Cave Expeditions and Artificial Substrates for Study of Cave Bacteria

One of our best study sites in Mammoth Cave National Park (MACA) was at the confluence of two underground rivers called the Hawkins and the Logsdon. The combined effluent constitutes the primary aquifer that today drains the Mammoth Cave system.

The Amos Hawkins Formation is one awesome and beautiful obstacle along the way. It is a giant flowstone mound formed by deposition of calcium carbonate from CO2-rich water seeping into the cave from the surface. The way past the formation is underneath to the right.

Photo copyright 2006 taken by Gary Berdeaux

Recently a book was published with a compendium of the most recent research at MACA by Rick Olson and Horton Hobbs called "Mammoth Cave: A Human and Natural History." I look forward to reading it in full, and I was honored to learn my DNA work was mentioned within it.

We deployed and a year later retrieved mesh bags containing a standardized substrate. The standardized substrate was needed to provide less variability among the consistencies of cave samples (e.g., sand vs. pebbles), and they could be used at different cave systems across the country or world.

Rick Olson (left) and Rick Fowler (right) at Mystic River in Mammoth Cave Nat'l. Park, 2006

The substrate was called "BioSep Beads" and was used in many published papers with broad applications. They consisted of small porous beads about 2-3 mm in diameter with 33% granules of limestone or calcium carbonate in 67% Nomex, similar to Kevlar. They were developed in collaboration with Kerry Sublette at the University of Tulsa and D.C. White at the University of Tennessee. Stay tuned for photomicrographs of the beads. Shown here are a few pictures from 2005-2006 during expeditions to deploy and collect some of the beads.

Photo by Rick Olson 2006

We used the 3 mm beads to leave in place inside mesh bags that were retrieved one year later. The water level In that particular aquifer varied from calm, as shown, to torrential and completely flooded.

Photo by Gary Berdeaux 2006

We extracted DNA from biofilms on the beads after a year in the cave. Along with fatty acid methyl ester (FAME) lipid analyses, eubacterial 16S rDNA sequences were determined and phylogenetic trees were constructed for each of the study sites.