The University of Arizona
Kartchner Caverns  

As part of the Kartchner Caverns Microbial Observatory NSF project, we are analyzing samples from various regions of the cave using 16S rRNA and metagenomic analysis.

Ortiz M, Neilson JW, Nelson WM, Legatzki A, Byrne A, Yu Y, Wing RA, Soderlund C, Pryor B, Pierson L, R Maier (2013) Profiling bacterial diversity and taxonomic composition on speleothem surfaces in Kartchner Caverns, AZ. Microb Ecol 65: 371-383. Link

Ortiz M, Legatzki A, Neilson JW, Fryslie B, Nelson WN, Wing RA, Soderlund C, Pryor B and R Maier (2013) Making a living while starving in the dark: metageno1mic insights into the energy dynamics of a carbonate cave. The ISME Journal doi: 10.1038/ismej.2013.159. Link

Kartchner 16S - Un-normalized

  1. Trimming & Filtering
  2. OTU Summaries
  3. Rarefaction Curves (Mothur rarefaction.single)
  4. Heat Maps (Mothur heatmap.sim)
  5. Similarity Measures (Mothur summary.shared)
  6. Taxonomy Tables
  7. Online BLAST (against 97% OTU reps or all unique seqs)

Kartchner 16S - Normalized

  1. OTU Summaries
  2. Similarity Measures
  3. Taxonomy Tables
  4. Heat Maps
Method: PW-CL (Esprit pairwise align + Mothur complete linkage cluster)
Representative OTU sequences were chosen by highest abundance (not Mothur method)
636 OTU removed for suspected contamination
Un-normalized analyzed with Mothur v1.11; normalized with Mothur v1.23.

Description of Samples

PrefixLocationTypeDescription
ABig WallSpeleothemClose to B, 28cm long. Dripping water and have a white layer over a yellowish surface.
BBig WallSpeleothemClose to A, 29cm long. Dripping water and have a white layer over a yellowish surface.
CBig WallSpeleothemA flowstone, commonly known as a bacon formation.
DBig WallSpeleothemA stalactite approximately 45 cm long, red, and close to the ceiling. Its tip is white and dripping water.
EBig WallSpeleothemA stalactite approximately 45 cm long, red, and close to the ceiling. Its tip is white and dripping water.
FBig WallSpeleothemA 110 cm stalactite that is dry and reddish brown with a coating of cave dust.
WBig WallSpeleothemA 39 cm stalactite with a uniform white to milky smooth and wet surface.
RockBig WallRockA composite of two rock surfaces, one two meters apart from speleothem C and the other behind speleothem D and W.
BlankBig WallBlank extractionIt was open in the cave to represent the sampling procedure and possible contamination throughout the process.
CarrotStrawberry AlcoveSpeleothem2.4 cm apart from stalactite. Originating as flow stone near the ceiling then dividing into arrays of highly crenulated stalactites of different sizes. Red color.
StalactiteStrawberry AlcoveSpeleothem2.4 cm apart from carrot. Originating as flow stone near the ceiling then dividing into arrays of highly crenulated stalactites of different sizes. Orcher color.
ORTRotunda RoomSoil20 cm below the surface in an area over the cave’s Rotunda Room. The area selected was as far as possible from plants to avoid rhizosphere effects.

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Last Modified Monday September 16, 2013 14:51 PM and 07 seconds