INBRE-2 GENOMICS OF ALASKAN SOIL TO MONITOR PATHOGENIC FUNGI

University Of Alaska Fairbanks, Fairbanks AK

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Abstract

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Soils are major environmental reservoirs of fungi that cause human diseases. Surveys of medically important fungi have been carried out using selective isolation approaches, but comprehensive molecular surveys of fungal diversity in soil haven't been applied to surveillance in medical mycology. The Taylor lab has spearheaded extensive soil sampling combined with in-depth sequencing of PCR clone libraries to characterize fungal diversity in Interior Alaska. We have generated roughly 100,000 fungal ITS clone sequences, surpassing the total number of fungal ITS sequences in GenBank. Here, we propose a pilot study investigating the diversity of fungi of concern to human health recovered from these soil PCR libraries. We will undertake comprehensive phylogenetic analyses of all fungi of medical interest in our massive sequence database. As exemplars, we present phylogenetic analyses of the genus Cryptococcus, a leading causative agent of respiratory diseases and meningitis in immune-compromised individuals, and the genus Candida, species of which belong to normal human flora, but which occasionally cause dangerous systemic infections. Sequences recovered from Alaskan soils in both fungal groups are diverse, and include putative new species with no prior known sequences. We also propose amplifying and sequencing additional loci where relationships of Alaskan entities to known clinical strains are uncertain based solely on ITS sequences. Our ultimate goal is obtaining external funding that expands this surveillance work by applying an Affymetrix microarray that is under development and through soil sampling in additional Alaskan regions, particularly the southeast where monitoring for the outbreak pathogen Cryptococcus gattii is warranted.