Biology ETDs

Publication Date



Lava tube caves possess a rich and patchy mosaic of nutrients and water that fosters a wide variety of microbial life. Water percolating past vegetation and through surface soils introduces dissolved carbon and nitrogen into caves. Roots provide even higher levels of carbon, nitrogen and microorganisms as they grow into the cave environment from surface vegetation. I hypothesized that this mosaic of nutrients and energy resources has a direct effect on the distribution and composition of microbial communities within caves. To test this hypothesis, I selected two lava tube caves in New Mexico, USA and identified six zones consisting of ceiling and floor sampling sites in areas with: (1) active root growth and active water percolation; (2) active water percolation from the surface, but no root growth and; (3) neither roots nor water. After determining percent carbon and nitrogen for each of the sites, I compared the results using ANOVA. I constructed 12 clone libraries using 16S rRNA-based culture-independent methods. Closest relatives were determined using the NCBI BLAST database and phylogenetic trees were constructed in MEGA 4. Diversity and community composition were compared using mothur, UniFrac and traditional statistics. Roots formed zones of isolated, increased carbon and nitrogen, but water percolating into caves without the presence of roots did not bring significantly more carbon or nitrogen into lava tubes. The microbial community compositions of the six zones were different from each other at the 97% OTU level, but were similar in diversity, phylum' level distribution and relatedness to other bacteria found in other soil, rhizosphere and cave environments. This study has numerous management implications, including highlighting the importance of roots and percolating water within the cave environment and therefore, the need to protect surface vegetation above caves. In addition, given that roots represent a conduit from the surface into the cave, this study shows the importance of native vegetation above critical cave habitats to preserve cave nutrient inputs and endemic microbial communities.




Cave, Microbial

Document Type


Degree Name


Level of Degree


Department Name

UNM Biology Department

First Committee Member (Chair)

Northup, Diana

Second Committee Member

Dahm, Cliff