, and 76), but are less well characterized, because they are more difficult to detect in microscopic analysis and are sometimes considered contaminants in mycorrhizal fungal studies. Growing evidence showing the broad distribution and high root colonization rates of DSF in different ecosystems suggests that their functional importance may rival that of arbuscular mycorrhizal fungi (AMF) (1, 43), particularly for plants growing in stressed environments, such as alpine habitats and arid grasslands (8, 45a, 54, 56, 75). In these habitats, endophytic DSF and other rootassociated fungi allow some plants to increase their resistance to drought and heat and facilitate the acquisition of nutrients (23, 43, 45a, 50, 57, 76, 81).Desert environments are one of the most challenging ecosystems for plants and microorganisms (18,51,87). Biological activity, dive...