Research

Fungi

 

Impact of Tourism on Kartchner Nonculture-Based Analysis Culture-Based Analysis Fungi Nematodes

In contrast to studies on cave bacterial communities, little data is available on cave fungal communities.  Over the last 30 years, a handful of papers on cave mycological diversity have been published, but these studies were usually surveys restricted to sampling cave soil and did not document diversity on various cave surfaces.  Several of these surveys focused on restricted groups of fungi such as thermophilic fungi or fungal-like taxa such as slime molds, but in no instance has a survey attempted to document fungal diversity across varied cave substrata and across varied taxonomic grouping, or has attempted to define and contrast different subterranean fungal communities.  Considering the importance of fungi in terrestrial microbial communities as primary decomposers, this absence of data is a major impediment to understanding the dynamics relating to cave fungal communities, their functions, and their contributions to cave ecological stability.  The Kartchner Caverns Microbial Observatory project is the first study on cave microbial communities that attempts to fill in this void of knowledge.

 

From a small number of preliminary samples collected in Kartchner Caverns in 2004, we documented the presence of 51 different fungal taxa representing 22 genera of filamentous fungi including Absidia, Alternaria, Aspergillus, Bipolaris, Catinula, Cephalosporium, Chaetomella, Cladosporium, Curvularia, Fusicoccum, Fusarium, Monilochaetes, Mucor, Oidiodendron, Penicillium, Peyronellaea, Pyrenochaeta, Rhizopus, Selenophoma, Trichoderma, Torula, and Verticillium. In addition to the filamentous fungi mentioned, numerous yeast strains were recovered and await identification.  These fungi were recovered from a variety of substrates including cave soil and mud flats, bat guano, and carbonate formations (Fig 1. left)) Thus, the high fungal diversity recovered from this initial limited sampling suggests that the Caverns are mycologically rich and that our proposed effort to define fungal community diversity and structure will likely be highly productive.

Subsequent sampling conducted in 2006-2007 expanded our initial culture collection to 273 isolates and increased taxon representation to 29 genera of filamentous fungi.  Identification to date has been based upon stimulating fungal sporulation through specific culture techniques (Fig 2a and 2b)...

 

	Figure 2a. (left) The Conviron Incubator allows the researchers to control the environmental conditions, such as temperature, humidity, and light, that the fungal isolates are grown in to induce sporulation.
	Figure 2b.(below) A small sampling of the fungi recovered from Kartchner Caverns growing on agar plates.  The diversity of morphological characteristics among the isolates helps us to identify the individuals.

 

...and using characteristics of the sporulation structures as diagnostic criteria Figures 3a, 3b, and 3c.

 

	Figure 3a. The sporing structure of an isolate of Aspergillus. Its small round spores form chains on special bottle shaped cells (phialides) that cluster on the swollen tips of the conidiophores.  This characteristic structure is mildly reminiscent of a toilet brush.
	Figure 3b. The spores of Bipolaris are multi-celled, bacilliform, and form at the tips of conidiophores.  The conidiophore then continues to grow creating a new tip for another spore to form.
	Figure 3c. Curvularia forms multiple spores at the tips of its conidiophores.  These spores are mulit-celled, with enlarged cells in the middle, giving the spore a distinctive curved shape.

 

To confirm identity of fungi based upon morphological characteristics, we are currently extracting genomic DNA from all recovered isolates and sequencing rDNA (ITS and 18S) for comparison with sequences from know species in each of the representative genera.  Considering the unique environment of the Caverns, we expect selection pressures distinct from those encountered at the cave surface.  Consequently, we expect that a proportion of the fungi recovered from the caverns will represent new species to mycology.

As with our studies on bacterial diversity, we will complement our culture-based fungal libraries with non-culturable libraries.  It is expected that culture based methods will uncover only a fraction of the true mycological diversity of Kartchner Caverns, and that including studies of non-culturable fungi will provide unprecedented insight into subterranean mycological communities.  Furthermore, DGGE profiling of these communities will enable a more quantitative approach to comparative studies  of communities recovered from diverse substrates found within the cave.

updated 7/2009