Microbial Ecology

, Volume 70, Issue 1, pp 175–187 | Cite as

Assessing Fungal Community Structure from Mineral Surfaces in Kartchner Caverns Using Multiplexed 454 Pyrosequencing

  • Michael Joe Vaughan
  • Will Nelson
  • Carol Soderlund
  • Raina M. Maier
  • Barry M. PryorEmail author
Environmental Microbiology


Research on the distribution and structure of fungal communities in caves is lacking. Kartchner Caverns is a wet and mineralogically diverse carbonate cave located in an escarpment of Mississippian Escabrosa limestone in the Whetstone Mountains, Arizona, USA. Fungal diversity from speleothem and rock wall surfaces was examined with 454 FLX Titanium sequencing technology using the Internal Transcribed Spacer 1 as a fungal barcode marker. Fungal diversity was estimated and compared between speleothem and rock wall surfaces, and its variation with distance from the natural entrance of the cave was quantified. Effects of environmental factors and nutrient concentrations in speleothem drip water at different sample sites on fungal diversity were also examined. Sequencing revealed 2,219 fungal operational taxonomic units (OTUs) at the 95 % similarity level. Speleothems supported a higher fungal richness and diversity than rock walls. However, community membership and the taxonomic distribution of fungal OTUs at the class level did not differ significantly between speleothems and rock walls. Both OTU richness and diversity decreased significantly with increasing distance from the natural cave entrance. Community membership and taxonomic distribution of fungal OTUs also differed significantly between the sampling sites closest to the entrance and those furthest away. There was no significant effect of temperature, CO2 concentration, or drip water nutrient concentration on fungal community structure on either speleothems or rock walls. Together, these results suggest that proximity to the natural entrance is a critical factor in determining fungal community structure on mineral surfaces in Kartchner Caverns.


Cave biology Speleology Community structure Cave microbiology Fungal ecology 454 sequencing 



The authors would like to thank Arizona State Parks, the RIM volunteers, and the Kartchner Caverns Cave Unit for all of the support they have provided in sampling and teaching us about Kartchner. Special thanks goes to Steve Willsey for leading the sampling expeditions and Dr. Bob Casavant for organizing them. We would also like to thank Jana U’Ren for her help with the statistical analyses. Thanks are also due to Mary Kay Amistadi at ALEC for analyzing the drip water samples. This study was supported in part by the College of Agriculture and Life Sciences, University of Arizona, by the Arizona State Parks system, and by the National Science Foundation (NSF-MCB #0604300).

Supplementary material

248_2014_560_Fig7_ESM.gif (54 kb)
Supp. Fig. 1

A principal component analysis (PCA) was conducted to examine the relationships among observed nutrient concentrations and sample sites. The PCA biplot reveals the relationship among measured drip water nutrient content and sites for water collection. The position of sampling sites in relation to the arrows for each nutrient depicts the relative concentration of each nutrient in each sample. Examination of the biplot reveals that separation of sites was strongly correlated with iron and sodium concentrations. The biplot also reveals that separation among samples reflects sampling sites rather than substrate types (GIF 54 kb)

248_2014_560_MOESM1_ESM.eps (438 kb)
High Resolution (EPS 437 kb)
248_2014_560_MOESM2_ESM.docx (189 kb)
Supp. Table 1 (DOCX 188 kb)
248_2014_560_MOESM3_ESM.pdf (281 kb)
Supp. Table 2 (PDF 281 kb)
248_2014_560_MOESM4_ESM.docx (111 kb)
Supp. Table 3 (DOCX 110 kb)


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Michael Joe Vaughan
    • 1
  • Will Nelson
    • 2
  • Carol Soderlund
    • 2
  • Raina M. Maier
    • 3
  • Barry M. Pryor
    • 1
    Email author
  1. 1.School of Plant SciencesUniversity of ArizonaTucsonUSA
  2. 2.BIO5 InstituteUniversity of ArizonaTucsonUSA
  3. 3.Department of Soil, Water and Environmental ScienceUniversity of ArizonaTucsonUSA

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